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.

May 1, 2026

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

We present a unique, multitask dataset comprising 143 drug and drug candidate molecules, each evaluated on in vitro, parallel artificial-membrane permeability assays (PAMPA) using six different model membranes. Using this resource, we systematically assess the effectiveness of various molecular descriptors and regression models in predicting passive membrane permeability. The studied models range from simple linear regression to a modern pre-trained transformer architecture. Particular attention is given to the trade-off between predictive performance and model interpretability, highlighting the challenges introduced by machine learning approaches. To our knowledge, this is the most comprehensive study on simultaneous modeling of multiple organ-specific PAMPA membranes to date, offering novel insights into membrane-specific permeability profiles. We found that expert-designed physico-chemical property descriptors are more fitting for a limited sample size permeabilty study than deep learning based representations.

Andrs Formanek, Anna Vincze, Richrd Bicsak +3

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

Multi-Task LearningMolecular Property PredictionMolecular Representation Learning
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Apr 30, 2026

Hyper-Dimensional Fingerprints as Molecular Representations

Computational molecular representations underpin virtual screening, property prediction, and materials discovery. Conventional fingerprints are efficient and deterministic but lose structural information through hash-based compression, particularly at low dimensionalities. Learned representations from graph neural networks recover this expressiveness but require task-specific training and substantial computational resources. Here we introduce hyperdimensional fingerprints (HDF), which replace the learned transformations of message-passing neural networks with algebraic operations on high-dimensional vectors, producing deterministic molecular representations without any training. Across diverse property prediction benchmarks, HDF outperforms conventional fingerprints in the majority of tasks while exhibiting greater consistency across datasets and models. Crucially, HDF embeddings preserve molecular similarity faithfully: at 32 dimensions, distances in HDF space achieve a 0.9 Pearson correlation with graph edit distance, compared to 0.55 for Morgan fingerprints at equivalent size. This structural fidelity persists at low dimensions where hash-based methods degrade, allowing simple nearest-neighbor regression to remain predictive with as few as 64 components. We further demonstrate the practical impact in Bayesian molecular optimization, where HDF-based surrogate models achieve substantially improved sample efficiency in regimes where Morgan fingerprints perform comparably to random search. HDF thus provides a general-purpose, training-free alternative to conventional molecular fingerprints, suggesting that the information loss long accepted as inherent to fixed-length fingerprints is a limitation of the hash-based encoding scheme rather than the fingerprint paradigm itself.

Jonas Teufel, Luca Torresi, André Eberhard +1

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.

Hyperdimensional ComputingMolecular Property PredictionMolecular Representation Learning
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Apr 29, 2026

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

The rapid growth of molecular foundation models and large language models (LLMs) has encouraged a scale centred view of AI in drug discovery, in which larger pretrained models are expected to supersede compact cheminformatics models. We test this assumption across 26 ADME, toxicity and bioactivity endpoints, covering 165,541 endpoint level compound label records. The benchmark contains 78 endpoint and split entries evaluated under random, Murcko scaffold and structure separated 5-fold cross validation protocols, representing increasing chemical generalization difficulty. Across 156 task and metric comparisons, classical machine learning (ML) provides the largest share of best performing entries (47.4%), followed by pretrained molecular sequence models (28.8%), graph neural networks (21.8%) and LLM based SAR baselines (1.9%). Classical ML dominates random split interpolation and remains the largest winner family overall. GNN and sequence models are competitive in selected harder splits, but their strict winner shares decrease under a fixed final-window readout, indicating sensitivity to training settings and model selection. Paired bootstrap analyses show that small numerical differences between individual models should not be read as decisive victories. SAR knowledge from training folds improves GPT5.5-SAR and Opus4.7-SAR metrics but does not make rule based reasoning a universal substitute for supervised predictors. Compact specialized models remain highly effective, and predictive performance depends on the fit among model, task and validation scenario, not on scale alone.

Jinjiang Guo, Sheng Ding

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

LLM EvaluationMolecular Property PredictionMolecular Foundation ModelsMolecular Representation LearningDrug Discovery
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Apr 27, 2026

Enhancing molecular dynamics with equivariant machine-learned densities

Machine-learning interatomic potentials (MLIPs) have enabled molecular dynamics at near ab initio accuracy, yet remain limited to energies and forces by construction, leaving electronic observables such as dipole moments and polarizabilities inaccessible. We introduce DenSNet, a density-first approach to machine-learned electronic structure that learns the Hohenberg--Kohn map from nuclear configurations to the ground-state electron density. Our approach employs an SE(3)-equivariant neural network to predict density coefficients of a flexible atom-centered Gaussian basis, combined with a ΔΔ-learning strategy that uses superposed atomic densities as a prior to accelerate training. A second equivariant network then maps the predicted density to the total energy, providing a unified framework for molecular dynamics and electronic structure. We validate DenSNet on ethanol, ethanethiol, and resorcinol, where infrared spectra from machine-learned trajectories show excellent agreement with experimental gas-phase measurements. To test scalability, we train on polythiophene oligomers with 1--6 monomers and extrapolate to chains of up to 12 monomers, generating stable long-time trajectories whose infrared spectra agree with reference density functional theory calculations. Here, we show that reinstating the electron density as the central learned quantity opens a practical route to transferable prediction of spectroscopic and electronic observables in large-scale molecular simulations.

