Chengbin Hou

Chengbin Hou, Xinyu Lin, Hanhui Huang et al.

Identification of fossil species is crucial to evolutionary studies. Recent advances from deep learning have shown promising prospects in fossil image identification. However, the quantity and quality of labeled fossil images are often limited due to fossil preservation, conditioned sampling, and expensive and inconsistent label annotation by domain experts, which pose great challenges to training deep learning based image classification models. To address these challenges, we follow the idea of the wisdom of crowds and propose a multiview ensemble framework, which collects Original (O), Gray (G), and Skeleton (S) views of each fossil image reflecting its different characteristics to train multiple base models, and then makes the final decision via soft voting. Experiments on the largest fusulinid dataset with 2400 images show that the proposed OGS consistently outperforms baselines (using a single model for each view), and obtains superior or comparable performance compared to OOO (using three base models for three the same Original views). Besides, as the training data decreases, the proposed framework achieves more gains. While considering the identification consistency estimation with respect to human experts, OGS receives the highest agreement with the original labels of dataset and with the re-identifications of two human experts. The validation performance provides a quantitative estimation of consistency across different experts and genera. We conclude that the proposed framework can present state-of-the-art performance in the fusulinid fossil identification case study. This framework is designed for general fossil identification and it is expected to see applications to other fossil datasets in future work. The source code is publicly available at https://github.com/houchengbin/Fossil-Image-Identification to benefit future research in fossil image identification.

Bingzhe Wu, Jintang Li, Junchi Yu et al.

Deep graph learning has achieved remarkable progresses in both business and scientific areas ranging from finance and e-commerce, to drug and advanced material discovery. Despite these progresses, how to ensure various deep graph learning algorithms behave in a socially responsible manner and meet regulatory compliance requirements becomes an emerging problem, especially in risk-sensitive domains. Trustworthy graph learning (TwGL) aims to solve the above problems from a technical viewpoint. In contrast to conventional graph learning research which mainly cares about model performance, TwGL considers various reliability and safety aspects of the graph learning framework including but not limited to robustness, explainability, and privacy. In this survey, we provide a comprehensive review of recent leading approaches in the TwGL field from three dimensions, namely, reliability, explainability, and privacy protection. We give a general categorization for existing work and review typical work for each category. To give further insights for TwGL research, we provide a unified view to inspect previous works and build the connection between them. We also point out some important open problems remaining to be solved in the future developments of TwGL.

Hongze Zhu, Guoyang Xie, Chengbin Hou et al.

High-resolution point clouds~(HRPCD) anomaly detection~(AD) plays a critical role in precision machining and high-end equipment manufacturing. Despite considerable 3D-AD methods that have been proposed recently, they still cannot meet the requirements of the HRPCD-AD task. There are several challenges: i) It is difficult to directly capture HRPCD information due to large amounts of points at the sample level; ii) The advanced transformer-based methods usually obtain anisotropic features, leading to degradation of the representation; iii) The proportion of abnormal areas is very small, which makes it difficult to characterize. To address these challenges, we propose a novel group-level feature-based network, called Group3AD, which has a significantly efficient representation ability. First, we design an Intercluster Uniformity Network~(IUN) to present the mapping of different groups in the feature space as several clusters, and obtain a more uniform distribution between clusters representing different parts of the point clouds in the feature space. Then, an Intracluster Alignment Network~(IAN) is designed to encourage groups within the cluster to be distributed tightly in the feature space. In addition, we propose an Adaptive Group-Center Selection~(AGCS) based on geometric information to improve the pixel density of potential anomalous regions during inference. The experimental results verify the effectiveness of our proposed Group3AD, which surpasses Reg3D-AD by the margin of 5\% in terms of object-level AUROC on Real3D-AD. We provide the code and supplementary information on our website: https://github.com/M-3LAB/Group3AD.

Tianyu Zhang, Chengbin Hou, Rui Jiang et al.

