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. Can Decision Trees Teach Large Language Models? Distilling Verbalized Knowledge for Molecular Property Prediction

    Mar 12, 2026Khiem Le, Sreejata Dey, Marcos Martínez Galindo +4Molecular Property PredictionKnowledge Distillation

    University of Notre Dame, IN, USA · IBM Research

  2. Hybrid Quantum-Classical Encoding for Accurate Residue-Level pKa Prediction

    Mar 9, 2026Van Le, Tan LeMolecular Property PredictionProtein Representation Learning

    the Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA · the School of Engineering, Architecture and Aviation, Hampton University, Hampton, VA 23669, USA

  3. MMAI Gym for Science: Training Liquid Foundation Models for Drug Discovery

    Mar 3, 2026Maksim Kuznetsov, Zulfat Miftahutdinov, Rim Shayakhmetov +17Molecular OptimizationMolecular Property Prediction

    Insilico Medicine · Liquid AI

  4. Information Routing in Atomistic Foundation Models: How Task Alignment and Equivariance Shape Linear Disentanglement

    Mar 3, 2026Joshua SteierMolecular Representation LearningRepresentation Disentanglement

    Independent Researcher

  5. ChemFlow:A Hierarchical Neural Network for Multiscale Representation Learning in Chemical Mixtures

    Mar 3, 2026Jinming Fan, Chao Qian, Wilhelm T. S. Huck +2Molecular Property PredictionMolecular Representation Learning

    College of Chemical and Biological Engineering, Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, Zhejiang University, 310027 Hangzhou (P. R. China) · Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands · Institute of Zhejiang University – Quzhou, 324000 Quzhou (P.R. China)

  6. GlassMol: Interpretable Molecular Property Prediction with Concept Bottleneck Models

    Mar 1, 2026Oscar Rivera, Ziqing Wang, Matthieu Dagommer +2Interpretable MLMolecular Property Prediction

    Northwestern University, Evanston, IL 60201, USA · AbbVie, Chicago, IL 60064, USA

  7. MultiPUFFIN: A Multimodal Domain-Constrained Foundation Model for Molecular Property Prediction of Small Molecules

    Mar 1, 2026Idelfonso B. R. Nogueira, Carine M. Rebello, Mumin Enis Leblebici +1Molecular Property PredictionMultimodal Foundation Models

    Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, 7034, Norway · Faculty of Industrial Engineering, KU Leuven, Diepenbeek, Belgium · University of Surrey, Guildford, United Kingdom

  8. Enhancing Molecular Property Predictions by Learning from Bond Modelling and Interactions

    Feb 28, 2026Yunqing Liu, Yi Zhou, Wenqi FanMolecular Property PredictionMolecular Representation Learning

    Department of Computing (COMP), The Hong Kong Polytechnic University · Department of Management and Marketing (MM), The Hong Kong Polytechnic University

  9. Tensor Hypercontraction Error Correction Using Regression

    Feb 27, 2026Ishna Satyarth, Eric C. Larson, Devin A. MatthewsComputational Quantum ChemistryQuantum Chemistry

    Department of Computer Science, Southern Methodist University, Dallas, TX 75275, USA · Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA

  10. Prediction of Diffusion Coefficients in Mixtures with Tensor Completion

    Feb 26, 2026Zeno Romero, Kerstin Münnemann, Hans Hasse +1Molecular Property PredictionTensor Completion

    Laboratory of Engineering Thermodynamics, RPTU Kaiserslautern, Erwin-Schrödinger-Str. 44, 67663 Kaiserslautern, Germany

  11. MolFM-Lite: Multi-Modal Molecular Property Prediction with Conformer Ensemble Attention and Cross-Modal Fusion

    Feb 25, 2026Syed Omer Shah, Mohammed Maqsood Ahmed, Danish Mohiuddin Mohammed +2Molecular Property PredictionMultimodal Fusion

    Department of Computer Science and Engineering, University at Buffalo, Buffalo, NY, USA · Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA · Department of Computer Science, Muffakham Jah College of Engineering and Technology, Hyderabad, India +1

  12. Zatom-1: Towards a Multimodal Foundation Model for 3D Molecules and Materials

    Feb 24, 2026Alex Morehead, Miruna Cretu, Antonia Panescu +143D Foundation ModelsMultimodal Foundation Models

    LBNL · ICSI · University of Cambridge +3

  13. MolGraphBench: A Benchmark of GNN Architectures for Molecular Regression Tasks

    Feb 24, 2026Rajan, Ishaan GuptaGraph Neural NetworksMolecular Property Prediction

    School of Interdisciplinary Research (SIRe), IIT Delhi, New Delhi-110016, India · Department of Biochemical Engineering and Biotechnology (DBEB), IIT Delhi, New Delhi-110016, India

