With the rise of contrastive learning, unsupervised graph representation learning has been booming recently, even surpassing the supervised counterparts in some machine learning tasks. Most of existing contrastive models for graph representation learning either focus on maximizing mutual information between local and global embeddings, or primarily depend on contrasting embeddings at node level. However, they are still not exquisite enough to comprehensively explore the local and global views of network topology. Although the former considers local-global relationship, its coarse global information leads to grudging cooperation between local and global views. The latter pays attention to node-level feature alignment, so that the role of global view appears inconspicuous. To avoid falling into these two extreme cases, we propose a novel unsupervised graph representation model by contrasting cluster assignments, called as GRCCA. It is motivated to make good use of local and global information synthetically through combining clustering algorithms and contrastive learning. This not only facilitates the contrastive effect, but also provides the more high-quality graph information. Meanwhile, GRCCA further excavates cluster-level information, which make it get insight to the elusive association between nodes beyond graph topology. Specifically, we first generate two augmented graphs with distinct graph augmentation strategies, then employ clustering algorithms to obtain their cluster assignments and prototypes respectively. The proposed GRCCA further compels the identical nodes from different augmented graphs to recognize their cluster assignments mutually by minimizing a cross entropy loss. To demonstrate its effectiveness, we compare with the state-of-the-art models in three different downstream tasks. The experimental results show that GRCCA has strong competitiveness in most tasks.
Recent advances in neuroimaging along with algorithmic innovations in statistical learning from network data offer a unique pathway to integrate brain structure and function, and thus facilitate revealing some of the brain's organizing principles at the system level. In this direction, we develop a supervised graph representation learning framework to model the relationship between brain structural connectivity (SC) and functional connectivity (FC) via a graph encoder-decoder system, where the SC is used as input to predict empirical FC. A trainable graph convolutional encoder captures direct and indirect interactions between brain regions-of-interest that mimic actual neural communications, as well as to integrate information from both the structural network topology and nodal (i.e., region-specific) attributes. The encoder learns node-level SC embeddings which are combined to generate (whole brain) graph-level representations for reconstructing empirical FC networks. The proposed end-to-end model utilizes a multi-objective loss function to jointly reconstruct FC networks and learn discriminative graph representations of the SC-to-FC mapping for downstream subject (i.e., graph-level) classification. Comprehensive experiments demonstrate that the learnt representations of said relationship capture valuable information from the intrinsic properties of the subject's brain networks and lead to improved accuracy in classifying a large population of heavy drinkers and non-drinkers from the Human Connectome Project. Our work offers new insights on the relationship between brain networks that support the promising prospect of using graph representation learning to discover more about human brain activity and function.
Mixed communities of organisms are found in many environments (from the human gut to marine ecosystems) and can have profound impact on human health and the environment. Metagenomics studies the genomic material of such communities through high-throughput sequencing that yields DNA subsequences for subsequent analysis. A fundamental problem in the standard workflow, called binning, is to discover clusters, of genomic subsequences, associated with the unknown constituent organisms. Inherent noise in the subsequences, various biological constraints that need to be imposed on them and the skewed cluster size distribution exacerbate the difficulty of this unsupervised learning problem. In this paper, we present a new formulation using a graph where the nodes are subsequences and edges represent homophily information. In addition, we model biological constraints providing heterophilous signal about nodes that cannot be clustered together. We solve the binning problem by developing new algorithms for (i) graph representation learning that preserves both homophily relations and heterophily constraints (ii) constraint-based graph clustering method that addresses the problems of skewed cluster size distribution. Extensive experiments, on real and synthetic datasets, demonstrate that our approach, called RepBin, outperforms a wide variety of competing methods. Our constraint-based graph representation learning and clustering methods, that may be useful in other domains as well, advance the state-of-the-art in both metagenomics binning and graph representation learning.
Controversial content refers to any content that attracts both positive and negative feedback. Its automatic identification, especially on social media, is a challenging task as it should be done on a large number of continuously evolving posts, covering a large variety of topics. Most of the existing approaches rely on the graph structure of a topic-discussion and/or the content of messages. This paper proposes a controversy detection approach based on both graph structure of a discussion and text features. Our proposed approach relies on Graph Neural Network (gnn) to encode the graph representation (including its texts) in an embedding vector before performing a graph classification task. The latter will classify the post as controversial or not. Two controversy detection strategies are proposed. The first one is based on a hierarchical graph representation learning. Graph user nodes are embedded hierarchically and iteratively to compute the whole graph embedding vector. The second one is based on the attention mechanism, which allows each user node to give more or less importance to its neighbors when computing node embeddings. We conduct experiments to evaluate our approach using different real-world datasets. Conducted experiments show the positive impact of combining textual features and structural information in terms of performance.
