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Period ending 2026-09-21

18 new papers

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Period ending 2026-09-14

9 new papers

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Period ending 2026-09-07

13 new papers

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  1. Accurate, Interdisciplinary and Transparent Structure-property Understanding with Deep Native Structural Reasoning

    Jul 8, 2026Chen Tang, Yizhou Wang, Jianyu Wu +26Vast Chemical SpaceScientific Discovery

  2. A hierarchical memory architecture overcomes context limits in long-horizon multi-agent computational modeling

    Jul 8, 2026Shivendra G. Tewari, Holly KimkoLong-Horizon AgentsSingle-Agent Baselines

  3. Asymmetric Focal Loss Improves Graph Neural Network Prediction of Drug-Drug Interactions

    Jul 8, 2026Faranak Hatami, Mousa MoradiDrug-Drug InteractionsFocal Loss

  4. AbICL: In-Context Learning for Antigen-Specific Antibody Affinity Ranking

    Jul 7, 2026Zhiyuan Chen, Jing Hu, Junzhe Wang +4AntibodyStructure-Based Drug Design

  5. A Quiet Failure in Calibrated Virtual Screening: Marginal Conformal Prediction Under-Covers the Minority Class, and a Class-Conditional Fix Recovers It

    Jul 7, 2026Muhammadjon Tursunbadalov, Mustafojon TursunbadalovConformal PredictionMinority

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

    Jul 6, 2026Xujun Che, Xiuxia Du, Depeng XuTandem Mass SpectraMolecular Structure Elucidation

  7. URSA: Chemistry-Aware Benchmark for Utilitarian Retrosynthesis Assessment

    Jul 6, 2026Bogdan Zagribelnyy, Ivan Ilin, Nikita Bondarev +7Vast Chemical SpaceDrug Discovery

  8. Folding, Reasoning, and Scaling with Open-source Drug Discovery Engine

    Jul 4, 2026Aureka AI OpenDDE projectDrug DiscoveryFolding

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

    Jul 3, 2026Emmanuel Bengio, Sanjeev Raja, Yui Tik Pang +5Molecular DynamicsPrevious Machine-Learning-Based Implicit Solvent

  10. Design-CP: Context Parallelism for Design of Protein Nanoparticles

    Jul 3, 2026Lorenzo Tarricone, Helen E. Eisenach, Aiko Muraishi +1Protein DesignMulti-Gpu Systems

  11. Back to Basics: Improving Molecular Understanding in LLMs via SMILES-Graph Translation

    Jul 3, 2026Wenda Wang, Jinjia Feng, Zhewei WeiMolecular Structure ElucidationGraph Language Models

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

    Jul 3, 2026Yujin Kim, Charmgil HongDrug DiscoveryDrug-Drug Interactions

  13. CoFEND: A Cross-Modal Fusion End-to-End Network for Cold-Start Drug-Drug Interaction Prediction

    Jul 3, 2026Di Wu, Hongyi Sun, Haichao Xu +3Drug-Drug InteractionsClinical Prediction

  14. Recovering Candidate Circadian Regulators of Arrhythmic Pituitary Hormone Genes Using Reliability-Weighted Magnetic Laplacian with rwMagLap

    Jul 3, 2026Shabnam Sodagari, Nick JaspersonGene-Regulatory NetworksDrug-Drug Interactions

  15. On the Design Space of Discrete Diffusion Online Adaptation for Molecular Optimization

    Jul 3, 2026Trevor Chen, Ariel Dai, Jason Yang +8Molecular OptimizationDiffusion Processes

  16. Q-Score: A Quantum-Native Scoring Function for Molecular Docking

    Jul 2, 2026Kangyu Zheng, Yidong Zhou, Ruihao Li +3Structure-Based Drug DesignQuantum Approximate Optimization Algorithm

  17. An Additive MLP-GNN Framework for Characterizing Chemical and Structural Contributions to Aqueous Solubility

    Jul 2, 2026Sampreeti Bhattacharya, Arkaprava RoyPrevious Machine-Learning-Based Implicit SolventMolecular Property Prediction

  18. Probing Chemical Language Models: Effects of Pre-training and Fine-tuning

    Jul 2, 2026Anna Karnysheva, Dietrich Klakow, Ji-Ung LeeMolecular Structure ElucidationModel Pretraining

  19. MolSight: A Graph-Aware Vision-Language Model for Unified Chemical Image Understanding

    Jul 2, 2026Wenda Wang, Yihan Tong, Yuwei Hu +1Molecular GraphsLarge Vision Language Models