Node Importance Estimation (NIE) is a task of inferring importance scores of the nodes in a graph. Due to the availability of richer data and knowledge, recent research interests of NIE have been dedicating to knowledge graphs for predicting future or missing node importance scores. Existing state-of-the-art NIE methods train the model by available labels, and they consider every interested node equally before training. However, the nodes with higher importance often require or receive more attention in real-world scenarios, e.g., people may care more about the movies or webpages with higher importance. To this end, we introduce Label Informed ContrAstive Pretraining (LICAP) to the NIE problem for being better aware of the nodes with high importance scores. Specifically, LICAP is a novel type of contrastive learning framework that aims to fully utilize the continuous labels to generate contrastive samples for pretraining embeddings. Considering the NIE problem, LICAP adopts a novel sampling strategy called top nodes preferred hierarchical sampling to first group all interested nodes into a top bin and a non-top bin based on node importance scores, and then divide the nodes within top bin into several finer bins also based on the scores. The contrastive samples are generated from those bins, and are then used to pretrain node embeddings of knowledge graphs via a newly proposed Predicate-aware Graph Attention Networks (PreGAT), so as to better separate the top nodes from non-top nodes, and distinguish the top nodes within top bin by keeping the relative order among finer bins. Extensive experiments demonstrate that the LICAP pretrained embeddings can further boost the performance of existing NIE methods and achieve the new state-of-the-art performance regarding both regression and ranking metrics. The source code for reproducibility is available at https://github.com/zhangtia16/LICAP

Jiazheng Quan, Xiaodong Li, Bin Wang et al.

Large language models (LLMs) have demonstrated strong capabilities in code generation, yet they remain prone to producing security vulnerabilities. Existing approaches commonly suffer from two key limitations: the scarcity of high-quality security data and coarse-grained reinforcement learning reward signals. To address these challenges, we propose Vul2Safe, a new secure code generation framework that leverages LLM self-reflection to construct high-confidence repair pairs from real-world vulnerabilities, and further generates diverse implicit prompts to build the PrimeVul+ dataset. Meanwhile, we introduce SRCode, a novel training framework that pioneers the use of token-level rewards in reinforcement learning for code security, which enables the model to continuously attend to and reinforce critical fine-grained security patterns during training. Compared with traditional instance-level reward schemes, our approach allows for more precise optimization of local security implementations. Extensive experiments show that PrimeVul+ and SRCode substantially reduce security vulnerabilities in generated code while improving overall code quality across multiple benchmarks.

Tianyu Zhang, Yuxiang Ren, Chengbin Hou et al.

Molecular property prediction is a crucial foundation for drug discovery. In recent years, pre-trained deep learning models have been widely applied to this task. Some approaches that incorporate prior biological domain knowledge into the pre-training framework have achieved impressive results. However, these methods heavily rely on biochemical experts, and retrieving and summarizing vast amounts of domain knowledge literature is both time-consuming and expensive. Large Language Models (LLMs) have demonstrated remarkable performance in understanding and efficiently providing general knowledge. Nevertheless, they occasionally exhibit hallucinations and lack precision in generating domain-specific knowledge. Conversely, Domain-specific Small Models (DSMs) possess rich domain knowledge and can accurately calculate molecular domain-related metrics. However, due to their limited model size and singular functionality, they lack the breadth of knowledge necessary for comprehensive representation learning. To leverage the advantages of both approaches in molecular property prediction, we propose a novel Molecular Graph representation learning framework that integrates Large language models and Domain-specific small models (MolGraph-LarDo). Technically, we design a two-stage prompt strategy where DSMs are introduced to calibrate the knowledge provided by LLMs, enhancing the accuracy of domain-specific information and thus enabling LLMs to generate more precise textual descriptions for molecular samples. Subsequently, we employ a multi-modal alignment method to coordinate various modalities, including molecular graphs and their corresponding descriptive texts, to guide the pre-training of molecular representations. Extensive experiments demonstrate the effectiveness of the proposed method.

Wenhao Mao, Chengbin Hou, Tianyu Zhang et al.

