Bryan Perozzi
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Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.
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HUGE: Huge Unsupervised Graph Embeddings with TPUs
SIGKDD Conference on Knowledge Discovery and Data Mining, ACM(2023) (to appear)
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Graphs are a representation of structured data that captures the relationships between sets of objects. With the ubiquity of available network data, there is increasing industrial and academic need to quickly analyze graphs with billions of nodes and trillions of edges. A common first step for network understanding is Graph Embedding, the process of creating a continuous representation of nodes in a graph. A continuous representation is often more amenable, especially at scale, for solving downstream machine learning tasks such as classification, link prediction, and clustering. A high-performance graph embedding architecture leveraging Tensor Processing Units (TPUs) with configurable amounts of high-bandwidth memory is presented that simplifies the graph embedding problem and can scale to graphs with billions of nodes and trillions of edges. We verify the embedding space quality on real and synthetic large-scale datasets.
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Tackling Provably Hard Representative Selection via Graph Neural Networks
Transactions on Machine Learning Research(2023)
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Representative Selection (RS) is the problem of finding a small subset of exemplars from a dataset that is representative of the dataset. In this paper, we study RS for attributed graphs, and focus on finding representative nodes that optimize the accuracy of a model trained on the selected representatives. Theoretically, we establish a new hardness result for RS (in the absence of a graph structure) by proving that a particular, highly practical variant of it (RS for Learning) is hard to approximate in polynomial time within any reasonable factor, which implies a significant potential gap between the optimum solution of widely-used surrogate functions and the actual accuracy of the model. We then study the setting where a (homophilous) graph structure is available, or can be constructed, between the data points. We show that with an appropriate modeling approach, the presence of such a structure can turn a hard RS (for learning) problem into one that can be effectively solved. To this end, we develop RS-GNN, a representation learning-based RS model based on Graph Neural Networks. Empirically, we demonstrate the effectiveness of RS-GNN on problems with predefined graph structures as well as problems with graphs induced from node feature similarities, by showing that RS-GNN achieves significant improvements over established baselines on a suite of eight benchmarks.
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TpuGraphs: Performance Prediction Datasets on Large Tensor Computational Graphs
Kaidi Cao
Charith Mendis
Advances in Neural Information Processing Systems(2023)
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Precise hardware performance models play a crucial role in code optimizations. They can assist compilers in making heuristic decisions or aid autotuners in identifying the optimal configuration for a given program. For example, the autotuner for XLA, a machine learning compiler, discovered 10–20\% speedup on state-of-the-art models serving substantial production traffic at Google. Although there exist a few datasets for program performance prediction, they target small sub-programs such as basic blocks or kernels. This paper introduces TpuGraphs, a performance prediction dataset on full tensor programs, represented as computational graphs, running on Tensor Processing Units (TPUs). Each graph in the dataset represents the main computation of a machine learning workload, eg, a training epoch or an inference step. Each data sample contains a computational graph, a compilation configuration, and the execution time of the graph when compiled with the configuration. The graphs in the dataset are collected from open-source machine learning programs, featuring popular model architectures (eg, ResNet, EfficientNet, Mask R-CNN, and Transformer). TpuGraphs provides 25x more graphs than the largest graph property prediction dataset (with comparable graph sizes), and 770x larger graphs on average compared to existing performance prediction datasets on machine learning programs. This graph-level prediction task on large graphs introduces new challenges in learning, ranging from scalability, training efficiency, to model quality.
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Graph Neural Networks (GNNs) have achieved state-of-the-art results on many graph analysis tasks such as node classification and link prediction. However, important unsupervised problems on graphs, such as graph clustering, have proved more resistant to advances in GNNs. Graph clustering has the same overall goal as node pooling in GNNs - does this mean that GNN pooling methods do a good job at clustering graphs?
Surprisingly, the answer is no - current GNN pooling methods often fail to recover the cluster structure in cases where simple baselines, such as k-means applied on learned representations, work well. We investigate further by carefully designing a set of experiments to study different signal-to-noise scenarios both in graph structure and attribute data. To address these methods' poor performance in clustering, we introduce Deep Modularity Networks (DMoN), an unsupervised pooling method inspired by the modularity measure of clustering quality, and show how it tackles recovery of the challenging clustering structure of real-world graphs. Similarly, on real-world data, we show that DMoN produces high quality clusters which correlate strongly with ground truth labels, achieving state-of-the-art results with over 40% improvement over other pooling methods across different metrics.
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Learning Large Graph Property Prediction via Graph Segment Training
Kaidi Cao
Charith Mendis
Jure Leskovec
Advances in Neural Information Processing Systems(2023)
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Learning to predict properties of large graphs is challenging because each prediction requires the knowledge of an entire graph, while the amount of memory available during training is bounded. Here we propose Graph Segment Training (GST), a general framework that utilizes a divide-and-conquer approach to allow learning large graph property prediction with a constant memory footprint. GST first divides a large graph into segments and then backpropagates through only a few segments sampled per training iteration. We refine the GST paradigm by introducing a historical embedding table to efficiently obtain embeddings for segments not sampled for backpropagation. To mitigate the staleness of historical embeddings, we design two novel techniques. First, we finetune the prediction head to fix the input distribution shift. Second, we introduce Stale Embedding Dropout to drop some stale embeddings during training to reduce bias. We evaluate our complete method GST-EFD (with all the techniques together) on two large graph property prediction benchmarks: MalNet and TpuGraphs. Our experiments show that GST-EFD is both memory-efficient and fast, while offering a slight boost on test accuracy over a typical full graph training regime.
