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.
By Sitong Chen, Xiaopeng Mao
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:2605. 26833v2 Announce Type: replace-cross Abstract: Polymers underpin applications across energy, healthcare, and materials science, yet their vast chemical space makes systematic discovery challenging.
By Yasharth Yadav, Tze Kwang Gerald Er, Atsushi Goto, Kelin Xia
Learning informative representations of mechanical Triply Periodic Minimal Surface (TPMS) metamaterials is important for mechanics analysis and structural design, yet existing methods have rarely expl...
arXiv:2610. 20684v1 Announce Type: new Abstract: Learning informative representations of mechanical Triply Periodic Minimal Surface (TPMS) metamaterials is important for mechanics analysis and structural design, yet existing methods have rarely explicitly supervised learned representations with information about global structural connectivity that is relevant to mechanical response.
By Songlin Duan, Shuo Yang, Yujia Zheng, Tobin Filleter
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
arXiv:2606. 09806v1 Announce Type: cross Abstract: We introduce Topological Neural Operators (TNOs), a principled framework for operator learning on cell complexes that lifts neural operators (NOs) from functions on points and/or edges to topological domains.
By Lennart Bastian, Samuel Leventhal, Mustafa Hajij, Tolga Birdal
arXiv:2607. 24818v1 Announce Type: cross Abstract: Accurate prediction of crystal properties remains a key challenge in computational materials science.
By Sanjay Chakraborty
Combinatorial Network-Based Manifold Topological Deep Learning (CNMTDL) is a new framework that represents medical images as discrete manifolds and decomposes them into three Hodge components. Features from these components are concatenated and fed into a combinatorial complex architecture, enabling higher‑order message passing between 0‑cells and 2‑cells via attention‑based blocks. CNMTDL was evaluated on six 2D and 3D datasets from the MedMNIST v2 benchmark, showing improved performance for medical image analysis.
By Alice Wachira, Xiang Liu, Zhe Su, Yiying Tong, Ge Wang, Guo-Wei Wei
arXiv:2607. 09998v1 Announce Type: new Abstract: Macrocyclic peptides are an increasingly important therapeutic modality, but existing computational methods for modeling their structures and properties are limited in scope and do not generalize well across the synthetically accessible chemical space.
By Vilya Research, :, Pascal Sturmfels, Milad Salem, Naozumi Hiranuma, Stephen Rettie, Xiaoliang Pan, Benjamin D. Sellers, Adam P. Moyer, Patrick J. Salveson, Ivan Anishchanka
arXiv:2606. 30961v1 Announce Type: cross Abstract: Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species.
By Jacob W. Toney, Samir Darouich, Yiran Wang, Aaron G. Garrison, Johannes K\"astner, Heather J. Kulik
arXiv:2607. 28755v1 Announce Type: new Abstract: Over the last decade, neural networks have been applied to an increasingly diverse range of applications, including data with rich geometric, topological, or symmetry-related structure.
By Brendan Kennedy, Tegan Emerson, Gregory Roek, Emilie Purvine, Henry Kvinge