miRKatAI: An Integrated Database and Multi-agent AI system for microRNA Research

TL;DR

miRKatAI is a multi-agent AI system integrated with a comprehensive miRNA database, designed to facilitate microRNA research through natural language queries, data visualization, and hypothesis support.

Contribution

The paper introduces the miRKat Suite, combining a curated miRNA database with an AI-powered query system using large language models and graph-based reasoning.

Findings

Provides a unified resource for miR-target interactions

Enables complex natural language queries about miRs

Supports data visualization and hypothesis generation

Abstract

MicroRNAs (miRs) are robust regulators of gene expression, implicated in most biological processes. microRNAs predominantly downregulate the expression of genes post-transcriptionally and each miR is predicted to target several hundred genes. The accurate identification and annotation of miR-mRNA target interactions is central to understanding miRs function and their therapeutic potential. However, computational target prediction is challenging due to imperfect complementarity of miRs with their targets and the growing volume and heterogeneity of experimental data present challenges in accessing, integrating, and analysing miR-target interaction information across biological contexts. This creates a need for integrated resources and intelligent query tools. We present the miRKat Suite, comprising miRKatDB, a comprehensive, curated database of predicted and validated miR-target interactions and associated annotations, and miRKatAI, a multi-agent system powered by large language models (LLMs) and LangGraph. miRKatDB integrates data from multiple publicly available sources, providing a comprehensive foundation for miR studies, including miR target genes and changes in levels of tissue expression previously reported. miRKatAI offers a natural language interface for complex querying of miRKatDB, facilitates grounded information retrieval from established sources in the field, and supports basic data visualisation. The miRKat Suite aims to accelerate miR research by streamlining data access, enhancing exploratory analysis, and supporting hypothesis generation.