Donald Loveland

Donald Loveland, Jiong Zhu, Mark Heimann et al.

Graph Neural Network (GNN) research has highlighted a relationship between high homophily (i.e., the tendency of nodes of the same class to connect) and strong predictive performance in node classification. However, recent work has found the relationship to be more nuanced, demonstrating that simple GNNs can learn in certain heterophilous settings. To resolve these conflicting findings and align closer to real-world datasets, we go beyond the assumption of a global graph homophily level and study the performance of GNNs when the local homophily level of a node deviates from the global homophily level. Through theoretical and empirical analysis, we systematically demonstrate how shifts in local homophily can introduce performance degradation, leading to performance discrepancies across local homophily levels. We ground the practical implications of this work through granular analysis on five real-world datasets with varying global homophily levels, demonstrating that (a) GNNs can fail to generalize to test nodes that deviate from the global homophily of a graph, and (b) high local homophily does not necessarily confer high performance for a node. We further show that GNNs designed for globally heterophilous graphs can alleviate performance discrepancy by improving performance across local homophily levels, offering a new perspective on how these GNNs achieve stronger global performance.

Donald Loveland, Jiong Zhu, Mark Heimann et al.

We study the task of node classification for graph neural networks (GNNs) and establish a connection between group fairness, as measured by statistical parity and equal opportunity, and local assortativity, i.e., the tendency of linked nodes to have similar attributes. Such assortativity is often induced by homophily, the tendency for nodes of similar properties to connect. Homophily can be common in social networks where systemic factors have forced individuals into communities which share a sensitive attribute. Through synthetic graphs, we study the interplay between locally occurring homophily and fair predictions, finding that not all node neighborhoods are equal in this respect -- neighborhoods dominated by one category of a sensitive attribute often struggle to obtain fair treatment, especially in the case of diverging local class and sensitive attribute homophily. After determining that a relationship between local homophily and fairness exists, we investigate if the issue of unfairness can be associated to the design of the applied GNN model. We show that by adopting heterophilous GNN designs capable of handling disassortative group labels, group fairness in locally heterophilous neighborhoods can be improved by up to 25% over homophilous designs in real and synthetic datasets.

Ioannis Tsaknakis, Bhavya Kailkhura, Sijia Liu et al.

Using deep learning (DL) to accelerate and/or improve scientific workflows can yield discoveries that are otherwise impossible. Unfortunately, DL models have yielded limited success in complex scientific domains due to large data requirements. In this work, we propose to overcome this issue by integrating the abundance of scientific knowledge sources (SKS) with the DL training process. Existing knowledge integration approaches are limited to using differentiable knowledge source to be compatible with first-order DL training paradigm. In contrast, our proposed approach treats knowledge source as a black-box in turn allowing to integrate virtually any knowledge source. To enable an end-to-end training of SKS-coupled-DL, we propose to use zeroth-order optimization (ZOO) based gradient-free training schemes, which is non-intrusive, i.e., does not require making any changes to the SKS. We evaluate the performance of our ZOO training scheme on two real-world material science applications. We show that proposed scheme is able to effectively integrate scientific knowledge with DL training and is able to outperform purely data-driven model for data-limited scientific applications. We also discuss some limitations of the proposed method and mention potentially worthwhile future directions.

Quang Truong, Yu Song, Donald Loveland et al.

Link prediction is a core challenge in graph machine learning, demanding models that capture rich and complex topological dependencies. While Graph Neural Networks (GNNs) are the standard solution, state-of-the-art pipelines often rely on explicit structural heuristics or memory-intensive node embeddings -- approaches that struggle to generalize or scale to massive graphs. Emerging Graph Transformers (GTs) offer a potential alternative but often incur significant overhead due to complex structural encodings, hindering their applications to large-scale link prediction. We challenge these sophisticated paradigms with PENCIL, an encoder-only plain Transformer that replaces hand-crafted priors with attention over sampled local subgraphs, retaining the scalability and hardware efficiency of standard Transformers. Through experimental and theoretical analysis, we show that PENCIL extracts richer structural signals than GNNs, implicitly generalizing a broad class of heuristics and subgraph-based expressivity. Empirically, PENCIL outperforms heuristic-informed GNNs and is far more parameter-efficient than ID-embedding--based alternatives, while remaining competitive across diverse benchmarks -- even without node features. Our results challenge the prevailing reliance on complex engineering techniques, demonstrating that simple design choices are potentially sufficient to achieve the same capabilities.

