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  1. MEGA-CL: A Molecular Foundation Model for Generalizable ADMET Prediction through Graph External Attention and Contrastive Learning

    Jul 27, 2026Tinghui Jin, Kedu Jin, Ying Li +8Drug-Drug InteractionsDrug Discovery

  2. MS-GPT: Rethinking MS/MS De Novo Structure Elucidation as Spectrum-Induced Posterior Querying of a Molecule-Language Model

    Jul 26, 2026Xin Zhao, Yumin Liu, Zhuo Li +5Tandem Mass SpectraMolecular Structure Elucidation

  3. Neonatal Hypoxic-ischaemic Encephalopathy Classification from the EEG and HRV Signals Using a Conformer based Masked Autoencoder

    Jul 26, 2026Shuwen Yu, William P Marnane, Geraldine B. Boylan +1Masked AutoencodersHeart Rate

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

    Jul 26, 2026Hengyuan Cao, Shizhuo Cheng, Mingxuan Liu +5Protein DesignConformational Ensembles

  5. A Multi-stage Constrained Optimization Framework for Data-driven Problems

    Jul 26, 2026Ye ShiConstrained OptimizationVariational Autoencoder

  6. PerturbPFN: Probing the Limits of Synthetic Priors in Drug Perturbation Modelling

    Jul 26, 2026Yuche Gao, José Miguel Hernández-Lobato, Siyuan GuoSingle-Cell Perturbation PredictionDrug-Drug Interactions

  7. Learning to Prepare Molecular Ground States with Transformer Models

    Jul 24, 2026Alex Koziell-Pipe, Jasmine Brewer, Jem Guhit +14Quantum Circuit SimulationN$-Qubit Stabilizer States

  8. Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs

    Jul 24, 2026Zhangzhi Xiong, Minzhang Li, Haotian Yu +6Protein Data BankFeature Alignment

  9. Closed-Loop Generative Selection: Convergence, Memory, and Noisy Oracles

    Jul 24, 2026Konstantin Fackeldey, Christof SchütteDrug DesignSharp Joint-Kl Oracle Theory

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

    Jul 24, 2026Yuliang Yan, Shuo Yan, Haochun Tang +2Structure-Based Drug DesignMolecular Generation

  11. LC-SEPLM: long-range contact-supervised adaptation for sequence-only protein representation learning

    Jul 24, 2026Chen Wang, Boming Kang, Qinghua CuiProtein Data BankSequence Modeling

  12. LatentFlow: Visual Analytics for Latent Space Analysis in Molecular Graph Neural Networks

    Jul 24, 2026Shiyi Liu, Jiaqing Chen, Nicholas Hadler +6Graph Neural NetworksVast Chemical Space

  13. Graph-Theoretic Neural Network Fragmentation with Covariant Direct Molecular Force Learning: Enabling Coupled-Cluster Accuracy AIMD for Fluxional Systems

    Jul 23, 2026Xiao Zhu, Srinivasan S. IyengarMolecular DynamicsComputational Chemistry

  14. Graph Learning on Ensembles of Cyclic Peptides: An Investigation of Molecular Ensemble Modeling

    Jul 23, 2026Aaron Feller, Kris Deibler, Maxim SecorCyclic PeptidesConformational Ensembles

  15. M3^3-Gen: Interpretable Multimodal Generation of Gene Expression Profiles Using Clinical and Imaging Data

    Jul 23, 2026Francesca Pia Panaccione, Carlo Sgaravatti, Marco VenereMultimodal Clinical DataCancer Genome Atlas

  16. Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad

    Jul 23, 2026Jiatong Li, Yuxuan Ren, Weida Wang +2Molecular Structure ElucidationHallucinations

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

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

  18. Machine-Learned Compact Subspace Generation for Quantum Selected Configuration Interaction within Density Matrix Embedding Framework

    Jul 22, 2026Ashish Kumar Patra, Anurag K. S. V., Ruchika Bhat +3Computational ChemistryStructure-Based Drug Design

  19. MOF-Sleuth: Tool-Grounded Reward Alignment for Explainable Fine-Grained MOF CIF Auditing

    Jul 22, 2026Yu Liu, Zhiwei Yang, Diandian Guo +7Vast Chemical SpaceMllm-Based

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

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

  21. Boltzmann-Expected Molecular Design with Decoupled Annealing Flows

    Jul 21, 2026Selma Moqvist, Richard Beckmann, Ross Irwin +2Molecular GenerationBoltzmann Distributions

