GANN: Graph Alignment Neural Network for Semi-Supervised Learning

Graph neural networks (GNNs) have been widely investigated in the field of semi-supervised graph machine learning. Most methods fail to exploit adequate graph information when labeled data is limited, leading to the problem of oversmoothing. To overcome this issue, we propose the Graph Alignment Neural Network (GANN), a simple and effective graph neural architecture. A unique learning algorithm with three alignment rules is proposed to thoroughly explore hidden information for insufficient labels. Firstly, to better investigate attribute specifics, we suggest the feature alignment rule to align the inner product of both the attribute and embedding matrices. Secondly, to properly utilize the higher-order neighbor information, we propose the cluster center alignment rule, which involves aligning the inner product of the cluster center matrix with the unit matrix. Finally, to get reliable prediction results with few labels, we establish the minimum entropy alignment rule by lining up the prediction probability matrix with its sharpened result. Extensive studies on graph benchmark datasets demonstrate that GANN can achieve considerable benefits in semi-supervised node classification and outperform state-of-the-art competitors

Revisiting Initializing Then Refining: An Incomplete and Missing Graph Imputation Network

With the development of various applications, such as social networks and knowledge graphs, graph data has been ubiquitous in the real world. Unfortunately, graphs usually suffer from being absent due to privacy-protecting policies or copyright restrictions during data collection. The absence of graph data can be roughly categorized into attribute-incomplete and attribute-missing circumstances. Specifically, attribute-incomplete indicates that a part of the attribute vectors of all nodes are incomplete, while attribute-missing indicates that the whole attribute vectors of partial nodes are missing. Although many efforts have been devoted, none of them is custom-designed for a common situation where both types of graph data absence exist simultaneously. To fill this gap, we develop a novel network termed Revisiting Initializing Then Refining (RITR), where we complete both attribute-incomplete and attribute-missing samples under the guidance of a novel initializing-then-refining imputation criterion. Specifically, to complete attribute-incomplete samples, we first initialize the incomplete attributes using Gaussian noise before network learning, and then introduce a structure-attribute consistency constraint to refine incomplete values by approximating a structure-attribute correlation matrix to a high-order structural matrix. To complete attribute-missing samples, we first adopt structure embeddings of attribute-missing samples as the embedding initialization, and then refine these initial values by adaptively aggregating the reliable information of attribute-incomplete samples according to a dynamic affinity structure. To the best of our knowledge, this newly designed method is the first unsupervised framework dedicated to handling hybrid-absent graphs. Extensive experiments on four datasets have verified that our methods consistently outperform existing state-of-the-art competitors

Attribute Graph Clustering via Learnable Augmentation

Contrastive deep graph clustering (CDGC) utilizes contrastive learning to group nodes into different clusters. Better augmentation techniques benefit the quality of the contrastive samples, thus being one of key factors to improve performance. However, the augmentation samples in existing methods are always predefined by human experiences, and agnostic from the downstream task clustering, thus leading to high human resource costs and poor performance. To this end, we propose an Attribute Graph Clustering method via Learnable Augmentation (\textbf{AGCLA}), which introduces learnable augmentors for high-quality and suitable augmented samples for CDGC. Specifically, we design two learnable augmentors for attribute and structure information, respectively. Besides, two refinement matrices, including the high-confidence pseudo-label matrix and the cross-view sample similarity matrix, are generated to improve the reliability of the learned affinity matrix. During the training procedure, we notice that there exist differences between the optimization goals for training learnable augmentors and contrastive learning networks. In other words, we should both guarantee the consistency of the embeddings as well as the diversity of the augmented samples. Thus, an adversarial learning mechanism is designed in our method. Moreover, a two-stage training strategy is leveraged for the high-confidence refinement matrices. Extensive experimental results demonstrate the effectiveness of AGCLA on six benchmark datasets

Large Language Models are Zero Shot Hypothesis Proposers

Significant scientific discoveries have driven the progress of human civilisation. The explosion of scientific literature and data has created information barriers across disciplines that have slowed the pace of scientific discovery. Large Language Models (LLMs) hold a wealth of global and interdisciplinary knowledge that promises to break down these information barriers and foster a new wave of scientific discovery. However, the potential of LLMs for scientific discovery has not been formally explored. In this paper, we start from investigating whether LLMs can propose scientific hypotheses. To this end, we construct a dataset consist of background knowledge and hypothesis pairs from biomedical literature. The dataset is divided into training, seen, and unseen test sets based on the publication date to control visibility. We subsequently evaluate the hypothesis generation capabilities of various top-tier instructed models in zero-shot, few-shot, and fine-tuning settings, including both closed and open-source LLMs. Additionally, we introduce an LLM-based multi-agent cooperative framework with different role designs and external tools to enhance the capabilities related to generating hypotheses. We also design four metrics through a comprehensive review to evaluate the generated hypotheses for both ChatGPT-based and human evaluations. Through experiments and analyses, we arrive at the following findings: 1) LLMs surprisingly generate untrained yet validated hypotheses from testing literature. 2) Increasing uncertainty facilitates candidate generation, potentially enhancing zero-shot hypothesis generation capabilities. These findings strongly support the potential of LLMs as catalysts for new scientific discoveries and guide further exploration.Comment: Instruction Workshop @ NeurIPS 202

