Daily Papers

Many real-world graphs frequently present challenges for graph learning due to the presence of both heterophily and heterogeneity. However, existing benchmarks for graph learning often focus on heterogeneous graphs with homophily or homogeneous graphs with heterophily, leaving a gap in understanding how methods perform on graphs that are both heterogeneous and heterophilic. To bridge this gap, we introduce H2GB, a novel graph benchmark that brings together the complexities of both the heterophily and heterogeneity properties of graphs. Our benchmark encompasses 9 diverse real-world datasets across 5 domains, 28 baseline model implementations, and 26 benchmark results. In addition, we present a modular graph transformer framework UnifiedGT and a new model variant, H2G-former, that excels at this challenging benchmark. By integrating masked label embeddings, cross-type heterogeneous attention, and type-specific FFNs, H2G-former effectively tackles graph heterophily and heterogeneity. Extensive experiments across 26 baselines on H2GB reveal inadequacies of current models on heterogeneous heterophilic graph learning, and demonstrate the superiority of our H2G-former over existing solutions. Both the benchmark and the framework are available on GitHub (https://github.com/junhongmit/H2GB) and PyPI (https://pypi.org/project/H2GB), and documentation can be found at https://junhongmit.github.io/H2GB/.

Large and sparse feed-forward layers (S-FFN) such as Mixture-of-Experts (MoE) have proven effective in scaling up Transformers model size for pretraining large language models. By only activating part of the FFN parameters conditioning on input, S-FFN improves generalization performance while keeping training and inference costs (in FLOPs) fixed. In this work, we analyzed two major design choices of S-FFN: the memory block (a.k.a. expert) size and the memory block selection method under a general conceptual framework of sparse neural memory. Using this unified framework, we compare several S-FFN architectures for language modeling and provide insights into their relative efficacy and efficiency. We found a simpler selection method -- \texttt{Avg-K} that selects blocks through their mean aggregated hidden states, achieving lower perplexity in language model pretraining compared to existing MoE architectures including Switch Transformer (Fedus et al., 2021) and HashLayer (Roller et al., 2021).

Fast feedforward networks (FFFs) are a class of neural networks that exploit the observation that different regions of the input space activate distinct subsets of neurons in wide networks. FFFs partition the input space into separate sections using a differentiable binary tree of neurons and during inference descend the binary tree in order to improve computational efficiency. Inspired by Mixture of Experts (MoE) research, we propose the incorporation of load balancing and Master Leaf techniques into the FFF architecture to improve performance and simplify the training process. We reproduce experiments found in literature and present results on FFF models enhanced using these techniques. The proposed architecture and training recipe achieves up to 16.3% and 3% absolute classification accuracy increase in training and test accuracy, respectively, compared to the original FFF architecture. Additionally, we observe a smaller variance in the results compared to those reported in prior research. These findings demonstrate the potential of integrating MoE-inspired techniques into FFFs for developing more accurate and efficient models.

Recent work has shown that feed-forward networks (FFNs) in pre-trained Transformers are a key component, storing various linguistic and factual knowledge. However, the computational patterns of FFNs are still unclear. In this work, we study the computational patterns of FFNs and observe that most inputs only activate a tiny ratio of neurons of FFNs. This phenomenon is similar to the sparsity of the human brain, which drives research on functional partitions of the human brain. To verify whether functional partitions also emerge in FFNs, we propose to convert a model into its MoE version with the same parameters, namely MoEfication. Specifically, MoEfication consists of two phases: (1) splitting the parameters of FFNs into multiple functional partitions as experts, and (2) building expert routers to decide which experts will be used for each input. Experimental results show that MoEfication can conditionally use 10% to 30% of FFN parameters while maintaining over 95% original performance for different models on various downstream tasks. Besides, MoEfication brings two advantages: (1) it significantly reduces the FLOPS of inference, i.e., 2x speedup with 25% of FFN parameters, and (2) it provides a fine-grained perspective to study the inner mechanism of FFNs. The source code of this paper can be obtained from https://github.com/thunlp/MoEfication.

Recent research has demonstrated that Feed-Forward Networks (FFNs) in Large Language Models (LLMs) play a pivotal role in storing diverse linguistic and factual knowledge. Conventional methods frequently face challenges due to knowledge confusion stemming from their monolithic and redundant architectures, which calls for more efficient solutions with minimal computational overhead, particularly for LLMs. In this paper, we explore the FFN computation paradigm in LLMs and introduce FactorLLM, a novel approach that decomposes well-trained dense FFNs into sparse sub-networks without requiring any further modifications, while maintaining the same level of performance. Furthermore, we embed a router from the Mixture-of-Experts (MoE), combined with our devised Prior-Approximate (PA) loss term that facilitates the dynamic activation of experts and knowledge adaptation, thereby accelerating computational processes and enhancing performance using minimal training data and fine-tuning steps. FactorLLM thus enables efficient knowledge factorization and activates select groups of experts specifically tailored to designated tasks, emulating the interactive functional segmentation of the human brain. Extensive experiments across various benchmarks demonstrate the effectiveness of our proposed FactorLLM which achieves comparable performance to the source model securing up to 85% model performance while obtaining over a 30% increase in inference speed. Code: https://github.com/zhenwuweihe/FactorLLM.

We analyze a family of large language models in such a lightweight manner that can be done on a single GPU. Specifically, we focus on the OPT family of models ranging from 125m to 66b parameters and rely only on whether an FFN neuron is activated or not. First, we find that the early part of the network is sparse and represents many discrete features. Here, many neurons (more than 70% in some layers of the 66b model) are "dead", i.e. they never activate on a large collection of diverse data. At the same time, many of the alive neurons are reserved for discrete features and act as token and n-gram detectors. Interestingly, their corresponding FFN updates not only promote next token candidates as could be expected, but also explicitly focus on removing the information about triggering them tokens, i.e., current input. To the best of our knowledge, this is the first example of mechanisms specialized at removing (rather than adding) information from the residual stream. With scale, models become more sparse in a sense that they have more dead neurons and token detectors. Finally, some neurons are positional: them being activated or not depends largely (or solely) on position and less so (or not at all) on textual data. We find that smaller models have sets of neurons acting as position range indicators while larger models operate in a less explicit manner.

Fourier Neural Operators (FNOs) have proven to be an efficient and effective method for resolution-independent operator learning in a broad variety of application areas across scientific machine learning. A key reason for their success is their ability to accurately model long-range dependencies in spatio-temporal data by learning global convolutions in a computationally efficient manner. To this end, FNOs rely on the discrete Fourier transform (DFT), however, DFTs cause visual and spectral artifacts as well as pronounced dissipation when learning operators in spherical coordinates since they incorrectly assume a flat geometry. To overcome this limitation, we generalize FNOs on the sphere, introducing Spherical FNOs (SFNOs) for learning operators on spherical geometries. We apply SFNOs to forecasting atmospheric dynamics, and demonstrate stable auto\-regressive rollouts for a year of simulated time (1,460 steps), while retaining physically plausible dynamics. The SFNO has important implications for machine learning-based simulation of climate dynamics that could eventually help accelerate our response to climate change.

Transformer, composed of self-attention and Feed-Forward Network, has revolutionized the landscape of network design across various vision tasks. FFN is a versatile operator seamlessly integrated into nearly all AI models to effectively harness rich representations. Recent works also show that FFN functions like key-value memories. Thus, akin to the query-key-value mechanism within self-attention, FFN can be viewed as a memory network, where the input serves as query and the two projection weights operate as keys and values, respectively. We hypothesize that the importance lies in query-key-value framework itself rather than in self-attention. To verify this, we propose converting self-attention into a more FFN-like efficient token mixer with only convolutions while retaining query-key-value framework, namely FFNification. Specifically, FFNification replaces query-key and attention coefficient-value interactions with large kernel convolutions and adopts GELU activation function instead of softmax. The derived token mixer, FFNified attention, serves as key-value memories for detecting locally distributed spatial patterns, and operates in the opposite dimension to the ConvNeXt block within each corresponding sub-operation of the query-key-value framework. Building upon the above two modules, we present a family of Fast-Forward Networks. Our FFNet achieves remarkable performance improvements over previous state-of-the-art methods across a wide range of tasks. The strong and general performance of our proposed method validates our hypothesis and leads us to introduce MetaMixer, a general mixer architecture that does not specify sub-operations within the query-key-value framework. We show that using only simple operations like convolution and GELU in the MetaMixer can achieve superior performance.

Transformer-based language models (LMs) are at the core of modern NLP, but their internal prediction construction process is opaque and largely not understood. In this work, we make a substantial step towards unveiling this underlying prediction process, by reverse-engineering the operation of the feed-forward network (FFN) layers, one of the building blocks of transformer models. We view the token representation as a changing distribution over the vocabulary, and the output from each FFN layer as an additive update to that distribution. Then, we analyze the FFN updates in the vocabulary space, showing that each update can be decomposed to sub-updates corresponding to single FFN parameter vectors, each promoting concepts that are often human-interpretable. We then leverage these findings for controlling LM predictions, where we reduce the toxicity of GPT2 by almost 50%, and for improving computation efficiency with a simple early exit rule, saving 20% of computation on average.

Large Language Models (LLMs) typically represent numbers using multiple tokens, which requires the model to aggregate these tokens to interpret numerical values. This fragmentation makes both training and inference less efficient and adversely affects the model's performance on number-related tasks. Inspired by the observation that pre-trained LLMs internally learn Fourier-like features for number tokens, we propose Fourier Number Embedding (FoNE), a novel method that directly maps numbers into the embedding space with their Fourier features. FoNE encodes each number as a single token with only two embedding dimensions per digit, effectively capturing numerical values without fragmentation. This compact representation accelerates both training and inference. Compared to traditional subword and digit-wise embeddings, FoNE not only reduces computational overhead but also achieves higher accuracy across various numerical tasks including addition, subtraction and multiplication. On 6-digit decimal addition, FoNE requires 64times less data to achieve 99% accuracy than subword and digit-wise embeddings while using 3times and 6times fewer tokens per number, respectively. Furthermore, FoNE is the only method that yields 100% accuracy on over 100,000 test examples for addition, subtraction, and multiplication. The codes and visualization are available at https://fouriernumber.github.io/.

Despite the recent success achieved by several two-stage prototypical networks in few-shot named entity recognition (NER) task, the over-detected false spans at span detection stage and the inaccurate and unstable prototypes at type classification stage remain to be challenging problems. In this paper, we propose a novel Type-Aware Decomposed framework, namely TadNER, to solve these problems. We first present a type-aware span filtering strategy to filter out false spans by removing those semantically far away from type names. We then present a type-aware contrastive learning strategy to construct more accurate and stable prototypes by jointly exploiting support samples and type names as references. Extensive experiments on various benchmarks prove that our proposed TadNER framework yields a new state-of-the-art performance.

We introduce FFN Fusion, an architectural optimization technique that reduces sequential computation in large language models by identifying and exploiting natural opportunities for parallelization. Our key insight is that sequences of Feed-Forward Network (FFN) layers, particularly those remaining after the removal of specific attention layers, can often be parallelized with minimal accuracy impact. We develop a principled methodology for identifying and fusing such sequences, transforming them into parallel operations that significantly reduce inference latency while preserving model behavior. Applying these techniques to Llama-3.1-405B-Instruct, we create Llama-Nemotron-Ultra-253B-Base (Ultra-253B-Base), an efficient and soon-to-be publicly available model that achieves a 1.71X speedup in inference latency and 35X lower per-token cost while maintaining strong performance across benchmarks. Through extensive experiments on models from 49B to 253B parameters, we demonstrate that FFN Fusion becomes increasingly effective at larger scales and can complement existing optimization techniques like quantization and pruning. Most intriguingly, we find that even full transformer blocks containing both attention and FFN layers can sometimes be parallelized, suggesting new directions for neural architecture design.

In this work, we aim to simultaneously enhance the effectiveness and efficiency of Mixture-of-Experts (MoE) methods. To achieve this, we propose MoE++, a general and heterogeneous MoE framework that integrates both Feed-Forward Network~(FFN) and zero-computation experts. Specifically, we introduce three types of zero-computation experts: the zero expert, copy expert, and constant expert, which correspond to discard, skip, and replace operations, respectively. This design offers three key advantages: (i) Low Computing Overhead: Unlike the uniform mixing mechanism for all tokens within vanilla MoE, MoE++ allows each token to engage with a dynamic number of FFNs, be adjusted by constant vectors, or even skip the MoE layer entirely. (ii) High Performance: By enabling simple tokens to utilize fewer FFN experts, MoE++ allows more experts to focus on challenging tokens, thereby unlocking greater performance potential than vanilla MoE. (iii) Deployment Friendly: Given that zero-computation experts have negligible parameters, we can deploy all zero-computation experts on each GPU, eliminating the significant communication overhead and expert load imbalance associated with FFN experts distributed across different GPUs. Moreover, we leverage gating residuals, enabling each token to consider the pathway taken in the previous layer when selecting the appropriate experts. Extensive experimental results demonstrate that MoE++ achieves better performance while delivering 1.1-2.1x expert forward throughput compared to a vanilla MoE model of the same size, which lays a solid foundation for developing advanced and efficient MoE-related models.

The impressive performance of ChatGPT and other foundation-model-based products in human language understanding has prompted both academia and industry to explore how these models can be tailored for specific industries and application scenarios. This process, known as the customization of domain-specific foundation models (FMs), addresses the limitations of general-purpose models, which may not fully capture the unique patterns and requirements of domain-specific data. Despite its importance, there is a notable lack of comprehensive overview papers on building domain-specific FMs, while numerous resources exist for general-purpose models. To bridge this gap, this article provides a timely and thorough overview of the methodology for customizing domain-specific FMs. It introduces basic concepts, outlines the general architecture, and surveys key methods for constructing domain-specific models. Furthermore, the article discusses various domains that can benefit from these specialized models and highlights the challenges ahead. Through this overview, we aim to offer valuable guidance and reference for researchers and practitioners from diverse fields to develop their own customized FMs.

The Transformer architecture consists of self-attention and feed-forward networks (FFNs) which can be viewed as key-value memories according to previous works. However, FFN and traditional memory utilize different activation functions (i.e., ReLU and Softmax respectively), which makes them not equivalent. In this paper, we first rebuild the connections between FFN and key-value memory by conducting extensive studies on ReLU and Softmax, and find they are equivalent when adding an additional layer normalization module on Softmax. In addition, ReLU outperforms Softmax on both FFN and key-value memory when the number of value slots is large. We analyze the reasons and then explore this good property of ReLU on the self-attention network where the original Softmax activation performs poorly on long input sequences. We then propose a full ReLU architecture named ReLUFormer which performs better than the baseline Transformer on long sequence tasks such as document translation. This paper sheds light on the following points: 1) Softmax and ReLU use different normalization methods over elements which lead to different variances of results, and ReLU is good at dealing with a large number of key-value slots; 2) FFN and key-value memory are equivalent, and thus the Transformer can be viewed as a memory network where FFNs and self-attention networks are both key-value memories.

We find arithmetic ability resides within a limited number of attention heads, with each head specializing in distinct operations. To delve into the reason, we introduce the Comparative Neuron Analysis (CNA) method, which identifies an internal logic chain consisting of four distinct stages from input to prediction: feature enhancing with shallow FFN neurons, feature transferring by shallow attention layers, feature predicting by arithmetic heads, and prediction enhancing among deep FFN neurons. Moreover, we identify the human-interpretable FFN neurons within both feature-enhancing and feature-predicting stages. These findings lead us to investigate the mechanism of LoRA, revealing that it enhances prediction probabilities by amplifying the coefficient scores of FFN neurons related to predictions. Finally, we apply our method in model pruning for arithmetic tasks and model editing for reducing gender bias. Code is on https://github.com/zepingyu0512/arithmetic-mechanism.

The large number of parameters in Pretrained Language Models enhance their performance, but also make them resource-intensive, making it challenging to deploy them on commodity hardware like a single GPU. Due to the memory and power limitations of these devices, model compression techniques are often used to decrease both the model's size and its inference latency. This usually results in a trade-off between model accuracy and efficiency. Therefore, optimizing this balance is essential for effectively deploying LLMs on commodity hardware. A significant portion of the efficiency challenge is the Feed-forward network (FFN) component, which accounts for roughly 2{3} total parameters and inference latency. In this paper, we first observe that only a few neurons of FFN module have large output norm for any input tokens, a.k.a. heavy hitters, while the others are sparsely triggered by different tokens. Based on this observation, we explicitly split the FFN into two parts according to the heavy hitters. We improve the efficiency-accuracy trade-off of existing compression methods by allocating more resource to FFN parts with heavy hitters. In practice, our method can reduce model size by 43.1\% and bring 1.25sim1.56times wall clock time speedup on different hardware with negligible accuracy drop.

