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Period ending 2026-09-21

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  1. Mat-Pref: Verifiable-Reward Training Improves Compositional Reasoning in Inorganic Materials

    Jun 20, 2026Sarrah R. Mikhail Leung, Taehan Kim, Jeongbin ParkVast Chemical SpaceVerifiable Rewards

  2. QBioFusion-QSAR: Morgan-Anchored Quantum Multiple Kernel Learning for Small-Data Ligand Classification

    Jun 19, 2026Azadeh Alavi, Fatemeh Kouchmeshki, Muhammad Usman +1Quantum KernelsStructure-Based Drug Design

  3. MMGNN: Multi-level, multi-color graph neural networks for molecular property prediction

    Jun 18, 2026Trung Nguyen, Duc Duy NguyenMolecular Property PredictionMolecular Structure Elucidation

  4. A large-scale foundation model enables simulation-to-real adaptation for nuclear magnetic resonance-based molecular structure analysis

    Jun 18, 2026Chen Yang, Zheng Fang, Hanyu Sun +7Molecular Structure ElucidationWireless Foundation Models

  5. Calibrating Generative Models to Feature Distributions with MMD Finetuning

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

  6. TxBench-PP: Analyzing AI Agent Performance on Small-Molecule Preclinical Pharmacology

    Jun 17, 2026Hannah Le, Ramesh Ramasamy, Alex Urrutia +3Drug Design

  7. AdsMind: A Physics-Grounded Multi-Agent System for Self-Correcting Discovery of Adsorption Configurations on Heterogeneous Catalyst Surfaces

    Jun 17, 2026Zongmin Zhang, Yuyang Lou, Bowen Zhang +6Heterogeneous CatalysisVast Chemical Space

  8. Be Your Own Teacher: Steering Protein Language Models via Unsupervised Reward Optimization

    Jun 17, 2026Lanqing Li, Shentong Mo, Yang Yu +1Protein DesignSteering

  9. Protein-Based Fish Species Identification: Dataset, Models, and Insights from Native Bangladeshi Fish

    Jun 16, 2026Md Nasiat Hasan Fahim, Md. Abid Ullah Muhib, Mohammad Shahidur RahmanFishProtein Data Bank

  10. Toward Controllable Catalyst Inverse Design via Large-Scale Autoregressive Pretraining

    Jun 16, 2026Dong Hyeon Mok, Jonggeol Na, Seoin BackHeterogeneous CatalysisMolecular Generation

  11. Latent space mapping of interpretable structural coordinates from stochastic single-molecule signals

    Jun 15, 2026Matteo Cartiglia, Sandro Kuppel, Wouter Botermans Wannes Peeters +7Multimodal Physiological SignalsMolecular Structure Elucidation

  12. Agentic Discovery of Non-Canonical Antimicrobial Peptides with AMPGAN v3

    Jun 15, 2026Jay Jung, Xiaohan Zhang, Shenghan Song +8Cyclic Peptides

  13. Learning Hybrid Biophysical Neuron Models with Neural ODEs

    Jun 15, 2026Jonas Beck, Michael Deistler, Dóra Viktória Molnár +2Neural Ordinary Differential EquationsDynamics Models

  14. BRICKS-WM: Building Reusability via Interface Composition Kinetics for Structured World Models

    Jun 15, 2026Shaowei Zhang, Jiahan Cao, Xunlan Zhou +2World ModelsLatent Dynamics

  15. DeepRoot: A KG-Coordinated Multi-Agent System for Therapeutic Reasoning over Historical Medical Texts

    Jun 14, 2026Zijian Carl Ma, Sean J. Wang, Sijbren Kramer +1Biomedical Knowledge GraphClinical Reasoning

  16. Pepti-Agent: An AI Agent for Peptide Design and Optimization

    Jun 13, 2026Houxu Chen, Achuth Chandrasekhar, Amir Barati FarimaniCyclic PeptidesCryptographically Authorized Mutation

  17. PepALD: Macrocyclic Peptide Generation via Autoregressive Latent Diffusion

    Jun 12, 2026Junming Zhang, Siyu Yi, Wei Ju +1Cyclic PeptidesMolecular Generation

  18. Emyx: Fast and efficient all-atom protein generation

    Jun 12, 2026Nicholas J. Williams, Ward Haddadin, Matteo P. Ferla +6Protein DesignProtein

  19. Where Black-box Drug-Target Interaction Prediction Models Look: Cross-Method Explainability

    Jun 12, 2026Ali Vefghi, Zahed Rahmati, Mohammad AkbariDrug-Drug InteractionsExplainability

