Title
A novel molecule generative model of VAE combined with Transformer for unseen structure generation Yasuhiro Yoshikai T. Mizuno Shumpei Nemoto Hiroyuki Kusuhara 25 2 0 19 Feb 2024
Pard: Permutation-Invariant Autoregressive Diffusion for Graph Generation Lingxiao Zhao Xueying Ding L. Akoglu DiffM 21 8 0 06 Feb 2024
A Graph is Worth $K$ Words: Euclideanizing Graph using Pure Transformer Zhangyang Gao Daize Dong Cheng Tan Jun-Xiong Xia Bozhen Hu Stan Z. Li 46 6 0 04 Feb 2024
Overcoming Order in Autoregressive Graph Generation Edo Cohen-Karlik Eyal Rozenberg Daniel Freedman 34 1 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 27 4 0 18 Jan 2024
De novo Drug Design using Reinforcement Learning with Multiple GPT Agents Xiuyuan Hu Guoqing Liu Yang Zhao Hao Zhang 15 19 0 21 Dec 2023
FSscore: A Machine Learning-based Synthetic Feasibility Score Leveraging Human Expertise Rebecca M. Neeser Bruno Correia Philippe Schwaller 19 1 0 20 Dec 2023
Large Language Models on Graphs: A Comprehensive Survey Bowen Jin Gang Liu Chi Han Meng-Long Jiang Heng Ji Jiawei Han AI4CE 28 136 0 05 Dec 2023
A Simple and Scalable Representation for Graph Generation Yunhui Jang Seul Lee Sungsoo Ahn 21 4 0 04 Dec 2023
LLamol: A Dynamic Multi-Conditional Generative Transformer for De Novo Molecular Design Niklas Dobberstein Astrid Maass J. Hamaekers 25 5 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 19 12 0 21 Nov 2023
Sparse Training of Discrete Diffusion Models for Graph Generation Yiming Qin Clément Vignac Pascal Frossard 21 12 0 03 Nov 2023
Discriminator Guidance for Autoregressive Diffusion Models Filip Ekstrom Kelvinius Fredrik Lindsten DiffM 17 5 0 24 Oct 2023
UniMAP: Universal SMILES-Graph Representation Learning Shikun Feng Lixin Yang Wei-Ying Ma Yanyan Lan OffRL 11 6 0 22 Oct 2023
Generative Marginalization Models Sulin Liu Peter J. Ramadge Ryan P. Adams 27 1 0 19 Oct 2023
Preference Optimization for Molecular Language Models Ryan Park Ryan Theisen Navriti Sahni Marcel Patek Anna Cichoñska Rayees Rahman 14 6 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 18 15 0 16 Oct 2023
Genetic algorithms are strong baselines for molecule generation Austin Tripp José Miguel Hernández-Lobato 32 16 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 28 0 0 28 Sep 2023
Navigating Healthcare Insights: A Birds Eye View of Explainability with Knowledge Graphs Satvik Garg Anh Nguyen Somya Garg 29 2 0 28 Sep 2023
Language models in molecular discovery Chaoqi Wang Yibo Jiang Chenghao Yang Han Liu Yuxin Chen 18 7 0 28 Sep 2023
Beam Enumeration: Probabilistic Explainability For Sample Efficient Self-conditioned Molecular Design Jeff Guo P. Schwaller 26 6 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 44 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 30 12 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 27 10 0 11 Sep 2023
Objective-Agnostic Enhancement of Molecule Properties via Multi-Stage VAE Chenghui Zhou Barnabás Póczós 25 0 0 24 Aug 2023
Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models Ziqi Chen B. Peng Srinivas Parthasarathy Xia Ning DiffM 29 5 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 16 0 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 T. Foster E. Tajkhorshid AI4CE 30 19 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 35 7 0 09 Jun 2023
