The recently emerged spectral clustering surpasses conventional clustering methods by detecting clusters of any shape without the convexity assumption. Unfortunately, with a computational complexity of $O(n^3)$, it was infeasible for multiple real applications, where $n$ could be large. This stimulates researchers to propose the approximate spectral clustering (ASC). However, most of ASC methods assumed that the number of clusters $k$ was known. In practice, manual setting of $k$ could be subjective or time consuming. The proposed algorithm has two relevance metrics for estimating $k$ in two vital steps of ASC. One for selecting the eigenvectors spanning the embedding space, and the other to discover the number of clusters in that space. The algorithm used a growing neural gas (GNG) approximation, GNG is superior in preserving input data topology. The experimental setup demonstrates the efficiency of the proposed algorithm and its ability to compete with similar methods where $k$ was set manually.
Spectral clustering became a popular choice for data clustering for its ability of uncovering clusters of different shapes. However, it is not always preferable over other clustering methods due to its computational demands. One of the effective ways to bypass these computational demands is to perform spectral clustering on a subset of points (data representatives) then generalize the clustering outcome, this is known as approximate spectral clustering (ASC). ASC uses sampling or quantization to select data representatives. This makes it vulnerable to 1) performance inconsistency (since these methods have a random step either in initialization or training), 2) local statistics loss (because the pairwise similarities are extracted from data representatives instead of data points). We proposed a refined version of $k$-nearest neighbor graph, in which we keep data points and aggressively reduce number of edges for computational efficiency. Local statistics were exploited to keep the edges that do not violate the intra-cluster distances and nullify all other edges in the $k$-nearest neighbor graph. We also introduced an optional step to automatically select the number of clusters $C$. The proposed method was tested on synthetic and real datasets. Compared to ASC methods, the proposed method delivered a consistent performance despite significant reduction of edges.
Whole slide image (WSI) has been widely used to assist automated diagnosis under the deep learning fields. However, most previous works only discuss the SINGLE task setting which is not aligned with real clinical setting, where pathologists often conduct multiple diagnosis tasks simultaneously. Also, it is commonly recognized that the multi-task learning paradigm can improve learning efficiency by exploiting commonalities and differences across multiple tasks. To this end, we present a novel multi-task framework (i.e., MulGT) for WSI analysis by the specially designed Graph-Transformer equipped with Task-aware Knowledge Injection and Domain Knowledge-driven Graph Pooling modules. Basically, with the Graph Neural Network and Transformer as the building commons, our framework is able to learn task-agnostic low-level local information as well as task-specific high-level global representation. Considering that different tasks in WSI analysis depend on different features and properties, we also design a novel Task-aware Knowledge Injection module to transfer the task-shared graph embedding into task-specific feature spaces to learn more accurate representation for different tasks. Further, we elaborately design a novel Domain Knowledge-driven Graph Pooling module for each task to improve both the accuracy and robustness of different tasks by leveraging different diagnosis patterns of multiple tasks. We evaluated our method on two public WSI datasets from TCGA projects, i.e., esophageal carcinoma and kidney carcinoma. Experimental results show that our method outperforms single-task counterparts and the state-of-theart methods on both tumor typing and staging tasks.
An important problem in network analysis is predicting a node attribute using both network covariates, such as graph embedding coordinates or local subgraph counts, and conventional node covariates, such as demographic characteristics. While standard regression methods that make use of both types of covariates may be used for prediction, statistical inference is complicated by the fact that the nodal summary statistics are often dependent in complex ways. We show that under a mild joint exchangeability assumption, a network analog of conformal prediction achieves finite sample validity for a wide range of network covariates. We also show that a form of asymptotic conditional validity is achievable. The methods are illustrated on both simulated networks and a citation network dataset.
