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Knowledge Graph Embedding (KGE) techniques play a pivotal role in transforming symbolic Knowledge Graphs (KGs) into numerical representations, thereby enhancing various deep learning models for knowledge-augmented applications. Unlike…
Knowledge Graphs (KGs) often have two characteristics: heterogeneous graph structure and text-rich entity/relation information. Text-based KG embeddings can represent entities by encoding descriptions with pre-trained language models, but…
Knowledge Graphs (KG) constitute a flexible representation of complex relationships between entities particularly useful for biomedical data. These KG, however, are very sparse with many missing edges (facts) and the visualisation of the…
Knowledge Graphs (KGs) have gained considerable attention recently from both academia and industry. In fact, incorporating graph technology and the copious of various graph datasets have led the research community to build sophisticated…
Recent advances in knowledge representation learning (KRL) highlight the urgent necessity to unify symbolic knowledge graphs (KGs) with language models (LMs) for richer semantic understanding. However, existing approaches typically…
In recent years, artificial intelligence has played an important role on accelerating the whole process of drug discovery. Various of molecular representation schemes of different modals (e.g. textual sequence or graph) are developed. By…
Interference between pharmacological substances can cause serious medical injuries. Correctly predicting so-called drug-drug interactions (DDI) does not only reduce these cases but can also result in a reduction of drug development cost.…
Recent advances in natural language processing (NLP) owe their success to pre-training language models on large amounts of unstructured data. Still, there is an increasing effort to combine the unstructured nature of LMs with structured…
Latent representations of drugs and their targets produced by contemporary graph autoencoder models have proved useful in predicting many types of node-pair interactions on large networks, including drug-drug, drug-target, and target-target…
Biomedical datasets are often modeled as knowledge graphs (KGs) because they capture the multi-relational, heterogeneous, and dynamic natures of biomedical systems. KG completion (KGC), can, therefore, help researchers make predictions to…
Due to its complexity, graph learning-based multi-modal integration and classification is one of the most challenging obstacles for disease prediction. To effectively offset the negative impact between modalities in the process of…
Irregular data in real-world are usually organized as heterogeneous graphs (HGs) consisting of multiple types of nodes and edges. To explore useful knowledge from real-world data, both the large-scale encyclopedic HG datasets and…
Knowledge graphs (KGs) that modelings the world knowledge as structural triples are inevitably incomplete. Such problems still exist for multimodal knowledge graphs (MMKGs). Thus, knowledge graph completion (KGC) is of great importance to…
Large language models (LLMs) offer new opportunities for constructing knowledge graphs (KGs) from unstructured clinical narratives. However, existing approaches often rely on structured inputs and lack robust validation of factual accuracy…
Much of biomedical and healthcare data is encoded in discrete, symbolic form such as text and medical codes. There is a wealth of expert-curated biomedical domain knowledge stored in knowledge bases and ontologies, but the lack of reliable…
Multilingual knowledge graph (KG) embeddings provide latent semantic representations of entities and structured knowledge with cross-lingual inferences, which benefit various knowledge-driven cross-lingual NLP tasks. However, precisely…
The ability of knowledge graphs to represent complex relationships at scale has led to their adoption for various needs including knowledge representation, question-answering, and recommendation systems. Knowledge graphs are often…
Knowledge Graphs (KGs) and their machine learning counterpart, Knowledge Graph Embedding Models (KGEMs), have seen ever-increasing use in a wide variety of academic and applied settings. In particular, KGEMs are typically applied to KGs to…
Extensive adoption of electronic health records (EHRs) offers opportunities for their use in various downstream clinical analyses. To accomplish this purpose, enriching an EHR cohort with external knowledge (e.g., standardized medical…
Representation learning for knowledge graphs (KGs) has focused on the problem of answering simple link prediction queries. In this work we address the more ambitious challenge of predicting the answers of conjunctive queries with multiple…