Document details

Development of an intelligent agent for knowledge extraction in the pathogens in foods (PIF) database with machine learning

Author(s): Silva, Lucas Ribeiro

Date: 2025

Persistent ID: http://hdl.handle.net/10198/35625

Origin: Biblioteca Digital da UPB

Subject(s): Natural language interface; Small language models; Food safety; Meta-analysis; Data visualization; Tool-using agents


Description

Scientific databases like the Pathogens in Foods (PIF) Database hold valuable public health data but are often inaccessible to experts lacking programming skills. This research addresses this gap by developing and evaluating a novel Visual Natural Language Interface (V-NLI) for the PIF database. The resulting PIF Intelligent Agent empowers users to perform complex queries, conduct meta-analyses, and generate dynamic reports using natural language. The agent uses a hybrid, dual-mode architecture separating language interpretation from statistical computation. An "Open Chat Mode" offers a flexible exploratory interface via a tool-calling Small Language Model (SLM) with Retrieval-Augmented Generation (RAG). A "Guided Meta-Analysis Mode" provides a structured workflow for generating reproducible scientific reports through a dedicated Rserver backend. A comprehensive evaluation benchmarked five SLMs: Phi-4 Mini (3.8B), MFDoom/deepseek-r1-tool-calling (14B), Cogito (14B), Qwen 3 (8B), and Gemini 2.5 Pro. While all models achieved flawless functional accuracy, their effectiveness was determined by interpretive quality. The ability to generate concise, factually coherent text was the key differentiator, with smaller, instruction-tuned models showing performance comparable or superior in conciseness to larger models. The end-to-end system proved highly reliable, validating the architecture and establishing interpretive fidelity as a critical benchmark for domain-specific agents.

Document Type Master thesis
Language English
Contributor(s) Biblioteca Digital da UPB; Alves, Paulo; Cadavez, Vasco
CC Licence
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