Hypothesis-Driven Deep Research with Large Language Models: A Structured Methodology for Automated Knowledge Discovery

TL;DR

This paper introduces HDRI, a novel hypothesis-driven methodology for organizing and automating deep research using large language models, transforming traditional search paradigms into proactive knowledge discovery.

Contribution

It presents the first framework that uses hypotheses to structure general-purpose deep research across domains, with innovative mechanisms for gap detection and iterative investigation.

Findings

Improved fact density by 22.4%

Achieved 90% subject matching accuracy

Attained 0.92 multi-source verification confidence

Abstract

Current AI-powered research systems adopt a direct search-then-summarize paradigm that treats hypotheses as end products of scientific discovery. We argue this leaves a critical gap: hypotheses can serve a far more powerful role as organizational instruments that structure the research process itself. We propose the Hypothesis-Driven Deep Research (HDRI) methodology - the first framework using hypotheses to organize general-purpose deep research across arbitrary domains, rather than merely validating claims within specific domains. This transforms research from reactive information retrieval into proactive, verifiable, and iterative knowledge discovery. HDRI is formalized with six core principles and an eight-stage pipeline. A central innovation is the gap-driven iterative research mechanism - a closed-loop quality assurance system that automatically identifies informational and logical gaps, triggering targeted supplementary investigation. We further introduce a fact reasoning framework with traceable reasoning chains and quantified confidence propagation, a subject locking mechanism to prevent entity confusion, and a multi-dimensional quality assessment scheme. The methodology is realized in the INFOMINER system. Experiments demonstrate improvements of 22.4% in fact density, 90% subject matching accuracy, 0.92 multi-source verification confidence, and 14% completeness gain from gap-driven supplementation. Five case studies validate its practical applicability, achieving an average quality rating of 4.46/5.0.