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

    Jul 21, 2026Yiming Qin, Kai Yi, Miruna Cretu +3Structure-Based Drug DesignMolecular Structure Elucidation

  23. Predicting Activities in Aqueous Electrolyte Solutions with Hybrid Machine Learning

    Jul 21, 2026Zeno Romero, Maximilian Kohns, Fabian JirasekMolecular Property PredictionMachine Learning

  24. Towards chemistries in dynamical systems

    Jul 21, 2026Martin Biehl, Nathaniel VirgoDynamical SystemsReaction

  25. Adopting Reinforcement Learning with Verifiable Rewards for Molecular Generation

    Jul 21, 2026Mingxuan Ouyang, Hao Lan, Wanyu LinMolecular GenerationVerifiable Rewards

  26. ABOPD: Antibody CDR Design via On-Policy Distillation

    Jul 21, 2026Zhuo Yang, Jiaying He, Jiaqing Xie +5AntibodyProtein Design

  27. Do AI-Native Biotechs Need Departments? Benchmarking Company World Models for AI-Driven Drug Development

    Jul 21, 2026Yinan WangAi-RanDrug Discovery

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

    Jul 20, 2026Tasfia Nuzhat Ornee, Elias Hossain, Ivan Garibay +1Molecular GraphsMotif

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

    Jul 20, 2026Thomas MacDougall, Maksim Kuznetsov, Roman Schutski +5Molecular GenerationDrug Design

  30. Chemical filters for ultra-high-throughput materials screening and generation

    Jul 20, 2026Kinga O. Mastej, Panyalak Detrattanawichai, Hyunsoo Park +3Vast Chemical SpaceMolecular Generation

  31. Trustworthy Protein-Ligand Binding Affinity Prediction via Reliability-Aware Multi-Engine Fusion

    Jul 20, 2026Yongchan Hong, Defu Cao, Wenjin Liu +6Structure-Based Drug DesignClinical Prediction

  32. Grounded verification of chemical and materials reasoning: detection is the bottleneck

    Jul 19, 2026Can Polat, Mustafa Kurban, Erchin Serpedin +1VerifierVast Chemical Space

  33. CORAL: Learning Amyloid Fibril Ligand Docking with Cooperative Binding Rewards

    Jul 19, 2026Yasheng Sun, Bohan Li, Youqi Tao +1Structure-Based Drug Design

  34. ChemHyperMag: Physics-informed magnetic hypergraph learning improves molecular ADMET prediction

    Jul 19, 2026Hexiao Ding, Hongzhao Chen, Jing Lan +12Molecular Property PredictionMolecular Graphs

  35. Neural spectroscopy of AlphaFold2 reveals encoded protein conformational landscapes

    Jul 17, 2026Kaustav MehtaConformational EnsemblesProtein Data Bank

  36. StructureClaw: Traceable LLM Agents and an Executable Benchmark for Structural Engineering Workflows

    Jul 16, 2026Sizhong Qin, Yi Gu, Yao Jiang +13EngineeringWorkflow Automation and Optimization

  37. Implementations of Quantum and Classical Topology-Aligned Architectures for Molecular Property Prediction

    Jul 15, 2026James T. Pegg, Hubert Okadome Valencia, Ronin WuQuantum Machine LearningComputational Chemistry

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

    Jul 14, 2026Daria A. Ryabchenko, Pavel Gurevich, Shamil Kadyrov +5Molecular GenerationDrug Discovery

  39. CoDiffGRN: Rethinking Gene Regulatory Network Inference via the BEELINE-KGC Benchmark and Co-evolutionary Discrete Diffusion

    Jul 14, 2026Jiaze Song, Runhao Zhao, Minghao Xu +2Gene-Regulatory NetworksBiomedical Knowledge Graph

  40. Learning Mechanistic Reasoning for Chemical Reactions with Large Language Models

    Jul 14, 2026Xingyu Dang, Haocheng Tang, Junmei Wang +1ReactionLarge Language Model Reasoning