This paper proposes a convolutional neural network (CNN)-based detector for faster-than-Nyquist (FTN) signaling that employs structured fixed kernel layers with domain-informed masking to mitigate intersymbol interference (ISI). Unlike standard CNNs with sliding kernels, the proposed method utilizes fixed-position kernels to directly capture ISI effects at varying distances from the central symbol. A hierarchical filter allocation strategy is also introduced, assigning more filters to earlier layers for strong ISI patterns and fewer to later layers for weaker ones. This design improves detection accuracy while reducing redundant operations. Simulation results show that the detector achieves near-optimal bit error rate (BER) performance for tau geq 0.7, closely matching the BCJR algorithm, and offers computational gains of up to 46% and 84% over M-BCJR for BPSK and QPSK, respectively. Comparative analysis with other methods further highlights the efficiency and effectiveness of the proposed approach. To the best of our knowledge, this is the first application of a fixed-kernel CNN architecture tailored for FTN detection in the literature.

Graph neural networks (GNNs) have achieved remarkable success across a wide range of applications, such as recommendation, drug discovery, and question answering. Behind the success of GNNs lies the backpropagation (BP) algorithm, which is the de facto standard for training deep neural networks (NNs). However, despite its effectiveness, BP imposes several constraints, which are not only biologically implausible, but also limit the scalability, parallelism, and flexibility in learning NNs. Examples of such constraints include storage of neural activities computed in the forward pass for use in the subsequent backward pass, and the dependence of parameter updates on non-local signals. To address these limitations, the forward-forward algorithm (FF) was recently proposed as an alternative to BP in the image classification domain, which trains NNs by performing two forward passes over positive and negative data. Inspired by this advance, we propose ForwardGNN in this work, a new forward learning procedure for GNNs, which avoids the constraints imposed by BP via an effective layer-wise local forward training. ForwardGNN extends the original FF to deal with graph data and GNNs, and makes it possible to operate without generating negative inputs (hence no longer forward-forward). Further, ForwardGNN enables each layer to learn from both the bottom-up and top-down signals without relying on the backpropagation of errors. Extensive experiments on real-world datasets show the effectiveness and generality of the proposed forward graph learning framework. We release our code at https://github.com/facebookresearch/forwardgnn.

Statically analyzing dynamically-typed code is a challenging endeavor, as even seemingly trivial tasks such as determining the targets of procedure calls are non-trivial without knowing the types of objects at compile time. Addressing this challenge, gradual typing is increasingly added to dynamically-typed languages, a prominent example being TypeScript that introduces static typing to JavaScript. Gradual typing improves the developer's ability to verify program behavior, contributing to robust, secure and debuggable programs. In practice, however, users only sparsely annotate types directly. At the same time, conventional type inference faces performance-related challenges as program size grows. Statistical techniques based on machine learning offer faster inference, but although recent approaches demonstrate overall improved accuracy, they still perform significantly worse on user-defined types than on the most common built-in types. Limiting their real-world usefulness even more, they rarely integrate with user-facing applications. We propose CodeTIDAL5, a Transformer-based model trained to reliably predict type annotations. For effective result retrieval and re-integration, we extract usage slices from a program's code property graph. Comparing our approach against recent neural type inference systems, our model outperforms the current state-of-the-art by 7.85% on the ManyTypes4TypeScript benchmark, achieving 71.27% accuracy overall. Furthermore, we present JoernTI, an integration of our approach into Joern, an open source static analysis tool, and demonstrate that the analysis benefits from the additional type information. As our model allows for fast inference times even on commodity CPUs, making our system available through Joern leads to high accessibility and facilitates security research.

Test-time scaling (TTS), which involves dynamic allocation of compute during inference, offers a promising way to improve reasoning in large language models. While existing TTS methods work well, they often rely on long decoding paths or require a large number of samples to be generated, increasing the token usage and inference latency. We observe the surprising fact that for reasoning tasks, shorter traces are much more likely to be correct than longer ones. Motivated by this, we introduce First Finish Search (FFS), a training-free parallel decoding strategy that launches n independent samples and returns as soon as any one completes. We evaluate FFS alongside simple decoding, beam search, majority voting, and budget forcing on four reasoning models (DeepSeek-R1, R1-Distill-Qwen-32B, QwQ-32B and Phi-4-Reasoning-Plus) and across four datasets (AIME24, AIME25-I, AIME25-II and GPQA Diamond). With DeepSeek-R1, FFS achieves 82.23% accuracy on the AIME datasets, a 15% improvement over DeepSeek-R1's standalone accuracy, nearly matching OpenAI's o4-mini performance. Our theoretical analysis explains why stopping at the shortest trace is likely to yield a correct answer and identifies the conditions under which early stopping may be suboptimal. The elegance and simplicity of FFS demonstrate that straightforward TTS strategies can perform remarkably well, revealing the untapped potential of simple approaches at inference time.

State-of-the-art results in large language models (LLMs) often rely on scale, which becomes computationally expensive. This has sparked a research agenda to reduce these models' parameter counts and computational costs without significantly impacting their performance. Our study focuses on transformer-based LLMs, specifically targeting the computationally intensive feedforward networks (FFNs), which are less studied than attention blocks. We consider three structured linear parameterizations of the FFN using efficient low-rank and block-diagonal matrices. In contrast to many previous works that examined these approximations, our study i) explores these structures from a training-from-scratch perspective, ii) scales up to 1.3B parameters, and iii) is conducted within recent Transformer-based LLMs rather than convolutional architectures. We demonstrate that these structures can lead to actual computational gains in various scenarios, including online decoding when using a pre-merge technique. Additionally, we propose a novel training regime, called self-guided training, aimed at improving the poor training dynamics that these approximations exhibit when used from initialization. Interestingly, the scaling performance of structured matrices is explored, revealing steeper curves in scaling training FLOPs, along with a favorable scaling trend in the overtraining regime. Specifically, we show that wide and structured networks can utilize training FLOPs more efficiently, with fewer parameters and lower loss than dense models at their optimal trade-off. Our code is available at https://github.com/CLAIRE-Labo/StructuredFFN/tree/main.

TypeScript and Python are two programming languages that support optional type annotations, which are useful but tedious to introduce and maintain. This has motivated automated type prediction: given an untyped program, produce a well-typed output program. Large language models (LLMs) are promising for type prediction, but there are challenges: fill-in-the-middle performs poorly, programs may not fit into the context window, generated types may not type check, and it is difficult to measure how well-typed the output program is. We address these challenges by building OpenTau, a search-based approach for type prediction that leverages large language models. We propose a new metric for type prediction quality, give a tree-based program decomposition that searches a space of generated types, and present fill-in-the-type fine-tuning for LLMs. We evaluate our work with a new dataset for TypeScript type prediction, and show that 47.4% of files type check (14.5% absolute improvement) with an overall rate of 3.3 type errors per file. All code, data, and models are available at: https://github.com/GammaTauAI/opentau.

Autoregressive Large Language Models (e.g., LLaMa, GPTs) are omnipresent achieving remarkable success in language understanding and generation. However, such impressive capability typically comes with a substantial model size, which presents significant challenges for autoregressive token-by-token generation. To mitigate computation overload incurred during generation, several early-exit and layer-dropping strategies have been proposed. Despite some promising success due to the redundancy across LLMs layers on metrics like Rough-L/BLUE, our careful knowledge-intensive evaluation unveils issues such as generation collapse, hallucination of wrong facts, and noticeable performance drop even at the trivial exit ratio of 10-15% of layers. We attribute these errors primarily to ineffective handling of the KV cache through state copying during early-exit. In this work, we observed the saturation of computationally expensive feed-forward blocks of LLM layers and proposed FFN-SkipLLM, which is a novel fine-grained skip strategy of autoregressive LLMs. More specifically, FFN-SkipLLM is an input-adaptive feed-forward skipping strategy that can skip 25-30% of FFN blocks of LLMs with marginal change in performance on knowledge-intensive generation tasks without any requirement to handle KV cache. Our extensive experiments and ablation across benchmarks like MT-Bench, Factoid-QA, and variable-length text summarization illustrate how our simple and ease-at-use method can facilitate faster autoregressive decoding.

We introduce a simple enhancement of vision transformers (ViTs) to improve accuracy while maintaining throughput. Our approach, Jumbo, creates a wider CLS token, which is split to match the patch token width before attention, processed with self-attention, and reassembled. After attention, Jumbo applies a dedicated, wider FFN to this token. Since there is only one Jumbo token, its cost is minimal, and because we share this FFN across layers, its parameter count is controlled. Jumbo significantly improves over ViT+Registers on ImageNet-1K and ImageNet-21K. These gains are largest at small sizes / high speeds, e.g., ViT-nano+Jumbo outperforms ViT-nano+Registers by 13%. In fact, our Jumbo models are so efficient that they outperform specialized compute-efficient models while preserving the architectural advantages of plain ViTs, such as support for token dropping and other modalities. Accordingly, we demonstrate that Jumbo excels in these two settings via masked autoencoding and on a suite of time series benchmarks. Code and weights available: https://github.com/antofuller/jumbo

Time series analysis is vital for numerous applications, and transformers have become increasingly prominent in this domain. Leading methods customize the transformer architecture from NLP and CV, utilizing a patching technique to convert continuous signals into segments. Yet, time series data are uniquely challenging due to significant distribution shifts and intrinsic noise levels. To address these two challenges,we introduce the Sparse Vector Quantized FFN-Free Transformer (Sparse-VQ). Our methodology capitalizes on a sparse vector quantization technique coupled with Reverse Instance Normalization (RevIN) to reduce noise impact and capture sufficient statistics for forecasting, serving as an alternative to the Feed-Forward layer (FFN) in the transformer architecture. Our FFN-free approach trims the parameter count, enhancing computational efficiency and reducing overfitting. Through evaluations across ten benchmark datasets, including the newly introduced CAISO dataset, Sparse-VQ surpasses leading models with a 7.84% and 4.17% decrease in MAE for univariate and multivariate time series forecasting, respectively. Moreover, it can be seamlessly integrated with existing transformer-based models to elevate their performance.

State-of-the-art LLMs often rely on scale with high computational costs, which has sparked a research agenda to reduce parameter counts and costs without significantly impacting performance. Our study focuses on Transformer-based LLMs, specifically applying low-rank parametrization to the computationally intensive feedforward networks (FFNs), which are less studied than attention blocks. In contrast to previous works, (i) we explore low-rank parametrization at scale, up to 1.3B parameters; (ii) within Transformer language models rather than convolutional architectures; and (iii) starting from training from scratch. Experiments on the large RefinedWeb dataset show that low-rank parametrization is both efficient (e.g., 2.6times FFN speed-up with 32\% parameters) and effective during training. Interestingly, these structured FFNs exhibit steeper scaling curves than the original models. Motivated by this finding, we develop the wide and structured networks surpassing the current medium-sized and large-sized Transformer in perplexity and throughput performance. Our code is available at https://github.com/CLAIRE-Labo/StructuredFFN/tree/main.

Implicit neural representations (INRs) use neural networks to provide continuous and resolution-independent representations of complex signals with a small number of parameters. However, existing INR models often fail to capture important frequency components specific to each task. To address this issue, in this paper, we propose a Fourier Kolmogorov Arnold network (FKAN) for INRs. The proposed FKAN utilizes learnable activation functions modeled as Fourier series in the first layer to effectively control and learn the task-specific frequency components. In addition, the activation functions with learnable Fourier coefficients improve the ability of the network to capture complex patterns and details, which is beneficial for high-resolution and high-dimensional data. Experimental results show that our proposed FKAN model outperforms three state-of-the-art baseline schemes, and improves the peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM) for the image representation task and intersection over union (IoU) for the 3D occupancy volume representation task, respectively.

We consider solving partial differential equations (PDEs) with Fourier neural operators (FNOs), which operate in the frequency domain. Since the laws of physics do not depend on the coordinate system used to describe them, it is desirable to encode such symmetries in the neural operator architecture for better performance and easier learning. While encoding symmetries in the physical domain using group theory has been studied extensively, how to capture symmetries in the frequency domain is under-explored. In this work, we extend group convolutions to the frequency domain and design Fourier layers that are equivariant to rotations, translations, and reflections by leveraging the equivariance property of the Fourier transform. The resulting G-FNO architecture generalizes well across input resolutions and performs well in settings with varying levels of symmetry. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Convolution models with long filters have demonstrated state-of-the-art reasoning abilities in many long-sequence tasks but lag behind the most optimized Transformers in wall-clock time. A major bottleneck is the Fast Fourier Transform (FFT)--which allows long convolutions to run in O(N logN) time in sequence length N but has poor hardware utilization. In this paper, we study how to optimize the FFT convolution. We find two key bottlenecks: the FFT does not effectively use specialized matrix multiply units, and it incurs expensive I/O between layers of the memory hierarchy. In response, we propose FlashFFTConv. FlashFFTConv uses a matrix decomposition that computes the FFT using matrix multiply units and enables kernel fusion for long sequences, reducing I/O. We also present two sparse convolution algorithms--1) partial convolutions and 2) frequency-sparse convolutions--which can be implemented simply by skipping blocks in the matrix decomposition, enabling further opportunities for memory and compute savings. FlashFFTConv speeds up exact FFT convolutions by up to 7.93times over PyTorch and achieves up to 4.4times speedup end-to-end. Given the same compute budget, FlashFFTConv allows Hyena-GPT-s to achieve 2.3 points better perplexity on the PILE and M2-BERT-base to achieve 3.3 points higher GLUE score--matching models with twice the parameter count. FlashFFTConv also achieves 96.1% accuracy on Path-512, a high-resolution vision task where no model had previously achieved better than 50%. Furthermore, partial convolutions enable longer-sequence models--yielding the first DNA model that can process the longest human genes (2.3M base pairs)--and frequency-sparse convolutions speed up pretrained models while maintaining or improving model quality.

Large Language Models (LLMs) have exhibited remarkable proficiency across a wide array of NLP tasks. However, the escalation in model size also engenders substantial deployment costs. While few efforts have explored model pruning techniques to reduce the size of LLMs, they mainly center on general or task-specific weights. This leads to suboptimal performance due to lacking specificity on the target domain or generality on different tasks when applied to domain-specific challenges. This work introduces an innovative unstructured dual-pruning methodology, D-Pruner, for domain-specific compression on LLM. It extracts a compressed, domain-specific, and task-agnostic LLM by identifying LLM weights that are pivotal for general capabilities, like linguistic capability and multi-task solving, and domain-specific knowledge. More specifically, we first assess general weight importance by quantifying the error incurred upon their removal with the help of an open-domain calibration dataset. Then, we utilize this general weight importance to refine the training loss, so that it preserves generality when fitting into a specific domain. Moreover, by efficiently approximating weight importance with the refined training loss on a domain-specific calibration dataset, we obtain a pruned model emphasizing generality and specificity. Our comprehensive experiments across various tasks in healthcare and legal domains show the effectiveness of D-Pruner in domain-specific compression. Our code is available at https://github.com/psunlpgroup/D-Pruner.

Proof-oriented programs mix computational content with proofs of program correctness. However, the human effort involved in programming and proving is still substantial, despite the use of Satisfiability Modulo Theories (SMT) solvers to automate proofs in languages such as F*. Seeking to spur research on using AI to automate the construction of proof-oriented programs, we curate a dataset of 600K lines of open-source F* programs and proofs, including software used in production systems ranging from Windows and Linux, to Python and Firefox. Our dataset includes around 32K top-level F* definitions, each representing a type-directed program and proof synthesis problem -- producing a definition given a formal specification expressed as an F* type. We provide a program-fragment checker that queries F* to check the correctness of candidate solutions. We believe this is the largest corpus of SMT-assisted program proofs coupled with a reproducible program-fragment checker. Grounded in this dataset, we investigate the use of AI to synthesize programs and their proofs in F*, with promising results. Our main finding in that the performance of fine-tuned smaller language models (such as Phi-2 or StarCoder) compare favorably with large language models (such as GPT-4), at a much lower computational cost. We also identify various type-based retrieval augmentation techniques and find that they boost performance significantly. With detailed error analysis and case studies, we identify potential strengths and weaknesses of models and techniques and suggest directions for future improvements.

Existing video recognition algorithms always conduct different training pipelines for inputs with different frame numbers, which requires repetitive training operations and multiplying storage costs. If we evaluate the model using other frames which are not used in training, we observe the performance will drop significantly (see Fig.1), which is summarized as Temporal Frequency Deviation phenomenon. To fix this issue, we propose a general framework, named Frame Flexible Network (FFN), which not only enables the model to be evaluated at different frames to adjust its computation, but also reduces the memory costs of storing multiple models significantly. Concretely, FFN integrates several sets of training sequences, involves Multi-Frequency Alignment (MFAL) to learn temporal frequency invariant representations, and leverages Multi-Frequency Adaptation (MFAD) to further strengthen the representation abilities. Comprehensive empirical validations using various architectures and popular benchmarks solidly demonstrate the effectiveness and generalization of FFN (e.g., 7.08/5.15/2.17% performance gain at Frame 4/8/16 on Something-Something V1 dataset over Uniformer). Code is available at https://github.com/BeSpontaneous/FFN.

