arXiv subjects

Danai Koutra

Publications and source records attributed to Danai Koutra.

At least 37 records · Page 2Linked to original sources

arXiv2025

GT2Vec: Large Language Models as Multi-Modal Encoders for Text and Graph-Structured Data

Graph-structured information offers rich contextual information that can enhance language models by providing structured relationships and hierarchies, leading to more expressive embeddings for various applications such as retrieval, question answering, and classification. However, existing methods for integrating graph and text embeddings, often based on Multi-layer Perceptrons (MLPs) or shallow transformers, are limited in their ability to fully exploit the heterogeneous nature of these modalities. To overcome this, we propose GT2Vec, a simple yet effective framework that leverages Large Language Models (LLMs) to jointly encode text and graph data. Specifically, GT2Vec employs an MLP adapter to project graph embeddings into the same space as text embeddings, allowing the LLM to process both modalities jointly. Unlike prior work, we also introduce contrastive learning to align the graph and text spaces more effectively, thereby improving the quality of learned joint embeddings. Empirical results across six datasets spanning three tasks, knowledge graph-contextualized question answering, graph-text pair classification, and retrieval, demonstrate that GT2Vec consistently outperforms existing baselines, achieving significant improvements across multiple datasets. These results highlight GT2Vec's effectiveness in integrating graph and text data. Ablation studies further validate the effectiveness of our method.

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arXiv2024

Accurate and Scalable Estimation of Epistemic Uncertainty for Graph Neural Networks

While graph neural networks (GNNs) are widely used for node and graph representation learning tasks, the reliability of GNN uncertainty estimates under distribution shifts remains relatively under-explored. Indeed, while post-hoc calibration strategies can be used to improve in-distribution calibration, they need not also improve calibration under distribution shift. However, techniques which produce GNNs with better intrinsic uncertainty estimates are particularly valuable, as they can always be combined with post-hoc strategies later. Therefore, in this work, we propose G-$Δ$UQ, a novel training framework designed to improve intrinsic GNN uncertainty estimates. Our framework adapts the principle of stochastic data centering to graph data through novel graph anchoring strategies, and is able to support partially stochastic GNNs. While, the prevalent wisdom is that fully stochastic networks are necessary to obtain reliable estimates, we find that the functional diversity induced by our anchoring strategies when sampling hypotheses renders this unnecessary and allows us to support G-$Δ$UQ on pretrained models. Indeed, through extensive evaluation under covariate, concept and graph size shifts, we show that G-$Δ$UQ leads to better calibrated GNNs for node and graph classification. Further, it also improves performance on the uncertainty-based tasks of out-of-distribution detection and generalization gap estimation. Overall, our work provides insights into uncertainty estimation for GNNs, and demonstrates the utility of G-$Δ$UQ in obtaining reliable estimates.

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arXiv2024

Multi-Stage Balanced Distillation: Addressing Long-Tail Challenges in Sequence-Level Knowledge Distillation

Large language models (LLMs) have significantly advanced various natural language processing tasks, but deploying them remains computationally expensive. Knowledge distillation (KD) is a promising solution, enabling the transfer of capabilities from larger teacher LLMs to more compact student models. Particularly, sequence-level KD, which distills rationale-based reasoning processes instead of merely final outcomes, shows great potential in enhancing students' reasoning capabilities. However, current methods struggle with sequence level KD under long-tailed data distributions, adversely affecting generalization on sparsely represented domains. We introduce the Multi-Stage Balanced Distillation (BalDistill) framework, which iteratively balances training data within a fixed computational budget. By dynamically selecting representative head domain examples and synthesizing tail domain examples, BalDistill achieves state-of-the-art performance across diverse long-tailed datasets, enhancing both the efficiency and efficacy of the distilled models.