Event analysis from news and social networks is very useful for a wide range of social studies and real-world applications. Recently, event graphs have been explored to model event datasets and their complex relationships, where events are vertices connected to other vertices representing locations, people's names, dates, and various other event metadata. Graph representation learning methods are promising for extracting latent features from event graphs to enable the use of different classification algorithms. However, existing methods fail to meet essential requirements for event graphs, such as (i) dealing with semi-supervised graph embedding to take advantage of some labeled events, (ii) automatically determining the importance of the relationships between event vertices and their metadata vertices, as well as (iii) dealing with the graph heterogeneity. This paper presents GNEE (GAT Neural Event Embeddings), a method that combines Graph Attention Networks and Graph Regularization. First, an event graph regularization is proposed to ensure that all graph vertices receive event features, thereby mitigating the graph heterogeneity drawback. Second, semi-supervised graph embedding with self-attention mechanism considers existing labeled events, as well as learns the importance of relationships in the event graph during the representation learning process. A statistical analysis of experimental results with five real-world event graphs and six graph embedding methods shows that our GNEE outperforms state-of-the-art semi-supervised graph embedding methods.
Graph representation learning is a fast-growing field where one of the main objectives is to generate meaningful representations of graphs in lower-dimensional spaces. The learned embeddings have been successfully applied to perform various prediction tasks, such as link prediction, node classification, clustering, and visualization. The collective effort of the graph learning community has delivered hundreds of methods, but no single method excels under all evaluation metrics such as prediction accuracy, running time, scalability, etc. This survey aims to evaluate all major classes of graph embedding methods by considering algorithmic variations, parameter selections, scalability, hardware and software platforms, downstream ML tasks, and diverse datasets. We organized graph embedding techniques using a taxonomy that includes methods from manual feature engineering, matrix factorization, shallow neural networks, and deep graph convolutional networks. We evaluated these classes of algorithms for node classification, link prediction, clustering, and visualization tasks using widely used benchmark graphs. We designed our experiments on top of PyTorch Geometric and DGL libraries and run experiments on different multicore CPU and GPU platforms. We rigorously scrutinize the performance of embedding methods under various performance metrics and summarize the results. Thus, this paper may serve as a comparative guide to help users select methods that are most suitable for their tasks.
The dynamic job-shop scheduling problem (DJSP) is a class of scheduling tasks that specifically consider the inherent uncertainties such as changing order requirements and possible machine breakdown in realistic smart manufacturing settings. Since traditional methods cannot dynamically generate effective scheduling strategies in face of the disturbance of environments, we formulate the DJSP as a Markov decision process (MDP) to be tackled by reinforcement learning (RL). For this purpose, we propose a flexible hybrid framework that takes disjunctive graphs as states and a set of general dispatching rules as the action space with minimum prior domain knowledge. The attention mechanism is used as the graph representation learning (GRL) module for the feature extraction of states, and the double dueling deep Q-network with prioritized replay and noisy networks (D3QPN) is employed to map each state to the most appropriate dispatching rule. Furthermore, we present Gymjsp, a public benchmark based on the well-known OR-Library, to provide a standardized off-the-shelf facility for RL and DJSP research communities. Comprehensive experiments on various DJSP instances confirm that our proposed framework is superior to baseline algorithms with smaller makespan across all instances and provide empirical justification for the validity of the various components in the hybrid framework.
Graph representation learning has drawn increasing attention in recent years, especially for learning the low dimensional embedding at both node and graph level for classification and recommendations tasks. To enable learning the representation on the large-scale graph data in the real world, numerous research has focused on developing different sampling strategies to facilitate the training process. Herein, we propose an adaptive Graph Policy-driven Sampling model (GPS), where the influence of each node in the local neighborhood is realized through the adaptive correlation calculation. Specifically, the selections of the neighbors are guided by an adaptive policy algorithm, contributing directly to the message aggregation, node embedding updating, and graph level readout steps. We then conduct comprehensive experiments against baseline methods on graph classification tasks from various perspectives. Our proposed model outperforms the existing ones by 3%-8% on several vital benchmarks, achieving state-of-the-art performance in real-world datasets.
