Title
Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks Xinyu Wang Jinbo Bi Minghu Song CLL 62 0 0 01 May 2025
Heterophily-informed Message Passing Haishan Wang Arno Solin Vikas K. Garg 27 0 0 28 Apr 2025
MetaMolGen: A Neural Graph Motif Generation Model for De Novo Molecular Design Zimo Yan Jie Zhang Zheng Xie Chang-rui Liu Y. Liu Yiping Song 36 0 0 22 Apr 2025
DMol: A Schedule-Driven Diffusion Model for Highly Efficient and Versatile Molecule Generation Peizhi Niu Yu-Hsiang Wang Vishal Rana Chetan Rupakheti Abhishek Pandey O. Milenkovic 30 0 0 08 Apr 2025
Improving Equivariant Networks with Probabilistic Symmetry Breaking Hannah Lawrence Vasco Portilheiro Yan Zhang Sékou-Oumar Kaba 42 3 0 27 Mar 2025
Towards Unified Latent Space for 3D Molecular Latent Diffusion Modeling Yanchen Luo Zhiyuan Liu Yi Zhao Sihang Li Kenji Kawaguchi Tat-Seng Chua X. Wang MedIm 61 0 0 19 Mar 2025
Backdoor Attacks on Discrete Graph Diffusion Models Jiawen Wang Samin Karim Yuan Hong Binghui Wang DiffM 65 0 0 08 Mar 2025
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation Mohit Pandey G. Subbaraj Artem Cherkasov Martin Ester Emmanuel Bengio AI4CE 74 1 0 08 Mar 2025
A Survey of Graph Transformers: Architectures, Theories and Applications Chaohao Yuan Kangfei Zhao Ercan Engin Kuruoglu Liang Wang Tingyang Xu Wenbing Huang Deli Zhao Hong Cheng Yu Rong 55 4 0 23 Feb 2025
FragFM: Efficient Fragment-Based Molecular Generation via Discrete Flow Matching Joongwon Lee Seonghwan Kim Wou Youn Kim 43 0 0 19 Feb 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Sihang Li Junfeng Fang Yaorui Shi X. Wang Kenji Kawaguchi Tat-Seng Chua 100 3 0 18 Feb 2025
Generating 3D Binding Molecules Using Shape-Conditioned Diffusion Models with Guidance Ziqi Chen B. Peng Tianhua Zhai Daniel Adu-Ampratwum Xia Ning 58 1 0 09 Feb 2025
Mol-MoE: Training Preference-Guided Routers for Molecule Generation Diego Calanzone P. DÓro Pierre-Luc Bacon 50 0 0 08 Feb 2025
Learning to generate feasible graphs using graph grammars Stefan Mautner Rolf Backofen Fabrizio Costa 41 0 0 10 Jan 2025
Unified Guidance for Geometry-Conditioned Molecular Generation Sirine Ayadi Leon Hetzel Johanna Sommer Fabian J. Theis Stephan Günnemann 30 0 0 05 Jan 2025
Graph Generative Pre-trained Transformer Xiaohui Chen Yinkai Wang Jiaxing He Yuanqi Du S. Hassoun Xiaolin Xu Li Liu 41 1 0 03 Jan 2025
The Jungle of Generative Drug Discovery: Traps, Treasures, and Ways Out Rıza Özçelik F. Grisoni 46 0 0 24 Dec 2024
Bayesian Flow Is All You Need to Sample Out-of-Distribution Chemical Spaces Nianze Tao OOD OODD BDL 97 0 0 16 Dec 2024
Rectified Flow For Structure Based Drug Design Daiheng Zhang Chengyue Gong Qiang Liu DiffM 75 0 0 02 Dec 2024
NPGPT: Natural Product-Like Compound Generation with GPT-based Chemical Language Models Koh Sakano Kairi Furui Masahito Ohue 62 0 0 19 Nov 2024
GraphXForm: Graph transformer for computer-aided molecular design Jonathan Pirnay Jan G. Rittig Alexander B. Wolf Martin Grohe Jakob Burger Alexander Mitsos D. G. Grimm AI4CE 51 1 0 03 Nov 2024
SAFE setup for generative molecular design Yassir El Mesbahi Emmanuel Noutahi 26 0 0 26 Oct 2024
Chemical Language Model Linker: blending text and molecules with modular adapters Yifan Deng Spencer S. Ericksen Anthony Gitter 23 1 0 26 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