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arXiv2024

Unveiling the Impact of Local Homophily on GNN Fairness: In-Depth Analysis and New Benchmarks

Graph Neural Networks (GNNs) often struggle to generalize when graphs exhibit both homophily (same-class connections) and heterophily (different-class connections). Specifically, GNNs tend to underperform for nodes with local homophily levels that differ significantly from the global homophily level. This issue poses a risk in user-centric applications where underrepresented homophily levels are present. Concurrently, fairness within GNNs has received substantial attention due to the potential amplification of biases via message passing. However, the connection between local homophily and fairness in GNNs remains underexplored. In this work, we move beyond global homophily and explore how local homophily levels can lead to unfair predictions. We begin by formalizing the challenge of fair predictions for underrepresented homophily levels as an out-of-distribution (OOD) problem. We then conduct a theoretical analysis that demonstrates how local homophily levels can alter predictions for differing sensitive attributes. We additionally introduce three new GNN fairness benchmarks, as well as a novel semi-synthetic graph generator, to empirically study the OOD problem. Across extensive analysis we find that two factors can promote unfairness: (a) OOD distance, and (b) heterophilous nodes situated in homophilous graphs. In cases where these two conditions are met, fairness drops by up to 24% on real world datasets, and 30% in semi-synthetic datasets. Together, our theoretical insights, empirical analysis, and algorithmic contributions unveil a previously overlooked source of unfairness rooted in the graph's homophily information.

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arXiv2024

On the Impact of Feature Heterophily on Link Prediction with Graph Neural Networks

Heterophily, or the tendency of connected nodes in networks to have different class labels or dissimilar features, has been identified as challenging for many Graph Neural Network (GNN) models. While the challenges of applying GNNs for node classification when class labels display strong heterophily are well understood, it is unclear how heterophily affects GNN performance in other important graph learning tasks where class labels are not available. In this work, we focus on the link prediction task and systematically analyze the impact of heterophily in node features on GNN performance. Theoretically, we first introduce formal definitions of homophilic and heterophilic link prediction tasks, and present a theoretical framework that highlights the different optimizations needed for the respective tasks. We then analyze how different link prediction encoders and decoders adapt to varying levels of feature homophily and introduce designs for improved performance. Our empirical analysis on a variety of synthetic and real-world datasets confirms our theoretical insights and highlights the importance of adopting learnable decoders and GNN encoders with ego- and neighbor-embedding separation in message passing for link prediction tasks beyond homophily.

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arXiv2024

LinkGPT: Teaching Large Language Models To Predict Missing Links

Large Language Models (LLMs) have shown promising results on various language and vision tasks. Recently, there has been growing interest in applying LLMs to graph-based tasks, particularly on Text-Attributed Graphs (TAGs). However, most studies have focused on node classification, while the use of LLMs for link prediction (LP) remains understudied. In this work, we propose a new task on LLMs, where the objective is to leverage LLMs to predict missing links between nodes in a graph. This task evaluates an LLM's ability to reason over structured data and infer new facts based on learned patterns. This new task poses two key challenges: (1) How to effectively integrate pairwise structural information into the LLMs, which is known to be crucial for LP performance, and (2) how to solve the computational bottleneck when teaching LLMs to perform LP. To address these challenges, we propose LinkGPT, the first end-to-end trained LLM for LP tasks. To effectively enhance the LLM's ability to understand the underlying structure, we design a two-stage instruction tuning approach where the first stage fine-tunes the pairwise encoder, projector, and node projector, and the second stage further fine-tunes the LLMs to predict links. To address the efficiency challenges at inference time, we introduce a retrieval-reranking scheme. Experiments show that LinkGPT can achieve state-of-the-art performance on real-world graphs as well as superior generalization in zero-shot and few-shot learning, surpassing existing benchmarks. At inference time, it can achieve $10\times$ speedup while maintaining high LP accuracy.

