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Period ending 2026-09-21

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  1. Agentic Molecular Recovery via Molecule-Aware Exploration

    Jun 4, 2026Suwan Yoon, Changhee LeeMolecular Structure ElucidationAutonomous Exploration Strategies

  2. MolE-RAG: Molecular Structure-Enhanced Retrieval-Augmented Generation for Chemistry

    Jun 4, 2026Joey Chan, Wonbin Kweon, Ashley Shin +4Molecular Property PredictionVast Chemical Space

  3. What's in a Name? Morphological Shortcuts by LLMs in Pharmacology

    Jun 4, 2026Kaijie Mo, Thomas Yang, Chantal Shaib +6Drug-Drug InteractionsName

  4. AlloGen: Conformation-Selective Binder Generation with Differential State Scoring

    Jun 3, 2026Hanqun Cao, Zachary Quinn, Aastha Pal +4Conformational Ensembles

  5. ProHiFlo: Hierarchical Flow Matching with Functional Guidance for De Novo Protein Generation

    Jun 3, 2026Chuanzhen Wang, Meade Cleti, Pete JanoProtein DesignHierarchical Flow Matching

  6. SC3: The Multi-Solvent Solubility Challenge and Benchmark

    Jun 3, 2026Vansh Ramani, Har Ashish Arora, Dhairya Kuchhal +4Previous Machine-Learning-Based Implicit SolventComputational Chemistry

  7. From Answers to States: Verifiable Process-Level Evaluation of Chemical Reasoning in Large Language Models

    Jun 2, 2026Hongyu Guo, Hao Li, He Cao +2Vast Chemical Space

  8. Learning Topological Representations for Molecular Dynamics

    Jun 2, 2026Dominik Geng, Florian Graf, Martin Uray +1Molecular DynamicsProtein

  9. CP-Agent: Context-Aware Multimodal Reasoning for Cellular Morphological Profiling under Chemical Perturbations

    Jun 2, 2026Yuxin Zhang, Yiyao Li, Ping Shu Ho +3Drug DiscoveryMultimodal Agents

  10. Rethinking Molecular Text Representations for LLMs: An Empirical Study

    Jun 2, 2026Arun Raja, Garrett M. Morris, Kian Ming A. ChaiVast Chemical SpaceEmpirical Study

  11. Fairness Definitions and Metrics in Deep Reinforcement Learning for Drug Discovery in Healthcare: A Rapid Evidence Review

    Jun 1, 2026Esmaeil Shakeri, Ronnie de Souza Santos, Behrouz FarDrug DiscoveryHealthcare

  12. Towards Automated Discovery: A Review of Generative Models, Multimodal Learning and Closed-Loop Workflows in Inverse Materials Design

    Jun 1, 2026Anand Babu, Rogério Almeida Gouvêa, Gian-Marco RignaneseData-Driven Materials DiscoveryGenerative Inverse Design

  13. AgentPLM: Agentic Protein Language Models with Reasoning-Augmented Decoding for Protein Sequence Design

    Jun 1, 2026Sahil Rahman, Maxx Richard RahmanProtein DesignAntibody

  14. Hybrid Neural Ordinary Differential Equations for Data-Efficient Polymerization Modeling with Incomplete Kinetics

    Jun 1, 2026Marah Almanasreh, Alexander Mitsos, Eike CramerPolymerNeural Ordinary Differential Equations

  15. SpliceBind: Isoform-Aware Prediction of Binding Pocket Druggability

    Jun 1, 2026Bryan Cheng, Austin Jin, Joshua ChangStructure-Based Drug Design

  16. Improvise, Adapt, Overcome: An On-The-Fly Multifidelity Algorithm for Efficient Machine Learning

    Jun 1, 2026Vivin Vinod, Peter ZaspelComputational ChemistryQuantum Machine Learning

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

    Jun 1, 2026Lina Wang, Yaning CuiMolecular GenerationGenerative Models

  18. Learning Implicit Bias in Generative Spaces for Accelerating Protein Dynamics Emulation

    Jun 1, 2026Kaihui Cheng, Zhiqiang Cai, Wenkai Xiang +4EmulatorsProtein Data Bank

  19. Site4Drug: Predicting Drug-Binding Target Sites with an AI Agent

    Jun 1, 2026Taehan Kim, Sarrah Rose Mikhail Leung, Bharat Mekala +1Structure-Based Drug DesignMultimodal Search Agents

