Attribute-Enhanced Similarity Ranking for Sparse Link Prediction

Link prediction is a fundamental problem in graph data. In its most realistic setting, the problem consists of predicting missing or future links between random pairs of nodes from the set of disconnected pairs. Graph Neural Networks (GNNs) have become the predominant framework for link prediction. GNN-based methods treat link prediction as a binary classification problem and handle the extreme class imbalance -- real graphs are very sparse -- by sampling (uniformly at random) a balanced number of disconnected pairs not only for training but also for evaluation. However, we show that the reported performance of GNNs for link prediction in the balanced setting does not translate to the more realistic imbalanced setting and that simpler topology-based approaches are often better at handling sparsity. These findings motivate Gelato, a similarity-based link-prediction method that applies (1) graph learning based on node attributes to enhance a topological heuristic, (2) a ranking loss for addressing class imbalance, and (3) a negative sampling scheme that efficiently selects hard training pairs via graph partitioning. Experiments show that Gelato outperforms existing GNN-based alternatives.

Normalized Space Alignment: A Versatile Metric for Representation Analysis

We introduce a manifold analysis technique for neural network representations. Normalized Space Alignment (NSA) compares pairwise distances between two point clouds derived from the same source and having the same size, while potentially possessing differing dimensionalities. NSA can act as both an analytical tool and a differentiable loss function, providing a robust means of comparing and aligning representations across different layers and models. It satisfies the criteria necessary for both a similarity metric and a neural network loss function. We showcase NSA's versatility by illustrating its utility as a representation space analysis metric, a structure-preserving loss function, and a robustness analysis tool. NSA is not only computationally efficient but it can also approximate the global structural discrepancy during mini-batching, facilitating its use in a wide variety of neural network training paradigms.

Global Human-guided Counterfactual Explanations for Molecular Properties via Reinforcement Learning

Counterfactual explanations of Graph Neural Networks (GNNs) offer a powerful way to understand data that can naturally be represented by a graph structure. Furthermore, in many domains, it is highly desirable to derive data-driven global explanations or rules that can better explain the high-level properties of the models and data in question. However, evaluating global counterfactual explanations is hard in real-world datasets due to a lack of human-annotated ground truth, which limits their use in areas like molecular sciences. Additionally, the increasing scale of these datasets provides a challenge for random search-based methods. In this paper, we develop a novel global explanation model RLHEX for molecular property prediction. It aligns the counterfactual explanations with human-defined principles, making the explanations more interpretable and easy for experts to evaluate. RLHEX includes a VAE-based graph generator to generate global explanations and an adapter to adjust the latent representation space to human-defined principles. Optimized by Proximal Policy Optimization (PPO), the global explanations produced by RLHEX cover 4.12% more input graphs and reduce the distance between the counterfactual explanation set and the input set by 0.47% on average across three molecular datasets. RLHEX provides a flexible framework to incorporate different human-designed principles into the counterfactual explanation generation process, aligning these explanations with domain expertise. The code and data are released at https://github.com/dqwang122/RLHEX.

Learning Neural Contracting Dynamics: Extended Linearization and Global Guarantees

Global stability and robustness guarantees in learned dynamical systems are essential to ensure well-behavedness of the systems in the face of uncertainty. We present Extended Linearized Contracting Dynamics (ELCD), the first neural network-based dynamical system with global contractivity guarantees in arbitrary metrics. The key feature of ELCD is a parametrization of the extended linearization of the nonlinear vector field. In its most basic form, ELCD is guaranteed to be (i) globally exponentially stable, (ii) equilibrium contracting, and (iii) globally contracting with respect to some metric. To allow for contraction with respect to more general metrics in the data space, we train diffeomorphisms between the data space and a latent space and enforce contractivity in the latent space, which ensures global contractivity in the data space. We demonstrate the performance of ELCD on the $2$D, $4$D, and $8$D LASA datasets.

DGCLUSTER: A Neural Framework for Attributed Graph Clustering via Modularity Maximization

Graph clustering is a fundamental and challenging task in the field of graph mining where the objective is to group the nodes into clusters taking into consideration the topology of the graph. It has several applications in diverse domains spanning social network analysis, recommender systems, computer vision, and bioinformatics. In this work, we propose a novel method, DGCluster, which primarily optimizes the modularity objective using graph neural networks and scales linearly with the graph size. Our method does not require the number of clusters to be specified as a part of the input and can also leverage the availability of auxiliary node level information. We extensively test DGCluster on several real-world datasets of varying sizes, across multiple popular cluster quality metrics. Our approach consistently outperforms the state-of-the-art methods, demonstrating significant performance gains in almost all settings.