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arXiv2024

Large Generative Graph Models

Large Generative Models (LGMs) such as GPT, Stable Diffusion, Sora, and Suno are trained on a huge amount of language corpus, images, videos, and audio that are extremely diverse from numerous domains. This training paradigm over diverse well-curated data lies at the heart of generating creative and sensible content. However, all previous graph generative models (e.g., GraphRNN, MDVAE, MoFlow, GDSS, and DiGress) have been trained only on one dataset each time, which cannot replicate the revolutionary success achieved by LGMs in other fields. To remedy this crucial gap, we propose a new class of graph generative model called Large Graph Generative Model (LGGM) that is trained on a large corpus of graphs (over 5000 graphs) from 13 different domains. We empirically demonstrate that the pre-trained LGGM has superior zero-shot generative capability to existing graph generative models. Furthermore, our pre-trained LGGM can be easily fine-tuned with graphs from target domains and demonstrate even better performance than those directly trained from scratch, behaving as a solid starting point for real-world customization. Inspired by Stable Diffusion, we further equip LGGM with the capability to generate graphs given text prompts (Text-to-Graph), such as the description of the network name and domain (i.e., "The power-1138-bus graph represents a network of buses in a power distribution system."), and network statistics (i.e., "The graph has a low average degree, suitable for modeling social media interactions."). This Text-to-Graph capability integrates the extensive world knowledge in the underlying language model, offering users fine-grained control of the generated graphs. We release the code, the model checkpoint, and the datasets at https://lggm-lg.github.io/.

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arXiv2023

Graph Coarsening via Convolution Matching for Scalable Graph Neural Network Training

Graph summarization as a preprocessing step is an effective and complementary technique for scalable graph neural network (GNN) training. In this work, we propose the Coarsening Via Convolution Matching (CONVMATCH) algorithm and a highly scalable variant, A-CONVMATCH, for creating summarized graphs that preserve the output of graph convolution. We evaluate CONVMATCH on six real-world link prediction and node classification graph datasets, and show it is efficient and preserves prediction performance while significantly reducing the graph size. Notably, CONVMATCH achieves up to 95% of the prediction performance of GNNs on node classification while trained on graphs summarized down to 1% the size of the original graph. Furthermore, on link prediction tasks, CONVMATCH consistently outperforms all baselines, achieving up to a 2x improvement.

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arXiv2023

Pitfalls in Link Prediction with Graph Neural Networks: Understanding the Impact of Target-link Inclusion & Better Practices

While Graph Neural Networks (GNNs) are remarkably successful in a variety of high-impact applications, we demonstrate that, in link prediction, the common practices of including the edges being predicted in the graph at training and/or test have outsized impact on the performance of low-degree nodes. We theoretically and empirically investigate how these practices impact node-level performance across different degrees. Specifically, we explore three issues that arise: (I1) overfitting; (I2) distribution shift; and (I3) implicit test leakage. The former two issues lead to poor generalizability to the test data, while the latter leads to overestimation of the model's performance and directly impacts the deployment of GNNs. To address these issues in a systematic way, we introduce an effective and efficient GNN training framework, SpotTarget, which leverages our insight on low-degree nodes: (1) at training time, it excludes a (training) edge to be predicted if it is incident to at least one low-degree node; and (2) at test time, it excludes all test edges to be predicted (thus, mimicking real scenarios of using GNNs, where the test data is not included in the graph). SpotTarget helps researchers and practitioners adhere to best practices for learning from graph data, which are frequently overlooked even by the most widely-used frameworks. Our experiments on various real-world datasets show that SpotTarget makes GNNs up to 15x more accurate in sparse graphs, and significantly improves their performance for low-degree nodes in dense graphs.

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arXiv2023

Leveraging Graph Diffusion Models for Network Refinement Tasks

Most real-world networks are noisy and incomplete samples from an unknown target distribution. Refining them by correcting corruptions or inferring unobserved regions typically improves downstream performance. Inspired by the impressive generative capabilities that have been used to correct corruptions in images, and the similarities between "in-painting" and filling in missing nodes and edges conditioned on the observed graph, we propose a novel graph generative framework, SGDM, which is based on subgraph diffusion. Our framework not only improves the scalability and fidelity of graph diffusion models, but also leverages the reverse process to perform novel, conditional generation tasks. In particular, through extensive empirical analysis and a set of novel metrics, we demonstrate that our proposed model effectively supports the following refinement tasks for partially observable networks: T1: denoising extraneous subgraphs, T2: expanding existing subgraphs and T3: performing "style" transfer by regenerating a particular subgraph to match the characteristics of a different node or subgraph.

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arXiv2023

On Performance Discrepancies Across Local Homophily Levels in Graph Neural Networks

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.

