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arXiv · 2310.08365

From Large Language Models to Knowledge Graphs for Biomarker Discovery in Cancer

Md. Rezaul Karim·Lina Molinas Comet·Md Shajalal·Oya Deniz Beyan·Dietrich Rebholz-Schuhmann·Stefan Decker
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Abstract

Domain experts often rely on most recent knowledge for apprehending and disseminating specific biological processes that help them design strategies for developing prevention and therapeutic decision-making in various disease scenarios. A challenging scenarios for artificial intelligence (AI) is using biomedical data (e.g., texts, imaging, omics, and clinical) to provide diagnosis and treatment recommendations for cancerous conditions.~Data and knowledge about biomedical entities like cancer, drugs, genes, proteins, and their mechanism is spread across structured (knowledge bases (KBs)) and unstructured (e.g., scientific articles) sources. A large-scale knowledge graph (KG) can be constructed by integrating and extracting facts about semantically interrelated entities and relations. Such a KG not only allows exploration and question answering (QA) but also enables domain experts to deduce new knowledge. However, exploring and querying large-scale KGs is tedious for non-domain users due to their lack of understanding of the data assets and semantic technologies. In this paper, we develop a domain KG to leverage cancer-specific biomarker discovery and interactive QA. For this, we constructed a domain ontology called OncoNet Ontology (ONO), which enables semantic reasoning for validating gene-disease (different types of cancer) relations. The KG is further enriched by harmonizing the ONO, metadata, controlled vocabularies, and biomedical concepts from scientific articles by employing BioBERT- and SciBERT-based information extractors. Further, since the biomedical domain is evolving, where new findings often replace old ones, without having access to up-to-date scientific findings, there is a high chance an AI system exhibits concept drift while providing diagnosis and treatment. Therefore, we fine-tune the KG using large language models (LLMs) based on more recent articles and KBs.

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Md. Rezaul Karim, Lina Molinas Comet, Md Shajalal, Oya Deniz Beyan, Dietrich Rebholz-Schuhmann, Stefan Decker. 2023-11-19. From Large Language Models to Knowledge Graphs for Biomarker Discovery in Cancer. https://arxiv.org/abs/2310.08365

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