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This paper describes the 2nd edition of the ICML Topological Deep Learning Challenge that was hosted within the ICML 2024 ELLIS Workshop on Geometry-grounded Representation Learning and Generative Modeling (GRaM). The challenge focused on the problem of representing data in different discrete topological domains in order to bridge the gap between Topological Deep Learning (TDL) and other types of structured datasets (e.g. point clouds, graphs). Specifically, participants were asked to design and implement topological liftings, i.e. mappings between different data structures and topological domains --like hypergraphs, or simplicial/cell/combinatorial complexes. The challenge received 52 submissions satisfying all the requirements. This paper introduces the main scope of the challenge, and summarizes the main results and findings., Comment: Proceedings of the Geometry-grounded Representation Learning and Generative Modeling Workshop (GRaM) at ICML 2024

Protein representation learning aims to learn informative protein embeddings capable of addressing crucial biological questions, such as protein function prediction. Although sequence-based transformer models have shown promising results by leveraging the vast amount of protein sequence data in a self-supervised way, there is still a gap in exploiting the available 3D protein structures. In this work, we propose a pre-training scheme going beyond trivial masking methods leveraging 3D and hierarchical structures of proteins. We propose a novel self-supervised method to pretrain 3D graph neural networks on 3D protein structures, by predicting the distances between local geometric centroids of protein subgraphs and the global geometric centroid of the protein. By considering subgraphs and their relationships to the global protein structure, our model can better learn the geometric properties of the protein structure. We experimentally show that our proposed pertaining strategy leads to significant improvements up to 6\%, in the performance of 3D GNNs in various protein classification tasks. Our work opens new possibilities in unsupervised learning for protein graph models while eliminating the need for multiple views, augmentations, or masking strategies which are currently used so far.

Graph neural networks excel at modeling pairwise interactions, but they cannot flexibly accommodate higher-order interactions and features. Topological deep learning (TDL) has emerged recently as a promising tool for addressing this issue. TDL enables the principled modeling of arbitrary multi-way, hierarchical higher-order interactions by operating on combinatorial topological spaces, such as simplicial or cell complexes, instead of graphs. However, little is known about how to leverage geometric features such as positions and velocities for TDL. This paper introduces E(n)-Equivariant Topological Neural Networks (ETNNs), which are E(n)-equivariant message-passing networks operating on combinatorial complexes, formal objects unifying graphs, hypergraphs, simplicial, path, and cell complexes. ETNNs incorporate geometric node features while respecting rotation, reflection, and translation equivariance. Moreover, ETNNs are natively ready for settings with heterogeneous interactions. We provide a theoretical analysis to show the improved expressiveness of ETNNs over architectures for geometric graphs. We also show how E(n)-equivariant variants of TDL models can be directly derived from our framework. The broad applicability of ETNNs is demonstrated through two tasks of vastly different scales: i) molecular property prediction on the QM9 benchmark and ii) land-use regression for hyper-local estimation of air pollution with multi-resolution irregular geospatial data. The results indicate that ETNNs are an effective tool for learning from diverse types of richly structured data, as they match or surpass SotA equivariant TDL models with a significantly smaller computational burden, thus highlighting the benefits of a principled geometric inductive bias., Comment: 41 pages, 11 figures, 12 tables

The increasing use of information technology has led to a significant share of energy consumption and carbon emissions from data centers. These contributions are expected to rise with the growing demand for big data analytics, increasing digitization, and the development of large artificial intelligence (AI) models. The need to address the environmental impact of software development has led to increased interest in green (sustainable) coding and claims that the use of AI models can lead to energy efficiency gains. Here, we provide an empirical study on green code and an overview of green coding practices, as well as metrics used to quantify the sustainability awareness of AI models. In this framework, we evaluate the sustainability of auto-generated code. The auto-generate codes considered in this study are produced by generative commercial AI language models, GitHub Copilot, OpenAI ChatGPT-3, and Amazon CodeWhisperer. Within our methodology, in order to quantify the sustainability awareness of these AI models, we propose a definition of the code's "green capacity", based on certain sustainability metrics. We compare the performance and green capacity of human-generated code and code generated by the three AI language models in response to easy-to-hard problem statements. Our findings shed light on the current capacity of AI models to contribute to sustainable software development.

