DisenSemi: Semi-supervised Graph Classification via Disentangled Representation Learning

Graph classification is a critical task in numerous multimedia applications, where graphs are employed to represent diverse types of multimedia data, including images, videos, and social networks. Nevertheless, in real-world scenarios, labeled graph data can be limited or scarce. To address this issue, we focus on the problem of semi-supervised graph classification, which involves both supervised and unsupervised models learning from labeled and unlabeled data. In contrast to recent approaches that transfer the entire knowledge from the unsupervised model to the supervised one, we argue that an effective transfer should only retain the relevant semantics that align well with the supervised task. In this paper, we propose a novel framework named DisenSemi, which learns disentangled representation for semi-supervised graph classification. Specifically, a disentangled graph encoder is proposed to generate factor-wise graph representations for both supervised and unsupervised models. Then we train two models via supervised objective and mutual information (MI)-based constraints respectively. To ensure the meaningful transfer of knowledge from the unsupervised encoder to the supervised one, we further define an MI-based disentangled consistency regularization between two models and identify the corresponding rationale that aligns well with the current graph classification task. Experimental results on a range of publicly accessible datasets reveal the effectiveness of our DisenSemi.

Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research

The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs to genomics and proteomics is still limited. To fill this gap, we propose a collection of finetuned LLMs and multimodal LLMs (MLLMs), known as Geneverse, for three novel tasks in genomic and proteomic research. The models in Geneverse are trained and evaluated based on domain-specific datasets, and we use advanced parameter-efficient finetuning techniques to achieve the model adaptation for tasks including the generation of descriptions for gene functions, protein function inference from its structure, and marker gene selection from spatial transcriptomic data. We demonstrate that adapted LLMs and MLLMs perform well for these tasks and may outperform closed-source large-scale models based on our evaluations focusing on both truthfulness and structural correctness. All of the training strategies and base models we used are freely accessible.

A Comprehensive Graph Pooling Benchmark: Effectiveness, Robustness and Generalizability

Graph pooling has gained attention for its ability to obtain effective node and graph representations for various downstream tasks. Despite the recent surge in graph pooling approaches, there is a lack of standardized experimental settings and fair benchmarks to evaluate their performance. To address this issue, we have constructed a comprehensive benchmark that includes 15 graph pooling methods and 21 different graph datasets. This benchmark systematically assesses the performance of graph pooling methods in three dimensions, i.e., effectiveness, robustness, and generalizability. We first evaluate the performance of these graph pooling approaches across different tasks including graph classification, graph regression and node classification. Then, we investigate their performance under potential noise attacks and out-of-distribution shifts in real-world scenarios. We also involve detailed efficiency analysis and parameter analysis. Extensive experiments validate the strong capability and applicability of graph pooling approaches in various scenarios, which can provide valuable insights and guidance for deep geometric learning research. The source code of our benchmark is available at https://github.com/goose315/Graph_Pooling_Benchmark.

Towards Graph Contrastive Learning: A Survey and Beyond

In recent years, deep learning on graphs has achieved remarkable success in various domains. However, the reliance on annotated graph data remains a significant bottleneck due to its prohibitive cost and time-intensive nature. To address this challenge, self-supervised learning (SSL) on graphs has gained increasing attention and has made significant progress. SSL enables machine learning models to produce informative representations from unlabeled graph data, reducing the reliance on expensive labeled data. While SSL on graphs has witnessed widespread adoption, one critical component, Graph Contrastive Learning (GCL), has not been thoroughly investigated in the existing literature. Thus, this survey aims to fill this gap by offering a dedicated survey on GCL. We provide a comprehensive overview of the fundamental principles of GCL, including data augmentation strategies, contrastive modes, and contrastive optimization objectives. Furthermore, we explore the extensions of GCL to other aspects of data-efficient graph learning, such as weakly supervised learning, transfer learning, and related scenarios. We also discuss practical applications spanning domains such as drug discovery, genomics analysis, recommender systems, and finally outline the challenges and potential future directions in this field.

DEMO: A Statistical Perspective for Efficient Image-Text Matching

Image-text matching has been a long-standing problem, which seeks to connect vision and language through semantic understanding. Due to the capability to manage large-scale raw data, unsupervised hashing-based approaches have gained prominence recently. They typically construct a semantic similarity structure using the natural distance, which subsequently provides guidance to the model optimization process. However, the similarity structure could be biased at the boundaries of semantic distributions, causing error accumulation during sequential optimization. To tackle this, we introduce a novel hashing approach termed Distribution-based Structure Mining with Consistency Learning (DEMO) for efficient image-text matching. From a statistical view, DEMO characterizes each image using multiple augmented views, which are considered as samples drawn from its intrinsic semantic distribution. Then, we employ a non-parametric distribution divergence to ensure a robust and precise similarity structure. In addition, we introduce collaborative consistency learning which not only preserves the similarity structure in the Hamming space but also encourages consistency between retrieval distribution from different directions in a self-supervised manner. Through extensive experiments on three benchmark image-text matching datasets, we demonstrate that DEMO achieves superior performance compared with many state-of-the-art methods.

Hypergraph-enhanced Dual Semi-supervised Graph Classification

In this paper, we study semi-supervised graph classification, which aims at accurately predicting the categories of graphs in scenarios with limited labeled graphs and abundant unlabeled graphs. Despite the promising capability of graph neural networks (GNNs), they typically require a large number of costly labeled graphs, while a wealth of unlabeled graphs fail to be effectively utilized. Moreover, GNNs are inherently limited to encoding local neighborhood information using message-passing mechanisms, thus lacking the ability to model higher-order dependencies among nodes. To tackle these challenges, we propose a Hypergraph-Enhanced DuAL framework named HEAL for semi-supervised graph classification, which captures graph semantics from the perspective of the hypergraph and the line graph, respectively. Specifically, to better explore the higher-order relationships among nodes, we design a hypergraph structure learning to adaptively learn complex node dependencies beyond pairwise relations. Meanwhile, based on the learned hypergraph, we introduce a line graph to capture the interaction between hyperedges, thereby better mining the underlying semantic structures. Finally, we develop a relational consistency learning to facilitate knowledge transfer between the two branches and provide better mutual guidance. Extensive experiments on real-world graph datasets verify the effectiveness of the proposed method against existing state-of-the-art methods.

