Molecular Generation

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10 papers in the last four weeks, up 67% on the four weeks before. 0.1% of all new papers.

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  1. Latent Flow Matching for Molecular Graph Generation

    Oct 5, 2026Mathis Goupillon, Roman Bresson, Konstantinos Divriotis +1Molecular Generation

    Mohamed bin Zayed University of Artificial Intelligence

  2. Higher-Order Molecular Grammars for Generative and Foundation Models in Chemistry

    Oct 1, 2026Yiming Huang, Yujie Zeng, Vijay Prakash Dwivedi +4Molecular GenerationMoleculenet

    Department of Computing, Imperial College London, London, UK · School of Electronic Engineering and Computer Science, Queen Mary University of London, London, UK · Department of Computer Science, Stanford University, Stanford, CA, USA +1

  3. Grand Canonical Generators

    Sep 30, 2026Andreas Burger, Malte Franke, Luka Mucko +2Boltzmann DistributionsMonte Carlo

    University of Toronto NVIDIA Vector Institute Toronto, Canada · NVIDIA · ETH Zurich NCCR Catalysis Zurich, Switzerland +2

  4. Riemannian Flow Models with Reinforcement Learning for Molecular Crystal Structure Prediction

    Sep 30, 2026Thomas Egg, Harry Winston Sullivan, Maya M. Martirossyan +8Crystal Structure PredictionMolecular Generation

    Center for Soft Matter Research, Department of Physics, New York University, New York 10003, USA · Simons Center for Computational Physical Chemistry, Department of Chemistry, New York University, New York 10003, USA · Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA +7

  5. Where Should Physics Enter a Molecular Crystal Generator?

    Sep 28, 2026Haocheng Tang, Junmei Wang, Wengong JinCrystal StructureCrystal Structure Prediction

    Khoury College of Computer Science Northeastern University Boston, MA 02115, USA · School of Pharmacy University of Pittsburgh Pittsburgh, PA 15213, USA

  6. Topology-Stratified Materials Discovery with A Flow-Based Generative Model

    Sep 22, 2026Jingyi Zhou, Oyshee Chowdhury, Noah Oyeniran +1Crystal StructureData-Driven Materials Discovery

    Department of Aerospace Engineering and Mechanics, University of Alabama, Tuscaloosa, 35487, Alabama, United States. · Alabama Materials Institute, The University of Alabama, Tuscaloosa, 35487, Alabama, United States.

  7. Deep Generative Crystal Structure Prediction: A Benchmark Study and a Controlled Test of Prototype Dependence

    Sep 22, 2026Lai Wei, Rongzhi Dong, Ying Feng +2Crystal Structure PredictionMolecular Generation

    Department of Computer Science and Engineering University of South Carolina Columbia, SC 29201 · Department of Computer Science and Cybersecurity, University of North Georgia, Dahlonega, GA 30597

  8. Ensemble-Conditioned Molecular Design

    Sep 14, 2026Ross Irwin, Alessandro Tibo, Jon Paul Janet +1Molecular DesignMolecular Generation

    Molecular AI Discovery Sciences, R&D AstraZeneca Gothenburg, Sweden · Department of Computer Science and Engineering Chalmers University of Technology and University of Gothenburg Gothenburg, Sweden

  9. A Systematic Evaluation of Molecule Generation Models for De Novo Drug Design: From Benchmarks to Practical Insights

    Sep 9, 2026Xinrui Xu, Xueer Wang, Dan Luo +2Molecular GenerationMolecular Design

    School of Computer Science, Xiangtan University, Xiangtan 411105, China · College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, China · School of Chinese Medicine, Hong Kong Baptist University, 15 Baptist University Road, Kowloon Tong 999077, Kowloon, Hong Kong SAR, China

  10. Fixed-Dimensional Latent Flow for Generating Variable-Size 3D Molecules

    Sep 8, 2026Weichi Yao, Cameron Gruich, Bryan R. Goldsmith +1Molecular GenerationMolecules

    Michigan Institute for Data & AI in Society University of Michigan, Ann Arbor, USA · Department of Chemical Engineering University of Michigan, Ann Arbor, USA · Department of Statistics University of Michigan, Ann Arbor, USA

