To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leveraged in many biomedical applications including drug repurposing. Our objective is to construct a knowledge graph from literature to study relations between Alzheimer's disease (AD) and chemicals, drugs and dietary supplements in order to identify opportunities to prevent or delay neurodegenerative progression. We collected biomedical annotations and extracted their relations using SemRep via SemMedDB. We used both a BERT-based classifier and rule-based methods during data preprocessing to exclude noise while preserving most AD-related semantic triples. The 1,672,110 filtered triples were used to train with knowledge graph completion algorithms (i.e., TransE, DistMult, and ComplEx) to predict candidates that might be helpful for AD treatment or prevention. Among three knowledge graph completion models, TransE outperformed the other two (MR = 13.45, Hits@1 = 0.306). We leveraged the time-slicing technique to further evaluate the prediction results. We found supporting evidence for most highly ranked candidates predicted by our model which indicates that our approach can inform reliable new knowledge. This paper shows that our graph mining model can predict reliable new relationships between AD and other entities (i.e., dietary supplements, chemicals, and drugs). The knowledge graph constructed can facilitate data-driven knowledge discoveries and the generation of novel hypotheses.

The effectiveness of knowledge graph embedding (KGE) largely depends on the ability to model intrinsic relation patterns and mapping properties. However, existing approaches can only capture some of them with insufficient modeling capacity. In this work, we propose a more powerful KGE framework named HousE, which involves a novel parameterization based on two kinds of Householder transformations: (1) Householder rotations to achieve superior capacity of modeling relation patterns; (2) Householder projections to handle sophisticated relation mapping properties. Theoretically, HousE is capable of modeling crucial relation patterns and mapping properties simultaneously. Besides, HousE is a generalization of existing rotation-based models while extending the rotations to high-dimensional spaces. Empirically, HousE achieves new state-of-the-art performance on five benchmark datasets. Our code is available at https://github.com/anrep/HousE.

How can we perform knowledge reasoning over temporal knowledge graphs (TKGs)? TKGs represent facts about entities and their relations, where each fact is associated with a timestamp. Reasoning over TKGs, i.e., inferring new facts from time-evolving KGs, is crucial for many applications to provide intelligent services. However, despite the prevalence of real-world data that can be represented as TKGs, most methods focus on reasoning over static knowledge graphs, or cannot predict future events. In this paper, we present a problem formulation that unifies the two major problems that need to be addressed for an effective reasoning over TKGs, namely, modeling the event time and the evolving network structure. Our proposed method EvoKG jointly models both tasks in an effective framework, which captures the ever-changing structural and temporal dynamics in TKGs via recurrent event modeling, and models the interactions between entities based on the temporal neighborhood aggregation framework. Further, EvoKG achieves an accurate modeling of event time, using flexible and efficient mechanisms based on neural density estimation. Experiments show that EvoKG outperforms existing methods in terms of effectiveness (up to 77% and 116% more accurate time and link prediction) and efficiency.

Recent years have witnessed the resurgence of knowledge engineering which is featured by the fast growth of knowledge graphs. However, most of existing knowledge graphs are represented with pure symbols, which hurts the machine's capability to understand the real world. The multi-modalization of knowledge graphs is an inevitable key step towards the realization of human-level machine intelligence. The results of this endeavor are Multi-modal Knowledge Graphs (MMKGs). In this survey on MMKGs constructed by texts and images, we first give definitions of MMKGs, followed with the preliminaries on multi-modal tasks and techniques. We then systematically review the challenges, progresses and opportunities on the construction and application of MMKGs respectively, with detailed analyses of the strength and weakness of different solutions. We finalize this survey with open research problems relevant to MMKGs.

In natural language processing and information retrieval, the bag of words representation is used to implicitly represent the meaning of the text. Implicit semantics, however, are insufficient in supporting text or natural language based interfaces, which are adopted by an increasing number of applications. Indeed, in applications ranging from automatic ontology construction to question answering, explicit representation of semantics is starting to play a more prominent role. In this paper, we introduce the task of conceptual labeling (CL), which aims at generating a minimum set of conceptual labels that best summarize a bag of words. We draw the labels from a data driven semantic network that contains millions of highly connected concepts. The semantic network provides meaning to the concepts, and in turn, it provides meaning to the bag of words through the conceptual labels we generate. To achieve our goal, we use an information theoretic approach to trade-off the semantic coverage of a bag of words against the minimality of the output labels. Specifically, we use Minimum Description Length (MDL) as the criteria in selecting the best concepts. Our extensive experimental results demonstrate the effectiveness of our approach in representing the explicit semantics of a bag of words.

