Insights from Network Science can advance Deep Graph Learning

Deep graph learning and network science both analyze graphs but approach similar problems from different perspectives. Whereas network science focuses on models and measures that reveal the organizational principles of complex systems with explicit assumptions, deep graph learning focuses on flexible and generalizable models that learn patterns in graph data in an automated fashion. Despite these differences, both fields share the same goal: to better model and understand patterns in graph-structured data. Early efforts to integrate methods, models, and measures from network science and deep graph learning indicate significant untapped potential. In this position, we explore opportunities at their intersection. We discuss open challenges in deep graph learning, including data augmentation, improved evaluation practices, higher-order models, and pooling methods. Likewise, we highlight challenges in network science, including scaling to massive graphs, integrating continuous gradient-based optimization, and developing standardized benchmarks.

Hierarchical Graph Pooling Based on Minimum Description Length

Graph pooling is an essential part of deep graph representation learning. We introduce MapEqPool, a principled pooling operator that takes the inherent hierarchical structure of real-world graphs into account. MapEqPool builds on the map equation, an information-theoretic objective function for community detection based on the minimum description length principle which naturally implements Occam's razor and balances between model complexity and fit. We demonstrate MapEqPool's competitive performance with an empirical comparison against various baselines across standard graph classification datasets.

Inference of Sequential Patterns for Neural Message Passing in Temporal Graphs

The modelling of temporal patterns in dynamic graphs is an important current research issue in the development of time-aware GNNs. Whether or not a specific sequence of events in a temporal graph constitutes a temporal pattern not only depends on the frequency of its occurrence. We consider whether it deviates from what is expected in a temporal graph where timestamps are randomly shuffled. While accounting for such a random baseline is important to model temporal patterns, it has mostly been ignored by current temporal graph neural networks. To address this issue we propose HYPA-DBGNN, a novel two-step approach that combines (i) the inference of anomalous sequential patterns in time series data on graphs based on a statistically principled null model, with (ii) a neural message passing approach that utilizes a higher-order De Bruijn graph whose edges capture overrepresented sequential patterns. Our method leverages hypergeometric graph ensembles to identify anomalous edges within both first- and higher-order De Bruijn graphs, which encode the temporal ordering of events. The model introduces an inductive bias that enhances model interpretability. We evaluate our approach for static node classification using benchmark datasets and a synthetic dataset that showcases its ability to incorporate the observed inductive bias regarding over- and under-represented temporal edges. We demonstrate the framework's effectiveness in detecting similar patterns within empirical datasets, resulting in superior performance compared to baseline methods in node classification tasks. To the best of our knowledge, our work is the first to introduce statistically informed GNNs that leverage temporal and causal sequence anomalies. HYPA-DBGNN represents a path for bridging the gap between statistical graph inference and neural graph representation learning, with potential applications to static GNNs.

Link Prediction with Untrained Message Passing Layers

Message passing neural networks (MPNNs) operate on graphs by exchanging information between neigbouring nodes. MPNNs have been successfully applied to various node-, edge-, and graph-level tasks in areas like molecular science, computer vision, natural language processing, and combinatorial optimization. However, most MPNNs require training on large amounts of labeled data, which can be costly and time-consuming. In this work, we explore the use of various untrained message passing layers in graph neural networks, i.e. variants of popular message passing architecture where we remove all trainable parameters that are used to transform node features in the message passing step. Focusing on link prediction, we find that untrained message passing layers can lead to competitive and even superior performance compared to fully trained MPNNs, especially in the presence of high-dimensional features. We provide a theoretical analysis of untrained message passing by relating the inner products of features implicitly produced by untrained message passing layers to path-based topological node similarity measures. As such, untrained message passing architectures can be viewed as a highly efficient and interpretable approach to link prediction.

From Link Prediction to Forecasting: Information Loss in Batch-based Temporal Graph Learning

Dynamic link prediction is an important problem considered by many recent works proposing various approaches for learning temporal edge patterns. To assess their efficacy, models are evaluated on publicly available benchmark datasets involving continuous-time and discrete-time temporal graphs. However, as we show in this work, the suitability of common batch-oriented evaluation depends on the datasets' characteristics, which can cause two issues: First, for continuous-time temporal graphs, fixed-size batches create time windows with different durations, resulting in an inconsistent dynamic link prediction task. Second, for discrete-time temporal graphs, the sequence of batches can additionally introduce temporal dependencies that are not present in the data. In this work, we empirically show that this common evaluation approach leads to skewed model performance and hinders the fair comparison of methods. We mitigate this problem by reformulating dynamic link prediction as a link forecasting task that better accounts for temporal information present in the data. We provide implementations of our new evaluation method for commonly used graph learning frameworks.

