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2305.05708
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Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB files
9 May 2023
Daniel Flam-Shepherd
Alán Aspuru-Guzik
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Papers citing
"Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB files"
38 / 38 papers shown
Title
RLDBF: Enhancing LLMs Via Reinforcement Learning With DataBase FeedBack
Weichen Dai
Zijie Dai
Zhijie Huang
Yixuan Pan
Xinhe Li
Xi Li
Yi Zhou
Ji Qi
Wu Jiang
24
0
0
28 Mar 2025
TransDiffSBDD: Causality-Aware Multi-Modal Structure-Based Drug Design
Xiuyuan Hu
Guoqing Liu
Can Chen
Yang Zhao
Hao Zhang
Xue Liu
50
2
0
26 Mar 2025
Invariant Tokenization of Crystalline Materials for Language Model Enabled Generation
Keqiang Yan
Xiner Li
Hongyi Ling
Kenna Ashen
Carl N. Edwards
...
Marinka Zitnik
Heng Ji
Xiaofeng Qian
X. Qian
Shuiwang Ji
33
2
0
28 Feb 2025
SymmCD: Symmetry-Preserving Crystal Generation with Diffusion Models
Daniel Levy
Siba Smarak Panigrahi
Sékou-Oumar Kaba
Qiang Zhu
Kin Long Kelvin Lee
Mikhail Galkin
Santiago Miret
Siamak Ravanbakhsh
192
11
0
05 Feb 2025
Establishing baselines for generative discovery of inorganic crystals
N. Szymanski
Christopher J. Bartel
40
1
0
04 Jan 2025
LLM4Mat-Bench: Benchmarking Large Language Models for Materials Property Prediction
Andre Niyongabo Rubungo
Kangming Li
Jason Hattrick-Simpers
Adji Bousso Dieng
23
4
0
31 Oct 2024
FlowLLM: Flow Matching for Material Generation with Large Language Models as Base Distributions
Anuroop Sriram
Benjamin Kurt Miller
Ricky T. Q. Chen
Brandon M. Wood
AI4CE
37
13
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
Bio2Token: All-atom tokenization of any biomolecular structure with Mamba
Andrew Liu
Axel Elaldi
Nathan Russell
Olivia Viessmann
Mamba
61
2
0
24 Oct 2024
nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder
Maksim Kuznetsov
Airat Valiev
Alex Aliper
Daniil Polykovskiy
E. Tutubalina
Rim Shayakhmetov
Z. Miftahutdinov
20
0
0
11 Oct 2024
Generative Hierarchical Materials Search
Sherry Yang
Simon L. Batzner
Ruiqi Gao
Muratahan Aykol
Alexander L. Gaunt
Brendan McMorrow
Danilo J. Rezende
Dale Schuurmans
Igor Mordatch
E. D. Cubuk
AI4CE
40
5
0
10 Sep 2024
Geometry Informed Tokenization of Molecules for Language Model Generation
Xiner Li
Limei Wang
Youzhi Luo
Carl N. Edwards
Shurui Gui
Yuchao Lin
Heng Ji
Shuiwang Ji
29
6
0
19 Aug 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
Efficient Evolutionary Search Over Chemical Space with Large Language Models
Haorui Wang
Marta Skreta
C. Ser
Wenhao Gao
Lingkai Kong
...
Yanqiao Zhu
Yuanqi Du
Alán Aspuru-Guzik
Kirill Neklyudov
Chao Zhang
37
12
0
23 Jun 2024
LLMatDesign: Autonomous Materials Discovery with Large Language Models
Shuyi Jia
Chao Zhang
Victor Fung
46
9
0
19 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
42
27
0
16 Jun 2024
FlowMM: Generating Materials with Riemannian Flow Matching
Benjamin Kurt Miller
Ricky T. Q. Chen
Anuroop Sriram
Brandon M. Wood
29
32
0
07 Jun 2024
BindGPT: A Scalable Framework for 3D Molecular Design via Language Modeling and Reinforcement Learning
Artem Zholus
Maksim Kuznetsov
Roman Schutski
Rim Shayakhmetov
Daniil Polykovskiy
Sarath Chandar
Alex Zhavoronkov
DiffM
AI4CE
35
4
0
06 Jun 2024
Structure-based drug design by denoising voxel grids
Pedro H. O. Pinheiro
Arian R. Jamasb
Omar Mahmood
Vishnu Sresht
Saeed Saremi
DiffM
34
8
0
07 May 2024
Are large language models superhuman chemists?
