Qi Liu

Dingmin Wang, Shengchao Liu, Hanchen Wang et al. · stanford

Graph Neural Networks (GNNs) are effective tools for graph representation learning. Most GNNs rely on a recursive neighborhood aggregation scheme, named message passing, thereby their theoretical expressive power is limited to the first-order Weisfeiler-Lehman test (1-WL). An effective approach to this challenge is to explicitly retrieve some annotated examples used to enhance GNN models. While retrieval-enhanced models have been proved to be effective in many language and vision domains, it remains an open question how effective retrieval-enhanced GNNs are when applied to graph datasets. Motivated by this, we want to explore how the retrieval idea can help augment the useful information learned in the graph neural networks, and we design a retrieval-enhanced scheme called GRAPHRETRIEVAL, which is agnostic to the choice of graph neural network models. In GRAPHRETRIEVAL, for each input graph, similar graphs together with their ground-true labels are retrieved from an existing database. Thus they can act as a potential enhancement to complete various graph property predictive tasks. We conduct comprehensive experiments over 13 datasets, and we observe that GRAPHRETRIEVAL is able to reach substantial improvements over existing GNNs. Moreover, our empirical study also illustrates that retrieval enhancement is a promising remedy for alleviating the long-tailed label distribution problem.

Zaixi Zhang, Qi Liu, Qingyong Hu et al.

The Transformer architecture has achieved remarkable success in a number of domains including natural language processing and computer vision. However, when it comes to graph-structured data, transformers have not achieved competitive performance, especially on large graphs. In this paper, we identify the main deficiencies of current graph transformers:(1) Existing node sampling strategies in Graph Transformers are agnostic to the graph characteristics and the training process. (2) Most sampling strategies only focus on local neighbors and neglect the long-range dependencies in the graph. We conduct experimental investigations on synthetic datasets to show that existing sampling strategies are sub-optimal. To tackle the aforementioned problems, we formulate the optimization strategies of node sampling in Graph Transformer as an adversary bandit problem, where the rewards are related to the attention weights and can vary in the training procedure. Meanwhile, we propose a hierarchical attention scheme with graph coarsening to capture the long-range interactions while reducing computational complexity. Finally, we conduct extensive experiments on real-world datasets to demonstrate the superiority of our method over existing graph transformers and popular GNNs.

Jingyu Peng, Qi Liu, Linan Yue et al.

Recent advancements in Graph Neural Networks (GNNs) have spurred an upsurge of research dedicated to enhancing the explainability of GNNs, particularly in critical domains such as medicine. A promising approach is the self-explaining method, which outputs explanations along with predictions. However, existing self-explaining models require a large amount of training data, rendering them unavailable in few-shot scenarios. To address this challenge, in this paper, we propose a Meta-learned Self-Explaining GNN (MSE-GNN), a novel framework that generates explanations to support predictions in few-shot settings. MSE-GNN adopts a two-stage self-explaining structure, consisting of an explainer and a predictor. Specifically, the explainer first imitates the attention mechanism of humans to select the explanation subgraph, whereby attention is naturally paid to regions containing important characteristics. Subsequently, the predictor mimics the decision-making process, which makes predictions based on the generated explanation. Moreover, with a novel meta-training process and a designed mechanism that exploits task information, MSE-GNN can achieve remarkable performance on new few-shot tasks. Extensive experimental results on four datasets demonstrate that MSE-GNN can achieve superior performance on prediction tasks while generating high-quality explanations compared with existing methods. The code is publicly available at https://github.com/jypeng28/MSE-GNN.

Qingchuan Li, Jiatong Li, Tongxuan Liu et al.

Large Language Models (LLMs) have exhibited remarkable potential across a wide array of reasoning tasks, including logical reasoning. Although massive efforts have been made to empower the logical reasoning ability of LLMs via external logical symbolic solvers, crucial challenges of the poor generalization ability to questions with different features and inevitable question information loss of symbolic solver-driven approaches remain unresolved. To mitigate these issues, we introduce LINA, a LLM-driven neuro-symbolic approach for faithful logical reasoning. By enabling an LLM to autonomously perform the transition from propositional logic extraction to sophisticated logical reasoning, LINA not only bolsters the resilience of the reasoning process but also eliminates the dependency on external solvers. Additionally, through its adoption of a hypothetical-deductive reasoning paradigm, LINA effectively circumvents the expansive search space challenge that plagues traditional forward reasoning methods. Empirical evaluations demonstrate that LINA substantially outperforms both established propositional logic frameworks and conventional prompting techniques across a spectrum of five logical reasoning tasks. Specifically, LINA achieves an improvement of 24.34% over LINC on the FOLIO dataset, while also surpassing prompting strategies like CoT and CoT-SC by up to 24.02%. Our code is available at https://github.com/wufeiwuwoshihua/nshy.

Lucas W. Remedios, Shunxing Bao, Samuel W. Remedios et al.

