Entity alignment (EA) is to identify equivalent entities across different knowledge graphs (KGs), which can help fuse these KGs into a more comprehensive one. Previous EA methods mainly focus on aligning a pair of KGs, and to the best of our knowledge, no existing EA method considers aligning multiple (more than two) KGs. To fill this research gap, in this work, we study a novel problem of aligning multiple KGs and propose an effective framework named MultiEA to solve the problem. First, we embed the entities of all the candidate KGs into a common feature space by a shared KG encoder. Then, we explore three alignment strategies to minimize the distances among pre-aligned entities. In particular, we propose an innovative inference enhancement technique to improve the alignment performance by incorporating high-order similarities. Finally, to verify the effectiveness of MultiEA, we construct two new real-world benchmark datasets and conduct extensive experiments on them. The results show that our MultiEA can effectively and efficiently align multiple KGs in a single pass.

Proteins play a vital role in biological processes and are indispensable for living organisms. Accurate representation of proteins is crucial, especially in drug development. Recently, there has been a notable increase in interest in utilizing machine learning and deep learning techniques for unsupervised learning of protein representations. However, these approaches often focus solely on the amino acid sequence of proteins and lack factual knowledge about proteins and their interactions, thus limiting their performance. In this study, we present GOProteinGNN, a novel architecture that enhances protein language models by integrating protein knowledge graph information during the creation of amino acid level representations. Our approach allows for the integration of information at both the individual amino acid level and the entire protein level, enabling a comprehensive and effective learning process through graph-based learning. By doing so, we can capture complex relationships and dependencies between proteins and their functional annotations, resulting in more robust and contextually enriched protein representations. Unlike previous fusion methods, GOProteinGNN uniquely learns the entire protein knowledge graph during training, which allows it to capture broader relational nuances and dependencies beyond mere triplets as done in previous work. We perform a comprehensive evaluation on several downstream tasks demonstrating that GOProteinGNN consistently outperforms previous methods, showcasing its effectiveness and establishing it as a state-of-the-art solution for protein representation learning.

The integration of knowledge graphs and graph machine learning (GML) in genomic data analysis offers several opportunities for understanding complex genetic relationships, especially at the RNA level. We present a comprehensive approach for leveraging these technologies to analyze genomic variants, specifically in the context of RNA sequencing (RNA-seq) data from COVID-19 patient samples. The proposed method involves extracting variant-level genetic information, annotating the data with additional metadata using SnpEff, and converting the enriched Variant Call Format (VCF) files into Resource Description Framework (RDF) triples. The resulting knowledge graph is further enhanced with patient metadata and stored in a graph database, facilitating efficient querying and indexing. We utilize the Deep Graph Library (DGL) to perform graph machine learning tasks, including node classification with GraphSAGE and Graph Convolutional Networks (GCNs). Our approach demonstrates significant utility using our proposed tool, VariantKG, in three key scenarios: enriching graphs with new VCF data, creating subgraphs based on user-defined features, and conducting graph machine learning for node classification.

This paper investigates the advantages of representing and processing semantic knowledge extracted into graphs within the emerging paradigm of semantic communications. The proposed approach leverages semantic and pragmatic aspects, incorporating recent advances on large language models (LLMs) to achieve compact representations of knowledge to be processed and exchanged between intelligent agents. This is accomplished by using the cascade of LLMs and graph neural networks (GNNs) as semantic encoders, where information to be shared is selected to be meaningful at the receiver. The embedding vectors produced by the proposed semantic encoder represent information in the form of triplets: nodes (semantic concepts entities), edges(relations between concepts), nodes. Thus, semantic information is associated with the representation of relationships among elements in the space of semantic concept abstractions. In this paper, we investigate the potential of achieving high compression rates in communication by incorporating relations that link elements within graph embeddings. We propose sending semantic symbols solely equivalent to node embeddings through the wireless channel and inferring the complete knowledge graph at the receiver. Numerical simulations illustrate the effectiveness of leveraging knowledge graphs to semantically compress and transmit information.

Knowledge Graph Embedding (KGE) is a popular approach, which aims to represent entities and relations of a knowledge graph in latent spaces. Their representations are known as embeddings. To measure the plausibility of triplets, score functions are defined over embedding spaces. Despite wide dissemination of KGE in various tasks, KGE methods have limitations in reasoning abilities. In this paper we propose a mathematical framework to compare reasoning abilities of KGE methods. We show that STransE has a higher capability than TransComplEx, and then present new STransCoRe method, which improves the STransE by combining it with the TransCoRe insights, which can reduce the STransE space complexity.

