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OntoProtein: Protein Pretraining With Gene Ontology Embedding
International Conference on Learning Representations (ICLR), 2022
23 January 2022
Ningyu Zhang
Zhen Bi
Xiaozhuan Liang
Shuyang Cheng
Haosen Hong
Shumin Deng
J. Lian
Qiang Zhang
Huajun Chen
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Papers citing
"OntoProtein: Protein Pretraining With Gene Ontology Embedding"
50 / 52 papers shown
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Zicheng Ma
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119
0
0
17 Aug 2025
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Xinzhe Zheng
Hao Du
Fanding Xu
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Yan Lu
Nanqing Dong
Yang-ting Zhang
304
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0
07 Jul 2025
DisProtEdit: Exploring Disentangled Representations for Multi-Attribute Protein Editing
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S. Sun
Ziqiao Wang
Wenhu Chen
269
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0
17 Jun 2025
AnnoDPO: Protein Functional Annotation Learning with Direct Preference Optimization
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Renjing Xu
240
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0
08 Jun 2025
PFMBench: Protein Foundation Model Benchmark
Zhangyang Gao
Hao Wang
Cheng Tan
Chenrui Xu
Mengdi Liu
Bozhen Hu
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Stan Z. Li
274
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0
01 Jun 2025
Rethinking Text-based Protein Understanding: Retrieval or LLM?
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Zijing Liu
He Cao
Hao Li
Bin Feng
Zishan Shu
Ke Yu
Li Yuan
Yu-Feng Li
485
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0
26 May 2025
Protein Large Language Models: A Comprehensive Survey
Yijia Xiao
Wanjia Zhao
Junkai Zhang
Yiqiao Jin
Han Zhang
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Xiao Luo
Yu Zhang
James Zou
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AI4CE
490
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0
21 Feb 2025
A Comprehensive Survey of Foundation Models in Medicine
IEEE Reviews in Biomedical Engineering (RBME), 2024
Wasif Khan
Seowung Leem
Kyle B. See
Joshua K. Wong
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AI4CE
LM&MA
VLM
869
100
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17 Jan 2025
MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering
Neural Information Processing Systems (NeurIPS), 2024
Yizhen Luo
Zikun Nie
Massimo Hong
Suyuan Zhao
Hao Zhou
Zaiqing Nie
351
2
0
30 Oct 2024
Long-context Protein Language Modeling Using Bidirectional Mamba with Shared Projection Layers
bioRxiv (bioRxiv), 2024
Yingheng Wang
Zichen Wang
Gil Sadeh
Luca Zancato
Alessandro Achille
George Karypis
Huzefa Rangwala
469
1
0
29 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
488
5
0
04 Oct 2024
SAC-KG: Exploiting Large Language Models as Skilled Automatic Constructors for Domain Knowledge Graphs
Annual Meeting of the Association for Computational Linguistics (ACL), 2024
Hanzhu Chen
Xu Shen
Qitan Lv
Jie Wang
Xiaoqi Ni
Jieping Ye
244
39
0
22 Sep 2024
OneEdit: A Neural-Symbolic Collaboratively Knowledge Editing System
Xin Xu
Zekun Xi
Yujie Luo
Peng Wang
Bozhong Tian
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Lei Liang
Qing Cui
Xiaowei Zhu
Jun Zhou
Huajun Chen
KELM
290
9
0
09 Sep 2024
ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding
Yijia Xiao
Edward Sun
Yiqiao Jin
Qifan Wang
Wei Wang
372
34
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21 Aug 2024
GOProteinGNN: Leveraging Protein Knowledge Graphs for Protein Representation Learning
Dan Kalifa
Uriel Singer
Kira Radinsky
608
3
0
31 Jul 2024
Multi-Modal CLIP-Informed Protein Editing
bioRxiv (bioRxiv), 2024
Mingze Yin
Hanjing Zhou
Yiheng Zhu
Miao Lin
YiXuan Wu
...
