Molecular Property Prediction

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19 papers in the last four weeks, up 46% on the four weeks before. 0.2% of all new papers.

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Latest papers 133

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Do LLMs Truly Generalize in the Molecular Domain? A Perturbation-Based Analysis
Jul 2, 2026Jiatong Li, Weida Wang, Changmeng Zheng +4In-Context Learning Molecular Property Prediction
The Hong Kong Polytechnic University · National University of Singapore · Shanghai AI Lab +1
Can Tabular In-Context Learners Generalize to Biomolecular Property Prediction?
Jun 30, 2026Davy Guan, Lu Zhang, Asiri Wijesinghe +7Tabular Foundation Models Protein Fitness Prediction
Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia
ElemeNet: Multiscale Molecular Machine Learning with Uncertainty Quantification Across the Periodic Table
Jun 29, 2026Jacob W. Toney, Samir Darouich, Yiran Wang +3Molecular Property Prediction Molecular Representation Learning
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA · Center for Computational Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA · Institute for Theoretical Chemistry, University of Stuttgart, Germany +2
Transformer-Based Active Learning for Data-Efficient Vaccine Epitope Selection in PRRS
Jun 27, 2026Aspen Erlandsson Brisebois, Zahed Khatooni, Connor Burbridge +5Transformer Active Learning
Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada · Engineering Science, Faculty of Applied Science, University of Toronto, Toronto, ON, Canada · Department of Mathematics and Statistics, University of Saskatchewan, Saskatoon, SK, Canada +4
ConSolv: Solvent-Conditional Machine Learning Implicit Solvent Potential
Jun 23, 2026Linying Zhang, Julija ZavadlavMachine Learning Interatomic Potentials Molecular Property Prediction
Multiscale Modeling of Fluid Materials, Department of Engineering Physics and Computation, TUM School of Engineering and Design, Technical University of Munich, Germany · Atomistic Modeling Center (AMC), Munich Data Science Institute (MDSI), Technical University of Munich, Germany
Closed-loop Auto Research for Molecular Property Prediction: Discovering and Certifying Generalizable Improvements
Jun 22, 2026Jingjie Ning, Xiaochuan Li, Ji Zeng +2Molecular Property Prediction Automated Machine Learning
School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA. · DP Technology, Beijing, China.
Residue-Level Attributions in Protein Language Models Do Not Recover Allergen Epitopes
Jun 20, 2026Jianzhou Yao, Anxiong Song, Katja Baerenfaller +1Gradient-Based Attribution Protein Language Models
Swiss Institute of Allergy and Asthma Research, Davos, Switzerland · ETH Zurich, Zurich, Switzerland · Swiss Institute of Bioinformatics, Lausanne, Switzerland
QBioFusion-QSAR: Morgan-Anchored Quantum Multiple Kernel Learning for Small-Data Ligand Classification
Jun 19, 2026Azadeh Alavi, Fatemeh Kouchmeshki, Muhammad Usman +1Quantum Machine Learning Quantum Kernel Methods
School of Computing Technologies, RMIT University, Melbourne 3000, Australia · Pattern Recognition Pty Ltd, Melbourne 3240, Australia · Data61, CSIRO, Clayton, VIC, Australia +1
MMGNN: Multi-level, multi-color graph neural networks for molecular property prediction
Jun 18, 2026Trung Nguyen, Duc Duy NguyenMessage Passing Neural Networks Molecular Property Prediction
The Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA · Department of Mathematics, University of Tennessee, Knoxville, TN 37996, USA
MOLAR: Learning Multimodal Molecular Representations from Noisy Labels
Jun 16, 2026Yingxu Wang, Kunyu Zhang, Nan Yin +2Molecular Property Prediction Learning with Noisy Labels
Department of Machine Learning, Mohamed bin Zayed University of Artificial Intelligence, AI Diyafah St, 7909, Abu Dhabi, United Arab Emirates · Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China · International College, Zhengzhou University, Daxue North Road, 450000, Henan, China +2
A Fixed-Point Neural Operator for Size- and Functional-Transferable Hamiltonian Prediction
Jun 12, 2026Yunhong Lou, Xihang Yue, Xinran Wei +2Quantum Chemistry Molecular Property Prediction
1Zhejiang University, Hangzhou, China. · 2Zhongguancun Academy, Beijing, China. · 3Zhongguancun Institute of Artificial Intelligence, Beijing, China.
Curvature-Informed Potential Energy Surface for Protein-Ligand Binding Affinity Prediction
Jun 12, 2026Peng-Fei Sun, Chuan-Xian Ren, Hong YanProtein-Ligand Binding Affinity Prediction Graph Neural Networks
School of Mathematics, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China · Department of Electrical Engineering, City University of Hong Kong, Hong Kong
Curvature-Guided Geometric Representation for Protein-Ligand Binding Affinity Prediction
Jun 12, 2026Shuai Li, Chuan-Xian Ren, Yuhao Li +4Protein-Ligand Binding Affinity Prediction Hierarchical Representation Learning
School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China · Department of Electrical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong
