Title
HyperHELM: Hyperbolic Hierarchy Encoding for mRNA Language Modeling Max van Spengler Artem Moskalev Tommaso Mansi Mangal Prakash Rui Liao 0 0 0 29 Sep 2025
PFMBench: Protein Foundation Model Benchmark Zhangyang Gao Hao Wang Cheng Tan Chenrui Xu Mengdi Liu Bozhen Hu Linlin Chao Xiaoming Zhang Stan Z. Li 118 0 0 01 Jun 2025
HELM: Hierarchical Encoding for mRNA Language Modeling Mehdi Yazdani-Jahromi Mangal Prakash Tommaso Mansi Artem Moskalev Rui Liao 208 8 0 13 Mar 2025
Protein Large Language Models: A Comprehensive Survey Yijia Xiao Wanjia Zhao Junkai Zhang Yiqiao Jin Han Zhang ... Xiao Luo Yu Zhang James Zou Yizhou Sun Wei Wang LM&MA AI4CE 278 9 0 21 Feb 2025
DataSciBench: An LLM Agent Benchmark for Data Science Dan Zhang Sining Zhoubian Min Cai Fengzu Li L. Yang Wei Wang Tianjiao Dong Ziniu Hu J. Tang Yisong Yue ALM ELM 143 16 0 20 Feb 2025
Recent Advances, Applications and Open Challenges in Machine Learning for Health: Reflections from Research Roundtables at ML4H 2024 Symposium A. Adibi Xu Cao Zongliang Ji Jivat Neet Kaur Winston Chen ... Mohsen Sadatsafavi Dennis L. Shung Shannon McWeeney Jessica Dafflon Sarah Jabbour OOD VLM AI4TS 207 1 0 10 Feb 2025
A Survey on Memory-Efficient Transformer-Based Model Training in AI for Science Kaiyuan Tian Linbo Qiao Baihui Liu Gongqingjian Jiang Shanshan Li Dongsheng Li 202 0 0 21 Jan 2025
S^2 ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning Mingze Yin Hanjing Zhou Jialu Wu Yiheng Zhu Yuxuan Zhan ... Hongxia Xu Chang-Yu Hsieh Jintai Chen Tingjun Hou Jian Wu 133 0 0 20 Nov 2024
Concept Bottleneck Language Models For protein design Aya Abdelsalam Ismail Tuomas Oikarinen Amy Wang Julius Adebayo Samuel Stanton ... J. Kleinhenz Allen Goodman H. C. Bravo Kyunghyun Cho Nathan C. Frey 180 10 0 09 Nov 2024
Training Compute-Optimal Protein Language Models Xingyi Cheng Bo Chen Pan Li Jing Gong Jie Tang Le Song 168 23 0 04 Nov 2024
MAMMAL -- Molecular Aligned Multi-Modal Architecture and Language Yoel Shoshan Moshiko Raboh Michal Ozery-Flato Vadim Ratner Alex Golts ... Sharon Kurant Joseph A. Morrone Parthasarathy Suryanarayanan Michal Rosen-Zvi Efrat Hexter 203 2 0 28 Oct 2024
pLDDT-Predictor: High-speed Protein Screening Using Transformer and ESM2 Joongwon Chae Zhenyu Wang I. Gul Jiansong Ji Zhenglin Chen Peiwu Qin 96 2 0 11 Oct 2024
Large-Scale Multi-omic Biosequence Transformers for Modeling Protein-Nucleic Acid Interactions Sully F. Chen Robert J. Steele Glen M. Hocky Beakal Lemeneh S. Lad Eric Oermann AI4CE 163 1 0 29 Aug 2024
ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding Yijia Xiao Edward Sun Yiqiao Jin Qifan Wang Wei Wang 145 19 0 21 Aug 2024
On the Limitations of Compute Thresholds as a Governance Strategy Sara Hooker 226 24 0 08 Jul 2024
Are Protein Language Models Compute Optimal? Yaiza Serrano Álvaro Ciudad Alexis Molina 90 9 0 11 Jun 2024
MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training Bo Chen Zhilei Bei Xingyi Cheng Pan Li Jie Tang Le Song 172 7 0 08 Jun 2024
