Molecular Property Prediction

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Overview

Molecular property prediction studies how to infer quantities such as solubility, toxicity, binding affinity, and quantum energies from molecules, mixtures, or molecular environments. Common approaches use fingerprints and physicochemical descriptors, graph neural networks, molecular language models, and 3D equivariant or multimodal models; some also encode physical laws or learn from experimental and simulated data together. Models are assessed on benchmarks such as MoleculeNet and TDC, with scaffold, temporal, and other out-of-distribution splits used to test transfer to unfamiliar chemistry. A central challenge is that strong in-distribution scores and larger pretrained models do not guarantee reliable extrapolation, while careful classical baselines, data quality, uncertainty estimates, and evaluation design can strongly affect results.

Latest papers

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204 papers29 papers in the last four weeks, level with the four weeks before. 0.2% of all new papers.

  1. A Comparative Study of QSPR Methods on a Unique Multitask PAMPA dataset

    May 1, 2026Andrs Formanek, Anna Vincze, Richrd Bicsak +3Multi-Task LearningMolecular Property Prediction

    Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems,May Signal Processing and Data Analytics, KU Leuven, 3001 Leuven, Belgium · Department of Artificial Intelligence and Systems Engineering, Faculty of Electrical Engineering and Informatics, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary[cs.LG] · Department of Chemical and Environmental Process Engineering, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary +2

  2. Hyper-Dimensional Fingerprints as Molecular Representations

    Apr 30, 2026Jonas Teufel, Luca Torresi, André Eberhard +1Hyperdimensional ComputingMolecular Property Prediction

    Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology (INT), Kaiserstraße 12, Karlsruhe, Germany. · Karlsruhe Institute of Technology (KIT), Institute of Anthropomatics and Robotics (IAR), Kaiserstraße 12, Karlsruhe, Germany.

  3. Do Larger Models Really Win in Drug Discovery? A Benchmark Assessment of Model Scaling in AI-Driven Molecular Property and Activity Prediction

    Apr 29, 2026Jinjiang Guo, Sheng DingLLM EvaluationMolecular Property Prediction

    Global Health Drug Discovery Institute, Beijing 100084, China · School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China

  4. Enhancing molecular dynamics with equivariant machine-learned densities

    Apr 27, 2026Mihail Bogojeski, Muhammad R. Hasyim, Leslie Vogt-Maranto +3Infrared SpectroscopyMachine Learning Interatomic Potentials

    BIFOLD and Machine Learning Group, Technische Universität Berlin, Franklinstr. 28/29, 10587 Berlin, Germany · Department of Chemistry, New York University, New York, NY 10003, USA · Department of Artificial Intelligence, Korea University, Seoul 02841, Korea +5

  5. h-MINT: Modeling Pocket-Ligand Binding with Hierarchical Molecular Interaction Network

    Apr 25, 2026Yanru Qu, Yijie Zhang, Wenjuan Tan +6Protein-Ligand Binding Affinity PredictionHierarchical Representation Learning

    Department of Computer Science, UIUC · School of Computer Science, McGill University · MILA-Québec AI Institute +4

  6. HBGSA: Hydrogen Bond Graph with Self-Attention for Drug-Target Binding Affinity Prediction

    Apr 25, 2026Junxiao Kong, Chupei Tang, Di Wang +4Protein-Ligand Binding Affinity PredictionGraph Neural Networks

    School of Mathematics and Statistics, Lanzhou University, 222 South Tianshui Road, 730000, Gansu, China · Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong 999077, China

  7. Graph-Theoretic Models for the Prediction of Molecular Measurements

    Apr 21, 2026Anna Niane, Prudence DjagbaMolecular Property Prediction

    African Institute for Mathematical Sciences (AIMS), Mbour, Senegal. · Lyman Briggs College, Michigan State University, East Lansing, Michigan, USA.

