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A Text-guided Protein Design Framework

A Text-guided Protein Design Framework

9 February 2023
Shengchao Liu
Yanjing Li
Zhuoxinran Li
A. Gitter
Yutao Zhu
Jiarui Lu
Zhao Xu
Weili Nie
Arvind Ramanathan
Chaowei Xiao
Jian Tang
Hongyu Guo
Anima Anandkumar
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Papers citing "A Text-guided Protein Design Framework"

50 / 50 papers shown
Title
Multimodal Large Language Models for Medicine: A Comprehensive Survey
Multimodal Large Language Models for Medicine: A Comprehensive Survey
Jiarui Ye
Hao Tang
LM&MA
74
0
0
29 Apr 2025
Protein Large Language Models: A Comprehensive Survey
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
45
3
0
21 Feb 2025
From large language models to multimodal AI: A scoping review on the potential of generative AI in medicine
From large language models to multimodal AI: A scoping review on the potential of generative AI in medicine
Lukas Buess
Matthias Keicher
Nassir Navab
Andreas K. Maier
Soroosh Tayebi Arasteh
LM&MA
108
0
0
13 Feb 2025
A Comprehensive Survey of Foundation Models in Medicine
A Comprehensive Survey of Foundation Models in Medicine
Wasif Khan
Seowung Leem
Kyle B. See
Joshua K. Wong
Shaoting Zhang
R. Fang
AI4CE
LM&MA
VLM
93
16
0
17 Jan 2025
Effective Fine-Tuning of Vision-Language Models for Accurate Galaxy
  Morphology Analysis
Effective Fine-Tuning of Vision-Language Models for Accurate Galaxy Morphology Analysis
Ruoqi Wang
Haitao Wang
Qiong Luo
59
0
0
29 Nov 2024
Chemical Language Model Linker: blending text and molecules with modular adapters
Chemical Language Model Linker: blending text and molecules with modular adapters
Yifan Deng
Spencer S. Ericksen
Anthony Gitter
19
0
0
26 Oct 2024
InstructBioMol: Advancing Biomolecule Understanding and Design Following
  Human Instructions
InstructBioMol: Advancing Biomolecule Understanding and Design Following Human Instructions
Xiang Zhuang
Keyan Ding
Tianwen Lyu
Yinuo Jiang
Xiaotong Li
...
Ming Qin
Kehua Feng
Jike Wang
Qiang Zhang
Huajun Chen
26
1
0
10 Oct 2024
Structure-Enhanced Protein Instruction Tuning: Towards General-Purpose
  Protein Understanding
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
23
0
0
04 Oct 2024
Harnessing LLMs for API Interactions: A Framework for Classification and
  Synthetic Data Generation
Harnessing LLMs for API Interactions: A Framework for Classification and Synthetic Data Generation
Chunliang Tao
Xiaojing Fan
Yahe Yang
18
19
0
18 Sep 2024
Large Language Models in Drug Discovery and Development: From Disease
  Mechanisms to Clinical Trials
Large Language Models in Drug Discovery and Development: From Disease Mechanisms to Clinical Trials
Yizhen Zheng
Huan Yee Koh
M. Yang
Li Li
Lauren T. May
Geoffrey I. Webb
Shirui Pan
George Church
LM&MA
37
9
0
06 Sep 2024
Emergence of Hidden Capabilities: Exploring Learning Dynamics in Concept
  Space
Emergence of Hidden Capabilities: Exploring Learning Dynamics in Concept Space
Core Francisco Park
Maya Okawa
Andrew Lee
Ekdeep Singh Lubana
Hidenori Tanaka
42
6
0
27 Jun 2024
Geometric Self-Supervised Pretraining on 3D Protein Structures using
  Subgraphs
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
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
33
17
0
16 Jun 2024
Improving Paratope and Epitope Prediction by Multi-Modal Contrastive
  Learning and Interaction Informativeness Estimation
Improving Paratope and Epitope Prediction by Multi-Modal Contrastive Learning and Interaction Informativeness Estimation
Zhiwei Wang
Yongkang Wang
Wen Zhang
24
2
0
31 May 2024
SysCaps: Language Interfaces for Simulation Surrogates of Complex Systems
SysCaps: Language Interfaces for Simulation Surrogates of Complex Systems
Patrick Emami
Zhaonan Li
Saumya Sinha
Truc Nguyen
48
1
0
30 May 2024
ProtT3: Protein-to-Text Generation for Text-based Protein Understanding
