Label-free Node Classification on Graphs with Large Language Models (LLMS)

In recent years, there have been remarkable advancements in node classification achieved by Graph Neural Networks (GNNs). However, they necessitate abundant high-quality labels to ensure promising performance. In contrast, Large Language Models (LLMs) exhibit impressive zero-shot proficiency on text-attributed graphs. Yet, they face challenges in efficiently processing structural data and suffer from high inference costs. In light of these observations, this work introduces a label-free node classification on graphs with LLMs pipeline, LLM-GNN. It amalgamates the strengths of both GNNs and LLMs while mitigating their limitations. Specifically, LLMs are leveraged to annotate a small portion of nodes and then GNNs are trained on LLMs' annotations to make predictions for the remaining large portion of nodes. The implementation of LLM-GNN faces a unique challenge: how can we actively select nodes for LLMs to annotate and consequently enhance the GNN training? How can we leverage LLMs to obtain annotations of high quality, representativeness, and diversity, thereby enhancing GNN performance with less cost? To tackle this challenge, we develop an annotation quality heuristic and leverage the confidence scores derived from LLMs to advanced node selection. Comprehensive experimental results validate the effectiveness of LLM-GNN. In particular, LLM-GNN can achieve an accuracy of 74.9% on a vast-scale dataset \products with a cost less than 1 dollar.

Amazon-M2: A Multilingual Multi-locale Shopping Session Dataset for Recommendation and Text Generation

Modeling customer shopping intentions is a crucial task for e-commerce, as it directly impacts user experience and engagement. Thus, accurately understanding customer preferences is essential for providing personalized recommendations. Session-based recommendation, which utilizes customer session data to predict their next interaction, has become increasingly popular. However, existing session datasets have limitations in terms of item attributes, user diversity, and dataset scale. As a result, they cannot comprehensively capture the spectrum of user behaviors and preferences. To bridge this gap, we present the Amazon Multilingual Multi-locale Shopping Session Dataset, namely Amazon-M2. It is the first multilingual dataset consisting of millions of user sessions from six different locales, where the major languages of products are English, German, Japanese, French, Italian, and Spanish. Remarkably, the dataset can help us enhance personalization and understanding of user preferences, which can benefit various existing tasks as well as enable new tasks. To test the potential of the dataset, we introduce three tasks in this work: (1) next-product recommendation, (2) next-product recommendation with domain shifts, and (3) next-product title generation. With the above tasks, we benchmark a range of algorithms on our proposed dataset, drawing new insights for further research and practice. In addition, based on the proposed dataset and tasks, we hosted a competition in the KDD CUP 2023 and have attracted thousands of users and submissions. The winning solutions and the associated workshop can be accessed at our website https://kddcup23.github.io/.

Exploring the Potential of Large Language Models (LLMs) in Learning on Graphs

Learning on Graphs has attracted immense attention due to its wide real-world applications. The most popular pipeline for learning on graphs with textual node attributes primarily relies on Graph Neural Networks (GNNs), and utilizes shallow text embedding as initial node representations, which has limitations in general knowledge and profound semantic understanding. In recent years, Large Language Models (LLMs) have been proven to possess extensive common knowledge and powerful semantic comprehension abilities that have revolutionized existing workflows to handle text data. In this paper, we aim to explore the potential of LLMs in graph machine learning, especially the node classification task, and investigate two possible pipelines: LLMs-as-Enhancers and LLMs-as-Predictors. The former leverages LLMs to enhance nodes' text attributes with their massive knowledge and then generate predictions through GNNs. The latter attempts to directly employ LLMs as standalone predictors. We conduct comprehensive and systematical studies on these two pipelines under various settings. From comprehensive empirical results, we make original observations and find new insights that open new possibilities and suggest promising directions to leverage LLMs for learning on graphs.

In-Process Global Interpretation for Graph Learning via Distribution Matching

Graphs neural networks (GNNs) have emerged as a powerful graph learning model due to their superior capacity in capturing critical graph patterns. To gain insights about the model mechanism for interpretable graph learning, previous efforts focus on post-hoc local interpretation by extracting the data pattern that a pre-trained GNN model uses to make an individual prediction. However, recent works show that post-hoc methods are highly sensitive to model initialization and local interpretation can only explain the model prediction specific to a particular instance. In this work, we address these limitations by answering an important question that is not yet studied: how to provide global interpretation of the model training procedure? We formulate this problem as in-process global interpretation, which targets on distilling high-level and human-intelligible patterns that dominate the training procedure of GNNs. We further propose Graph Distribution Matching (GDM) to synthesize interpretive graphs by matching the distribution of the original and interpretive graphs in the feature space of the GNN as its training proceeds. These few interpretive graphs demonstrate the most informative patterns the model captures during training. Extensive experiments on graph classification datasets demonstrate multiple advantages of the proposed method, including high explanation accuracy, time efficiency and the ability to reveal class-relevant structure.

Demystifying Structural Disparity in Graph Neural Networks: Can One Size Fit All?