  41. Improving Molecular Property Prediction in Small Language Models Using Graph-based Tools

    Jul 14, 2026Konstantinos Bougiatiotis, Dimitrios Kelesis, Georgios PaliourasMolecular Property PredictionSmall Language Models

  42. Sample Efficient Generative Optimization for Molecular Design

    Jul 14, 2026Sarina Kopf, Cristina Nevado, Philippe SchwallerMolecular OptimizationBayesian Optimization

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

    Jul 14, 2026Yuxuan Ren, Fan Yang, Jianhua Yao +1Molecular GenerationMasked Autoencoders

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

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

  45. CatRetriever: Contrastive Representation Learning for Slab-to-Bulk Retrieval in Generative Catalyst Discovery

    Jul 13, 2026Jungho Oh, Woosung Kim, Dong Hyeon Mok +2Heterogeneous CatalysisVast Chemical Space

  46. Q2SAR\mathtt{Q^2SAR}: overcoming classical bottlenecks in drug discovery via quantum multiple kernel learning

    Jul 13, 2026Mariano Caruso, Daniel Ruiz, Alejandro Giraldo +1Quantum KernelsDrug Discovery

  47. Advancing Optimal Subset Oracle via Learning Relaxation of Neural Set Functions

    Jul 13, 2026Yongquan Shi, Zijing Ou, Shiping Wang +1Variational InferenceTime-Step-Wise Learnable Surrogate Gradient Function

  48. AutoMatBench: An Automatic Optimization Toolkit for the Acceleration of Material Properties Prediction Benchmarking

    Jul 13, 2026Hongxiao Li, Wanling GaoData-Driven Materials DiscoveryMle-Bench Lite

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

    Jul 13, 2026Hang Yuan, Chen Li, Wenjun Ma +2Molecular GenerationSpatial Transcriptomics

  50. Adapting Evidential Neural Networks to Test-Time Neighbor Fusion Improves Molecular Property Prediction

    Jul 13, 2026Cameron Gruich, Weichi Yao, Yixin Wang +1Molecular Property PredictionEvidential Learning

  51. Transferable Implicit Solvent Machine Learning Potential for Drugs and Proteins Approaching Ab Initio Accuracy

    Jul 12, 2026Jan Eckwert, Julija ZavadlavPrevious Machine-Learning-Based Implicit SolventInteratomic Potentials

  52. Scaffold splits hide structural-frontier failures in ADMET models

    Jul 12, 2026Jiacheng Zheng, Chang Guo, Zixuan Wang +1Molecular Property PredictionLabel-Free

  53. Vilya-1: An all-atom foundation model for macrocycle structure prediction and design

    Jul 10, 2026Vilya Research, :, Pascal Sturmfels +8Cyclic PeptidesDrug Discovery

  54. Inverse-IMPRESSION: A Graph-based Platform for Molecular Structure Elucidation from Experimental NMR Spectroscopic Properties

    Jul 10, 2026Zheqi Jin, Grace Armitage, Richard Cox +3Molecular Structure ElucidationImprint

  55. Entropy-Constrained Machine Learning with Residual Data Augmentation for Modeling Chemical Kinetics

    Jul 10, 2026Okezzi Ukorigho, Opeoluwa OwoyeleCombustion ControlReaction

  56. Autoregressive latent diffusion for 3D molecule generation

    Jul 10, 2026Federico Ottomano, Gaopeng Ren, Yingzhen Li +2Molecular GenerationAutoregressive Diffusion

  57. Variable-Length Generative Protein Design via Generalized Poisson Flow

    Jul 10, 2026Chaoran Cheng, Zhanghan Ni, Yanru Qu +4Protein DesignGenerative Flow Networks

  58. Model Agnostic Graph Prompt Learning for Crystal Property Prediction

    Jul 9, 2026Shrimon Mukherjee, Kishalay Das, Partha Basuchowdhuri +2Graph Neural NetworksGraph Representation Learning

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

    Jul 9, 2026Ali Motahharynia, Mohammadreza Ghaffarzadeh-Esfahani, Mahsa Sheikholeslami +4Drug DesignDrug Discovery

  60. path_boost: A Python Package for Interpretable Graph-Level Prediction using Path-Based Gradient Boosting

    Jul 8, 2026Claudio Meggio, Johan Pensar, Riccardo De BinGraph Representation LearningGraph Neural Networks