  20. Structure-Guided Adaptive Propagation for Protein-Protein Interaction Site Prediction

    Jun 1, 2026Enqiang Zhu, Yizi Liu, Yilong Luo +3ProteinGraph Neural Networks

  21. Demystifying Multimodal Biomolecular Co-design With Intrinsic Geodesic Coupling

    Jun 1, 2026Keyue Qiu, Xintong Wang, Zhilong Zhang +2Protein DesignStructure-Based Drug Design

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

    Jun 1, 2026Fang Wan, Jingxiang Qu, Yi LiuMolecular GenerationMolecular Graphs

  23. 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

  24. Leaf Spectral Reflectance Prediction Using Multi-Head Attention Neural Networks

    May 31, 2026Parastoo Farajpoor, Alireza Pourreza, Mohammadreza Narimani +2Spectral ReflectanceCanopy

  25. UniD3^3: A Knowledge Graph-Enhanced RAG Framework for Drug-Disease Discovery and Reasoning

    May 31, 2026Qing Wang, Tianshi Liu, Minghao Zhou +5Biomedical Knowledge GraphDrug Discovery

  26. Conditioned free-energy density of proteins using unbalanced solutions to constraint satisfaction problems

    May 31, 2026Pratik Worah, Subhash Khot, Srinivasa VaradhanConformational EnsemblesFree Energy Principle

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

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

  28. CryoProt: A Protein Pretraining Framework with Cross-Box Interactions on Cryo-EM Density Maps

    May 31, 2026Dan Luo, Xuan Lin, Peng Zhou +4Cryo-Electron MicroscopyProtein Data Bank

  29. Latent Diffusion Pretraining for Crystal Property Prediction

    May 30, 2026Shrimon Mukherjee, Kishalay Das, Partha Basuchowdhuri +2Crystal StructureCrystal

  30. Manifold Diffusion for Structure Generation of Transition Metal Complexes

    May 30, 2026Luca Schaufelberger, Kjell JornerMolecular GenerationData Generation

  31. Probe Before You Edit: Probing-Guided Molecular Optimization for LLM Agents in Structure-Based Drug Design

    May 30, 2026Zaifei Yang, Weiyu Chen, Yaqing Wang +1Structure-Based Drug DesignDrug Design

  32. Enhancing Protein-Protein Interaction Prediction with Hierarchical Motif-based Multimodal Protein Embedding

    May 30, 2026Zaifei Yang, Samuel Ping-Man Choi, James KwokProteinModality-Specific Encoders

  33. ProtStructQA: A Denotation Threshold in Protein Structural Reasoning

    May 30, 2026Aravind Mandiga, Guoming Li, Jin Lu +3Protein Data BankProtein

  34. Chem-PerturBridge: a harmonized compendium of small molecule perturbation transcriptomic effects

    May 29, 2026Artur Szałata, Olga Novitskaia, Maiia Shulman +3Single-Cell Perturbation PredictionSpatial Transcriptomics

  35. TadA-Bench: A Million-Variant Benchmark for Future-Round Discovery Toward Agentic Protein Engineering

    May 29, 2026Jin Gao, Juntu Zhao, Zirui Zeng +5Protein DesignLarge-Scale Benchmark

  36. AMix-2: Establishing Protein as a Native Modality in Large Language Models

    May 29, 2026Keyue Qiu, Yixin Wu, Lihao Wang +19Protein DesignProtein Data Bank

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

    May 29, 2026Thang Dang, Haderbache Amir, Tzanakakis Alexandros +1Crystallographic Plane IndicesMolecular Generation

  38. OOD-GraphLLM: Graph Large Language Model for Out-of-Distribution Generalized Drug Synergy Prediction

    May 28, 2026Xin Wang, Linxin Xiao, Yang Yao +1Drug-Drug InteractionsSynergy

  39. What drives performance in molecular MPNNs? An operator-level factorial benchmark

    May 28, 2026Panyu Jiao, Shuizhou Chen, Yiheng Shen +3Message Passing Neural NetworksMolecular Property Prediction

  40. OmniMatBench: A Human-Calibrated Multimodal Reasoning Benchmark Across 19 Materials Science Subfields

    May 28, 2026Wanhao Liu, Jiaqing Xie, Qian Tan +10Materials ScienceMultimodal Reasoning Benchmarks

  41. A Systematic Evaluation of Molecular Mixture Behavior Prediction

    May 28, 2026Roel J. Leenhouts, Nathan K. Morgan, William Green +2Molecular Property PredictionMixtures

