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Period ending 2026-09-21

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  1. The Montparnasse Algorithm for RNA Design

    May 25, 2026Tristan CazenaveMessenger RnaMolecular Optimization

  2. Co-folding model guided by structural proteomics

    May 25, 2026Alon Shtrikman, Nitzan Simchi, Michal Ran Shchory +3Previous Machine-Learning-Based Implicit Solvent

  3. UNATE: UNsupervised ATomic Embedding for crystal structures property prediction

    May 25, 2026Laura Solà-Garcia, Àlex Solé, Javier Ruiz-HidalgoCrystal StructureMolecular Property Prediction

  4. Don't Retrain, Just Reuse: Recovering Dual-Target Molecules from Single-Target Diffusion Models

    May 25, 2026Qingyuan Zeng, Pengxiang Cai, Zixin Guan +5Drug-Drug InteractionsReuse

  5. Geometric Flow Matching for Molecular Conformation Generation via Manifold Decomposition

    May 25, 2026Yunqing Liu, Yi Zhou, Wenqi FanConformational EnsemblesHierarchical Flow Matching

  6. What Molecular Structure Cannot Tell Us: A Taxonomy of Explainability Gaps in GNN-Based Drug Toxicity Prediction

    May 25, 2026Juergen DietrichDrug-Drug InteractionsMolecular Graphs

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

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

  8. Aligning Molecular Graph Explanations with Chemical Identity via InChIfied Invariants

    May 23, 2026Emanuele Guidotti, Sara PuglioliMolecular GraphsVast Chemical Space

  9. Representation-Guided Discrete Molecular Graph Retrosynthesis

    May 23, 2026Jiahai Huang, Anjie Qiao, Zhen Wang +2Molecular GraphsVast Chemical Space

  10. Learning dynamical systems with biochemically informed neural ordinary differential equations

    May 22, 2026Luis L. Fonseca, Reinhard C. Laubenbacher, Lucas BöttcherNeural Ordinary Differential EquationsDynamical Systems

  11. An accurate nucleic acid-small molecule docking framework via geometric deep learning with large-scale pretraining

    May 22, 2026Shi Li, Xujun Zhang, Mingquan Liu +5Structure-Based Drug DesignDrug Design

  12. A Large-Scale Dataset and Benchmark: Do Protein-Ligand Models Learn Binding Sites or Just Binding Likelihood?

    May 21, 2026Zhaohan Meng, Zhen Bai, Ke Yuan +4Structure-Based Drug DesignLikelihood

  13. LLM-AutoSciLab: Closed-Loop Scientific Discovery via Active Experimentation with LLMs

    May 21, 2026Sanchit Kabra, Nikhil Abhyankar, Saaketh Desai +2Scientific DiscoveryDrug Discovery

  14. Molecular Lead Optimization via Agentic Tool Planning

    May 21, 2026Lingxiao Li, Haobo Zhang, Ruohao Fan +2Molecular OptimizationDrug Discovery

  15. Epicure: Navigating the Emergent Geometry of Food Ingredient Embeddings

    May 21, 2026Jakub Radzikowski, Josef ChenRecipeNutrient Reasoning

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

    May 21, 2026Yuxuan Chen, Changwei Lv, Yunduo Xiao +5Molecular Structure ElucidationMolecular Generation

  17. Spectra as Language: Large Language Models for Scalable Stellar Parameter and Abundance Inference

    May 21, 2026Hai-Ling Lu, Yu-Yang Li, Yin-Bi Li +4SpectraVast Chemical Space

  18. Atom-level Protein Representation Learning Improves Protein Structure Prediction

    May 21, 2026Taewon Kim, Hyosoon Jang, Hyunjin Seo +6Protein Data BankProtein

  19. SMDD-Bench: Can LLMs Solve Real-World Small Molecule Drug Design Tasks?

    May 20, 2026Kevin Han, Renfei Zhang, Kathy Wei +3Drug DesignDrug Discovery

  20. ConTact: Contact-First Antibody CDR Design via Explicit Interface Reasoning

    May 20, 2026Mansoor Ahmed, Spencer VonBank, Nadeem Taj +3AntibodyStructure-Based Drug Design

  21. From swept contact to pose: Probe-aware registration via complementary-shape docking

    May 20, 2026Chen Chen, Yunwen Li, Yifan Xu +5Feature MatchingContact-Rich Manipulation