The Transformer architecture has two main non-embedding components: Attention and the Feed Forward Network (FFN). Attention captures interdependencies between words regardless of their position, while the FFN non-linearly transforms each input token independently. In this work we explore the role of the FFN, and find that despite taking up a significant fraction of the model's parameters, it is highly redundant. Concretely, we are able to substantially reduce the number of parameters with only a modest drop in accuracy by removing the FFN on the decoder layers and sharing a single FFN across the encoder. Finally we scale this architecture back to its original size by increasing the hidden dimension of the shared FFN, achieving substantial gains in both accuracy and latency with respect to the original Transformer Big.

Recent advancements in operator-type neural networks have shown promising results in approximating the solutions of spatiotemporal Partial Differential Equations (PDEs). However, these neural networks often entail considerable training expenses, and may not always achieve the desired accuracy required in many scientific and engineering disciplines. In this paper, we propose a new Spatiotemporal Fourier Neural Operator (SFNO) that learns maps between Bochner spaces, and a new learning framework to address these issues. This new paradigm leverages wisdom from traditional numerical PDE theory and techniques to refine the pipeline of commonly adopted end-to-end neural operator training and evaluations. Specifically, in the learning problems for the turbulent flow modeling by the Navier-Stokes Equations (NSE), the proposed architecture initiates the training with a few epochs for SFNO, concluding with the freezing of most model parameters. Then, the last linear spectral convolution layer is fine-tuned without the frequency truncation. The optimization uses a negative Sobolev norm for the first time as the loss in operator learning, defined through a reliable functional-type a posteriori error estimator whose evaluation is almost exact thanks to the Parseval identity. This design allows the neural operators to effectively tackle low-frequency errors while the relief of the de-aliasing filter addresses high-frequency errors. Numerical experiments on commonly used benchmarks for the 2D NSE demonstrate significant improvements in both computational efficiency and accuracy, compared to end-to-end evaluation and traditional numerical PDE solvers.

In solving partial differential equations (PDEs), Fourier Neural Operators (FNOs) have exhibited notable effectiveness compared to Convolutional Neural Networks (CNNs). This paper presents clear empirical evidence through spectral analysis to elucidate the superiority of FNO over CNNs: FNO is significantly more capable of learning low-frequencies. This empirical evidence also unveils FNO's distinct low-frequency bias, which limits FNO's effectiveness in learning high-frequency information from PDE data. To tackle this challenge, we introduce SpecBoost, an ensemble learning framework that employs multiple FNOs to better capture high-frequency information. Specifically, a secondary FNO is utilized to learn the overlooked high-frequency information from the prediction residual of the initial FNO. Experiments demonstrate that SpecBoost noticeably enhances FNO's prediction accuracy on diverse PDE applications, achieving an up to 71% improvement.

The design choices in Transformer feed-forward neural networks have resulted in significant computational and parameter overhead. In this work, we emphasize the importance of hidden dimension in designing lightweight FFNs, a factor often overlooked in previous architectures. Guided by this principle, we introduce PartialFormer, a parameter-efficient Transformer architecture utilizing multiple smaller FFNs to reduce parameters and computation while maintaining essential hidden dimensions. These smaller FFNs are integrated into a multi-head attention system to enable effective collaboration. We also propose a tailored head scaling strategy to enhance PartialFormer's capabilities. Furthermore, we present a residual-like attention calculation to improve depth scaling within PartialFormer. Extensive experiments on 9 translation tasks and 1 abstractive summarization task validate the effectiveness of our PartialFormer approach. Our code would be available at: https://github.com/zhengkid/PartialFormer.

We present the first simulations of core-collapse supernovae in axial symmetry with feedback from fast neutrino flavor conversion (FFC). Our schematic treatment of FFCs assumes instantaneous flavor equilibration under the constraint of lepton-number conservation individually for each flavor. Systematically varying the spatial domain where FFCs are assumed to occur, we find that they facilitate SN explosions in low-mass (9-12 solar masses) progenitors that otherwise explode with longer time delays, whereas FFCs weaken the tendency to explode of higher-mass (around 20 solar masses) progenitors.

Neural networks have shown tremendous growth in recent years to solve numerous problems. Various types of neural networks have been introduced to deal with different types of problems. However, the main goal of any neural network is to transform the non-linearly separable input data into more linearly separable abstract features using a hierarchy of layers. These layers are combinations of linear and nonlinear functions. The most popular and common non-linearity layers are activation functions (AFs), such as Logistic Sigmoid, Tanh, ReLU, ELU, Swish and Mish. In this paper, a comprehensive overview and survey is presented for AFs in neural networks for deep learning. Different classes of AFs such as Logistic Sigmoid and Tanh based, ReLU based, ELU based, and Learning based are covered. Several characteristics of AFs such as output range, monotonicity, and smoothness are also pointed out. A performance comparison is also performed among 18 state-of-the-art AFs with different networks on different types of data. The insights of AFs are presented to benefit the researchers for doing further research and practitioners to select among different choices. The code used for experimental comparison is released at: https://github.com/shivram1987/ActivationFunctions.

Foundation Models (FMs) serve as a general class for the development of artificial intelligence systems, offering broad potential for generalization across a spectrum of downstream tasks. Despite extensive research into self-supervised learning as the cornerstone of FMs, several outstanding issues persist in Graph Foundation Models that rely on graph self-supervised learning, namely: 1) Homogenization. The extent of generalization capability on downstream tasks remains unclear. 2) Scalability. It is unknown how effectively these models can scale to large datasets. 3) Efficiency. The training time and memory usage of these models require evaluation. 4) Training Stop Criteria. Determining the optimal stopping strategy for pre-training across multiple tasks to maximize performance on downstream tasks. To address these questions, we have constructed a rigorous benchmark that thoroughly analyzes and studies the generalization and scalability of self-supervised Graph Neural Network (GNN) models. Regarding generalization, we have implemented and compared the performance of various self-supervised GNN models, trained to generate node representations, across tasks such as node classification, link prediction, and node clustering. For scalability, we have compared the performance of various models after training using full-batch and mini-batch strategies. Additionally, we have assessed the training efficiency of these models by conducting experiments to test their GPU memory usage and throughput. Through these experiments, we aim to provide insights to motivate future research. The code for this benchmark is publicly available at https://github.com/NYUSHCS/GraphFM.

The Transformer architecture is widely used in natural language processing. Despite its success, the design principle of the Transformer remains elusive. In this paper, we provide a novel perspective towards understanding the architecture: we show that the Transformer can be mathematically interpreted as a numerical Ordinary Differential Equation (ODE) solver for a convection-diffusion equation in a multi-particle dynamic system. In particular, how words in a sentence are abstracted into contexts by passing through the layers of the Transformer can be interpreted as approximating multiple particles' movement in the space using the Lie-Trotter splitting scheme and the Euler's method. Given this ODE's perspective, the rich literature of numerical analysis can be brought to guide us in designing effective structures beyond the Transformer. As an example, we propose to replace the Lie-Trotter splitting scheme by the Strang-Marchuk splitting scheme, a scheme that is more commonly used and with much lower local truncation errors. The Strang-Marchuk splitting scheme suggests that the self-attention and position-wise feed-forward network (FFN) sub-layers should not be treated equally. Instead, in each layer, two position-wise FFN sub-layers should be used, and the self-attention sub-layer is placed in between. This leads to a brand new architecture. Such an FFN-attention-FFN layer is "Macaron-like", and thus we call the network with this new architecture the Macaron Net. Through extensive experiments, we show that the Macaron Net is superior to the Transformer on both supervised and unsupervised learning tasks. The reproducible codes and pretrained models can be found at https://github.com/zhuohan123/macaron-net

We propose a scalable Forward-Forward (FF) algorithm that eliminates the need for backpropagation by training each layer separately. Unlike backpropagation, FF avoids backward gradients and can be more modular and memory efficient, making it appealing for large networks. We extend FF to modern convolutional architectures, such as MobileNetV3 and ResNet18, by introducing a new way to compute losses for convolutional layers. Experiments show that our method achieves performance comparable to standard backpropagation. Furthermore, when we divide the network into blocks, such as the residual blocks in ResNet, and apply backpropagation only within each block, but not across blocks, our hybrid design tends to outperform backpropagation baselines while maintaining a similar training speed. Finally, we present experiments on small datasets and transfer learning that confirm the adaptability of our method.

Transformer-based large language models (e.g., BERT and GPT) achieve great success, and fine-tuning, which tunes a pre-trained model on a task-specific dataset, is the standard practice to utilize these models for downstream tasks. However, Transformer fine-tuning has long running time and high memory consumption due to the large size of the models. We propose the SPT system to fine-tune Transformer-based models efficiently by introducing sparsity. We observe that the memory consumption of Transformer mainly comes from storing attention weights for multi-head attention (MHA), and the majority of running time is spent on feed-forward network (FFN). Thus, we design the sparse MHA module, which computes and stores only large attention weights to reduce memory consumption, and the routed FFN module, which dynamically activates a subset of model parameters for each token to reduce computation cost. We implement SPT on PyTorch and customize CUDA kernels to run sparse MHA and routed FFN efficiently. Specifically, we use product quantization to identify the large attention weights and compute attention via sparse matrix multiplication for sparse MHA. For routed FFN, we batch the tokens according to their activated model parameters for efficient computation. We conduct extensive experiments to evaluate SPT on various model configurations. The results show that SPT consistently outperforms well-optimized baselines, reducing the peak memory consumption by up to 50% and accelerating fine-tuning by up to 2.2x.

Conventional self-attention mechanisms incur quadratic complexity, limiting their scalability on long sequences. We introduce FFTNet, an adaptive spectral filtering framework that leverages the Fast Fourier Transform (FFT) to achieve global token mixing in O(nlog n) time. By transforming inputs into the frequency domain, FFTNet exploits the orthogonality and energy preservation guaranteed by Parseval's theorem to capture long-range dependencies efficiently. A learnable spectral filter and modReLU activation dynamically emphasize salient frequency components, providing a rigorous and adaptive alternative to traditional self-attention. Experiments on the Long Range Arena and ImageNet benchmarks validate our theoretical insights and demonstrate superior performance over fixed Fourier and standard attention models.

Fine-tuning Large Language Models (LLMs) on specific datasets is a common practice to improve performance on target tasks. However, this performance gain often leads to overfitting, where the model becomes too specialized in either the task or the characteristics of the training data, resulting in a loss of generalization. This paper introduces Selective Self-to-Supervised Fine-Tuning (S3FT), a fine-tuning approach that achieves better performance than the standard supervised fine-tuning (SFT) while improving generalization. S3FT leverages the existence of multiple valid responses to a query. By utilizing the model's correct responses, S3FT reduces model specialization during the fine-tuning stage. S3FT first identifies the correct model responses from the training set by deploying an appropriate judge. Then, it fine-tunes the model using the correct model responses and the gold response (or its paraphrase) for the remaining samples. The effectiveness of S3FT is demonstrated through experiments on mathematical reasoning, Python programming and reading comprehension tasks. The results show that standard SFT can lead to an average performance drop of up to 4.4 on multiple benchmarks, such as MMLU and TruthfulQA. In contrast, S3FT reduces this drop by half, i.e. 2.5, indicating better generalization capabilities than SFT while performing significantly better on the fine-tuning tasks.

In this paper, we present an improved feedforward sequential memory networks (FSMN) architecture, namely Deep-FSMN (DFSMN), by introducing skip connections between memory blocks in adjacent layers. These skip connections enable the information flow across different layers and thus alleviate the gradient vanishing problem when building very deep structure. As a result, DFSMN significantly benefits from these skip connections and deep structure. We have compared the performance of DFSMN to BLSTM both with and without lower frame rate (LFR) on several large speech recognition tasks, including English and Mandarin. Experimental results shown that DFSMN can consistently outperform BLSTM with dramatic gain, especially trained with LFR using CD-Phone as modeling units. In the 2000 hours Fisher (FSH) task, the proposed DFSMN can achieve a word error rate of 9.4% by purely using the cross-entropy criterion and decoding with a 3-gram language model, which achieves a 1.5% absolute improvement compared to the BLSTM. In a 20000 hours Mandarin recognition task, the LFR trained DFSMN can achieve more than 20% relative improvement compared to the LFR trained BLSTM. Moreover, we can easily design the lookahead filter order of the memory blocks in DFSMN to control the latency for real-time applications.

Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes grow. Moreover, existing GFMs are constrained by rigid output formats, limiting their applicability to various genomic tasks. In this work, we revisit the transformer-based auto-regressive models and introduce Omni-DNA, a family of cross-modal multi-task models ranging from 20 million to 1 billion parameters. Our approach consists of two stages: (i) pretraining on DNA sequences with next token prediction objective, and (ii) expanding the multi-modal task-specific tokens and finetuning for multiple downstream tasks simultaneously. When evaluated on the Nucleotide Transformer and GB benchmarks, Omni-DNA achieves state-of-the-art performance on 18 out of 26 tasks. Through multi-task finetuning, Omni-DNA addresses 10 acetylation and methylation tasks at once, surpassing models trained on each task individually. Finally, we design two complex genomic tasks, DNA2Function and Needle-in-DNA, which map DNA sequences to textual functional descriptions and images, respectively, indicating Omni-DNA's cross-modal capabilities to broaden the scope of genomic applications. All the models are available through https://huggingface.co/collections/zehui127

We introduce Probabilistic Dependent Type Systems (PDTS) via a functional language based on a subsystem of intuitionistic type theory including dependent sums and products, which is expanded to include stochastic functions. We provide a sampling-based semantics for the language based on non-deterministic beta reduction. Further, we derive a probabilistic logic from the PDTS introduced as a direct result of the Curry-Howard isomorphism. The probabilistic logic derived is shown to provide a universal representation for finite discrete distributions.

This paper investigates the key role of Feed-Forward Networks (FFNs) in transformer models by utilizing the Parallel Attention and Feed-Forward Net Design (PAF) architecture, and comparing it to their Series Attention and Feed-Forward Net Design (SAF) counterparts. Central to the effectiveness of PAF are two main assumptions regarding the FFN block and the attention block within a layer: 1) the primary function of the FFN block is to maintain isotropy among token embeddings and prevent their degeneration, and 2) the residual norm computed in the attention block is substantially smaller than the input token embedding norm. To empirically validate these assumptions, we train PAF variants of two large language models (RoBERTa-large and bert-large-uncased). Our results demonstrate that both assumptions hold true in the PAF design. This study contributes to a deeper understanding of the roles and interactions between FFNs and self-attention mechanisms in transformer architectures.

We present any4, a learned 4-bit weight quantization solution for large language models (LLMs) providing arbitrary numeric representations without requiring pre-processing of weights or activations. any4 yields higher accuracy compared to other related 4-bit numeric representation types: int4, fp4 and nf4, as evaluated on a range of model sizes, generations and families (Llama 2, Llama 3, Mistral and Mixtral). While any4 does not require preprocessing of weights or activations, it is also competitive with orthogonal techniques that require such preprocessing (e.g., AWQ and GPTQ). We also experiment with any3 and any2 and show competitiveness at lower bits. Additionally, we show that we can calibrate using a single curated diverse sample rather than hundreds of samples from a dataset as done in most quantization approaches. We also open source tinygemm, a latency optimized GPU matrix multiplication library for LLMs, that implements any4 using a GPU-efficient lookup table strategy along with other common quantization methods. We open source our code at https://github.com/facebookresearch/any4 .

Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built from shorter subsequences by classifying them as applicable or inapplicable for the synthesis method using three different machine learning methods: Support Vector Machines (SVMs), random forest, and Convolution Neural Networks (CNNs). Before applying these methods to the data, a series of feature selection, curation, and reduction steps are applied to create an accurate and representative feature space. Following these preprocessing steps, three different pipelines are proposed to classify subsequences based on their nucleotide sequence and other relevant features corresponding to the restriction sites of over 200 endonucleases. The sensitivity using SVMs, random forest, and CNNs are 94.9%, 92.7%, 91.4%, respectively. Moreover, each method scores lower in specificity with SVMs, random forest, and CNNs resulting in 77.4%, 85.7%, and 82.4%, respectively. In addition to analyzing these results, the misclassifications in SVMs and CNNs are investigated. Across these two models, different features with a derived nucleotide specificity visually contribute more to classification compared to other features. This observation is an important factor when considering new nucleotide sensitivity features for future studies.

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

Modern instruction-tuned large language models (LLMs) have made remarkable progress in code generation. However, these LLMs fine-tuned with standard supervised fine-tuning (SFT) sometimes generate plausible-looking but functionally incorrect code variants. This issue likely stems from the limitation of standard SFT, which treats all tokens equally during optimization and fails to emphasize the error-sensitive segments-specific code differences between correct implementations and similar incorrect variants. To address this problem, we propose Fault-Aware Fine-Tuning (FAIT), a novel fine-tuning technique that enhances LLMs' code generation by (1) extracting multi-granularity (line/token-level) differences between correct and incorrect yet similar implementations to identify error-sensitive segments, and (2) dynamically prioritizing those segments during training via dynamic loss weighting. Through extensive experiments on seven LLMs across three widely-used benchmarks, our method achieves an average relative improvement of 6.9% on pass@1 with just one epoch of training, with some enhanced 6.7B LLMs outperforming closed-source models, e.g., GPT-3.5-Turbo. Furthermore, our fine-tuning technique demonstrates strong generalization with performance improvements ranging from 3.8% to 19.1% across diverse instruction-tuned LLMs, and our ablation studies confirm the contributions of different granularities of differences and loss function components.