SupraBench: A Benchmark for Supramolecular Chemistry
Jun 11, 2026Tianyi Ma, Yijun Ma, Zehong Wang +6LLM Evaluation Molecular Property Prediction
University of Notre Dame · University of Connecticut
A green solvent screening tool for emerging materials via uncertainty aware, transformer enhanced transfer learning
Jun 11, 2026Ioannis Kouroudis, Simon Ternes, Zhaosu Gu +5Molecular Property Prediction
Chair of Simulation of Nanosystems for Energy Conversion, Department of Electrical Engineering, TUM School of Computation, Information and Technology, Atomistic Modeling Center (AMC) · Munich Data Science Institute (MDSI), Technical University of Munich, Hans-Piloty-Straße 1, 85748 Garching, Germany · Institute of Structure of Matter – National Research Council Rome (ISM-CNR), via del Fosso del Cavaliere 100, Rome, 00133, RM,Italy +2
Physics-Aware Auxiliary Losses Improve Out-of-Distribution Generalization of a GNN Synthesizability Filter
Jun 10, 2026Riya Bisht, Dhruv AgarwalGraph Neural Networks OOD Generalization
Comprehensive pKa Data Augmentation from Limited Real Data through an Engineered Models-Quantum Framework
Jun 10, 2026Wang Rui, Liu DinghaoSynthetic Data Augmentation Quantum Annealing
Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China · Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China · School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
Probabilistic Contrastive Pretraining for Multi-task ADME Property Prediction
Jun 9, 2026Yifan Xue, Srimukh Prasad Veccham, Saee Paliwal +2Contrastive Learning Self-Supervised Pre-Training
NVIDIA Santa Clara, CA 95051
GLACIER: A Multimodal Student-Teacher Foundation Model for Molecular Property Prediction
Jun 9, 2026Emily Nguyen, Yongchan Hong, Harsh Toshniwal +2Multimodal Pretraining Molecular Property Prediction
Department of Medical Biochemistry and Biophysics Science for Life Laboratory Karolinska Institutet Stockholm, Sweden · Amazon
Flexible Kernels for Protein Property Prediction
Jun 9, 2026Martin Jankowiak, Yerdos Ordabayev, Rudraksh Tuwani +4Kernel Methods Molecular Property Prediction
Generate Biomedicines, Somerville, MA, USA
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 Prediction Molecular Representation Learning
Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan. · 4Interdisciplinary Program of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan. · School of Medicine, National Tsing Hua University, Hsinchu, Taiwan. +1
Constraint-Aware Optimization for Robust Protein Stability Prediction
Jun 6, 2026A Shivram, Aneesh S. Chivukula, Manik Gupta +1OOD Generalization Protein Language Models
Department of Computer Science and Information Systems, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, 500078, Telangana, India · Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, 500078, Telangana, India
MolE-RAG: Molecular Structure-Enhanced Retrieval-Augmented Generation for Chemistry
Jun 4, 2026Joey Chan, Wonbin Kweon, Ashley Shin +4Retrieval-Augmented Generation LLM Inference
University of Illinois Urbana-Champaign · University of California, San Diego
SC3: The Multi-Solvent Solubility Challenge and Benchmark
Jun 3, 2026Vansh Ramani, Har Ashish Arora, Dhairya Kuchhal +4Benchmark Construction Benchmark Validity
Indian Institute of Technology Delhi, India · Kurnakov Institute of General and Inorganic Chemistry RAS, Russia
Structure-Aware Prediction of PROTAC-Mediated Protein Degradability via Graph Neural Networks
Jun 1, 2026Bryan Cheng, Austin JinGraph Neural Networks Molecular Property Prediction
Independent Researcher USA
Improvise, Adapt, Overcome: An On-The-Fly Multifidelity Algorithm for Efficient Machine Learning
Jun 1, 2026Vivin Vinod, Peter ZaspelQuantum Chemistry Multifidelity Modeling
School of Mathematics and Natural Sciences, University of Wuppertal, Germany.
CryoProt: A Protein Pretraining Framework with Cross-Box Interactions on Cryo-EM Density Maps
May 31, 2026Dan Luo, Xuan Lin, Peng Zhou +4Cryo-Electron Microscopy 3D Representation Learning
College of Computer Science and Electronic Engineering, Hunan University · School of Computer Science, Xiangtan University
TadA-Bench: A Million-Variant Benchmark for Future-Round Discovery Toward Agentic Protein Engineering
May 29, 2026Jin Gao, Juntu Zhao, Zirui Zeng +5Protein Fitness Prediction Benchmark Design
Shanghai Jiao Tong University · Shanghai Innovation Institute.
What drives performance in molecular MPNNs? An operator-level factorial benchmark
May 28, 2026Panyu Jiao, Shuizhou Chen, Yiheng Shen +3Message Passing Neural Networks Molecular Property Prediction
Materials Genome Institute, Shanghai University, Shanghai 200444, China · School of Computer Engineering and Science, Shanghai University, Shanghai 200444, China · School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
A Systematic Evaluation of Molecular Mixture Behavior Prediction
May 28, 2026Roel J. Leenhouts, Nathan K. Morgan, William Green +2OOD Generalization Molecular Property Prediction
KU Leuven Leuven, Belgium · MIT Cambridge, USA · RWTH Aachen University Aachen, Germany