Mihail Bogojeski, Muhammad R. Hasyim, Leslie Vogt-Maranto +3

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

Infrared SpectroscopyMachine Learning Interatomic PotentialsQuantum ChemistryMolecular Property PredictionMolecular Dynamics Simulation
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Apr 25, 2026

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

Accurate molecular representations are critical for drug discovery, and a central challenge lies in capturing the chemical environment of molecular fragments, as key interactions, such as H-bond and π stacking, occur only under specific local conditions. Most existing approaches represent molecules as atom-level graphs; however, atom-level representations can hardly express higher-order chemical context (e.g., stereochemistry, lone pairs, conjugation). Fragment-based methods (e.g., principal subgraph, predefined functional groups) fail to preserve essential information such as chirality, aromaticity, and ionic states. This work addresses these limitations from two aspects. (i) OverlapBPE tokenization. We propose a novel data-driven molecule tokenization method. Unlike existing approaches, our method allows overlapping fragments, reflecting the inherently fuzzy boundaries of small-molecule substructures and, together with enriched chemical information at the token level, thereby preserving a more complete chemical context. (ii) h-MINT model. OverlapBPE induces many-to-many atom-fragment mappings, which necessitate a new hierarchical architecture. We therefore develop a hierarchical molecular interaction network capable of jointly modeling interactions at both atom and fragment levels. By supporting fragment overlaps, the model naturally accommodates the many-to-many atom-fragment mappings introduced by the OverlapBPE scheme. Extensive evaluation against state-of-the-art methods shows our method improves binding affinity prediction by 2-4% Pearson/Spearman correlation on PDBBind and LBA, enhances virtual screening by 1-3% in key metrics on DUD-E and LIT-PCBA, and achieves the best overall HTS performance on PubChem assays. Further analysis demonstrates that our method effectively captures interactive information while maintaining good generalization.

Yanru Qu, Yijie Zhang, Wenjuan Tan +6

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

Protein-Ligand Binding Affinity PredictionHierarchical Representation LearningAI-Assisted Scientific ResearchMolecular Property PredictionMolecular Representation LearningDrug Discovery
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Apr 25, 2026

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

Accurate prediction of drug-target binding affinity accelerates drug discovery by prioritizing compounds for experimental validation. Current methods face three limitations: sequence-based approaches discard spatial geometric constraints, structure-based methods fail to exploit hydrogen bond features, and conventional loss functions neglect prediction-target correlation, a key factor for identifying high-affinity compounds in virtual screening. We developed HBGSA (Hydrogen Bond Graph with Self-Attention), a 3.06M-parameter model that encodes hydrogen bond spatial features. HBGSA uses graph neural networks to model hydrogen bond spatial topology with self-attention enhancement and Pearson correlation loss. Experimental results on PDBbind Core Set and CSAR-HiQ dataset demonstrate that HBGSA outperforms baseline methods with strong generalization capability. Ablation studies confirm the effectiveness of hydrogen bond modeling and Pearson correlation loss.

Junxiao Kong, Chupei Tang, Di Wang +4

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

Protein-Ligand Binding Affinity PredictionGraph Neural NetworksMolecular Property PredictionDrug Discovery
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Apr 21, 2026

Graph-Theoretic Models for the Prediction of Molecular Measurements

Graph-theoretic approaches offer simplicity, interpretability, and low computational cost for molecular property prediction. Among these, the model proposed by Mukwembi and Nyabadza, based on the external activity D(G)D(G) and internal activity ζ(G)ζ(G) indices, achieved strong results on a small flavonoid dataset. However, its ability to generalize to larger and chemically diverse datasets has not been tested. This study evaluates the baseline D(G)D(G)-ζ(G)ζ(G) polynomial model on five benchmark datasets from MoleculeNet, covering biological activity (BACE, 1,513 molecules), lipophilicity (LogP synthetic, 14,610 molecules; LogP experimental, 753 molecules), aqueous solubility (ESOL, 1,128 molecules), and hydration free energy (SAMPL, 642 molecules). The baseline model achieves an average R2=0.24R^2 = 0.24, confirming limited transferability. To address this, a systematic enhancement framework is proposed, progressively incorporating Ridge regularization, additional graph descriptors, physicochemical properties, ensemble learning with Gradient Boosting, Lasso feature selection, and a hybrid approach combining topological indices with Morgan fingerprints. The enhanced models raise the average best R2R^2 to 0.79, with individual improvements ranging from 165% to 274%. All improvements are statistically significant (p<0.001p < 0.001). A direct comparison with a Graph Convolutional Network under identical experimental conditions shows that the enhanced classical models match or outperform deep learning on all five datasets. Comparison with the recent GNN+PGM hybrid of Djagba et al.\ further confirms competitiveness, with the enhanced models achieving the best results on two datasets and tying on one. The entire framework requires no GPU, trains in under five minutes, and uses only open-source tools, making it accessible for researchers in resource-limited settings.