Liam Collins, Bhuvesh Kumar, Clark Mingxuan Ju et al.

Modern Sequential Recommendation (SR) models commonly utilize modality features to represent items, motivated in large part by recent advancements in language and vision modeling. To do so, several works completely replace ID embeddings with modality embeddings, claiming that modality embeddings render ID embeddings unnecessary because they can match or even exceed ID embedding performance. On the other hand, many works jointly utilize ID and modality features, but posit that complex fusion strategies, such as multi-stage training and/or intricate alignment architectures, are necessary for this joint utilization. However, underlying both these lines of work is a lack of understanding of the complementarity of ID and modality features. In this work, we address this gap by studying the complementarity of ID- and text-based SR models. We show that these models do learn complementary signals, meaning that either should provide performance gain when used properly alongside the other. Motivated by this, we propose a new SR method that preserves ID-text complementarity through independent model training, then harnesses it through a simple ensembling strategy. Despite this method's simplicity, we show it outperforms several competitive SR baselines, implying that both ID and text features are necessary to achieve state-of-the-art SR performance but complex fusion architectures are not.

Donald Loveland, Rajmonda Caceres

Graph Neural Network (GNN) research has produced strategies to modify a graph's edges using gradients from a trained GNN, with the goal of network design. However, the factors which govern gradient-based editing are understudied, obscuring why edges are chosen and if edits are grounded in an edge's importance. Thus, we begin by analyzing the gradient computation in previous works, elucidating the factors that influence edits and highlighting the potential over-reliance on structural properties. Specifically, we find that edges can achieve high gradients due to structural biases, rather than importance, leading to erroneous edits when the factors are unrelated to the design task. To improve editing, we propose ORE, an iterative editing method that (a) edits the highest scoring edges and (b) re-embeds the edited graph to refresh gradients, leading to less biased edge choices. We empirically study ORE through a set of proposed design tasks, each with an external validation method, demonstrating that ORE improves upon previous methods by up to 50%.

Donald Loveland, Xinyi Wu, Tong Zhao et al.

Collaborative Filtering (CF) methods dominate real-world recommender systems given their ability to learn high-quality, sparse ID-embedding tables that effectively capture user preferences. These tables scale linearly with the number of users and items, and are trained to ensure high similarity between embeddings of interacted user-item pairs, while maintaining low similarity for non-interacted pairs. Despite their high performance, encouraging dispersion for non-interacted pairs necessitates expensive regularization (e.g., negative sampling), hurting runtime and scalability. Existing research tends to address these challenges by simplifying the learning process, either by reducing model complexity or sampling data, trading performance for runtime. In this work, we move beyond model-level modifications and study the properties of the embedding tables under different learning strategies. Through theoretical analysis, we find that the singular values of the embedding tables are intrinsically linked to different CF loss functions. These findings are empirically validated on real-world datasets, demonstrating the practical benefits of higher stable rank, a continuous version of matrix rank which encodes the distribution of singular values. Based on these insights, we propose an efficient warm-start strategy that regularizes the stable rank of the user and item embeddings. We show that stable rank regularization during early training phases can promote higher-quality embeddings, resulting in training speed improvements of up to 66%. Additionally, stable rank regularization can act as a proxy for negative sampling, allowing for performance gains of up to 21% over loss functions with small negative sampling ratios. Overall, our analysis unifies current CF methods under a new perspective, their optimization of stable rank, motivating a flexible regularization method.

Donald Loveland, Yao-An Yang, Danai Koutra

Learning on text-attributed graphs has motivated the use of Large Language Models (LLMs) for graph learning. However, most fusion strategies are applied uniformly across all nodes and attain only small overall performance gains. We argue this result stems from aggregate metrics that obscure when LLMs provide benefit, inhibiting actionable signals for new strategies. In this work, we reframe LLM-GNN fusion around nodes where GNNs typically falter. We first show that performance can significantly differ between GNNs and LLMs, with each excelling on distinct structural patterns, such as local homophily. To leverage this finding, we propose GLANCE (GNN with LLM Assistance for Neighbor- and Context-aware Embeddings), a framework that invokes an LLM to refine a GNN's prediction. GLANCE employs a lightweight router that, given inexpensive per-node signals, decides whether to query the LLM. Since the LLM calls are non-differentiable, the router is trained with an advantage-based objective that compares the utility of querying the LLM against relying solely on the GNN. Across multiple benchmarks, GLANCE achieves the best performance balance across node subgroups, achieving significant gains on heterophilous nodes (up to $+13\%$) while simultaneously achieving top overall performance. Our findings highlight the value of adaptive, node-aware GNN-LLM architectures, where selectively invoking the LLM enables scalable deployment on large graphs without incurring high computational costs.

