Shirui Pan

Griffith University · School of Information and Communication Technology (ICT)

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications, where data are generated from...

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction toward cognition and human-level intelligence. In this survey, we provide a comprehensive review of the knowledge graph covering overall research topics about: 1)...

One-shot neural architecture search (NAS) has recently become mainstream in the NAS community because it significantly improves computational efficiency through weight sharing. However, the supernet training paradigm in one-shot NAS introduces catastrophic forgetting. To overcome this problem of catastrophic forgetting, we formulate supernet traini...

Conversational Recommender Systems (CRSs) aim to provide personalized recommendations through dynamically capturing user preferences in interactive conversations. Conventional CRSs often extract user preferences as hidden representations, which are criticized for their lack of interpretability. This diminishes the transparency and trustworthiness o...

Graph Neural Networks (GNNs) have achieved impressive performance in many tasks on graph data. Recent studies show that they are vulnerable to adversarial attacks. Deliberate and unnoticeable perturbations on topology structure could render them near-useless in applications. How to design effective methods to improve the robustness of GNNs is a cru...

Traffic accident prediction plays a vital role in Intelligent Transportation Systems (ITS), where a large number of traffic streaming data are generated on a daily basis for spatiotemporal big data analysis. The rarity of accidents and the absent interconnection information make it hard for spatiotemporal modeling. Moreover, the inherent characteri...

Knowledge Graph Query Embedding (KGQE) aims to embed First-Order Logic (FOL) queries in a low-dimensional KG space for complex reasoning over incomplete KGs. To enhance the generalization of KGQE models, recent studies integrate various external information (such as entity types and relation context) to better capture the logical semantics of FOL q...

Unsupervised graph representation learning (UGRL) based on graph neural networks (GNNs), has received increasing attention owing to its efficacy in handling graph-structured data. However, existing UGRL methods ideally assume that the node features are noise-free, which makes them fail to distinguish between useful information and noise when applie...

The Large Visual Language Models (LVLMs) enhances user interaction and enriches user experience by integrating visual modality on the basis of the Large Language Models (LLMs). It has demonstrated their powerful information processing and generation capabilities. However, the existence of hallucinations has limited the potential and practical effec...

Molecular optimization (MO) is a crucial stage in drug discovery in which task-oriented generated molecules are optimized to meet practical industrial requirements. Existing mainstream MO approaches primarily utilize external property predictors to guide iterative property optimization. However, learning all molecular samples in the vast chemical s...

Scaling laws offer valuable insights into the design of time series foundation models (TSFMs). However, previous research has largely focused on the scaling laws of TSFMs for in-distribution (ID) data, leaving their out-of-distribution (OOD) scaling behavior and the influence of model architectures less explored. In this work, we examine two common...

Large language models (LLMs) have demonstrated impressive reasoning abilities, but they still struggle with faithful reasoning due to knowledge gaps and hallucinations. To address these issues, knowledge graphs (KGs) have been utilized to enhance LLM reasoning through their structured knowledge. However, existing KG-enhanced methods, either retriev...

Multiple-choice question answering (MCQA) becomes particularly challenging when all choices are relevant to the question and are semantically similar. Yet this setting of MCQA can potentially provide valuable clues for choosing the right answer. Existing models often rank each choice separately, overlooking the context provided by other choices. Sp...

Motivation Predicting the binding affinity between antigens and antibodies accurately is crucial for assessing therapeutic antibody effectiveness and enhancing antibody engineering and vaccine design. Traditional machine learning methods have been widely used for this purpose, relying on interfacial amino acids’ structural information. Nevertheless...

Increasing multiple behavior recommendation models have achieved great successes. However, many models do not consider commonalities and differences between behaviors and data sparsity of the target behavior. This paper proposes a novel Multi-behavior Recommendation Model (MBRCC) based on Contrastive Clustering Learning. Specifically, the graph con...

Owing to the unprecedented capability in semantic understanding and logical reasoning, the pre-trained large language models (LLMs) have shown fantastic potential in developing the next-generation recommender systems (RSs). However, the static index paradigm adopted by current methods greatly restricts the utilization of LLMs capacity for recommend...

The integration of Large Language Models (LLMs) into the drug discovery and development field marks a significant paradigm shift, offering novel methodologies for understanding disease mechanisms, facilitating drug discovery, and optimizing clinical trial processes. This review highlights the expanding role of LLMs in revolutionizing various stages...

