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Apr 23

UAlign: Pushing the Limit of Template-free Retrosynthesis Prediction with Unsupervised SMILES Alignment

Retrosynthesis planning poses a formidable challenge in the organic chemical industry, particularly in pharmaceuticals. Single-step retrosynthesis prediction, a crucial step in the planning process, has witnessed a surge in interest in recent years due to advancements in AI for science. Various deep learning-based methods have been proposed for this task in recent years, incorporating diverse levels of additional chemical knowledge dependency. This paper introduces UAlign, a template-free graph-to-sequence pipeline for retrosynthesis prediction. By combining graph neural networks and Transformers, our method can more effectively leverage the inherent graph structure of molecules. Based on the fact that the majority of molecule structures remain unchanged during a chemical reaction, we propose a simple yet effective SMILES alignment technique to facilitate the reuse of unchanged structures for reactant generation. Extensive experiments show that our method substantially outperforms state-of-the-art template-free and semi-template-based approaches. Importantly, Our template-free method achieves effectiveness comparable to, or even surpasses, established powerful template-based methods. Scientific contribution: We present a novel graph-to-sequence template-free retrosynthesis prediction pipeline that overcomes the limitations of Transformer-based methods in molecular representation learning and insufficient utilization of chemical information. We propose an unsupervised learning mechanism for establishing product-atom correspondence with reactant SMILES tokens, achieving even better results than supervised SMILES alignment methods. Extensive experiments demonstrate that UAlign significantly outperforms state-of-the-art template-free methods and rivals or surpasses template-based approaches, with up to 5\% (top-5) and 5.4\% (top-10) increased accuracy over the strongest baseline.

KL3M Tokenizers: A Family of Domain-Specific and Character-Level Tokenizers for Legal, Financial, and Preprocessing Applications

We present the KL3M tokenizers, a family of specialized tokenizers for legal, financial, and governmental text. Despite established work on tokenization, specialized tokenizers for professional domains remain understudied. Our paper offers two main contributions to this area. First, we introduce domain-specific BPE tokenizers for legal, financial, and governmental text. Our kl3m-004-128k-cased tokenizer uses 9-17% fewer tokens than GPT-4o and Llama3 for domain-specific documents, despite having a smaller vocabulary. For specialized terminology, our cased tokenizer is even more efficient, using up to 83% fewer tokens for legal terms and 39% fewer tokens for financial terms. Second, we develop character-level BPE tokenizers (4K, 8K, and 16K vocabulary sizes) for text correction tasks like OCR post-processing. These tokenizers keep consistent token boundaries between error-containing and correct text, making it easier for models to learn correction patterns. These tokenizers help professional applications by fitting more text in context windows, reducing computational needs, and preserving the meaning of domain-specific terms. Our analysis shows these efficiency gains directly benefit the processing of long legal and financial documents. We release all tokenizers and code through GitHub and Hugging Face to support further research in specialized tokenization.

DENTEX: An Abnormal Tooth Detection with Dental Enumeration and Diagnosis Benchmark for Panoramic X-rays

Panoramic X-rays are frequently used in dentistry for treatment planning, but their interpretation can be both time-consuming and prone to error. Artificial intelligence (AI) has the potential to aid in the analysis of these X-rays, thereby improving the accuracy of dental diagnoses and treatment plans. Nevertheless, designing automated algorithms for this purpose poses significant challenges, mainly due to the scarcity of annotated data and variations in anatomical structure. To address these issues, the Dental Enumeration and Diagnosis on Panoramic X-rays Challenge (DENTEX) has been organized in association with the International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) in 2023. This challenge aims to promote the development of algorithms for multi-label detection of abnormal teeth, using three types of hierarchically annotated data: partially annotated quadrant data, partially annotated quadrant-enumeration data, and fully annotated quadrant-enumeration-diagnosis data, inclusive of four different diagnoses. In this paper, we present the results of evaluating participant algorithms on the fully annotated data, additionally investigating performance variation for quadrant, enumeration, and diagnosis labels in the detection of abnormal teeth. The provision of this annotated dataset, alongside the results of this challenge, may lay the groundwork for the creation of AI-powered tools that can offer more precise and efficient diagnosis and treatment planning in the field of dentistry. The evaluation code and datasets can be accessed at https://github.com/ibrahimethemhamamci/DENTEX

Interpretable Bangla Sarcasm Detection using BERT and Explainable AI

A positive phrase or a sentence with an underlying negative motive is usually defined as sarcasm that is widely used in today's social media platforms such as Facebook, Twitter, Reddit, etc. In recent times active users in social media platforms are increasing dramatically which raises the need for an automated NLP-based system that can be utilized in various tasks such as determining market demand, sentiment analysis, threat detection, etc. However, since sarcasm usually implies the opposite meaning and its detection is frequently a challenging issue, data meaning extraction through an NLP-based model becomes more complicated. As a result, there has been a lot of study on sarcasm detection in English over the past several years, and there's been a noticeable improvement and yet sarcasm detection in the Bangla language's state remains the same. In this article, we present a BERT-based system that can achieve 99.60\% while the utilized traditional machine learning algorithms are only capable of achieving 89.93\%. Additionally, we have employed Local Interpretable Model-Agnostic Explanations that introduce explainability to our system. Moreover, we have utilized a newly collected bangla sarcasm dataset, BanglaSarc that was constructed specifically for the evaluation of this study. This dataset consists of fresh records of sarcastic and non-sarcastic comments, the majority of which are acquired from Facebook and YouTube comment sections.