Anna Niane, Prudence Djagba

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

Molecular Property Prediction
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Apr 17, 2026

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

Large Language Models (LLMs) have the potential to accelerate small molecule drug design due to their ability to reason about information from diverse sources and formats. However, their practical utility remains unclear due to the lack of benchmarks that reflect real-world scenarios. In this work, we introduce a suite of chemically-grounded tasks spanning molecular property prediction, molecular representation transformations, and molecular design. Importantly, we formulate these tasks as reinforcement learning (RL) environments, enabling a unified approach for evaluation and post-training. Across three model families, we find that frontier models are increasingly proficient at chemical tasks, but that there is significant room for improvement, especially in experimental settings with low data. Critically, we show that RL-based post-training can substantially improve performance. A smaller model post-trained on our environments becomes competitive with state-of-the-art frontier models, despite a significantly weaker base model. This suggests a practical route toward employing LLMs in drug discovery; by combining carefully-designed evaluation tasks with targeted post-training, we can both elucidate and close critical capability gaps.

Shriram Chennakesavalu, Kirill Shmilovich, Hayley Weir +5

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

LLM EvaluationMolecular Property PredictionLLM Post-TrainingDrug Discovery
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Apr 17, 2026

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

Molecular property prediction integrates quantum chemistry, cheminformatics, and deep learning to connect molecular structure with physicochemical and biological behavior. This survey traces four complementary paradigms, including Quantum, Descriptor Machine Learning, Geometric Deep Learning, and Foundation Models, and outlines a unified taxonomy linking molecular representations, model architectures, and interdisciplinary applications. Benchmark analyses integrate evidence from both widely used datasets and datasets reflecting industry perspectives, encompassing quantum, physicochemical, physiological, and biophysical domains. The survey examines current standards in data curation, splitting strategies, and evaluation protocols, highlighting challenges including inconsistent stereochemistry, heterogeneous assay sources, and reproducibility limitations under random or poorly defined splits. These observations motivate the modernization of benchmark design toward more transparent, time- and scaffold-aware methodologies. We further propose three forward-looking directions: (i) physics-aware learning embedding quantum consistency, (ii) uncertainty-calibrated foundation models for trustworthy inference, and (iii) realistic multimodal benchmark ecosystems integrating computational and experimental data. Repository: https://github.com/Zongru-Li/Survey-and-Benchmarks-of-DL-for-Molecular-Property-Prediction-in-the-Foundation-Model-Era.

Zongru Li, Xingsheng Chen, Honggang Wen +8

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

Molecular Property PredictionMolecular Foundation ModelsMolecular Representation Learning
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Apr 17, 2026

Tabular foundation models for in-context prediction of molecular properties

Accurate molecular property prediction is central to drug discovery, catalysis, and process design, yet real-world applications are often limited by small datasets. Molecular foundation models provide a promising direction by learning transferable molecular representations; however, they typically involve task-specific fine-tuning, require machine learning expertise, and often fail to outperform classical baselines. Tabular foundation models (TFMs) offer a fundamentally different paradigm: they perform predictions through in-context learning, enabling inference without task-specific training. Here, we evaluate TFMs in the low- to medium-data regime across both standardized pharmaceutical benchmarks and chemical engineering datasets. We evaluate both frozen molecular foundation model representations, as well as classical descriptors and fingerprints. Across the benchmarks, the approach shows excellent predictive performance while reducing computational cost, compared to fine-tuning, with these advantages also transferring to practical engineering data settings. In particular, combining TFMs with CheMeleon embeddings yields up to 100% win rates on 30 MoleculeACE tasks, while compact RDKit2d and Mordred descriptors provide strong descriptor-based alternatives. Molecular representation emerges as a key determinant in TFM performance, with molecular foundation model embeddings and 2D descriptor sets both providing substantial gains over classic molecular fingerprints on many tasks. These results suggest that in-context learning with TFMs provides a highly accurate and cost-efficient alternative for property prediction in practical applications.

Karim K. Ben Hicham, Jan G. Rittig, Martin Grohe +1

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

Tabular Foundation ModelsMolecular Property PredictionTabular ICLMolecular Representation LearningMolecular Foundation Models
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Apr 13, 2026

TriFit: Trimodal Fusion with Protein Dynamics for Mutation Fitness Prediction

Predicting the functional impact of single amino acid substitutions (SAVs) is central to understanding genetic disease and engineering therapeutic proteins. While protein language models and structure-based methods have achieved strong performance on this task, they systematically neglect protein dynamics; residue flexibility, correlated motions, and allosteric coupling are well-established determinants of mutational tolerance in structural biology, yet have not been incorporated into supervised variant effect predictors. We present TriFit, a multimodal framework that integrates sequence, structure, and protein dynamics through a four-expert Mixture-of-Experts (MoE) fusion module with trimodal cross-modal contrastive learning. Sequence embeddings are extracted via masked marginal scoring with ESM-2 (650M); structural embeddings from AlphaFold2-predicted C-alpha geometries; and dynamics embeddings from Gaussian Network Model (GNM) B-factors, mode shapes, and residue-residue cross-correlations. The MoE router adaptively weights modality combinations conditioned on the input, enabling protein-specific fusion without fixed modality assumptions. On the ProteinGym substitution benchmark (217 DMS assays, 696k SAVs), TriFit achieves AUROC 0.897 +/- 0.0002, outperforming all supervised baselines including Kermut (0.864) and ProteinNPT (0.844), and the best zero-shot model ESM3 (0.769). Ablation studies confirm that dynamics provides the largest marginal contribution over pairwise modality combinations, and TriFit achieves well-calibrated probabilistic outputs (ECE = 0.044) without post-hoc correction.

