Puja Trivedi

April Chen, Ryan A. Rossi, Namyong Park et al.

Graph Neural Networks (GNNs) have become increasingly important due to their representational power and state-of-the-art predictive performance on many fundamental learning tasks. Despite this success, GNNs suffer from fairness issues that arise as a result of the underlying graph data and the fundamental aggregation mechanism that lies at the heart of the large class of GNN models. In this article, we examine and categorize fairness techniques for improving the fairness of GNNs. Previous work on fair GNN models and techniques are discussed in terms of whether they focus on improving fairness during a preprocessing step, during training, or in a post-processing phase. Furthermore, we discuss how such techniques can be used together whenever appropriate, and highlight the advantages and intuition as well. We also introduce an intuitive taxonomy for fairness evaluation metrics including graph-level fairness, neighborhood-level fairness, embedding-level fairness, and prediction-level fairness metrics. In addition, graph datasets that are useful for benchmarking the fairness of GNN models are summarized succinctly. Finally, we highlight key open problems and challenges that remain to be addressed.

Puja Trivedi, Danai Koutra, Jayaraman J. Thiagarajan

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.

Puja Trivedi, Ekdeep Singh Lubana, Mark Heimann et al.

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.

Puja Trivedi, Mark Heimann, Rushil Anirudh et al.

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.

Puja Trivedi, Ryan Rossi, David Arbour et al.

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.

Puja Trivedi, Danai Koutra, Jayaraman J. Thiagarajan

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.

Puja Trivedi, Danai Koutra, Jayaraman J. Thiagarajan

While directly fine-tuning (FT) large-scale, pretrained models on task-specific data is well-known to induce strong in-distribution task performance, recent works have demonstrated that different adaptation protocols, such as linear probing (LP) prior to FT, can improve out-of-distribution generalization. However, the design space of such adaptation protocols remains under-explored and the evaluation of such protocols has primarily focused on distribution shifts. Therefore, in this work, we evaluate common adaptation protocols across distributions shifts and machine learning safety metrics (e.g., anomaly detection, calibration, robustness to corruptions). We find that protocols induce disparate trade-offs that were not apparent from prior evaluation. Further, we demonstrate that appropriate pairing of data augmentation and protocol can substantially mitigate this trade-off. Finally, we hypothesize and empirically see that using hardness-promoting augmentations during LP and then FT with augmentations may be particularly effective for trade-off mitigation.

Jayaraman J. Thiagarajan, Vivek Narayanaswamy, Puja Trivedi et al.

Safe deployment of AI models requires proactive detection of failures to prevent costly errors. To this end, we study the important problem of detecting failures in deep regression models. Existing approaches rely on epistemic uncertainty estimates or inconsistency w.r.t the training data to identify failure. Interestingly, we find that while uncertainties are necessary they are insufficient to accurately characterize failure in practice. Hence, we introduce PAGER (Principled Analysis of Generalization Errors in Regressors), a framework to systematically detect and characterize failures in deep regressors. Built upon the principle of anchored training in deep models, PAGER unifies both epistemic uncertainty and complementary manifold non-conformity scores to accurately organize samples into different risk regimes.

Tek Raj Chhetri, Yibei Chen, Puja Trivedi et al.

The ability to extract structured information from unstructured sources-such as free-text documents and scientific literature-is critical for accelerating scientific discovery and knowledge synthesis. Large Language Models (LLMs) have demonstrated remarkable capabilities in various natural language processing tasks, including structured information extraction. However, their effectiveness often diminishes in specialized, domain-specific contexts that require nuanced understanding and expert-level domain knowledge. In addition, existing LLM-based approaches frequently exhibit poor transferability across tasks and domains, limiting their scalability and adaptability. To address these challenges, we introduce StructSense, a modular, task-agnostic, open-source framework for structured information extraction built on LLMs. StructSense is guided by domain-specific symbolic knowledge encoded in ontologies, enabling it to navigate complex domain content more effectively. It further incorporates agentic capabilities through self-evaluative judges that form a feedback loop for iterative refinement, and includes human-in-the-loop mechanisms to ensure quality and validation. We demonstrate that StructSense can overcome both the limitations of domain sensitivity and the lack of cross-task generalizability, as shown through its application to diverse neuroscience information extraction tasks.

Namyong Park, Xing Wang, Antoine Simoulin et al.

Graph neural networks (GNNs) have achieved remarkable success across a wide range of applications, such as recommendation, drug discovery, and question answering. Behind the success of GNNs lies the backpropagation (BP) algorithm, which is the de facto standard for training deep neural networks (NNs). However, despite its effectiveness, BP imposes several constraints, which are not only biologically implausible, but also limit the scalability, parallelism, and flexibility in learning NNs. Examples of such constraints include storage of neural activities computed in the forward pass for use in the subsequent backward pass, and the dependence of parameter updates on non-local signals. To address these limitations, the forward-forward algorithm (FF) was recently proposed as an alternative to BP in the image classification domain, which trains NNs by performing two forward passes over positive and negative data. Inspired by this advance, we propose ForwardGNN in this work, a new forward learning procedure for GNNs, which avoids the constraints imposed by BP via an effective layer-wise local forward training. ForwardGNN extends the original FF to deal with graph data and GNNs, and makes it possible to operate without generating negative inputs (hence no longer forward-forward). Further, ForwardGNN enables each layer to learn from both the bottom-up and top-down signals without relying on the backpropagation of errors. Extensive experiments on real-world datasets show the effectiveness and generality of the proposed forward graph learning framework. We release our code at https://github.com/facebookresearch/forwardgnn.

