Zhili Wang

Zhili Wang, Shimin Di, Lei Chen et al.

Recently, graph neural networks (GNNs) have shown its unprecedented success in many graph-related tasks. However, GNNs face the label scarcity issue as other neural networks do. Thus, recent efforts try to pre-train GNNs on a large-scale unlabeled graph and adapt the knowledge from the unlabeled graph to the target downstream task. The adaptation is generally achieved by fine-tuning the pre-trained GNNs with a limited number of labeled data. Despite the importance of fine-tuning, current GNNs pre-training works often ignore designing a good fine-tuning strategy to better leverage transferred knowledge and improve the performance on downstream tasks. Only few works start to investigate a better fine-tuning strategy for pre-trained GNNs. But their designs either have strong assumptions or overlook the data-aware issue for various downstream datasets. Therefore, we aim to design a better fine-tuning strategy for pre-trained GNNs to improve the model performance in this paper. Given a pre-trained GNN, we propose to search to fine-tune pre-trained graph neural networks for graph-level tasks (S2PGNN), which adaptively design a suitable fine-tuning framework for the given labeled data on the downstream task. To ensure the improvement brought by searching fine-tuning strategy, we carefully summarize a proper search space of fine-tuning framework that is suitable for GNNs. The empirical studies show that S2PGNN can be implemented on the top of 10 famous pre-trained GNNs and consistently improve their performance. Besides, S2PGNN achieves better performance than existing fine-tuning strategies within and outside the GNN area. Our code is publicly available at \url{https://anonymous.4open.science/r/code_icde2024-A9CB/}.

Jialiang Wang, Hanmo Liu, Shimin Di et al.

High-level automation is increasingly critical in AI, driven by rapid advances in large language models (LLMs) and AI agents. However, LLMs, despite their general reasoning power, struggle significantly in specialized, data-sensitive tasks such as designing Graph Neural Networks (GNNs). This difficulty arises from (1) the inherent knowledge gaps in modeling the intricate, varying relationships between graph properties and suitable architectures and (2) the external noise from misleading descriptive inputs, often resulting in generic or even misleading model suggestions. Achieving proficiency in designing data-aware models -- defined as the meta-level capability to systematically accumulate, interpret, and apply data-specific design knowledge -- remains challenging for existing automated approaches, due to their inefficient construction and application of meta-knowledge. To achieve meta-level proficiency, we propose DesiGNN, a knowledge-centered framework that systematically converts past model design experience into structured, fine-grained knowledge priors well-suited for meta-learning with LLMs. To account for the inherent variability and external noise, DesiGNN aligns empirical property filtering from extensive benchmarks with adaptive elicitation of literature insights via LLMs. By constructing a solid meta-knowledge between unseen graph understanding and known effective architecture patterns, DesiGNN can deliver top-5.77% initial model proposals for unseen datasets within seconds and achieve consistently superior performance with minimal search cost compared to baselines.

Yubo Wang, Shimin Di, Zhili Wang et al.

Recently, Hyper-relational Knowledge Graphs (HKGs) have been proposed as an extension of traditional Knowledge Graphs (KGs) to better represent real-world facts with additional qualifiers. As a result, researchers have attempted to adapt classical Knowledge Graph Embedding (KGE) models for HKGs by designing extra qualifier processing modules. However, it remains unclear whether the superior performance of Hyper-relational KGE (HKGE) models arises from their base KGE model or the specially designed extension module. Hence, in this paper, we data-wise convert HKGs to KG format using three decomposition methods and then evaluate the performance of several classical KGE models on HKGs. Our results show that some KGE models achieve performance comparable to that of HKGE models. Upon further analysis, we find that the decomposition methods alter the original HKG topology and fail to fully preserve HKG information. Moreover, we observe that current HKGE models are either insufficient in capturing the graph's long-range dependency or struggle to integrate main-triple and qualifier information due to the information compression issue. To further justify our findings and offer a potential direction for future HKGE research, we propose the FormerGNN framework. This framework employs a qualifier integrator to preserve the original HKG topology, and a GNN-based graph encoder to capture the graph's long-range dependencies, followed by an improved approach for integrating main-triple and qualifier information to mitigate compression issues. Our experimental results demonstrate that FormerGNN outperforms existing HKGE models.

Jialiang Wang, Hanmo Liu, Shimin Di et al.

Database systems have recently advocated for embedding machine learning (ML) capabilities, offering declarative model queries over large, managed model repositories, thereby circumventing the huge computational overhead of traditional ML-based algorithms in automated neural network model selection. Pioneering database studies aim to organize existing benchmark repositories as model bases (MB), querying them for the model records with the highest performance estimation metrics for given tasks. However, this static model selection practice overlooks the fine-grained, evolving relational dependencies between diverse task queries and model architecture variations, resulting in suboptimal matches and failing to further refine the model effectively. To fill the model refinement gap in database research, we propose M-DESIGN, a curated model knowledge base (MKB) pipeline for mastering neural network refinement by adaptively weaving prior insights about model architecture modification. First, we propose a knowledge weaving engine that reframes model refinement as an adaptive query problem over task metadata. Given a user's task query, M-DESIGN quickly matches and iteratively refines candidate models by leveraging a graph-relational knowledge schema that explicitly encodes data properties, architecture variations, and pairwise performance deltas as joinable relations. This schema supports fine-grained relational analytics over architecture tweaks and drives a predictive query planner that can detect and adapt to out-of-distribution (OOD) tasks. We instantiate M-DESIGN for graph analytics tasks, where our model knowledge base enriches existing benchmarks with structured metadata covering 3 graph tasks and 22 graph datasets, contributing data records of 67,760 graph models. Empirical results demonstrate that M-DESIGN delivers the optimal model in 26 of 33 data-task pairs within limited budgets.

Zhili Wang, Shimin Di, Lei Chen

Recently, Graph Neural Networks (GNNs) have gained popularity in a variety of real-world scenarios. Despite the great success, the architecture design of GNNs heavily relies on manual labor. Thus, automated graph neural network (AutoGNN) has attracted interest and attention from the research community, which makes significant performance improvements in recent years. However, existing AutoGNN works mainly adopt an implicit way to model and leverage the link information in the graphs, which is not well regularized to the link prediction task on graphs, and limits the performance of AutoGNN for other graph tasks. In this paper, we present a novel AutoGNN work that explicitly models the link information, abbreviated to AutoGEL. In such a way, AutoGEL can handle the link prediction task and improve the performance of AutoGNNs on the node classification and graph classification task. Specifically, AutoGEL proposes a novel search space containing various design dimensions at both intra-layer and inter-layer designs and adopts a more robust differentiable search algorithm to further improve efficiency and effectiveness. Experimental results on benchmark data sets demonstrate the superiority of AutoGEL on several tasks.

Shenghao Wang, Huajie Han, Kun Gao et al.

X-ray phase-contrast imaging can provide greatly improved contrast over conventional absorption-based imaging for weakly absorbing samples, such as biological soft tissues and fibre composites. In this manuscript, we introduce an easy and fast way to develop a user-friendly software platform dedicated to the new grating-based X-ray phase-contrast imaging setup recently built at the National Synchrotron Radiation Laboratory of the University of Science and Technology of China. Unified management and control of 21 motorized positioning stages, of an ultra-precision piezoelectric translation stage and of the X-ray tube are achieved with this platform. The software package also covers the automatic image acquisition of the phase-stepping scanning with a flat panel detector. Moreover, a data post-processing module for signals retrieval and other custom features are in principle available. With a seamless integration of all necessary functions in a unique package, this software platform will greatly support the user activity during experimental runs.