Critical Tokens Matter: Token-Level Contrastive Estimation Enhence LLM's Reasoning Capability

Large Language Models (LLMs) have exhibited remarkable performance on reasoning tasks. They utilize autoregressive token generation to construct reasoning trajectories, enabling the development of a coherent chain of thought. In this work, we explore the impact of individual tokens on the final outcomes of reasoning tasks. We identify the existence of ``critical tokens'' that lead to incorrect reasoning trajectories in LLMs. Specifically, we find that LLMs tend to produce positive outcomes when forced to decode other tokens instead of critical tokens. Motivated by this observation, we propose a novel approach - cDPO - designed to automatically recognize and conduct token-level rewards for the critical tokens during the alignment process. Specifically, we develop a contrastive estimation approach to automatically identify critical tokens. It is achieved by comparing the generation likelihood of positive and negative models. To achieve this, we separately fine-tune the positive and negative models on various reasoning trajectories, consequently, they are capable of identifying identify critical tokens within incorrect trajectories that contribute to erroneous outcomes. Moreover, to further align the model with the critical token information during the alignment process, we extend the conventional DPO algorithms to token-level DPO and utilize the differential likelihood from the aforementioned positive and negative model as important weight for token-level DPO learning.Experimental results on GSM8K and MATH500 benchmarks with two-widely used models Llama-3 (8B and 70B) and deepseek-math (7B) demonstrate the effectiveness of the propsoed approach cDPO.

Model Cards for Model Reporting

Trained machine learning models are increasingly used to perform high-impact tasks in areas such as law enforcement, medicine, education, and employment. In order to clarify the intended use cases of machine learning models and minimize their usage in contexts for which they are not well suited, we recommend that released models be accompanied by documentation detailing their performance characteristics. In this paper, we propose a framework that we call model cards, to encourage such transparent model reporting. Model cards are short documents accompanying trained machine learning models that provide benchmarked evaluation in a variety of conditions, such as across different cultural, demographic, or phenotypic groups (e.g., race, geographic location, sex, Fitzpatrick skin type) and intersectional groups (e.g., age and race, or sex and Fitzpatrick skin type) that are relevant to the intended application domains. Model cards also disclose the context in which models are intended to be used, details of the performance evaluation procedures, and other relevant information. While we focus primarily on human-centered machine learning models in the application fields of computer vision and natural language processing, this framework can be used to document any trained machine learning model. To solidify the concept, we provide cards for two supervised models: One trained to detect smiling faces in images, and one trained to detect toxic comments in text. We propose model cards as a step towards the responsible democratization of machine learning and related AI technology, increasing transparency into how well AI technology works. We hope this work encourages those releasing trained machine learning models to accompany model releases with similar detailed evaluation numbers and other relevant documentation.

A 106K Multi-Topic Multilingual Conversational User Dataset with Emoticons

Instant messaging has become a predominant form of communication, with texts and emoticons enabling users to express emotions and ideas efficiently. Emoticons, in particular, have gained significant traction as a medium for conveying sentiments and information, leading to the growing importance of emoticon retrieval and recommendation systems. However, one of the key challenges in this area has been the absence of datasets that capture both the temporal dynamics and user-specific interactions with emoticons, limiting the progress of personalized user modeling and recommendation approaches. To address this, we introduce the emoticon dataset, a comprehensive resource that includes time-based data along with anonymous user identifiers across different conversations. As the largest publicly accessible emoticon dataset to date, it comprises 22K unique users, 370K emoticons, and 8.3M messages. The data was collected from a widely-used messaging platform across 67 conversations and 720 hours of crawling. Strict privacy and safety checks were applied to ensure the integrity of both text and image data. Spanning across 10 distinct domains, the emoticon dataset provides rich insights into temporal, multilingual, and cross-domain behaviors, which were previously unavailable in other emoticon-based datasets. Our in-depth experiments, both quantitative and qualitative, demonstrate the dataset's potential in modeling user behavior and personalized recommendation systems, opening up new possibilities for research in personalized retrieval and conversational AI. The dataset is freely accessible.

SELFormer: Molecular Representation Learning via SELFIES Language Models

Automated computational analysis of the vast chemical space is critical for numerous fields of research such as drug discovery and material science. Representation learning techniques have recently been employed with the primary objective of generating compact and informative numerical expressions of complex data. One approach to efficiently learn molecular representations is processing string-based notations of chemicals via natural language processing (NLP) algorithms. Majority of the methods proposed so far utilize SMILES notations for this purpose; however, SMILES is associated with numerous problems related to validity and robustness, which may prevent the model from effectively uncovering the knowledge hidden in the data. In this study, we propose SELFormer, a transformer architecture-based chemical language model that utilizes a 100% valid, compact and expressive notation, SELFIES, as input, in order to learn flexible and high-quality molecular representations. SELFormer is pre-trained on two million drug-like compounds and fine-tuned for diverse molecular property prediction tasks. Our performance evaluation has revealed that, SELFormer outperforms all competing methods, including graph learning-based approaches and SMILES-based chemical language models, on predicting aqueous solubility of molecules and adverse drug reactions. We also visualized molecular representations learned by SELFormer via dimensionality reduction, which indicated that even the pre-trained model can discriminate molecules with differing structural properties. We shared SELFormer as a programmatic tool, together with its datasets and pre-trained models. Overall, our research demonstrates the benefit of using the SELFIES notations in the context of chemical language modeling and opens up new possibilities for the design and discovery of novel drug candidates with desired features.