Designing domain specific neural networks is a time-consuming, error-prone, and expensive task. Neural Architecture Search (NAS) exists to simplify domain-specific model development but there is a gap in the literature for time series classification on microcontrollers. Therefore, we adapt the concept of differentiable neural architecture search (DNAS) to solve the time-series classification problem on resource-constrained microcontrollers (MCUs). We introduce MicroNAS, a domain-specific HW-NAS system integration of DNAS, Latency Lookup Tables, dynamic convolutions and a novel search space specifically designed for time-series classification on MCUs. The resulting system is hardware-aware and can generate neural network architectures that satisfy user-defined limits on the execution latency and peak memory consumption. Our extensive studies on different MCUs and standard benchmark datasets demonstrate that MicroNAS finds MCU-tailored architectures that achieve performance (F1-score) near to state-of-the-art desktop models. We also show that our approach is superior in adhering to memory and latency constraints compared to domain-independent NAS baselines such as DARTS.

Deep learning techniques have provided significant improvements in hyperspectral image (HSI) classification. The current deep learning based HSI classifiers follow a patch-based learning framework by dividing the image into overlapping patches. As such, these methods are local learning methods, which have a high computational cost. In this paper, a fast patch-free global learning (FPGA) framework is proposed for HSI classification. In FPGA, an encoder-decoder based FCN is utilized to consider the global spatial information by processing the whole image, which results in fast inference. However, it is difficult to directly utilize the encoder-decoder based FCN for HSI classification as it always fails to converge due to the insufficiently diverse gradients caused by the limited training samples. To solve the divergence problem and maintain the abilities of FCN of fast inference and global spatial information mining, a global stochastic stratified sampling strategy is first proposed by transforming all the training samples into a stochastic sequence of stratified samples. This strategy can obtain diverse gradients to guarantee the convergence of the FCN in the FPGA framework. For a better design of FCN architecture, FreeNet, which is a fully end-to-end network for HSI classification, is proposed to maximize the exploitation of the global spatial information and boost the performance via a spectral attention based encoder and a lightweight decoder. A lateral connection module is also designed to connect the encoder and decoder, fusing the spatial details in the encoder and the semantic features in the decoder. The experimental results obtained using three public benchmark datasets suggest that the FPGA framework is superior to the patch-based framework in both speed and accuracy for HSI classification. Code has been made available at: https://github.com/Z-Zheng/FreeNet.

Communications satellite network (CSN), as an integral component of the next generation of communication systems, has the capability to offer services globally. Data transmission in this network primarily relies on two modes: inter-satellite communication and satellite-to-ground station communication. The latter directly impacts the successful reception of data by users. However, due to resource and task limitations, finding a satisfactory solution poses a significant challenge. The communication satellite-ground station network scheduling problem (CS-GSNSP) aims to optimize CSN effectiveness by devising a plan that maximizes link construction time while considering constraints associated with satellite operation modes. The large number of tasks and numerous constraints in the problem result in a time-consuming evaluation of fitness function values. To address this issue, we propose a fuzzy fitness evaluation method (FFEM) that employs fuzzy or real evaluation methods based on individual similarity degrees. Additionally, we introduce an evolutionary algorithm based on FFEM, called evolutionary algorithm based on FFEM (FFEEA), for iteratively searching high-quality network construction schemes. In FFEEA, an adaptive crossover approach is used for efficient population search. Finally, extensive experiments are conducted to demonstrate that our proposed fuzzy fitness evaluation method and other improvement strategies significantly enhance satellite network service time. The study introduces a novel approach to enhance the efficiency of solving combinatorial optimization problems, such as CS-GSNSP, by mitigating the complexity associated with fitness evaluation.

Large language models (LLMs) achieve impressive performance by scaling model parameters, but this comes with significant inference overhead. Feed-forward networks (FFNs), which dominate LLM parameters, exhibit high activation sparsity in hidden neurons. To exploit this, researchers have proposed using a mixture-of-experts (MoE) architecture, where only a subset of parameters is activated. However, existing approaches often require extensive training data and resources, limiting their practicality. We propose CMoE (Carved MoE), a novel framework to efficiently carve MoE models from dense models. CMoE achieves remarkable performance through efficient expert grouping and lightweight adaptation. First, neurons are grouped into shared and routed experts based on activation rates. Next, we construct a routing mechanism without training from scratch, incorporating a differentiable routing process and load balancing. Using modest data, CMoE produces a well-designed, usable MoE from a 7B dense model within five minutes. With lightweight fine-tuning, it achieves high-performance recovery in under an hour. We make our code publicly available at https://github.com/JarvisPei/CMoE.

Pruning is a model compression method that removes redundant parameters in deep neural networks (DNNs) while maintaining accuracy. Most available filter pruning methods require complex treatments such as iterative pruning, features statistics/ranking, or additional optimization designs in the training process. In this paper, we propose a simple and effective regularization strategy from a new perspective of evolution of features, which we call feature flow regularization (FFR), for improving structured sparsity and filter pruning in DNNs. Specifically, FFR imposes controls on the gradient and curvature of feature flow along the neural network, which implicitly increases the sparsity of the parameters. The principle behind FFR is that coherent and smooth evolution of features will lead to an efficient network that avoids redundant parameters. The high structured sparsity obtained from FFR enables us to prune filters effectively. Experiments with VGGNets, ResNets on CIFAR-10/100, and Tiny ImageNet datasets demonstrate that FFR can significantly improve both unstructured and structured sparsity. Our pruning results in terms of reduction of parameters and FLOPs are comparable to or even better than those of state-of-the-art pruning methods.

The discovery of the lazy neuron phenomenon in trained Transformers, where the vast majority of neurons in their feed-forward networks (FFN) are inactive for each token, has spurred tremendous interests in activation sparsity for enhancing large model efficiency. While notable progress has been made in translating such sparsity to wall-time benefits, modern Transformers have moved away from the ReLU activation function crucial to this phenomenon. Existing efforts on re-introducing activation sparsity often degrade model quality, increase parameter count, complicate or slow down training. Sparse attention, the application of sparse activation to the attention mechanism, often faces similar challenges. This paper introduces the Spark Transformer, a novel architecture that achieves a high level of activation sparsity in both FFN and the attention mechanism while maintaining model quality, parameter count, and standard training procedures. Our method realizes sparsity via top-k masking for explicit control over sparsity level. Crucially, we introduce statistical top-k, a hardware-accelerator-friendly, linear-time approximate algorithm that avoids costly sorting and mitigates significant training slowdown from standard top-k operators. Furthermore, Spark Transformer reallocates existing FFN parameters and attention key embeddings to form a low-cost predictor for identifying activated entries. This design not only mitigates quality loss from enforced sparsity, but also enhances wall-time benefit. Pretrained with the Gemma-2 recipe, Spark Transformer demonstrates competitive performance on standard benchmarks while exhibiting significant sparsity: only 8% of FFN neurons are activated, and each token attends to a maximum of 256 tokens. This sparsity translates to a 2.5x reduction in FLOPs, leading to decoding wall-time speedups of up to 1.79x on CPU and 1.40x on GPU.

With large Foundation Models (FMs), language technologies (AI in general) are entering a new paradigm: eliminating the need for developing large-scale task-specific datasets and supporting a variety of tasks through set-ups ranging from zero-shot to few-shot learning. However, understanding FMs capabilities requires a systematic benchmarking effort by comparing FMs performance with the state-of-the-art (SOTA) task-specific models. With that goal, past work focused on the English language and included a few efforts with multiple languages. Our study contributes to ongoing research by evaluating FMs performance for standard Arabic NLP and Speech processing, including a range of tasks from sequence tagging to content classification across diverse domains. We start with zero-shot learning using GPT-3.5-turbo, Whisper, and USM, addressing 33 unique tasks using 59 publicly available datasets resulting in 96 test setups. For a few tasks, FMs performs on par or exceeds the performance of the SOTA models but for the majority it under-performs. Given the importance of prompt for the FMs performance, we discuss our prompt strategies in detail and elaborate on our findings. Our future work on Arabic AI will explore few-shot prompting, expand the range of tasks, and investigate additional open-source models.

As mathematical computing becomes more democratized in high-level languages, high-performance symbolic-numeric systems are necessary for domain scientists and engineers to get the best performance out of their machine without deep knowledge of code optimization. Naturally, users need different term types either to have different algebraic properties for them, or to use efficient data structures. To this end, we developed Symbolics.jl, an extendable symbolic system which uses dynamic multiple dispatch to change behavior depending on the domain needs. In this work we detail an underlying abstract term interface which allows for speed without sacrificing generality. We show that by formalizing a generic API on actions independent of implementation, we can retroactively add optimized data structures to our system without changing the pre-existing term rewriters. We showcase how this can be used to optimize term construction and give a 113x acceleration on general symbolic transformations. Further, we show that such a generic API allows for complementary term-rewriting implementations. We demonstrate the ability to swap between classical term-rewriting simplifiers and e-graph-based term-rewriting simplifiers. We showcase an e-graph ruleset which minimizes the number of CPU cycles during expression evaluation, and demonstrate how it simplifies a real-world reaction-network simulation to halve the runtime. Additionally, we show a reaction-diffusion partial differential equation solver which is able to be automatically converted into symbolic expressions via multiple dispatch tracing, which is subsequently accelerated and parallelized to give a 157x simulation speedup. Together, this presents Symbolics.jl as a next-generation symbolic-numeric computing environment geared towards modeling and simulation.

Physics-Informed Neural Networks (PINNs), which incorporate PDEs as soft constraints, train with a composite loss function that contains multiple training point types: different types of collocation points chosen during training to enforce each PDE and initial/boundary conditions, and experimental points which are usually costly to obtain via experiments or simulations. Training PINNs using this loss function is challenging as it typically requires selecting large numbers of points of different types, each with different training dynamics. Unlike past works that focused on the selection of either collocation or experimental points, this work introduces PINN Adaptive ColLocation and Experimental points selection (PINNACLE), the first algorithm that jointly optimizes the selection of all training point types, while automatically adjusting the proportion of collocation point types as training progresses. PINNACLE uses information on the interaction among training point types, which had not been considered before, based on an analysis of PINN training dynamics via the Neural Tangent Kernel (NTK). We theoretically show that the criterion used by PINNACLE is related to the PINN generalization error, and empirically demonstrate that PINNACLE is able to outperform existing point selection methods for forward, inverse, and transfer learning problems.

Text-to-Speech (TTS) systems face ongoing challenges in processing complex linguistic features, handling polyphonic expressions, and producing natural-sounding multilingual speech - capabilities that are crucial for future AI applications. In this paper, we present Fish-Speech, a novel framework that implements a serial fast-slow Dual Autoregressive (Dual-AR) architecture to enhance the stability of Grouped Finite Scalar Vector Quantization (GFSQ) in sequence generation tasks. This architecture improves codebook processing efficiency while maintaining high-fidelity outputs, making it particularly effective for AI interactions and voice cloning. Fish-Speech leverages Large Language Models (LLMs) for linguistic feature extraction, eliminating the need for traditional grapheme-to-phoneme (G2P) conversion and thereby streamlining the synthesis pipeline and enhancing multilingual support. Additionally, we developed FF-GAN through GFSQ to achieve superior compression ratios and near 100\% codebook utilization. Our approach addresses key limitations of current TTS systems while providing a foundation for more sophisticated, context-aware speech synthesis. Experimental results show that Fish-Speech significantly outperforms baseline models in handling complex linguistic scenarios and voice cloning tasks, demonstrating its potential to advance TTS technology in AI applications. The implementation is open source at https://github.com/fishaudio/fish-speech{https://github.com/fishaudio/fish-speech}.

We explore different ways to utilize position-based cross-attention in seq2seq networks to enable length generalization in algorithmic tasks. We show that a simple approach of interpolating the original and reversed encoded representations combined with relative attention allows near-perfect length generalization for both forward and reverse lookup tasks or copy tasks that had been generally hard to tackle. We also devise harder diagnostic tasks where the relative distance of the ideal attention position varies with timestep. In such settings, the simple interpolation trick with relative attention is not sufficient. We introduce novel variants of location attention building on top of Dubois et al. (2020) to address the new diagnostic tasks. We also show the benefits of our approaches for length generalization in SCAN (Lake & Baroni, 2018) and CFQ (Keysers et al., 2020). Our code is available on GitHub.

Despite the remarkable success achieved by neural networks, particularly those represented by MLP and Transformer, we reveal that they exhibit potential flaws in the modeling and reasoning of periodicity, i.e., they tend to memorize the periodic data rather than genuinely understanding the underlying principles of periodicity. However, periodicity is a crucial trait in various forms of reasoning and generalization, underpinning predictability across natural and engineered systems through recurring patterns in observations. In this paper, we propose FAN, a novel network architecture based on Fourier Analysis, which empowers the ability to efficiently model and reason about periodic phenomena. By introducing Fourier Series, the periodicity is naturally integrated into the structure and computational processes of the neural network, thus achieving a more accurate expression and prediction of periodic patterns. As a promising substitute to multi-layer perceptron (MLP), FAN can seamlessly replace MLP in various models with fewer parameters and FLOPs. Through extensive experiments, we demonstrate the effectiveness of FAN in modeling and reasoning about periodic functions, and the superiority and generalizability of FAN across a range of real-world tasks, including symbolic formula representation, time series forecasting, and language modeling.

FP8 is a natural progression for accelerating deep learning training inference beyond the 16-bit formats common in modern processors. In this paper we propose an 8-bit floating point (FP8) binary interchange format consisting of two encodings - E4M3 (4-bit exponent and 3-bit mantissa) and E5M2 (5-bit exponent and 2-bit mantissa). While E5M2 follows IEEE 754 conventions for representatio of special values, E4M3's dynamic range is extended by not representing infinities and having only one mantissa bit-pattern for NaNs. We demonstrate the efficacy of the FP8 format on a variety of image and language tasks, effectively matching the result quality achieved by 16-bit training sessions. Our study covers the main modern neural network architectures - CNNs, RNNs, and Transformer-based models, leaving all the hyperparameters unchanged from the 16-bit baseline training sessions. Our training experiments include large, up to 175B parameter, language models. We also examine FP8 post-training-quantization of language models trained using 16-bit formats that resisted fixed point int8 quantization.

We present FFCV, a library for easy and fast machine learning model training. FFCV speeds up model training by eliminating (often subtle) data bottlenecks from the training process. In particular, we combine techniques such as an efficient file storage format, caching, data pre-loading, asynchronous data transfer, and just-in-time compilation to (a) make data loading and transfer significantly more efficient, ensuring that GPUs can reach full utilization; and (b) offload as much data processing as possible to the CPU asynchronously, freeing GPU cycles for training. Using FFCV, we train ResNet-18 and ResNet-50 on the ImageNet dataset with competitive tradeoff between accuracy and training time. For example, we are able to train an ImageNet ResNet-50 model to 75\% in only 20 mins on a single machine. We demonstrate FFCV's performance, ease-of-use, extensibility, and ability to adapt to resource constraints through several case studies. Detailed installation instructions, documentation, and Slack support channel are available at https://ffcv.io/ .

How to evaluate Large Language Models (LLMs) in code generation remains an open question. Existing benchmarks have two limitations - data leakage and lack of domain-specific evaluation. The former hurts the fairness of benchmarks, and the latter hinders practitioners from selecting superior LLMs for specific programming domains. To address these two limitations, we propose a new benchmark - EvoCodeBench, which has the following advances: (1) Evolving data. EvoCodeBench will be dynamically updated every period (e.g., 6 months) to avoid data leakage. This paper releases the first version - EvoCodeBench-2403, containing 275 samples from 25 repositories. (2) A domain taxonomy and domain labels. Based on the statistics of open-source communities, we design a programming domain taxonomy consisting of 10 popular domains. Based on the taxonomy, we annotate each sample in EvoCodeBench with a domain label. (3) Domain-specific evaluations. Besides the Pass@k, we compute the Domain-Specific Improvement (DSI) and define LLMs' comfort and strange domains. These evaluations help practitioners select superior LLMs in specific domains and discover the shortcomings of existing LLMs. We evaluate 8 popular LLMs (e.g., gpt-4, DeepSeek Coder) on EvoCodeBench and summarize some insights. EvoCodeBench reveals the actual abilities of these LLMs in real-world repositories. For example, the highest Pass@1 of gpt-4 on EvoCodeBench-2403 is only 20.74%. Besides, we evaluate LLMs in different domains and discover their comfort and strange domains. For example, gpt-4 performs best in most domains but falls behind others in the Internet domain. StarCoder 2-15B unexpectedly performs well in the Database domain and even outperforms 33B LLMs. EvoCodeBench has been released.