Seungik Cho

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

Protein Fitness PredictionMolecular Property PredictionMultimodal Learning
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Apr 10, 2026

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

Generative models can now propose thousands of de novo antibody sequences, yet translating these designs into viable therapeutics remains constrained by the cost of biophysical characterization. Here we present CrossAbSense, a framework of property-specific neural oracles that combine frozen protein language model encoders with configurable attention decoders, identified through a systematic hyperparameter campaign totaling over 200 runs per property. On the GDPa1 benchmark of 242 therapeutic IgGs, our oracles achieve notable improvements of 12--20% over established baselines on three of five developability assays and competitive performance on the remaining two. The central finding is that optimal decoder architectures invert our initial biological hypotheses: self-attention alone suffices for aggregation-related properties (hydrophobic interaction chromatography, polyreactivity), where the relevant sequence signatures -- such as CDR-H3 hydrophobic patches -- are already fully resolved within single-chain embeddings by the high-capacity 6B encoder. Bidirectional cross-attention, by contrast, is required for expression yield and thermal stability -- properties that inherently depend on the compatibility between heavy and light chains. Learned chain fusion weights independently confirm heavy-chain dominance in aggregation (wH=0.62w_H = 0.62) versus balanced contributions for stability (wH=0.51w_H = 0.51). We demonstrate practical utility by deploying CrossAbSense on 100 IgLM-generated antibody designs, illustrating a path toward substantial reduction in experimental screening costs.

Simon J. Crouzet

Molecular Property PredictionProtein DesignCross-Attention
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Apr 9, 2026

Active Learning for Generalizable Detonation Performance Prediction of Energetic Materials

The discovery of new energetic materials is critical for advancing technologies from defense to private industry. However, experimental approaches remain slow and expensive while computational alternatives require accurate material property inputs that are often costly to obtain, limiting their ability to efficiently predict detonation performance across a vast chemical space. We address this challenge through an active learning strategy that integrates density functional theory calculations, thermochemical modeling, message-passing neural networks, and Bayesian optimization. The resulting high-throughput workflow iteratively expands the training dataset by selecting new molecules in a targeted manner that balances the exploration of broad chemical space with the exploitation of promising high-performing candidates. This approach yields the largest publicly available database of potential CHNO explosives drawn from an initial pool of more than 70 billion candidates and a generalizable surrogate model capable of accurately predicting detonation performance (R2^2 > 0.98). Feature importance analysis on this largest-to-date dataset reveals that oxygen balance is the dominant driver of detonation performance, complemented by contributions from local electronic structure, density, and the presence of specific functional groups. Cheminformatics analysis highlights how energetic materials with similar performance metrics tend to cluster in distinct chemical spaces offering a clearer direction for future synthesis studies. Together, the surrogate model, database, and resulting chemical insights provide a valuable foundation for high-throughput screening and targeted discovery of new energetic materials spanning diverse and previously unexplored regions of chemical space.

R. Seaton Ullberg, Megan C. Davis, Jeremy N. Schroeder +5

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

Materials Property PredictionMaterials ScienceMolecular Property Prediction
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Apr 8, 2026

Predicting Activity Cliffs for Autonomous Medicinal Chemistry

Activity cliff prediction - identifying positions where small structural changes cause large potency shifts - has been a persistent challenge in computational medicinal chemistry. This work focuses on a parsimonious definition: which small modifications, at which positions, confer the highest probability of an outcome change. Position-level sensitivity is calculated using 25 million matched molecular pairs from 50 ChEMBL targets across six protein families, revealing that two questions have fundamentally different answers. "Which positions vary most?" is answered by scaffold size alone (NDCG@3 = 0.966), requiring no machine learning. "Which are true activity cliffs?" - where small modifications cause disproportionately large effects, as captured by SALI normalization - requires an 11-feature model with 3D pharmacophore context (NDCG@3 = 0.910 vs. 0.839 random), generalizing across all six protein families, novel scaffolds (0.913), and temporal splits (0.878). The model identifies the cliff-prone position first 53% of the time (vs. 27% random - 2x lift), reducing positions a chemist must explore from 3.1 to 2.1 - a 31% reduction in first-round experiments. Predicting which modification to make is not tractable from structure alone (Spearman 0.268, collapsing to -0.31 on novel scaffolds). The system is released as open-source code and an interactive webapp.

