Related papers: BioGraphFusion: Graph Knowledge Embedding for Biol…

Identifying relationships between concepts is a key aspect of scientific knowledge synthesis. Finding these links often requires a researcher to laboriously search through scien- tific papers and databases, as the size of these resources…

Knowledge Graphs (KGs) provide a structured representation of knowledge but often suffer from challenges of incompleteness. To address this, link prediction or knowledge graph completion (KGC) aims to infer missing new facts based on…

Geospatial Knowledge Graphs (GeoKGs) model geoentities (e.g., places and natural features) and spatial relationships in an interconnected manner, providing strong knowledge support for geographic applications, including data retrieval,…

Drug repurposing is often framed as a candidate identification task, but existing approaches provide limited guidance for distinguishing biologically plausible candidates from historically well-connected ones. Here we introduce DrugKLM, a…

Graph Neural Networks (GNNs) have attracted increasing attention in recent years and have achieved excellent performance in semi-supervised node classification tasks. The success of most GNNs relies on one fundamental assumption, i.e., the…

Knowledge graphs (KGs) are crucial in the field of artificial intelligence and are widely applied in downstream tasks, such as enhancing Question Answering (QA) systems. The construction of KGs typically requires significant effort from…

Recent research on integrating Large Language Models (LLMs) with Graph Neural Networks (GNNs) typically follows two approaches: LLM-centered models, which convert graph data into tokens for LLM processing, and GNN-centered models, which use…

Knowledge graph embedding (KGE) focuses on representing the entities and relations of a knowledge graph (KG) into the continuous vector spaces, which can be employed to predict the missing triples to achieve knowledge graph completion…

Knowledge graphs and ontologies represent entities and their relationships in a structured way, having gained significance in the development of modern AI applications. Integrating these semantic resources with machine learning models often…

Knowledge Graphs (KGs) are crucial in the field of artificial intelligence and are widely used in downstream tasks, such as question-answering (QA). The construction of KGs typically requires significant effort from domain experts. Large…

The task of data integration for multi-omics data has emerged as a powerful strategy to unravel the complex biological underpinnings of cancer. Recent advancements in graph neural networks (GNNs) offer an effective framework to model…

Term clustering is important in biomedical knowledge graph construction. Using similarities between terms embedding is helpful for term clustering. State-of-the-art term embeddings leverage pretrained language models to encode terms, and…

Knowledge Graph (KG) is a flexible structure that is able to describe the complex relationship between data entities. Currently, most KG embedding models are trained based on negative sampling, i.e., the model aims to maximize some…

The advent of large language models (LLMs) has revolutionized the integration of knowledge graphs (KGs) in biomedical and cognitive sciences, overcoming limitations in traditional machine learning methods for capturing intricate semantic…

A key component of deep learning (DL) for natural language processing (NLP) is word embeddings. Word embeddings that effectively capture the meaning and context of the word that they represent can significantly improve the performance of…

Leveraging Large Language Models (LLMs) for Knowledge Graph Completion (KGC) is promising but hindered by a fundamental granularity mismatch. LLMs operate on fragmented token sequences, whereas entities are the fundamental units in…

There is an emerging trend of embedding knowledge graphs (KGs) in continuous vector spaces in order to use those for machine learning tasks. Recently, many knowledge graph embedding (KGE) models have been proposed that learn low dimensional…

Understanding mechanistic relationships among genes and their impacts on biological pathways is essential for elucidating disease mechanisms and advancing precision medicine. Despite the availability of extensive molecular interaction and…

Integrating Pre-trained Language Models (PLMs) with Graph Neural Networks (GNNs) remains a central challenge in text-rich heterophilic graph learning. We propose a novel integration framework that enables effective fusion between powerful…

Advancements in Artificial Intelligence (AI) and deep neural networks have driven significant progress in vision and text processing. However, achieving human-like reasoning and interpretability in AI systems remains a substantial…