Foundation Models (FMs) are models trained on large corpora of data that, at very large scale, can generalize to new tasks without any task-specific finetuning. As these models continue to grow in size, innovations continue to push the boundaries of what these models can do on language and image tasks. This paper aims to understand an underexplored area of FMs: classical data tasks like cleaning and integration. As a proof-of-concept, we cast five data cleaning and integration tasks as prompting tasks and evaluate the performance of FMs on these tasks. We find that large FMs generalize and achieve SoTA performance on data cleaning and integration tasks, even though they are not trained for these data tasks. We identify specific research challenges and opportunities that these models present, including challenges with private and domain specific data, and opportunities to make data management systems more accessible to non-experts. We make our code and experiments publicly available at: https://github.com/HazyResearch/fm_data_tasks.

This paper presents NT-Java-1.1B, an open-source specialized code language model built on StarCoderBase-1.1B, designed for coding tasks in Java programming. NT-Java-1.1B achieves state-of-the-art performance, surpassing its base model and majority of other models of similar size on MultiPL-E Java code benchmark. While there have been studies on extending large, generic pre-trained models to improve proficiency in specific programming languages like Python, similar investigations on small code models for other programming languages are lacking. Large code models require specialized hardware like GPUs for inference, highlighting the need for research into building small code models that can be deployed on developer desktops. This paper addresses this research gap by focusing on the development of a small Java code model, NT-Java-1.1B, and its quantized versions, which performs comparably to open models around 1.1B on MultiPL-E Java code benchmarks, making them ideal for desktop deployment. This paper establishes the foundation for specialized models across languages and sizes for a family of NT Models.

While Foundation Models provide a general tool for rapid content creation, they regularly require task-specific adaptation. Traditionally, this exercise involves careful curation of datasets and repeated fine-tuning of the underlying model. Fine-tuning techniques enable practitioners to adapt foundation models for many new applications but require expensive and lengthy training while being notably sensitive to hyperparameter choices. To overcome these limitations, we introduce Text-to-LoRA (T2L), a model capable of adapting large language models (LLMs) on the fly solely based on a natural language description of the target task. T2L is a hypernetwork trained to construct LoRAs in a single inexpensive forward pass. After training T2L on a suite of 9 pre-trained LoRA adapters (GSM8K, Arc, etc.), we show that the ad-hoc reconstructed LoRA instances match the performance of task-specific adapters across the corresponding test sets. Furthermore, T2L can compress hundreds of LoRA instances and zero-shot generalize to entirely unseen tasks. This approach provides a significant step towards democratizing the specialization of foundation models and enables language-based adaptation with minimal compute requirements. Our code is available at https://github.com/SakanaAI/text-to-lora

Following its success for vision and text, the "foundation model" (FM) paradigm -- pretraining large models on massive data, then fine-tuning on target tasks -- has rapidly expanded to domains in the sciences, engineering, healthcare, and beyond. Has this achieved what the original FMs accomplished, i.e. the supplanting of traditional supervised learning in their domains? To answer we look at three modalities -- genomics, satellite imaging, and time series -- with multiple recent FMs and compare them to a standard supervised learning workflow: model development, hyperparameter tuning, and training, all using only data from the target task. Across these three specialized domains, we find that it is consistently possible to train simple supervised models -- no more complicated than a lightly modified wide ResNet or UNet -- that match or even outperform the latest foundation models. Our work demonstrates that the benefits of large-scale pretraining have yet to be realized in many specialized areas, reinforces the need to compare new FMs to strong, well-tuned baselines, and introduces two new, easy-to-use, open-source, and automated workflows for doing so.

Time series foundation models have demonstrated impressive performance as zero-shot forecasters. However, achieving effectively unified training on time series remains an open challenge. Existing approaches introduce some level of model specialization to account for the highly heterogeneous nature of time series data. For instance, Moirai pursues unified training by employing multiple input/output projection layers, each tailored to handle time series at a specific frequency. Similarly, TimesFM maintains a frequency embedding dictionary for this purpose. We identify two major drawbacks to this human-imposed frequency-level model specialization: (1) Frequency is not a reliable indicator of the underlying patterns in time series. For example, time series with different frequencies can display similar patterns, while those with the same frequency may exhibit varied patterns. (2) Non-stationarity is an inherent property of real-world time series, leading to varied distributions even within a short context window of a single time series. Frequency-level specialization is too coarse-grained to capture this level of diversity. To address these limitations, this paper introduces Moirai-MoE, using a single input/output projection layer while delegating the modeling of diverse time series patterns to the sparse mixture of experts (MoE) within Transformers. With these designs, Moirai-MoE reduces reliance on human-defined heuristics and enables automatic token-level specialization. Extensive experiments on 39 datasets demonstrate the superiority of Moirai-MoE over existing foundation models in both in-distribution and zero-shot scenarios. Furthermore, this study conducts comprehensive model analyses to explore the inner workings of time series MoE foundation models and provides valuable insights for future research.

Large Language Models (LLMs) demonstrate impressive performance in diverse applications, yet they face significant drawbacks, including high inference latency, expensive training cost, and generation of hallucination. Collaborative decoding between large and small language models (SLMs) offers a novel approach to address these challenges. Inspired by dual-process cognitive theory, we integrate these methods into a unified framework termed Fast and Slow Generating (FS-GEN). This paper explores several techniques within the FS-GEN framework, including speculative decoding, contrastive decoding, and emulator or proxy fine-tuning. We provide a comprehensive analysis of these methodologies, offering insights into their similarities and differences under this framework. Our study delves into the differential knowledge capabilities of LLMs versus SLMs through the FS-GEN lens, revealing that fewer than 20% of collaborative interactions are required across various methods. These interactions adhere to a scaling law relative to the parameter ratios, thereby facilitating predictable collaboration. Furthermore, we investigate the specific positions where collaboration is most effective from an uncertainty perspective, yielding novel insights that could refine FS-GEN methods. Our findings reveal that the essential difference between models of different sizes lies in the uncertainty of the next token prediction, where interventions by larger models are most needed to assist the smaller ones. Code for Reproduction: https://github.com/TsinghuaC3I/FS-GEN

In this note we examine the autoregressive generalization of the FNet algorithm, in which self-attention layers from the standard Transformer architecture are substituted with a trivial sparse-uniformsampling procedure based on Fourier transforms. Using the Wikitext-103 benchmark, we demonstratethat FNetAR retains state-of-the-art performance (25.8 ppl) on the task of causal language modelingcompared to a Transformer-XL baseline (24.2 ppl) with only half the number self-attention layers,thus providing further evidence for the superfluity of deep neural networks with heavily compoundedattention mechanisms. The autoregressive Fourier transform could likely be used for parameterreduction on most Transformer-based time-series prediction models.

DL compiler's primary function is to translate DNN programs written in high-level DL frameworks such as PyTorch and TensorFlow into portable executables. These executables can then be flexibly executed by the deployed host programs. However, existing DL compilers rely on a tracing mechanism, which involves feeding a runtime input to a neural network program and tracing the program execution paths to generate the computational graph necessary for compilation. Unfortunately, this mechanism falls short when dealing with modern dynamic neural networks (DyNNs) that possess varying computational graphs depending on the inputs. Consequently, conventional DL compilers struggle to accurately compile DyNNs into executable code. To address this limitation, we propose \tool, a general approach that enables any existing DL compiler to successfully compile DyNNs. \tool tackles the dynamic nature of DyNNs by introducing a compilation mechanism that redistributes the control and data flow of the original DNN programs during the compilation process. Specifically, \tool develops program analysis and program transformation techniques to convert a dynamic neural network into multiple sub-neural networks. Each sub-neural network is devoid of conditional statements and is compiled independently. Furthermore, \tool synthesizes a host module that models the control flow of the DyNNs and facilitates the invocation of the sub-neural networks. Our evaluation demonstrates the effectiveness of \tool, achieving a 100\% success rate in compiling all dynamic neural networks. Moreover, the compiled executables generated by \tool exhibit significantly improved performance, running between 1.12times and 20.21times faster than the original DyNNs executed on general-purpose DL frameworks.

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

Learned image compression (LIC) has gained traction as an effective solution for image storage and transmission in recent years. However, existing LIC methods are redundant in latent representation due to limitations in capturing anisotropic frequency components and preserving directional details. To overcome these challenges, we propose a novel frequency-aware transformer (FAT) block that for the first time achieves multiscale directional ananlysis for LIC. The FAT block comprises frequency-decomposition window attention (FDWA) modules to capture multiscale and directional frequency components of natural images. Additionally, we introduce frequency-modulation feed-forward network (FMFFN) to adaptively modulate different frequency components, improving rate-distortion performance. Furthermore, we present a transformer-based channel-wise autoregressive (T-CA) model that effectively exploits channel dependencies. Experiments show that our method achieves state-of-the-art rate-distortion performance compared to existing LIC methods, and evidently outperforms latest standardized codec VTM-12.1 by 14.5%, 15.1%, 13.0% in BD-rate on the Kodak, Tecnick, and CLIC datasets.

Retrieval-Augmented Generation (RAG) enhances coding tasks by incorporating retrieved code examples into prompts. However, lengthy prompts, often exceeding tens of thousands of tokens, introduce challenges related to limited context windows of language models (LMs) and high computational costs. Existing prompt compression techniques focus on natural language, lacking tailored solutions for code. To address the gap, we propose CodePromptZip, a framework that compresses code examples before integrating into RAG workflows. Our framework employs a type-aware, priority-driven strategy to construct training samples for training code compression model. By using program analysis, we identify token types (e.g., Identifier) and perform ablation analysis to rank their removal priorities based on their impact on task performance. We then train a small LM as the compressor on these samples, enabling flexible compression conditioned on specified ratios while minimizing performance degradation. Specially, the compressor is augmented with a copy mechanism, allowing tokens to be directly copied from the original code snippets. Evaluation results show that CodePromptZip surpasses SOTA entropy-based and distillation-based baselines, improving by 23.4%, 28.7%, and 8.7% over the best baseline for Assertion Generation, Bugs2Fix, and Code Suggestion, respectively.

We consider higher-order linear-chain conditional random fields (HO-LC-CRFs) for sequence modelling, and use sum-product networks (SPNs) for representing higher-order input- and output-dependent factors. SPNs are a recently introduced class of deep models for which exact and efficient inference can be performed. By combining HO-LC-CRFs with SPNs, expressive models over both the output labels and the hidden variables are instantiated while still enabling efficient exact inference. Furthermore, the use of higher-order factors allows us to capture relations of multiple input segments and multiple output labels as often present in real-world data. These relations can not be modelled by the commonly used first-order models and higher-order models with local factors including only a single output label. We demonstrate the effectiveness of our proposed models for sequence labeling. In extensive experiments, we outperform other state-of-the-art methods in optical character recognition and achieve competitive results in phone classification.

Toeplitz Neural Networks (TNNs) have exhibited outstanding performance in various sequence modeling tasks. They outperform commonly used Transformer-based models while benefiting from log-linear space-time complexities. On the other hand, State Space Models (SSMs) achieve lower performance than TNNs in language modeling but offer the advantage of constant inference complexity. In this paper, we aim to combine the strengths of TNNs and SSMs by converting TNNs to SSMs during inference, thereby enabling TNNs to achieve the same constant inference complexities as SSMs. To accomplish this, we formulate the conversion process as an optimization problem and provide a closed-form solution. We demonstrate how to transform the target equation into a Vandermonde linear system problem, which can be efficiently solved using the Discrete Fourier Transform (DFT). Notably, our method requires no training and maintains numerical stability. It can be also applied to any LongConv-based model. To assess its effectiveness, we conduct extensive experiments on language modeling tasks across various settings. Additionally, we compare our method to other gradient-descent solutions, highlighting the superior numerical stability of our approach. The source code is available at https://github.com/OpenNLPLab/ETSC-Exact-Toeplitz-to-SSM-Conversion.

Pretrained foundation models offer substantial benefits for a wide range of downstream tasks, which can be one of the most potential techniques to access artificial general intelligence. However, scaling up foundation transformers for maximal task-agnostic knowledge has brought about computational challenges, especially on resource-limited devices such as mobiles. This work proposes the first Binary Pretrained Foundation Transformer (BiPFT) for natural language understanding (NLU) tasks, which remarkably saves 56 times operations and 28 times memory. In contrast to previous task-specific binary transformers, BiPFT exhibits a substantial enhancement in the learning capabilities of binary neural networks (BNNs), promoting BNNs into the era of pre-training. Benefiting from extensive pretraining data, we further propose a data-driven binarization method. Specifically, we first analyze the binarization error in self-attention operations and derive the polynomials of binarization error. To simulate full-precision self-attention, we define binarization error as binarization residual polynomials, and then introduce low-rank estimators to model these polynomials. Extensive experiments validate the effectiveness of BiPFTs, surpassing task-specific baseline by 15.4% average performance on the GLUE benchmark. BiPFT also demonstrates improved robustness to hyperparameter changes, improved optimization efficiency, and reduced reliance on downstream distillation, which consequently generalize on various NLU tasks and simplify the downstream pipeline of BNNs. Our code and pretrained models are publicly available at https://github.com/Xingrun-Xing/BiPFT.

As deep learning models grow, sparsity is becoming an increasingly critical component of deep neural networks, enabling improved performance and reduced storage. However, existing frameworks offer poor support for sparsity. Specialized sparsity engines focus exclusively on sparse inference, while general frameworks primarily focus on sparse tensors in classical formats and neglect the broader sparsification pipeline necessary for using sparse models, especially during training. Further, existing frameworks are not easily extensible: adding a new sparse tensor format or operator is challenging and time-consuming. To address this, we propose STen, a sparsity programming model and interface for PyTorch, which incorporates sparsity layouts, operators, and sparsifiers, in an efficient, customizable, and extensible framework that supports virtually all sparsification methods. We demonstrate this by developing a high-performance grouped n:m sparsity layout for CPU inference at moderate sparsity. STen brings high performance and ease of use to the ML community, making sparsity easily accessible.

Current state of the art methods in Domain Adaptation follow adversarial approaches, making training a challenge. Existing non-adversarial methods learn mappings between the source and target domains, to achieve reasonable performance. However, even these methods do not focus on a key aspect: maintaining performance on the source domain, even after optimizing over the target domain. Additionally, there exist very few methods in low resource supervised domain adaptation. This work proposes a method, LRS-DAG, that aims to solve these current issues in the field. By adding a set of "encoder layers" which map the target domain to the source, and can be removed when dealing directly with the source data, the model learns to perform optimally on both domains. LRS-DAG showcases its uniqueness by being a new algorithm for low resource domain adaptation which maintains performance over the source domain, with a new metric for learning mappings between domains being introduced. We show that, in the case of FCNs, when transferring from MNIST to SVHN, LRS-DAG performs comparably to fine tuning, with the advantage of maintaining performance over the source domain. LRS-DAG outperforms fine tuning when transferring to a synthetic dataset similar to MNIST, which is a setting more representative of low resource supervised domain adaptation.

Backward Filtering Forward Guiding (BFFG) is a bidirectional algorithm proposed in Mider et al. [2021] and studied more in depth in a general setting in Van der Meulen and Schauer [2022]. In category theory, optics have been proposed for modelling systems with bidirectional data flow. We connect BFFG with optics and prove that different ways of composing the building blocks of BFFG correspond to equivalent optics.

Spectral analysis provides one of the most effective paradigms for information-preserving dimensionality reduction, as simple descriptions of naturally occurring signals are often obtained via few terms of periodic basis functions. In this work, we study deep neural networks designed to harness the structure in frequency domain for efficient learning of long-range correlations in space or time: frequency-domain models (FDMs). Existing FDMs are based on complex-valued transforms i.e. Fourier Transforms (FT), and layers that perform computation on the spectrum and input data separately. This design introduces considerable computational overhead: for each layer, a forward and inverse FT. Instead, this work introduces a blueprint for frequency domain learning through a single transform: transform once (T1). To enable efficient, direct learning in the frequency domain we derive a variance-preserving weight initialization scheme and investigate methods for frequency selection in reduced-order FDMs. Our results noticeably streamline the design process of FDMs, pruning redundant transforms, and leading to speedups of 3x to 10x that increase with data resolution and model size. We perform extensive experiments on learning the solution operator of spatio-temporal dynamics, including incompressible Navier-Stokes, turbulent flows around airfoils and high-resolution video of smoke. T1 models improve on the test performance of FDMs while requiring significantly less computation (5 hours instead of 32 for our large-scale experiment), with over 20% reduction in average predictive error across tasks.