  22. AIMBio-Mat: An AI-Native FAIR Platform for Closed-Loop Materials Discovery and Biomedical Translation

    May 20, 2026D. -M. Mei, K. Acharya, C. M. Adhikari +51Data-Driven Materials DiscoveryBiomedical Knowledge

  23. Training distribution determines the ceiling of drug-blind cancer sensitivity prediction

    May 20, 2026Taekyung HeoDrug-Drug InteractionsCancer Genome Atlas

  24. Distribution-Aware Reward: Reinforcement Learning over Predictive Distributions for LLM Regression

    May 20, 2026Jungsoo Park, Hyungjoo Chae, Ethan Mendes +4Process Reward ModelingLarge Language Model Post-Training

  25. Beyond Text and Tables: Vision-Language Model Integration in ComProScanner for Extracting Materials Data from Scientific Figures with High Accuracy

    May 19, 2026Aritra Roy, Enrico Grisan, Chiara Gattinoni +1Image-Text PairsVast Chemical Space

  26. Hierarchical Contrastive Learning for Multi-Domain Protein-Ligand Binding

    May 19, 2026Shuo Zhang, Rongqi Hong, Huifeng Zhang +1Structure-Based Drug DesignMulti-Domain

  27. MSAlign: Aligning Molecule and Mass Spectra Foundation Models for Metabolite Identification

    May 19, 2026Paul Krzakala, Gabriel Melo, Camille Lançon +4Tandem Mass SpectraMetabolic

  28. Protein Thoughts: Interpretable Reasoning with Tree of Thoughts and Embedding-Space Flow Matching for Protein-Protein Interaction Discovery

    May 19, 2026Kingsley Yeon, Xuefeng Liu, Promit GhosalProteinTree Search

  29. Generative Pseudo-Force Fields for Molecular Generation

    May 18, 2026Stefaan Simon Pierre Hessmann, Khaled Kahouli, Stefan Gugler +4Molecular GenerationConformational Ensembles

  30. Protein Fold Classification at Scale: Benchmarking and Pretraining

    May 18, 2026Dexiong Chen, Andrei Manolache, Mathias Niepert +1Protein Data BankProtein

  31. Generating Physically Consistent Molecules with Energy-Based Models

    May 18, 2026Christoph Griesbacher, Lea Bogensperger, Andreas Habring +1Molecular GenerationFree-Energy Landscape

  32. DCFold: Efficient Protein Structure Generation with Single Forward Pass

    May 18, 2026Zhe Zhang, Yuanning Feng, Yuxuan Song +3Protein DesignSingle Forward Pass

  33. LEAP: A closed-loop framework for perovskite precursor additive discovery

    May 18, 2026Xin-De Wang, Zhi-Rui Chen, Ze-Feng Gao +3Vast Chemical SpacePhotovoltaic

  34. Fine-tuning Pocket-Aware Diffusion Models via Denoising Policy Optimization

    May 17, 2026Yuan Xue, Daniel Kudenko, Megha KhoslaDrug DesignMolecular Optimization

  35. When Molecular Similarity Works: Property Cliffs Reveal Hidden Errors

    May 17, 2026Di Hu, Kun Li, Haojie Rao +6Molecular Property PredictionPrevious Machine-Learning-Based Implicit Solvent

  36. ChemVA: Advancing Large Language Models on Chemical Reaction Diagrams Understanding

    May 17, 2026Mingyang Rao, Kehua Feng, Zhihui Zhu +4Vast Chemical SpaceReaction

  37. Provably Learning Diffusion Models under the Manifold Hypothesis: Collapse and Refine

    May 16, 2026Wei Huang, Andi Han, Mingyuan Bai +4Score-Based Diffusion ModelDiscrete Diffusion Model

  38. Tensor Channel Equivariant Graph Neural Networks for Molecular Polarizability Prediction

    May 16, 2026Jean Philip Filling, Daniel Franzen, Michael WandMolecular Property PredictionTensor Networks

  39. Cross-Domain Molecular Relational Learning: Leveraging Chemical Structure-Activity Analysis

    May 16, 2026Peiliang Zhang, Jingling Yuan, Shiqing Wu +4Structure-Based Drug DesignRelational Deep Learning

  40. Structure-Aware Masking for Protein Representation Learning

    May 15, 2026Thomas Walton, Ayan Goel, Amirali AghazadehProtein Data BankSequence Modeling