In this paper, we propose a framework to detect topics in social media based on Human Word Association. Identifying topics discussed in these media has become a critical and significant challenge. Most of the work done in this area is in English, but much has been done in the Persian language, especially microblogs written in Persian. Also, the existing works focused more on exploring frequent patterns or semantic relationships and ignored the structural methods of language. In this paper, a topic detection framework using HWA, a method for Human Word Association, is proposed. This method uses the concept of imitation of mental ability for word association. This method also calculates the Associative Gravity Force that shows how words are related. Using this parameter, a graph can be generated. The topics can be extracted by embedding this graph and using clustering methods. This approach has been applied to a Persian language dataset collected from Telegram. Several experimental studies have been performed to evaluate the proposed framework's performance. Experimental results show that this approach works better than other topic detection methods.
Spectral clustering became a popular choice for data clustering for its ability of uncovering clusters of different shapes. However, it is not always preferable over other clustering methods due to its computational demands. One of the effective ways to bypass these computational demands is to perform spectral clustering on a subset of points (data representatives) then generalize the clustering outcome, this is known as approximate spectral clustering (ASC). ASC uses sampling or quantization to select data representatives. This makes it vulnerable to 1) performance inconsistency (since these methods have a random step either in initialization or training), 2) local statistics loss (because the pairwise similarities are extracted from data representatives instead of data points). We proposed a refined version of -nearest neighbor graph, in which we keep data points and aggressively reduce number of edges for computational efficiency. Local statistics were exploited to keep the edges that do not violate the intra-cluster distances and nullify all other edges in the -nearest neighbor graph. We also introduced an optional step to automatically select the number of clusters . The proposed method was tested on synthetic and real datasets. Compared to ASC methods, the proposed method delivered a consistent performance despite significant reduction of edges
Recent applications of pattern recognition techniques on brain connectome classification using functional connectivity (FC) are shifting towards acknowledging the non-Euclidean topology and dynamic aspects of brain connectivity across time. In this paper, a deep spatiotemporal variational Bayes (DSVB) framework is proposed to learn time-varying topological structures in dynamic FC networks for identifying autism spectrum disorder (ASD) in human participants. The framework incorporates a spatial-aware recurrent neural network with an attention-based message passing scheme to capture rich spatiotemporal patterns across dynamic FC networks. To overcome model overfitting on limited training datasets, an adversarial training strategy is introduced to learn graph embedding models that generalize well to unseen brain networks. Evaluation on the ABIDE resting-state functional magnetic resonance imaging dataset shows that our proposed framework substantially outperforms state-of-the-art methods in identifying patients with ASD. Dynamic FC analyses with DSVB-learned embeddings reveal apparent group differences between ASD and healthy controls in brain network connectivity patterns and switching dynamics of brain states. The code is available at https://github.com/Monash-NeuroAI/Deep-Spatiotemporal-Variational-Bayes.
Temporal interaction graphs (TIGs), consisting of sequences of timestamped interaction events, are prevalent in fields like e-commerce and social networks. To better learn dynamic node embeddings that vary over time, researchers have proposed a series of temporal graph neural networks for TIGs. However, due to the entangled temporal and structural dependencies, existing methods have to process the sequence of events chronologically and consecutively to ensure node representations are up-to-date. This prevents existing models from parallelization and reduces their flexibility in industrial applications. To tackle the above challenge, in this paper, we propose TIGER, a TIG embedding model that can restart at any timestamp. We introduce a restarter module that generates surrogate representations acting as the warm initialization of node representations. By restarting from multiple timestamps simultaneously, we divide the sequence into multiple chunks and naturally enable the parallelization of the model. Moreover, in contrast to previous models that utilize a single memory unit, we introduce a dual memory module to better exploit neighborhood information and alleviate the staleness problem. Extensive experiments on four public datasets and one industrial dataset are conducted, and the results verify both the effectiveness and the efficiency of our work.