Hongxia Xu
Chang-Yu Hsieh
Tingjun Hou
Jintai Chen
Jian Wu
320
7
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27 Jul 2024
Ontology Embedding: A Survey of Methods, Applications and Resources
Jiaoyan Chen
Olga Mashkova
Fernando Zhapa-Camacho
Robert Hoehndorf
Yuan He
Ian Horrocks
633
26
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16 Jun 2024
Learning Multi-view Molecular Representations with Structured and Unstructured Knowledge
Knowledge Discovery and Data Mining (KDD), 2024
Yizhen Luo
Kai Yang
Massimo Hong
Xing Yi Liu
Zikun Nie
Hao Zhou
Zaiqing Nie
243
15
0
14 Jun 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
387
33
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21 May 2024
Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship
Eunji Ko
Seul Lee
Minseon Kim
Dongki Kim
249
1
0
29 Apr 2024
Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey
Qizhi Pei
Lijun Wu
Ran Bi
Jinhua Zhu
Yue Wang
Guoqing Liu
Tao Qin
Lijun Wu
Rui Yan
AI4CE
545
25
0
03 Mar 2024
PQA: Zero-shot Protein Question Answering for Free-form Scientific Enquiry with Large Language Models
Eli M. Carrami
Sahand Sharifzadeh
232
3
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21 Feb 2024
ProtChatGPT: Towards Understanding Proteins with Large Language Models
Chao Wang
Hehe Fan
Ruijie Quan
Yi Yang
363
24
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15 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
302
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13 Feb 2024
Large Knowledge Model: Perspectives and Challenges
Data Intelligence (DI), 2023
Huajun Chen
KELM
428
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05 Dec 2023
xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data
bioRxiv (bioRxiv), 2023
Jing Gong
Minsheng Hao
Xingyi Cheng
Xin Zeng
Chiming Liu
Jianzhu Ma
Xuegong Zhang
Taifeng Wang
Leo T. Song
402
39
0
26 Nov 2023
BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphs
International Conference on Learning Representations (ICLR), 2023
Zifeng Wang
Zichen Wang
Ninad Kulkarni
V. Ioannidis
Huzefa Rangwala
Rishita Anubhai
AI4CE
373
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05 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
475
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29 Sep 2023
Otter-Knowledge: benchmarks of multimodal knowledge graph representation learning from different sources for drug discovery
Hoang Thanh Lam
M. Sbodio
Marcos Martínez Galindo
Mykhaylo Zayats
Raúl Fernández-Díaz
Víctor Valls
Gabriele Picco
Cesar Berrospi Ramis
V. López
431
11
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22 Jun 2023
UUKG: Unified Urban Knowledge Graph Dataset for Urban Spatiotemporal Prediction
Neural Information Processing Systems (NeurIPS), 2023
Yansong Ning
Hao Liu
Hao Wang
Zhenyu Zeng
Hui Xiong
AI4TS
289
37
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20 Jun 2023
Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials
Neural Information Processing Systems (NeurIPS), 2023
Shengchao Liu
Weitao Du
Yanjing Li
Zhuoxinran Li
Zhiling Zheng
...
Anima Anandkumar
C. Borgs
J. Chayes
Ziqiao Wang
Jian Tang
AI4CE
310
42
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15 Jun 2023
Multi-level Protein Representation Learning for Blind Mutational Effect Prediction
Y. Tan
Bingxin Zhou
Yuanhong Jiang
Yu Wang
Liang Hong
179
2
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08 Jun 2023
Knowledge-Design: Pushing the Limit of Protein Design via Knowledge Refinement
Zhangyang Gao
Cheng Tan
Stan Z. Li
441
17
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20 May 2023
Towards Unified AI Drug Discovery with Multiple Knowledge Modalities
Yi Luo
Xing Yi Liu
Kai Yang
Kui Huang
Massimo Hong
Jiahuan Zhang
Yushuai Wu
Zaiqing Nie
OffRL
179
6
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17 Apr 2023
Biological Factor Regulatory Neural Network
Xinnan Dai
Caihua Shan
Jie Zheng
Xiaoxiao Li
Dongsheng Li
208
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11 Apr 2023
ChatGPT for Shaping the Future of Dentistry: The Potential of Multi-Modal Large Language Model
International Journal of Oral Science (IJOS), 2023
Hanyao Huang
Ou Zheng
Dongdong Wang
Jiayi Yin
Zijin Wang
...