  8. Evaluating the Progression of Large Language Model Capabilities for Small-Molecule Drug Design

    Apr 17, 2026Shriram Chennakesavalu, Kirill Shmilovich, Hayley Weir +5LLM EvaluationMolecular Property Prediction

    Prescient Design, Genentech, South San Francisco, CA, USA

  9. A Systematic Survey and Benchmark of Deep Learning for Molecular Property Prediction in the Foundation Model Era

    Apr 17, 2026Zongru Li, Xingsheng Chen, Honggang Wen +8Molecular Property PredictionMolecular Foundation Models

    The University of Hong Kong, Hong Kong SAR · Nanyang Technological University, Singapore · University of Cambridge, United Kingdom +4

  10. Tabular foundation models for in-context prediction of molecular properties

    Apr 17, 2026Karim K. Ben Hicham, Jan G. Rittig, Martin Grohe +1Tabular Foundation ModelsMolecular Property Prediction

    RWTH Aachen University, Process Systems Engineering (AVT.SVT), Aachen, Germany. · Lehrstuhl Informatik 7, RWTH Aachen University, Aachen, Germany. · JARA-CSD, Aachen, Germany. +1

  11. TriFit: Trimodal Fusion with Protein Dynamics for Mutation Fitness Prediction

    Apr 13, 2026Seungik ChoProtein Fitness PredictionMolecular Property Prediction

    Department of Physics and Astronomy, Rice University, Texas, USA.

  12. Biologically-Grounded Multi-Encoder Architectures as Developability Oracles for Antibody Design

    Apr 10, 2026Simon J. CrouzetMolecular Property PredictionProtein Design

  13. Active Learning for Generalizable Detonation Performance Prediction of Energetic Materials

    Apr 9, 2026R. Seaton Ullberg, Megan C. Davis, Jeremy N. Schroeder +5Materials Property PredictionMaterials Science

    Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA · Department of Mechanical Engineering, Texas Tech University, Lubbock, TX 79409, USA · Weapon Stockpile Modernization Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

  14. Predicting Activity Cliffs for Autonomous Medicinal Chemistry

    Apr 8, 2026Michael CuccareseDrug DiscoveryMolecular Property Prediction

  15. When Does Context Help? A Systematic Study of Target-Conditional Molecular Property Prediction

    Apr 8, 2026Bryan Cheng, Jasper ZhangMolecular Property PredictionMolecular Representation Learning

    Great Neck South High School

  16. BiScale-GTR: Fragment-Aware Graph Transformers for Multi-Scale Molecular Representation Learning

    Apr 7, 2026Yi Yang, Ovidiu DaescuMolecular Representation LearningGraph Transformer

    Department of Computer Science, The University of Texas at Dallas

  17. ToxReason: A Benchmark for Mechanistic Chemical Toxicity Reasoning via Adverse Outcome Pathway

    Apr 7, 2026Jueon Park, Wonjune Jang, Chanhwi Kim +2Toxicity DetectionLLM Evaluation

    Korea University · Myongji University · University of Texas Health Science Center at Houston +1

  18. DPD-Cancer: Explainable Graph-Based Deep Learning for Small Molecule Anti-Cancer Activity Prediction

    Mar 27, 2026Magnus H. Strømme, Alex G. C. de Sá, David B. AscherCancer Drug Response PredictionMolecular Property Prediction

    The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia · Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, 3004, Australia

  19. In-Context Molecular Property Prediction with LLMs: A Blinding Study on Memorization and Knowledge Conflicts

    Mar 26, 2026Matthias Busch, Marius Tacke, Sviatlana V. Lamaka +4LLM EvaluationKnowledge Conflicts in Language Models

    Institute for Continuum and Material Mechanics, Technical University of Hamburg, Eißendorfer Straße, 21073 Hamburg, Germany · Institute of Material Systems Modeling, Helmholtz-Zentrum Hereon, Max-Planck-Straße, 21502 Geesthacht, Germany · Institute of Surface Science, Helmholtz-Zentrum Hereon, Max-Planck-Straße, 21502 Geesthacht, Germany +2