Unsupervised graph representation learning has recently gained interest in several application domains such as neuroscience, where modeling the diverse morphology of cell types in the brain is one of the key challenges. It is currently unknown how many excitatory cortical cell types exist and what their defining morphological features are. Here we present GraphDINO, a purely data-driven approach to learn low-dimensional representations of 3D neuronal morphologies from unlabeled large-scale datasets. GraphDINO is a novel transformer-based representation learning method for spatially-embedded graphs. To enable self-supervised learning on transformers, we (1) developed data augmentation strategies for spatially-embedded graphs, (2) adapted the positional encoding and (3) introduced a novel attention mechanism, AC-Attention, which combines attention-based global interaction between nodes and classic graph convolutional processing. We show, in two different species and across multiple brain areas, that this method yields morphological cell type clusterings that are on par with manual feature-based classification by experts, but without using prior knowledge about the structural features of neurons. Moreover, it outperforms previous approaches on quantitative benchmarks predicting expert labels. Our method could potentially enable data-driven discovery of novel morphological features and cell types in large-scale datasets. It is applicable beyond neuroscience in settings where samples in a dataset are graphs and graph-level embeddings are desired.
Self-supervised learning on graphs has recently drawn a lot of attention due to its independence from labels and its robustness in representation. Current studies on this topic mainly use static information such as graph structures but cannot well capture dynamic information such as timestamps of edges. Realistic graphs are often dynamic, which means the interaction between nodes occurs at a specific time. This paper proposes a self-supervised dynamic graph representation learning framework (DySubC), which defines a temporal subgraph contrastive learning task to simultaneously learn the structural and evolutional features of a dynamic graph. Specifically, a novel temporal subgraph sampling strategy is firstly proposed, which takes each node of the dynamic graph as the central node and uses both neighborhood structures and edge timestamps to sample the corresponding temporal subgraph. The subgraph representation function is then designed according to the influence of neighborhood nodes on the central node after encoding the nodes in each subgraph. Finally, the structural and temporal contrastive loss are defined to maximize the mutual information between node representation and temporal subgraph representation. Experiments on five real-world datasets demonstrate that (1) DySubC performs better than the related baselines including two graph contrastive learning models and four dynamic graph representation learning models in the downstream link prediction task, and (2) the use of temporal information can not only sample more effective subgraphs, but also learn better representation by temporal contrastive loss.
Unsupervised graph-level representation learning plays a crucial role in a variety of tasks such as molecular property prediction and community analysis, especially when data annotation is expensive. Currently, most of the best-performing graph embedding methods are based on Infomax principle. The performance of these methods highly depends on the selection of negative samples and hurt the performance, if the samples were not carefully selected. Inter-graph similarity-based methods also suffer if the selected set of graphs for similarity matching is low in quality. To address this, we focus only on utilizing the current input graph for embedding learning. We are motivated by an observation from real-world graph generation processes where the graphs are formed based on one or more global factors which are common to all elements of the graph (e.g., topic of a discussion thread, solubility level of a molecule). We hypothesize extracting these common factors could be highly beneficial. Hence, this work proposes a new principle for unsupervised graph representation learning: Graph-wise Common latent Factor EXtraction (GCFX). We further propose a deep model for GCFX, deepGCFX, based on the idea of reversing the above-mentioned graph generation process which could explicitly extract common latent factors from an input graph and achieve improved results on downstream tasks to the current state-of-the-art. Through extensive experiments and analysis, we demonstrate that, while extracting common latent factors is beneficial for graph-level tasks to alleviate distractions caused by local variations of individual nodes or local neighbourhoods, it also benefits node-level tasks by enabling long-range node dependencies, especially for disassortative graphs.
Recent research has achieved impressive progress in the session-based recommendation. However, information such as item knowledge and click time interval, which could be potentially utilized to improve the performance, remains largely unexploited. In this paper, we propose a framework called Knowledge-enhanced Session-based Recommendation with Temporal Transformer (KSTT) to incorporate such information when learning the item and session embeddings. Specifically, a knowledge graph, which models contexts among items within a session and their corresponding attributes, is proposed to obtain item embeddings through graph representation learning. We introduce time interval embedding to represent the time pattern between the item that needs to be predicted and historical click, and use it to replace the position embedding in the original transformer (called temporal transformer). The item embeddings in a session are passed through the temporal transformer network to get the session embedding, based on which the final recommendation is made. Extensive experiments demonstrate that our model outperforms state-of-the-art baselines on four benchmark datasets.