Fusion Dynamical Systems with Machine Learning in Imitation Learning: A Comprehensive Overview

Imitation Learning (IL), also referred to as Learning from Demonstration (LfD), holds significant promise for capturing expert motor skills through efficient imitation, facilitating adept navigation of complex scenarios. A persistent challenge in IL lies in extending generalization from historical demonstrations, enabling the acquisition of new skills without re-teaching. Dynamical system-based IL (DSIL) emerges as a significant subset of IL methodologies, offering the ability to learn trajectories via movement primitives and policy learning based on experiential abstraction. This paper emphasizes the fusion of theoretical paradigms, integrating control theory principles inherent in dynamical systems into IL. This integration notably enhances robustness, adaptability, and convergence in the face of novel scenarios. This survey aims to present a comprehensive overview of DSIL methods, spanning from classical approaches to recent advanced approaches. We categorize DSIL into autonomous dynamical systems and non-autonomous dynamical systems, surveying traditional IL methods with low-dimensional input and advanced deep IL methods with high-dimensional input. Additionally, we present and analyze three main stability methods for IL: Lyapunov stability, contraction theory, and diffeomorphism mapping. Our exploration also extends to popular policy improvement methods for DSIL, encompassing reinforcement learning, deep reinforcement learning, and evolutionary strategies.

Fast Inference of Removal-Based Node Influence

Graph neural networks (GNNs) are widely utilized to capture the information spreading patterns in graphs. While remarkable performance has been achieved, there is a new trending topic of evaluating node influence. We propose a new method of evaluating node influence, which measures the prediction change of a trained GNN model caused by removing a node. A real-world application is, "In the task of predicting Twitter accounts' polarity, had a particular account been removed, how would others' polarity change?". We use the GNN as a surrogate model whose prediction could simulate the change of nodes or edges caused by node removal. Our target is to obtain the influence score for every node, and a straightforward way is to alternately remove every node and apply the trained GNN on the modified graph to generate new predictions. It is reliable but time-consuming, so we need an efficient method. The related lines of work, such as graph adversarial attack and counterfactual explanation, cannot directly satisfy our needs, since their problem settings are different. We propose an efficient, intuitive, and effective method, NOde-Removal-based fAst GNN inference (NORA), which uses the gradient information to approximate the node-removal influence. It only costs one forward propagation and one backpropagation to approximate the influence score for all nodes. Extensive experiments on six datasets and six GNN models verify the effectiveness of NORA. Our code is available at https://github.com/weikai-li/NORA.git.

A Survey of Graph Neural Networks in Real world: Imbalance, Noise, Privacy and OOD Challenges

Graph-structured data exhibits universality and widespread applicability across diverse domains, such as social network analysis, biochemistry, financial fraud detection, and network security. Significant strides have been made in leveraging Graph Neural Networks (GNNs) to achieve remarkable success in these areas. However, in real-world scenarios, the training environment for models is often far from ideal, leading to substantial performance degradation of GNN models due to various unfavorable factors, including imbalance in data distribution, the presence of noise in erroneous data, privacy protection of sensitive information, and generalization capability for out-of-distribution (OOD) scenarios. To tackle these issues, substantial efforts have been devoted to improving the performance of GNN models in practical real-world scenarios, as well as enhancing their reliability and robustness. In this paper, we present a comprehensive survey that systematically reviews existing GNN models, focusing on solutions to the four mentioned real-world challenges including imbalance, noise, privacy, and OOD in practical scenarios that many existing reviews have not considered. Specifically, we first highlight the four key challenges faced by existing GNNs, paving the way for our exploration of real-world GNN models. Subsequently, we provide detailed discussions on these four aspects, dissecting how these solutions contribute to enhancing the reliability and robustness of GNN models. Last but not least, we outline promising directions and offer future perspectives in the field.

COOL: A Conjoint Perspective on Spatio-Temporal Graph Neural Network for Traffic Forecasting

This paper investigates traffic forecasting, which attempts to forecast the future state of traffic based on historical situations. This problem has received ever-increasing attention in various scenarios and facilitated the development of numerous downstream applications such as urban planning and transportation management. However, the efficacy of existing methods remains sub-optimal due to their tendency to model temporal and spatial relationships independently, thereby inadequately accounting for complex high-order interactions of both worlds. Moreover, the diversity of transitional patterns in traffic forecasting makes them challenging to capture for existing approaches, warranting a deeper exploration of their diversity. Toward this end, this paper proposes Conjoint Spatio-Temporal graph neural network (abbreviated as COOL), which models heterogeneous graphs from prior and posterior information to conjointly capture high-order spatio-temporal relationships. On the one hand, heterogeneous graphs connecting sequential observation are constructed to extract composite spatio-temporal relationships via prior message passing. On the other hand, we model dynamic relationships using constructed affinity and penalty graphs, which guide posterior message passing to incorporate complementary semantic information into node representations. Moreover, to capture diverse transitional properties to enhance traffic forecasting, we propose a conjoint self-attention decoder that models diverse temporal patterns from both multi-rank and multi-scale views. Experimental results on four popular benchmark datasets demonstrate that our proposed COOL provides state-of-the-art performance compared with the competitive baselines.