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Deep Learning/Graph Neural Networks

Yuankai Luo, Lei Shi, Veronika Thost

Self-supervised learning (SSL) has great potential for molecular representation learning given the complexity of molecular graphs, the large amounts of unlabelled data available, the considerable cost of obtaining labels experimentally, and the hence often only small training datasets. The importance of the topic is reflected in the variety of paradigms and architectures that have been investigated recently, most focus on designing views for contrastive learning.In this paper, we study SSL based on persistent homology (PH), a mathematical tool for modeling topological features of data that persist across multiple scales. It has several unique features which particularly suit SSL, naturally offering: different views of the data, stability in terms of distance preservation, and the opportunity to flexibly incorporate domain knowledge.We (1) investigate an autoencoder, which shows the general representational power of PH, and (2) propose a contrastive loss that complements existing approaches. We rigorously evaluate our approach for molecular property prediction and demonstrate its particular features in improving the embedding space:after SSL, the representations are better and offer considerably more predictive power than the baselines over different probing tasks; our loss increases baseline performance, sometimes largely; and we often obtain substantial improvements over very small datasets, a common scenario in practice.

Deep Learning/Graph Neural Networks

Jinwoo Kim, Dat Nguyen, Ayhan Suleymanzade, Hyeokjun An, Seunghoon Hong

We present a novel framework to overcome the limitations of equivariant architectures in learning functions with group symmetries. In contrary to equivariant architectures, we use an arbitrary base model such as an MLP or a transformer and symmetrize it to be equivariant to the given group by employing a small equivariant network that parameterizes the probabilistic distribution underlying the symmetrization. The distribution is end-to-end trained with the base model which can maximize performance while reducing sample complexity of symmetrization. We show that this approach ensures not only equivariance to given group but also universal approximation capability in expectation. We implement our method on various base models, including patch-based transformers that can be initialized from pretrained vision transformers, and test them for a wide range of symmetry groups including permutation and Euclidean groups and their combinations. Empirical tests show competitive results against tailored equivariant architectures, suggesting the potential for learning equivariant functions for diverse groups using a non-equivariant universal base architecture. We further show evidence of enhanced learning in symmetric modalities, like graphs, when pretrained from non-symmetric modalities, like vision. Code is available at https://github.com/jw9730/lps.

Deep Learning/Graph Neural Networks

Honghua Dong, Jiawei Xu, Yu Yang, Rui Zhao, Shiwen Wu, Chun Yuan, Xiu Li, Chris Maddison, Lei Han

Graph neural networks, which typically exchange information between local neighbors, often struggle to capture long-range interactions (LRIs) within the graph. Building a graph hierarchy via graph pooling methods is a promising approach to address this challenge; however, hierarchical information propagation cannot entirely take over the role of local information aggregation. To balance locality and hierarchy, we integrate the local and hierarchical structures, represented by intra- and inter-graphs respectively, of a multi-scale graph hierarchy into a single mega graph. Our proposed MeGraph model consists of multiple layers alternating between local and hierarchical information aggregation on the mega graph. Each layer first performs local-aware message-passing on graphs of varied scales via the intra-graph edges, then fuses information across the entire hierarchy along the bidirectional pathways formed by inter-graph edges. By repeating this fusion process, local and hierarchical information could intertwine and complement each other. To evaluate our model, we establish a new Graph Theory Benchmark designed to assess LRI capture ability, in which MeGraph demonstrates dominant performance. Furthermore, MeGraph exhibits superior or equivalent performance to state-of-the-art models on the Long Range Graph Benchmark. The experimental results on commonly adopted real-world datasets further demonstrate the broad applicability of MeGraph.

Deep Learning/Graph Neural Networks

Xingyue Huang, Miguel Romero, Ismail Ceylan, Pablo Barceló

Graph neural networks are prominent models for representation learning over graph-structured data. While the capabilities and limitations of these models are well-understood for simple graphs, our understanding remains incomplete in the context of knowledge graphs. Our goal is to provide a systematic understanding of the landscape of graph neural networks for knowledge graphs pertaining to the prominent task of link prediction. Our analysis entails a unifying perspective on seemingly unrelated models and unlocks a series of other models. The expressive power of various models is characterized via a corresponding relational Weisfeiler-Leman algorithm. This analysis is extended to provide a precise logical characterization of the class of functions captured by a class of graph neural networks. The theoretical findings presented in this paper explain the benefits of some widely employed practical design choices, which are validated empirically.

Deep Learning/Graph Neural Networks

Anthony Gruber, Kookjin Lee, Nathaniel Trask

Recent works have shown that physics-inspired architectures allow the training of deep graph neural networks (GNNs) without oversmoothing. The role of these physics is unclear, however, with successful examples of both reversible (e.g., Hamiltonian) and irreversible (e.g., diffusion) phenomena producing comparable results despite diametrically opposed mechanisms, and further complications arising due to empirical departures from mathematical theory. This work presents a series of novel GNN architectures based upon structure-preserving bracket-based dynamical systems, which are provably guaranteed to either conserve energy or generate positive dissipation with increasing depth. It is shown that the theoretically principled framework employed here allows for inherently explainable constructions, which contextualize departures from theory in current architectures and better elucidate the roles of reversibility and irreversibility in network performance. Code is available at the Github repository \url{https://github.com/natrask/BracketGraphs}.

Deep Learning/Graph Neural Networks

Aseem Baranwal, Kimon Fountoulakis, Aukosh Jagannath

We study the node classification problem on feature-decorated graphs in the sparse setting, i.e., when the expected degree of a node is $O(1)$ in the number of nodes, in the fixed-dimensional asymptotic regime, i.e., the dimension of the feature data is fixed while the number of nodes is large. Such graphs are typically known to be locally tree-like. We introduce a notion of Bayes optimality for node classification tasks, called asymptotic local Bayes optimality, and compute the optimal classifier according to this criterion for a fairly general statistical data model with arbitrary distributions of the node features and edge connectivity. The optimal classifier is implementable using a message-passing graph neural network architecture. We then compute the generalization error of this classifier and compare its performance against existing learning methods theoretically on a well-studied statistical model with naturally identifiable signal-to-noise ratios (SNRs) in the data. We find that the optimal message-passing architecture interpolates between a standard MLP in the regime of low graph signal and a typical convolution in the regime of high graph signal. Furthermore, we prove a corresponding non-asymptotic result.

Deep Learning/Graph Neural Networks

Aditya Shahane, Saripilli Swapna Manjiri, Ankesh Jain, Sandeep Kumar

The design automation of analog circuits poses significant challenges in terms of the large design space, complex interdependencies between circuit specifications, and resource-intensive simulations. To address these challenges, this paper presents an innovative framework called the Graph of Circuits Explorer (GCX). Leveraging graph structure learning along with graph neural networks, GCX enables the creation of a surrogate model that facilitates efficient exploration of the optimal design space within a semi-supervised learning framework which reduces the need for large labelled datasets. The proposed approach comprises three key stages. First, we learn the geometric representation of circuits and enrich it with technology information to create a comprehensive feature vector. Subsequently, integrating feature-based graph learning with few-shot and zero-shot learning enhances the generalizability in predictions for unseen circuits. Finally, we introduce two algorithms namely, EASCO and ASTROG which upon integration with GCX optimize the available samples to yield the optimal circuit configuration meeting the designer's criteria. The effectiveness of the proposed approach is demonstrated through simulated performance evaluation of various circuits, using derived parameters in 180nm CMOS technology. Furthermore, the generalizability of the approach is extended to higher-order topologies and different technology nodes such as 65nm and 45nm CMOS process nodes.