Diffusion probabilistic models (DPMs) have shown remarkable performance in visual synthesis but are computationally expensive due to the need for multiple evaluations during the sampling. Recent predictor-corrector diffusion samplers have significantly reduced the required number of function evaluations (NFE), but inherently suffer from a misalignment issue caused by the extra corrector step, especially with a large classifier-free guidance scale (CFG). In this paper, we introduce a new fast DPM sampler called DC-Solver, which leverages dynamic compensation (DC) to mitigate the misalignment of the predictor-corrector samplers. The dynamic compensation is controlled by compensation ratios that are adaptive to the sampling steps and can be optimized on only 10 datapoints by pushing the sampling trajectory toward a ground truth trajectory. We further propose a cascade polynomial regression (CPR) which can instantly predict the compensation ratios on unseen sampling configurations. Additionally, we find that the proposed dynamic compensation can also serve as a plug-and-play module to boost the performance of predictor-only samplers. Extensive experiments on both unconditional sampling and conditional sampling demonstrate that our DC-Solver can consistently improve the sampling quality over previous methods on different DPMs with a wide range of resolutions up to 1024times1024. Notably, we achieve 10.38 FID (NFE=5) on unconditional FFHQ and 0.394 MSE (NFE=5, CFG=7.5) on Stable-Diffusion-2.1. Code is available at https://github.com/wl-zhao/DC-Solver

From optical sensors to microwave radars, leveraging the complementary strengths of remote sensing (RS) sensors is crucial for achieving dense spatio-temporal monitoring of our planet. In contrast, recent deep learning models, whether task-specific or foundational, are often specific to single sensors or to fixed combinations: adapting such models to different sensory inputs requires both architectural changes and re-training, limiting scalability and generalization across multiple RS sensors. On the contrary, a single model able to modulate its feature representations to accept diverse sensors as input would pave the way to agile and flexible multi-sensor RS data processing. To address this, we introduce SMARTIES, a generic and versatile foundation model lifting sensor-specific/dependent efforts and enabling scalability and generalization to diverse RS sensors: SMARTIES projects data from heterogeneous sensors into a shared spectrum-aware space, enabling the use of arbitrary combinations of bands both for training and inference. To obtain sensor-agnostic representations, we train a single, unified transformer model reconstructing masked multi-sensor data with cross-sensor token mixup. On both single- and multi-modal tasks across diverse sensors, SMARTIES outperforms previous models that rely on sensor-specific pretraining. Our code and pretrained models are available at https://gsumbul.github.io/SMARTIES.

Flow matching in the continuous simplex has emerged as a promising strategy for DNA sequence design, but struggles to scale to higher simplex dimensions required for peptide and protein generation. We introduce Gumbel-Softmax Flow and Score Matching, a generative framework on the simplex based on a novel Gumbel-Softmax interpolant with a time-dependent temperature. Using this interpolant, we introduce Gumbel-Softmax Flow Matching by deriving a parameterized velocity field that transports from smooth categorical distributions to distributions concentrated at a single vertex of the simplex. We alternatively present Gumbel-Softmax Score Matching which learns to regress the gradient of the probability density. Our framework enables high-quality, diverse generation and scales efficiently to higher-dimensional simplices. To enable training-free guidance, we propose Straight-Through Guided Flows (STGFlow), a classifier-based guidance method that leverages straight-through estimators to steer the unconditional velocity field toward optimal vertices of the simplex. STGFlow enables efficient inference-time guidance using classifiers pre-trained on clean sequences, and can be used with any discrete flow method. Together, these components form a robust framework for controllable de novo sequence generation. We demonstrate state-of-the-art performance in conditional DNA promoter design, sequence-only protein generation, and target-binding peptide design for rare disease treatment.

Decompilers are important tools for reverse engineers that help them analyze software at a higher level of abstraction than assembly. Unfortunately, because compilation is lossy, deterministic decompilers produce code that is missing many of the details that make source code readable in the first place, like variable names and types. Neural decompilers, on the other hand, offer the ability to statistically fill in these details. Existing work in neural decompilation, however, suffers from substantial drawbacks that limits its ability to handle real code: it is unable to handle user-defined composite types, which are essential to fully specifying many functions' semantics, or require test cases. In this work, we introduce a new training process to finetune any LLM into a neural decompiler capable of generating the appropriate user-defined types alongside the decompilation. We introduce a new dataset, Realtype, that includes substantially more complicated and realistic types than existing neural decompilation benchmarks. Motivated by the intuition that different parts of data structures can be operated upon by different parts of the program, we show that interprocedural context can help improve neural decompilers' ability to handle user-defined types. We show that our training process yields state-of-the-art results in neural decompilation. We also publicly release the Idioms series of finetuned neural decompilation models in support of open science. In summary, we identify the need for joint code and type prediction, show that it is a hard problem, and take the first steps towards solving it.

Tokenization, the division of input text into input tokens, is an often overlooked aspect of the large language model (LLM) pipeline and could be the source of useful or harmful inductive biases. Historically, LLMs have relied on byte pair encoding, without care to specific input domains. With the increased use of LLMs for reasoning, various number-specific tokenization schemes have been adopted, with popular models like LLaMa and PaLM opting for single-digit tokenization while GPT-3.5 and GPT-4 have separate tokens for each 1-, 2-, and 3-digit numbers. In this work, we study the effect this choice has on numerical reasoning through the use of arithmetic tasks. We consider left-to-right and right-to-left tokenization for GPT-3.5 and -4, finding that right-to-left tokenization (enforced by comma separating numbers at inference time) leads to largely improved performance. Furthermore, we find that model errors when using standard left-to-right tokenization follow stereotyped error patterns, suggesting that model computations are systematic rather than approximate. We show that the model is able to convert between tokenizations easily, thus allowing chain-of-thought-inspired approaches to recover performance on left-to-right tokenized inputs. We also find the gap between tokenization directions decreases when models are scaled, possibly indicating that larger models are better able to override this tokenization-dependent inductive bias. In summary, our work performs the first study of how number tokenization choices lead to differences in model performance on arithmetic tasks, accompanied by a thorough analysis of error patterns. We hope this work inspires practitioners to more carefully ablate number tokenization-related choices when working towards general models of numerical reasoning.

We extend JAX with the capability to automatically differentiate higher-order functions (functionals and operators). By representing functions as a generalization of arrays, we seamlessly use JAX's existing primitive system to implement higher-order functions. We present a set of primitive operators that serve as foundational building blocks for constructing several key types of functionals. For every introduced primitive operator, we derive and implement both linearization and transposition rules, aligning with JAX's internal protocols for forward and reverse mode automatic differentiation. This enhancement allows for functional differentiation in the same syntax traditionally use for functions. The resulting functional gradients are themselves functions ready to be invoked in python. We showcase this tool's efficacy and simplicity through applications where functional derivatives are indispensable. The source code of this work is released at https://github.com/sail-sg/autofd .

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

In this paper, we explore FP8 low-bit data formats for efficient training of large language models (LLMs). Our key insight is that most variables, such as gradients and optimizer states, in LLM training can employ low-precision data formats without compromising model accuracy and requiring no changes to hyper-parameters. Specifically, we propose a new FP8 automatic mixed-precision framework for training LLMs. This framework offers three levels of FP8 utilization to streamline mixed-precision and distributed parallel training for LLMs. It gradually incorporates 8-bit gradients, optimizer states, and distributed learning in an incremental manner. Experiment results show that, during the training of GPT-175B model on H100 GPU platform, our FP8 mixed-precision training framework not only achieved a remarkable 42% reduction in real memory usage but also ran 64% faster than the widely adopted BF16 framework (i.e., Megatron-LM), surpassing the speed of Nvidia Transformer Engine by 17%. This largely reduces the training costs for large foundation models. Furthermore, our FP8 mixed-precision training methodology is generic. It can be seamlessly applied to other tasks such as LLM instruction tuning and reinforcement learning with human feedback, offering savings in fine-tuning expenses. Our FP8 low-precision training framework is open-sourced at {https://github.com/Azure/MS-AMP}{aka.ms/MS.AMP}.

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

Existing pre-trained models are generally geared towards a particular class of problems. To date, there seems to be still no consensus on what the right architecture and pre-training setup should be. This paper presents a unified framework for pre-training models that are universally effective across datasets and setups. We begin by disentangling architectural archetypes with pre-training objectives -- two concepts that are commonly conflated. Next, we present a generalized & unified perspective for self-supervision in NLP and show how different pre-training objectives can be cast as one another and how interpolating between different objectives can be effective. We then propose Mixture-of-Denoisers (MoD), a pre-training objective that combines diverse pre-training paradigms together. We furthermore introduce a notion of mode switching, wherein downstream fine-tuning is associated with specific pre-training schemes. We conduct extensive ablative experiments to compare multiple pre-training objectives and find that our method pushes the Pareto-frontier by outperforming T5 & GPT-like models across multiple diverse setups. By scaling our model up to 20B parameters, we achieve SOTA performance on 50 well-established supervised finetuning based NLP tasks. Our model also achieve strong results at in-context learning, outperforming 175B GPT-3 on zero-shot SuperGLUE and tripling the performance of T5-XXL on one-shot summarization. On 0-shot MMLU, UL2 20B outperforms T0 and T5 models. UL2 20B also works well with chain-of-thought prompting and reasoning, making it an appealing choice for research into reasoning at a small to medium scale of 20B parameters. Finally, we apply FLAN instruction tuning to the UL2 20B model, achieving MMLU and Big-Bench scores competitive to FLAN-PaLM 62B. We release Flax-based T5X checkpoints for the UL2 20B & Flan-UL2 20B.

Radio frequency fingerprint identification (RFFI) is an emerging device authentication technique that relies on intrinsic hardware characteristics of wireless devices. We designed an RFFI scheme for Long Range (LoRa) systems based on spectrogram and convolutional neural network (CNN). Specifically, we used spectrogram to represent the fine-grained time-frequency characteristics of LoRa signals. In addition, we revealed that the instantaneous carrier frequency offset (CFO) is drifting, which will result in misclassification and significantly compromise the system stability; we demonstrated CFO compensation is an effective mitigation. Finally, we designed a hybrid classifier that can adjust CNN outputs with the estimated CFO. The mean value of CFO remains relatively stable, hence it can be used to rule out CNN predictions whose estimated CFO falls out of the range. We performed experiments in real wireless environments using 20 LoRa devices under test (DUTs) and a Universal Software Radio Peripheral (USRP) N210 receiver. By comparing with the IQ-based and FFT-based RFFI schemes, our spectrogram-based scheme can reach the best classification accuracy, i.e., 97.61% for 20 LoRa DUTs.

Few-shot class-incremental learning (FSCIL) confronts the challenge of integrating new classes into a model with minimal training samples while preserving the knowledge of previously learned classes. Traditional methods widely adopt static adaptation relying on a fixed parameter space to learn from data that arrive sequentially, prone to overfitting to the current session. Existing dynamic strategies require the expansion of the parameter space continually, leading to increased complexity. To address these challenges, we integrate the recently proposed selective state space model (SSM) into FSCIL. Concretely, we propose a dual selective SSM projector that dynamically adjusts the projection parameters based on the intermediate features for dynamic adaptation. The dual design enables the model to maintain the robust features of base classes, while adaptively learning distinctive feature shifts for novel classes. Additionally, we develop a class-sensitive selective scan mechanism to guide dynamic adaptation. It minimizes the disruption to base-class representations caused by training on novel data, and meanwhile, forces the selective scan to perform in distinct patterns between base and novel classes. Experiments on miniImageNet, CUB-200, and CIFAR-100 demonstrate that our framework outperforms the existing state-of-the-art methods. The code is available at https://github.com/xiaojieli0903/Mamba-FSCIL.

Dimensionality reduction in vector databases is pivotal for streamlining AI data management, enabling efficient storage, faster computation, and improved model performance. This paper explores the benefits of reducing vector database dimensions, with a focus on computational efficiency and overcoming the curse of dimensionality. We introduce a novel application of Fast Fourier Transform (FFT) to dimensionality reduction, a method previously underexploited in this context. By demonstrating its utility across various AI domains, including Retrieval-Augmented Generation (RAG) models and image processing, this FFT-based approach promises to improve data retrieval processes and enhance the efficiency and scalability of AI solutions. The incorporation of FFT may not only optimize operations in real-time processing and recommendation systems but also extend to advanced image processing techniques, where dimensionality reduction can significantly improve performance and analysis efficiency. This paper advocates for the broader adoption of FFT in vector database management, marking a significant stride towards addressing the challenges of data volume and complexity in AI research and applications. Unlike many existing approaches, we directly handle the embedding vectors produced by the model after processing a test input.

Large pre-trained time series foundation models (TSFMs) have demonstrated promising zero-shot performance across a wide range of domains. However, a question remains: Do TSFMs succeed solely by memorizing training patterns, or do they possess the ability to reason? While reasoning is a topic of great interest in the study of Large Language Models (LLMs), it is undefined and largely unexplored in the context of TSFMs. In this work, inspired by language modeling literature, we formally define compositional reasoning in forecasting and distinguish it from in-distribution generalization. We evaluate the reasoning and generalization capabilities of 23 popular deep learning forecasting models on multiple synthetic and real-world datasets. Additionally, through controlled studies, we systematically examine which design choices in TSFMs contribute to improved reasoning abilities. Our study yields key insights into the impact of TSFM architecture design on compositional reasoning and generalization. We find that patch-based Transformers have the best reasoning performance, closely followed by residualized MLP-based architectures, which are 97\% less computationally complex in terms of FLOPs and 86\% smaller in terms of the number of trainable parameters. Interestingly, in some zero-shot out-of-distribution scenarios, these models can outperform moving average and exponential smoothing statistical baselines trained on in-distribution data. Only a few design choices, such as the tokenization method, had a significant (negative) impact on Transformer model performance.

In practical federated learning scenarios, the participating devices may have different bitwidths for computation and memory storage by design. However, despite the progress made in device-heterogeneous federated learning scenarios, the heterogeneity in the bitwidth specifications in the hardware has been mostly overlooked. We introduce a pragmatic FL scenario with bitwidth heterogeneity across the participating devices, dubbed as Bitwidth Heterogeneous Federated Learning (BHFL). BHFL brings in a new challenge, that the aggregation of model parameters with different bitwidths could result in severe performance degeneration, especially for high-bitwidth models. To tackle this problem, we propose ProWD framework, which has a trainable weight dequantizer at the central server that progressively reconstructs the low-bitwidth weights into higher bitwidth weights, and finally into full-precision weights. ProWD further selectively aggregates the model parameters to maximize the compatibility across bit-heterogeneous weights. We validate ProWD against relevant FL baselines on the benchmark datasets, using clients with varying bitwidths. Our ProWD largely outperforms the baseline FL algorithms as well as naive approaches (e.g. grouped averaging) under the proposed BHFL scenario.

Recent work has shown that fine-tuning large pre-trained language models on a collection of tasks described via instructions, a.k.a. instruction-tuning, improves their zero and few-shot generalization to unseen tasks. However, there is a limited understanding of the performance trade-offs of different decisions made during the instruction-tuning process. These decisions include the scale and diversity of the instruction-tuning benchmark, different task sampling strategies, fine-tuning with and without demonstrations, training using specialized datasets for reasoning and dialogue, and finally, the fine-tuning objectives themselves. In this paper, we characterize the effect of instruction-tuning decisions on downstream task performance when scaling both model and benchmark sizes. To this end, we create OPT-IML Bench: a large benchmark for Instruction Meta-Learning (IML) of 2000 NLP tasks consolidated into task categories from 8 existing benchmarks, and prepare an evaluation framework to measure three types of model generalizations: to tasks from fully held-out categories, to held-out tasks from seen categories, and to held-out instances from seen tasks. Through the lens of this framework, we first present insights about instruction-tuning decisions as applied to OPT-30B and further exploit these insights to train OPT-IML 30B and 175B, which are instruction-tuned versions of OPT. OPT-IML demonstrates all three generalization abilities at both scales on four different evaluation benchmarks with diverse tasks and input formats -- PromptSource, FLAN, Super-NaturalInstructions, and UnifiedSKG. Not only does it significantly outperform OPT on all benchmarks but is also highly competitive with existing models fine-tuned on each specific benchmark. We release OPT-IML at both scales, together with the OPT-IML Bench evaluation framework.

Large language models (LLMs) have exhibited impressive reasoning abilities on a wide range of complex tasks. However, enhancing these capabilities through post-training remains resource intensive, particularly in terms of data and computational cost. Although recent efforts have sought to improve sample efficiency through selective data curation, existing methods often rely on heuristic or task-specific strategies that hinder scalability. In this work, we introduce InfiAlign, a scalable and sample-efficient post-training framework that integrates supervised fine-tuning (SFT) with Direct Preference Optimization (DPO) to align LLMs for enhanced reasoning. At the core of InfiAlign is a robust data selection pipeline that automatically curates high-quality alignment data from open-source reasoning datasets using multidimensional quality metrics. This pipeline enables significant performance gains while drastically reducing data requirements and remains extensible to new data sources. When applied to the Qwen2.5-Math-7B-Base model, our SFT model achieves performance on par with DeepSeek-R1-Distill-Qwen-7B, while using only approximately 12% of the training data, and demonstrates strong generalization across diverse reasoning tasks. Additional improvements are obtained through the application of DPO, with particularly notable gains in mathematical reasoning tasks. The model achieves an average improvement of 3.89% on AIME 24/25 benchmarks. Our results highlight the effectiveness of combining principled data selection with full-stage post-training, offering a practical solution for aligning large reasoning models in a scalable and data-efficient manner. The model checkpoints are available at https://huggingface.co/InfiX-ai/InfiAlign-Qwen-7B-SFT.