Offering rich contexts to Large Language Models (LLMs) has shown to boost the performance in various tasks, but the resulting longer prompt would increase the computational cost and might exceed the input limit of LLMs. Recently, some prompt compression methods have been suggested to shorten the length of prompts by using language models to generate shorter prompts or by developing computational models to select important parts of original prompt. The generative compression methods would suffer from issues like hallucination, while the selective compression methods have not involved linguistic rules and overlook the global structure of prompt. To this end, we propose a novel selective compression method called PartPrompt. It first obtains a parse tree for each sentence based on linguistic rules, and calculates local information entropy for each node in a parse tree. These local parse trees are then organized into a global tree according to the hierarchical structure such as the dependency of sentences, paragraphs, and sections. After that, the root-ward propagation and leaf-ward propagation are proposed to adjust node values over the global tree. Finally, a recursive algorithm is developed to prune the global tree based on the adjusted node values. The experiments show that PartPrompt receives the state-of-the-art performance across various datasets, metrics, compression ratios, and target LLMs for inference. The in-depth ablation studies confirm the effectiveness of designs in PartPrompt, and other additional experiments also demonstrate its superiority in terms of the coherence of compressed prompts and in the extreme long prompt scenario.

Xinyu Lin, Tianyu Zhang, Chengbin Hou et al.

Node Importance Estimation (NIE) is a task that quantifies the importance of node in a graph. Recent research has investigated to exploit various information from Knowledge Graphs (KGs) to estimate node importance scores. However, the semantic information in KGs could be insufficient, missing, and inaccurate, which would limit the performance of existing NIE models. To address these issues, we leverage Large Language Models (LLMs) for semantic augmentation thanks to the LLMs' extra knowledge and ability of integrating knowledge from both LLMs and KGs. To this end, we propose the LLMs Empowered Node Importance Estimation (LENIE) method to enhance the semantic information in KGs for better supporting NIE tasks. To our best knowledge, this is the first work incorporating LLMs into NIE. Specifically, LENIE employs a novel clustering-based triplet sampling strategy to extract diverse knowledge of a node sampled from the given KG. After that, LENIE adopts the node-specific adaptive prompts to integrate the sampled triplets and the original node descriptions, which are then fed into LLMs for generating richer and more precise augmented node descriptions. These augmented descriptions finally initialize node embeddings for boosting the downstream NIE model performance. Extensive experiments demonstrate LENIE's effectiveness in addressing semantic deficiencies in KGs, enabling more informative semantic augmentation and enhancing existing NIE models to achieve the state-of-the-art performance. The source code of LENIE is freely available at \url{https://github.com/XinyuLin-FZ/LENIE}.

Chengbin Hou, Han Zhang, Shan He et al.

Learning low-dimensional topological representation of a network in dynamic environments is attracting much attention due to the time-evolving nature of many real-world networks. The main and common objective of Dynamic Network Embedding (DNE) is to efficiently update node embeddings while preserving network topology at each time step. The idea of most existing DNE methods is to capture the topological changes at or around the most affected nodes (instead of all nodes) and accordingly update node embeddings. Unfortunately, this kind of approximation, although can improve efficiency, cannot effectively preserve the global topology of a dynamic network at each time step, due to not considering the inactive sub-networks that receive accumulated topological changes propagated via the high-order proximity. To tackle this challenge, we propose a novel node selecting strategy to diversely select the representative nodes over a network, which is coordinated with a new incremental learning paradigm of Skip-Gram based embedding approach. The extensive experiments show GloDyNE, with a small fraction of nodes being selected, can already achieve the superior or comparable performance w.r.t. the state-of-the-art DNE methods in three typical downstream tasks. Particularly, GloDyNE significantly outperforms other methods in the graph reconstruction task, which demonstrates its ability of global topology preservation. The source code is available at https://github.com/houchengbin/GloDyNE

Chengbin Hou, Han Zhang, Ke Tang et al.