This paper addresses the challenge of extending general finite sequences of real numbers within a subinterval of the real line, maintaining their inherent statistical properties by employing machine learning. Our focus lies on preserving the gap distribution and pair correlation function of these point sets. Leveraging advancements in deep learning applied to point processes, this paper explores the use of an auto-regressive \textit{Sequence Extension Mixture Model} (SEMM) for extending finite sequences, by estimating directly the conditional density, instead of the intensity function. We perform comparative experiments on multiple types of point processes, including Poisson, locally attractive, and locally repelling sequences, and we perform a case study on the prediction of Riemann $\zeta$ function zeroes. The results indicate that the proposed mixture model outperforms traditional neural network architectures in sequence extension with the retention of statistical properties. Given this motivation, we showcase the capabilities of a mixture model to extend sequences, maintaining specific statistical properties, i.e. the gap distribution, and pair correlation indicators., Comment: 17 pages

Graph unlearning, which involves deleting graph elements such as nodes, node labels, and relationships from a trained graph neural network (GNN) model, is crucial for real-world applications where data elements may become irrelevant, inaccurate, or privacy-sensitive. However, existing methods for graph unlearning either deteriorate model weights shared across all nodes or fail to effectively delete edges due to their strong dependence on local graph neighborhoods. To address these limitations, we introduce GNNDelete, a novel model-agnostic layer-wise operator that optimizes two critical properties, namely, Deleted Edge Consistency and Neighborhood Influence, for graph unlearning. Deleted Edge Consistency ensures that the influence of deleted elements is removed from both model weights and neighboring representations, while Neighborhood Influence guarantees that the remaining model knowledge is preserved after deletion. GNNDelete updates representations to delete nodes and edges from the model while retaining the rest of the learned knowledge. We conduct experiments on seven real-world graphs, showing that GNNDelete outperforms existing approaches by up to 38.8% (AUC) on edge, node, and node feature deletion tasks, and 32.2% on distinguishing deleted edges from non-deleted ones. Additionally, GNNDelete is efficient, taking 12.3x less time and 9.3x less space than retraining GNN from scratch on WordNet18., Comment: Accepted to ICLR2023

Graph autoencoders (GAE) and variational graph autoencoders (VGAE) emerged as powerful methods for link prediction (LP). Their performances are less impressive on community detection (CD), where they are often outperformed by simpler alternatives such as the Louvain method. It is still unclear to what extent one can improve CD with GAE and VGAE, especially in the absence of node features. It is moreover uncertain whether one could do so while simultaneously preserving good performances on LP in a multi-task setting. In this workshop paper, summarizing results from our journal publication (Salha-Galvan et al. 2022), we show that jointly addressing these two tasks with high accuracy is possible. For this purpose, we introduce a community-preserving message passing scheme, doping our GAE and VGAE encoders by considering both the initial graph and Louvain-based prior communities when computing embedding spaces. Inspired by modularity-based clustering, we further propose novel training and optimization strategies specifically designed for joint LP and CD. We demonstrate the empirical effectiveness of our approach, referred to as Modularity-Aware GAE and VGAE, on various real-world graphs., Comment: This NeurIPS 2022 GLFrontiers workshop paper summarizes results from the following journal article: arXiv:2202.00961. arXiv admin note: text overlap with arXiv:2205.14651

Artificial intelligence for graphs has achieved remarkable success in modeling complex systems, ranging from dynamic networks in biology to interacting particle systems in physics. However, the increasingly heterogeneous graph datasets call for multimodal methods that can combine different inductive biases: the set of assumptions that algorithms use to make predictions for inputs they have not encountered during training. Learning on multimodal datasets presents fundamental challenges because the inductive biases can vary by data modality and graphs might not be explicitly given in the input. To address these challenges, multimodal graph AI methods combine different modalities while leveraging cross-modal dependencies using graphs. Diverse datasets are combined using graphs and fed into sophisticated multimodal architectures, specified as image-intensive, knowledge-grounded and language-intensive models. Using this categorization, we introduce a blueprint for multimodal graph learning, use it to study existing methods and provide guidelines to design new models., Comment: 27 pages, 5 figures, 2 boxes

Graph Neural Networks (GNNs) have been successfully used in many problems involving graph-structured data, achieving state-of-the-art performance. GNNs typically employ a message-passing scheme, in which every node aggregates information from its neighbors using a permutation-invariant aggregation function. Standard well-examined choices such as the mean or sum aggregation functions have limited capabilities, as they are not able to capture interactions among neighbors. In this work, we formalize these interactions using an information-theoretic framework that notably includes synergistic information. Driven by this definition, we introduce the Graph Ordering Attention (GOAT) layer, a novel GNN component that captures interactions between nodes in a neighborhood. This is achieved by learning local node orderings via an attention mechanism and processing the ordered representations using a recurrent neural network aggregator. This design allows us to make use of a permutation-sensitive aggregator while maintaining the permutation-equivariance of the proposed GOAT layer. The GOAT model demonstrates its increased performance in modeling graph metrics that capture complex information, such as the betweenness centrality and the effective size of a node. In practical use-cases, its superior modeling capability is confirmed through its success in several real-world node classification benchmarks., Comment: Accepted at AAAI 2023