  20. MKGR: Multimodal Knowledge-Graph Representation Learning for Cold-Start Protein-Protein Interaction Prediction

    Jul 2, 2026Wenbo ZhangProteinBiomedical Knowledge Graph

  21. From Monolingual to Multilingual: Evaluating Mamba for ASR in South African Languages

    Jul 1, 2026Jesujoba O. Alabi, Julian Herreilers, Badr M. Abdullah +1Multilingual Automatic Speech RecognitionAfrican Languages

  22. Agentic generation of verifiable rules for deterministic, self-expanding reaction classification

    Jul 1, 2026Daniel Armstrong, Maarten Dobbelaere, Valentas Olikauskas +4ReactionVast Chemical Space

  23. Diffeomorphic Optimization

    Jul 1, 2026Ludwig Winkler, Andrew Leaver-Fay, Joseph Kleinhenz +1Protein DesignManifolds

  24. Active-GRPO: Adaptive Imitation and Self-Improving Reasoning for Molecular Optimization

    Jul 1, 2026Xuefeng Liu, Mingxuan Cao, Qinan Huang +3Molecular OptimizationGroup Relative Policy Optimization

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

    Jul 1, 2026Tong Xu, Xinzhe Cao, Zhihui Zhu +2Safety EvaluationSafety

  26. CryoACE: An Atom-centric Framework for Accurate and Automated Model Building in Cryo-EM

    Jun 30, 2026Minzhang Li, Mingrui Li, Weichen Qin +5Cryo-Electron MicroscopyConformational Ensembles

  27. Can Tabular In-Context Learners Generalize to Biomolecular Property Prediction?

    Jun 30, 2026Davy Guan, Lu Zhang, Asiri Wijesinghe +7Molecular Property PredictionTabular Foundation Models

  28. DDIAgents: Mechanism-Conditioned Context Flow for Drug-Drug Interaction Prediction

    Jun 30, 2026Zhenqian Shen, Yu Liu, Xiaoyi Fu +1Drug-Drug InteractionsMulti-Agent Reasoning

  29. ElemeNet: Multiscale Molecular Machine Learning with Uncertainty Quantification Across the Periodic Table

    Jun 29, 2026Jacob W. Toney, Samir Darouich, Yiran Wang +3Molecular Property PredictionAtoms

  30. ReactionAtlas: Ab origine exploration of chemical reaction networks with machine learning

    Jun 29, 2026Stefan Gugler, Max Eissler, Khaled Kahouli +1Vast Chemical SpaceAutonomous Exploration Strategies

  31. Bridging the NISQ and Fault-Tolerant Regimes: Generative-ML-Assisted Quantum Selected CI for Molecular Simulations

    Jun 29, 2026Anurag K. S. V., Ashish Kumar Patra, Manas Mukherjee +4Computational ChemistryStructure-Based Drug Design

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

    Jun 29, 2026Matthias Blaschke, Daniel Kienzle, Zsuzsanna Koczor-Benda +3Molecular OptimizationDrug Discovery

  33. Towards Generalizable and Evidential Nuclear Magnetic Resonance-Based Molecular Structure Elucidation via Large Language Model Agent

    Jun 29, 2026Zheng Fang, Chen Yang, Yusen Tan +9Molecular Structure ElucidationVast Chemical Space

  34. Modeling Cell-Cycle-Aware Single-Cell Drug Perturbation Responses

    Jun 29, 2026Dingping Zhao, Jie Lin, Feng Xu +1Single-Cell Perturbation PredictionDrug-Drug Interactions

  35. Geometric Algebra Meets Cartesian Tensors: Higher-Order Equivariance for Interatomic Potentials

    Jun 28, 2026Can Polat, Erchin Serpedin, Mustafa Kurban +1Interatomic PotentialsCosine Similarity

  36. Unsupervised Thermodynamics of Molecular Diffusion Models: Action-Operator Semantics and Auditable Free-Energy Readout

    Jun 28, 2026Wenjie XiDiffusion DynamicsThermodynamics

  37. GLACIER: Rethinking Mass Spectrum Prediction as an Object Detection Problem

    Jun 28, 2026Rui-Xi Wang, Runzhong Wang, Connor W. ColeyTandem Mass SpectraMolecular Structure Elucidation

  38. Few-Step Boltzmann Generators via Scalable Likelihood Flow Maps

    Jun 27, 2026RuiKang OuYang, Hanlin Yu, Xinyue Ai +7Generative Flow NetworksBoltzmann Distributions