The Self-Loop Paradox: Investigating the Impact of Self-Loops on Graph Neural Networks

Many Graph Neural Networks (GNNs) add self-loops to a graph to include feature information about a node itself at each layer. However, if the GNN consists of more than one layer, this information can return to its origin via cycles in the graph topology. Intuition suggests that this "backflow" of information should be larger in graphs with self-loops compared to graphs without. In this work, we counter this intuition and show that for certain GNN architectures, the information a node gains from itself can be smaller in graphs with self-loops compared to the same graphs without. We adopt an analytical approach for the study of statistical graph ensembles with a given degree sequence and show that this phenomenon, which we call the self-loop paradox, can depend both on the number of GNN layers $k$ and whether $k$ is even or odd. We experimentally validate our theoretical findings in a synthetic node classification task and investigate its practical relevance in 23 real-world graphs.

Using Causality-Aware Graph Neural Networks to Predict Temporal Centralities in Dynamic Graphs

Node centralities play a pivotal role in network science, social network analysis, and recommender systems. In temporal data, static path-based centralities like closeness or betweenness can give misleading results about the true importance of nodes in a temporal graph. To address this issue, temporal generalizations of betweenness and closeness have been defined that are based on the shortest time-respecting paths between pairs of nodes. However, a major issue of those generalizations is that the calculation of such paths is computationally expensive. Addressing this issue, we study the application of De Bruijn Graph Neural Networks (DBGNN), a causality-aware graph neural network architecture, to predict temporal path-based centralities in time series data. We experimentally evaluate our approach in 13 temporal graphs from biological and social systems and show that it considerably improves the prediction of both betweenness and closeness centrality compared to a static Graph Convolutional Neural Network.

The Map Equation Goes Neural

Community detection and graph clustering are essential for unsupervised data exploration and understanding the high-level organisation of networked systems. Recently, graph clustering has been highlighted as an under-explored primary task for graph neural networks. While hierarchical graph pooling has been shown to improve performance in graph and node classification tasks, it performs poorly in identifying meaningful clusters. Community detection has a long history in network science, but typically relies on optimising objective functions with custom-tailored search algorithms, not leveraging recent advances in deep learning, particularly from graph neural networks. In this paper, we narrow this gap between the deep learning and network science communities. We consider the map equation, an information-theoretic objective function for community detection. Expressing it in a fully differentiable tensor form that produces soft cluster assignments, we optimise the map equation with deep learning through gradient descent. More specifically, the reformulated map equation is a loss function compatible with any graph neural network architecture, enabling flexible clustering and graph pooling that clusters both graph structure and data features in an end-to-end way, automatically finding an optimum number of clusters without explicit regularisation. We evaluate our approach experimentally using different neural network architectures for unsupervised clustering in synthetic and real data. Our results show that our approach achieves competitive performance against baselines, naturally detects overlapping communities, and avoids over-partitioning sparse graphs.

Bayesian Inference of Transition Matrices from Incomplete Graph Data with a Topological Prior

Many network analysis and graph learning techniques are based on models of random walks which require to infer transition matrices that formalize the underlying stochastic process in an observed graph. For weighted graphs, it is common to estimate the entries of such transition matrices based on the relative weights of edges. However, we are often confronted with incomplete data, which turns the construction of the transition matrix based on a weighted graph into an inference problem. Moreover, we often have access to additional information, which capture topological constraints of the system, i.e. which edges in a weighted graph are (theoretically) possible and which are not, e.g. transportation networks, where we have access to passenger trajectories as well as the physical topology of connections, or a set of social interactions with the underlying social structure. Combining these two different sources of information to infer transition matrices is an open challenge, with implications on the downstream network analysis tasks. Addressing this issue, we show that including knowledge on such topological constraints can improve the inference of transition matrices, especially for small datasets. We derive an analytically tractable Bayesian method that uses repeated interactions and a topological prior to infer transition matrices data-efficiently. We compare it against commonly used frequentist and Bayesian approaches both in synthetic and real-world datasets, and we find that it recovers the transition probabilities with higher accuracy and that it is robust even in cases when the knowledge of the topological constraint is partial. Lastly, we show that this higher accuracy improves the results for downstream network analysis tasks like cluster detection and node ranking, which highlights the practical relevance of our method for analyses of various networked systems.

One Graph to Rule them All: Using NLP and Graph Neural Networks to analyse Tolkien's Legendarium

Natural Language Processing and Machine Learning have considerably advanced Computational Literary Studies. Similarly, the construction of co-occurrence networks of literary characters, and their analysis using methods from social network analysis and network science, have provided insights into the micro- and macro-level structure of literary texts. Combining these perspectives, in this work we study character networks extracted from a text corpus of J.R.R. Tolkien's Legendarium. We show that this perspective helps us to analyse and visualise the narrative style that characterises Tolkien's works. Addressing character classification, embedding and co-occurrence prediction, we further investigate the advantages of state-of-the-art Graph Neural Networks over a popular word embedding method. Our results highlight the large potential of graph learning in Computational Literary Studies.