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
44
14
0
21 May 2024
Functional Protein Design with Local Domain Alignment
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
21
2
0
18 Apr 2024
Foundation Model for Advancing Healthcare: Challenges, Opportunities,
  and Future Directions
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
71
26
0
04 Apr 2024
PAPERCLIP: Associating Astronomical Observations and Natural Language
  with Multi-Modal Models
PAPERCLIP: Associating Astronomical Observations and Natural Language with Multi-Modal Models
S. Mishra-Sharma
Yiding Song
Jesse Thaler
21
7
0
13 Mar 2024
Bridging Text and Molecule: A Survey on Multimodal Frameworks for
  Molecule
Bridging Text and Molecule: A Survey on Multimodal Frameworks for Molecule
Yi Xiao
Xiangxin Zhou
Qiang Liu
Liang Wang
AI4CE
27
3
0
07 Mar 2024
Leveraging Biomolecule and Natural Language through Multi-Modal
  Learning: A Survey
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
39
19
0
03 Mar 2024
BioT5+: Towards Generalized Biological Understanding with IUPAC
  Integration and Multi-task Tuning
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning
Qizhi Pei
Lijun Wu
Kaiyuan Gao
Xiaozhuan Liang
Yin Fang
Jinhua Zhu
Shufang Xie
Tao Qin
Rui Yan
AI4CE
39
19
0
27 Feb 2024
Generative AI for Controllable Protein Sequence Design: A Survey
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
25
6
0
16 Feb 2024
ChemReasoner: Heuristic Search over a Large Language Model's Knowledge
  Space using Quantum-Chemical Feedback
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
18
7
0
15 Feb 2024
Data-Centric Foundation Models in Computational Healthcare: A Survey
Data-Centric Foundation Models in Computational Healthcare: A Survey
Yunkun Zhang
Jin Gao
Zheling Tan
Lingfeng Zhou
Kexin Ding
Mu Zhou
Shaoting Zhang
Dequan Wang
AI4CE
13
20
0
04 Jan 2024
A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide
  Generation
A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation
Yongkang Wang
Xuan Liu
Feng Huang
Zhankun Xiong
Wen Zhang
42
13
0
25 Dec 2023
Form follows Function: Text-to-Text Conditional Graph Generation based
  on Functional Requirements
Form follows Function: Text-to-Text Conditional Graph Generation based on Functional Requirements
Peter Zachares
Vahan Hovhannisyan
Alan Mosca
Yarin Gal
16
1
0
01 Nov 2023
Defining a New NLP Playground
Defining a New NLP Playground
Sha Li
Chi Han
Pengfei Yu
Carl N. Edwards
Manling Li
...
Yi Ren Fung
Charles Yu
Joel R. Tetreault
Eduard H. Hovy
Heng Ji
23
5
0
31 Oct 2023
Monte Carlo Thought Search: Large Language Model Querying for Complex
  Scientific Reasoning in Catalyst Design
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
20
10
0
22 Oct 2023
Generative artificial intelligence for de novo protein design
Generative artificial intelligence for de novo protein design
Adam Winnifrith
C. Outeiral
Brian L. Hie
AI4CE
11
13
0
15 Oct 2023
BioT5: Enriching Cross-modal Integration in Biology with Chemical
  Knowledge and Natural Language Associations
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
20
60
0
11 Oct 2023
BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphs
BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphs
Zifeng Wang
Zichen Wang
Balasubramaniam Srinivasan
V. Ioannidis
Huzefa Rangwala
Rishita Anubhai
AI4CE
24
15
0
05 Oct 2023
Prot2Text: Multimodal Protein's Function Generation with GNNs and
  Transformers
Prot2Text: Multimodal Protein's Function Generation with GNNs and Transformers
Hadi Abdine
Michail Chatzianastasis
Costas Bouyioukos
Michalis Vazirgiannis
13
38
0
25 Jul 2023
Symmetry-Informed Geometric Representation for Molecules, Proteins, and
  Crystalline Materials
Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials
Shengchao Liu
Weitao Du
Yanjing Li
Zhuoxinran Li
Zhiling Zheng
...