  11. PocketVE: Stable and Property-Guided Structure-Based Drug Design with Variance-Exploding Diffusion

    Sep 8, 2026Peining Zhang, Jinbo BiMolecular GenerationDiffusion Models

    University of Connecticut Storrs, Connecticut 06269, USA

  12. Text-guided flow matching enables sample-efficient crystal structure generation

    Sep 1, 2026Wentao LiCrystal StructureCrystal Structure Prediction

    1Tsinghua University

  13. Probabilistic Model Checking of Autoregressive Neural Sequence Models

    Sep 1, 2026Helge Spieker, Dennis Gross, Arnaud GotliebProbabilistic Model CheckingProbabilistic Model

    Simula Research Laboratory, Oslo, Norway

  14. Language-Informed Flow Matching for Trend-Guided Structure-Based 3D Molecular Generation

    Aug 31, 2026Tianyu Gao, Zhikai Su, Jiashu Li +5Molecular GenerationDrug Design

    1City University of Hong Kong · 2The University of Hong Kong · 3Stanford University

  15. S3C-LLM: Skill-Code Guided Agentic Language Models for Spectrum-to-Structure Elucidation

    Aug 31, 2026Xuanle Zhao, Xinyuan Cai, Xiang Cheng +1Laser-Induced Breakdown SpectroscopyMolecular Generation

    The Key Laboratory of Cognition and Decision Intelligence for Complex Systems, Institute of Automation, Chinese Academy of Sciences · School of Artificial Intelligence, University of Chinese Academy of Sciences

  16. Symmetry-Breaking De Novo Crystal Generation via Markovian Jump Diffusion

    Aug 13, 2026Van Khoa Nguyen, Alexandros KalousisCrystal StructureCrystal

    HES-SO Geneva · University of Geneva

  17. NAE: Normalizing AutoEncoder

    Aug 12, 2026Muhammad Abdur Rafae, Niels LandwehrAutoencoder ArchitecturesSurrogate Gradient

    University of Hildeshiem

  18. DynaCrys: Crystal Generation with Dynamic Space-Group Diffusion

    Aug 7, 2026Zhuotao Jin, Xiaoyun Wang, Nicholas Brawand +5Crystal StructureCrystal

    NVIDIA · Center for Computational Science and Engineering, Massachusetts Institute of Technology · Department of Materials Science and Engineering, Massachusetts Institute of Technology +4

  19. How Molecular Generative Models Organize Molecular Identity

    Aug 7, 2026Raul Ortega-Ochoa, Tejs Vegge, Jens S. Bakander +3Molecular GenerationMoleculenet

    Toyota Research Institute, Los Altos, California, USA · Department of Energy Conversion and Storage, Technical University of Denmark · CAPeX Pioneer Center for Accelerating P2X Materials Discovery, Kgs. Lyngby, Denmark +8

  20. MolGVR: A Chemistry-Grounded Framework for Text-to-Molecule Generation

    Jul 31, 2026Qian Tan, Xuanyu Zhu, Lei Jiang +3Molecular GenerationMoleculenet

    University of Science and Technology of China · Shanghai Jiao Tong University · Shanghai Artificial Intelligence Laboratory

  21. TriGlue: a Biology-Inspired Generative Model for Generating Molecular Glue-Induced Ternary Complex

    Jul 24, 2026Yuliang Yan, Shuo Yan, Haochun Tang +2Molecular DesignMolecular Generation

    The Hong Kong University of Science and Technology (Guangzhou) · Jilin University · University of Sydney

  22. M3^3-Gen: Interpretable Multimodal Generation of Gene Expression Profiles Using Clinical and Imaging Data

    Jul 23, 2026Francesca Pia Panaccione, Carlo Sgaravatti, Marco VenereMultimodal Clinical DataTranscriptomics

    DEIB - Dipartimento Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, 20133, Italy

  23. Hypothesis-and-Refinement Learning of Organic Structures from Multimodal Spectroscopic Data

    Jul 22, 2026Chengchun Liu, Zhiyuan Yan, Li Yuan +5Laser-Induced Breakdown SpectroscopyMolecules

