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update task families and add new datasets in README
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README.md
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@@ -49,12 +49,13 @@ Currently, Patho-Bench contains the following task families. We will add more ta
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| **Family** | **Description** | **Tasks** |
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|--------------------------------------|---------------------------------------------------------------------------------------|----------|
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| **Morphological Subtyping** | Classifying distinct morphological patterns associated with different disease subtypes |
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## π₯ Latest updates
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- **April 2025**: Patho-Bench has been updated with 53 new tasks! Now Patho-Bench contains a total of 95 public tasks across 33 datasets.
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@@ -147,6 +148,19 @@ For each dataset in Patho-Bench, please visit the respective repository below to
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| BOEHMK | [https://www.synapse.org/Synapse:syn25946117/wiki/611576](https://www.synapse.org/Synapse:syn25946117/wiki/611576) |
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| MBC | [https://www.synapse.org/Synapse:syn59490671/wiki/628046](https://www.synapse.org/Synapse:syn59490671/wiki/628046) |
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| SURGEN | [https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1285](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1285) / [arXiv](https://arxiv.org/abs/2502.04946) |
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## π Contact
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For any questions, contact:
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| **Family** | **Description** | **Tasks** |
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|--------------------------------------|---------------------------------------------------------------------------------------|----------|
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| **Morphological Subtyping** | Classifying distinct morphological patterns associated with different disease subtypes | 11 |
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| **TME Characterization** | Predicting morphological features from the tissue microenvironment (e.g., vascular invasion, necrosis, immune response) | 16 |
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| **Tumor Grading** | Assigning a grade based on cellular differentiation and growth patterns | 9 |
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| **Molecular Subtyping** | Predicting antigen presence (e.g., via IHC staining) | 6 |
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| **Mutation Prediction** | Predicting specific genetic mutations in tumors | 34 |
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| **Treatment Response & Assessment** | Evaluating patient response to treatment | 7 |
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| **Survival Prediction** | Predicting survival outcomes and risk stratification | 12 |
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## π₯ Latest updates
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- **April 2025**: Patho-Bench has been updated with 53 new tasks! Now Patho-Bench contains a total of 95 public tasks across 33 datasets.
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| BOEHMK | [https://www.synapse.org/Synapse:syn25946117/wiki/611576](https://www.synapse.org/Synapse:syn25946117/wiki/611576) |
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| MBC | [https://www.synapse.org/Synapse:syn59490671/wiki/628046](https://www.synapse.org/Synapse:syn59490671/wiki/628046) |
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| SURGEN | [https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1285](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1285) / [arXiv](https://arxiv.org/abs/2502.04946) |
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| CPTAC-UCEC | [https://www.cancerimagingarchive.net/collection/cptac-ucec/](https://www.cancerimagingarchive.net/collection/cptac-ucec/) |
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| CPTAC-OV | [https://www.cancerimagingarchive.net/collection/cptac-ov/](https://www.cancerimagingarchive.net/collection/cptac-ov/) |
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| VisioMel | [https://www.drivendata.org/competitions/148/visiomel-melanoma/](https://www.drivendata.org/competitions/148/visiomel-melanoma/) |
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| UCLA Lung | [https://idr.openmicroscopy.org/webclient/?show=project-1251](https://idr.openmicroscopy.org/webclient/?show=project-1251) |
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| HER2-Tumor-ROIs | [https://www.cancerimagingarchive.net/collection/her2-tumor-rois/](https://www.cancerimagingarchive.net/collection/her2-tumor-rois/) |
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| DHMC LUAD | [https://bmirds.github.io/LungCancer/](https://bmirds.github.io/LungCancer/) |
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| DHMC CCRCC | [https://bmirds.github.io/KidneyCancer/](https://bmirds.github.io/KidneyCancer/) |
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| Hancock | [https://hancock.research.fau.eu/download](https://hancock.research.fau.eu/download) |
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| BC Therapy | [https://zenodo.org/records/6337925\#.Y30d1y-l1Ls](https://zenodo.org/records/6337925\#.Y30d1y-l1Ls) |
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| COMET | [https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1714](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1714) |
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| Multiscanner | [https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1343](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1343) |
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| IMP-Cervical | [https://rdm.inesctec.pt/dataset/nis-2024-003](https://rdm.inesctec.pt/dataset/nis-2024-003) |
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| Valentino-CRC, BRAF-CRC | [https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1407?query=czi](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1407?query=czi) |
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## π Contact
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For any questions, contact:
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