In the last few years, the solution to Knowledge Graph (KG) completion via learning embeddings of entities and relations has attracted a surge of interest. Temporal KGs(TKGs) extend traditional Knowledge Graphs (KGs) by associating static triples with timestamps forming quadruples. Different from KGs and TKGs in the transductive setting, constantly emerging entities and relations in incomplete TKGs create demand to predict missing facts with unseen components, which is the extrapolation setting. Traditional temporal knowledge graph embedding (TKGE) methods are limited in the extrapolation setting since they are trained within a fixed set of components. In this paper, we propose a Meta-Learning based Temporal Knowledge Graph Extrapolation (MTKGE) model, which is trained on link prediction tasks sampled from the existing TKGs and tested in the emerging TKGs with unseen entities and relations. Specifically, we meta-train a GNN framework that captures relative position patterns and temporal sequence patterns between relations. The learned embeddings of patterns can be transferred to embed unseen components. Experimental results on two different TKG extrapolation datasets show that MTKGE consistently outperforms both the existing state-of-the-art models for knowledge graph extrapolation and specifically adapted KGE and TKGE baselines.
Predicting missing links between entities in a knowledge graph is a fundamental task to deal with the incompleteness of data on the Web. Knowledge graph embeddings map nodes into a vector space to predict new links, scoring them according to geometric criteria. Relations in the graph may follow patterns that can be learned, e.g., some relations might be symmetric and others might be hierarchical. However, the learning capability of different embedding models varies for each pattern and, so far, no single model can learn all patterns equally well. In this paper, we combine the query representations from several models in a unified one to incorporate patterns that are independently captured by each model. Our combination uses attention to select the most suitable model to answer each query. The models are also mapped onto a non-Euclidean manifold, the Poincar\'e ball, to capture structural patterns, such as hierarchies, besides relational patterns, such as symmetry. We prove that our combination provides a higher expressiveness and inference power than each model on its own. As a result, the combined model can learn relational and structural patterns. We conduct extensive experimental analysis with various link prediction benchmarks showing that the combined model outperforms individual models, including state-of-the-art approaches.
(Dis)agreement detection aims to identify the authors' attitudes or positions (\textit{{agree, disagree, neutral}}) towards a specific text. It is limited for existing methods merely using textual information for identifying (dis)agreements, especially for cross-domain settings. Social relation information can play an assistant role in the (dis)agreement task besides textual information. We propose a novel method to extract such relation information from (dis)agreement data into an inductive social relation graph, merely using the comment-reply pairs without any additional platform-specific information. The inductive social relation globally considers the historical discussion and the relation between authors. Textual information based on a pre-trained language model and social relation information encoded by pre-trained RGCN are jointly considered for (dis)agreement detection. Experimental results show that our model achieves state-of-the-art performance for both the in-domain and cross-domain tasks on the benchmark -- DEBAGREEMENT. We find social relations can boost the performance of the (dis)agreement detection model, especially for the long-token comment-reply pairs, demonstrating the effectiveness of the social relation graph. We also explore the effect of the knowledge graph embedding methods, the information fusing method, and the time interval in constructing the social relation graph, which shows the effectiveness of our model.
Federated Learning (FL) recently emerges as a paradigm to train a global machine learning model across distributed clients without sharing raw data. Knowledge Graph (KG) embedding represents KGs in a continuous vector space, serving as the backbone of many knowledge-driven applications. As a promising combination, federated KG embedding can fully take advantage of knowledge learned from different clients while preserving the privacy of local data. However, realistic problems such as data heterogeneity and knowledge forgetting still remain to be concerned. In this paper, we propose FedLU, a novel FL framework for heterogeneous KG embedding learning and unlearning. To cope with the drift between local optimization and global convergence caused by data heterogeneity, we propose mutual knowledge distillation to transfer local knowledge to global, and absorb global knowledge back. Moreover, we present an unlearning method based on cognitive neuroscience, which combines retroactive interference and passive decay to erase specific knowledge from local clients and propagate to the global model by reusing knowledge distillation. We construct new datasets for assessing realistic performance of the state-of-the-arts. Extensive experiments show that FedLU achieves superior results in both link prediction and knowledge forgetting.