  14. Protein Language Models Diverge from Natural Language: Comparative Analysis and Improved Inference

    Feb 24, 2026Anna Hart, Chi Han, Jeonghwan Kim +2Protein Language ModelsProtein Representation Learning

    Siebel School of Data Science and Computing, University of Illinois Urbana-Champaign, 201 N Goodwin Ave, Urbana, IL 61801, USA · DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, 1206 W Gregory Drive, Urbana, IL 61801, USA · Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, 600 S Matthews Ave, Urbana, IL 61801, USA

  15. MACE-POLAR-1: A Polarisable Electrostatic Foundation Model for Molecular Chemistry

    Feb 23, 2026Ilyes Batatia, William J. Baldwin, Domantas Kuryla +10Molecular Foundation ModelsMachine Learning Interatomic Potentials

    Engineering Laboratory, University of Cambridge, Trumpington St, Cambridge, UK · Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK · Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge, UK +6

  16. KEMP-PIP: A Feature-Fusion Based Approach for Pro-inflammatory Peptide Prediction

    Feb 22, 2026Soumik Deb Niloy, Md. Fahmid-Ul-Alam Juboraj, Swakkhar ShatabdaMolecular Property PredictionFeature Fusion

    Department of Computer Science and Engineering, BRAC University, Dhaka 1212, Bangladesh

  17. Clapeyron Neural Networks for Single-Species Vapor-Liquid Equilibria

    Feb 20, 2026Jan Pavšek, Alexander Mitsos, Elvis J. Sim +1Molecular Property PredictionMaterials Property Prediction

    Process Systems Engineering (AVT.SVT), RWTH Aachen University · JARA Center for Simulation and Data Science (CSD) · Institute of Climate and Energy Systems ICE-1: Energy Systems Engineering, Forschungszentrum Jülich GmbH

  18. DuaDeep-SeqAffinity: Dual-Branch Deep Learning for Tri-Stream Sequence-Based Antibody--Antigen Affinity Prediction

    Dec 26, 2025Aicha Boutorh, Soumia Bouyahiaoui, Manel Kara Laouar +3Hybrid CNN-Transformer ArchitecturesMolecular Property Prediction

    National School of Artificial Intelligence (ENSIA) Sidi Abdallah Campus, Algiers, Algeria · Lamine Debaghine University Hospital Center, CHU Bab El Oued, Algiers, Algeria

  19. Freeze, Diffuse, Decode: Task-Aware Adaptation of Transformer Embeddings for Antimicrobial Peptide Design

    Nov 28, 2025Pankhil Gawade, Adam Izdebski, Myriam Lizotte +4Representation LearningGeometric Representation Learning

    Institute of AI for Health, Helmholtz Munich · School of Computation, Information and Technology, Technical University of Munich · Mila - Quebec AI institute; Univ. de Montreal +3

  20. Structure-Aware Compound-Protein Affinity Prediction via Graph Neural Networks with Group Lasso Regularization

    Jul 4, 2025Zanyu Shi, Yang Wang, Pathum M. Weerawarna +4Protein-Ligand Binding Affinity PredictionMolecular Property Prediction

    Department of Biostatistics & Health Data Science, Indiana University Fairbanks School of Public Health, Indianapolis, 46202 IN, USA. · Department of Computer Science, Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, 47405 IN, USA. · Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, 46202 IN, USA. +2

  21. A Machine Learning Benchmarking Framework for Lipid Nanoparticle Transfection Efficiency Prediction

    Jul 3, 2025Asal Mehradfar, Mohammad Shahab Sepehri, Jose Miguel Hernandez-Lobato +4Graph Representation LearningMolecular Property Prediction

    Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA · Department of Engineering, University of Cambridge, Cambridge, UK · Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI +1

  22. BOOM: Benchmarking Out-Of-distribution Molecular Property Predictions of Machine Learning Models

    May 3, 2025Evan R. Antoniuk, Shehtab Zaman, Tal Ben-Nun +10OOD GeneralizationMolecular Property Prediction

    Lawrence Livermore National Laboratory, Livermore, CA · Binghamton University, Binghamton, NY

  23. GenShin: Guiding Rational Liposome Design by Ranking Liposomal Protein Corona through a Docking-Pose-Free GNN

    Mar 16, 2025Pingfei Zhu, Hongyi Liu, Xueyan Liu +2Graph Neural NetworksMaterials Science

    Key Laboratory of symbolic Computation and Knowledge Engineering of ministry of education, Jilin University, Qianjin Street 2699, Changchun, Jilin Province, 130012, China · State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China

  24. Active Learning Enables Generation of Molecules that Advance the Known Pareto Front

    Jan 3, 2025Evan R. Antoniuk, Peggy Li, Nathan Keilbart +3Molecular OptimizationOOD Generalization