MAGNet: Motif-Agnostic Generation of Molecules from Shapes Leon Hetzel Johanna Sommer Bastian Alexander Rieck Fabian J. Theis Stephan Günnemann 18 6 0 30 May 2023
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation Han Huang Leilei Sun Bowen Du Weifeng Lv DiffM 24 16 0 21 May 2023
RGCVAE: Relational Graph Conditioned Variational Autoencoder for Molecule Design Davide Rigoni Nicoló Navarin A. Sperduti BDL 20 1 0 19 May 2023
Augmented Memory: Capitalizing on Experience Replay to Accelerate De Novo Molecular Design Jeff Guo P. Schwaller 29 10 0 10 May 2023
Efficient and Degree-Guided Graph Generation via Discrete Diffusion Modeling Xiaohui Chen Jiaxing He Xuhong Han Liping Liu DiffM 30 46 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 30 6 0 11 Apr 2023
The power of motifs as inductive bias for learning molecular distributions Johanna Sommer Leon Hetzel David Ludke Fabian J. Theis Stephan Günnemann 25 5 0 04 Apr 2023
Cloud Services Enable Efficient AI-Guided Simulation Workflows across Heterogeneous Resources Logan T. Ward J. G. Pauloski Valérie Hayot-Sasson Ryan Chard Y. Babuji Ganesh Sivaraman Sutanay Choudhury Kyle Chard R. Thakur Ian T. Foster 32 9 0 15 Mar 2023
Automated patent extraction powers generative modeling in focused chemical spaces Akshay Subramanian Kevin P. Greenman Alexis Gervaix Tzuhsiung Yang Rafael Gómez-Bombarelli 33 6 0 14 Mar 2023
Bridging the Gap between Chemical Reaction Pretraining and Conditional Molecule Generation with a Unified Model Bo Qiang Yiran Zhou Yuheng Ding Ningfeng Liu Song Song L. Zhang Bowei Huang Zhenming Liu AI4CE 21 9 0 13 Mar 2023
Domain-Agnostic Molecular Generation with Chemical Feedback Yin Fang Ningyu Zhang Zhuo Chen Lingbing Guo Xiaohui Fan Huajun Chen 33 11 0 26 Jan 2023
Domain-agnostic and Multi-level Evaluation of Generative Models G. Tadesse Jannis Born C. Cintas William Ogallo Dmitry Zubarev Matteo Manica Komminist Weldemariam ELM 27 1 0 20 Jan 2023
Improving Molecule Properties Through 2-Stage VAE Chenghui Zhou Barnabás Póczós DRL 18 1 0 06 Dec 2022
Group SELFIES: A Robust Fragment-Based Molecular String Representation Austin H. Cheng Andy Cai Santiago Miret Gustavo Malkomes Mariano Phielipp Alán Aspuru-Guzik 21 27 0 23 Nov 2022
DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding Haitao Lin Yufei Huang Odin Zhang Siqi Ma Meng Liu X. Li Lirong Wu Shuiwang Ji Tingjun Hou Stan Z. Li DiffM 18 60 0 21 Nov 2022
ParticleGrid: Enabling Deep Learning using 3D Representation of Materials Shehtab Zaman E. Ferguson Cécile Pereira D. Akhiyarov Mauricio Araya-Polo Kenneth Chiu DiffM AI4CE 21 2 0 15 Nov 2022
Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES E. Bjerrum Christian Margreitter Thomas Blaschke Raquel Lopez-Rios de Castro 32 11 0 22 Oct 2022
An efficient graph generative model for navigating ultra-large combinatorial synthesis libraries Aryan Pedawi P. Gniewek Chao-Ling Chang Brandon M. Anderson H. V. D. Bedem 19 5 0 19 Oct 2022
A Transformer-based Generative Model for De Novo Molecular Design Wenlu Wang Ye Wang Honggang Zhao Simone Sciabola 8 0 0 17 Oct 2022
Modular Flows: Differential Molecular Generation Yogesh Verma Samuel Kaski Markus Heinonen Vikas K. Garg 29 14 0 12 Oct 2022