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arXiv2023

Accurate and Scalable Estimation of Epistemic Uncertainty for Graph Neural Networks

Safe deployment of graph neural networks (GNNs) under distribution shift requires models to provide accurate confidence indicators (CI). However, while it is well-known in computer vision that CI quality diminishes under distribution shift, this behavior remains understudied for GNNs. Hence, we begin with a case study on CI calibration under controlled structural and feature distribution shifts and demonstrate that increased expressivity or model size do not always lead to improved CI performance. Consequently, we instead advocate for the use of epistemic uncertainty quantification (UQ) methods to modulate CIs. To this end, we propose G-$Δ$UQ, a new single model UQ method that extends the recently proposed stochastic centering framework to support structured data and partial stochasticity. Evaluated across covariate, concept, and graph size shifts, G-$Δ$UQ not only outperforms several popular UQ methods in obtaining calibrated CIs, but also outperforms alternatives when CIs are used for generalization gap prediction or OOD detection. Overall, our work not only introduces a new, flexible GNN UQ method, but also provides novel insights into GNN CIs on safety-critical tasks.

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arXiv2023

Interpretable Sparsification of Brain Graphs: Better Practices and Effective Designs for Graph Neural Networks

Brain graphs, which model the structural and functional relationships between brain regions, are crucial in neuroscientific and clinical applications involving graph classification. However, dense brain graphs pose computational challenges including high runtime and memory usage and limited interpretability. In this paper, we investigate effective designs in Graph Neural Networks (GNNs) to sparsify brain graphs by eliminating noisy edges. While prior works remove noisy edges based on explainability or task-irrelevant properties, their effectiveness in enhancing performance with sparsified graphs is not guaranteed. Moreover, existing approaches often overlook collective edge removal across multiple graphs. To address these issues, we introduce an iterative framework to analyze different sparsification models. Our findings are as follows: (i) methods prioritizing interpretability may not be suitable for graph sparsification as they can degrade GNNs' performance in graph classification tasks; (ii) simultaneously learning edge selection with GNN training is more beneficial than post-training; (iii) a shared edge selection across graphs outperforms separate selection for each graph; and (iv) task-relevant gradient information aids in edge selection. Based on these insights, we propose a new model, Interpretable Graph Sparsification (IGS), which enhances graph classification performance by up to 5.1% with 55.0% fewer edges. The retained edges identified by IGS provide neuroscientific interpretations and are supported by well-established literature.

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arXiv2023

On the Efficacy of Generalization Error Prediction Scoring Functions

Generalization error predictors (GEPs) aim to predict model performance on unseen distributions by deriving dataset-level error estimates from sample-level scores. However, GEPs often utilize disparate mechanisms (e.g., regressors, thresholding functions, calibration datasets, etc), to derive such error estimates, which can obfuscate the benefits of a particular scoring function. Therefore, in this work, we rigorously study the effectiveness of popular scoring functions (confidence, local manifold smoothness, model agreement), independent of mechanism choice. We find, absent complex mechanisms, that state-of-the-art confidence- and smoothness- based scores fail to outperform simple model-agreement scores when estimating error under distribution shifts and corruptions. Furthermore, on realistic settings where the training data has been compromised (e.g., label noise, measurement noise, undersampling), we find that model-agreement scores continue to perform well and that ensemble diversity is important for improving its performance. Finally, to better understand the limitations of scoring functions, we demonstrate that simplicity bias, or the propensity of deep neural networks to rely upon simple but brittle features, can adversely affect GEP performance. Overall, our work carefully studies the effectiveness of popular scoring functions in realistic settings and helps to better understand their limitations.

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arXiv2023

Simplifying Distributed Neural Network Training on Massive Graphs: Randomized Partitions Improve Model Aggregation

