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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 Janus, a simple yet effective framework that leverages Large Language Models (LLMs) to jointly encode text and graph data. Specifically, Janus 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 Janus consistently outperforms existing baselines, achieving significant improvements across multiple datasets, with gains of up to 11.4% in QA tasks. These results highlight Janus's effectiveness in integrating graph and text data. Ablation studies further validate the effectiveness of our method.

Graphs are a fundamental data structure used to represent relationships in domains as diverse as the social sciences, bioinformatics, cybersecurity, the Internet, and more. One of the central observations in network science is that real-world graphs are globally sparse, yet contains numerous "pockets" of high edge density. A fundamental task in graph mining is to discover these dense subgraphs. Most common formulations of the problem involve finding a single (or a few) "optimally" dense subsets. But in most real applications, one does not care for the optimality. Instead, we want to find a large collection of dense subsets that covers a significant fraction of the input graph. We give a mathematical formulation of this problem, using a new definition of regularly triangle-rich (RTR) families. These families capture the notion of dense subgraphs that contain many triangles and have degrees comparable to the subgraph size. We design a provable algorithm, RTRExtractor, that can discover RTR families that approximately cover any RTR set. The algorithm is efficient and is inspired by recent results that use triangle counts for community testing and clustering. We show that RTRExtractor has excellent behavior on a large variety of real-world datasets. It is able to process graphs with hundreds of millions of edges within minutes. Across many datasets, RTRExtractor achieves high coverage using high edge density datasets. For example, the output covers a quarter of the vertices with subgraphs of edge density more than (say) $0.5$, for datasets with 10M+ edges. We show an example of how the output of RTRExtractor correlates with meaningful sets of similar vertices in a citation network, demonstrating the utility of RTRExtractor for unsupervised graph discovery tasks.

Graph Neural Networks (GNNs) have attracted immense attention in the past decade due to their numerous real-world applications built around graph-structured data. On the other hand, Large Language Models (LLMs) with extensive pretrained knowledge and powerful semantic comprehension abilities have recently shown a remarkable ability to benefit applications using vision and text data. In this paper, we investigate how LLMs can be leveraged in a computationally efficient fashion to benefit rich graph-structured data, a modality relatively unexplored in LLM literature. Prior works in this area exploit LLMs to augment every node features in an ad-hoc fashion (not scalable for large graphs), use natural language to describe the complex structural information of graphs, or perform computationally expensive finetuning of LLMs in conjunction with GNNs. We propose E-LLaGNN (Efficient LLMs augmented GNNs), a framework with an on-demand LLM service that enriches message passing procedure of graph learning by enhancing a limited fraction of nodes from the graph. More specifically, E-LLaGNN relies on sampling high-quality neighborhoods using LLMs, followed by on-demand neighborhood feature enhancement using diverse prompts from our prompt catalog, and finally information aggregation using message passing from conventional GNN architectures. We explore several heuristics-based active node selection strategies to limit the computational and memory footprint of LLMs when handling millions of nodes. Through extensive experiments & ablation on popular graph benchmarks of varying scales (Cora, PubMed, ArXiv, & Products), we illustrate the effectiveness of our E-LLaGNN framework and reveal many interesting capabilities such as improved gradient flow in deep GNNs, LLM-free inference ability etc.

Deep learning techniques have shown promising results in the automatic classification of respiratory sounds. However, accurately distinguishing these sounds in real-world noisy conditions poses challenges for clinical deployment. Additionally, predicting signals with only background noise could undermine user trust in the system. This paper aims to investigate the feasibility and effectiveness of incorporating a deep learning-based audio enhancement preprocessing step into automatic respiratory sound classification systems to improve robustness and clinical applicability. Multiple experiments were conducted using different audio enhancement model structures and classification models. The classification performance was compared to the baseline method of noise injection data augmentation. Experiments were performed on two datasets: the ICBHI respiratory sound dataset, which includes 5.5 hours of recordings, and the Formosa Archive of Breath Sounds (FABS) dataset, comprising 14.6 hours of recordings. Additionally, a physician validation study was conducted by 7 senior physicians to assess the clinical utility of the system.The integration of the audio enhancement pipeline resulted in a 21.88% increase in the ICBHI classification score on the ICBHI dataset and a 4.10% improvement on the FABS dataset in multi-class noisy scenarios. Quantitative analysis from the physician validation study revealed improvements in efficiency, diagnostic confidence, and trust during model-assisted diagnosis, with workflows integrating enhanced audio leading to an 11.61% increase in diagnostic sensitivity and facilitating high-confidence diagnoses. Incorporating an audio enhancement algorithm significantly enhances the robustness and clinical utility of automatic respiratory sound classification systems, improving performance in noisy environments and fostering greater trust among medical professionals., Comment: Demo website: https://rogertzeng.github.io/ReSC-AE/

