Title
BioVERSE: Representation Alignment of Biomedical Modalities to LLMs for Multi-Modal Reasoning Ching-Huei Tsou Michal Ozery-Flato Ella Barkan Diwakar Mahajan Ben Shapira AI4CE 76 1 0 01 Oct 2025
Agentic AI for Scientific Discovery: A Survey of Progress, Challenges, and Future Directions Mourad Gridach Jay Nanavati Khaldoun Zine El Abidine Lenon Mendes Christina Mack 335 49 0 12 Mar 2025
Leveraging Large Language Models to Predict Antibody Biological Activity Against Influenza A HemagglutininComputational and Structural Biotechnology Journal (CSBJ), 2025 Ella Barkan Ibrahim Siddiqui Kevin J. Cheng Alex Golts Yoel Shoshan J. Weber Yailin Campos Mota Michal Ozery-Flato Giuseppe A. Sautto AI4CE 210 2 0 02 Feb 2025
Toward AI-Driven Digital Organism: Multiscale Foundation Models for Predicting, Simulating and Programming Biology at All Levels Le Song Eran Segal Eric P. Xing AI4CE 130 10 0 09 Dec 2024
Regress, Don't Guess -- A Regression-like Loss on Number Tokens for Language Models Jonas Zausinger Lars Pennig Anamarija Kozina Sean Sdahl Julian Sikora ... Anna Ketteler Thorben Prein Vishwa Mohan Singh Michael Morris Danziger Jannis Born 337 5 0 04 Nov 2024
How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities Charlotte Bunne Yusuf Roohani Yanay Rosen Ankit Gupta Xikun Zhang ... Theofanis Karaletsos Aviv Regev Emma Lundberg J. Leskovec Stephen R. Quake 311 74 0 18 Sep 2024
Tx-LLM: A Large Language Model for Therapeutics Juan Manuel Zambrano Chaves Eric Wang Tao Tu E. D. Vaishnav Byron Lee S. S. Mahdavi Christopher Semturs David Fleet Vivek Natarajan Shekoofeh Azizi LM&MA 223 31 0 10 Jun 2024
Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization Xiangxin Zhou Dongyu Xue Ruizhe Chen Zaixiang Zheng Liang Wang Quanquan Gu DiffM 367 33 0 25 Mar 2024
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning Qizhi Pei Lijun Wu Ran Bi Xiaozhuan Liang Yin Fang Jinhua Zhu Shufang Xie Tao Qin Rui Yan AI4CE 387 55 0 27 Feb 2024
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation Xiangru Tang Howard Dai Elizabeth Knight Fang Wu Yunyang Li Tianxiao Li Mark B. Gerstein 225 62 0 13 Feb 2024
xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of ProteinbioRxiv (bioRxiv), 2024 Bo Chen Xingyi Cheng Pan Li Yangli-ao Geng Jing Gong ... Chiming Liu Aohan Zeng Yuxiao Dong Jie Tang Leo T. Song 228 134 0 11 Jan 2024
BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language AssociationsConference on Empirical Methods in Natural Language Processing (EMNLP), 2023 Qizhi Pei Wei Zhang Jinhua Zhu Kehan Wu Ran Bi Lijun Wu Ziheng Lu Rui Yan 252 102 0 11 Oct 2023
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End-to-End Full-Atom Antibody DesignInternational Conference on Machine Learning (ICML), 2023 Xiangzhe Kong Wenbing Huang Yang Liu 497 68 0 01 Feb 2023
Conditional Antibody Design as 3D Equivariant Graph TranslationInternational Conference on Learning Representations (ICLR), 2022 Xiangzhe Kong Wenbing Huang Yang Liu DiffM 397 105 0 12 Aug 2022
Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement Wengong Jin Regina Barzilay Tommi Jaakkola 123 29 0 14 Jul 2022
PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence UnderstandingNeural Information Processing Systems (NeurIPS), 2022 Minghao Xu Zuobai Zhang Jiarui Lu Zhaocheng Zhu Yang Zhang Chang Ma Runcheng Liu Jian Tang 166 125 0 05 Jun 2022
Regression Transformer: Concurrent sequence regression and generation for molecular language modelingNature Machine Intelligence (Nat. Mach. Intell.), 2022 Jannis Born Matteo Manica 261 121 0 01 Feb 2022
Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-designInternational Conference on Learning Representations (ICLR), 2021 Wengong Jin Jeremy Wohlwend Regina Barzilay Tommi Jaakkola 223 157 0 09 Oct 2021
Large-Scale Chemical Language Representations Capture Molecular Structure and PropertiesNature Machine Intelligence (Nat. Mach. Intell.), 2021 Jerret Ross Brian M. Belgodere Vijil Chenthamarakshan Inkit Padhi Youssef Mroueh Payel Das AI4CE 230 429 0 17 Jun 2021
TITAN: T Cell Receptor Specificity Prediction with Bimodal Attention Networks Anna Weber Jannis Born María Rodríguez Martínez 101 149 0 21 Apr 2021
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development Kexin Huang Tianfan Fu Wenhao Gao Yue Zhao Yusuf Roohani J. Leskovec Connor W. Coley Cao Xiao Jimeng Sun Marinka Zitnik OOD LM&MA 227 356 0 18 Feb 2021
ProGen: Language Modeling for Protein GenerationbioRxiv (bioRxiv), 2020 Ali Madani Bryan McCann Nikhil Naik N. Keskar N. Anand Raphael R. Eguchi Po-Ssu Huang R. Socher 199 315 0 08 Mar 2020
Exploring the Limits of Transfer Learning with a Unified Text-to-Text TransformerJournal of machine learning research (JMLR), 2019 Colin Raffel Noam M. Shazeer Adam Roberts Katherine Lee Sharan Narang Michael Matena Yanqi Zhou Wei Li Peter J. Liu AIMat 1.5K 23,572 0 23 Oct 2019
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Attention Is All You NeedNeural Information Processing Systems (NeurIPS), 2017 Ashish Vaswani Noam M. Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan Gomez Lukasz Kaiser Illia Polosukhin 3DV 2.7K 159,241 0 12 Jun 2017
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