Contrastive learning has emerged as a premier method for learning representations with or without supervision. Recent studies have shown its utility in graph representation learning for pre-training. Despite successes, the understanding of how to design effective graph augmentations that can capture structural properties common to many different types of downstream graphs remains incomplete. We propose a set of well-motivated graph transformation operations derived via graph spectral analysis to provide a bank of candidates when constructing augmentations for a graph contrastive objective, enabling contrastive learning to capture useful structural representation from pre-training graph datasets. We first present a spectral graph cropping augmentation that involves filtering nodes by applying thresholds to the eigenvalues of the leading Laplacian eigenvectors. Our second novel augmentation reorders the graph frequency components in a structural Laplacian-derived position graph embedding. Further, we introduce a method that leads to improved views of local subgraphs by performing alignment via global random walk embeddings. Our experimental results indicate consistent improvements in out-of-domain graph data transfer compared to state-of-the-art graph contrastive learning methods, shedding light on how to design a graph learner that is able to learn structural properties common to diverse graph types.
Knowledge graphs represent known facts using triplets. While existing knowledge graph embedding methods only consider the connections between entities, we propose considering the relationships between triplets. For example, let us consider two triplets $T_1$ and $T_2$ where $T_1$ is (Academy_Awards, Nominates, Avatar) and $T_2$ is (Avatar, Wins, Academy_Awards). Given these two base-level triplets, we see that $T_1$ is a prerequisite for $T_2$. In this paper, we define a higher-level triplet to represent a relationship between triplets, e.g., $\langle T_1$, PrerequisiteFor, $T_2\rangle$ where PrerequisiteFor is a higher-level relation. We define a bi-level knowledge graph that consists of the base-level and the higher-level triplets. We also propose a data augmentation strategy based on the random walks on the bi-level knowledge graph to augment plausible triplets. Our model called BiVE learns embeddings by taking into account the structures of the base-level and the higher-level triplets, with additional consideration of the augmented triplets. We propose two new tasks: triplet prediction and conditional link prediction. Given a triplet $T_1$ and a higher-level relation, the triplet prediction predicts a triplet that is likely to be connected to $T_1$ by the higher-level relation, e.g., $\langle T_1$, PrerequisiteFor, ?$\rangle$. The conditional link prediction predicts a missing entity in a triplet conditioned on another triplet, e.g., $\langle T_1$, PrerequisiteFor, (Avatar, Wins, ?)$\rangle$. Experimental results show that BiVE significantly outperforms all other methods in the two new tasks and the typical base-level link prediction in real-world bi-level knowledge graphs.
Research publications are the primary vehicle for sharing scientific progress in the form of new discoveries, methods, techniques, and insights. Unfortunately, the lack of a large-scale, comprehensive, and easy-to-use resource capturing the myriad relationships between publications, their authors, and venues presents a barrier to applications for gaining a deeper understanding of science. In this paper, we present PubGraph, a new resource for studying scientific progress that takes the form of a large-scale knowledge graph (KG) with more than 385M entities, 13B main edges, and 1.5B qualifier edges. PubGraph is comprehensive and unifies data from various sources, including Wikidata, OpenAlex, and Semantic Scholar, using the Wikidata ontology. Beyond the metadata available from these sources, PubGraph includes outputs from auxiliary community detection algorithms and large language models. To further support studies on reasoning over scientific networks, we create several large-scale benchmarks extracted from PubGraph for the core task of knowledge graph completion (KGC). These benchmarks present many challenges for knowledge graph embedding models, including an adversarial community-based KGC evaluation setting, zero-shot inductive learning, and large-scale learning. All of the aforementioned resources are accessible at https://pubgraph.isi.edu/ and released under the CC-BY-SA license. We plan to update PubGraph quarterly to accommodate the release of new publications.
Knowledge graphs (KGs) have become valuable knowledge resources in various applications, and knowledge graph embedding (KGE) methods have garnered increasing attention in recent years. However, conventional KGE methods still face challenges when it comes to handling unseen entities or relations during model testing. To address this issue, much effort has been devoted to various fields of KGs. In this paper, we use a set of general terminologies to unify these methods and refer to them collectively as Knowledge Extrapolation. We comprehensively summarize these methods, classified by our proposed taxonomy, and describe their interrelationships. Additionally, we introduce benchmarks and provide comparisons of these methods based on aspects that are not captured by the taxonomy. Finally, we suggest potential directions for future research.
