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ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts

28 January 2023

Jian Tang

Papers citing "ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts"

50 / 51 papers shown

Title
AnnoDPO: Protein Functional Annotation Learning with Direct Preference Optimization Zixuan Jiang Renjing Xu 20 0 0 08 Jun 2025
Modeling All-Atom Glycan Structures via Hierarchical Message Passing and Multi-Scale Pre-training Minghao Xu Jiaze Song Keming Wu Xiangxin Zhou Bin Cui Wentao Zhang 67 0 0 02 Jun 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 12 0 0 01 Jun 2025
Rethinking Text-based Protein Understanding: Retrieval or LLM? Juntong Wu Zijing Liu He Cao Hao Li Bin Feng Zishan Shu Ke Yu Li Yuan Yu-Feng Li 83 1 0 26 May 2025
Object-level Cross-view Geo-localization with Location Enhancement and Multi-Head Cross Attention Zheyang Huang Jagannath Aryal S. Nahavandi Xuequan Lu C. Lim Lei Wei Hailing Zhou ObjD 66 0 0 23 May 2025
Interpretable Multimodal Learning for Tumor Protein-Metal Binding: Progress, Challenges, and Perspectives Xiaokun Liu Sayedmohammadreza Rastegari Yijun Huang Sxe Chang Cheong Weikang Liu ... Sina Tabakhi Xianyuan Liu Zheqing Zhu Wei Sang Haiping Lu 84 1 0 04 Apr 2025
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery Yiheng Zhu Mingyang Li Junlong Liu Kun Fu Jian Wu Yue Liu Mingze Yin Jieping Ye Jian Wu Zehua Wang 143 0 0 06 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 133 4 0 21 Feb 2025
Can linguists better understand DNA? Wang Liang 148 1 0 20 Jan 2025
Towards Scientific Discovery with Generative AI: Progress, Opportunities, and Challenges Chandan K. Reddy Parshin Shojaee 150 11 0 16 Dec 2024
SeqProFT: Applying LoRA Finetuning for Sequence-only Protein Property Predictions Shuo Zhang Jian K. Liu 120 1 0 18 Nov 2024
MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering Yizhen Luo Zikun Nie Massimo Hong Suyuan Zhao Hao Zhou Zaiqing Nie 149 1 0 30 Oct 2024
MatExpert: Decomposing Materials Discovery by Mimicking Human Experts Qianggang Ding Santiago Miret Bang Liu MoE 69 8 0 26 Oct 2024
Structure-Enhanced Protein Instruction Tuning: Towards General-Purpose Protein Understanding with LLMs Wei Wu Chao Wang L. Chen Mingze Yin Yiheng Zhu Kun Fu Jieping Ye Hui Xiong Zheng Wang 143 1 0 04 Oct 2024
Recent advances in interpretable machine learning using structure-based protein representations L. Vecchietti Minji Lee Begench Hangeldiyev Hyunkyu Jung Hahnbeom Park Tae-Kyun Kim Meeyoung Cha Ho Min Kim AI4CE 125 1 0 26 Sep 2024
GP-GPT: Large Language Model for Gene-Phenotype Mapping Yanjun Lyu Zihao Wu Lu Zhang Jing Zhang Yiwei Li ... Rongjie Liu Chao Huang Wentao Li Tianming Liu Dajiang Zhu LM&MA 52 4 0 15 Sep 2024
TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering Yiqing Shen Zan Chen Michail Mamalakis Yungeng Liu Tianbin Li Yanzhou Su Junjun He Pietro Liò Yu Guang Wang LLMAG 86 9 0 27 Aug 2024
GOProteinGNN: Leveraging Protein Knowledge Graphs for Protein Representation Learning Dan Kalifa Uriel Singer Kira Radinsky 146 1 0 31 Jul 2024
Multi-Modal CLIP-Informed Protein Editing Mingze Yin Hanjing Zhou Yiheng Zhu Miao Lin YiXuan Wu ... Hongxia Xu Chang-Yu Hsieh Tingjun Hou Jintai Chen Jian Wu 93 7 0 27 Jul 2024
MatText: Do Language Models Need More than Text & Scale for Materials Modeling? Nawaf Alampara Santiago Miret Kevin Maik Jablonka 92 10 0 25 Jun 2024
Geometric Self-Supervised Pretraining on 3D Protein Structures using Subgraphs Michail Chatzianastasis George Dasoulas Michalis Vazirgiannis SSL 72 0 0 20 Jun 2024
A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery Yu Zhang Xiusi Chen Bowen Jin Sheng Wang Shuiwang Ji Wei Wang Jiawei Han 140 42 0 16 Jun 2024
Learning Multi-view Molecular Representations with Structured and Unstructured Knowledge Yizhen Luo Kai Yang Massimo Hong Xing Yi Liu Zikun Nie Hao Zhou Zaiqing Nie 68 4 0 14 Jun 2024
Gentle-CLIP: Exploring Aligned Semantic In Low-Quality Multimodal Data With Soft Alignment Zijia Song Z. Zang Yelin Wang Guozheng Yang Jiangbin Zheng Kaicheng Yu Wanyu Chen Stan Z. Li 75 1 0 09 Jun 2024