XplainLLM: A QA Explanation Dataset for Understanding LLM Decision-Making

Large Language Models (LLMs) have recently made impressive strides in natural language understanding tasks. Despite their remarkable performance, understanding their decision-making process remains a big challenge. In this paper, we look into bringing some transparency to this process by introducing a new explanation dataset for question answering (QA) tasks that integrates knowledge graphs (KGs) in a novel way. Our dataset includes 12,102 question-answer-explanation (QAE) triples. Each explanation in the dataset links the LLM's reasoning to entities and relations in the KGs. The explanation component includes a why-choose explanation, a why-not-choose explanation, and a set of reason-elements that underlie the LLM's decision. We leverage KGs and graph attention networks (GAT) to find the reason-elements and transform them into why-choose and why-not-choose explanations that are comprehensible to humans. Through quantitative and qualitative evaluations, we demonstrate the potential of our dataset to improve the in-context learning of LLMs, and enhance their interpretability and explainability. Our work contributes to the field of explainable AI by enabling a deeper understanding of the LLMs decision-making process to make them more transparent and thereby, potentially more reliable, to researchers and practitioners alike. Our dataset is available at: https://github.com/chen-zichen/XplainLLM_dataset.git

Fragment-based Pretraining and Finetuning on Molecular Graphs

Property prediction on molecular graphs is an important application of Graph Neural Networks (GNNs). Recently, unlabeled molecular data has become abundant, which facilitates the rapid development of self-supervised learning for GNNs in the chemical domain. In this work, we propose pretraining GNNs at the fragment level, which serves as a promising middle ground to overcome the limitations of node-level and graph-level pretraining. Borrowing techniques from recent work on principle subgraph mining, we obtain a compact vocabulary of prevalent fragments that span a large pretraining dataset. From the extracted vocabulary, we introduce several fragment-based contrastive and predictive pretraining tasks. The contrastive learning task jointly pretrains two different GNNs: one based on molecular graphs and one based on fragment graphs, which represents high-order connectivity within molecules. By enforcing the consistency between the fragment embedding and the aggregated embedding of the corresponding atoms from the molecular graphs, we ensure that both embeddings capture structural information at multiple resolutions. The structural information of the fragment graphs is further exploited to extract auxiliary labels for the graph-level predictive pretraining. We employ both the pretrained molecular-based and fragment-based GNNs for downstream prediction, thus utilizing the fragment information during finetuning. Our models advance the performances on 5 out of 8 common molecular benchmarks and improve the performances on long-range biological benchmarks by at least 11.5%.

GNNX-BENCH: Unravelling the Utility of Perturbation-based GNN Explainers through In-depth Benchmarking

Numerous explainability methods have been proposed to shed light on the inner workings of GNNs. Despite the inclusion of empirical evaluations in all the proposed algorithms, the interrogative aspects of these evaluations lack diversity. As a result, various facets of explainability pertaining to GNNs, such as a comparative analysis of counterfactual reasoners, their stability to variational factors such as different GNN architectures, noise, stochasticity in non-convex loss surfaces, feasibility amidst domain constraints, and so forth, have yet to be formally investigated. Motivated by this need, we present a benchmarking study on perturbation-based explainability methods for GNNs, aiming to systematically evaluate and compare a wide range of explainability techniques. Among the key findings of our study, we identify the Pareto-optimal methods that exhibit superior efficacy and stability in the presence of noise. Nonetheless, our study reveals that all algorithms are affected by stability issues when faced with noisy data. Furthermore, we have established that the current generation of counterfactual explainers often fails to provide feasible recourses due to violations of topological constraints encoded by domain-specific considerations. Overall, this benchmarking study empowers stakeholders in the field of GNNs with a comprehensive understanding of the state-of-the-art explainability methods, potential research problems for further enhancement, and the implications of their application in real-world scenarios.

Graph Encoding and Neural Network Approaches for Volleyball Analytics: From Game Outcome to Individual Play Predictions

This research aims to improve the accuracy of complex volleyball predictions and provide more meaningful insights to coaches and players. We introduce a specialized graph encoding technique to add additional contact-by-contact volleyball context to an already available volleyball dataset without any additional data gathering. We demonstrate the potential benefits of using graph neural networks (GNNs) on this enriched dataset for three different volleyball prediction tasks: rally outcome prediction, set location prediction, and hit type prediction. We compare the performance of our graph-based models to baseline models and analyze the results to better understand the underlying relationships in a volleyball rally. Our results show that the use of GNNs with our graph encoding yields a much more advanced analysis of the data, which noticeably improves prediction results overall. We also show that these baseline tasks can be significantly improved with simple adjustments, such as removing blocked hits. Lastly, we demonstrate the importance of choosing a model architecture that will better extract the important information for a certain task. Overall, our study showcases the potential strengths and weaknesses of using graph encodings in sports data analytics and hopefully will inspire future improvements in machine learning strategies across sports and applications by using graphbased encodings.

Robust Ante-hoc Graph Explainer using Bilevel Optimization

Explaining the decisions made by machine learning models for high-stakes applications is critical for increasing transparency and guiding improvements to these decisions. This is particularly true in the case of models for graphs, where decisions often depend on complex patterns combining rich structural and attribute data. While recent work has focused on designing so-called post-hoc explainers, the question of what constitutes a good explanation remains open. One intuitive property is that explanations should be sufficiently informative to enable humans to approximately reproduce the predictions given the data. However, we show that post-hoc explanations do not achieve this goal as their explanations are highly dependent on fixed model parameters (e.g., learned GNN weights). To address this challenge, this paper proposes RAGE (Robust Ante-hoc Graph Explainer), a novel and flexible ante-hoc explainer designed to discover explanations for a broad class of graph neural networks using bilevel optimization. RAGE is able to efficiently identify explanations that contain the full information needed for prediction while still enabling humans to rank these explanations based on their influence. Our experiments, based on graph classification and regression, show that RAGE explanations are more robust than existing post-hoc and ante-hoc approaches and often achieve similar or better accuracy than state-of-the-art models.