Learning topological representation of a network in dynamic environments has recently attracted considerable attention due to the time-evolving nature of many real-world networks i.e. nodes/links might be added/removed as time goes on. Dynamic network embedding aims to learn low dimensional embeddings for unseen and seen nodes by using any currently available snapshots of a dynamic network. For seen nodes, the existing methods either treat them equally important or focus on the $k$ most affected nodes at each time step. However, the former solution is time-consuming, and the later solution that relies on incoming changes may lose the global topology---an important feature for downstream tasks. To address these challenges, we propose a dynamic network embedding method called DynWalks, which includes two key components: 1) An online network embedding framework that can dynamically and efficiently learn embeddings based on the selected nodes; 2) A novel online node selecting scheme that offers the flexible choices to balance global topology and recent changes, as well as to fulfill the real-time constraint if needed. The empirical studies on six real-world dynamic networks under three different slicing ways show that DynWalks significantly outperforms the state-of-the-art methods in graph reconstruction tasks, and obtains comparable results in link prediction tasks. Furthermore, the wall-clock time and complexity analysis demonstrate its excellent time and space efficiency. The source code of DynWalks is available at https://github.com/houchengbin/DynWalks

Hanzhe Liang, Guoyang Xie, Chengbin Hou et al.

3D anomaly detection has recently become a significant focus in computer vision. Several advanced methods have achieved satisfying anomaly detection performance. However, they typically concentrate on the external structure of 3D samples and struggle to leverage the internal information embedded within samples. Inspired by the basic intuition of why not look inside for more, we introduce a straightforward method named Internal Spatial Modality Perception~(ISMP) to explore the feature representation from internal views fully. Specifically, our proposed ISMP consists of a critical perception module, Spatial Insight Engine~(SIE), which abstracts complex internal information of point clouds into essential global features. Besides, to better align structural information with point data, we propose an enhanced key point feature extraction module for amplifying spatial structure feature representation. Simultaneously, a novel feature filtering module is incorporated to reduce noise and redundant features for further aligning precise spatial structure. Extensive experiments validate the effectiveness of our proposed method, achieving object-level and pixel-level AUROC improvements of 3.2\% and 13.1\%, respectively, on the Real3D-AD benchmarks. Note that the strong generalization ability of SIE has been theoretically proven and is verified in both classification and segmentation tasks.

Jiarui Song, Yunheng Shen, Chengbin Hou et al.

Personalized Federated Learning (PFL) aims to address the statistical heterogeneity of data across clients by learning the personalized model for each client. Among various PFL approaches, the personalized aggregation-based approach conducts parameter aggregation in the server-side aggregation phase to generate personalized models, and focuses on learning appropriate collaborative relationships among clients for aggregation. However, the collaborative relationships vary in different scenarios and even at different stages of the FL process. To this end, we propose Personalized Federated Learning with Attentive Graph HyperNetworks (FedAGHN), which employs Attentive Graph HyperNetworks (AGHNs) to dynamically capture fine-grained collaborative relationships and generate client-specific personalized initial models. Specifically, AGHNs empower graphs to explicitly model the client-specific collaborative relationships, construct collaboration graphs, and introduce tunable attentive mechanism to derive the collaboration weights, so that the personalized initial models can be obtained by aggregating parameters over the collaboration graphs. Extensive experiments can demonstrate the superiority of FedAGHN. Moreover, a series of visualizations are presented to explore the effectiveness of collaboration graphs learned by FedAGHN.

Ziming Tang, Chengbin Hou, Tianyu Zhang et al.

Parkinson's disease (PD) is one of the most common neurodegenerative disorder. PD telemonitoring emerges as a novel assessment modality enabling self-administered at-home tests of Unified Parkinson's Disease Rating Scale (UPDRS) scores, enhancing accessibility for PD patients. However, three types of noise would occur during measurements: (1) patient-induced measurement inaccuracies, (2) environmental noise, and (3) data packet loss during transmission, resulting in higher prediction errors. To address these challenges, NoRo, a noise-robust UPDRS prediction framework is proposed. First, the original speech features are grouped into ordered bins, based on the continuous values of a selected feature, to construct contrastive pairs. Second, the contrastive pairs are employed to train a multilayer perceptron encoder for generating noise-robust features. Finally, these features are concatenated with the original features as the augmented features, which are then fed into the UPDRS prediction models. Notably, we further introduces a novel evaluation approach with customizable noise injection module, and extensive experiments show that NoRo can successfully enhance the noise robustness of UPDRS prediction across various downstream prediction models under different noisy environments.