Time series anomaly detection is important for a wide range of research fields and applications, including financial markets, economics, earth sciences, manufacturing, and healthcare. The presence of anomalies can indicate novel or unexpected events, such as production faults, system defects, and heart palpitations, and is therefore of particular i...

Multiple-choice question answering (MCQA) becomes particularly challenging when all choices are relevant to the question and are semantically similar. Yet this setting of MCQA can potentially provide valuable clues for choosing the right answer. Existing models often rank each choice separately, overlooking the context provided by other choices. Sp...

Time series are the primary data type used to record dynamic system measurements and generated in great volume by both physical sensors and online processes (virtual sensors). Time series analytics is therefore crucial to unlocking the wealth of information implicit in available data. With the recent advancements in graph neural networks (GNNs), th...

Dynamic graph learning aims to uncover evolutionary laws in real-world systems, enabling accurate social recommendation (link prediction) or early detection of cancer cells (classification). Inspired by the success of state space models, e.g., Mamba, for efficiently capturing long-term dependencies in language modeling, we propose DyG-Mamba, a new...

Motivation The asymmetrical distribution of expressed mRNAs tightly controls the precise synthesis of proteins within human cells. This non-uniform distribution, a cornerstone of developmental biology, plays a pivotal role in numerous cellular processes. To advance our comprehension of gene regulatory networks, it is essential to develop computatio...

Heterogeneous graph data are ubiquitous and extracting information from them is increasingly crucial. Existing approaches for modeling heterogeneous graphs often rely on the splitting strategy guided by meta-paths or relations. However, the splitting strategy falls short in capturing the rich semantic information and topological structure of hetero...

Knowledge graphs (KGs) store enormous facts as relationships between entities. Due to the long-tailed distribution of relations and the incompleteness of KGs, there is growing interest in few-shot knowledge graph completion (FKGC). Existing FKGC methods often assume the existence of all entities in KGs, which may not be practical since new relation...

Graph Neural Network (GNN) is powerful in graph embedding learning, but its performance has been shown to be heavily degraded under adversarial attacks. Deep graph structure learning (GSL) is proposed to defend attack by jointly learning graph structure and graph embedding, typically in node classification task. Label supervision is expensive in re...

In recommender systems, graph neural networks (GNN) can integrate interactions between users and items with their attributes, which makes GNN-based methods more powerful. However, directly stacking multiple layers in a graph neural network can easily lead to over-smoothing, hence recommendation systems based on graph neural networks typically under...

Graph Transformers (GTs) have demonstrated their advantages across a wide range of tasks. However, the self-attention mechanism in GTs overlooks the graph's inductive biases, particularly biases related to structure, which are crucial for the graph tasks. Although some methods utilize positional encoding and attention bias to model inductive biases...

As a popular task in graph learning, node classification seeks to assign labels to nodes, taking into account both their features and connections. However, an important challenge for its application in real-world scenarios is the presence of newly-emerged out-of-distribution samples and noisy samples, which affect the quality and robustness of lear...

Unsupervised graph representation learning (UGRL) based on graph neural networks (GNNs), has received increasing attention owing to its efficacy in handling graph-structured data. However, existing UGRL methods ideally assume that the node features are noise-free, which makes them fail to distinguish between useful information and noise when applie...

Cross-modal hashing encodes different modalities of multimodal data into low-dimensional Hamming space for fast cross-modal retrieval. In multi-label cross-modal retrieval, multimodal data are often annotated with multiple labels, and some labels, e.g.“, ocean” and “cloud”, often co-occur. However, existing cross-modal hashing methods overlook labe...

Message passing (MP) is crucial for effective graph neural networks (GNNs). Most local message-passing schemes have been shown to underperform on heterophily graphs due to the perturbation of updated representations caused by local redundant heterophily information. However, our experiment findings indicate that the distribution of heterophily info...

Large language models (LLMs), such as ChatGPT and GPT4, are making new waves in the field of natural language processing and artificial intelligence, due to their emergent ability and generalizability. However, LLMs are black-box models, which often fall short of capturing and accessing factual knowledge. In contrast, Knowledge Graphs (KGs), Wikipe...

Recommender systems are pivotal in enhancing user experiences across various web applications by analyzing the complicated relationships between users and items. Knowledge graphs(KGs) have been widely used to enhance the performance of recommender systems. However, KGs are known to be noisy and incomplete, which are hard to provide reliable explana...