Graph convolutional networks (GCNs) -- which are effective in modeling graph structures -- have been increasingly popular in knowledge graph completion (KGC). GCN-based KGC models first use GCNs to generate expressive entity representations and then use knowledge graph embedding (KGE) models to capture the interactions among entities and relations. However, many GCN-based KGC models fail to outperform state-of-the-art KGE models though introducing additional computational complexity. This phenomenon motivates us to explore the real effect of GCNs in KGC. Therefore, in this paper, we build upon representative GCN-based KGC models and introduce variants to find which factor of GCNs is critical in KGC. Surprisingly, we observe from experiments that the graph structure modeling in GCNs does not have a significant impact on the performance of KGC models, which is in contrast to the common belief. Instead, the transformations for entity representations are responsible for the performance improvements. Based on the observation, we propose a simple yet effective framework named LTE-KGE, which equips existing KGE models with linearly transformed entity embeddings. Experiments demonstrate that LTE-KGE models lead to similar performance improvements with GCN-based KGC methods, while being more computationally efficient. These results suggest that existing GCNs are unnecessary for KGC, and novel GCN-based KGC models should count on more ablation studies to validate their effectiveness. The code of all the experiments is available on GitHub at https://github.com/MIRALab-USTC/GCN4KGC.

The use of symbolic knowledge representation and reasoning as a way to resolve the lack of transparency of machine learning classifiers is a research area that lately attracts many researchers. In this work, we use knowledge graphs as the underlying framework providing the terminology for representing explanations for the operation of a machine learning classifier. In particular, given a description of the application domain of the classifier in the form of a knowledge graph, we introduce a novel method for extracting and representing black-box explanations of its operation, in the form of first-order logic rules expressed in the terminology of the knowledge graph.

Knowledge graph completion (a.k.a.~link prediction), i.e.,~the task of inferring missing information from knowledge graphs, is a widely used task in many applications, such as product recommendation and question answering. The state-of-the-art approaches of knowledge graph embeddings and/or rule mining and reasoning are data-driven and, thus, solely based on the information the input knowledge graph contains. This leads to unsatisfactory prediction results which make such solutions inapplicable to crucial domains such as healthcare. To further enhance the accuracy of knowledge graph completion we propose to loosely-couple the data-driven power of knowledge graph embeddings with domain-specific reasoning stemming from experts or entailment regimes (e.g., OWL2). In this way, we not only enhance the prediction accuracy with domain knowledge that may not be included in the input knowledge graph but also allow users to plugin their own knowledge graph embedding and reasoning method. Our initial results show that we enhance the MRR accuracy of vanilla knowledge graph embeddings by up to 3x and outperform hybrid solutions that combine knowledge graph embeddings with rule mining and reasoning up to 3.5x MRR.

The ongoing COVID-19 pandemic has taught us many valuable lessons. One of them is that we need to modernise our healthcare system and make it more accessible to all people. Governments around the world have thrown a huge sum of money into digitalisation (here and here). But two years into the pandemic, rich countries such as Germany still use fax and buggy software in their hospitals to transmit data. This glaring technological gap costs lives.

Representing words by vectors, or embeddings, enables computational reasoning and is foundational to automating natural language tasks. For example, if word embeddings of similar words contain similar values, word similarity can be readily assessed, whereas judging that from their spelling is often impossible (e.g. cat /feline) and to predetermine and store similarities between all words is prohibitively time-consuming, memory intensive and subjective. We focus on word embeddings learned from text corpora and knowledge graphs. Several well-known algorithms learn word embeddings from text on an unsupervised basis by learning to predict those words that occur around each word, e.g. word2vec and GloVe. Parameters of such word embeddings are known to reflect word co-occurrence statistics, but how they capture semantic meaning has been unclear. Knowledge graph representation models learn representations both of entities (words, people, places, etc.) and relations between them, typically by training a model to predict known facts in a supervised manner. Despite steady improvements in fact prediction accuracy, little is understood of the latent structure that enables this. The limited understanding of how latent semantic structure is encoded in the geometry of word embeddings and knowledge graph representations makes a principled means of improving their performance, reliability or interpretability unclear. To address this: 1. we theoretically justify the empirical observation that particular geometric relationships between word embeddings learned by algorithms such as word2vec and GloVe correspond to semantic relations between words; and 2. we extend this correspondence between semantics and geometry to the entities and relations of knowledge graphs, providing a model for the latent structure of knowledge graph representation linked to that of word embeddings.