Can LLMs Generate Diverse Molecules? Towards Alignment with Structural Diversity Hyosoon Jang Yunhui Jang Jaehyung Kim Sungsoo Ahn 23 2 0 04 Oct 2024
SynthFormer: Equivariant Pharmacophore-based Generation of Synthesizable Molecules for Ligand-Based Drug Design Zygimantas Jocys Henriette M. G. Willems Katayoun Farrahi Katayoun Farrahi 13 0 0 03 Oct 2024
Conformal Generative Modeling with Improved Sample Efficiency through Sequential Greedy Filtering K. K. Bernhard Schölkopf Michael Muehlebach 26 0 0 02 Oct 2024
A Bayesian Flow Network Framework for Chemistry Tasks Nianze Tao Minori Abe BDL 27 2 0 28 Jul 2024
A Large Encoder-Decoder Family of Foundation Models For Chemical Language Eduardo Soares Victor Shirasuna E. V. Brazil Renato F. G. Cerqueira Dmitry Zubarev Kristin Schmidt AI4CE 27 7 0 24 Jul 2024
Diff4VS: HIV-inhibiting Molecules Generation with Classifier Guidance Diffusion for Virtual Screening Jiaqing Lyu Changjie Chen Bing Liang Yijia Zhang 26 0 0 20 Jul 2024
Any-Property-Conditional Molecule Generation with Self-Criticism using Spanning Trees Alexia Jolicoeur-Martineau A. Baratin Kisoo Kwon Boris Knyazev Yan Zhang 36 1 0 12 Jul 2024
Generative Modelling of Structurally Constrained Graphs Manuel Madeira Clément Vignac D. Thanou Pascal Frossard DiffM 48 0 0 25 Jun 2024
Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Space Mohamed Amine Ketata Nicholas Gao Johanna Sommer Tom Wollschlager Stephan Günnemann DiffM 36 1 0 15 Jun 2024
Cometh: A continuous-time discrete-state graph diffusion model Antoine Siraudin Fragkiskos D. Malliaros Christopher Morris 31 3 0 10 Jun 2024
$Diffusion Models in $\textit{De Novo}$ Drug Design$ Diffusion Models in $\textit{De Novo}$ Drug Design Amira Alakhdar Barnabás Póczos Newell Washburn MedIm 36 13 0 07 Jun 2024
Structure-based Drug Design Benchmark: Do 3D Methods Really Dominate? Kangyu Zheng Yingzhou Lu Zaixi Zhang Zhongwei Wan Yao Ma Marinka Zitnik Tianfan Fu ELM 32 6 0 04 Jun 2024
Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation Jeff Guo Philippe Schwaller Mamba 49 7 0 27 May 2024
Discrete-state Continuous-time Diffusion for Graph Generation Zhe Xu Ruizhong Qiu Yuzhong Chen Huiyuan Chen Xiran Fan Menghai Pan Zhichen Zeng Mahashweta Das Hanghang Tong 32 8 0 19 May 2024
Improving Targeted Molecule Generation through Language Model Fine-Tuning Via Reinforcement Learning Salma J. Ahmed Mustafa A. Alattar 52 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 40 4 0 07 May 2024
Data-Efficient Molecular Generation with Hierarchical Textual Inversion Seojin Kim Jaehyun Nam Sihyun Yu Younghoon Shin Jinwoo Shin 33 2 0 05 May 2024
Optimized Drug Design using Multi-Objective Evolutionary Algorithms with SELFIES Tomoya Hömberg Sanaz Mostaghim S. Hiwa Tomoyuki Hiroyasu 18 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 19 14 0 24 Apr 2024
ControlMol: Adding Substruture Control To Molecule Diffusion Models Zhengyang Qi Zijing Liu Jiying Zhang He Cao Yu Li 40 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 36 5 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 35 2 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 33 2 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 29 15 0 07 Mar 2024
Graph Diffusion Policy Optimization Yijing Liu Chao Du Tianyu Pang Chongxuan Li Wei Chen Min-Bin Lin 29 7 0 26 Feb 2024
L+M-24: Building a Dataset for Language + Molecules @ ACL 2024 Carl N. Edwards Qingyun Wang Lawrence Zhao Heng Ji 38 17 0 22 Feb 2024