To build safe and reliable graph machine learning systems, unsupervised graph-level anomaly detection (GLAD) and unsupervised graph-level out-of-distribution (OOD) detection (GLOD) have received significant attention in recent years. Though those two lines of research indeed share the same objective, they have been studied independently in the comm...

Graph Neural Networks (GNNs) have become pivotal tools for a range of graph-based learning tasks. Notably, most current GNN architectures operate under the assumption of homophily, whether explicitly or implicitly. While this underlying assumption is frequently adopted, it is not universally applicable, which can result in potential shortcomings in...

In drug discovery, determining the binding affinity and functional effects of small-molecule ligands on proteins is critical. Current computational methods can predict these protein–ligand interaction properties but often lose accuracy without high-resolution protein structures and falter in predicting functional effects. Here we introduce PSICHIC...

The Type III Secretion Systems (T3SSs) play a pivotal role in host-pathogen interactions by mediating the secretion of type III secretion system effectors (T3SEs) into host cells. These T3SEs mimic host cell protein functions, influencing interactions between Gram-negative bacterial pathogens and their hosts. Identifying T3SEs is essential in biome...

In recent years, there has been notable interest in investigating combinatorial optimization (CO) problems by neural-based framework. An emerging strategy to tackle these challenging problems involves the adoption of graph neural networks (GNNs) as an alternative to traditional algorithms, a subject that has attracted considerable attention. Despit...

The vision-and-language navigation (VLN) task necessitates an agent to perceive the surroundings, follow natural language instructions, and act in photo-realistic unseen environments. Most of the existing methods employ the entire image or object features to represent navigable viewpoints. However, these representations are insufficient for proper...

This research introduces the Variational Graph Attention Dynamics (VarGATDyn), addressing the complexities of dynamic graph representation learning, where existing models, tailored for static graphs, prove inadequate. VarGATDyn melds attention mechanisms with a Markovian assumption to surpass the challenges of maintaining temporal consistency and t...

Accurate geographical traffic forecasting plays a critical role in urban transportation planning, traffic management, and geospatial artificial intelligence (GeoAI). Although deep learning models have made significant progress in geographical traffic forecasting, they still face challenges in effectively capturing long-term temporal dependencies an...

Graph Neural Networks (GNNs) have gained significant attention as a powerful modeling and inference method, especially for homophilic graph-structured data. To empower GNNs in heterophilic graphs, where adjacent nodes exhibit dissimilar labels or features, Signed Message Passing (SMP) has been widely adopted. However, there is a lack of theoretical...

The Large Language Model (LLM) watermark is a newly emerging technique that shows promise in addressing concerns surrounding LLM copyright, monitoring AI-generated text, and preventing its misuse. The LLM watermark scheme commonly includes generating secret keys to partition the vocabulary into green and red lists, applying a perturbation to the lo...

Graph anomaly detection (GAD), which aims to identify abnormal nodes that differ from the majority within a graph, has garnered significant attention. However, current GAD methods necessitate training specific to each dataset, resulting in high training costs, substantial data requirements, and limited generalizability when being applied to new dat...

Social recommendation models weave social interactions into their design to provide uniquely personalized recommendation results for users. However, social networks not only amplify the popularity bias in recommendation models, resulting in more frequent recommendation of hot items and fewer long-tail items, but also include a substantial amount of...

Temporal Knowledge Graph Reasoning (TKGR) is the process of utilizing temporal information to capture complex relations within a Temporal Knowledge Graph (TKG) to infer new knowledge. Conventional methods in TKGR typically depend on deep learning algorithms or temporal logical rules. However, deep learning-based TKGRs often lack interpretability, w...

Graph unlearning has emerged as an essential tool for safeguarding user privacy and mitigating the negative impacts of undesirable data. Meanwhile, the advent of dynamic graph neural networks (DGNNs) marks a significant advancement due to their superior capability in learning from dynamic graphs, which encapsulate spatial-temporal variations in div...

Graph Neural Networks (GNNs) have demonstrated superior performance across various graph learning tasks but face significant computational challenges when applied to large-scale graphs. One effective approach to mitigate these challenges is graph sparsification, which involves removing non-essential edges to reduce computational overhead. However,...

Drug response prediction (DRP) is a crucial phase in drug discovery, and the most important metric for its evaluation is the IC50 score. DRP results are heavily dependent on the quality of the generated molecules. Existing molecule generation methods typically employ classifier-based guidance, enabling sampling within the IC50 classification range....

