Hao Yuan

Shurui Gui, Hao Yuan, Jie Wang et al.

We investigate the explainability of graph neural networks (GNNs) as a step toward elucidating their working mechanisms. While most current methods focus on explaining graph nodes, edges, or features, we argue that, as the inherent functional mechanism of GNNs, message flows are more natural for performing explainability. To this end, we propose a novel method here, known as FlowX, to explain GNNs by identifying important message flows. To quantify the importance of flows, we propose to follow the philosophy of Shapley values from cooperative game theory. To tackle the complexity of computing all coalitions' marginal contributions, we propose a flow sampling scheme to compute Shapley value approximations as initial assessments of further training. We then propose an information-controlled learning algorithm to train flow scores toward diverse explanation targets: necessary or sufficient explanations. Experimental studies on both synthetic and real-world datasets demonstrate that our proposed FlowX and its variants lead to improved explainability of GNNs. The code is available at https://github.com/divelab/DIG.

Li Cai, Xin Mao, Meirong Ma et al.

Entity alignment (EA) aims to find entities in different knowledge graphs (KGs) that refer to the same object in the real world. Recent studies incorporate temporal information to augment the representations of KGs. The existing methods for EA between temporal KGs (TKGs) utilize a time-aware attention mechanism to incorporate relational and temporal information into entity embeddings. The approaches outperform the previous methods by using temporal information. However, we believe that it is not necessary to learn the embeddings of temporal information in KGs since most TKGs have uniform temporal representations. Therefore, we propose a simple graph neural network (GNN) model combined with a temporal information matching mechanism, which achieves better performance with less time and fewer parameters. Furthermore, since alignment seeds are difficult to label in real-world applications, we also propose a method to generate unsupervised alignment seeds via the temporal information of TKG. Extensive experiments on public datasets indicate that our supervised method significantly outperforms the previous methods and the unsupervised one has competitive performance.

Xin Ai, Qiange Wang, Chunyu Cao et al.

Graph Neural Networks (GNNs) have demonstrated outstanding performance in various applications. Existing frameworks utilize CPU-GPU heterogeneous environments to train GNN models and integrate mini-batch and sampling techniques to overcome the GPU memory limitation. In CPU-GPU heterogeneous environments, we can divide sample-based GNN training into three steps: sample, gather, and train. Existing GNN systems use different task orchestrating methods to employ each step on CPU or GPU. After extensive experiments and analysis, we find that existing task orchestrating methods fail to fully utilize the heterogeneous resources, limited by inefficient CPU processing or GPU resource contention. In this paper, we propose NeutronOrch, a system for sample-based GNN training that incorporates a layer-based task orchestrating method and ensures balanced utilization of the CPU and GPU. NeutronOrch decouples the training process by layer and pushes down the training task of the bottom layer to the CPU. This significantly reduces the computational load and memory footprint of GPU training. To avoid inefficient CPU processing, NeutronOrch only offloads the training of frequently accessed vertices to the CPU and lets GPU reuse their embeddings with bounded staleness. Furthermore, NeutronOrch provides a fine-grained pipeline design for the layer-based task orchestrating method, fully overlapping different tasks on heterogeneous resources while strictly guaranteeing bounded staleness. The experimental results show that compared with the state-of-the-art GNN systems, NeutronOrch can achieve up to 11.51x performance speedup.

ZhiChao Yan, Hui Xue, Yi Zhu et al.

Accurate segmentation of lesions in pancreatic endoscopic ultrasound (EUS) images is crucial for effective diagnosis and treatment. However, the collection of enough crisp EUS images for effective diagnosis is arduous. Recently, domain adaptation (DA) has been employed to address these challenges by leveraging related knowledge from other domains. Most DA methods only focus on multi-view representations of the same organ, which makes it still tough to clearly depict the tumor lesion area with limited semantic information. Although transferring homogeneous similarity from different organs could benefit the issue, there is a lack of relevant work due to the enormous domain gap between them. To address these challenges, we propose the Cross-Organ Tumor Segmentation Networks (COTS-Nets), consisting of a universal network and an auxiliary network. The universal network utilizes boundary loss to learn common boundary information of different tumors, enabling accurate delineation of tumors in EUS despite limited and low-quality data. Simultaneously, we incorporate consistency loss in the universal network to align the prediction of pancreatic EUS with tumor boundaries from other organs to mitigate the domain gap. To further reduce the cross-organ domain gap, the auxiliary network integrates multi-scale features from different organs, aiding the universal network in acquiring domain-invariant knowledge. Systematic experiments demonstrate that COTS-Nets significantly improves the accuracy of pancreatic cancer diagnosis. Additionally, we developed the Pancreatic Cancer Endoscopic Ultrasound (PCEUS) dataset, comprising 501 pathologically confirmed pancreatic EUS images, to facilitate model development.