    School of AI for Science, Peking University Shenzhen Graduate School, Shenzhen 518055, China · State Key Laboratory of Advanced Waterproof Materials, School of Materials Science and Engineering, Peking University, Beijing 100871, China · School of Electronic and Computer Engineering, Peking University Shenzhen Graduate School, Shenzhen 518055, China +6

  24. Adopting Reinforcement Learning with Verifiable Rewards for Molecular Generation

    Jul 21, 2026Mingxuan Ouyang, Hao Lan, Wanyu LinMolecular GenerationMolecular Design

  25. Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints

    Jul 20, 2026Thomas MacDougall, Maksim Kuznetsov, Roman Schutski +5Molecular GenerationDrug Design

    Insilico Medicine Canada Inc. · Insilico Medicine Hong Kong Ltd. · Insilico Medicine AI Limited

  26. Chemical filters for ultra-high-throughput materials screening and generation

    Jul 20, 2026Kinga O. Mastej, Panyalak Detrattanawichai, Hyunsoo Park +3Data-Driven Materials DiscoveryChemical Structures

    Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom

  27. HEDGEHOG: Hierarchical Evaluation of Drug Generators Through Rigorous Filtration

    Jul 14, 2026Daria A. Ryabchenko, Pavel Gurevich, Shamil Kadyrov +5Molecular GenerationDrug Discovery

    Ligand Pro, Moscow, Russia · Skolkovo Institute of Science and Technology, Artificial Intelligence Center, Moscow, Russia · 1Ligand Pro, Moscow, Russia +1

  28. SinAE: A Single-Architecture Flow-Matching Autoencoder for Cross-Domain Atomic Systems

    Jul 14, 2026Yuxuan Ren, Fan Yang, Jianhua Yao +1Molecular GenerationAutoencoder Architectures

    Department of Computer Science National University of Singapore · Tencent AI for Life Science Lab

  29. Generating Developable 3D Molecules via Pocket-Conditioned Diffusion and Property-Aware Optimization

    Jul 14, 2026Ruoxi Gao, Jiangweizhi Peng, Ziqi Chen +10Drug DesignMolecular Design

    Computer Science and Engineering, The Ohio State University, Columbus, OH 43210. · Industrial and System Engineering, University of Minnesota, Minneapolis, MN 55455. · Google Cloud, Google LLC, Mountain View, CA 94043. +6

  30. Gene Expression-Informed Jointly Controlled Generative Modeling for Precision Molecular Design

    Jul 13, 2026Hang Yuan, Chen Li, Wenjun Ma +2Molecular DesignMolecular Generation

    School of Artificial Intelligence South China Normal University Foshan, Guangdong, China · D3 Center The University of Osaka Suita, Osaka, Japan · School of Computer Science South China Normal University Guangzhou, Guangdong, China

  31. Autoregressive latent diffusion for 3D molecule generation

    Jul 10, 2026Federico Ottomano, Gaopeng Ren, Yingzhen Li +2Molecular GenerationAutoregressive Diffusion

    Department of Chemistry Imperial College London · Department of Computing Imperial College London

  32. DrugGen 2: A disease-aware language model for enhancing drug discovery

    Jul 9, 2026Ali Motahharynia, Mohammadreza Ghaffarzadeh-Esfahani, Mahsa Sheikholeslami +4Drug DesignDrug Discovery

    Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran · Isfahan Neuroscience Research Center, Isfahan University of Medical Sciences, Isfahan, Iran · Department of Medicinal Chemistry, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran +3

  33. A Precedent-Guided Co-Scientist for Side-Effect-Aware Drug Redesign

    Jul 3, 2026Yujin Kim, Charmgil HongDrug DiscoveryPharmacokinetics

    Department of Computer Science and Electrical Engineering, Handong Global University, Pohang, Republic of Korea.

