arXiv AI September 28, 2026 By Sitong Chen, Xiaopeng Mao

Predicting Transmembrane Protein Topology from 3D Structure

This paper introduces a new method for predicting transmembrane protein topology by employing the graph neural network SchNet. The model is trained on the same dataset used for DeepTMHMM, using 5‑fold cross‑validation, and incorporates all atom‑level embeddings rather than just sequence or alpha‑carbon features. Results indicate that GNNs hold significant promise for topological predictions without relying on pre‑trained weights.

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arXiv Machine Learning

Aug 18

EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction

EquiPocket is an E(3)-equivariant Graph Neural Network designed to predict ligand binding sites on proteins. It processes proteins as geometric graphs, extracting local surface atom geometry, modeling chemical and spatial relationships, and performing equivariant message passing to capture surface geometry. A dense attention output layer mitigates issues caused by variable protein sizes, and experiments show the method outperforms current state‑of‑the‑art approaches.

By Yang Zhang, Zhewei Wei, Ye Yuan, Chongxuan Li, Wenbing Huang

benchmarks

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

Jul 31

TopoFormer: Topology Meets Attention for Graph Learning

arXiv:2607. 28259v1 Announce Type: new Abstract: We introduce Topoformer, a lightweight and scalable framework for graph representation learning that encodes topological structure into attention-friendly sequences.

By Md Joshem Uddin, Astrit Tola, Cuneyt Gurcan Akcora, Baris Coskunuzer

llms rag benchmarks

arXiv AI

Jun 19

Protein Representation Learning with Secondary-Structure and Energy-Filtered Hydrogen-Bond Graphs

arXiv:2606. 19374v1 Announce Type: cross Abstract: Graph-based representations are widely used in protein modeling, yet many existing approaches rely primarily on sequence adjacency or geometric proximity, which only partially reflect the principles governing protein folding.

By Mohamed Mouhajir, Limei Wang, El Houcine Bergou, Hajar El Hammouti, Lamiae Azizi, Dongqi Fu

benchmarks safety

arXiv Machine Learning

Jun 15

Traditional machine learning vs. deep learning from dynamic graph representations of proteins' 3D folds in the task of protein structure classification

arXiv:2605. 29228v2 Announce Type: replace Abstract: Protein structure classification (PSC) uses supervised learning to predict a protein's CATH/SCOP(e) class from the protein's sequence or 3D structural feature(s).

By Aydin Wells, Francis A. Gatsi, Aaron Striegel, Tijana Milenkovi\'c

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

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Related stories

EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction

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

TopoFormer: Topology Meets Attention for Graph Learning

Protein Representation Learning with Secondary-Structure and Energy-Filtered Hydrogen-Bond Graphs

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