Michael Cuccarese

Drug DiscoveryMolecular Property Prediction
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Apr 8, 2026

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

We present the first systematic study of when target context helps molecular property prediction, evaluating context conditioning across 10 diverse protein families, 4 fusion architectures, data regimes spanning 67-9,409 training compounds, and both temporal and random evaluation splits. Using NestDrug, a FiLM-based architecture that conditions molecular representations on target identity, we characterize both success and failure modes with three principal findings. First, fusion architecture dominates: FiLM outperforms concatenation by 24.2 percentage points and additive conditioning by 8.6 pp; how you incorporate context matters more than whether you include it. Second, context enables otherwise impossible predictions: on data-scarce CYP3A4 (67 training compounds), multi-task transfer achieves 0.686 AUC where per-target Random Forest collapses to 0.238. Third, context can systematically hurt: distribution mismatch causes 10.2 pp degradation on BACE1; few-shot adaptation consistently underperforms zero-shot. Beyond methodology, we expose fundamental flaws in standard benchmarking: 1-nearest-neighbor Tanimoto achieves 0.991 AUC on DUD-E without any learning, and 50% of actives leak from training data, rendering absolute performance metrics meaningless. Our temporal split evaluation (train up to 2020, test 2021-2024) achieves stable 0.843 AUC with no degradation, providing the first rigorous evidence that context-conditional molecular representations generalize to future chemical space.

Bryan Cheng, Jasper Zhang

Great Neck South High School

Molecular Property PredictionMolecular Representation LearningMulti-Task LearningBenchmark Contamination
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Apr 7, 2026

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

Fragment-level representations provide a natural way to capture recurring molecular substructures and reuse their learned representations across molecules. However, a shared fragment identity alone may not fully describe how a fragment is instantiated in a particular molecule, since the same fragment can exhibit different chemical behavior depending on its surrounding atomic environment. Effective fragment-based molecular learning therefore requires representations that are both reusable across molecules and sensitive to local atomic context. We introduce BiScale-GTR, a self-supervised molecular representation framework built around context-grounded shared fragment tokens. BiScale-GTR constructs a reusable graph Byte Pair Encoding (graph-BPE) vocabulary using Weisfeiler-Lehman (WL)-based fragment identity, chemical validity filtering, and recursive out-of-vocabulary (OOV) decomposition. Each shared fragment token is then grounded with atom-level GNN representations through atom-to-fragment pooling and gated fusion, allowing the same fragment identity to acquire context-dependent representations in different molecular environments. A structure-aware fragment Transformer performs global reasoning over these atom-grounded tokens, capturing reusable substructure identity, local chemical context, and long-range molecular dependencies. Experiments on MoleculeNet, PharmaBench, and the Long Range Graph Benchmark demonstrate strong performance across classification and regression tasks. Attribution analysis further shows that BiScale-GTR highlights chemically meaningful recurring motifs, providing interpretable links between molecular structure and predicted properties.

Yi Yang, Ovidiu Daescu

Department of Computer Science, The University of Texas at Dallas

Molecular Representation LearningGraph TransformerGraph SSLMolecular Property Prediction
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Apr 7, 2026

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

Recent advances in large language models (LLMs) have enabled molecular reasoning for property prediction. However, toxicity arises from complex biological mechanisms beyond chemical structure, necessitating mechanistic reasoning for reliable prediction. Despite its importance, current benchmarks fail to systematically evaluate this capability. LLMs can generate fluent but biologically unfaithful explanations, making it difficult to assess whether predicted toxicities are grounded invalid mechanisms. To bridge this gap, we introduce ToxReason, a benchmark grounded in the Adverse Outcome Pathway (AOP) that evaluates organ-level toxicity reasoning across multiple organs. ToxReason integrates experimental drug-target interaction evidence with toxicity labels, requiring models to infer both toxic outcomes and their underlying mechanisms from Molecular Initiating Event (MIE) to Adverse Outcome (AO). Using ToxReason, we evaluate toxicity prediction performance and reasoning quality across diverse LLMs. We find that strong predictive performance does not necessarily imply reliable reasoning. Furthermore, we show that reasoning-aware training improves mechanistic reasoning and, consequently, toxicity prediction performance. Together, these results underscore the necessity of integrating reasoning into both evaluation and training for trustworthy toxicity modeling.

Jueon Park, Wonjune Jang, Chanhwi Kim +2

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

Toxicity DetectionLLM EvaluationMolecular Property Prediction
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Mar 27, 2026

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

DPD-Cancer is a graph-attention deep learning framework for predicting small-molecule DPD-Cancer is a graph-attention deep learning framework for predicting small-molecule anti-cancer activity across the NCI-60 panel, trained and evaluated under a strict chemistry-aware data-partitioning scheme. On the hold-out test set, the classifier achieved an Area Under the Receiver Operating Characteristic Curve (AUROC) of 0.87 (95% CI [0.86, 0.88]) and Area Under the Precision-Recall Curve (AUPRC) of 0.73 (95% CI [0.70, 0.76]); per-cell-line regression models for 73 cell lines produced a median Pearson's Correlation Coefficient (Pearson's R) of 0.64 and median Root Mean Squared Error (RMSE) of 0.67 for pGI50-value prediction. Benchmarks against pdCSM-Cancer, MLASM, and ACLPred under matched data conditions yielded consistently higher Matthew's Correlation Coefficient (MCC) scores, an occlusion-based attribution analysis confirmed that model explanations were quantitatively faithful to classifier decisions, and an applicability-domain analysis characterised reliability as a function of chemical distance. To facilitate widespread adoption, DPD-Cancer is available as a free, user-friendly web server for unrestricted use at https://biosig.lab.uq.edu.au/dpd_cancer/.