  20. Curvature-Informed Potential Energy Surface for Protein-Ligand Binding Affinity Prediction

    Jun 12, 2026Peng-Fei Sun, Chuan-Xian Ren, Hong YanStructure-Based Drug DesignConformational Ensembles

  21. Protein Representation Learning with Secondary-Structure and Energy-Filtered Hydrogen-Bond Graphs

    Jun 12, 2026Mohamed Mouhajir, Limei Wang, El Houcine Bergou +3Protein Data BankProtein

  22. Curvature-Guided Geometric Representation for Protein-Ligand Binding Affinity Prediction

    Jun 12, 2026Shuai Li, Chuan-Xian Ren, Yuhao Li +4Structure-Based Drug Design

  23. Applicability Condition Extraction for Therapeutic Drug-Disease Relations

    Jun 12, 2026Guanting Luo, Noriki Nishida, Yuji Matsumoto +1Biomedical TextDrug-Drug Interactions

  24. XRDiff: Crystal Structure Prediction from Powder X-Ray Diffraction Data Using Diffusion Models

    Jun 12, 2026Nofit Segal, Mingda Li, Benjamin Kurt Miller +1Crystallographic Plane IndicesCryo-Electron Microscopy

  25. Smoothing Dark Areas in Molecular Latent Diffusion

    Jun 11, 2026Xi Wang, Jiahan Li, Yuxuan Xia +3Molecular GenerationVariational Autoencoder

  26. Uncertainty Estimation for Molecular Diffusion Models

    Jun 11, 2026Paul Seij, Christian A. Naesseth, Stephan Mandt +1Diffusion DynamicsMolecular Generation

  27. A green solvent screening tool for emerging materials via uncertainty aware, transformer enhanced transfer learning

    Jun 11, 2026Ioannis Kouroudis, Simon Ternes, Zhaosu Gu +5Previous Machine-Learning-Based Implicit SolventData-Driven Materials Discovery

  28. APCyc: Property-Informed Design of Cyclic Peptides via Automated Cyclization

    Jun 11, 2026Yifan Zhao, Lang Qin, Jintai ChenCyclic PeptidesDrug Discovery

  29. Physics-Informed Neural Networks for Chemotherapy Pharmacokinetics: Benchmarking the Clinical Estimator and Exposing Parameter Identifiability

    Jun 10, 2026Riya Bisht, Dhruv AgarwalDrug-Drug InteractionsIdentifiability

  30. Physics-Aware Auxiliary Losses Improve Out-of-Distribution Generalization of a GNN Synthesizability Filter

    Jun 10, 2026Riya Bisht, Dhruv AgarwalOut-Of-DistributionGraph Neural Networks

  31. The Metric Picks the Winner: Evaluation Choice Flips Model Rankings for Drug-Response Prediction in Unseen Chemistry

    Jun 10, 2026Dhruv Agarwal, Riya BishtDrug-Drug InteractionsClinical Prediction

  32. MARD: Mirror-Augmented Reasoning Distillation for Mechanism-Level Drug-Drug Interaction Prediction

    Jun 10, 2026Mohammadreza Riyazat, Vian Lelo, Rameen Jafri +2Drug-Drug InteractionsMemorization

  33. Adjoint Method versus Physics-Informed Neural Networks in PDE-Constrained Inverse Problems

    Jun 10, 2026Zhen Zhang, Alessandro Alla, George Em KarniadakisConventional Physics-Informed Neural NetworksIll-Posed Inverse Problem

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

    Jun 10, 2026Wang Rui, Liu DinghaoMolecular GenerationDrug-Drug Interactions

  35. MemNovo: Look Back at the Spectrum for Balanced De Novo Peptide Sequencing from Mass Spectrometry

    Jun 10, 2026Dongxin Lyu, Jingbo Zhou, Hongxin Xiang +2Cyclic PeptidesTandem Mass Spectra

  36. DeepRHP: A Hybrid Variational Autoencoder for Designing Random Heteropolymers as Protein Mimics

    Jun 10, 2026Shuni Li, Zhiyuan Ruan, Andy Shen +3Protein DesignPolymer

  37. Probabilistic Contrastive Pretraining for Multi-task ADME Property Prediction

    Jun 9, 2026Yifan Xue, Srimukh Prasad Veccham, Saee Paliwal +2Molecular Property PredictionDrug-Drug Interactions

  38. GLACIER: A Multimodal Student-Teacher Foundation Model for Molecular Property Prediction

    Jun 9, 2026Emily Nguyen, Yongchan Hong, Harsh Toshniwal +2Molecular Property PredictionVast Chemical Space

  39. Flexible Kernels for Protein Property Prediction

    Jun 9, 2026Martin Jankowiak, Yerdos Ordabayev, Rudraksh Tuwani +4Protein Data BankProtein Design

