| Autor: |
Ivanisenko TV; The Artificial Intelligence Research Center of Novosibirsk State University, Pirogova Street 1, Novosibirsk 630090, Russia.; Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia., Demenkov PS; The Artificial Intelligence Research Center of Novosibirsk State University, Pirogova Street 1, Novosibirsk 630090, Russia.; Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia., Ivanisenko VA; The Artificial Intelligence Research Center of Novosibirsk State University, Pirogova Street 1, Novosibirsk 630090, Russia.; Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia. |
| Abstrakt: |
The rapid growth of biomedical literature makes it challenging for researchers to stay current. Integrating knowledge from various sources is crucial for studying complex biological systems. Traditional text-mining methods often have limited accuracy because they don't capture semantic and contextual nuances. Deep-learning models can be computationally expensive and typically have low interpretability, though efforts in explainable AI aim to mitigate this. Furthermore, transformer-based models have a tendency to produce false or made-up information-a problem known as hallucination-which is especially prevalent in large language models (LLMs). This study proposes a hybrid approach combining text-mining techniques with graph neural networks (GNNs) and fine-tuned large language models (LLMs) to extend biomedical knowledge graphs and interpret predicted edges based on published literature. An LLM is used to validate predictions and provide explanations. Evaluated on a corpus of experimentally confirmed protein interactions, the approach achieved a Matthews correlation coefficient (MCC) of 0.772. Applied to insomnia, the approach identified 25 interactions between 32 human proteins absent in known knowledge bases, including regulatory interactions between MAOA and 5-HT2C, binding between ADAM22 and 14-3-3 proteins, which is implicated in neurological diseases, and a circadian regulatory loop involving RORB and NR1D1. The hybrid GNN-LLM method analyzes biomedical literature efficiency to uncover potential molecular interactions for complex disorders. It can accelerate therapeutic target discovery by focusing expert verification on the most relevant automatically extracted information. |