  20. MolEvolve: LLM-Guided Evolutionary Search for Interpretable Molecular Optimization

    Mar 25, 2026Xiangsen Chen, Ruilong Wu, Yanyan Lan +2Molecular OptimizationLarge Language Model-Guided Optimization

    Hong Kong Polytechnic University · Hong Kong University of Science and Technology(Guangzhou) · Tsinghua University +1

  21. KANEL: Kolmogorov-Arnold Network Ensemble Learning Enables Early Hit Enrichment in High-Throughput Virtual Screening

    Mar 25, 2026Pavel Koptev, Nikita Krainov, Konstantin Malkov +1Virtual ScreeningMolecular Property Prediction

    AI1 Technologies · KAN Technologies, LLC · UNC-Chapel Hill

  22. ChargeFlow: Flow-Matching Refinement of Charge-Conditioned Electron Densities

    Mar 25, 2026Tri Minh Nguyen, Sherif Abdulkader Tawfik, Truyen Tran +1Computational Materials ScienceQuantum Chemistry

    Deakin University, Geelong, VIC 3216, Australia

  23. Deep Convolutional Neural Networks for predicting highest priority functional group in organic molecules

    Mar 25, 2026Kunal Khatri, Vineet MehtaInfrared SpectroscopyMolecular Property Prediction

    Dhirubhai Ambani Institute of Information & Communication Technology

  24. ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural Embeddings

    Mar 24, 2026Josef Hanke, Sebastian Pujalte Ojeda, Shengyu Zhang +3Molecular Property PredictionMolecular Representation Learning

    Yusuf Hamied Department of Chemistry, University of Cambridge, UK · Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK · Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R and D, AstraZeneca, Sweden +1

  25. Suiren-1.0 Technical Report: A Family of Molecular Foundation Models

    Mar 23, 2026Junyi An, Xinyu Lu, Yun-Fei Shi +5Molecular Foundation ModelsMolecular Representation Learning

    Shanghai Academy of AI for Science (SAIS)

  26. DMMRL: Disentangled Multi-Modal Representation Learning via Variational Autoencoders for Molecular Property Prediction

    Mar 22, 2026Long Xu, Junping Guo, Jianbo Zhao +2Molecular Representation LearningMultimodal Disentangled Representation Learning

    Guangxi Key Lab of Human-machine Interaction and Intelligent Decision, Nanning Normal University, Nanning, China · College of Big Data and Software Engineering, Zhejiang Wanli University, Ningbo, China

  27. Multi-RF Fusion with Multi-GNN Blending for Molecular Property Prediction

    Mar 21, 2026Zacharie BugaudMolecular Property PredictionEnsemble Learning

  28. BERTology of Molecular Property Prediction

    Mar 13, 2026Mohammad Mostafanejad, Paul Saxe, T. Daniel CrawfordChemical Language ModelsMolecular Property Prediction

    Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA · Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA

  29. Multimodal Protein Language Models for Enzyme Kinetic Parameters: From Substrate Recognition to Conformational Adaptation

    Mar 13, 2026Fei Wang, Xinye Zheng, Kun Li +5Molecular Property PredictionCross-Modal Representation Learning

    School of Computer Science and Information Engineering, Hefei University of Technology · Institute of Artificial Intelligence, Hefei Comprehensive National Science Center · CVLab, College of Information Technology, United Arab Emirates University +2

  30. A Multitask Large Reasoning Model for Molecular Science

    Mar 13, 2026Pengfei Liu, Shuang Ge, Xiaobo Wang +6Scientific ReasoningMulti-Task Learning

    Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, Southern Medical University, Guangzhou, Guangdong, 510515, China · Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong 518000, China · Guangdong Provincial Key Laboratory of Psychoactive Substances Monitoring and Safety, Anti-Drug Technology Center of Guangdong Province (National Anti-Drug Laboratory Guangdong Regional Center), Guangzhou, 510230, China +4