Distributed training of GNNs enables learning on massive graphs (e.g., social and e-commerce networks) that exceed the storage and computational capacity of a single machine. To reach performance comparable to centralized training, distributed frameworks focus on maximally recovering cross-instance node dependencies with either communication across instances or periodic fallback to centralized training, which create overhead and limit the framework scalability. In this work, we present a simplified framework for distributed GNN training that does not rely on the aforementioned costly operations, and has improved scalability, convergence speed and performance over the state-of-the-art approaches. Specifically, our framework (1) assembles independent trainers, each of which asynchronously learns a local model on locally-available parts of the training graph, and (2) only conducts periodic (time-based) model aggregation to synchronize the local models. Backed by our theoretical analysis, instead of maximizing the recovery of cross-instance node dependencies -- which has been considered the key behind closing the performance gap between model aggregation and centralized training -- , our framework leverages randomized assignment of nodes or super-nodes (i.e., collections of original nodes) to partition the training graph such that it improves data uniformity and minimizes the discrepancy of gradient and loss function across instances. In our experiments on social and e-commerce networks with up to 1.3 billion edges, our proposed RandomTMA and SuperTMA approaches -- despite using less training data -- achieve state-of-the-art performance and 2.31x speedup compared to the fastest baseline, and show better robustness to trainer failures.

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arXiv2023

A Closer Look at Model Adaptation using Feature Distortion and Simplicity Bias

Advances in the expressivity of pretrained models have increased interest in the design of adaptation protocols which enable safe and effective transfer learning. Going beyond conventional linear probing (LP) and fine tuning (FT) strategies, protocols that can effectively control feature distortion, i.e., the failure to update features orthogonal to the in-distribution, have been found to achieve improved out-of-distribution generalization (OOD). In order to limit this distortion, the LP+FT protocol, which first learns a linear probe and then uses this initialization for subsequent FT, was proposed. However, in this paper, we find when adaptation protocols (LP, FT, LP+FT) are also evaluated on a variety of safety objectives (e.g., calibration, robustness, etc.), a complementary perspective to feature distortion is helpful to explain protocol behavior. To this end, we study the susceptibility of protocols to simplicity bias (SB), i.e. the well-known propensity of deep neural networks to rely upon simple features, as SB has recently been shown to underlie several problems in robust generalization. Using a synthetic dataset, we demonstrate the susceptibility of existing protocols to SB. Given the strong effectiveness of LP+FT, we then propose modified linear probes that help mitigate SB, and lead to better initializations for subsequent FT. We verify the effectiveness of the proposed LP+FT variants for decreasing SB in a controlled setting, and their ability to improve OOD generalization and safety on three adaptation datasets.

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arXiv2023

Leveraging the Graph Structure of Neural Network Training Dynamics

Understanding the training dynamics of deep neural networks (DNNs) is important as it can lead to improved training efficiency and task performance. Recent works have demonstrated that representing the wirings of static graph cannot capture how DNNs change over the course of training. Thus, in this work, we propose a compact, expressive temporal graph framework that effectively captures the dynamics of many workhorse architectures in computer vision. Specifically, it extracts an informative summary of graph properties (e.g., eigenvector centrality) over a sequence of DNN graphs obtained during training. We demonstrate that our framework captures useful dynamics by accurately predicting trained, task performance when using a summary over early training epochs (<5) across four different architectures and two image datasets. Moreover, by using a novel, highly-scalable DNN graph representation, we also show that the proposed framework captures generalizable dynamics as summaries extracted from smaller-width networks are effective when evaluated on larger widths.

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arXiv2023

Analyzing Data-Centric Properties for Graph Contrastive Learning

Recent analyses of self-supervised learning (SSL) find the following data-centric properties to be critical for learning good representations: invariance to task-irrelevant semantics, separability of classes in some latent space, and recoverability of labels from augmented samples. However, given their discrete, non-Euclidean nature, graph datasets and graph SSL methods are unlikely to satisfy these properties. This raises the question: how do graph SSL methods, such as contrastive learning (CL), work well? To systematically probe this question, we perform a generalization analysis for CL when using generic graph augmentations (GGAs), with a focus on data-centric properties. Our analysis yields formal insights into the limitations of GGAs and the necessity of task-relevant augmentations. As we empirically show, GGAs do not induce task-relevant invariances on common benchmark datasets, leading to only marginal gains over naive, untrained baselines. Our theory motivates a synthetic data generation process that enables control over task-relevant information and boasts pre-defined optimal augmentations. This flexible benchmark helps us identify yet unrecognized limitations in advanced augmentation techniques (e.g., automated methods). Overall, our work rigorously contextualizes, both empirically and theoretically, the effects of data-centric properties on augmentation strategies and learning paradigms for graph SSL.

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