Magnus H. Strømme, Alex G. C. de Sá, David B. Ascher

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

Cancer Drug Response PredictionMolecular Property PredictionDrug Discovery
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Mar 26, 2026

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

The capabilities of large language models (LLMs) have expanded beyond natural language processing to scientific prediction tasks, including molecular property prediction. However, their effectiveness in in-context learning remains ambiguous, particularly given the potential for training data contamination in widely used benchmarks. This paper investigates whether LLMs perform genuine in-context regression on molecular properties or instead rely on verbatim retrieval of memorized target values. Furthermore, we analyze the interplay between pre-trained knowledge and in-context information through a series of progressively blinded experiments. We evaluate nine LLM variants across three families (GPT-4.1, GPT-5, Gemini 2.5) on three MoleculeNet datasets (Delaney solubility, Lipophilicity, QM7 atomization energy) using a systematic blinding approach that iteratively reduces available information, complemented by 0-, 60-, and 1000-shot in-context sample sizes as an additional control for information access. To validate the memorization analysis and the blinding experiments, we add a positive and a negative control for the memorization experiments and structural reference baselines for the multi-shot experiments as well as bootstrap confidence intervals for all results. We find no evidence of verbatim retrieval on the legacy benchmarks and show that blinding exposes conflicts between pre-trained knowledge and in-context information. This work provides a principled framework for evaluating molecular property prediction under controlled information access.

Matthias Busch, Marius Tacke, Sviatlana V. Lamaka +4

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

LLM EvaluationKnowledge Conflicts in Language ModelsIn-Context LearningMolecular Property Prediction
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Mar 25, 2026

MolEvolve: LLM-Guided Evolutionary Search for Interpretable Molecular Optimization

Despite deep learning's success in chemistry, its impact is hindered by a lack of interpretability and an inability to resolve activity cliffs, where minor structural nuances trigger drastic property shifts. Current representation learning, bound by the similarity principle, often fails to capture these structural-activity discontinuities. To address this, we introduce MolEvolve, an evolutionary framework that reformulates molecular discovery as an autonomous, look-ahead planning problem. Unlike traditional methods that depend on human-engineered features or rigid prior knowledge, MolEvolve leverages a Large Language Model (LLM) to actively explore and evolve a library of executable chemical symbolic operations. By utilizing the LLM to cold start and an Monte Carlo Tree Search (MCTS) engine for test-time planning with external tools (e.g. RDKit), the system self-discovers optimal trajectories autonomously. This process evolves transparent reasoning chains that translate complex structural transformations into actionable, human-readable chemical insights. Experimental results demonstrate that MolEvolve's autonomous search not only evolves transparent, human-readable chemical insights, but also outperforms baselines in both property prediction and molecule optimization tasks.

Xiangsen Chen, Ruilong Wu, Yanyan Lan +2

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

Molecular OptimizationLarge Language Model-Guided OptimizationMolecular Property Prediction
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Mar 25, 2026

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

Machine learning models of chemical bioactivity are increasingly used for prioritizing a small number of compounds in virtual screening libraries for experimental follow-up. In these applications, assessing model accuracy by early hit enrichment such as Positive Predicted Value (PPV) calculated for top N hits (PPV@N) is more appropriate and actionable than traditional global metrics such as AUC. We present KANEL, an ensemble workflow that combines interpretable Kolmogorov-Arnold Networks (KANs) with XGBoost, random forest, and multilayer perceptron models trained on complementary molecular representations (LillyMol descriptors, RDKit-derived descriptors, and Morgan fingerprints).

Pavel Koptev, Nikita Krainov, Konstantin Malkov +1

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

Virtual ScreeningMolecular Property PredictionEnsemble Learning
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Mar 25, 2026

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

Accurate charge densities are central to electronic-structure theory, but computing charge-state-dependent densities with density functional theory remains too expensive for large-scale screening and defect workflows. We present ChargeFlow, a flow-matching refinement model that transforms a charge-conditioned superposition of atomic densities into the corresponding DFT electron density on the native periodic real-space grid using a 3D U-Net velocity field. Trained on 9,502 charged Materials Project-derived calculations and evaluated on an external 1,671-structure benchmark spanning perovskites, charged defects, diamond defects, metal-organic frameworks, and organic crystals, ChargeFlow is not uniformly best on every in-distribution class but is strongest on problems dominated by nonlocal charge redistribution and charge-state extrapolation, improving deformation-density error from 3.62% to 3.21% and charge- response cosine similarity from 0.571 to 0.655 relative to a ResNet baseline. The predicted densities remain chemically useful under downstream analysis, yielding successful Bader partitioning on all 1,671 benchmark structures and high-fidelity electrostatic potentials, which positions flow matching as a practical density-refinement strategy for charged materials.