Lingyue Fu, Hao Guan, Bolun Zhang et al.

As Large Language Models (LLMs) demonstrate increasingly sophisticated code processing capabilities, evaluating their performance on engineering-level code remains challenging. Existing repository-level benchmarks primarily focus on single scenarios, such as code generation or bug fixing, without adequately capturing the diversity and complexity of real-world software or project engineering workflows. Furthermore, these benchmarks suffer from limited controllability in question positioning and reliability issues in their generated test cases. To address these limitations, we present CorePipe, a fully automated pipeline that converts repositories into comprehensive test cases, and introduce CoreCodeBench, a configurable multi-scenario repository-level benchmark. To simulate real engineering scenarios, CorePipe generates three types of atomic questions (Development, BugFix, and Test-Driven Development) specifically targeting core code segments. These atomic questions are further combined into three types of composite questions, with difficulty levels flexibly adjusted through hyperparameter tuning. CoreCodeBench provides a comprehensive and extensive repository-level benchmark to investigate the applicability of LLMs in real-world engineering projects. Experiments with 16 LLMs across diverse scenarios reveal varying capabilities and offer multi-dimensional insights into LLM performance in engineering contexts. The code for CorePipe is available at https://github.com/AGI-Eval-Official/CoreCodeBench, and the data for CoreCodeBench can be accessed at https://huggingface.co/collections/tubehhh/corecodebench-68256d2faabf4b1610a08caa.

Hao Yuan, Haiyang Yu, Shurui Gui et al.

Deep learning methods are achieving ever-increasing performance on many artificial intelligence tasks. A major limitation of deep models is that they are not amenable to interpretability. This limitation can be circumvented by developing post hoc techniques to explain the predictions, giving rise to the area of explainability. Recently, explainability of deep models on images and texts has achieved significant progress. In the area of graph data, graph neural networks (GNNs) and their explainability are experiencing rapid developments. However, there is neither a unified treatment of GNN explainability methods, nor a standard benchmark and testbed for evaluations. In this survey, we provide a unified and taxonomic view of current GNN explainability methods. Our unified and taxonomic treatments of this subject shed lights on the commonalities and differences of existing methods and set the stage for further methodological developments. To facilitate evaluations, we generate a set of benchmark graph datasets specifically for GNN explainability. We summarize current datasets and metrics for evaluating GNN explainability. Altogether, this work provides a unified methodological treatment of GNN explainability and a standardized testbed for evaluations.

Mohammad Kachuee, Hao Yuan, Young-Bum Kim et al.

Turn-level user satisfaction is one of the most important performance metrics for conversational agents. It can be used to monitor the agent's performance and provide insights about defective user experiences. Moreover, a powerful satisfaction model can be used as an objective function that a conversational agent continuously optimizes for. While end-to-end deep learning has shown promising results, having access to a large number of reliable annotated samples required by these methods remains challenging. In a large-scale conversational system, there is a growing number of newly developed skills, making the traditional data collection, annotation, and modeling process impractical due to the required annotation costs as well as the turnaround times. In this paper, we suggest a self-supervised contrastive learning approach that leverages the pool of unlabeled data to learn user-agent interactions. We show that the pre-trained models using the self-supervised objective are transferable to the user satisfaction prediction. In addition, we propose a novel few-shot transfer learning approach that ensures better transferability for very small sample sizes. The suggested few-shot method does not require any inner loop optimization process and is scalable to very large datasets and complex models. Based on our experiments using real-world data from a large-scale commercial system, the suggested approach is able to significantly reduce the required number of annotations, while improving the generalization on unseen out-of-domain skills.