Adrian Mirza
Nawaf Alampara
Sreekanth Kunchapu
Benedict Emoekabu
Aswanth Krishnan
...
Leanne M. Stafast
Dinga Wonanke
Michael Pieler
P. Schwaller
K. Jablonka
ELM
AI4MH
LRM
LM&MA
29
4
0
01 Apr 2024
Space Group Informed Transformer for Crystalline Materials Generation
Zhendong Cao
Xiaoshan Luo
Jianwei Lv
Lei Wang
AI4CE
31
16
0
23 Mar 2024
Are LLMs Ready for Real-World Materials Discovery?
Santiago Miret
N. M. A. Krishnan
40
27
0
07 Feb 2024
Fine-Tuned Language Models Generate Stable Inorganic Materials as Text
Nate Gruver
Anuroop Sriram
Andrea Madotto
A. Wilson
C. L. Zitnick
Zachary W. Ulissi
27
55
0
06 Feb 2024
Swallowing the Bitter Pill: Simplified Scalable Conformer Generation
Yuyang Wang
Ahmed A. A. Elhag
Navdeep Jaitly
J. Susskind
Miguel Angel Bautista
DiffM
27
20
0
27 Nov 2023
Scalable Diffusion for Materials Generation
Mengjiao Yang
KwangHwan Cho
Amil Merchant
Pieter Abbeel
Dale Schuurmans
Igor Mordatch
E. D. Cubuk
27
38
0
18 Oct 2023
Transformers and Large Language Models for Chemistry and Drug Discovery
Andres M Bran
Philippe Schwaller
LM&MA
MedIm
AI4CE
30
14
0
09 Oct 2023
Atom-by-atom protein generation and beyond with language models
Daniel Flam-Shepherd
Kevin Zhu
Alán Aspuru-Guzik
28
2
0
16 Aug 2023
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
31
19
0
15 Jun 2023
3D molecule generation by denoising voxel grids
Pedro H. O. Pinheiro
Joshua Rackers
J. Kleinhenz
Michael R. Maser
Omar Mahmood
Andrew Watkins
Stephen Ra
Vishnu Sresht
Saeed Saremi
DiffM
34
20
0
13 Jun 2023
14 Examples of How LLMs Can Transform Materials Science and Chemistry: A Reflection on a Large Language Model Hackathon
K. Jablonka
Qianxiang Ai
Alexander H Al-Feghali
S. Badhwar
Joshua D. Bocarsly Andres M Bran
...
Aristana Scourtas
K. J. Schmidt
Ian T. Foster
Andrew D. White
B. Blaiszik
38
100
0
09 Jun 2023
From Words to Wires: Generating Functioning Electronic Devices from Natural Language Descriptions
Peter Alexander Jansen
22
2
0
24 May 2023
Computational modeling of semantic change
Nina Tahmasebi
Haim Dubossarsky
26
6
0
13 Apr 2023
Emergent autonomous scientific research capabilities of large language models
Daniil A. Boiko
R. MacKnight
Gabe Gomes
ELM
LM&Ro
AI4CE
LLMAG
104
117
0
11 Apr 2023
A 3D Generative Model for Structure-Based Drug Design
Shitong Luo
Jiaqi Guan
Jianzhu Ma
Jian-wei Peng
DiffM
65
178
0
20 Mar 2022
Keeping it Simple: Language Models can learn Complex Molecular Distributions
Daniel Flam-Shepherd
Kevin Zhu
A. Aspuru‐Guzik
129
142
0
06 Dec 2021
The Open Catalyst 2020 (OC20) Dataset and Community Challenges
L. Chanussot
Abhishek Das
Siddharth Goyal
Thibaut Lavril
Muhammed Shuaibi
...
Brandon M. Wood
Junwoong Yoon
Devi Parikh
C. L. Zitnick
Zachary W. Ulissi
223
503
0
20 Oct 2020
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation
Jiaxuan You
Bowen Liu
Rex Ying
Vijay S. Pande
J. Leskovec
GNN
200
885
0
07 Jun 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation
Wengong Jin
Regina Barzilay
Tommi Jaakkola
224
1,337
0
12 Feb 2018
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