H. Yin
Chuan Xu
Renjie Yang
Q. Zheng
B. Shi
MedIm
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375
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23 Mar 2023
A Systematic Study of Joint Representation Learning on Protein Sequences and Structures
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Chuanrui Wang
Minghao Xu
Vijil Chenthamarakshan
A. Lozano
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238
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11 Mar 2023
Retrieved Sequence Augmentation for Protein Representation Learning
bioRxiv (bioRxiv), 2023
Chang Ma
Haiteng Zhao
Lin Zheng
Jiayi Xin
Qintong Li
Lijun Wu
Zhihong Deng
Yang Lu
Qi Liu
Lingpeng Kong
AI4TS
221
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24 Feb 2023
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability
ACM Computing Surveys (ACM Comput. Surv.), 2023
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Davide Mottin
300
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16 Feb 2023
A Text-guided Protein Design Framework
Shengchao Liu
Yanjing Li
Zhuoxinran Li
A. Gitter
Yutao Zhu
...
Arvind Ramanathan
Chaowei Xiao
Jian Tang
Ziqiao Wang
Anima Anandkumar
605
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09 Feb 2023
Protein Representation Learning via Knowledge Enhanced Primary Structure Modeling
bioRxiv (bioRxiv), 2023
Hong-Yu Zhou
Yunxiang Fu
Zhicheng Zhang
Cheng Bian
Yizhou Yu
266
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30 Jan 2023
ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts
International Conference on Machine Learning (ICML), 2023
Minghao Xu
Xinyu Yuan
Santiago Miret
Jian Tang
AI4TS
423
144
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28 Jan 2023
Editing Language Model-based Knowledge Graph Embeddings
AAAI Conference on Artificial Intelligence (AAAI), 2023
Shuyang Cheng
Ningyu Zhang
Bo Tian
Feiyu Xiong
Wei Guo
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545
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25 Jan 2023
Ontology Pre-training for Poison Prediction
Deutsche Jahrestagung für Künstliche Intelligenz (KI), 2023
Martin Glauer
Fabian Neuhaus
Till Mossakowski
Janna Hastings
292
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20 Jan 2023
Protein Language Models and Structure Prediction: Connection and Progression
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Jun Xia
Jiangbin Zheng
Cheng Tan
Yufei Huang
Yongjie Xu
Stan Z. Li
256
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30 Nov 2022
Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design
bioRxiv (bioRxiv), 2022
Ran Bi
Lijun Wu
Jinhua Zhu
Tianbo Peng
Ziheng Lu
...
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Tao Qin
Haiguang Liu
Kun He
Tie-Yan Liu
382
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26 Oct 2022
Construction and Applications of Billion-Scale Pre-Trained Multimodal Business Knowledge Graph
IEEE International Conference on Data Engineering (ICDE), 2022
Shumin Deng
Chengming Wang
Zhoubo Li
Ningyu Zhang
Zelin Dai
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Mosha Chen
Jiaoyan Chen
Jeff Z. Pan
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VLM
396
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30 Sep 2022
CoSP: Co-supervised pretraining of pocket and ligand
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Cheng Tan
Lirong Wu
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352
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23 Jun 2022
Relphormer: Relational Graph Transformer for Knowledge Graph Representations
Neurocomputing (Neurocomputing), 2022
Zhen Bi
Shuyang Cheng
Jing Chen
Xiaozhuan Liang
Feiyu Xiong
Ningyu Zhang
613
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22 May 2022
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