  34. MolSafeEval: A Benchmark for Uncovering Safety Risks in AI-Generated Molecules

    Jul 1, 2026Tong Xu, Xinzhe Cao, Zhihui Zhu +2Molecular GenerationMolecular Design

    Zhejiang University · ZJU-Hangzhou Global Scientific and Technological Innovation Center · University of Oxford

  35. Multi-Objective Molecular Generation with Frequency-Controlled Evolutionary Dynamics

    Jun 25, 2026Elia Colleoni, Paolo Guida, Didier Barradas-Bautista +1Molecular GenerationDrug Discovery

    Clean Energy Research Center (CERP) Physical Science and Engineering (PSE) Division King Abdullah University of Science and Technology Thuwal, Saudi Arabia 23955 · Kaust Visualization Lab (KVL) Core Lab Division King Abdullah University of Science and Technology Thuwal, Saudi Arabia 23955

  36. Autoregressive Boltzmann Generators

    Jun 25, 2026Danyal Rehman, Charlie B. Tan, Yoshua Bengio +2Autoregressive GenerationMolecular Generation

    Mila – Québec AI Institute · Broad Institute of MIT & Harvard · Aithyra +4

  37. Project Ariadne: Prompt-Conditioned Route Generation for Synthesis Planning

    Jun 23, 2026Anton Morgunov, Victor S. BatistaMolecular GenerationSynthesis

    Yale University

  38. Sesame: Structure-Aware Molecular Generation via Spatial Density-Map Conditioning

    Jun 22, 2026Konstantin Yatsenko, Arvind ThiagarajanMolecular GenerationDrug Design

    Tessel Biosciences, Inc., 750 Main Street, Cambridge, MA 02139

  39. Substitution-Based Analysis of Structural Novelty for Generative Models of Materials

    Jun 22, 2026Masahiro Negishi, Aron WalshCrystal StructureCrystal

    Department of Materials, Imperial College London, Exhibition Road, South Kensington, SW7 2AZ, London, United Kingdom.

  40. JEDEL: Zero-Shot DNA-Encoded Library Design for Early-Stage Drug Discovery

    Jun 21, 2026Zygimantas Jocys, Zhanxing Zhu, Henriette M. G. Willems +1Drug DesignDrug Discovery

    School of Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, United Kingdom. · The ALBORADA Drug Discovery Institute, University of Cambridge,2026 Hills Road, Cambridge, CB2 0AH, United Kingdom.

  41. Multigrid Training for Molecular Generation using Graph Neural Networks

    Jun 21, 2026Zixuan Ling, Paula Mercurio, Di LiuMolecular GenerationAlgebraic Multigrid

    Department of Mathematics, Michigan State University, East Lansing, MI. · Department of Mathematics, Hamline University, Saint Paul, MN.

  42. Calibrating Generative Models to Feature Distributions with MMD Finetuning

    Jun 17, 2026Nathaniel L. Diamant, Brian L. TrippeMolecular GenerationGenerative Models

    Stanford University

  43. Circuit Tracing in Autoregressive Protein Language Models

    Jun 14, 2026Darin Tsui, William Deinzer, Daniel Saeedi +1Mechanistic InterpretabilityMolecular Generation

    School of Electrical and Computer Engineering, Georgia Institute of Technology, Atltanta, GA.

  44. PepALD: Macrocyclic Peptide Generation via Autoregressive Latent Diffusion

    Jun 12, 2026Junming Zhang, Siyu Yi, Wei Ju +1Molecular GenerationAutoregressive Diffusion

    College of Computer Science, Sichuan University, Chengdu, 610065, China · School of Mathematics, Sichuan University, Chengdu, 610065, China · School of Artificial Intelligence, Sichuan University, Chengdu, 610065, China +1

  45. LapidaryEngine: Fully Conversational Crystal Generation

    Jun 12, 2026Yusei Ito, Yuta Suzuki, Tomoya Murata +1CrystalMolecular Generation

    Lattice Lab, Toyota Motor Corporation

  46. Smoothing Dark Areas in Molecular Latent Diffusion

    Jun 11, 2026Xi Wang, Jiahan Li, Yuxuan Xia +3Molecular GenerationStar-Vae

    New York University · Stanford University

  47. Uncertainty Estimation for Molecular Diffusion Models

    Jun 11, 2026Paul Seij, Christian A. Naesseth, Stephan Mandt +1Diffusion ModelsDiffusion Dynamics

    UvA-Bosch Delta Lab, University of Amsterdam · University of California, Irvine

  48. Comprehensive pKa Data Augmentation from Limited Real Data through an Engineered Models-Quantum Framework

    Jun 10, 2026Wang Rui, Liu DinghaoMolecular GenerationAugmentation

    Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China · Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China · School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China