Representing deep neural networks (DNNs) in low-precision is a promising approach to enable efficient acceleration and memory reduction. Previous methods that train DNNs in low-precision typically keep a copy of weights in high-precision during the weight updates. Directly training with low-precision weights leads to accuracy degradation due to complex interactions between the low-precision number systems and the learning algorithms. To address this issue, we develop a co-designed low-precision training framework, termed LNS-Madam, in which we jointly design a logarithmic number system (LNS) and a multiplicative weight update algorithm (Madam). We prove that LNS-Madam results in low quantization error during weight updates, leading to stable performance even if the precision is limited. We further propose a hardware design of LNS-Madam that resolves practical challenges in implementing an efficient datapath for LNS computations. Our implementation effectively reduces energy overhead incurred by LNS-to-integer conversion and partial sum accumulation. Experimental results show that LNS-Madam achieves comparable accuracy to full-precision counterparts with only 8 bits on popular computer vision and natural language tasks. Compared to FP32 and FP8, LNS-Madam reduces the energy consumption by over 90% and 55%, respectively.

Large Language Models (LLMs) have demonstrated remarkable proficiency in understanding and generating natural language. However, their capabilities wane in highly specialized domains underrepresented in the pretraining corpus, such as physical and biomedical sciences. This work explores how to repurpose general LLMs into effective task solvers for specialized domains. We introduce a novel, model-agnostic framework for learning custom input tags, which are parameterized as continuous vectors appended to the LLM's embedding layer, to condition the LLM. We design two types of input tags: domain tags are used to delimit specialized representations (e.g., chemical formulas) and provide domain-relevant context; function tags are used to represent specific functions (e.g., predicting molecular properties) and compress function-solving instructions. We develop a three-stage protocol to learn these tags using auxiliary data and domain knowledge. By explicitly disentangling task domains from task functions, our method enables zero-shot generalization to unseen problems through diverse combinations of the input tags. It also boosts LLM's performance in various specialized domains, such as predicting protein or chemical properties and modeling drug-target interactions, outperforming expert models tailored to these tasks.

To alleviate the computational burden of large language models (LLMs), architectures with activation sparsity, represented by mixture-of-experts (MoE), have attracted increasing attention. However, the non-differentiable and inflexible routing of vanilla MoE hurts model performance. Moreover, while each token activates only a few parameters, these sparsely-activated architectures exhibit low chunk-level sparsity, indicating that the union of multiple consecutive tokens activates a large ratio of parameters. Such a sparsity pattern is unfriendly for acceleration under low-resource conditions (e.g., end-side devices) and incompatible with mainstream acceleration techniques (e.g., speculative decoding). To address these challenges, we introduce a novel MoE architecture, BlockFFN, as well as its efficient training and deployment techniques. Specifically, we use a router integrating ReLU activation and RMSNorm for differentiable and flexible routing. Next, to promote both token-level sparsity (TLS) and chunk-level sparsity (CLS), CLS-aware training objectives are designed, making BlockFFN more acceleration-friendly. Finally, we implement efficient acceleration kernels, combining activation sparsity and speculative decoding for the first time. The experimental results demonstrate the superior performance of BlockFFN over other MoE baselines, achieving over 80% TLS and 70% 8-token CLS. Our kernels achieve up to 3.67times speedup on real end-side devices than dense models. All codes and checkpoints are available publicly (https://github.com/thunlp/BlockFFN).

Python type inference is challenging in practice. Due to its dynamic properties and extensive dependencies on third-party libraries without type annotations, the performance of traditional static analysis techniques is limited. Although semantics in source code can help manifest intended usage for variables (thus help infer types), they are usually ignored by existing tools. In this paper, we propose PYInfer, an end-to-end learning-based type inference tool that automatically generates type annotations for Python variables. The key insight is that contextual code semantics is critical in inferring the type for a variable. For each use of a variable, we collect a few tokens within its contextual scope, and design a neural network to predict its type. One challenge is that it is difficult to collect a high-quality human-labeled training dataset for this purpose. To address this issue, we apply an existing static analyzer to generate the ground truth for variables in source code. Our main contribution is a novel approach to statically infer variable types effectively and efficiently. Formulating the type inference as a classification problem, we can handle user-defined types and predict type probabilities for each variable. Our model achieves 91.2% accuracy on classifying 11 basic types in Python and 81.2% accuracy on classifying 500 most common types. Our results substantially outperform the state-of-the-art type annotators. Moreover, PYInfer achieves 5.2X more code coverage and is 187X faster than a state-of-the-art learning-based tool. With similar time consumption, our model annotates 5X more variables than a state-of-the-art static analysis tool. Our model also outperforms a learning-based function-level annotator on annotating types for variables and function arguments. All our tools and datasets are publicly available to facilitate future research in this direction.

We propose a neural network for both forward and inverse continuous nonlinear Fourier transforms, NFT and INFT respectively. We demonstrate the network's capability to perform NFT and INFT for a random mix of NFDM-QAM signals. The network transformations (NFT and INFT) exhibit true characteristics of these transformations; they are significantly different for low and high-power input pulses. The network shows adequate accuracy with an RMSE of 5e-3 for forward and 3e-2 for inverse transforms. We further show that the trained network can be used to perform general nonlinear Fourier transforms on arbitrary pulses beyond the training pulse types.

Recent advances in deep learning methods such as LLMs and Diffusion models have created a need for improved quantization methods that can meet the computational demands of these modern architectures while maintaining accuracy. Towards this goal, we study the advantages of FP8 data formats for post-training quantization across 75 unique network architectures covering a wide range of tasks, including machine translation, language modeling, text generation, image classification, generation, and segmentation. We examine three different FP8 representations (E5M2, E4M3, and E3M4) to study the effects of varying degrees of trade-off between dynamic range and precision on model accuracy. Based on our extensive study, we developed a quantization workflow that generalizes across different network architectures. Our empirical results show that FP8 formats outperform INT8 in multiple aspects, including workload coverage (92.64% vs. 65.87%), model accuracy and suitability for a broader range of operations. Furthermore, our findings suggest that E4M3 is better suited for NLP models, whereas E3M4 performs marginally better than E4M3 on computer vision tasks. The code is publicly available on Intel Neural Compressor: https://github.com/intel/neural-compressor.

The transformer model is known to be computationally demanding, and prohibitively costly for long sequences, as the self-attention module uses a quadratic time and space complexity with respect to sequence length. Many researchers have focused on designing new forms of self-attention or introducing new parameters to overcome this limitation, however a large portion of them prohibits the model to inherit weights from large pretrained models. In this work, the transformer's inefficiency has been taken care of from another perspective. We propose Fourier Transformer, a simple yet effective approach by progressively removing redundancies in hidden sequence using the ready-made Fast Fourier Transform (FFT) operator to perform Discrete Cosine Transformation (DCT). Fourier Transformer is able to significantly reduce computational costs while retain the ability to inherit from various large pretrained models. Experiments show that our model achieves state-of-the-art performances among all transformer-based models on the long-range modeling benchmark LRA with significant improvement in both speed and space. For generative seq-to-seq tasks including CNN/DailyMail and ELI5, by inheriting the BART weights our model outperforms the standard BART and other efficient models. Our code is publicly available at \url{https://github.com/LUMIA-Group/FourierTransformer}

Recent vision transformers, large-kernel CNNs and MLPs have attained remarkable successes in broad vision tasks thanks to their effective information fusion in the global scope. However, their efficient deployments, especially on mobile devices, still suffer from noteworthy challenges due to the heavy computational costs of self-attention mechanisms, large kernels, or fully connected layers. In this work, we apply conventional convolution theorem to deep learning for addressing this and reveal that adaptive frequency filters can serve as efficient global token mixers. With this insight, we propose Adaptive Frequency Filtering (AFF) token mixer. This neural operator transfers a latent representation to the frequency domain via a Fourier transform and performs semantic-adaptive frequency filtering via an elementwise multiplication, which mathematically equals to a token mixing operation in the original latent space with a dynamic convolution kernel as large as the spatial resolution of this latent representation. We take AFF token mixers as primary neural operators to build a lightweight neural network, dubbed AFFNet. Extensive experiments demonstrate the effectiveness of our proposed AFF token mixer and show that AFFNet achieve superior accuracy and efficiency trade-offs compared to other lightweight network designs on broad visual tasks, including visual recognition and dense prediction tasks.

Large language models (LLMs) show great performance in various tasks, but face deployment challenges from limited memory capacity and bandwidth. Low-bit weight quantization can save memory and accelerate inference. Although floating-point (FP) formats show good performance in LLM quantization, they tend to perform poorly with small group sizes or sub-4 bits. We find the reason is that the absence of asymmetry in previous FP quantization makes it unsuitable for handling asymmetric value distribution of LLM weight tensors. In this work, we propose asymmetric FP quantization (AFPQ), which sets separate scales for positive and negative values. Our method leads to large accuracy improvements and can be easily plugged into other quantization methods, including GPTQ and AWQ, for better performance. Besides, no additional storage is needed compared with asymmetric integer (INT) quantization. The code is available at https://github.com/zhangsichengsjtu/AFPQ.

Extending Large Language Models (LLMs) to advanced applications requires reliable structured output generation. Existing methods which often rely on rigid JSON schemas, can lead to unreliable outputs, diminished reasoning capabilities, and increased computational overhead, limiting LLMs' adaptability for complex tasks. We introduce Meaning Typed Prompting (MTP), a technique for efficient structured output generation that integrates types, meanings, and abstractions, such as variables and classes, into the prompting process. By utilizing expressive type definitions, MTP enhances output clarity and reduces dependence on complex abstractions, simplifying development, and improving implementation efficiency. This enables LLMs to understand relationships and generate structured data more effectively. Empirical evaluations on multiple benchmarks demonstrate that MTP outperforms existing frameworks in accuracy, reliability, consistency, and token efficiency. We present Semantix, a framework that implements MTP, providing practical insights into its application.

Machine learning (ML)-based weather models have rapidly risen to prominence due to their greater accuracy and speed than traditional forecasts based on numerical weather prediction (NWP), recently outperforming traditional ensembles in global probabilistic weather forecasting. This paper presents FGN, a simple, scalable and flexible modeling approach which significantly outperforms the current state-of-the-art models. FGN generates ensembles via learned model-perturbations with an ensemble of appropriately constrained models. It is trained directly to minimize the continuous rank probability score (CRPS) of per-location forecasts. It produces state-of-the-art ensemble forecasts as measured by a range of deterministic and probabilistic metrics, makes skillful ensemble tropical cyclone track predictions, and captures joint spatial structure despite being trained only on marginals.

We consider the problem of computing the Walsh-Hadamard Transform (WHT) of some N-length input vector in the presence of noise, where the N-point Walsh spectrum is K-sparse with K = {O}(N^{delta}) scaling sub-linearly in the input dimension N for some 0<delta<1. Over the past decade, there has been a resurgence in research related to the computation of Discrete Fourier Transform (DFT) for some length-N input signal that has a K-sparse Fourier spectrum. In particular, through a sparse-graph code design, our earlier work on the Fast Fourier Aliasing-based Sparse Transform (FFAST) algorithm computes the K-sparse DFT in time {O}(Klog K) by taking {O}(K) noiseless samples. Inspired by the coding-theoretic design framework, Scheibler et al. proposed the Sparse Fast Hadamard Transform (SparseFHT) algorithm that elegantly computes the K-sparse WHT in the absence of noise using {O}(Klog N) samples in time {O}(Klog^2 N). However, the SparseFHT algorithm explicitly exploits the noiseless nature of the problem, and is not equipped to deal with scenarios where the observations are corrupted by noise. Therefore, a question of critical interest is whether this coding-theoretic framework can be made robust to noise. Further, if the answer is yes, what is the extra price that needs to be paid for being robust to noise? In this paper, we show, quite interestingly, that there is {\it no extra price} that needs to be paid for being robust to noise other than a constant factor. In other words, we can maintain the same sample complexity {O}(Klog N) and the computational complexity {O}(Klog^2 N) as those of the noiseless case, using our SParse Robust Iterative Graph-based Hadamard Transform (SPRIGHT) algorithm.

While tabular classification has traditionally relied on from-scratch training, a recent breakthrough called prior-data fitted networks (PFNs) challenges this approach. Similar to large language models, PFNs make use of pretraining and in-context learning to achieve strong performance on new tasks in a single forward pass. However, current PFNs have limitations that prohibit their widespread adoption. Notably, TabPFN achieves very strong performance on small tabular datasets but is not designed to make predictions for datasets of size larger than 1000. In this work, we overcome these limitations and substantially improve the performance of PFNs via context optimization. We introduce TuneTables, a parameter-efficient fine-tuning strategy for PFNs that compresses large datasets into a smaller learned context. We conduct extensive experiments on 19 algorithms over 98 datasets and find that TuneTables achieves the best performance on average, outperforming boosted trees such as CatBoost, while optimizing fewer than 5% of TabPFN's parameters. Furthermore, we show that TuneTables can be used as an interpretability tool and can even be used to mitigate biases by optimizing a fairness objective. We open-source our code and raw results at https://github.com/penfever/TuneTables.

With easier access to powerful compute resources, there is a growing trend in the field of AI for software development to develop larger and larger language models (LLMs) to address a variety of programming tasks. Even LLMs applied to tasks from the high-performance computing (HPC) domain are huge in size (e.g., billions of parameters) and demand expensive compute resources for training. We found this design choice confusing - why do we need large LLMs trained on natural languages and programming languages unrelated to HPC for HPC-specific tasks? In this line of work, we aim to question design choices made by existing LLMs by developing smaller LLMs for specific domains - we call them domain-specific LLMs. Specifically, we start off with HPC as a domain and propose a novel tokenizer named Tokompiler, designed specifically for preprocessing code in HPC and compilation-centric tasks. Tokompiler leverages knowledge of language primitives to generate language-oriented tokens, providing a context-aware understanding of code structure while avoiding human semantics attributed to code structures completely. We applied Tokompiler to pre-train two state-of-the-art models, SPT-Code and Polycoder, for a Fortran code corpus mined from GitHub. We evaluate the performance of these models against the conventional LLMs. Results demonstrate that Tokompiler significantly enhances code completion accuracy and semantic understanding compared to traditional tokenizers in normalized-perplexity tests, down to ~1 perplexity score. This research opens avenues for further advancements in domain-specific LLMs, catering to the unique demands of HPC and compilation tasks.

Recently, the release of INSTRUCTEVAL has provided valuable insights into the performance of large language models (LLMs) that utilize encoder-decoder or decoder-only architecture. Interestingly, despite being introduced four years ago, T5-based LLMs, such as FLAN-T5, continue to outperform the latest decoder-based LLMs, such as LLAMA and VICUNA, on tasks that require general problem-solving skills. This performance discrepancy can be attributed to three key factors: (1) Pre-training data, (2) Backbone architecture, and (3) Instruction dataset. In this technical report, our main focus is on investigating the impact of the third factor by leveraging VICUNA, a large language model based on LLAMA, which has undergone fine-tuning on ChatGPT conversations. To achieve this objective, we fine-tuned VICUNA using a customized instruction dataset collection called FLANMINI. This collection includes a subset of the large-scale instruction dataset known as FLAN, as well as various code-related datasets and conversational datasets derived from ChatGPT/GPT-4. This dataset comprises a large number of tasks that demand problem-solving skills. Our experimental findings strongly indicate that the enhanced problem-solving abilities of our model, FLACUNA, are obtained through fine-tuning VICUNA on the FLAN dataset, leading to significant improvements across numerous benchmark datasets in INSTRUCTEVAL. FLACUNA is publicly available at https://huggingface.co/declare-lab/flacuna-13b-v1.0.

The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information between RNA sequences and structures. In this study, we introduce OmniGenome, an RNA FM trained to align RNA sequences with respect to secondary structures based on structure-contextualised modelling. The alignment enables free and bidirectional mappings between sequences and structures by utilising the flexible RNA modelling paradigm that supports versatile input and output modalities, i.e., sequence and/or structure as input/output. We implement RNA design and zero-shot secondary structure prediction as case studies to evaluate the Seq2Str and Str2Seq mapping capacity of OmniGenome. Results on the EternaV2 benchmark show that OmniGenome solved 74% of puzzles, whereas existing FMs only solved up to 3% of the puzzles due to the oversight of sequence-structure alignment. We leverage four comprehensive in-silico genome modelling benchmarks to evaluate performance across a diverse set of genome downstream tasks, where the results show that OmniGenome achieves state-of-the-art performance on RNA and DNA benchmarks, even without any training on DNA genomes.