  42. Mixing Vector Model for Copolymer Inference via Mixed Integer Linear Programming

    May 28, 2026Jianshen Zhu, Raveena Rai, Taiyo Sohkawa +4PolymerMolecular Property Prediction

  43. Traditional machine learning vs. deep learning from dynamic graph representations of proteins' 3D folds in the task of protein structure classification

    May 28, 2026Aydin Wells, Francis A. Gatsi, Aaron Striegel +1Protein Data BankProtein

  44. PROTOCOL: Late Interaction Retrieval for Protein Homolog Search

    May 27, 2026Gabrielle Cohn, Rohan Gumaste, Minh Hoang +1ProteinFeature Alignment

  45. Bridging Chemists and AI: An Expert-Augmented Framework for Interpretable Route Evaluation

    May 27, 2026Yujia Guo, Mikhail Kabeshov, Tat Hong Duong Le +6Vast Chemical SpaceAutomated Synthesis Techniques

  46. Evaluating the Realism of LLM-powered Social Agents: A Case Study of Reactions to Spanish Online News

    May 27, 2026Alejandro Buitrago López, Alberto Ortega Pastor, Javier Pastor-Galindo +1Large Language Model BiasImplicit Bias

  47. Thermodynamic properties of chemically disordered compounds via AI-driven estimation of partition function with the PULSE method

    May 27, 2026Baptiste Bernard, Luca Messina, Eiji Kawasaki +1ThermodynamicsBoltzmann Distributions

  48. Machine Learning methods for event classification and vertex reconstruction of the 12C + 12C reaction with the MATE-TPC

    May 27, 2026Minghui Zhang, Xiaobin Li, Jie Chen +11Nuclear DataBeamline

  49. AtomComposer: Discovering Chemical Space from First Principles with Reinforcement Learning

    May 27, 2026Bjarke Hastrup, Francois Cornet, Tejs Vegge +1Vast Chemical SpaceGenerative Models

  50. PhAME: Phenotype-Aware Molecular Editing via Latent Diffusion

    May 27, 2026Łukasz Janisiów, Sebastian Musiał, Bartosz Zieliński +2Molecular OptimizationDrug Design

  51. MACReD: A Multi-Agent Collaborative Reasoning Framework for Reaction Diagram Parsing

    May 27, 2026Chuang Tang, Chenhao Lin, Yin Xu +5ReactionDiagrams

  52. Computational Modeling of Antibody-Antigen Complexes: PLM-Based and MSA-Based Approaches

    May 27, 2026Xiao LuoAntibodyProtein

  53. From Detection to Mechanism: Cross-Attention Graph Neural Networks Enable Drug-Drug Interaction Type Prediction An Ablation Study with Acetylsalicylic Acid Validation

    May 27, 2026Juergen DietrichDrug-Drug InteractionsGraph Neural Networks

  54. MolLingo: Molecule-Native Representations for LLM-Powered Scientific Agents

    May 27, 2026Thao Nguyen, Heng JiStructure-Based Drug DesignAutoresearch

  55. SCENT: Aligning Mass Spectra with Molecular Structure for Olfactory Perception

    May 26, 2026Ziqi Zhang, Eunyeong Jin, Miguel Vasco +6Tandem Mass SpectraOlfactory Perception

  56. Periodic Topological Deep Learning for Polymer Design and Discovery

    May 26, 2026Yasharth Yadav, Tze Kwang Gerald Er, Atsushi Goto +1PolymerMolecular Property Prediction

  57. Self-Improvement Imitation with Biologically Guided Search for Protein Design Under Oracle Budgets

    May 26, 2026Ashima Khanna, Dominik GrimmProtein DesignCryptographically Authorized Mutation

  58. DGLD: Domain-Gated Latent Diffusion for the Discovery of Novel Energetic Materials

    May 26, 2026Yehudit Aperstein, Alexander ApartsinVast Chemical SpaceMolecular Structure Elucidation

  59. SurfDesign: Effective Protein Design on Molecular Surfaces

    May 25, 2026Fang Wu, Shuting Jin, Xiangru Tang +5Protein DesignGenerative Inverse Design

  60. Goal-driven Bayesian Optimal Experimental Design for Robust Decision-Making Under Model Uncertainty

    May 25, 2026Jinwoo Go, Xiaoning Qian, Byung-Jun YoonBayesian Experimental DesignOptimal Design