We propose an entity-agnostic representation learning method for handling the problem of inefficient parameter storage costs brought by embedding knowledge graphs. Conventional knowledge graph embedding methods map elements in a knowledge graph, including entities and relations, into continuous vector spaces by assigning them one or multiple specific embeddings (i.e., vector representations). Thus the number of embedding parameters increases linearly as the growth of knowledge graphs. In our proposed model, Entity-Agnostic Representation Learning (EARL), we only learn the embeddings for a small set of entities and refer to them as reserved entities. To obtain the embeddings for the full set of entities, we encode their distinguishable information from their connected relations, k-nearest reserved entities, and multi-hop neighbors. We learn universal and entity-agnostic encoders for transforming distinguishable information into entity embeddings. This approach allows our proposed EARL to have a static, efficient, and lower parameter count than conventional knowledge graph embedding methods. Experimental results show that EARL uses fewer parameters and performs better on link prediction tasks than baselines, reflecting its parameter efficiency.
Graph alignment, which aims at identifying corresponding entities across multiple networks, has been widely applied in various domains. As the graphs to be aligned are usually constructed from different sources, the inconsistency issues of structures and features between two graphs are ubiquitous in real-world applications. Most existing methods follow the ``embed-then-cross-compare'' paradigm, which computes node embeddings in each graph and then processes node correspondences based on cross-graph embedding comparison. However, we find these methods are unstable and sub-optimal when structure or feature inconsistency appears. To this end, we propose SLOTAlign, an unsupervised graph alignment framework that jointly performs Structure Learning and Optimal Transport Alignment. We convert graph alignment to an optimal transport problem between two intra-graph matrices without the requirement of cross-graph comparison. We further incorporate multi-view structure learning to enhance graph representation power and reduce the effect of structure and feature inconsistency inherited across graphs. Moreover, an alternating scheme based algorithm has been developed to address the joint optimization problem in SLOTAlign, and the provable convergence result is also established. Finally, we conduct extensive experiments on six unsupervised graph alignment datasets and the DBP15K knowledge graph (KG) alignment benchmark dataset. The proposed SLOTAlign shows superior performance and strongest robustness over seven unsupervised graph alignment methods and five specialized KG alignment methods.
Empirical data plays an important role in evolutionary computation research. To make better use of the available data, ontologies have been proposed in the literature to organize their storage in a structured way. However, the full potential of these formal methods to capture our domain knowledge has yet to be demonstrated. In this work, we evaluate a performance prediction model built on top of the extension of the recently proposed OPTION ontology. More specifically, we first extend the OPTION ontology with the vocabulary needed to represent modular black-box optimization algorithms. Then, we use the extended OPTION ontology, to create knowledge graphs with fixed-budget performance data for two modular algorithm frameworks, modCMA, and modDE, for the 24 noiseless BBOB benchmark functions. We build the performance prediction model using a knowledge graph embedding-based methodology. Using a number of different evaluation scenarios, we show that a triple classification approach, a fairly standard predictive modeling task in the context of knowledge graphs, can correctly predict whether a given algorithm instance will be able to achieve a certain target precision for a given problem instance. This approach requires feature representation of algorithms and problems. While the latter is already well developed, we hope that our work will motivate the community to collaborate on appropriate algorithm representations.
In Human-Robot Interaction (HRI) systems, a challenging task is sharing the representation of the operational environment, fusing symbolic knowledge and perceptions, between users and robots. With the existing HRI pipelines, users can teach the robots some concepts to increase their knowledge base. Unfortunately, the data coming from the users are usually not enough dense for building a consistent representation. Furthermore, the existing approaches are not able to incrementally build up their knowledge base, which is very important when robots have to deal with dynamic contexts. To this end, we propose an architecture to gather data from users and environments in long-runs of continual learning. We adopt Knowledge Graph Embedding techniques to generalize the acquired information with the goal of incrementally extending the robot's inner representation of the environment. We evaluate the performance of the overall continual learning architecture by measuring the capabilities of the robot of learning entities and relations coming from unknown contexts through a series of incremental learning sessions.