  40. Physics-Constrained Neural Surrogate for Domain Growth Prediction in Systems with Conserved Kinetics

    Jun 9, 2026Vijay Yadav, Pallvi Pandey, Madhu Priya +2Physics-Guided Deep Learning FrameworkPorous Media

  41. Unsupervised Deep Learning for Limited-Angle STEM-EDX Tomography -- Application to 3D Chemical Analysis of Phase-Change Memory Devices

    Jun 9, 2026Daniel del Pozo Bueno, Serge Brosset, Theo Monniez +3Transmission Electron MicroscopyTomography

  42. Flexible Flows for Biological Sequence Design

    Jun 9, 2026Yogesh Verma, Dani Korpela, Harri Lähdesmäki +1Protein DesignGenerative Flow Networks

  43. My Chemical Harness: Evolutionary Molecular Design over Synthetic Pathways with Large Language Model Agents

    Jun 8, 2026César Ojeda, Darius A. Faroughy, Maryam Karimi +3Vast Chemical SpaceLarge Language

  44. VFUSE: Virulent Feature Understanding with Sparse autoEncoders

    Jun 8, 2026Michael Yu, Matthew L. OlsonProtein DesignMechanistic Interpretability

  45. In-Context Learning for Latent Space Bayesian Optimization

    Jun 8, 2026Tuan A. Vu, Harri Lähdesmäki, Julien MartinelliBayesian OptimizationMolecular Optimization

  46. Automating the Expert Eye: A System-Agnostic Deep Learning Framework for Rare Event Discovery in Imbalanced Force Spectroscopy

    Jun 8, 2026Jorge Rodriguez-RamosMicroscopyDeep Learning Framework

  47. Closing the Prior-Posterior Loop: Self-Reflective Molecular Design with Analysis-Driven LLM Iteration

    Jun 8, 2026Junyi Gong, Zijie Qiu, Ben Zhong TangStructure-Based Drug DesignLarge Language Model Backbones

  48. Loss-Guided Adaptive Scale Refinement for Molecular Force Prediction

    Jun 8, 2026Limin YuMolecular DynamicsMolecular Property Prediction

  49. A systematic investigation of molecular encoding methods for drug property predictions across neural network and Transformer encoder-based model

    Jun 8, 2026Sheng-Ya Chen, Shan-Ju YehMolecular Property PredictionMechanistic Interpretability

  50. Active Flow Expansion for Out-of-Distribution Discovery: from Theory to Molecules

    Jun 7, 2026Riccardo De Santi, Bruce Lee, Cristian Perez Jensen +6Generative Flow NetworksMolecular Generation

  51. Few-step Cofolding with All-Atom Flow Maps

    Jun 7, 2026Gianluca Scarpellini, Ron Shprints, Peter Holderrieth +7Conformational EnsemblesStructure-Based Drug Design

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

    Jun 6, 2026Haozhe Huang, Manuel Gonzalez Lastre, Hyun Suk Park +3Molecular GenerationVast Chemical Space

  53. Constraint-Aware Optimization for Robust Protein Stability Prediction

    Jun 6, 2026A Shivram, Aneesh S. Chivukula, Manik Gupta +1Protein Data BankCryptographically Authorized Mutation

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

    Jun 5, 2026Zhan'ao Yao, Boxuan Zhang, Jingyuan Shu +10Data-Driven Materials DiscoveryMaterials Science

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

    Jun 5, 2026Malte Franke, Stefan P. Schmid, Zarko Ivkovic +2Molecular GenerationGenerative Models

  56. Pharmacogenomic Knowledge Graph Augmentation for Graph Neural Network-Based Drug-Drug Interaction Prediction

    Jun 5, 2026Juergen DietrichDrug-Drug InteractionsMetabolic

  57. ShallowBench: Benchmarking Generative Drug Design Models on Shallow-Pocket Targets

    Jun 4, 2026Saket Reddy, Shiwei LiuStructure-Based Drug DesignDrug Discovery

  58. End-to-End Subgraph Detection with GraphDETR

    Jun 4, 2026Dexiong Chen, Till Hendrik Schulz, Karsten BorgwardtSubgraphsGraph Neural Networks

  59. Reactive Flux Matching: Mechanism Discovery and Adaptive Sampling of Rare Events

    Jun 4, 2026Rishal Aggarwal, David Ryan Koes, Nicholas M. Boffi +1Conditional Flow MatchingReaction

  60. Unsupervised Pattern Analysis in Japanese Veterinary Toxicology: A Regulatory-Compliant Framework for Cross-Species Risk Assessment

    Jun 4, 2026Yukiko Kawakami, Mohammad Shirazi, Ryo Shimizuwa +3Drug-Drug InteractionsRegulation