Molecular Generation

Latest papers 172

All topics
CardsList
  1. Evolutionary One-Step Generators: Fast and Diverse Sampling for Discrete Design

    Oct 6, 2026Marcus Vukojevic, Erik Nielsen, Veronica Lachi +2Constrained Generative ModelingGraph Generation

  2. Latent Flow Matching for Molecular Graph Generation

    Oct 5, 2026Mathis Goupillon, Roman Bresson, Konstantinos Divriotis +1Flow MatchingMolecular Graph Generation

  3. From Benchmark to Bench: Can Agents Survive Real-World Drug Discovery?

    Oct 5, 2026Pierre Llompart, Levent Guner, Helen Lai +2AI Agents for Scientific DiscoveryLLM Agent Orchestration

  4. Bridging the Evidence-to-Execution Gap:A Reflective Agent for Multi-Objective Peptide Design

    Oct 5, 2026Haosen Zhang, Yang YangAI Agents for Scientific DiscoveryLarge Language Model-Guided Optimization

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

    Oct 1, 2026Yiming Huang, Yujie Zeng, Vijay Prakash Dwivedi +4Graph Representation LearningMolecular Generation

  6. CODesign: Consistency from Data to Trajectory in All-Atom Protein Binder Co-Design

    Oct 1, 2026Yuanle Mo, Bo Qiang, Haitao Lin +4Molecular GenerationProtein Design

  7. Grand Canonical Generators

    Sep 30, 2026Andreas Burger, Malte Franke, Luka Mucko +2Generative ModelingMolecular Generation

  8. Analysis of Quantized and Efficiently Adapted Protein Language Models

    Sep 30, 2026Ilan Yaniv Zeisler, Sebastian Clancy, Pouriya Bayat +8Protein Language ModelsQuantization-Aware LoRA

  9. RetroGEF: Dynamic Graph Edit Flow for Single-Step Retrosynthesis

    Sep 29, 2026Xiaozhuang Song, Xuemin Chen, Xinjian Zhao +2One-Step Generative ModelingMolecular Generation

  10. AbGaze: Attentive Geometric Representation Learning for End-to-End Antibody Design

    Sep 28, 2026Jiashuo Wang, Siqi Fan, Yizhen Luo +1Geometric Representation LearningMolecular Generation

  11. Learning to Re-Draft: A Variational Stackelberg Game for Discrete Diffusion

    Sep 28, 2026Dmitrii Moor, Federico Tomasi, Paul N. Bennett +2Bilevel OptimizationMolecular Generation

  12. Continuous Variational Synthesis

    Sep 28, 2026Alan N. Amin, Mattia G. Gollub, Andrei Slabodkin +2Variational AutoencodersConstrained Generative Modeling

  13. One Sequence, Many Decodings: CAGenMol-2 Recasts Drug Design as Masked Molecular Inference

    Sep 28, 2026Yanting Li, Enyan Dai, Lei Wang +2Molecular OptimizationMasked Diffusion Models

  14. MolDesignBench: Evaluating LLM-based Agent for Scenario-grounded Molecular Design

    Sep 23, 2026Yongjun Jeong, Hanbum Ko, Ye Rin Kim +6Molecular OptimizationLLM Agent Evaluation

  15. TorchCraft: Unified binder design by inverting an all-atom structure predictor

    Sep 17, 2026TorchCraft Team, Yu Liu, Zhouhanyu Shen +8Molecular GenerationProtein Design

  16. Ensemble-Conditioned Molecular Design

    Sep 14, 2026Ross Irwin, Alessandro Tibo, Jon Paul Janet +1Molecular OptimizationStructure-Based Drug Design

  17. 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 +2Structure-Based Drug DesignMolecular Generation

  18. Mode Coverage in Normalizing Flow Boltzmann Generators via Log-Ratio Variation

    Sep 8, 2026Qi Feng, Rongjie Lai, Di Qi +1Normalizing FlowsMolecular Generation

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

    Sep 8, 2026Weichi Yao, Cameron Gruich, Bryan R. Goldsmith +13D Molecular GenerationMolecular Generation

  20. SimpleDesign: A Joint Model for Protein Sequence and Structure Codesign

    Sep 3, 2026Jiarui Lu, Yuyang Wang, Yizhe Zhang +4Unified Multimodal ModelsGenerative Modeling

  21. HiPoly: a hierarchical polymer-native AI framework for property prediction and generative design

    Sep 2, 2026Ge Sun, Gervasio Zaldivar, Yuan Tian +5Materials Property PredictionMaterials Science

  22. Schrödinger Bridges on Lie Group Manifolds for Probabilistic Intrinsic Generation

    Sep 2, 2026Shizhe Zhang, Mingyang Zhao, Lei MaSchrödinger BridgesGenerative Modeling

  23. Elite-Weighted Supervised Fine-tuning for Goal-Directed Molecular Optimization

    Aug 31, 2026Shiyun Wa, Yifei Wang, Anna G. Green +2Supervised Fine-TuningMolecular Optimization

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

    Aug 31, 2026Tianyu Gao, Zhikai Su, Jiashu Li +5Flow MatchingStructure-Based Drug Design

  25. How Molecular Generative Models Organize Molecular Identity

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

  26. Genotypic Triggers: Exposing Pharmacogenomic Blind Spots via Host-Specific Backdoors in Generative Antimicrobial Peptide Models

    Aug 7, 2026Doniyorkhon Obidov, Xiaolong Guo, Yonghui Li +1Backdoor AttacksMolecular Generation