A few-shot font generation (FFG) method has to satisfy two objectives: the generated images should preserve the underlying global structure of the target character and present the diverse local reference style. Existing FFG methods aim to disentangle content and style either by extracting a universal representation style or extracting multiple component-wise style representations. However, previous methods either fail to capture diverse local styles or cannot be generalized to a character with unseen components, e.g., unseen language systems. To mitigate the issues, we propose a novel FFG method, named Multiple Localized Experts Few-shot Font Generation Network (MX-Font). MX-Font extracts multiple style features not explicitly conditioned on component labels, but automatically by multiple experts to represent different local concepts, e.g., left-side sub-glyph. Owing to the multiple experts, MX-Font can capture diverse local concepts and show the generalizability to unseen languages. During training, we utilize component labels as weak supervision to guide each expert to be specialized for different local concepts. We formulate the component assign problem to each expert as the graph matching problem, and solve it by the Hungarian algorithm. We also employ the independence loss and the content-style adversarial loss to impose the content-style disentanglement. In our experiments, MX-Font outperforms previous state-of-the-art FFG methods in the Chinese generation and cross-lingual, e.g., Chinese to Korean, generation. Source code is available at https://github.com/clovaai/mxfont.

In this paper, we present ManyTypes4Py, a large Python dataset for machine learning (ML)-based type inference. The dataset contains a total of 5,382 Python projects with more than 869K type annotations. Duplicate source code files were removed to eliminate the negative effect of the duplication bias. To facilitate training and evaluation of ML models, the dataset was split into training, validation and test sets by files. To extract type information from abstract syntax trees (ASTs), a lightweight static analyzer pipeline is developed and accompanied with the dataset. Using this pipeline, the collected Python projects were analyzed and the results of the AST analysis were stored in JSON-formatted files. The ManyTypes4Py dataset is shared on zenodo and its tools are publicly available on GitHub.

Large language models (LLMs) have achieved impressive performance across various domains. However, the substantial hardware resources required for their training present a significant barrier to efficiency and scalability. To mitigate this challenge, low-precision training techniques have been widely adopted, leading to notable advancements in training efficiency. Despite these gains, low-precision training involves several componentsx2013such as weights, activations, and gradientsx2013each of which can be represented in different numerical formats. The resulting diversity has created a fragmented landscape in low-precision training research, making it difficult for researchers to gain a unified overview of the field. This survey provides a comprehensive review of existing low-precision training methods. To systematically organize these approaches, we categorize them into three primary groups based on their underlying numerical formats, which is a key factor influencing hardware compatibility, computational efficiency, and ease of reference for readers. The categories are: (1) fixed-point and integer-based methods, (2) floating-point-based methods, and (3) customized format-based methods. Additionally, we discuss quantization-aware training approaches, which share key similarities with low-precision training during forward propagation. Finally, we highlight several promising research directions to advance this field. A collection of papers discussed in this survey is provided in https://github.com/Hao840/Awesome-Low-Precision-Training.

We report the delivery to the Mikulski Archive for Space Telescopes of target pixel and light curve files for up to 160,000 targets selected from full-frame images (FFI) for each TESS Northern hemisphere observing sector. The data include calibrated target pixels, simple aperture photometry flux time series, and presearch data conditioning corrected flux time series. These data provide TESS users with high quality, uniform pipeline products for a selection of FFI targets, that would otherwise not be readily available. Additionally, we deliver cotrending basis vectors derived from the FFI targets to allow users to perform their own systematic error corrections. The selected targets include all 2-minute targets and additional targets selected from the TESS Input Catalog with a maximum of 10,000 targets per sector on each of the sixteen TESS CCDs. The data products are in the same format as the project-delivered files for the TESS 2-minute targets. All of the TESS-SPOC data products are available at the MAST as a High Level Science Product via https://doi.org/10.17909/t9-wpz1-8s54.

Current PEFT methods for LLMs can achieve either high quality, efficient training, or scalable serving, but not all three simultaneously. To address this limitation, we investigate sparse fine-tuning and observe a remarkable improvement in generalization ability. Utilizing this key insight, we propose a family of Structured Sparse Fine-Tuning (S^{2}FT) methods for LLMs, which concurrently achieve state-of-the-art fine-tuning performance, training efficiency, and inference scalability. S^{2}FT accomplishes this by "selecting sparsely and computing densely". It selects a few heads and channels in the MHA and FFN modules for each Transformer block, respectively. Next, it co-permutes weight matrices on both sides of the coupled structures in LLMs to connect the selected components in each layer into a dense submatrix. Finally, S^{2}FT performs in-place gradient updates on all submatrices. Through theoretical analysis and empirical results, our method prevents forgetting while simplifying optimization, delivers SOTA performance on both commonsense and arithmetic reasoning with 4.6% and 1.3% average improvements compared to LoRA, and surpasses full FT by 11.5% when generalizing to various domains after instruction tuning. Using our partial backpropagation algorithm, S^{2}FT saves training memory up to 3times and improves latency by 1.5-2.7times compared to full FT, while delivering an average 10% improvement over LoRA on both metrics. We further demonstrate that the weight updates in S^{2}FT can be decoupled into adapters, enabling effective fusion, fast switch, and efficient parallelism for serving multiple fine-tuned models.

Keyphrase Generation (KPG) is a longstanding task in NLP with widespread applications. The advent of sequence-to-sequence (seq2seq) pre-trained language models (PLMs) has ushered in a transformative era for KPG, yielding promising performance improvements. However, many design decisions remain unexplored and are often made arbitrarily. This paper undertakes a systematic analysis of the influence of model selection and decoding strategies on PLM-based KPG. We begin by elucidating why seq2seq PLMs are apt for KPG, anchored by an attention-driven hypothesis. We then establish that conventional wisdom for selecting seq2seq PLMs lacks depth: (1) merely increasing model size or performing task-specific adaptation is not parameter-efficient; (2) although combining in-domain pre-training with task adaptation benefits KPG, it does partially hinder generalization. Regarding decoding, we demonstrate that while greedy search achieves strong F1 scores, it lags in recall compared with sampling-based methods. Based on these insights, we propose DeSel, a likelihood-based decode-select algorithm for seq2seq PLMs. DeSel improves greedy search by an average of 4.7% semantic F1 across five datasets. Our collective findings pave the way for deeper future investigations into PLM-based KPG.

In many applications of machine learning, like drug discovery and material design, the goal is to generate candidates that simultaneously maximize a set of objectives. As these objectives are often conflicting, there is no single candidate that simultaneously maximizes all objectives, but rather a set of Pareto-optimal candidates where one objective cannot be improved without worsening another. Moreover, in practice, these objectives are often under-specified, making the diversity of candidates a key consideration. The existing multi-objective optimization methods focus predominantly on covering the Pareto front, failing to capture diversity in the space of candidates. Motivated by the success of GFlowNets for generation of diverse candidates in a single objective setting, in this paper we consider Multi-Objective GFlowNets (MOGFNs). MOGFNs consist of a novel Conditional GFlowNet which models a family of single-objective sub-problems derived by decomposing the multi-objective optimization problem. Our work is the first to empirically demonstrate conditional GFlowNets. Through a series of experiments on synthetic and benchmark tasks, we empirically demonstrate that MOGFNs outperform existing methods in terms of Hypervolume, R2-distance and candidate diversity. We also demonstrate the effectiveness of MOGFNs over existing methods in active learning settings. Finally, we supplement our empirical results with a careful analysis of each component of MOGFNs.

This work studies discrete diffusion probabilistic models with applications to natural language generation. We derive an alternative yet equivalent formulation of the sampling from discrete diffusion processes and leverage this insight to develop a family of reparameterized discrete diffusion models. The derived generic framework is highly flexible, offers a fresh perspective of the generation process in discrete diffusion models, and features more effective training and decoding techniques. We conduct extensive experiments to evaluate the text generation capability of our model, demonstrating significant improvements over existing diffusion models.

The derivation of mathematical results in specialised fields using Large Language Models (LLMs) is an emerging research direction that can help identify models' limitations, and potentially support mathematical discovery. In this paper, we leverage a symbolic engine to generate derivations of equations at scale, and investigate the capabilities of LLMs when deriving goal equations from premises. Specifically, we employ in-context learning for GPT and fine-tune a range of T5 models to compare the robustness and generalisation of pre-training strategies to specialised models. Empirical results show that fine-tuned FLAN-T5-large (MathT5) outperforms GPT models on all static and out-of-distribution test sets in terms of absolute performance. However, an in-depth analysis reveals that the fine-tuned models are more sensitive to perturbations involving unseen symbols and (to a lesser extent) changes to equation structure. In addition, we analyse 1.7K equations and over 200 derivations to highlight common reasoning errors such as the inclusion of incorrect, irrelevant, and redundant equations, along with the tendency to skip derivation steps. Finally, we explore the suitability of existing metrics for evaluating mathematical derivations finding evidence that, while they capture general properties such as sensitivity to perturbations, they fail to highlight fine-grained reasoning errors and essential differences between models. Overall, this work demonstrates that training models on synthetic data can improve their mathematical capabilities beyond larger architectures.

We propose Multiple Experts Fine-tuning Framework to build a financial large language model (LLM), DISC-FinLLM. Our methodology improves general LLMs by endowing them with multi-turn question answering abilities, domain text processing capabilities, mathematical computation skills, and retrieval-enhanced generation capabilities. We build a financial instruction-tuning dataset named DISC-FIN-SFT, including instruction samples of four categories (consulting, NLP tasks, computing and retrieval-augmented generation). Evaluations conducted on multiple benchmarks demonstrate that our model performs better than baseline models in various financial scenarios. Further resources can be found at https://github.com/FudanDISC/DISC-FinLLM.

Transformer-based foundation models have emerged as a dominant paradigm in time series analysis, offering unprecedented capabilities in tasks such as forecasting, anomaly detection, classification, trend analysis and many more time series analytical tasks. This survey provides a comprehensive overview of the current state of the art pre-trained foundation models, introducing a novel taxonomy to categorize them across several dimensions. Specifically, we classify models by their architecture design, distinguishing between those leveraging patch-based representations and those operating directly on raw sequences. The taxonomy further includes whether the models provide probabilistic or deterministic predictions, and whether they are designed to work with univariate time series or can handle multivariate time series out of the box. Additionally, the taxonomy encompasses model scale and complexity, highlighting differences between lightweight architectures and large-scale foundation models. A unique aspect of this survey is its categorization by the type of objective function employed during training phase. By synthesizing these perspectives, this survey serves as a resource for researchers and practitioners, providing insights into current trends and identifying promising directions for future research in transformer-based time series modeling.

Cell type annotation is a key task in analyzing the heterogeneity of single-cell RNA sequencing data. Although recent foundation models automate this process, they typically annotate cells independently, without considering batch-level cellular context or providing explanatory reasoning. In contrast, human experts often annotate distinct cell types for different cell clusters based on their domain knowledge. To mimic this workflow, we introduce the CellPuzzles task, where the objective is to assign unique cell types to a batch of cells. This benchmark spans diverse tissues, diseases, and donor conditions, and requires reasoning across the batch-level cellular context to ensure label uniqueness. We find that off-the-shelf large language models (LLMs) struggle on CellPuzzles, with the best baseline (OpenAI's o1) achieving only 19.0% batch-level accuracy. To fill this gap, we propose Cell-o1, a 7B LLM trained via supervised fine-tuning on distilled reasoning traces, followed by reinforcement learning with batch-level rewards. Cell-o1 achieves state-of-the-art performance, outperforming o1 by over 73% and generalizing well across contexts. Further analysis of training dynamics and reasoning behaviors provides insights into batch-level annotation performance and emergent expert-like reasoning. Code and data are available at https://github.com/ncbi-nlp/cell-o1.

Radio Frequency Neural Networks (RFNNs) have demonstrated advantages in realizing intelligent applications across various domains. However, as the model size of deep neural networks rapidly increases, implementing large-scale RFNN in practice requires an extensive number of RF interferometers and consumes a substantial amount of energy. To address this challenge, we propose to utilize low-rank decomposition to transform a large-scale RFNN into a compact RFNN while almost preserving its accuracy. Specifically, we develop a Tensor-Train RFNN (TT-RFNN) where each layer comprises a sequence of low-rank third-order tensors, leading to a notable reduction in parameter count, thereby optimizing RF interferometer utilization in comparison to the original large-scale RFNN. Additionally, considering the inherent physical errors when mapping TT-RFNN to RF device parameters in real-world deployment, from a general perspective, we construct the Robust TT-RFNN (RTT-RFNN) by incorporating a robustness solver on TT-RFNN to enhance its robustness. To adapt the RTT-RFNN to varying requirements of reshaping operations, we further provide a reconfigurable reshaping solution employing RF switch matrices. Empirical evaluations conducted on MNIST and CIFAR-10 datasets show the effectiveness of our proposed method.

Pre-trained language models (PLMs) demonstrate excellent abilities to understand texts in the generic domain while struggling in a specific domain. Although continued pre-training on a large domain-specific corpus is effective, it is costly to tune all the parameters on the domain. In this paper, we investigate whether we can adapt PLMs both effectively and efficiently by only tuning a few parameters. Specifically, we decouple the feed-forward networks (FFNs) of the Transformer architecture into two parts: the original pre-trained FFNs to maintain the old-domain knowledge and our novel domain-specific adapters to inject domain-specific knowledge in parallel. Then we adopt a mixture-of-adapters gate to fuse the knowledge from different domain adapters dynamically. Our proposed Mixture-of-Domain-Adapters (MixDA) employs a two-stage adapter-tuning strategy that leverages both unlabeled data and labeled data to help the domain adaptation: i) domain-specific adapter on unlabeled data; followed by ii) the task-specific adapter on labeled data. MixDA can be seamlessly plugged into the pretraining-finetuning paradigm and our experiments demonstrate that MixDA achieves superior performance on in-domain tasks (GLUE), out-of-domain tasks (ChemProt, RCT, IMDB, Amazon), and knowledge-intensive tasks (KILT). Further analyses demonstrate the reliability, scalability, and efficiency of our method. The code is available at https://github.com/Amano-Aki/Mixture-of-Domain-Adapters.

Low-precision formats such as float8 have been introduced in machine learning accelerated hardware to improve computational efficiency for large language models training and inference. Nevertheless, adoption by the ML community has been slowed down by the complex, and sometimes brittle, techniques required to match higher precision training accuracy. In this work, we present Scalify, a end-to-end scale propagation paradigm for computational graphs, generalizing and formalizing existing tensor scaling methods. Experiment results show that Scalify supports out-of-the-box float8 matrix multiplication and gradients representation, as well as float16 optimizer state storage. Our JAX implementation of Scalify is open-sourced at https://github.com/graphcore-research/jax-scalify

Feature selection in deep learning remains a critical challenge, particularly for high-dimensional tabular data where interpretability and computational efficiency are paramount. We present GFSNetwork, a novel neural architecture that performs differentiable feature selection through temperature-controlled Gumbel-Sigmoid sampling. Unlike traditional methods, where the user has to define the requested number of features, GFSNetwork selects it automatically during an end-to-end process. Moreover, GFSNetwork maintains constant computational overhead regardless of the number of input features. We evaluate GFSNetwork on a series of classification and regression benchmarks, where it consistently outperforms recent methods including DeepLasso, attention maps, as well as traditional feature selectors, while using significantly fewer features. Furthermore, we validate our approach on real-world metagenomic datasets, demonstrating its effectiveness in high-dimensional biological data. Concluding, our method provides a scalable solution that bridges the gap between neural network flexibility and traditional feature selection interpretability. We share our python implementation of GFSNetwork at https://github.com/wwydmanski/GFSNetwork, as well as a PyPi package (gfs_network).

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

We demonstrate, for the first time, fully quantized training (FQT) of large language models (LLMs) using predominantly 4-bit floating-point (FP4) precision for weights, activations, and gradients on datasets up to 200 billion tokens. We extensively investigate key design choices for FP4, including block sizes, scaling formats, and rounding methods. Our analysis shows that the NVFP4 format, where each block of 16 FP4 values (E2M1) shares a scale represented in E4M3, provides optimal results. We use stochastic rounding for backward and update passes and round-to-nearest for the forward pass to enhance stability. Additionally, we identify a theoretical and empirical threshold for effective quantized training: when the gradient norm falls below approximately 3 times the quantization noise, quantized training becomes less effective. Leveraging these insights, we successfully train a 7-billion-parameter model on 256 Intel Gaudi2 accelerators. The resulting FP4-trained model achieves downstream task performance comparable to a standard BF16 baseline, confirming that FP4 training is a practical and highly efficient approach for large-scale LLM training. A reference implementation is supplied in https://github.com/Anonymous1252022/fp4-all-the-way .

In this work, we present several deep learning models for the automatic diacritization of Arabic text. Our models are built using two main approaches, viz. Feed-Forward Neural Network (FFNN) and Recurrent Neural Network (RNN), with several enhancements such as 100-hot encoding, embeddings, Conditional Random Field (CRF) and Block-Normalized Gradient (BNG). The models are tested on the only freely available benchmark dataset and the results show that our models are either better or on par with other models, which require language-dependent post-processing steps, unlike ours. Moreover, we show that diacritics in Arabic can be used to enhance the models of NLP tasks such as Machine Translation (MT) by proposing the Translation over Diacritization (ToD) approach.