Graph autoencoders (GAE) and variational graph autoencoders (VGAE) emerged as powerful methods for link prediction. Their performances are less impressive on community detection problems where, according to recent and concurring experimental evaluations, they are often outperformed by simpler alternatives such as the Louvain method. It is currently still unclear to which extent one can improve community detection with GAE and VGAE, especially in the absence of node features. It is moreover uncertain whether one could do so while simultaneously preserving good performances on link prediction. In this paper, we show that jointly addressing these two tasks with high accuracy is possible. For this purpose, we introduce and theoretically study a community-preserving message passing scheme, doping our GAE and VGAE encoders by considering both the initial graph structure and modularity-based prior communities when computing embedding spaces. We also propose novel training and optimization strategies, including the introduction of a modularity-inspired regularizer complementing the existing reconstruction losses for joint link prediction and community detection. We demonstrate the empirical effectiveness of our approach, referred to as Modularity-Aware GAE and VGAE, through in-depth experimental validation on various real-world graphs., Comment: Accepted for publication in Elsevier's Neural Networks journal in 2022

Graph neural networks (GNNs) have recently emerged as a dominant paradigm for machine learning with graphs. Research on GNNs has mainly focused on the family of message passing neural networks (MPNNs). Similar to the Weisfeiler-Leman (WL) test of isomorphism, these models follow an iterative neighborhood aggregation procedure to update vertex representations, and they next compute graph representations by aggregating the representations of the vertices. Although very successful, MPNNs have been studied intensively in the past few years. Thus, there is a need for novel architectures which will allow research in the field to break away from MPNNs. In this paper, we propose a new graph neural network model, so-called $\pi$-GNN which learns a "soft" permutation (i.e., doubly stochastic) matrix for each graph, and thus projects all graphs into a common vector space. The learned matrices impose a "soft" ordering on the vertices of the input graphs, and based on this ordering, the adjacency matrices are mapped into vectors. These vectors can be fed into fully-connected or convolutional layers to deal with supervised learning tasks. In case of large graphs, to make the model more efficient in terms of running time and memory, we further relax the doubly stochastic matrices to row stochastic matrices. We empirically evaluate the model on graph classification and graph regression datasets and show that it achieves performance competitive with state-of-the-art models., Comment: Accepted at IEEE Transactions on Pattern Analysis and Machine Intelligence

Neural Architecture Search (NAS) has recently gained increased attention, as a class of approaches that automatically searches in an input space of network architectures. A crucial part of the NAS pipeline is the encoding of the architecture that consists of the applied computational blocks, namely the operations and the links between them. Most of the existing approaches either fail to capture the structural properties of the architectures or use hand-engineered vector to encode the operator information. In this paper, we propose the replacement of fixed operator encoding with learnable representations in the optimization process. This approach, which effectively captures the relations of different operations, leads to smoother and more accurate representations of the architectures and consequently to improved performance of the end task. Our extensive evaluation in ENAS benchmark demonstrates the effectiveness of the proposed operation embeddings to the generation of highly accurate models, achieving state-of-the-art performance. Finally, our method produces top-performing architectures that share similar operation and graph patterns, highlighting a strong correlation between the structural properties of the architecture and its performance., Comment: 12 pages, 10 figures

Attention based neural networks are state of the art in a large range of applications. However, their performance tends to degrade when the number of layers increases. In this work, we show that enforcing Lipschitz continuity by normalizing the attention scores can significantly improve the performance of deep attention models. First, we show that, for deep graph attention networks (GAT), gradient explosion appears during training, leading to poor performance of gradient-based training algorithms. To address this issue, we derive a theoretical analysis of the Lipschitz continuity of attention modules and introduce LipschitzNorm, a simple and parameter-free normalization for self-attention mechanisms that enforces the model to be Lipschitz continuous. We then apply LipschitzNorm to GAT and Graph Transformers and show that their performance is substantially improved in the deep setting (10 to 30 layers). More specifically, we show that a deep GAT model with LipschitzNorm achieves state of the art results for node label prediction tasks that exhibit long-range dependencies, while showing consistent improvements over their unnormalized counterparts in benchmark node classification tasks., Comment: 18 pages. Proceedings of the 38th International Conference on Machine Learning, PMLR 139, 2021. Copyright 2021 by the author(s)

Machine learning on graph-structured data has attracted high research interest due to the emergence of Graph Neural Networks (GNNs). Most of the proposed GNNs are based on the node homophily, i.e neighboring nodes share similar characteristics. However, in many complex networks, nodes that lie to distant parts of the graph share structurally equivalent characteristics and exhibit similar roles (e.g chemical properties of distant atoms in a molecule, type of social network users). A growing literature proposed representations that identify structurally equivalent nodes. However, most of the existing methods require high time and space complexity. In this paper, we propose VNEstruct, a simple approach, based on entropy measures of the neighborhood's topology, for generating low-dimensional structural representations, that is time-efficient and robust to graph perturbations. Empirically, we observe that VNEstruct exhibits robustness on structural role identification tasks. Moreover, VNEstruct can achieve state-of-the-art performance on graph classification, without incorporating the graph structure information in the optimization, in contrast to GNN competitors., Comment: Accepted to ICASSP 2021. arXiv admin note: substantial text overlap with arXiv:2003.00553

