Neural injective functions for multisets, measures and graphs via a finite witness theorem

T Amir, S Gortler, I Avni, R Ravina… - Advances in Neural …, 2024 - proceedings.neurips.cc
Injective multiset functions have a key role in the theoretical study of machine learning on
multisets and graphs. Yet, there remains a gap between the provably injective multiset …

A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems

A Duval, SV Mathis, CK Joshi, V Schmidt… - arxiv preprint arxiv …, 2023 - arxiv.org
Recent advances in computational modelling of atomic systems, spanning molecules,
proteins, and materials, represent them as geometric graphs with atoms embedded as …

On the Completeness of Invariant Geometric Deep Learning Models

Z Li, X Wang, S Kang, M Zhang - arxiv preprint arxiv:2402.04836, 2024 - arxiv.org
Invariant models, one important class of geometric deep learning models, are capable of
generating meaningful geometric representations by leveraging informative geometric …

Transferable deep generative modeling of intrinsically disordered protein conformations

G Janson, M Feig - PLOS Computational Biology, 2024 - journals.plos.org
Intrinsically disordered proteins have dynamic structures through which they play key
biological roles. The elucidation of their conformational ensembles is a challenging problem …

On dimensionality of feature vectors in MPNNs

CÊ Bravo, A Kozachinskiy, Cà Rojas - arxiv preprint arxiv:2402.03966, 2024 - arxiv.org
We revisit the classical result of Morris et al.~(AAAI'19) that message-passing graphs neural
networks (MPNNs) are equal in their distinguishing power to the Weisfeiler--Leman (WL) …

Geometric Representation Condition Improves Equivariant Molecule Generation

Z Li, C Zhou, X Wang, X Peng, M Zhang - arxiv preprint arxiv:2410.03655, 2024 - arxiv.org
Recent advancements in molecular generative models have demonstrated substantial
potential in accelerating scientific discovery, particularly in drug design. However, these …

Towards Stable, Globally Expressive Graph Representations with Laplacian Eigenvectors

J Zhou, C Zhou, X Wang, P Li, M Zhang - arxiv preprint arxiv:2410.09737, 2024 - arxiv.org
Graph neural networks (GNNs) have achieved remarkable success in a variety of machine
learning tasks over graph data. Existing GNNs usually rely on message passing, ie …

Weisfeiler Leman for Euclidean Equivariant Machine Learning

S Hordan, T Amir, N Dym - arxiv preprint arxiv:2402.02484, 2024 - arxiv.org
The $ k $-Weifeiler-Leman ($ k $-WL) graph isomorphism test hierarchy is a common
method for assessing the expressive power of graph neural networks (GNNs). Recently, the …

VisDiff: SDF-Guided Polygon Generation for Visibility Reconstruction and Recognition

R Moorthy, V Isler - arxiv preprint arxiv:2410.05530, 2024 - arxiv.org
The capability to learn latent representations plays a key role in the effectiveness of recent
machine learning methods. An active frontier in representation learning is understanding …

On the Expressive Power of Sparse Geometric MPNNs

Y Sverdlov, N Dym - arxiv preprint arxiv:2407.02025, 2024 - arxiv.org
Motivated by applications in chemistry and other sciences, we study the expressive power of
message-passing neural networks for geometric graphs, whose node features correspond to …