Title
NovoMolGen: Rethinking Molecular Language Model Pretraining Kamran Chitsaz Roshan Balaji Quentin Fournier Nirav Pravinbhai Bhatt Sarath Chandar AI4CE 68 0 0 19 Aug 2025
Sparse Probabilistic Graph Circuits Martin Rektoris Milan Papez Václav Smídl Tomás Pevný TPM 30 0 0 11 Aug 2025
MolSnap: Snap-Fast Molecular Generation with Latent Variational Mean Flow Md Atik Ahamed Qiang Ye Q. Cheng BDL 32 0 0 07 Aug 2025
One Small Step with Fingerprints, One Giant Leap for De Novo Molecule Generation from Mass Spectra Neng Kai Nigel Neo Lim Jing Ngoui Yong Zhau Preston Koh Xue Ting Serene Bingquan Shen 4 0 0 06 Aug 2025
Look the Other Way: Designing 'Positive' Molecules with Negative Data via Task Arithmetic Rıza Özçelik Sarah de Ruiter F. Grisoni 31 0 0 23 Jul 2025
Bures-Wasserstein Flow Matching for Graph Generation Keyue Jiang Jiahao Cui Xiaowen Dong Laura Toni 119 1 0 16 Jun 2025
Polymorphism Crystal Structure Prediction with Adaptive Space Group Diversity Control Sadman Sadeed Omee Lai Wei Sourin Dey Jianjun Hu 39 3 0 12 Jun 2025
HSG-12M: A Large-Scale Spatial Multigraph Dataset Xianquan Yan Hakan Akgün Kenji Kawaguchi N. Duane Loh Ching Hua Lee 76 1 0 10 Jun 2025
A Comprehensive Benchmarking Platform for Deep Generative Models in Molecular Design Adarsh Singh ELM 89 0 0 19 May 2025
El Agente: An Autonomous Agent for Quantum Chemistry Yunheng Zou Austin H. Cheng Abdulrahman Aldossary Jiaru Bai Shi Xuan Leong ... Ilya Yakavets Han Hao Chris Crebolder Varinia Bernales Alán Aspuru-Guzik 108 5 0 05 May 2025
Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks Xinyu Wang Jinbo Bi Minghu Song CLL 170 0 0 01 May 2025
Heterophily-informed Message Passing Haishan Wang Arno Solin Vikas Garg 164 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 Teli Ma Yiping Song 194 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 274 0 0 08 Apr 2025
Improving Equivariant Networks with Probabilistic Symmetry Breaking Hannah Lawrence Vasco Portilheiro Yan Zhang Sékou-Oumar Kaba 195 7 0 27 Mar 2025
Towards Unified and Lossless Latent Space for 3D Molecular Latent Diffusion Modeling Yanchen Luo Zhiyuan Liu Yi Zhao Changhao Nai Kenji Kawaguchi Tat-Seng Chua Xiang Wang Yang Zhang Xiang Wang MedIm 211 0 0 19 Mar 2025
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation Mohit Pandey G. Subbaraj Artem Cherkasov Martin Ester Emmanuel Bengio AI4CE 202 1 0 08 Mar 2025
Backdoor Attacks on Discrete Graph Diffusion Models Jiawen Wang Samin Karim Yuan Hong Binghui Wang DiffM 261 0 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 292 7 0 23 Feb 2025
FragFM: Hierarchical Framework for Efficient Molecule Generation via Fragment-Level Discrete Flow Matching Joongwon Lee Seonghwan Kim Wou Youn Kim H. Kim Woo Youn Kim 214 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 Changhao Nai Cunchun Li Yaorui Shi Xiang Wang Kenji Kawaguchi Tat-Seng Chua 279 6 0 18 Feb 2025
Generating 3D Binding Molecules Using Shape-Conditioned Diffusion Models with Guidance Ziqi Chen Bo Peng Tianhua Zhai Daniel Adu-Ampratwum Xia Ning 203 1 0 09 Feb 2025
Mol-MoE: Training Preference-Guided Routers for Molecule Generation Diego Calanzone P. DÓro Pierre-Luc Bacon 121 1 0 08 Feb 2025
Learning to generate feasible graphs using graph grammars Stefan Mautner Rolf Backofen Fabrizio Costa 158 0 0 10 Jan 2025
Unified Guidance for Geometry-Conditioned Molecular Generation Sirine Ayadi Leon Hetzel Johanna Sommer Fabian J. Theis Stephan Günnemann 136 2 0 05 Jan 2025
Graph Generative Pre-trained Transformer Xiaohui Chen Yinkai Wang Jiaxing He Yuanqi Du S. Hassoun Xiaolin Xu Li Liu 226 5 0 02 Jan 2025
The Jungle of Generative Drug Discovery: Traps, Treasures, and Ways Out Rıza Özçelik F. Grisoni 118 2 0 24 Dec 2024
Bayesian Flow Is All You Need to Sample Out-of-Distribution Chemical Spaces Nianze Tao OOD OODD BDL 350 0 0 16 Dec 2024
Rectified Flow For Structure Based Drug Design Daiheng Zhang Chengyue Gong Qiang Liu DiffM 149 2 0 02 Dec 2024
NPGPT: Natural Product-Like Compound Generation with GPT-based Chemical Language Models Koh Sakano Kairi Furui Masahito Ohue 130 4 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 207 3 0 03 Nov 2024
SAFE setup for generative molecular design Yassir El Mesbahi Emmanuel Noutahi 91 1 0 26 Oct 2024
Chemical Language Model Linker: blending text and molecules with modular adapters Yifan Deng Spencer S. Ericksen Anthony Gitter 238 0 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 97 0 0 11 Oct 2024
Can LLMs Generate Diverse Molecules? Towards Alignment with Structural Diversity Hyosoon Jang Yunhui Jang Jaehyung Kim SungSoo Ahn 88 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 99 0 0 03 Oct 2024
Conformal Generative Modeling with Improved Sample Efficiency through Sequential Greedy Filtering Kemal Kurniawan Bernhard Schölkopf Michael Muehlebach 270 1 0 02 Oct 2024
A Bayesian Flow Network Framework for Chemistry Tasks Nianze Tao Minori Abe BDL 171 5 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 144 10 0 24 Jul 2024
Diff4VS: HIV-inhibiting Molecules Generation with Classifier Guidance Diffusion for Virtual Screening Jiaqing Lyu Changjie Chen Bing Liang Yijia Zhang 73 1 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 142 1 0 12 Jul 2024
Generative Modelling of Structurally Constrained Graphs Manuel Madeira Clément Vignac D. Thanou Pascal Frossard DiffM 129 6 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 151 2 0 15 Jun 2024
Cometh: A continuous-time discrete-state graph diffusion model Antoine Siraudin Fragkiskos D. Malliaros Christopher Morris 86 8 0 10 Jun 2024
$Diffusion Models in $\textit{De Novo}$ Drug Design$ Diffusion Models in $\textit{De Novo}$ Drug Design Amira Alakhdar Barnabas Poczos Newell Washburn MedIm 127 35 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 101 9 0 04 Jun 2024
Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation Jeff Guo Philippe Schwaller Mamba 137 8 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 143 32 0 19 May 2024
Improving Targeted Molecule Generation through Language Model Fine-Tuning Via Reinforcement Learning Salma J. Ahmed Emad A. Mohammed 87 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 145 14 0 07 May 2024