Graph representation learning received increasing attentions in recent years. Most of existing methods ignore the complexity of the graph structures and restrict graphs in a single constant-curvature representation space, which is only suitable to particular kinds of graph structure indeed. Additionally, these methods follow the supervised or semi-supervised learning paradigm, and thereby notably limit their deployment on the unlabeled graphs in real applications. To address these aforementioned limitations, we take the first attempt to study the self-supervised graph representation learning in the mixed-curvature spaces. In this paper, we present a novel Self-supervised Mixed-curvature Graph Neural Network (SelfMGNN). Instead of working on one single constant-curvature space, we construct a mixed-curvature space via the Cartesian product of multiple Riemannian component spaces and design hierarchical attention mechanisms for learning and fusing the representations across these component spaces. To enable the self-supervisd learning, we propose a novel dual contrastive approach. The mixed-curvature Riemannian space actually provides multiple Riemannian views for the contrastive learning. We introduce a Riemannian projector to reveal these views, and utilize a well-designed Riemannian discriminator for the single-view and cross-view contrastive learning within and across the Riemannian views. Finally, extensive experiments show that SelfMGNN captures the complicated graph structures in reality and outperforms state-of-the-art baselines.
We investigate quantum circuits for graph representation learning, and propose equivariant quantum graph circuits (EQGCs), as a class of parameterized quantum circuits with strong relational inductive bias for learning over graph-structured data. Conceptually, EQGCs serve as a unifying framework for quantum graph representation learning, allowing us to define several interesting subclasses which subsume existing proposals. In terms of the representation power, we prove that the studied subclasses of EQGCs are universal approximators for functions over the bounded graph domain. This theoretical perspective on quantum graph machine learning methods opens many directions for further work, and could lead to models with capabilities beyond those of classical approaches. We empirically verify the expressive power of EQGCs through a dedicated experiment on synthetic data, and additionally observe that the performance of EQGCs scales well with the depth of the model and does not suffer from barren plateu issues.
Graph representation learning (GRL) on attribute-missing graphs, which is a common yet challenging problem, has recently attracted considerable attention. We observe that existing literature: 1) isolates the learning of attribute and structure embedding thus fails to take full advantages of the two types of information; 2) imposes too strict distribution assumption on the latent space variables, leading to less discriminative feature representations. In this paper, based on the idea of introducing intimate information interaction between the two information sources, we propose our Siamese Attribute-missing Graph Auto-encoder (SAGA). Specifically, three strategies have been conducted. First, we entangle the attribute embedding and structure embedding by introducing a siamese network structure to share the parameters learned by both processes, which allows the network training to benefit from more abundant and diverse information. Second, we introduce a K-nearest neighbor (KNN) and structural constraint enhanced learning mechanism to improve the quality of latent features of the missing attributes by filtering unreliable connections. Third, we manually mask the connections on multiple adjacent matrices and force the structural information embedding sub-network to recover the true adjacent matrix, thus enforcing the resulting network to be able to selectively exploit more high-order discriminative features for data completion. Extensive experiments on six benchmark datasets demonstrate the superiority of our SAGA against the state-of-the-art methods.
Prediction using the ground truth sounds like an oxymoron in machine learning. However, such an unrealistic setting was used in hundreds, if not thousands of papers in the area of finding graph representations. To evaluate the multi-label problem of node classification by using the obtained representations, many works assume in the prediction stage that the number of labels of each test instance is known. In practice such ground truth information is rarely available, but we point out that such an inappropriate setting is now ubiquitous in this research area. We detailedly investigate why the situation occurs. Our analysis indicates that with unrealistic information, the performance is likely over-estimated. To see why suitable predictions were not used, we identify difficulties in applying some multi-label techniques. For the use in future studies, we propose simple and effective settings without using practically unknown information. Finally, we take this chance to conduct a fair and serious comparison of major graph-representation learning methods on multi-label node classification.