ABodyBuilder3: Improved and scalable antibody structure predictions Henry Kenlay Frédéric A. Dreyer Daniel Cutting Daniel A. Nissley Charlotte M. Deane 89 14 0 31 May 2024
OpenCarbonEval: A Unified Carbon Emission Estimation Framework in Large-Scale AI Models Zhaojian Yu Yinghao Wu Zhuotao Deng Yansong Tang Xiao-Ping Zhang 116 3 0 21 May 2024
Continual Learning of Large Language Models: A Comprehensive Survey Haizhou Shi Zihao Xu Hengyi Wang Weiyi Qin Wenyuan Wang Yibin Wang Zifeng Wang Sayna Ebrahimi Hao Wang CLL KELM LRM 257 117 0 25 Apr 2024
Foundation Model for Advancing Healthcare: Challenges, Opportunities, and Future Directions Yuting He Fuxiang Huang Xinrui Jiang Yuxiang Nie Minghao Wang Jiguang Wang Hao Chen LM&MA AI4CE 211 67 0 04 Apr 2024
Large scale paired antibody language models Henry Kenlay Frédéric A. Dreyer A. Kovaltsuk Dom Miketa Douglas Pires Charlotte M. Deane 103 36 0 26 Mar 2024
AI for Biomedicine in the Era of Large Language Models Zhenyu Bi Sajib Acharjee Dip Daniel Hajialigol Sindhura Kommu Hanwen Liu Meng Lu Xuan Wang LM&MA AI4CE 97 8 0 23 Mar 2024
A system capable of verifiably and privately screening global DNA synthesis Carsten Baum Jens Berlips Walther Chen Hongrui Cui I. Damgård ... Stephen Wooster Andrew C. Yao Yu Yu Haoling Zhang Kaiyi Zhang 68 6 0 20 Mar 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 351 35 0 01 Mar 2024
RiNALMo: General-Purpose RNA Language Models Can Generalize Well on Structure Prediction Tasks Rafael Josip Penić Tin Vlasic Roland G. Huber Yue Wan M. Šikić AI4CE 91 46 0 29 Feb 2024
A Survey on Knowledge Distillation of Large Language Models Xiaohan Xu Ming Li Chongyang Tao Tao Shen Reynold Cheng Jinyang Li Can Xu Dacheng Tao Wanrong Zhu KELM VLM 266 175 0 20 Feb 2024
Generative AI for Controllable Protein Sequence Design: A Survey Yiheng Zhu Zitai Kong Jialun Wu Weize Liu Yuqiang Han Mingze Yin Hongxia Xu Chang-Yu Hsieh Tingjun Hou AI4CE 155 9 0 16 Feb 2024
Progress and Opportunities of Foundation Models in Bioinformatics Qing Li Zhihang Hu Yixuan Wang Lei Li Yimin Fan Irwin King Le Song Yu Li AI4CE 127 28 0 06 Feb 2024
Pre-Training Protein Bi-level Representation Through Span Mask Strategy On 3D Protein Chains Jiale Zhao Wanru Zhuang Jia Song Yaqi Li Shuqi Lu AI4CE 212 9 0 02 Feb 2024
Endowing Protein Language Models with Structural Knowledge Dexiong Chen Philip Hartout Paolo Pellizzoni Carlos Oliver Karsten Borgwardt 143 16 0 26 Jan 2024
PETA: Evaluating the Impact of Protein Transfer Learning with Sub-word Tokenization on Downstream Applications Yang Tan Mingchen Li P. Tan Ziyi Zhou Huiqun Yu Guisheng Fan Liang Hong 87 0 0 26 Oct 2023
Large AI Models in Health Informatics: Applications, Challenges, and the Future Jianing Qiu Lin Li Jiankai Sun Jiachuan Peng Peilun Shi ... Bo Xiao Wu Yuan Ningli Wang Dong Xu Benny Lo AI4MH LM&MA 159 157 0 21 Mar 2023
A Systematic Study of Joint Representation Learning on Protein Sequences and Structures Zuobai Zhang Chuanrui Wang Minghao Xu Vijil Chenthamarakshan A. Lozano Payel Das Jian Tang 129 33 0 11 Mar 2023