The problem of search relevance in the E-commerce domain is a challenging one since it involves understanding the intent of a user's short nuanced query and matching it with the appropriate products in the catalog. This problem has traditionally been addressed using language models (LMs) and graph neural networks (GNNs) to capture semantic and inter-product behavior signals, respectively. However, the rapid development of new architectures has created a gap between research and the practical adoption of these techniques. Evaluating the generalizability of these models for deployment requires extensive experimentation on complex, real-world datasets, which can be non-trivial and expensive. Furthermore, such models often operate on latent space representations that are incomprehensible to humans, making it difficult to evaluate and compare the effectiveness of different models. This lack of interpretability hinders the development and adoption of new techniques in the field. To bridge this gap, we propose Plug and Play Graph LAnguage Model (PP-GLAM), an explainable ensemble of plug and play models. Our approach uses a modular framework with uniform data processing pipelines. It employs additive explanation metrics to independently decide whether to include (i) language model candidates, (ii) GNN model candidates, and (iii) inter-product behavioral signals. For the task of search relevance, we show that PP-GLAM outperforms several state-of-the-art baselines as well as a proprietary model on real-world multilingual, multi-regional e-commerce datasets. To promote better model comprehensibility and adoption, we also provide an analysis of the explainability and computational complexity of our model. We also provide the public codebase and provide a deployment strategy for practical implementation., Comment: Accepted to The Web Conference 2024 (Industry)

Training Graph Neural Networks (GNNs) on real-world graphs consisting of billions of nodes and edges is quite challenging, primarily due to the substantial memory needed to store the graph and its intermediate node and edge features, and there is a pressing need to speed up the training process. A common approach to achieve speed up is to divide the graph into many smaller subgraphs, which are then distributed across multiple GPUs in one or more machines and processed in parallel. However, existing distributed methods require frequent and substantial cross-GPU communication, leading to significant time overhead and progressively diminishing scalability. Here, we introduce CoFree-GNN, a novel distributed GNN training framework that significantly speeds up the training process by implementing communication-free training. The framework utilizes a Vertex Cut partitioning, i.e., rather than partitioning the graph by cutting the edges between partitions, the Vertex Cut partitions the edges and duplicates the node information to preserve the graph structure. Furthermore, the framework maintains high model accuracy by incorporating a reweighting mechanism to handle a distorted graph distribution that arises from the duplicated nodes. We also propose a modified DropEdge technique to further speed up the training process. Using an extensive set of experiments on real-world networks, we demonstrate that CoFree-GNN speeds up the GNN training process by up to 10 times over the existing state-of-the-art GNN training approaches.

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., Comment: 14 pages, 3 figures

Link prediction is central to many real-world applications, but its performance may be hampered when the graph of interest is sparse. To alleviate issues caused by sparsity, we investigate a previously overlooked phenomenon: in many cases, a densely connected, complementary graph can be found for the original graph. The denser graph may share nodes with the original graph, which offers a natural bridge for transferring selective, meaningful knowledge. We identify this setting as Graph Intersection-induced Transfer Learning (GITL), which is motivated by practical applications in e-commerce or academic co-authorship predictions. We develop a framework to effectively leverage the structural prior in this setting. We first create an intersection subgraph using the shared nodes between the two graphs, then transfer knowledge from the source-enriched intersection subgraph to the full target graph. In the second step, we consider two approaches: a modified label propagation, and a multi-layer perceptron (MLP) model in a teacher-student regime. Experimental results on proprietary e-commerce datasets and open-source citation graphs show that the proposed workflow outperforms existing transfer learning baselines that do not explicitly utilize the intersection structure., Comment: Accepted in TMLR (https://openreview.net/forum?id=Nn71AdKyYH)

Although the bipartite shopping graphs are straightforward to model search behavior, they suffer from two challenges: 1) The majority of items are sporadically searched and hence have noisy/sparse query associations, leading to a \textit{long-tail} distribution. 2) Infrequent queries are more likely to link to popular items, leading to another hurdle known as \textit{disassortative mixing}. To address these two challenges, we go beyond the bipartite graph to take a hypergraph perspective, introducing a new paradigm that leverages \underline{auxiliary} information from anonymized customer engagement sessions to assist the \underline{main task} of query-item link prediction. This auxiliary information is available at web scale in the form of search logs. We treat all items appearing in the same customer session as a single hyperedge. The hypothesis is that items in a customer session are unified by a common shopping interest. With these hyperedges, we augment the original bipartite graph into a new \textit{hypergraph}. We develop a \textit{\textbf{D}ual-\textbf{C}hannel \textbf{A}ttention-Based \textbf{H}ypergraph Neural Network} (\textbf{DCAH}), which synergizes information from two potentially noisy sources (original query-item edges and item-item hyperedges). In this way, items on the tail are better connected due to the extra hyperedges, thereby enhancing their link prediction performance. We further integrate DCAH with self-supervised graph pre-training and/or DropEdge training, both of which effectively alleviate disassortative mixing. Extensive experiments on three proprietary E-Commerce datasets show that DCAH yields significant improvements of up to \textbf{24.6\% in mean reciprocal rank (MRR)} and \textbf{48.3\% in recall} compared to GNN-based baselines. Our source code is available at \url{https://github.com/amazon-science/dual-channel-hypergraph-neural-network}., Comment: WSDM 2023