  41. Hypergraph Pattern Machine: Compositional Tokenization for Higher-Order Interactions

    May 15, 2026Kyrie Zhao, Zehong Wang, Tianyi Ma +5HypergraphsDrug-Drug Interactions

  42. MoleCode unlocks structural intelligence in large language models

    May 15, 2026Zhiyuan Yan, Chen Liu, Boxuan Zhao +8Molecular Structure ElucidationMolecular Graphs

  43. Multi-level Self-supervised Pretraining on Compositional Hierarchical Graph for Molecular Property Prediction

    May 15, 2026Xiayu Liu, Zhengyi Lu, Hou-biao LiMolecular Property PredictionVast Chemical Space

  44. Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design

    May 15, 2026Chen Wei, Fanding Xu, Minghao Sun +5Protein DesignProtein

  45. CrystalBoltz: End-to-End Protein Structure Determination via Experiment-Guided Diffusion for X-Ray Crystallography

    May 15, 2026Minseo Kim, Huanghao Mai, Jay Shenoy +3Crystallographic Plane IndicesProtein Data Bank

  46. DrugSAGE:Self-evolving Agent Experience for Efficient State-of-the-Art Drug Discovery

    May 14, 2026Yikun Zhang, Xiwei Cheng, Tianyu Liu +2Drug DiscoverySelf-Evolving Agents

  47. Controllable Molecular Generative Foundation Models

    May 14, 2026Yihan Zhu, Yuhan Liu, Weijiang Li +2Molecular GenerationGenerative Models

  48. Solvita: Enhancing Large Language Models for Competitive Programming via Agentic Evolution

    May 14, 2026Han Li, Jinyu Tian, Rili Feng +10Self-Evolving AgentsPrevious Machine-Learning-Based Implicit Solvent

  49. Composable Crystals: Controllable Materials Discovery via Concept Learning

    May 14, 2026Nian Liu, Yuwei Zeng, Ryoji Kubo +7CrystalData-Driven Materials Discovery

  50. Crys-JEPA: Accelerating Crystal Discovery via Embedding Screening and Generative Refinement

    May 14, 2026Nian Liu, Nikita Kazeev, Stephen Gregory Dale +8CrystalMolecular Generation

  51. All-atomistic Transferable Neural Potentials for Protein Solvation

    May 14, 2026Rishabh Dey, Salvina Sharipova, Konstantin PopovPrevious Machine-Learning-Based Implicit SolventNeural Solvers

  52. Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design

    May 14, 2026Ziyu Xu, Zijian Zhang, Liang Wang +4Drug DesignSpatial Transcriptomics

  53. CrystalReasoner: Reasoning and RL for Property-Conditioned Crystal Structure Generation

    May 14, 2026Yuyang Wu, Stefano Falletta, Delia McGrath +1Crystal StructureCrystallographic Plane Indices

  54. AIM-DDI: A Model-Agnostic Multimodal Integration Module for Drug-Drug Interaction Prediction

    May 14, 2026Yerin Park, Sangseon LeeDrug-Drug Interactions

  55. Reducing cross-sample prediction churn in scientific machine learning

    May 13, 2026Gordan Prastalo, Kevin Maik JablonkaCross ValidationChurn Prediction

  56. ENSEMBITS: an alphabet of protein conformational ensembles

    May 13, 2026Kaiwen Shi, Carlos OliverProtein Data BankConformational Ensembles

  57. Rethinking Molecular OOD Generalization via Target-Aware Source Selection

    May 13, 2026Zhuohao Lin, Kun Li, Jiameng Chen +4Drug DiscoveryOut-Of-Distribution

  58. Chem-GMNet: A Sphere-Native Geometric Transformer for Molecular Property Prediction

    May 13, 2026Deepak Warrier, Raja Sekhar PappalaMolecular Structure ElucidationMolecular Property Prediction

  59. CoRe-Gen: Robust Spectrum-to-Structure Generation under Imperfect Fingerprint Conditions

    May 13, 2026Tianbo Liu, Chixiang Lu, Jing Hao +4Tandem Mass SpectraMolecular Structure Elucidation

  60. A Non-Destructive Methodological Framework for Modernizing Legacy Clinical Reporting Systems for AI-Driven Pharmacoinformatics: A SAS Case Study

    May 13, 2026Jaime YanMedical Report GenerationClinical Notes