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 / 50 papers shown

Title
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 29 0 0 04 Apr 2025
Multimodal Language Modeling for High-Accuracy Single Cell Transcriptomics Analysis and Generation Yaorui Shi Jiaqi Yang Sihang Li Junfeng Fang X. Wang Zhiyuan Liu Yang Zhang 126 0 0 12 Mar 2025
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery Yiheng Zhu Mingyang Li Junlong Liu Kun Fu J. Wu Q. Li Mingze Yin Jieping Ye Jian Wu Z. Wang 60 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-Jie Zhang James Y. Zou Y. Sun Wei Wang LM&MA AI4CE 49 3 0 21 Feb 2025
Can linguists better understand DNA? Wang Liang 82 1 0 20 Jan 2025
Towards Scientific Discovery with Generative AI: Progress, Opportunities, and Challenges Chandan K. Reddy Parshin Shojaee 73 4 0 16 Dec 2024
SeqProFT: Applying LoRA Finetuning for Sequence-only Protein Property Predictions Shuo Zhang Jian K. Liu 59 0 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 31 0 0 30 Oct 2024
MatExpert: Decomposing Materials Discovery by Mimicking Human Experts Qianggang Ding Santiago Miret Bang Liu MoE 32 7 0 26 Oct 2024
Structure-Enhanced Protein Instruction Tuning: Towards General-Purpose Protein Understanding Wei Yu Wu Chao Wang Liyi Chen Mingze Yin Yiheng Zhu Kun Fu Jieping Ye Hui Xiong Zheng Wang 28 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 21 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 25 3 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 36 9 0 27 Aug 2024
GOProteinGNN: Leveraging Protein Knowledge Graphs for Protein Representation Learning Dan Kalifa Uriel Singer Kira Radinsky 36 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 33 7 0 27 Jul 2024
MatText: Do Language Models Need More than Text & Scale for Materials Modeling? Nawaf Alampara Santiago Miret K. Jablonka 48 8 0 25 Jun 2024
Geometric Self-Supervised Pretraining on 3D Protein Structures using Subgraphs Michail Chatzianastasis George Dasoulas Michalis Vazirgiannis SSL 19 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 40 27 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 38 2 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 31 0 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 24 9 0 08 Jun 2024
FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction Zhaohan Meng Zaiqiao Meng I. Ounis 49 4 0 03 Jun 2024
SysCaps: Language Interfaces for Simulation Surrogates of Complex Systems Patrick Emami Zhaonan Li Saumya Sinha Truc Nguyen 48 1 0 30 May 2024
Boosting Protein Language Models with Negative Sample Mining Yaoyao Xu Xinjian Zhao Xiaozhuang Song Benyou Wang Tianshu Yu 33 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 52 16 0 21 May 2024
LangCell: Language-Cell Pre-training for Cell Identity Understanding Suyuan Zhao Jiahuan Zhang Yushuai Wu Yizhen Luo Zaiqing Nie VLM 26 6 0 09 May 2024
Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship Eunji Ko Seul Lee Minseon Kim Dongki Kim 23 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 29 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 21 7 0 23 Mar 2024
Bridging Text and Molecule: A Survey on Multimodal Frameworks for Molecule Yi Xiao Xiangxin Zhou Qiang Liu Liang Wang AI4CE 30 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 47 19 0 03 Mar 2024
PQA: Zero-shot Protein Question Answering for Free-form Scientific Enquiry with Large Language Models Eli M. Carrami Sahand Sharifzadeh 27 2 0 21 Feb 2024
ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback Henry W Sprueill Carl N. Edwards Khushbu Agarwal Mariefel V. Olarte Udishnu Sanyal Conrad Johnston Hongbin Liu Heng Ji Sutanay Choudhury LRM 26 7 0 15 Feb 2024
ProtChatGPT: Towards Understanding Proteins with Large Language Models Chao Wang Hehe Fan Ruijie Quan Yi Yang 26 12 0 15 Feb 2024
Are LLMs Ready for Real-World Materials Discovery? Santiago Miret N. M. A. Krishnan 35 27 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-Hu Li AI4CE 35 9 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 30 4 0 03 Feb 2024
Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Design Henry W Sprueill Carl N. Edwards Mariefel V. Olarte Udishnu Sanyal Heng Ji Sutanay Choudhury LRM 30 10 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 28 60 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 27 15 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 16 28 0 05 Oct 2023
GeRA: Label-Efficient Geometrically Regularized Alignment Dustin Klebe Tal Shnitzer Mikhail Yurochkin Leonid Karlinsky Justin Solomon 11 1 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 19 11 0 29 Sep 2023
Prot2Text: Multimodal Protein's Function Generation with GNNs and Transformers Hadi Abdine Michail Chatzianastasis Costas Bouyioukos Michalis Vazirgiannis 26 39 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 30 1 0 20 Jun 2023
SynerGPT: In-Context Learning for Personalized Drug Synergy Prediction and Drug Design Carl N. Edwards Aakanksha Naik Tushar Khot Martin Burke Heng Ji Tom Hope 23 13 0 19 Jun 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 27 29 0 11 Mar 2023
Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval Pascal Notin M. Dias J. Frazer Javier Marchena-Hurtado Aidan N. Gomez D. Marks Y. Gal 53 174 0 27 May 2022
OntoProtein: Protein Pretraining With Gene Ontology Embedding Ningyu Zhang Zhen Bi Xiaozhuan Liang Shuyang Cheng Haosen Hong Shumin Deng J. Lian Qiang Zhang Huajun Chen 91 90 0 23 Jan 2022
VideoCLIP: Contrastive Pre-training for Zero-shot Video-Text Understanding Hu Xu Gargi Ghosh Po-Yao (Bernie) Huang Dmytro Okhonko Armen Aghajanyan Florian Metze Luke Zettlemoyer Florian Metze Luke Zettlemoyer Christoph Feichtenhofer CLIP VLM 245 557 0 28 Sep 2021