Jul 2, 2026, cs.LGJ/K move · Enter open · S save

Do LLMs Truly Generalize in the Molecular Domain? A Perturbation-Based Analysis

Jiatong Li, Weida Wang, Changmeng Zheng, Shufei Zhang+3

The Hong Kong Polytechnic University · National University of Singapore · Shanghai AI Lab+1

In-Context Learning Molecular Property Prediction Language Model Robustness

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Large Language Models (LLMs) have recently shown promise in molecular discovery, yet a gap remains between their probabilistic nature over discrete sequential tokens and the rigid topological constraints of chemical space. This raises the question of whether molecular LLMs can generalize beyond the local neighborhoods induced by their sequence-based representations. To systematically investigate this question, we introduce a Molecular Perturbation framework that generates syntax-valid structural variants of training molecules under controlled Graph Edit Distance (GED) to probe the manifold regularity of molecular LLMs. Our analysis shows that even a single edit can cause substantial performance drops on common molecular tasks, revealing a narrow local trust region and fragile sensitivity to structural changes. Since similar molecules tend to exhibit similar properties, In-Context Tuning (ICT), which anchors predictions on structurally similar molecules, offers a natural way to mitigate such fragility. Our experiments also examine whether ICT confers robustness under controlled structural perturbations, and the results suggest that it can partially expand the local trust region and offer a promising direction for stabilizing molecular LLMs against structural variation.

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