  39. Transformer-Based Active Learning for Data-Efficient Vaccine Epitope Selection in PRRS

    Jun 27, 2026Aspen Erlandsson Brisebois, Zahed Khatooni, Connor Burbridge +5Epitope PredictionActive Learning

  40. Surrogate-Gated Generation and Foundation-Model Embeddings for Bayesian Materials Design

    Jun 26, 2026Sk Md Ahnaf Akif Alvi, Jan Janssen, Danny Perez +2Data-Driven Materials DiscoveryCrystal

  41. Two-Stage Fine-Tuning for Protein Sequence Generation with Targeted Amino-Acid Composition

    Jun 26, 2026Violeta Basten-Romero, Rubén Muñoz-Tafalla, Anna María Díaz-Rovira +3Protein DesignSequence Modeling

  42. Pepti-drift: Toxicity-Repulsive Drifting for Antigen-Conditioned Discrete Peptide Generation

    Jun 26, 2026Takashi Fujiwara, Hikaru Shindo, Kaushalya Madhawa +2Cyclic PeptidesMolecular Property Prediction

  43. Reduction of Probabilistic Chemical Reaction Networks

    Jun 26, 2026Mauricio Montes, Gregoire Sergeant-PerthuisBayesian NetworksReaction

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

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

  45. PairSAE: Mechanistic Interpretability from Pair Representations in Protein Co-Folding

    Jun 25, 2026Giosue Migliorini, Aristofanis Rontogiannis, Grigori Guitchounts +3Protein Data BankProtein

  46. Autoregressive Boltzmann Generators

    Jun 25, 2026Danyal Rehman, Charlie B. Tan, Yoshua Bengio +2Autoregressive GenerationBoltzmann Distributions

  47. Target-Aware Bandit Allocation for Scalable Surrogate Optimization in Chemical Space

    Jun 25, 2026Mohammad Haddadnia, Yuvan Chali, Abhilash Jayaraj +4Bayesian OptimizationDrug Design

  48. Implementation of reinforcement learning in chemical reaction networks: application to phototaxis as curiosity-driven exploration

    Jun 24, 2026Ruyi Tang, Grégoire Sergeant-Perthuis, David ColliauxPartially Observable Markov Decision ProcessReaction

  49. Scalable Peptide Design via Memory-Efficient Equivariant Transformer

    Jun 23, 2026Rui Jiao, Xiangzhe Kong, Yinjun Jia +4Cyclic PeptidesVariational Autoencoder

  50. Uncertainty-aware reinforcement learning for chemical language models

    Jun 23, 2026Borja Medina, Jon Paul JanetLarge Language Model UncertaintyUncertainty-Aware Inference

  51. ConSolv: Solvent-Conditional Machine Learning Implicit Solvent Potential

    Jun 23, 2026Linying Zhang, Julija ZavadlavPrevious Machine-Learning-Based Implicit SolventMachine Learning

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

    Jun 22, 2026Konstantin Yatsenko, Arvind ThiagarajanMolecular GenerationDrug Design

  53. Rethinking Molecular Graph Backdoors under Chemistry-aware Admission

    Jun 22, 2026Thinh T. H. Nguyen, Sze Jue Yang, Khoa D. Doan +2Molecular GraphsBackdoor Attacks

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

    Jun 22, 2026Masahiro Negishi, Aron WalshCrystal StructureCrystal

  55. Closed-loop Auto Research for Molecular Property Prediction: Discovering and Certifying Generalizable Improvements

    Jun 22, 2026Jingjie Ning, Xiaochuan Li, Ji Zeng +2Molecular Property PredictionAutoresearch

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

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

  57. Mitigating Measurement-Induced Training Instability in Hybrid Quantum Neural Networks for Protein Classification

    Jun 21, 2026Milton Mondal, Sushovan Chanda, Mohamad Mahdi Alawieh +6Hybrid Quantum Neural NetworksLogit Lens

  58. Multigrid Training for Molecular Generation using Graph Neural Networks

    Jun 21, 2026Zixuan Ling, Paula Mercurio, Di LiuMolecular GenerationVariational Autoencoder

  59. Enhancing Protein Representation Learning via Manifold Restore Mixing

    Jun 21, 2026Yizhou Dang, Chuang Zhao, Lianbo Ma +3Protein Data BankSynthetic Data Augmentation

  60. Protein contacts are already in the attention: a single-forward-pass alternative to the Categorical Jacobian

    Jun 20, 2026Rome ThorstensonProteinJacobian