  27. PolymerGPT: Multi-property Optimization with a Decoder-Based GPT Model for Generative Polymer Design

    Aug 2, 2026Charlie Pyle, Adarsh Gadari, C. Adrian Figg +3Molecular OptimizationMolecular Generation

  28. Fused Bayesian Flow Networks for Dual-Target Molecular Design

    Aug 2, 2026Jingyuan Zhou, Shikui Tu, Lei XuStructure-Based Drug DesignMolecular Generation

  29. Evolutionary Curriculum Learning Improves Biological Sequence Modeling

    Aug 1, 2026Richard Zhu, Kento NishiVariational AutoencodersCurriculum Learning

  30. A Synthetically-accessible Universe of Chemically Recyclable Polymers

    Jul 31, 2026Anagha Savit, Wei Xiong, Harikrishna Sahu +3Synthetic Data GenerationMaterials Science

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

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

  32. Oracle-Budgeted Molecular Optimization with Short-Term Graph Memory

    Jul 30, 2026Jiannan Yang, Veronika Thost, Xiang Ling +1Molecular OptimizationSurrogate-Assisted Optimization

  33. SE(3)-MeanFlow: Few-Step Protein Backbone Generation on Lie Groups

    Jul 29, 2026Yikun Bai, Binghang Lu, Yikai Liu +7Flow MatchingLie Group Methods

  34. Chamaileon: Cross-Context Binder Design with Contextualized Modeling and Mixed Sampling

    Jul 26, 2026Hengyuan Cao, Shizhuo Cheng, Mingxuan Liu +5Molecular GenerationProtein Design

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

    Jul 24, 2026Yuliang Yan, Shuo Yan, Haochun Tang +2Molecular GenerationDrug Discovery

  36. OLEDLM: A Unified Language Model for OLED Molecular Design

    Jul 22, 2026Fukang Wen, Yuchong Tang, Jingyuan Li +9Molecular OptimizationMaterials Science

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

    Jul 22, 2026Chengchun Liu, Zhiyuan Yan, Li Yuan +5Molecular Generation

  38. Boltzmann-Expected Molecular Design with Decoupled Annealing Flows

    Jul 21, 2026Selma Moqvist, Richard Beckmann, Ross Irwin +2Molecular OptimizationMolecular Graph Generation

  39. DBMol: Design of High-Affinity, Target-Specific Small Molecules through Structure Prediction Models

    Jul 21, 2026Yiming Qin, Kai Yi, Miruna Cretu +3Protein-Ligand Binding Affinity PredictionMolecular Optimization

  40. Parallel Noising in Neural Markov Logic Networks

    Jul 21, 2026Peter Jung, Giuseppe Marra, Ondrej KuzelkaMarkov Chain Monte CarloGraph Generation

  41. Decafs: Disentangled Conditional adversarial Flows

    Jul 21, 2026Anirudh jain, Sakshi Varshney, Samuel Kaski +1Disentangled Representation LearningNormalizing Flows

  42. MotifRole-Diff: Risk-Optimal Role-Aware Corruption for Masked Molecular Graph Diffusion

    Jul 20, 2026Tasfia Nuzhat Ornee, Elias Hossain, Ivan Garibay +1Masked Diffusion ModelsMolecular Graph Generation

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

    Jul 20, 2026Thomas MacDougall, Maksim Kuznetsov, Roman Schutski +5Constrained Generative ModelingLLM Evaluation

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

    Jul 14, 2026Daria A. Ryabchenko, Pavel Gurevich, Shamil Kadyrov +5Molecular GenerationGenerative AI Evaluation

  45. Sample Efficient Generative Optimization for Molecular Design

    Jul 14, 2026Sarina Kopf, Cristina Nevado, Philippe SchwallerMolecular OptimizationSurrogate-Assisted Optimization

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

    Jul 14, 2026Yuxuan Ren, Fan Yang, Jianhua Yao +1Autoencoders3D Molecular Generation

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

    Jul 14, 2026Ruoxi Gao, Jiangweizhi Peng, Ziqi Chen +10Molecular OptimizationStructure-Based Drug Design

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

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

  49. Autoregressive latent diffusion for 3D molecule generation

    Jul 10, 2026Federico Ottomano, Gaopeng Ren, Yingzhen Li +2Latent Diffusion ModelsMolecular Graph Generation

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

    Jul 9, 2026Ali Motahharynia, Mohammadreza Ghaffarzadeh-Esfahani, Mahsa Sheikholeslami +4Molecular GenerationConditional Generative Modeling

  51. MARLIN: De Novo Molecular Structure Elucidation from Tandem Mass Spectra without a Ground-Truth Formula

    Jul 6, 2026Xujun Che, Xiuxia Du, Depeng XuMolecular GenerationMass Spectrometry

  52. AquaGen: Scaling generative models to molecular dynamics precision on thousands of atoms

    Jul 3, 2026Emmanuel Bengio, Sanjeev Raja, Yui Tik Pang +5Free Energy CalculationGenerative Modeling

  53. SynLaD: Latent Diffusion for Generating Synthesizable Molecules Conditioned on 3D Pharmacophore Profiles

    Jul 1, 2026Miruna Cretu, John Bradshaw, Patricia Suriana +6Latent Diffusion Models3D Molecular Generation

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

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

  55. Beyond Drug Discovery: The Nanotechnology Molecular Optimization (NMO) Benchmark

    Jun 29, 2026Matthias Blaschke, Daniel Kienzle, Zsuzsanna Koczor-Benda +3Molecular OptimizationBenchmark Design