arXiv Machine Learning

Physics-Based Molecular Fingerprints from Spectral Graph Theory Provide Efficient Geometry-Aware Measures of Chemical Similarity

arXiv:2608. 05336v1 Announce Type: cross Abstract: Molecular representations are essential for the evaluation of molecular similarity and the development of structure-property relationships.

arXiv AI

Jun 3

Learning the Neighborhood: Contrast-Free Multimodal Self-Supervised Molecular Graph Pretraining

arXiv:2509. 22468v2 Announce Type: replace-cross Abstract: High-quality molecular representations are essential for property prediction and molecular design, yet large labeled datasets remain scarce.

By Boshra Ariguib, Mathias Niepert, Andrei Manolache

llms rag diffusion fine-tuning multimodal benchmarks

arXiv Machine Learning

Jun 16

Spectral Analysis of Molecular Features: When Richer Features Do Not Guarantee Better Generalization

arXiv:2510. 14217v2 Announce Type: replace Abstract: The spectral properties of feature embeddings offer critical insights into model generalization and representation quality.

By Asma Jamali, Tin Sum Cheng, Rodrigo A. Vargas-Hern\'andez

llms rag benchmarks

arXiv Machine Learning

Jun 9

Hyper-Dimensional Fingerprints as Molecular Representations

arXiv:2604. 27810v2 Announce Type: replace Abstract: Computational molecular representations underpin virtual screening, property prediction, and materials discovery.

By Jonas Teufel, Luca Torresi, Andr\'e Eberhard, Pascal Friederich

rag benchmarks

arXiv Machine Learning

Aug 26

MolGA: Molecular Graph Adaptation with Pre-trained 2D Graph Encoder

arXiv:2510.07289v2 Announce Type: replace Abstract: Molecular graph representation learning is widely used in chemical and biomedical research. While pre-trained 2D graph encoders have demonstrated s...

By Xingtong Yu, Chang Zhou, Xinming Zhang, Yuan Fang

safety

arXiv Machine Learning

Jul 3

An Additive MLP-GNN Framework for Characterizing Chemical and Structural Contributions to Aqueous Solubility

arXiv:2607. 02212v1 Announce Type: cross Abstract: Aqueous solubility is a key property in early-stage drug discovery, but most predictive models merge physicochemical descriptors and molecular graph information into a single representation, obscuring whether a prediction is driven by global chemistry, molecular structure, or both.

By Sampreeti Bhattacharya, Arkaprava Roy

rag fine-tuning

arXiv Machine Learning

Aug 11

RAVEN: Frozen Random Graph Reservoirs with Physics-Informed Interaction Fingerprints for Protein-Ligand Binding Affinity Prediction

arXiv:2608. 09099v1 Announce Type: new Abstract: Quantitative estimation of protein-ligand binding affinity from three-dimensional complex structures is a fundamental task in structure-based computational chemistry and molecular modeling.

By Qingyang Zou, Jiaye Huang, Hangbo Xie, Jiayue Yin, Youyi Song, Jinfeng Liu

arXiv Machine Learning

Jun 15

Curvature-Informed Potential Energy Surface for Protein-Ligand Binding Affinity Prediction

arXiv:2606. 14217v1 Announce Type: new Abstract: Accurate prediction of protein-ligand binding affinity is essential for structure-based drug discovery.

By Peng-Fei Sun, Chuan-Xian Ren, Hong Yan

benchmarks safety

arXiv AI

Aug 12

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

arXiv:2604. 06336v2 Announce Type: replace-cross Abstract: Fragment-level representations provide a natural way to capture recurring molecular substructures and reuse their learned representations across molecules.

By Yi Yang, Ovidiu Daescu

llms benchmarks

arXiv Machine Learning

Jul 8

Multimodal Molecular Representation Learning with Graph Neural Networks, Deep & Cross Networks, and SMILES Embeddings

arXiv:2607. 05736v1 Announce Type: new Abstract: Molecular property prediction often relies on isolated data modalities, where continuous 3D graph neural networks (GNNs) struggle to efficiently capture long-range topological dependencies and exact macroscopic heuristics.

By Qiwei Han, Chi Zhou, Ruobing Wang, Zheng Ma

rag diffusion efficiency multimodal benchmarks safety

arXiv AI

Sep 15

Multi-View Molecular Representation Learning with Hierarchical Graphs and Contextualized Fingerprints

arXiv:2609.15611v1 Announce Type: cross Abstract: Molecular property prediction requires representations that generalize from limited labeled data to structurally novel compounds. Existing molecular...

By Gwang-Hyeon Yun, Jong-Hoon Park, Bing Hu, Helen Chen, Anita Layton, Young-Rae Cho

rag fine-tuning benchmarks

arXiv AI

Jul 24

SenCos-GEM: SENet-Calibrated and Law-of-Cosines-Constrained Geometry-Enhanced Molecular Representation for Property Prediction

arXiv:2607. 20551v1 Announce Type: cross Abstract: Effective molecular representation learning is crucial for accurate molecular property prediction.

By Tianming Han, Li Zhang, Qi Zhao

benchmarks

arXiv Machine Learning

Jun 11

GLACIER: A Multimodal Student-Teacher Foundation Model for Molecular Property Prediction

arXiv:2606. 11382v1 Announce Type: new Abstract: Deep learning models facilitate the discovery of molecules with tailored properties among billions of candidate compounds.

By Emily Nguyen, Yongchan Hong, Harsh Toshniwal, Yan Liu, Andreas Luttens

llms rag multimodal benchmarks safety

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