In many domains data is currently represented as graphs and therefore, the graph representation of this data becomes increasingly important in machine learning. Network data is, implicitly or explicitly, always represented using a graph shift operator (GSO) with the most common choices being the adjacency, Laplacian matrices and their normalisations. In this paper, a novel parametrised GSO (PGSO) is proposed, where specific parameter values result in the most commonly used GSOs and message-passing operators in graph neural network (GNN) frameworks. The PGSO is suggested as a replacement of the standard GSOs that are used in state-of-the-art GNN architectures and the optimisation of the PGSO parameters is seamlessly included in the model training. It is proved that the PGSO has real eigenvalues and a set of real eigenvectors independent of the parameter values and spectral bounds on the PGSO are derived. PGSO parameters are shown to adapt to the sparsity of the graph structure in a study on stochastic blockmodel networks, where they are found to automatically replicate the GSO regularisation found in the literature. On several real-world datasets the accuracy of state-of-the-art GNN architectures is improved by the inclusion of the PGSO in both node- and graph-classification tasks., Comment: 17 pages, 8 figures

Neural networks are the pinnacle of Artificial Intelligence, as in recent years we witnessed many novel architectures, learning and optimization techniques for deep learning. Capitalizing on the fact that neural networks inherently constitute multipartite graphs among neuron layers, we aim to analyze directly their structure to extract meaningful information that can improve the learning process. To our knowledge graph mining techniques for enhancing learning in neural networks have not been thoroughly investigated. In this paper we propose an adapted version of the k-core structure for the complete weighted multipartite graph extracted from a deep learning architecture. As a multipartite graph is a combination of bipartite graphs, that are in turn the incidence graphs of hypergraphs, we design k-hypercore decomposition, the hypergraph analogue of k-core degeneracy. We applied k-hypercore to several neural network architectures, more specifically to convolutional neural networks and multilayer perceptrons for image recognition tasks after a very short pretraining. Then we used the information provided by the hypercore numbers of the neurons to re-initialize the weights of the neural network, thus biasing the gradient optimization scheme. Extensive experiments proved that k-hypercore outperforms the state-of-the-art initialization methods.

In complex networks, nodes that share similar structural characteristics often exhibit similar roles (e.g type of users in a social network or the hierarchical position of employees in a company). In order to leverage this relationship, a growing literature proposed latent representations that identify structurally equivalent nodes. However, most of the existing methods require high time and space complexity. In this paper, we propose VNEstruct, a simple approach for generating low-dimensional structural node embeddings, that is both time efficient and robust to perturbations of the graph structure. The proposed approach focuses on the local neighborhood of each node and employs the Von Neumann entropy, an information-theoretic tool, to extract features that capture the neighborhood's topology. Moreover, on graph classification tasks, we suggest the utilization of the generated structural embeddings for the transformation of an attributed graph structure into a set of augmented node attributes. Empirically, we observe that the proposed approach exhibits robustness on structural role identification tasks and state-of-the-art performance on graph classification tasks, while maintaining very high computational speed., Comment: 7 pages, 4 figures

In this paper, we show that a simple coloring scheme can improve, both theoretically and empirically, the expressive power of Message Passing Neural Networks(MPNNs). More specifically, we introduce a graph neural network called Colored Local Iterative Procedure (CLIP) that uses colors to disambiguate identical node attributes, and show that this representation is a universal approximator of continuous functions on graphs with node attributes. Our method relies on separability , a key topological characteristic that allows to extend well-chosen neural networks into universal representations. Finally, we show experimentally that CLIP is capable of capturing structural characteristics that traditional MPNNs fail to distinguish,while being state-of-the-art on benchmark graph classification datasets., Comment: 17 pages, 2 figures

Graph neural networks (GNNs) have emerged recently as a powerful architecture for learning node and graph representations. Standard GNNs have the same expressive power as the Weisfeiler-Leman test of graph isomorphism in terms of distinguishing non-isomorphic graphs. However, it was recently shown that this test cannot identify fundamental graph properties such as connectivity and triangle freeness. We show that GNNs also suffer from the same limitation. To address this limitation, we propose a more expressive architecture, k-hop GNNs, which updates a node's representation by aggregating information not only from its direct neighbors, but from its k-hop neighborhood. We show that the proposed architecture can identify fundamental graph properties. We evaluate the proposed architecture on standard node classification and graph classification datasets. Our experimental evaluation confirms our theoretical findings since the proposed model achieves performance better or comparable to standard GNNs and to state-of-the-art algorithms., Comment: Accepted at Neural Networks