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Unsupervised Embedding Quality Evaluation
Marina Munkhoeva
Topology, Algebra, and Geometry in Machine Learning(2023)
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Unsupervised learning has recently significantly gained in popularity, especially with deep learning-based approaches. Despite numerous successes and approaching supervised-level performance on a variety of academic benchmarks, it is still hard to train and evaluate SSL models in practice due to the unsupervised nature of the problem. Even with networks trained in a supervised fashion, it is often unclear whether they will perform well when transferred to another domain.
Past works have focused on assessing the amount of information contained in the embeddings. This works chooses to follow a different approach: can we quantify how easy it is to linearly separate the data in a stable way? We survey the literature and uncover three methods that could be potentially used for evaluating quality of representations. We also introduce one novel method based on recent advances in understanding the high-dimensional geometric structure self-supervised learning.
We conduct extensive experiments and study the properties of these metrics and ones introduced in the previous work. Our results suggest that while there is no free lunch, there are metrics that can robustly estimate embedding quality in an unsupervised way.
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Machine Learning on Graphs: A Model and Comprehensive Taxonomy
Ines Chami
Sami Abu-El-Haija
Chris Ré
Journal of Machine Learning Research, 23(2022), pp. 1-64
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There has been a surge of recent interest in graph representation learning (GRL). GRL methods have generally fallen into three main categories, based on the availability of labeled data. The first, network embedding, focuses on learning unsupervised representations of relational structure. The second, graph regularized neural networks, leverages graphs to augment neural network losses with a regularization objective for semi-supervised learning. The third, graph neural networks, aims to learn differentiable functions over discrete topologies with arbitrary structure. However, despite the popularity of these areas there has been surprisingly little work on unifying the three paradigms. Here, we aim to bridge the gap between network embedding, graph regularization and graph neural networks. We propose a comprehensive taxonomy of GRL methods, aiming to unify several disparate bodies of work. Specifically, we propose the GraphEDM framework, which generalizes popular algorithms for semi-supervised learning (e.g. GraphSage, GCN, GAT), and unsupervised learning (e.g. DeepWalk, node2vec) of graph representations into a single consistent approach. To illustrate the generality of GraphEDM, we fit over thirty existing methods into this framework. We believe that this unifying view both provides a solid foundation for understanding the intuition behind these methods, and enables future research in the area.
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Zero-shot Transfer Learning within a Heterogeneous Graph via Knowledge Transfer Networks
Minji Yoon
Ziniu Hu
Ruslan Salakhutdinov
Advances in Neural Information Processing Systems(2022)
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Data continuously emitted from industrial ecosystems such as social or e-commerce platforms are commonly represented as heterogeneous graphs (HG) composed of multiple node/edge types. State-of-the-art graph learning methods for HGs known as heterogeneous graph neural networks (HGNNs) are applied to learn deep context-informed node representations. However, many HG datasets from industrial applications suffer from label imbalance between node types. As there is no direct way to learn using labels rooted at different node types, HGNNs have been applied to only a few node types with abundant labels. We propose a zero-shot transfer learning module for HGNNs called a Knowledge Transfer Network (KTN) that transfers knowledge from label-abundant node types to zero-labeled node types through rich relational information given in the HG. KTN is derived from the theoretical relationship, which we introduce in this work, between distinct feature extractors for each node type given in an HGNN model. KTN improves the performance of 6 different types of HGNN models by up to 960% for inference on zero-labeled node types and outperforms state-of-the-art transfer learning baselines by up to 73% across 18 different transfer learning tasks on HGs.
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GraphWorld: Fake Graphs Bring Real Insights for GNNs
Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining(2022)
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The continuing maturity of the deep learning subfield of graph neural networks (GNNs) has motivated recent studies into the standard datasets used to benchmark GNNs. While important improvements have been made to GNN datasets and experimental design, any one dataset provides only a singular, potentially spurious insight into the performance of any GNN being tested. We show that state-of-the-art GNN task datasets do not cover the distribution of graphs in a much larger real-data graph repository, with respect to several key graph metrics. Motivated by this finding, we introduce GraphWorld, a novel distributed framework and software package for testing GNN models on an arbitrarily-large population of \emph{synthetic} task datasets.
GraphWorld allows a user to efficiently generate a \emph{world} of millions of graph datasets, with fine-grained control over graph generator parameters, and benchmark arbitrary GNN models, with built-in hyperparameter tuning. Using GraphWorld to generate diverse graph worlds corresponding to node classification, graph classification, and link prediction tasks, we provide insight into the sensitivity of 10,000+ GNN models to various parameters of graphs and node features and} show comparisons between models that have not been possible to make in any previous work. We also introduce a novel metric with which to explore each models' performance on the graph world, conditioning on graph metrics and graph generator parameters.
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