Anima Anandkumar
C. Borgs
J. Chayes
Hongyu Guo
Jian Tang
AI4CE
21
17
0
15 Jun 2023
Protein Design with Guided Discrete Diffusion
Protein Design with Guided Discrete Diffusion
Nate Gruver
Samuel Stanton
Nathan C. Frey
Tim G. J. Rudner
I. Hotzel
J. Lafrance-Vanasse
A. Rajpal
Kyunghyun Cho
A. Wilson
DiffM
16
100
0
31 May 2023
ChatGPT-powered Conversational Drug Editing Using Retrieval and Domain
  Feedback
ChatGPT-powered Conversational Drug Editing Using Retrieval and Domain Feedback
Shengchao Liu
Jiong Wang
Yijin Yang
Chengpeng Wang
Ling Liu
Hongyu Guo
Chaowei Xiao
LM&MA
KELM
AI4MH
18
36
0
29 May 2023
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining
Shengchao Liu
Weitao Du
Zhiming Ma
Hongyu Guo
Jian Tang
16
29
0
28 May 2023
Computational modeling of semantic change
Computational modeling of semantic change
Nina Tahmasebi
Haim Dubossarsky
23
6
0
13 Apr 2023
Muse: Text-To-Image Generation via Masked Generative Transformers
Muse: Text-To-Image Generation via Masked Generative Transformers
Huiwen Chang
Han Zhang
Jarred Barber
AJ Maschinot
José Lezama
...
Kevin Patrick Murphy
William T. Freeman
Michael Rubinstein
Yuanzhen Li
Dilip Krishnan
DiffM
197
515
0
02 Jan 2023
Designing Biological Sequences via Meta-Reinforcement Learning and
  Bayesian Optimization
Designing Biological Sequences via Meta-Reinforcement Learning and Bayesian Optimization
Leo Feng
Padideh Nouri
Aneri Muni
Yoshua Bengio
Pierre-Luc Bacon
103
4
0
13 Sep 2022
A Molecular Multimodal Foundation Model Associating Molecule Graphs with
  Natural Language
A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language
Bing-Huang Su
Dazhao Du
Zhao-Qing Yang
Yujie Zhou
Jiangmeng Li
Anyi Rao
Haoran Sun
Zhiwu Lu
Ji-Rong Wen
38
84
0
12 Sep 2022
Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance
  Matching
Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching
Shengchao Liu
Hongyu Guo
Jian Tang
13
77
0
27 Jun 2022
Diffusion-LM Improves Controllable Text Generation
Diffusion-LM Improves Controllable Text Generation
Xiang Lisa Li
John Thickstun
Ishaan Gulrajani
Percy Liang
Tatsunori B. Hashimoto
AI4CE
163
537
0
27 May 2022
Tranception: protein fitness prediction with autoregressive transformers
  and inference-time retrieval
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
45
172
0
27 May 2022
Protein Structure and Sequence Generation with Equivariant Denoising
  Diffusion Probabilistic Models
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models
N. Anand
Tudor Achim
DiffM
175
170
0
26 May 2022
OntoProtein: Protein Pretraining With Gene Ontology Embedding
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
85
86
0
23 Jan 2022
Pre-training Molecular Graph Representation with 3D Geometry
Pre-training Molecular Graph Representation with 3D Geometry
Shengchao Liu
Hanchen Wang
Weiyang Liu
Joan Lasenby
Hongyu Guo
Jian Tang
106
294
0
07 Oct 2021
Zero-Shot Text-to-Image Generation
Zero-Shot Text-to-Image Generation
Aditya A. Ramesh
Mikhail Pavlov
Gabriel Goh
Scott Gray
Chelsea Voss
Alec Radford
Mark Chen
Ilya Sutskever
VLM
253
3,790
0
24 Feb 2021
Argmax Flows and Multinomial Diffusion: Learning Categorical
  Distributions
Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions
Emiel Hoogeboom
Didrik Nielsen
P. Jaini
Patrick Forré
Max Welling
DiffM
191
392
0
10 Feb 2021
A Style-Based Generator Architecture for Generative Adversarial Networks
A Style-Based Generator Architecture for Generative Adversarial Networks
Tero Karras
S. Laine
Timo Aila
262
10,183
0
12 Dec 2018
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