Sparse Knowledge Graphs (KGs), frequently encountered in real-world applications, contain fewer facts in the form of (head entity, relation, tail entity) compared to more populated KGs. The sparse KG completion task, which reasons answers for given queries in the form of (head entity, relation, ?) for sparse KGs, is particularly challenging due to the necessity of reasoning missing facts based on limited facts. Path-based models, known for excellent explainability, are often employed for this task. However, existing path-based models typically rely on external models to fill in missing facts and subsequently perform path reasoning. This approach introduces unexplainable factors or necessitates meticulous rule design. In light of this, this paper proposes an alternative approach by looking inward instead of seeking external assistance. We introduce a two-stage path reasoning model called LoGRe (Look Globally and Reason) over sparse KGs. LoGRe constructs a relation-path reasoning schema by globally analyzing the training data to alleviate the sparseness problem. Based on this schema, LoGRe then aggregates paths to reason out answers. Experimental results on five benchmark sparse KG datasets demonstrate the effectiveness of the proposed LoGRe model.

Knowledge Graph Alignment (KGA) aims to integrate knowledge from multiple sources to address the limitations of individual Knowledge Graphs (KGs) in terms of coverage and depth. However, current KGA models fall short in achieving a ``complete'' knowledge graph alignment. Existing models primarily emphasize the linkage of cross-graph entities but overlook aligning relations across KGs, thereby providing only a partial solution to KGA. The semantic correlations embedded in relations are largely overlooked, potentially restricting a comprehensive understanding of cross-KG signals. In this paper, we propose to conceptualize relation alignment as an independent task and conduct KGA by decomposing it into two distinct but highly correlated sub-tasks: entity alignment and relation alignment. To capture the mutually reinforcing correlations between these objectives, we propose a novel Expectation-Maximization-based model, EREM, which iteratively optimizes both sub-tasks. Experimental results on real-world datasets demonstrate that EREM consistently outperforms state-of-the-art models in both entity alignment and relation alignment tasks.

This paper discusses how to generate general graph node embeddings from knowledge graph representations. The embedded space is composed of a number of sub-features to mimic both local affinity and remote structural relevance. These sub-feature dimensions are defined by several indicators that we speculate to catch nodal similarities, such as hop-based topological patterns, the number of overlapping labels, the transitional probabilities (markov-chain probabilities), and the cluster indices computed by our recursive spectral bisection (RSB) algorithm. These measures are flattened over the one dimensional vector space into their respective sub-component ranges such that the entire set of vector similarity functions could be used for finding similar nodes. The error is defined by the sum of pairwise square differences across a randomly selected sample of graph nodes between the assumed embeddings and the ground truth estimates as our novel loss function. The ground truth is estimated to be a combination of pairwise Jaccard similarity and the number of overlapping labels. Finally, we demonstrate a multi-variate stochastic gradient descent (SGD) algorithm to compute the weighing factors among sub-vector spaces to minimize the average error using a random sampling logic.

Abstraction -- the process of generalizing specific examples into broad reusable patterns -- is central to how people efficiently process and store information and apply their knowledge to new data. Promisingly, research has shown that ML models learn representations that span levels of abstraction, from specific concepts like "bolo tie" and "car tire" to more general concepts like "CEO" and "model". However, existing techniques analyze these representations in isolation, treating learned concepts as independent artifacts rather than an interconnected web of abstraction. As a result, although we can identify the concepts a model uses to produce its output, it is difficult to assess if it has learned a human-aligned abstraction of the concepts that will generalize to new data. To address this gap, we introduce abstraction alignment, a methodology to measure the agreement between a model's learned abstraction and the expected human abstraction. We quantify abstraction alignment by comparing model outputs against a human abstraction graph, such as linguistic relationships or medical disease hierarchies. In evaluation tasks interpreting image models, benchmarking language models, and analyzing medical datasets, abstraction alignment provides a deeper understanding of model behavior and dataset content, differentiating errors based on their agreement with human knowledge, expanding the verbosity of current model quality metrics, and revealing ways to improve existing human abstractions.

Fine-tuning pre-trained language models (PLMs) has recently shown a potential to improve knowledge graph completion (KGC). However, most PLM-based methods encode only textual information, neglecting various topological structures of knowledge graphs (KGs). In this paper, we empirically validate the significant relations between the structural properties of KGs and the performance of the PLM-based methods. To leverage the structural knowledge, we propose a Subgraph-Aware Training framework for KGC (SATKGC) that combines (i) subgraph-aware mini-batching to encourage hard negative sampling, and (ii) a new contrastive learning method to focus more on harder entities and harder negative triples in terms of the structural properties. To the best of our knowledge, this is the first study to comprehensively incorporate the structural inductive bias of the subgraphs into fine-tuning PLMs. Extensive experiments on four KGC benchmarks demonstrate the superiority of SATKGC. Our code is available.