Despite recent advances in Graph Neural Networks (GNNs), their training strategies remain largely under-explored. The conventional training strategy learns over all nodes in the original graph(s) equally, which can be sub-optimal as certain nodes are often more difficult to learn than others. Here we present TuneUp, a simple curriculum-based training strategy for improving the predictive performance of GNNs. TuneUp trains a GNN in two stages. In the first stage, TuneUp applies conventional training to obtain a strong base GNN. The base GNN tends to perform well on head nodes (nodes with large degrees) but less so on tail nodes (nodes with small degrees). Therefore, the second stage of TuneUp focuses on improving prediction on the difficult tail nodes by further training the base GNN on synthetically generated tail node data. We theoretically analyze TuneUp and show it provably improves generalization performance on tail nodes. TuneUp is simple to implement and applicable to a broad range of GNN architectures and prediction tasks. Extensive evaluation of TuneUp on five diverse GNN architectures, three types of prediction tasks, and both transductive and inductive settings shows that TuneUp significantly improves the performance of the base GNN on tail nodes, while often even improving the performance on head nodes. Altogether, TuneUp produces up to 57.6% and 92.2% relative predictive performance improvement in the transductive and the challenging inductive settings, respectively.

Graph Neural Networks (GNNs) have emerged as powerful tools to encode graph-structured data. Due to their broad applications, there is an increasing need to develop tools to explain how GNNs make decisions given graph-structured data. Existing learning-based GNN explanation approaches are task-specific in training and hence suffer from crucial drawbacks. Specifically, they are incapable of producing explanations for a multitask prediction model with a single explainer. They are also unable to provide explanations in cases where the GNN is trained in a self-supervised manner, and the resulting representations are used in future downstream tasks. To address these limitations, we propose a Task-Agnostic GNN Explainer (TAGE) that is independent of downstream models and trained under self-supervision with no knowledge of downstream tasks. TAGE enables the explanation of GNN embedding models with unseen downstream tasks and allows efficient explanation of multitask models. Our extensive experiments show that TAGE can significantly speed up the explanation efficiency by using the same model to explain predictions for multiple downstream tasks while achieving explanation quality as good as or even better than current state-of-the-art GNN explanation approaches. Our code is pubicly available as part of the DIG library at https://github.com/divelab/DIG/tree/main/dig/xgraph/TAGE/., Comment: Accepted by NeurIPS 2022

Studies of active learning traditionally assume the target and source data stem from a single domain. However, in realistic applications, practitioners often require active learning with multiple sources of out-of-distribution data, where it is unclear a priori which data sources will help or hurt the target domain. We survey a wide variety of techniques in active learning (AL), domain shift detection (DS), and multi-domain sampling to examine this challenging setting for question answering and sentiment analysis. We ask (1) what family of methods are effective for this task? And, (2) what properties of selected examples and domains achieve strong results? Among 18 acquisition functions from 4 families of methods, we find H-Divergence methods, and particularly our proposed variant DAL-E, yield effective results, averaging 2-3% improvements over the random baseline. We also show the importance of a diverse allocation of domains, as well as room-for-improvement of existing methods on both domain and example selection. Our findings yield the first comprehensive analysis of both existing and novel methods for practitioners faced with multi-domain active learning for natural language tasks.

Graph Neural Networks (GNNs) have achieved state-of-the-art performance in node classification, regression, and recommendation tasks. GNNs work well when rich and high-quality connections are available. However, their effectiveness is often jeopardized in many real-world graphs in which node degrees have power-law distributions. The extreme case of this situation, where a node may have no neighbors, is called Strict Cold Start (SCS). SCS forces the prediction to rely completely on the node's own features. We propose Cold Brew, a teacher-student distillation approach to address the SCS and noisy-neighbor challenges for GNNs. We also introduce feature contribution ratio (FCR), a metric to quantify the behavior of inductive GNNs to solve SCS. We experimentally show that FCR disentangles the contributions of different graph data components and helps select the best architecture for SCS generalization. We further demonstrate the superior performance of Cold Brew on several public benchmark and proprietary e-commerce datasets, where many nodes have either very few or noisy connections. Our source code is available at https://github.com/amazon-research/gnn-tail-generalization., Comment: Published as a conference paper in ICLR 2022

Alzheimer's disease (AD) and Parkinson's disease (PD) are the two most common neurodegenerative disorders in humans. Because a significant percentage of patients have clinical and pathological features of both diseases, it has been hypothesized that the patho-cascades of the two diseases overlap. Despite this evidence, these two diseases are rarely studied in a joint manner. In this paper, we utilize clinical, imaging, genetic, and biospecimen features to cluster AD and PD patients into the same feature space. By training a machine learning classifier on the combined feature space, we predict the disease stage of patients two years after their baseline visits. We observed a considerable improvement in the prediction accuracy of Parkinson's dementia patients due to combined training on Alzheimer's and Parkinson's patients, thereby affirming the claim that these two diseases can be jointly studied., Comment: 7 pages