Jintang Li, Bingzhe Wu, Chengbin Hou et al.

Deep graph learning (DGL) has achieved remarkable progress in both business and scientific areas ranging from finance and e-commerce to drug and advanced material discovery. Despite the progress, applying DGL to real-world applications faces a series of reliability threats including inherent noise, distribution shift, and adversarial attacks. This survey aims to provide a comprehensive review of recent advances for improving the reliability of DGL algorithms against the above threats. In contrast to prior related surveys which mainly focus on adversarial attacks and defense, our survey covers more reliability-related aspects of DGL, i.e., inherent noise and distribution shift. Additionally, we discuss the relationships among above aspects and highlight some important issues to be explored in future research.

Chengbin Hou, Guoji Fu, Peng Yang et al.

Dynamic Network Embedding (DNE) has recently attracted considerable attention due to the advantage of network embedding in various fields and the dynamic nature of many real-world networks. An input dynamic network to DNE is often assumed to have smooth changes over snapshots, which however would not hold for all real-world scenarios. It is natural to ask if existing DNE methods can perform well for an input dynamic network without smooth changes. To quantify it, an index called Degree of Changes (DoCs) is suggested so that the smaller DoCs indicates the smoother changes. Our comparative study shows several DNE methods are not robust enough to different DoCs even if the corresponding input dynamic networks come from the same dataset, which would make these methods unreliable and hard to use for unknown real-world applications. To propose an effective and more robust DNE method, we follow the notion of ensembles where each base learner adopts an incremental Skip-Gram embedding model. To further boost the performance, a simple yet effective strategy is designed to enhance the diversity among base learners at each timestep by capturing different levels of local-global topology. Extensive experiments demonstrate the superior effectiveness and robustness of the proposed method compared to state-of-the-art DNE methods, as well as the benefits of special designs in the proposed method and its scalability.

Guoji Fu, Chengbin Hou, Xin Yao

The topological information is essential for studying the relationship between nodes in a network. Recently, Network Representation Learning (NRL), which projects a network into a low-dimensional vector space, has been shown their advantages in analyzing large-scale networks. However, most existing NRL methods are designed to preserve the local topology of a network, they fail to capture the global topology. To tackle this issue, we propose a new NRL framework, named HSRL, to help existing NRL methods capture both the local and global topological information of a network. Specifically, HSRL recursively compresses an input network into a series of smaller networks using a community-awareness compressing strategy. Then, an existing NRL method is used to learn node embeddings for each compressed network. Finally, the node embeddings of the input network are obtained by concatenating the node embeddings from all compressed networks. Empirical studies for link prediction on five real-world datasets demonstrate the advantages of HSRL over state-of-the-art methods.

Chengbin Hou, Shan He, Ke Tang

Attributed networks are ubiquitous since a network often comes with auxiliary attribute information e.g. a social network with user profiles. Attributed Network Embedding (ANE) has recently attracted considerable attention, which aims to learn unified low dimensional node embeddings while preserving both structural and attribute information. The resulting node embeddings can then facilitate various network downstream tasks e.g. link prediction. Although there are several ANE methods, most of them cannot deal with incomplete attributed networks with missing links and/or missing node attributes, which often occur in real-world scenarios. To address this issue, we propose a robust ANE method, the general idea of which is to reconstruct a unified denser network by fusing two sources of information for information enhancement, and then employ a random walks based network embedding method for learning node embeddings. The experiments of link prediction, node classification, visualization, and parameter sensitivity analysis on six real-world datasets validate the effectiveness of our method to incomplete attributed networks.