Tri Minh Nguyen, Sherif Abdulkader Tawfik, Truyen Tran +1

Deakin University, Geelong, VIC 3216, Australia

Computational Materials ScienceQuantum ChemistryMolecular Property PredictionDensity Functional TheoryFlow Matching
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Mar 25, 2026

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

Our work addresses the problem of predicting the highest priority functional group present in an organic molecule. Functional Groups are groups of bound atoms that determine the physical and chemical properties of organic molecules. In the presence of multiple functional groups, the dominant functional group determines the compound's properties. Fourier-transform Infrared spectroscopy (FTIR) is a commonly used spectroscopic method for identifying the presence or absence of functional groups within a compound. We propose the use of a Deep Convolutional Neural Networks (CNN) to predict the highest priority functional group from the Fourier-transform infrared spectrum (FTIR) of the organic molecule. We have compared our model with other previously applied Machine Learning (ML) method Support Vector Machine (SVM) and reasoned why CNN outperforms it.

Kunal Khatri, Vineet Mehta

Dhirubhai Ambani Institute of Information & Communication Technology

Infrared SpectroscopyMolecular Property Prediction
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Mar 24, 2026

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

The accurate prediction of protein-RNA binding affinity remains an unsolved problem in structural biology, limiting opportunities in understanding gene regulation and designing RNA-targeting therapeutics. A central obstacle is the structural flexibility of RNA, as, unlike proteins, RNA molecules exist as dynamic conformational ensembles. Thus, committing to a single predicted structure discards information relevant to binding. Here, we show that this obstacle can be addressed by extracting pre-structural embeddings, which are intermediate representations from a biomolecular foundation model captured before the structure decoding step. Pre-structural embeddings implicitly encode conformational ensemble information without requiring predicted structures. We build ZeroFold, a transformer-based model that combines pre-structural embeddings from Boltz-2 for both protein and RNA molecules through a cross-modal attention mechanism to predict binding affinity directly from sequence. To support training and evaluation, we construct PRADB, a curated dataset of 2,621 unique protein-RNA pairs with experimentally measured affinities drawn from four complementary databases. On a held-out test set constructed with 40% sequence identity thresholds, ZeroFold achieves a Spearman correlation of 0.65, a value approaching the ceiling imposed by experimental measurement noise. Under progressively fairer evaluation conditions that control for training-set overlap, ZeroFold compares favourably with respect to leading structure-based and leading sequence-based predictors, with the performance gap widening as sequence similarity to competitor training data is reduced. These results illustrate how pre-structural embeddings offer a representation strategy for flexible biomolecules, opening a route to affinity prediction for protein-RNA pairs for which no structural data exist.

Josef Hanke, Sebastian Pujalte Ojeda, Shengyu Zhang +3

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

Molecular Property PredictionMolecular Representation Learning
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Mar 23, 2026

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

We introduce Suiren-1.0, a family of molecular foundation models for the accurate modeling of diverse organic systems. Suiren-1.0 comprising three specialized variants (Suiren-Base, Suiren-Dimer, and Suiren-ConfAvg) is integrated within an algorithmic framework that bridges the gap between 3D conformational geometry and 2D statistical ensemble spaces. We first pre-train Suiren-Base (1.8B parameters) on a 70M-sample Density Functional Theory dataset using spatial self-supervision and SE(3)-equivariant architectures, achieving robust performance in quantum property prediction. Suiren-Dimer extends this capability through continued pre-training on 13.5M intermolecular interaction samples. To enable efficient downstream application, we propose Conformation Compression Distillation (CCD), a diffusion-based framework that distills complex 3D structural representations into 2D conformation-averaged representations. This yields the lightweight Suiren-ConfAvg, which generates high-fidelity representations from SMILES or molecular graphs. Our extensive evaluations demonstrate that Suiren-1.0 establishes state-of-the-art results across a range of tasks. All models and benchmarks are open-sourced.

Junyi An, Xinyu Lu, Yun-Fei Shi +5

Shanghai Academy of AI for Science (SAIS)

Molecular Foundation ModelsMolecular Representation LearningMolecular Property Prediction3D Representation Learning
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Mar 22, 2026

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

Molecular property prediction constitutes a cornerstone of drug discovery and materials science, necessitating models capable of disentangling complex structure-property relationships across diverse molecular modalities. Existing approaches frequently exhibit entangled representations--conflating structural, chemical, and functional factors--thereby limiting interpretability and transferability. Furthermore, conventional methods inadequately exploit complementary information from graphs, sequences, and geometries, often relying on naive concatenation that neglects inter-modal dependencies. In this work, we propose DMMRL, which employs variational autoencoders to disentangle molecular representations into shared (structure-relevant) and private (modality-specific) latent spaces, enhancing both interpretability and predictive performance. The proposed variational disentanglement mechanism effectively isolates the most informative features for property prediction, while orthogonality and alignment regularizations promote statistical independence and cross-modal consistency. Additionally, a gated attention fusion module adaptively integrates shared representations, capturing complex inter-modal relationships. Experimental validation across seven benchmark datasets demonstrates DMMRL's superior performance relative to state-of-the-art approaches. The code and data underlying this article are freely available at https://github.com/xulong0826/DMMRL.