Drug-target interaction (DTI) prediction is a critical component of the drug discovery process. In the drug development engineering field, predicting novel drug-target interactions is extremely crucial.However, although existing methods have achieved high accuracy levels in predicting known drugs and drug targets, they fail to utilize global protei...

Temporal knowledge graphs (TKGs) are receiving increased attention due to their time-dependent properties and the evolving nature of knowledge over time. TKGs typically contain complex geometric structures, such as hierarchical, ring, and chain structures, which can often be mixed together. However, embedding TKGs into Euclidean space, as is typica...

Graph Masked Autoencoders (GMAEs) have emerged as a notable self-supervised learning approach for graph-structured data. Existing GMAE models primarily focus on reconstructing node-level information, categorizing them as single-scale GMAEs. This methodology, while effective in certain contexts, tends to overlook the complex hierarchical structures...

Conversational recommender systems (CRSs) utilize natural language interactions and dialog history to infer user preferences and provide accurate recommendations. Due to the limited conversation context and background knowledge, existing CRSs rely on external sources such as knowledge graphs (KGs) to enrich the context and model entities based on t...

Graph Neural Networks (GNNs) have achieved remarkable success in diverse real-world applications. Traditional GNNs are designed based on homophily, which leads to poor performance under heterophily scenarios. Most current solutions deal with heterophily mainly by modeling the heterophily edges as data noises or high-frequency signals, treating all...

The study of time series data is crucial for understanding trends and anomalies over time, enabling predictive insights across various sectors. Spatio-temporal data, on the other hand, is vital for analyzing phenomena in both space and time, providing a dynamic perspective on complex system interactions. Recently, diffusion models have seen widespr...

Adapting Foundation Models (FMs) for downstream tasks through Federated Learning (FL) emerges a promising strategy for protecting data privacy and valuable FMs. Existing methods finetune FM by allocating sub-FM to clients in FL, however, leading to suboptimal performance due to insufficient tuning and inevitable error accumulations of gradients. In...

Answering complex queries with First-order logical operators over knowledge graphs, such as conjunction (∧\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\wedge $$\end{...

Self-supervised learning (SSL) has recently achieved impressive performance on various time series tasks. The most prominent advantage of SSL is that it reduces the dependence on labeled data. Based on the pre-training and fine-tuning strategy, even a small amount of labeled data can achieve high performance. Compared with many published self-super...

Federated learning is a new learning paradigm that decouples data collection and model training via multi-party computation and model aggregation. As a flexible learning setting, federated learning has the potential to integrate with other learning frameworks. We conduct a focused survey of federated learning in conjunction with other learning algo...

Deep neural networks for graphs (DNNGs) represent an emerging field that studies how the deep learning method can be generalized to graph-structured data. Since graphs are a powerful and flexible tool to represent complex information in the form of patterns and their relationships, ranging from molecules to protein-to-protein interaction networks,...

Model extraction attacks (MEAs) enable an attacker to replicate the functionality of a victim deep neural network (DNN) model by only querying its API service remotely, posing a severe threat to the security and integrity of pay-per-query DNN-based services. Although the majority of current research on MEAs has primarily concentrated on neural clas...

The vision-and-language navigation (VLN) task necessitates an agent to perceive the surroundings, follow natural language instructions, and act in photo-realistic unseen environments. Most of the existing methods employ the entire image or object features to represent navigable viewpoints. However, these representations are insufficient for proper...

Graph neural networks (GNNs) have found widespread application in modeling graph data across diverse domains. While GNNs excel in scenarios where the testing data shares the distribution of their training counterparts (in distribution, ID), they often exhibit incorrect predictions when confronted with samples from an unfamiliar distribution (out-of...

Open-set graph learning is a practical task that aims to classify the known class nodes and to identify unknown class samples as unknowns. Conventional node classification methods usually perform unsatisfactorily in open-set scenarios due to the complex data they encounter, such as out-of-distribution (OOD) data and in-distribution (IND) noise. OOD...

Reasoning with knowledge graphs (KGs) has primarily focused on triple-shaped facts. Recent advancements have been explored to enhance the semantics of these facts by incorporating more potent representations, such as hyper-relational facts. However, these approaches are limited to atomic facts, which describe a single piece of information. This pap...

Identifying circRNA (circular RNA) associated with diseases holds promise as diagnostic and prognostic biomarkers, offering potential avenues for novel therapeutics. Several computational methods have been designed to predict circRNA-disease associations. Unfortunately, current computational models face issues stemming from the integration of data...