Expressivity and Generalization: Fragment-Biases for Molecular GNNs

Tom Wollschläger; Niklas Kemper; Leon Hetzel; Johanna Sommer; Stephan Günnemann

Home/Archive/arXiv

arXiv · 2406.08210

Expressivity and Generalization: Fragment-Biases for Molecular GNNs

Tom Wollschläger·Niklas Kemper·Leon Hetzel·Johanna Sommer·Stephan Günnemann

View original source ↗Read source document ↗Export metadata ↓

Abstract

Although recent advances in higher-order Graph Neural Networks (GNNs) improve the theoretical expressiveness and molecular property predictive performance, they often fall short of the empirical performance of models that explicitly use fragment information as inductive bias. However, for these approaches, there exists no theoretic expressivity study. In this work, we propose the Fragment-WL test, an extension to the well-known Weisfeiler & Leman (WL) test, which enables the theoretic analysis of these fragment-biased GNNs. Building on the insights gained from the Fragment-WL test, we develop a new GNN architecture and a fragmentation with infinite vocabulary that significantly boosts expressiveness. We show the effectiveness of our model on synthetic and real-world data where we outperform all GNNs on Peptides and have 12% lower error than all GNNs on ZINC and 34% lower error than other fragment-biased models. Furthermore, we show that our model exhibits superior generalization capabilities compared to the latest transformer-based architectures, positioning it as a robust solution for a range of molecular modeling tasks.

Explore related subjects

cs.LG

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Tom Wollschläger, Niklas Kemper, Leon Hetzel, Johanna Sommer, Stephan Günnemann. 2024-07-25. Expressivity and Generalization: Fragment-Biases for Molecular GNNs. https://arxiv.org/abs/2406.08210

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Random Polytope Descriptors

We introduce a class of random polytopes which simultaneously generalizes several known constructions. While being fairly general, these polytopes are also computationally exceptionally benign. We indicate how these properties can be exploited for classification and clustering tasks in data analysis. Crucially, our construction lets users smoothly trade off between a tighter description of the data and faster computation.

cs.LG↗

arXiv2026

CurvFed: Curvature-Aligned Federated Learning for Fairness without Demographics

Modern human sensing applications often rely on data distributed across users and devices, where privacy concerns prevent centralized training. Federated Learning (FL) addresses this challenge by enabling collaborative model training without exposing raw data or attributes. However, achieving fairness in such settings remains difficult, as most human sensing datasets lack demographic labels, and FL's privacy guarantees limit the use of sensitive attributes. This paper introduces CurvFed: Curvature Aligned Federated Learning for Fairness without Demographics, a theoretically grounded framework that promotes fairness in FL without requiring any demographic or sensitive attribute information, a concept termed Fairness without Demographics (FWD), by optimizing the underlying loss landscape curvature. Building on the theory that equivalent loss landscape curvature corresponds to consistent model efficacy across sensitive attribute groups, CurvFed regularizes the top eigenvalue of the Fisher Information Matrix (FIM) as an efficient proxy for loss landscape curvature, both within and across clients. This alignment promotes uniform model behavior across diverse bias inducing factors, offering an attribute agnostic route to algorithmic fairness. CurvFed is especially suitable for real world human sensing FL scenarios involving single or multi user edge devices with unknown or multiple bias factors. We validated CurvFed through theoretical and empirical justifications, as well as comprehensive evaluations using three real world datasets and a deployment on a heterogeneous testbed of resource constrained devices. Additionally, we conduct sensitivity analyses on local training data volume, client sampling, communication overhead, resource costs, and runtime performance to demonstrate its feasibility for practical FL edge device deployment.

cs.LG↗

arXiv2026

Path Regularization: A Near-Complete and Optimal Nonasymptotic Generalization Theory for Multilayer Neural Networks and Double Descent Phenomenon

Path regularization has shown to be a very effective regularization to train neural networks, leading to a better generalization property than common regularizations i.e. weight decay, etc. We propose a first near-complete (as will be made explicit in the main text) nonasymptotic generalization theory for multilayer neural networks with path regularizations for general learning problems. In particular, it does not require the boundedness of the loss function, as is commonly assumed in the literature. Our theory goes beyond the bias-variance tradeoff and aligns with phenomena typically encountered in deep learning. It is therefore sharply different from other existing nonasymptotic generalization error bounds. More explicitly, we propose an explicit generalization error upper bound for multilayer neural networks with $σ(0)=0$ and sufficiently broad Lipschitz loss functions, without requiring the width, depth, or other hyperparameters of the neural network to approach infinity, a specific neural network architecture (e.g., sparsity), or boundedness of the loss function, while also taking approximation error into consideration. In particular, we solve an open problem proposed by Weinan E et. al. in 2020 regarding the approximation rates in generalized Barron spaces. Furthermore, we show the near-minimax optimality of our theory for regression problems with ReLU activations. Notably, our upper bound exhibits the famous double descent phenomenon for such networks, which is the most distinguished characteristic compared with other existing results. Our subsequent work will prove the matching lower bounds in the minimax sense, meaning that it is highly possible that our theory reveals the true underlying mechanism of the double descent phenomenon. We can also explain scaling law from this theory.

cs.LG↗