Large-Scale Biomedical Relation Extraction Across Diverse Relation Types: Model Development and Usability Study on COVID-19. Journal of medical Internet research BACKGROUND:Biomedical relation extraction (RE) is of great importance for researchers to conduct systematic biomedical studies. It not only helps knowledge mining, such as knowledge graphs and novel knowledge discovery, but also promotes translational applications, such as clinical diagnosis, decision-making, and precision medicine. However, the relations between biomedical entities are complex and diverse, and comprehensive biomedical RE is not yet well established. OBJECTIVE:We aimed to investigate and improve large-scale RE with diverse relation types and conduct usability studies with application scenarios to optimize biomedical text mining. METHODS:Data sets containing 125 relation types with different entity semantic levels were constructed to evaluate the impact of entity semantic information on RE, and performance analysis was conducted on different model architectures and domain models. This study also proposed a continued pretraining strategy and integrated models with scripts into a tool. Furthermore, this study applied RE to the COVID-19 corpus with article topics and application scenarios of clinical interest to assess and demonstrate its biological interpretability and usability. RESULTS:The performance analysis revealed that RE achieves the best performance when the detailed semantic type is provided. For a single model, PubMedBERT with continued pretraining performed the best, with an F1-score of 0.8998. Usability studies on COVID-19 demonstrated the interpretability and usability of RE, and a relation graph database was constructed, which was used to reveal existing and novel drug paths with edge explanations. The models (including pretrained and fine-tuned models), integrated tool (Docker), and generated data (including the COVID-19 relation graph database and drug paths) have been made publicly available to the biomedical text mining community and clinical researchers. CONCLUSIONS:This study provided a comprehensive analysis of RE with diverse relation types. Optimized RE models and tools for diverse relation types were developed, which can be widely used in biomedical text mining. Our usability studies provided a proof-of-concept demonstration of how large-scale RE can be leveraged to facilitate novel research. 10.2196/48115

KRAGEN: a knowledge graph-enhanced RAG framework for biomedical problem solving using large language models. Bioinformatics (Oxford, England) MOTIVATION:Answering and solving complex problems using a large language model (LLM) given a certain domain such as biomedicine is a challenging task that requires both factual consistency and logic, and LLMs often suffer from some major limitations, such as hallucinating false or irrelevant information, or being influenced by noisy data. These issues can compromise the trustworthiness, accuracy, and compliance of LLM-generated text and insights. RESULTS:Knowledge Retrieval Augmented Generation ENgine (KRAGEN) is a new tool that combines knowledge graphs, Retrieval Augmented Generation (RAG), and advanced prompting techniques to solve complex problems with natural language. KRAGEN converts knowledge graphs into a vector database and uses RAG to retrieve relevant facts from it. KRAGEN uses advanced prompting techniques: namely graph-of-thoughts (GoT), to dynamically break down a complex problem into smaller subproblems, and proceeds to solve each subproblem by using the relevant knowledge through the RAG framework, which limits the hallucinations, and finally, consolidates the subproblems and provides a solution. KRAGEN's graph visualization allows the user to interact with and evaluate the quality of the solution's GoT structure and logic. AVAILABILITY AND IMPLEMENTATION:KRAGEN is deployed by running its custom Docker containers. KRAGEN is available as open-source from GitHub at: https://github.com/EpistasisLab/KRAGEN. 10.1093/bioinformatics/btae353

PluDG: enhancing task-oriented dialogue system with knowledge graph plug-in module. PeerJ. Computer science Task-oriented dialogue systems continue to face significant challenges as they require not only an understanding of dialogue history but also domain-specific knowledge. However, knowledge is often dynamic, making it difficult to effectively integrate into the learning process. Existing large language model approaches primarily treat knowledge bases as textual resources, neglecting to capture the underlying relationships between facts within the knowledge base. To address this limitation, we propose a novel dialogue system called PluDG. We regard the knowledge as a knowledge graph and propose a knowledge extraction plug-in, Kg-Plug, to capture the features of the graph and generate prompt entities to assist the system's dialogue generation. Besides, we propose Unified Memory Integration, a module that enhances the comprehension of the sentence's internal structure and optimizes the knowledge base's encoding location. We conduct experiments on three public datasets and compare PluDG with several state-of-the-art dialogue models. The experimental results indicate that PluDG achieves significant improvements in both accuracy and diversity, outperforming the current state-of-the-art dialogue system models and achieving state-of-the-art performance. 10.7717/peerj-cs.1707