A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding Yiqing Shen Zan Chen Michail Mamalakis Luhan He Haiyang Xia Tianbin Li Yanzhou Su Junjun He Yu Guang Wang AI4MH 150 10 0 08 Jun 2024
FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction Zhaohan Meng Zaiqiao Meng I. Ounis 89 4 0 03 Jun 2024
SysCaps: Language Interfaces for Simulation Surrogates of Complex Systems Patrick Emami Zhaonan Li Saumya Sinha Truc Nguyen 155 1 0 30 May 2024
Boosting Protein Language Models with Negative Sample Mining Yaoyao Xu Xinjian Zhao Xiaozhuang Song Benyou Wang Tianshu Yu 79 0 0 28 May 2024
ProtT3: Protein-to-Text Generation for Text-based Protein Understanding Zhiyuan Liu An Zhang Hao Fei Enzhi Zhang Xiang Wang Kenji Kawaguchi Tat-Seng Chua 111 19 0 21 May 2024
LangCell: Language-Cell Pre-training for Cell Identity Understanding Suyuan Zhao Jiahuan Zhang Yushuai Wu Yizhen Luo Zaiqing Nie VLM 142 8 0 09 May 2024
Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship Eunji Ko Seul Lee Minseon Kim Dongki Kim 56 0 0 29 Apr 2024
Functional Protein Design with Local Domain Alignment Chaohao Yuan Songyou Li Geyan Ye Yikun Zhang Long-Kai Huang Wenbing Huang Wei Liu Jianhua Yao Yu Rong 91 1 0 18 Apr 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 73 8 0 23 Mar 2024
Bridging Text and Molecule: A Survey on Multimodal Frameworks for Molecule Yi Xiao Xiangxin Zhou Qiang Liu Liang Wang AI4CE 64 3 0 07 Mar 2024
Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey Qizhi Pei Lijun Wu Kaiyuan Gao Jinhua Zhu Yue Wang Zun Wang Tao Qin Rui Yan AI4CE 127 18 0 03 Mar 2024
PQA: Zero-shot Protein Question Answering for Free-form Scientific Enquiry with Large Language Models Eli M. Carrami Sahand Sharifzadeh 63 2 0 21 Feb 2024
ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback Henry W Sprueill Carl Edwards Khushbu Agarwal Mariefel V. Olarte Udishnu Sanyal Conrad Johnston Hongbin Liu Heng Ji Sutanay Choudhury LRM 114 9 0 15 Feb 2024
ProtChatGPT: Towards Understanding Proteins with Large Language Models Chao Wang Hehe Fan Ruijie Quan Yi Yang 108 16 0 15 Feb 2024
Are LLMs Ready for Real-World Materials Discovery? Santiago Miret N. M. A. Krishnan 101 34 0 07 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 85 18 0 06 Feb 2024
Future Directions in the Theory of Graph Machine Learning Christopher Morris Fabrizio Frasca Nadav Dym Haggai Maron .Ismail .Ilkan Ceylan Ron Levie Derek Lim Michael M. Bronstein Martin Grohe Stefanie Jegelka AI4CE 141 7 0 03 Feb 2024
Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Design Henry W Sprueill Carl Edwards Mariefel V. Olarte Udishnu Sanyal Heng Ji Sutanay Choudhury LRM 117 11 0 22 Oct 2023
BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations Qizhi Pei Wei Zhang Jinhua Zhu Kehan Wu Kaiyuan Gao Lijun Wu Yingce Xia Rui Yan 116 73 0 11 Oct 2023
BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphs Zifeng Wang Zichen Wang Balasubramaniam Srinivasan V. Ioannidis Huzefa Rangwala Rishita Anubhai AI4CE 80 18 0 05 Oct 2023
InstructProtein: Aligning Human and Protein Language via Knowledge Instruction Zeyuan Wang Qiang Zhang Keyan Ding Ming Qin Zhuang Xiang Xiaotong Li Huajun Chen 104 32 0 05 Oct 2023
GeRA: Label-Efficient Geometrically Regularized Alignment Dustin Klebe Tal Shnitzer Mikhail Yurochkin Leonid Karlinsky Justin Solomon 81 2 0 01 Oct 2023
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities Jiaoyan Chen Hang Dong Janna Hastings Ernesto Jiménez-Ruiz Vanessa Lopez Pierre Monnin Catia Pesquita Petr vSkoda Valentina A. M. Tamma 90 12 0 29 Sep 2023
Prot2Text: Multimodal Protein's Function Generation with GNNs and Transformers Hadi Abdine Michail Chatzianastasis Costas Bouyioukos Michalis Vazirgiannis 71 45 0 25 Jul 2023
A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design Zaixin Zhang Jiaxian Yan Qi Liu Enhong Chen Marinka Zitnik 131 1 0 20 Jun 2023
SynerGPT: In-Context Learning for Personalized Drug Synergy Prediction and Drug Design Carl Edwards Aakanksha Naik Tushar Khot Martin D. Burke Heng Ji Tom Hope 124 16 0 19 Jun 2023