Understanding the way cells communicate, co-locate, and interrelate is essential to understanding human physiology. Hematoxylin and eosin (H&E) staining is ubiquitously available both for clinical studies and research. The Colon Nucleus Identification and Classification (CoNIC) Challenge has recently innovated on robust artificial intelligence labeling of six cell types on H&E stains of the colon. However, this is a very small fraction of the number of potential cell classification types. Specifically, the CoNIC Challenge is unable to classify epithelial subtypes (progenitor, endocrine, goblet), lymphocyte subtypes (B, helper T, cytotoxic T), or connective subtypes (fibroblasts, stromal). In this paper, we propose to use inter-modality learning to label previously un-labelable cell types on virtual H&E. We leveraged multiplexed immunofluorescence (MxIF) histology imaging to identify 14 subclasses of cell types. We performed style transfer to synthesize virtual H&E from MxIF and transferred the higher density labels from MxIF to these virtual H&E images. We then evaluated the efficacy of learning in this approach. We identified helper T and progenitor nuclei with positive predictive values of $0.34 \pm 0.15$ (prevalence $0.03 \pm 0.01$) and $0.47 \pm 0.1$ (prevalence $0.07 \pm 0.02$) respectively on virtual H&E. This approach represents a promising step towards automating annotation in digital pathology.

Zaixi Zhang, Qingyong Hu, Yang Yu et al.

Graphs are widely used to model relational data. As graphs are getting larger and larger in real-world scenarios, there is a trend to store and compute subgraphs in multiple local systems. For example, recently proposed \emph{subgraph federated learning} methods train Graph Neural Networks (GNNs) distributively on local subgraphs and aggregate GNN parameters with a central server. However, existing methods have the following limitations: (1) The links between local subgraphs are missing in subgraph federated learning. This could severely damage the performance of GNNs that follow message-passing paradigms to update node/edge features. (2) Most existing methods overlook the subgraph heterogeneity issue, brought by subgraphs being from different parts of the whole graph. To address the aforementioned challenges, we propose a scalable \textbf{Fed}erated \textbf{G}raph \textbf{T}ransformer (\textbf{FedGT}) in the paper. Firstly, we design a hybrid attention scheme to reduce the complexity of the Graph Transformer to linear while ensuring a global receptive field with theoretical bounds. Specifically, each node attends to the sampled local neighbors and a set of curated global nodes to learn both local and global information and be robust to missing links. The global nodes are dynamically updated during training with an online clustering algorithm to capture the data distribution of the corresponding local subgraph. Secondly, FedGT computes clients' similarity based on the aligned global nodes with optimal transport. The similarity is then used to perform weighted averaging for personalized aggregation, which well addresses the data heterogeneity problem. Moreover, local differential privacy is applied to further protect the privacy of clients. Finally, extensive experimental results on 6 datasets and 2 subgraph settings demonstrate the superiority of FedGT.

Zaixi Zhang, Qi Liu, Hao Wang et al.

Despite the recent progress in Graph Neural Networks (GNNs), it remains challenging to explain the predictions made by GNNs. Existing explanation methods mainly focus on post-hoc explanations where another explanatory model is employed to provide explanations for a trained GNN. The fact that post-hoc methods fail to reveal the original reasoning process of GNNs raises the need of building GNNs with built-in interpretability. In this work, we propose Prototype Graph Neural Network (ProtGNN), which combines prototype learning with GNNs and provides a new perspective on the explanations of GNNs. In ProtGNN, the explanations are naturally derived from the case-based reasoning process and are actually used during classification. The prediction of ProtGNN is obtained by comparing the inputs to a few learned prototypes in the latent space. Furthermore, for better interpretability and higher efficiency, a novel conditional subgraph sampling module is incorporated to indicate which part of the input graph is most similar to each prototype in ProtGNN+. Finally, we evaluate our method on a wide range of datasets and perform concrete case studies. Extensive results show that ProtGNN and ProtGNN+ can provide inherent interpretability while achieving accuracy on par with the non-interpretable counterparts.

Hanshuang Tong, Zhen Wang, Yun Zhou et al.

Knowledge tracing (KT) which aims at predicting learner's knowledge mastery plays an important role in the computer-aided educational system. In recent years, many deep learning models have been applied to tackle the KT task, which have shown promising results. However, limitations still exist. Most existing methods simplify the exercising records as knowledge sequences, which fail to explore rich information that existed in exercises. Besides, the existing diagnosis results of knowledge tracing are not convincing enough since they neglect prior relations between exercises. To solve the above problems, we propose a hierarchical graph knowledge tracing model called HGKT to explore the latent hierarchical relations between exercises. Specifically, we introduce the concept of problem schema to construct a hierarchical exercise graph that could model the exercise learning dependencies. Moreover, we employ two attention mechanisms to highlight the important historical states of learners. In the testing stage, we present a K&S diagnosis matrix that could trace the transition of mastery of knowledge and problem schema, which can be more easily applied to different applications. Extensive experiments show the effectiveness and interpretability of our proposed models.

Shuai Zhang, Yi Tay, Lina Yao et al.

In this work, we move beyond the traditional complex-valued representations, introducing more expressive hypercomplex representations to model entities and relations for knowledge graph embeddings. More specifically, quaternion embeddings, hypercomplex-valued embeddings with three imaginary components, are utilized to represent entities. Relations are modelled as rotations in the quaternion space. The advantages of the proposed approach are: (1) Latent inter-dependencies (between all components) are aptly captured with Hamilton product, encouraging a more compact interaction between entities and relations; (2) Quaternions enable expressive rotation in four-dimensional space and have more degree of freedom than rotation in complex plane; (3) The proposed framework is a generalization of ComplEx on hypercomplex space while offering better geometrical interpretations, concurrently satisfying the key desiderata of relational representation learning (i.e., modeling symmetry, anti-symmetry and inversion). Experimental results demonstrate that our method achieves state-of-the-art performance on four well-established knowledge graph completion benchmarks.