Representation learning models for Knowledge Graphs (KG) have proven to be effective in encoding structural information and performing reasoning over KGs. In this paper, we propose a novel pre-training-then-fine-tuning framework for knowledge graph representation learning, in which a KG model is firstly pre-trained with triple classification task, followed by discriminative fine-tuning on specific downstream tasks such as entity type prediction and entity alignment. Drawing on the general ideas of learning deep contextualized word representations in typical pre-trained language models, we propose SCoP to learn pre-trained KG representations with structural and contextual triples of the target triple encoded. Experimental results demonstrate that fine-tuning SCoP not only outperforms results of baselines on a portfolio of downstream tasks but also avoids tedious task-specific model design and parameter training.
In recent years, owing to the outstanding performance in graph representation learning, graph neural network (GNN) techniques have gained considerable interests in many real-world scenarios, such as recommender systems and social networks. In recommender systems, the main challenge is to learn the effective user/item representations from their interactions. However, many recent publications using GNNs for recommender systems cannot be directly compared, due to their difference on datasets and evaluation metrics. Furthermore, many of them only provide a demo to conduct experiments on small datasets, which is far away to be applied in real-world recommender systems. To address this problem, we introduce Graph4Rec, a universal toolkit that unifies the paradigm to train GNN models into the following parts: graphs input, random walk generation, ego graphs generation, pairs generation and GNNs selection. From this training pipeline, one can easily establish his own GNN model with a few configurations. Besides, we develop a large-scale graph engine and a parameter server to support distributed GNN training. We conduct a systematic and comprehensive experiment to compare the performance of different GNN models on several scenarios in different scale. Extensive experiments are demonstrated to identify the key components of GNNs. We also try to figure out how the sparse and dense parameters affect the performance of GNNs. Finally, we investigate methods including negative sampling, ego graph construction order, and warm start strategy to find a more effective and efficient GNNs practice on recommender systems. Our toolkit is based on PGL https://github.com/PaddlePaddle/PGL and the code is opened source in https://github.com/PaddlePaddle/PGL/tree/main/apps/Graph4Rec.
The contemporary visual captioning models frequently hallucinate objects that are not actually in a scene, due to the visual misclassification or over-reliance on priors that resulting in the semantic inconsistency between the visual information and the target lexical words. The most common way is to encourage the captioning model to dynamically link generated object words or phrases to appropriate regions of the image, i.e., the grounded image captioning (GIC). However, GIC utilizes an auxiliary task (grounding objects) that has not solved the key issue of object hallucination, i.e., the semantic inconsistency. In this paper, we take a novel perspective on the issue above - exploiting the semantic coherency between the visual and language modalities. Specifically, we propose the Consensus Rraph Representation Learning framework (CGRL) for GIC that incorporates a consensus representation into the grounded captioning pipeline. The consensus is learned by aligning the visual graph (e.g., scene graph) to the language graph that consider both the nodes and edges in a graph. With the aligned consensus, the captioning model can capture both the correct linguistic characteristics and visual relevance, and then grounding appropriate image regions further. We validate the effectiveness of our model, with a significant decline in object hallucination (-9% CHAIRi) on the Flickr30k Entities dataset. Besides, our CGRL also evaluated by several automatic metrics and human evaluation, the results indicate that the proposed approach can simultaneously improve the performance of image captioning (+2.9 Cider) and grounding (+2.3 F1LOC).
Despite significant advances in graph representation learning, little attention has been paid to the more practical continual learning scenario in which new categories of nodes (e.g., new research areas in citation networks, or new types of products in co-purchasing networks) and their associated edges are continuously emerging, causing catastrophic forgetting on previous categories. Existing methods either ignore the rich topological information or sacrifice plasticity for stability. To this end, we present Hierarchical Prototype Networks (HPNs) which extract different levels of abstract knowledge in the form of prototypes to represent the continuously expanded graphs. Specifically, we first leverage a set of Atomic Feature Extractors (AFEs) to encode both the elemental attribute information and the topological structure of the target node. Next, we develop HPNs to adaptively select relevant AFEs and represent each node with three levels of prototypes. In this way, whenever a new category of nodes is given, only the relevant AFEs and prototypes at each level will be activated and refined, while others remain uninterrupted to maintain the performance over existing nodes. Theoretically, we first demonstrate that the memory consumption of HPNs is bounded regardless of how many tasks are encountered. Then, we prove that under mild constraints, learning new tasks will not alter the prototypes matched to previous data, thereby eliminating the forgetting problem. The theoretical results are supported by experiments on five datasets, showing that HPNs not only outperform state-of-the-art baseline techniques but also consume relatively less memory.