Long Xu, Junping Guo, Jianbo Zhao +2

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

Molecular Representation LearningMultimodal Disentangled Representation LearningMolecular Property PredictionVariational Autoencoders
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Mar 21, 2026

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

Multi-RF Fusion achieves a test ROC-AUC of 0.8476 +/- 0.0002 on ogbg-molhiv (10 seeds), placing #1 on the OGB leaderboard ahead of HyperFusion (0.8475 +/- 0.0003). The core of the method is a rank-averaged ensemble of 12 Random Forest models trained on concatenated molecular fingerprints (FCFP, ECFP, MACCS, atom pairs -- 4,263 dimensions total), blended with deep-ensembled GNN predictions at 12% weight. Two findings drive the result: (1) setting max_features to 0.20 instead of the default sqrt(d) gives a +0.008 AUC gain on this scaffold split, and (2) averaging GNN predictions across 10 seeds before blending with the RF eliminates GNN seed variance entirely, dropping the final standard deviation from 0.0008 to 0.0002. No external data or pre-training is used.

Zacharie Bugaud

Molecular Property PredictionEnsemble LearningRandom Forest
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Mar 13, 2026

BERTology of Molecular Property Prediction

Chemical language models (CLMs) have emerged as promising competitors to popular classical machine learning models for molecular property prediction (MPP) tasks. However, an increasing number of studies have reported inconsistent and contradictory results for the performance of CLMs across various MPP benchmark tasks. In this study, we conduct and analyze hundreds of meticulously controlled experiments to systematically investigate the effects of various factors, such as dataset size, model size, and standardization, on the pre-training and fine-tuning performance of CLMs for MPP. In the absence of well-established scaling laws for encoder-only masked language models, our aim is to provide comprehensive numerical evidence and a deeper understanding of the underlying mechanisms affecting the performance of CLMs for MPP tasks, some of which appear to be entirely overlooked in the literature.

Mohammad Mostafanejad, Paul Saxe, T. Daniel Crawford

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

Chemical Language ModelsMolecular Property PredictionMolecular Representation LearningLanguage Model PretrainingLLM Fine-TuningLanguage Modeling+1
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Mar 13, 2026

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

Predicting enzyme kinetic parameters quantifies how efficiently an enzyme catalyzes a specific substrate under defined biochemical conditions. Canonical parameters such as the turnover number (kcatk_\text{cat}), Michaelis constant (KmK_\text{m}), and inhibition constant (KiK_\text{i}) depend jointly on the enzyme sequence, the substrate chemistry, and the conformational adaptation of the active site during binding. Many learning pipelines simplify this process to a static compatibility problem between the enzyme and substrate, fusing their representations through shallow operations and regressing a single value. Such formulations overlook the staged nature of catalysis, which involves both substrate recognition and conformational adaptation. In this regard, we reformulate kinetic prediction as a staged multimodal conditional modeling problem and introduce the Enzyme-Reaction Bridging Adapter (ERBA), which injects cross-modal information via fine-tuning into Protein Language Models (PLMs) while preserving their biochemical priors. ERBA performs conditioning in two stages: Molecular Recognition Cross-Attention (MRCA) first injects substrate information into the enzyme representation to capture specificity; Geometry-aware Mixture-of-Experts (G-MoE) then integrates active-site structure and routes samples to pocket-specialized experts to reflect induced fit. To maintain semantic fidelity, Enzyme-Substrate Distribution Alignment (ESDA) enforces distributional consistency within the PLM manifold in a reproducing kernel Hilbert space. Experiments across three kinetic endpoints and multiple PLM backbones, ERBA delivers consistent gains and stronger out-of-distribution performance compared with sequence-only and shallow-fusion baselines, offering a biologically grounded route to scalable kinetic prediction and a foundation for adding cofactors, mutations, and time-resolved structural cues.

Fei Wang, Xinye Zheng, Kun Li +5

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

Molecular Property PredictionCross-Modal Representation LearningProtein Representation Learning
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Mar 13, 2026

A Multitask Large Reasoning Model for Molecular Science

Artificial intelligence in molecular science must move beyond pattern recognition toward chemically valid and interpretable reasoning. We present a task-adaptive large reasoning model that integrates chemical knowledge through a synergistic multispecialist architecture, chain-of-thought supervision, and molecule-informed reinforcement learning. Task-conditioned routing coordinates prediction and inference specialists across 10 molecular tasks spanning molecular description and generation, nomenclature translation, property prediction, and reaction prediction. The model outperforms more than 20 general-purpose and molecular large language models, improves aggregate performance over the base model by 50.3%, and surpasses the leading molecular multitask baseline on most tasks. Analyses of specialist representations and reasoning pathways reveal task-specific adaptation while retaining interpretable chemical inference. A case study further demonstrates an integrated workflow for central nervous system candidate generation, property screening, molecular interpretation, and retrosynthetic planning. These results demonstrate a versatile multi-task framework for knowledge-guided molecular reasoning and design, with the potential to serve as a core task engine for future molecular science agents.

Pengfei Liu, Shuang Ge, Xiaobo Wang +6

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

Scientific ReasoningMulti-Task LearningMolecular GenerationMolecular Property Prediction
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