Donald Loveland, Jiayi Pan, Aaresh Farrokh Bhathena et al.

Graph Neural Networks (GNNs) have proven to excel in predictive modeling tasks where the underlying data is a graph. However, as GNNs are extensively used in human-centered applications, the issue of fairness has arisen. While edge deletion is a common method used to promote fairness in GNNs, it fails to consider when data is inherently missing fair connections. In this work we consider the unexplored method of edge addition, accompanied by deletion, to promote fairness. We propose two model-agnostic algorithms to perform edge editing: a brute force approach and a continuous approximation approach, FairEdit. FairEdit performs efficient edge editing by leveraging gradient information of a fairness loss to find edges that improve fairness. We find that FairEdit outperforms standard training for many data sets and GNN methods, while performing comparably to many state-of-the-art methods, demonstrating FairEdit's ability to improve fairness across many domains and models.

Donald Loveland, Shusen Liu, Bhavya Kailkhura et al.

Graph neural network (GNN) explanations have largely been facilitated through post-hoc introspection. While this has been deemed successful, many post-hoc explanation methods have been shown to fail in capturing a model's learned representation. Due to this problem, it is worthwhile to consider how one might train a model so that it is more amenable to post-hoc analysis. Given the success of adversarial training in the computer vision domain to train models with more reliable representations, we propose a similar training paradigm for GNNs and analyze the respective impact on a model's explanations. In instances without ground truth labels, we also determine how well an explanation method is utilizing a model's learned representation through a new metric and demonstrate adversarial training can help better extract domain-relevant insights in chemistry.

Jiong Zhu, Junchen Jin, Donald Loveland et al.

We bridge two research directions on graph neural networks (GNNs), by formalizing the relation between heterophily of node labels (i.e., connected nodes tend to have dissimilar labels) and the robustness of GNNs to adversarial attacks. Our theoretical and empirical analyses show that for homophilous graph data, impactful structural attacks always lead to reduced homophily, while for heterophilous graph data the change in the homophily level depends on the node degrees. These insights have practical implications for defending against attacks on real-world graphs: we deduce that separate aggregators for ego- and neighbor-embeddings, a design principle which has been identified to significantly improve prediction for heterophilous graph data, can also offer increased robustness to GNNs. Our comprehensive experiments show that GNNs merely adopting this design achieve improved empirical and certifiable robustness compared to the best-performing unvaccinated model. Additionally, combining this design with explicit defense mechanisms against adversarial attacks leads to an improved robustness with up to 18.33% performance increase under attacks compared to the best-performing vaccinated model.

Shusen Liu, Bhavya Kailkhura, Jize Zhang et al.

The scientific community has been increasingly interested in harnessing the power of deep learning to solve various domain challenges. However, despite the effectiveness in building predictive models, fundamental challenges exist in extracting actionable knowledge from deep neural networks due to their opaque nature. In this work, we propose techniques for exploring the behavior of deep learning models by injecting domain-specific actionable attributes as tunable "knobs" in the analysis pipeline. By incorporating the domain knowledge in a generative modeling framework, we are not only able to better understand the behavior of these black-box models, but also provide scientists with actionable insights that can potentially lead to fundamental discoveries.

Shusen Liu, Bhavya Kailkhura, Jize Zhang et al.

The scientific community has been increasingly interested in harnessing the power of deep learning to solve various domain challenges. However, despite the effectiveness in building predictive models, fundamental challenges exist in extracting actionable knowledge from the deep neural network due to their opaque nature. In this work, we propose techniques for exploring the behavior of deep learning models by injecting domain-specific actionable concepts as tunable ``knobs'' in the analysis pipeline. By incorporating the domain knowledge with generative modeling, we are not only able to better understand the behavior of these black-box models, but also provide scientists with actionable insights that can potentially lead to fundamental discoveries.

Shusen Liu, Bhavya Kailkhura, Donald Loveland et al.

In this work, we propose an introspection technique for deep neural networks that relies on a generative model to instigate salient editing of the input image for model interpretation. Such modification provides the fundamental interventional operation that allows us to obtain answers to counterfactual inquiries, i.e., what meaningful change can be made to the input image in order to alter the prediction. We demonstrate how to reveal interesting properties of the given classifiers by utilizing the proposed introspection approach on both the MNIST and the CelebA dataset.