Entity-Augmented Neuroscience Knowledge Retrieval Using Ontology and Semantic Understanding Capability of LLM

Neuroscience research publications encompass a vast wealth of knowledge. Accurately retrieving existing information and discovering new insights from this extensive literature is essential for advancing the field. However, when knowledge is dispersed across multiple sources, current state-of-the-art retrieval methods often struggle to extract the necessary information. A knowledge graph (KG) can integrate and link knowledge from multiple sources, but existing methods for constructing KGs in neuroscience often rely on labeled data and require domain expertise. Acquiring large-scale, labeled data for a specialized area like neuroscience presents significant challenges. This work proposes novel methods for constructing KG from unlabeled large-scale neuroscience research corpus utilizing large language models (LLM), neuroscience ontology, and text embeddings. We analyze the semantic relevance of neuroscience text segments identified by LLM for building the knowledge graph. We also introduce an entity-augmented information retrieval algorithm to extract knowledge from the KG. Several experiments were conducted to evaluate the proposed approaches, and the results demonstrate that our methods significantly enhance knowledge discovery from the unlabeled neuroscience research corpus. It achieves an F1 score of 0.84 for entity extraction, and the knowledge obtained from the KG improves answers to over 54% of the questions.

@article{ta2025_2506.03145,
  title={ Entity-Augmented Neuroscience Knowledge Retrieval Using Ontology and Semantic Understanding Capability of LLM },
  author={ Pralaypati Ta and Sriram Venkatesaperumal and Keerthi Ram and Mohanasankar Sivaprakasam },
  journal={arXiv preprint arXiv:2506.03145},
  year={ 2025 }
}