Recent studies on Graph Neural Networks(GNNs) provide both empirical and theoretical evidence supporting their effectiveness in capturing structural patterns on both homophilic and certain heterophilic graphs. Notably, most real-world homophilic and heterophilic graphs are comprised of a mixture of nodes in both homophilic and heterophilic structural patterns, exhibiting a structural disparity. However, the analysis of GNN performance with respect to nodes exhibiting different structural patterns, e.g., homophilic nodes in heterophilic graphs, remains rather limited. In the present study, we provide evidence that Graph Neural Networks(GNNs) on node classification typically perform admirably on homophilic nodes within homophilic graphs and heterophilic nodes within heterophilic graphs while struggling on the opposite node set, exhibiting a performance disparity. We theoretically and empirically identify effects of GNNs on testing nodes exhibiting distinct structural patterns. We then propose a rigorous, non-i.i.d PAC-Bayesian generalization bound for GNNs, revealing reasons for the performance disparity, namely the aggregated feature distance and homophily ratio difference between training and testing nodes. Furthermore, we demonstrate the practical implications of our new findings via (1) elucidating the effectiveness of deeper GNNs; and (2) revealing an over-looked distribution shift factor on graph out-of-distribution problem and proposing a new scenario accordingly.

Estimating Continuous Muscle Fatigue For Multi-Muscle Coordinated Exercise: A Pilot Study

Assessing the progression of muscle fatigue for daily exercises provides vital indicators for precise rehabilitation, personalized training dose, especially under the context of Metaverse. Assessing fatigue of multi-muscle coordination-involved daily exercises requires the neuromuscular features that represent the fatigue-induced characteristics of spatiotemporal adaptions of multiple muscles and the estimator that captures the time-evolving progression of fatigue. In this paper, we propose to depict fatigue by the features of muscle compensation and spinal module activation changes and estimate continuous fatigue by a physiological rationale model. First, we extract muscle synergy fractionation and the variance of spinal module spikings as features inspired by the prior of fatigue-induced neuromuscular adaptations. Second, we treat the features as observations and develop a Bayesian Gaussian process to capture the time-evolving progression. Third, we solve the issue of lacking supervision information by mathematically formulating the time-evolving characteristics of fatigue as the loss function. Finally, we adapt the metrics that follow the physiological principles of fatigue to quantitatively evaluate the performance. Our extensive experiments present a 0.99 similarity between days, a over 0.7 similarity with other views of fatigue and a nearly 1 weak monotonicity, which outperform other methods. This study would aim the objective assessment of muscle fatigue.

Single-Cell Multimodal Prediction via Transformers

The recent development of multimodal single-cell technology has made the possibility of acquiring multiple omics data from individual cells, thereby enabling a deeper understanding of cellular states and dynamics. Nevertheless, the proliferation of multimodal single-cell data also introduces tremendous challenges in modeling the complex interactions among different modalities. The recently advanced methods focus on constructing static interaction graphs and applying graph neural networks (GNNs) to learn from multimodal data. However, such static graphs can be suboptimal as they do not take advantage of the downstream task information; meanwhile GNNs also have some inherent limitations when deeply stacking GNN layers. To tackle these issues, in this work, we investigate how to leverage transformers for multimodal single-cell data in an end-to-end manner while exploiting downstream task information. In particular, we propose a scMoFormer framework which can readily incorporate external domain knowledge and model the interactions within each modality and cross modalities. Extensive experiments demonstrate that scMoFormer achieves superior performance on various benchmark datasets. Note that scMoFormer won a Kaggle silver medal with the rank of $24\ /\ 1221$ (Top 2%) without ensemble in a NeurIPS 2022 competition. Our implementation is publicly available at Github.

Toward Degree Bias in Embedding-Based Knowledge Graph Completion

A fundamental task for knowledge graphs (KGs) is knowledge graph completion (KGC). It aims to predict unseen edges by learning representations for all the entities and relations in a KG. A common concern when learning representations on traditional graphs is degree bias. It can affect graph algorithms by learning poor representations for lower-degree nodes, often leading to low performance on such nodes. However, there has been limited research on whether there exists degree bias for embedding-based KGC and how such bias affects the performance of KGC. In this paper, we validate the existence of degree bias in embedding-based KGC and identify the key factor to degree bias. We then introduce a novel data augmentation method, KG-Mixup, to generate synthetic triples to mitigate such bias. Extensive experiments have demonstrated that our method can improve various embedding-based KGC methods and outperform other methods tackling the bias problem on multiple benchmark datasets.

Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Imputation

Spatially resolved transcriptomics brings exciting breakthroughs to single-cell analysis by providing physical locations along with gene expression. However, as a cost of the extremely high spatial resolution, the cellular level spatial transcriptomic data suffer significantly from missing values. While a standard solution is to perform imputation on the missing values, most existing methods either overlook spatial information or only incorporate localized spatial context without the ability to capture long-range spatial information. Using multi-head self-attention mechanisms and positional encoding, transformer models can readily grasp the relationship between tokens and encode location information. In this paper, by treating single cells as spatial tokens, we study how to leverage transformers to facilitate spatial tanscriptomics imputation. In particular, investigate the following two key questions: (1) $\textit{how to encode spatial information of cells in transformers}$, and (2) $\textit{ how to train a transformer for transcriptomic imputation}$. By answering these two questions, we present a transformer-based imputation framework, SpaFormer, for cellular-level spatial transcriptomic data. Extensive experiments demonstrate that SpaFormer outperforms existing state-of-the-art imputation algorithms on three large-scale datasets.

Test-Time Training for Graph Neural Networks

Graph Neural Networks (GNNs) have made tremendous progress in the graph classification task. However, a performance gap between the training set and the test set has often been noticed. To bridge such gap, in this work we introduce the first test-time training framework for GNNs to enhance the model generalization capacity for the graph classification task. In particular, we design a novel test-time training strategy with self-supervised learning to adjust the GNN model for each test graph sample. Experiments on the benchmark datasets have demonstrated the effectiveness of the proposed framework, especially when there are distribution shifts between training set and test set. We have also conducted exploratory studies and theoretical analysis to gain deeper understandings on the rationality of the design of the proposed graph test time training framework (GT3).