Ekdeep Singh Lubana, Puja Trivedi, Danai Koutra et al.

Catastrophic forgetting undermines the effectiveness of deep neural networks (DNNs) in scenarios such as continual learning and lifelong learning. While several methods have been proposed to tackle this problem, there is limited work explaining why these methods work well. This paper has the goal of better explaining a popularly used technique for avoiding catastrophic forgetting: quadratic regularization. We show that quadratic regularizers prevent forgetting of past tasks by interpolating current and previous values of model parameters at every training iteration. Over multiple training iterations, this interpolation operation reduces the learning rates of more important model parameters, thereby minimizing their movement. Our analysis also reveals two drawbacks of quadratic regularization: (a) dependence of parameter interpolation on training hyperparameters, which often leads to training instability and (b) assignment of lower importance to deeper layers, which are generally the place forgetting occurs in DNNs. Via a simple modification to the order of operations, we show these drawbacks can be easily avoided, resulting in 6.2\% higher average accuracy at 4.5\% lower average forgetting. We confirm the robustness of our results by training over 2000 models in different settings. Code available at \url{https://github.com/EkdeepSLubana/QRforgetting}

Ekdeep Singh Lubana, Puja Trivedi, Conrad Hougen et al.

Network pruning in Convolutional Neural Networks (CNNs) has been extensively investigated in recent years. To determine the impact of pruning a group of filters on a network's accuracy, state-of-the-art pruning methods consistently assume filters of a CNN are independent. This allows the importance of a group of filters to be estimated as the sum of importances of individual filters. However, overparameterization in modern networks results in highly correlated filters that invalidate this assumption, thereby resulting in incorrect importance estimates. To address this issue, we propose OrthoReg, a principled regularization strategy that enforces orthonormality on a network's filters to reduce inter-filter correlation, thereby allowing reliable, efficient determination of group importance estimates, improved trainability of pruned networks, and efficient, simultaneous pruning of large groups of filters. When used for iterative pruning on VGG-13, MobileNet-V1, and ResNet-34, OrthoReg consistently outperforms five baseline techniques, including the state-of-the-art, on CIFAR-100 and Tiny-ImageNet. For the recently proposed Early-Bird Ticket hypothesis, which claims networks become amenable to pruning early-on in training and can be pruned after a few epochs to minimize training expenditure, we find OrthoReg significantly outperforms prior work. Code available at https://github.com/EkdeepSLubana/OrthoReg.

Puja Trivedi, Mark Heimann, Rushil Anirudh et al.

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.

Jiaji Ma, Puja Trivedi, Danai Koutra

Text-attributed graphs (TAGs), which combine structural and textual node information, are ubiquitous across many domains. Recent work integrates Large Language Models (LLMs) with Graph Neural Networks (GNNs) to jointly model semantics and structure, resulting in more general and expressive models that achieve state-of-the-art performance on TAG benchmarks. However, this integration introduces dual vulnerabilities: GNNs are sensitive to structural perturbations, while LLM-derived features are vulnerable to prompt injection and adversarial phrasing. While existing adversarial attacks largely perturb structure or text independently, we find that uni-modal attacks cause only modest degradation in LLM-enhanced GNNs. Moreover, many existing attacks assume unrealistic capabilities, such as white-box access or direct modification of graph data. To address these gaps, we propose GRAPHTEXTACK, the first black-box, multi-modal{, poisoning} node injection attack for LLM-enhanced GNNs. GRAPHTEXTACK injects nodes with carefully crafted structure and semantics to degrade model performance, operating under a realistic threat model without relying on model internals or surrogate models. To navigate the combinatorial, non-differentiable search space of connectivity and feature assignments, GRAPHTEXTACK introduces a novel evolutionary optimization framework with a multi-objective fitness function that balances local prediction disruption and global graph influence. Extensive experiments on five datasets and two state-of-the-art LLM-enhanced GNN models show that GRAPHTEXTACK significantly outperforms 12 strong baselines.

Yu Wang, Ryan A. Rossi, Namyong Park et al.

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/.

Fatemeh Vahedian, Ruiyu Li, Puja Trivedi et al.

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.

Puja Trivedi, Ekdeep Singh Lubana, Yujun Yan et al.

Unsupervised graph representation learning is critical to a wide range of applications where labels may be scarce or expensive to procure. Contrastive learning (CL) is an increasingly popular paradigm for such settings and the state-of-the-art in unsupervised visual representation learning. Recent work attributes the success of visual CL to use of task-relevant augmentations and large, diverse datasets. Interestingly, graph CL frameworks report strong performance despite using orders of magnitude smaller datasets and employing domain-agnostic graph augmentations (DAGAs). Motivated by this discrepancy, we probe the quality of representations learnt by popular graph CL frameworks using DAGAs. We find that DAGAs can destroy task-relevant information and harm the model's ability to learn discriminative representations. On small benchmark datasets, we show the inductive bias of graph neural networks can significantly compensate for this weak discriminability. Based on our findings, we propose several sanity checks that enable practitioners to quickly assess the quality of their model's learned representations. We further propose a broad strategy for designing task-aware augmentations that are amenable to graph CL and demonstrate its efficacy on two large-scale, complex graph applications. For example, in graph-based document classification, we show task-aware augmentations improve accuracy up to 20%.