Dink-Net: Neural Clustering on Large Graphs

Deep graph clustering, which aims to group the nodes of a graph into disjoint clusters with deep neural networks, has achieved promising progress in recent years. However, the existing methods fail to scale to the large graph with million nodes. To solve this problem, a scalable deep graph clustering method (Dink-Net) is proposed with the idea of dilation and shrink. Firstly, by discriminating nodes, whether being corrupted by augmentations, representations are learned in a self-supervised manner. Meanwhile, the cluster centres are initialized as learnable neural parameters. Subsequently, the clustering distribution is optimized by minimizing the proposed cluster dilation loss and cluster shrink loss in an adversarial manner. By these settings, we unify the two-step clustering, i.e., representation learning and clustering optimization, into an end-to-end framework, guiding the network to learn clustering-friendly features. Besides, Dink-Net scales well to large graphs since the designed loss functions adopt the mini-batch data to optimize the clustering distribution even without performance drops. Both experimental results and theoretical analyses demonstrate the superiority of our method. Compared to the runner-up, Dink-Net achieves 9.62% NMI improvement on the ogbn-papers100M dataset with 111 million nodes and 1.6 billion edges. The source code is released at https://github.com/yueliu1999/Dink-Net. Besides, a collection (papers, codes, and datasets) of deep graph clustering is shared at https://github.com/yueliu1999/Awesome-Deep-Graph-Clustering.Comment: 19 pages, 5 figure

Self-Supervised Temporal Graph learning with Temporal and Structural Intensity Alignment

Temporal graph learning aims to generate high-quality representations for graph-based tasks along with dynamic information, which has recently drawn increasing attention. Unlike the static graph, a temporal graph is usually organized in the form of node interaction sequences over continuous time instead of an adjacency matrix. Most temporal graph learning methods model current interactions by combining historical information over time. However, such methods merely consider the first-order temporal information while ignoring the important high-order structural information, leading to sub-optimal performance. To solve this issue, by extracting both temporal and structural information to learn more informative node representations, we propose a self-supervised method termed S2T for temporal graph learning. Note that the first-order temporal information and the high-order structural information are combined in different ways by the initial node representations to calculate two conditional intensities, respectively. Then the alignment loss is introduced to optimize the node representations to be more informative by narrowing the gap between the two intensities. Concretely, besides modeling temporal information using historical neighbor sequences, we further consider the structural information from both local and global levels. At the local level, we generate structural intensity by aggregating features from the high-order neighbor sequences. At the global level, a global representation is generated based on all nodes to adjust the structural intensity according to the active statuses on different nodes. Extensive experiments demonstrate that the proposed method S2T achieves at most 10.13% performance improvement compared with the state-of-the-art competitors on several datasets

Reinforcement Graph Clustering with Unknown Cluster Number

Deep graph clustering, which aims to group nodes into disjoint clusters by neural networks in an unsupervised manner, has attracted great attention in recent years. Although the performance has been largely improved, the excellent performance of the existing methods heavily relies on an accurately predefined cluster number, which is not always available in the real-world scenario. To enable the deep graph clustering algorithms to work without the guidance of the predefined cluster number, we propose a new deep graph clustering method termed Reinforcement Graph Clustering (RGC). In our proposed method, cluster number determination and unsupervised representation learning are unified into a uniform framework by the reinforcement learning mechanism. Concretely, the discriminative node representations are first learned with the contrastive pretext task. Then, to capture the clustering state accurately with both local and global information in the graph, both node and cluster states are considered. Subsequently, at each state, the qualities of different cluster numbers are evaluated by the quality network, and the greedy action is executed to determine the cluster number. In order to conduct feedback actions, the clustering-oriented reward function is proposed to enhance the cohesion of the same clusters and separate the different clusters. Extensive experiments demonstrate the effectiveness and efficiency of our proposed method. The source code of RGC is shared at https://github.com/yueliu1999/RGC and a collection (papers, codes and, datasets) of deep graph clustering is shared at https://github.com/yueliu1999/Awesome-Deep-Graph-Clustering on Github

A Survey of Knowledge Graph Reasoning on Graph Types: Static, Dynamic, and Multimodal

Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering, recommendation systems, and etc. According to the graph types, existing KGR models can be roughly divided into three categories, i.e., static models, temporal models, and multi-modal models. Early works in this domain mainly focus on static KGR, and recent works try to leverage the temporal and multi-modal information, which are more practical and closer to real-world. However, no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a first survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the models are reviewed based on bi-level taxonomy, i.e., top-level (graph types) and base-level (techniques and scenarios). Besides, the performances, as well as datasets, are summarized and presented. Moreover, we point out the challenges and potential opportunities to enlighten the readers. The corresponding open-source repository is shared on GitHub https://github.com/LIANGKE23/Awesome-Knowledge-Graph-Reasoning.Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessibl