arXiv AI

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.

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

arXiv Machine Learning

Aug 4

Differentiable Lifting for Topological Neural Networks

arXiv:2608. 01160v1 Announce Type: new Abstract: Topological neural networks (TNNs) enable leveraging high-order structures on graphs (e.

By Jorge Luiz Franco, Gabriel Duarte, Alexander Nikitin, Moacir Ponti, Diego Mesquita, Amauri H. Souza

benchmarks

arXiv Machine Learning

4d ago

TopoEmbedX: A General Framework for Representation Learning on Topological Domains

arXiv:2609.37884v1 Announce Type: new Abstract: Topological structures such as simplicial complexes, hypergraphs, and cell complexes extend standard graph models by modeling higher-order relationship...

By Florian Frantzen, Ibrahem AlJabea, Ines Henriques-Cadby, Theodore Papamarkou, Mustafa Hajij, Michael T. Schaub

rag

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 24

Writhe-Based Polymer Link Classification Using Machine Learning

arXiv:2607. 20657v1 Announce Type: cross Abstract: Unique and rapid classification of knots and links is an open mathematical problem that is relevant to a range of (bio)physical systems, including polymer melts, DNA, and proteins.

By Jack Beda, Djordje Mihajlovic, Kasturi Barkataki, Davide Michieletto

arXiv Machine Learning

5d ago

WEECFP-SuRGE: A Position-Aware Substructure Encoding Method for Molecular Property Prediction

WEECFP-SuRGE introduces a position‑aware substructure encoding method that combines tokenized hierarchical Morgan fingerprints with graph‑distance‑dependent rotations applied at the input and within transformer self‑attention. The approach captures local chemistry, long‑range interactions, and molecular topology without requiring external pretraining or 3‑D conformer generation. Benchmarks on MoleculeNet and the Therapeutic Data Commons ADMET datasets show competitive performance, and a reconstruction procedure correctly identifies constitutional isomers for 92.6% of a 4,200‑molecule library.

By Robert Epps

llms benchmarks

arXiv Machine Learning

Sep 17

Topology-enhanced machine learning for speech signal processing

The paper introduces TopCap, a topology‑enhanced method for extracting features from speech time series. TopCap captures fine structural details, such as vibrations, that traditional spectral analysis may miss. When applied to classifying voiced versus voiceless consonants, TopCap matches neural network accuracy, and when combined with neural networks it improves robustness to noise, accuracy, stability, convergence, and interpretability.

By Pingyao Feng, Qingrui Qu, Haiyu Zhang, Siheng Yi, Zhiwang Yu, Zeyang Ding, Yifei Zhu

benchmarks safety

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