  49. De novo molecular generation with optical property preconditioning at the token level

    Jun 6, 2026Haozhe Huang, Manuel Gonzalez Lastre, Hyun Suk Park +3Molecular GenerationAutoregressive Language Models

    Department of Computer Science, University of Toronto, 40 St George St., Toronto, ON M5S 2E4, Canada · 2Vector Institute for Artificial Intelligence, W1140-108 College St., Schwartz Reisman Innovation Campus, Toronto, ON M5G 0C6, Canada · 3Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, 28049, Madrid, Spain. +6

  50. MatMind: A Structure-Activity Knowledge-Driven Generative Foundation Model for Materials Science

    Jun 5, 2026Zhan'ao Yao, Boxuan Zhang, Jingyuan Shu +10Materials ScienceMolecular Generation

    State Key Laboratory of High Performance Ceramics, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, China. · Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China. · State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, 95 Zhongguancun East Road, Beijing, 100190, China. +5

  51. Generative Molecular Morphing for Flexible-Size Design via Unbalanced Optimal Transport

    Jun 5, 2026Malte Franke, Stefan P. Schmid, Zarko Ivkovic +2Molecular GenerationMolecular Design

    ETH Zürich · NCCR Catalysis

  52. Scaling Novel Graph Generation via Lightweight Structure-Guided Autoregressive Models

    Jun 2, 2026Alessio Barboni, Massimiliano Lupo Pasini, Bishal Lakha +1Graph Representation LearningGraph Representations

    Boise State University Boise, Idaho, USA · Oak Ridge National Laboratory Oak Ridge, Tennessee, USA

  53. Mos-Gen: A Generative Molecular Framework for Mosquito Insecticide Design

    Jun 1, 2026Lina Wang, Yaning CuiMolecular GenerationGenerative Models

    Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Xuhui District, Shanghai, China · DP Technology, Shanghai, China

  54. Uncertainty-Calibrated Diffusion for Reliable 3D Molecular Graph Generation

    Jun 1, 2026Fang Wan, Jingxiang Qu, Yi LiuMolecular GenerationDiffusion Dynamics

    State University of New York at Stony Brook

  55. Genotype-Conditioned Molecular Generation via Evidence-Grounded Multi-Objective Latent Perturbation in Diffusion Models

    May 31, 2026Brenda Nogueira, Gisela A. Gonzalez-Montiel, Nitesh V. Chawla +1Drug DiscoveryMolecular Generation

    Department of Computer Science and Engineering University of Notre Dame Notre Dame, IN, 46556 · Department of Chemistry and Biochemistry University of Notre Dame Notre Dame, IN, 46556 · Lucy Family Institute for Data & Society University of Notre Dame Notre Dame, IN, 46556

  56. Fine-Tuning Diffusion Models for Molecular Generation via Reinforcement Learning and Fast Sampling

    May 31, 2026Guang Lin, Shikui Tu, Lei XuMolecular GenerationDrug Design

    Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China · Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen, Guangdong, China

  57. Manifold Diffusion for Structure Generation of Transition Metal Complexes

    May 30, 2026Luca Schaufelberger, Kjell JornerMolecular GenerationDynamic Environments

    Institute of Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich. · NCCR Catalysis, Switzerland.

  58. A Padding Method for Enhanced Encoding of Inorganic Structures with Varying Chemical Compositions

    May 29, 2026Thang Dang, Haderbache Amir, Tzanakakis Alexandros +1Crystal StructureMolecular Generation

    Fujitsu Limited, Japan · National Technical University of Athens, Greece

  59. DriftingMol: Decoder-Coupled Drift for One-Pass Property-Conditional Molecular Generation

    May 24, 2026Jiangjie Qiu, Yijun Li, Wentao Li +1Molecular Generation

    Beijing Key Laboratory of Artificial Intelligence for Advanced Chemical Engineering Materials

  60. SciCore-Mol: Augmenting Large Language Models with Pluggable Molecular Cognition Modules

    May 21, 2026Yuxuan Chen, Changwei Lv, Yunduo Xiao +5Molecular GenerationScientific Discovery

    School of Electronic and Computer Engineering, Peking University, Shenzhen, China · Tsinghua University, Beijing, China · School of Intelligence Science and Technology, Nanjing University, Suzhou, China