Title
Improving Targeted Molecule Generation through Language Model Fine-Tuning Via Reinforcement Learning Salma J. Ahmed Emad A. Mohammed 91 2 0 10 May 2024
ACEGEN: Reinforcement learning of generative chemical agents for drug discovery Albert Bou Morgan Thomas Sebastian Dittert Carles Navarro Ramírez Maciej Majewski ... Mazen Ahmad Vincent Moens Woody Sherman Simone Sciabola Gianni De Fabritiis 169 14 0 07 May 2024
Data-Efficient Molecular Generation with Hierarchical Textual Inversion Seojin Kim Jaehyun Nam Sihyun Yu Younghoon Shin Jinwoo Shin 205 4 0 05 May 2024
Optimized Drug Design using Multi-Objective Evolutionary Algorithms with SELFIES Tomoya Hömberg Sanaz Mostaghim S. Hiwa Tomoyuki Hiroyasu 59 0 0 01 May 2024
A Comprehensive Survey on Evaluating Large Language Model Applications in the Medical Industry Yining Huang Keke Tang Meilian Chen Boyuan Wang ELM LM&MA 112 18 0 24 Apr 2024
ControlMol: Adding Substruture Control To Molecule Diffusion Models Zhengyang Qi Zijing Liu Jiying Zhang He Cao Yu-Feng Li 110 2 0 22 Apr 2024
GP-MoLFormer: A Foundation Model For Molecular Generation Jerret Ross Brian M. Belgodere Samuel C. Hoffman Vijil Chenthamarakshan Youssef Mroueh Payel Das Payel Das 155 11 0 04 Apr 2024
Representing Molecules as Random Walks Over Interpretable Grammars Michael Sun Minghao Guo Weize Yuan Veronika Thost C. Owens ... Hassan Mohiuddin Benjamin J Pedretti Zachary P Smith Jie Chen Wojciech Matusik 148 4 0 13 Mar 2024
CardioGenAI: A Machine Learning-Based Framework for Re-Engineering Drugs for Reduced hERG Liability Gregory W. Kyro Matthew T. Martin Eric D. Watt Victor S. Batista 133 5 0 12 Mar 2024
DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization Xiangxin Zhou Xiwei Cheng Yuwei Yang Yu Bao Liang Wang Quanquan Gu 122 21 0 07 Mar 2024
Graph Diffusion Policy Optimization Yijing Liu Chao Du Tianyu Pang Chongxuan Li Wei Chen Min Lin 124 12 0 26 Feb 2024
L+M-24: Building a Dataset for Language + Molecules @ ACL 2024 Carl Edwards Qingyun Wang Lawrence Zhao Heng Ji 164 24 0 22 Feb 2024
A novel molecule generative model of VAE combined with Transformer for unseen structure generation Yasuhiro Yoshikai T. Mizuno Shumpei Nemoto Hiroyuki Kusuhara 58 3 0 19 Feb 2024
A quantitative analysis of knowledge-learning preferences in large language models in molecular science Pengfei Liu Jun Tao Zhixiang Ren 56 6 0 06 Feb 2024
Pard: Permutation-Invariant Autoregressive Diffusion for Graph Generation Lingxiao Zhao Xueying Ding Leman Akoglu DiffM 148 12 0 06 Feb 2024
A Graph is Worth $K$ Words: Euclideanizing Graph using Pure Transformer Zhangyang Gao Daize Dong Cheng Tan Jun Xia Bozhen Hu Stan Z. Li 160 8 0 04 Feb 2024
Overcoming Order in Autoregressive Graph Generation Edo Cohen-Karlik Eyal Rozenberg Daniel Freedman 87 2 0 04 Feb 2024
FREED++: Improving RL Agents for Fragment-Based Molecule Generation by Thorough Reproduction Alexander Telepov Artem Tsypin Kuzma Khrabrov Sergey Yakukhnov Pavel Strashnov ... Egor Rumiantsev Daniel Ezhov Manvel Avetisian Olga Popova Artur Kadurin 108 5 0 18 Jan 2024
De novo Drug Design using Reinforcement Learning with Multiple GPT Agents Xiuyuan Hu Guoqing Liu Yang Zhao Hao Zhang 122 24 0 21 Dec 2023
FSscore: A Machine Learning-based Synthetic Feasibility Score Leveraging Human Expertise Rebecca M. Neeser Bruno Correia Philippe Schwaller 75 1 0 20 Dec 2023
Large Language Models on Graphs: A Comprehensive Survey Bowen Jin Gang Liu Chi Han Meng Jiang Heng Ji Jiawei Han AI4CE 182 199 0 05 Dec 2023
A Simple and Scalable Representation for Graph Generation Yunhui Jang Seul Lee SungSoo Ahn 113 8 0 04 Dec 2023
LLamol: A Dynamic Multi-Conditional Generative Transformer for De Novo Molecular Design Niklas Dobberstein Astrid Maass J. Hamaekers 104 9 0 24 Nov 2023
nach0: Multimodal Natural and Chemical Languages Foundation Model M. Livne Z. Miftahutdinov E. Tutubalina Maksim Kuznetsov Daniil Polykovskiy ... Aastha Jhunjhunwala Anthony Costa Alex Aliper Alán Aspuru-Guzik Alex Zhavoronkov AI4CE 163 21 0 21 Nov 2023
Sparse Training of Discrete Diffusion Models for Graph Generation Yiming Qin Clément Vignac Pascal Frossard 88 16 0 03 Nov 2023
Discriminator Guidance for Autoregressive Diffusion Models Filip Ekstrom Kelvinius Fredrik Lindsten DiffM 82 6 0 24 Oct 2023
UniMAP: Universal SMILES-Graph Representation Learning Shikun Feng Lixin Yang Wei-Ying Ma Yanyan Lan OffRL 98 7 0 22 Oct 2023
Generative Marginalization Models Sulin Liu Peter J. Ramadge Ryan P. Adams 102 1 0 19 Oct 2023
Preference Optimization for Molecular Language Models Ryan Park Ryan Theisen Navriti Sahni Marcel Patek Anna Cichoñska Rayees Rahman 27 8 0 18 Oct 2023
Gotta be SAFE: A New Framework for Molecular Design Emmanuel Noutahi Cristian Gabellini Michael Craig Jonathan S.C Lim Prudencio Tossou 136 28 0 16 Oct 2023
Genetic algorithms are strong baselines for molecule generation Austin Tripp José Miguel Hernández-Lobato 94 24 0 13 Oct 2023
Neural scaling laws for phenotypic drug discovery Drew Linsley John Griffin Jason Parker Brown Adam N Roose Michael Frank Peter Linsley Steven Finkbeiner Jeremy W. Linsley 118 0 0 28 Sep 2023
Navigating Healthcare Insights: A Birds Eye View of Explainability with Knowledge Graphs Satvik Garg Anh Nguyen Somya Garg 105 3 0 28 Sep 2023
Language models in molecular discovery Chaoqi Wang Yibo Jiang Chenghao Yang Han Liu Yuxin Chen 97 9 0 28 Sep 2023
Beam Enumeration: Probabilistic Explainability For Sample Efficient Self-conditioned Molecular Design Jeff Guo P. Schwaller 85 7 0 25 Sep 2023
Curiosity as a Self-Supervised Method to Improve Exploration in De novo Drug Design M. Chadi H. Mousannif Ahmed Aamouche BDL 101 2 0 24 Sep 2023
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation Gregory W. Kyro Anton Morgunov Rafael I. Brent Victor S. Batista 124 17 0 11 Sep 2023
From Artificially Real to Real: Leveraging Pseudo Data from Large Language Models for Low-Resource Molecule Discovery Yuhan Chen Nuwa Xi Yanrui Du Hao Wang Jianyu Chen Sendong Zhao Bing Qin 136 13 0 11 Sep 2023
Objective-Agnostic Enhancement of Molecule Properties via Multi-Stage VAE Chenghui Zhou Barnabás Póczós 116 2 0 24 Aug 2023
Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models Ziqi Chen Bo Peng Srinivas Parthasarathy Xia Ning DiffM 119 13 0 23 Aug 2023
DiffDTM: A conditional structure-free framework for bioactive molecules generation targeted for dual proteins Lei Huang Zheng Yuan Huihui Yan Rong Sheng Linjing Liu ... Nanjun Chen Fei Huang Songfang Huang Ka-Chun Wong Yaoyun Zhang 91 1 0 24 Jun 2023
A generative artificial intelligence framework based on a molecular diffusion model for the design of metal-organic frameworks for carbon capture Hyun Park Xiaoli Yan Ruijie Zhu Eliu A. Huerta Santanu Chaudhuri Donny Cooper Ian Foster E. Tajkhorshid AI4CE 123 31 0 14 Jun 2023
Molecule Design by Latent Space Energy-Based Modeling and Gradual Distribution Shifting Deqian Kong Bo Pang Tian Han Ying Nian Wu DiffM 110 7 0 09 Jun 2023
MAGNet: Motif-Agnostic Generation of Molecules from Shapes Leon Hetzel Johanna Sommer Bastian Rieck Fabian J. Theis Stephan Günnemann 139 6 0 30 May 2023
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation Han Huang Leilei Sun Bowen Du Weifeng Lv DiffM 180 19 0 21 May 2023
RGCVAE: Relational Graph Conditioned Variational Autoencoder for Molecule Design Davide Rigoni Nicoló Navarin A. Sperduti BDL 86 3 0 19 May 2023
Augmented Memory: Capitalizing on Experience Replay to Accelerate De Novo Molecular Design Jeff Guo P. Schwaller 100 10 0 10 May 2023
Efficient and Degree-Guided Graph Generation via Discrete Diffusion Modeling Xiaohui Chen Jiaxing He Xuhong Han Liping Liu DiffM 161 63 0 06 May 2023
GraphGANFed: A Federated Generative Framework for Graph-Structured Molecules Towards Efficient Drug Discovery Daniel Manu Jingjing Yao Wuji Liu Xiang Sun FedML 96 11 0 11 Apr 2023
The power of motifs as inductive bias for learning molecular distributions Johanna Sommer Leon Hetzel David Lüdke Fabian J. Theis Stephan Günnemann 90 6 0 04 Apr 2023