AquiLLM: Evaluating Faithfulness in Open-Weight RAG-LLM Systems for Scientific Research
Authors: Bernie Boscoe, Srinath Saikrishnan, Vikram Seenivasan, Jack Stark, Andrew Lizarraga, Morgan Himes, Jonathan Soriano, PJ Allen, +1 more
Organizations: Dept. of Computer Science, Southern Oregon University, USA · Dept. of Computer Science, University of California, Los Angeles, USA · Dept. of Physics & Astronomy, University of California, Los Angeles, USA · Dept. of Statistics, University of California, Los Angeles, USA
Scientific research increasingly relies on large, heterogeneous data sources, motivating interest in retrieval-augmented generation (RAG) systems that provide natural language access to scientific knowledge and research workflows. Researchers are exploring the viability of these systems as natural language interfaces for document search and for generating analysis code and pipeline components. At the same time, concerns about data privacy and control over research infrastructure have motivated interest in open-weight models and open-source deployments hosted within research institutions. In astronomy, this development follows a long history of computational infrastructure development, from archival databases and Structured Query Language (SQL)-based systems to large language model (LLM)-assisted research tools. This paper presents a domain-expert evaluation of faithfulness for AquiLLM, an open-weight, offline RAG-LLM platform designed to support scientific research groups in the use and preservation of tacit and formal knowledge. We define faithfulness as the extent to which generated responses remain grounded in retrieved scientific context without unsupported claims or omissions. We report results from an astronomy case study evaluating AquiLLM across retrieval and scientific analysis tasks. AquiLLM performs most reliably on explicit retrieval-oriented questions grounded in the RAG collection, while faithfulness degrades for queries requiring synthesis or ambiguity resolution. These results highlight both the promise and limitations of open-weight RAG-LLM systems for scientific research and demonstrate the importance of domain-expert evaluation beyond standard benchmark leaderboards.
Recent advances in retrieval-augmented generation (RAG) and large language models (LLMs) enable researchers to integrate AI into scientific workflows. However, using proprietary commercial AI systems raises concerns about transparency, reproducibility and privacy, which are essential for scientific practices. To this end, AquiLLM was developed as an open-source modular RAG-LLM framework using open-weight models, designed to support research groups in capturing tacit knowledge. In this work, we present a series of architectural improvements and feature enhancements to AquiLLM, including local embedding and reranking, multimodal capabilities, OpenAI-compatible inference interfaces, user interface improvements, semantic and episodic memory capabilities, and skills support. These enhancements were informed by discussions with domain experts, including astrophysicists and environmental researchers, and represent a step toward AI systems more closely aligned with scientific research practices.
Jack Stark, Srinath Saikrishnan, Vikram Seenivasan +3
Large language models (LLMs) demonstrate strong performance in natural language processing but often generate factual errors when relying solely on parametric knowledge. Retrieval-Augmented Generation (RAG) mitigates these errors by grounding responses in external evidence, yet conventional retrieve-and-dump approaches frequently introduce irrelevant context that degrades answer quality. In this work, we present AstroRAG -- a PageRank-based retrieval-augmented generation (RAG) pipeline adapted for question answering in astronomy. The system performs token-aware chunking and per-instance, ephemeral indexing in Elasticsearch, then executes a two-stage retrieval: (i) Maximal Marginal Relevance (MMR) to obtain a small, diverse candidate set and (ii) a reader-driven PageRank (PR) re-ranking on a similarity graph to identify a compact, mutually supportive context under a strict token budget. Our design is training-free, privacy-preserving, and reproducible, as each instance is processed through transient indexing to prevent cross-task leakage. We evaluate the pipeline on the AstroQA benchmark for astronomy QA, and demonstrate competitive performance across all difficulty levels. In particular, the RAG-enhanced Mistral-7B achieves \textbf{79.49% accuracy} and \textbf{79.49% F1-score}, nearly doubling the performance of its non-RAG counterpart. These results highlight the effectiveness of disciplined retrieval and refinement in boosting domain-specific reasoning, establishing a robust foundation for extending RAG to other scientific fields.
LLM systems for scientific discovery increasingly assist with ideation, literature synthesis, experiment planning, and report generation, but the first research question they propose can remain difficult to audit: it may sound plausible without exposing the mechanism, falsifier, or assumption that a scientist should inspect. We introduce FirstResearch, a first-principles research-question formation framework for scientific LLM agents whose core artifact is a structured Research Question Certificate. The certificate records primitive definitions, assumptions, a mechanism model, a tension or contradiction, a falsifiable hypothesis, a minimal decisive test, and a failure update rule, making the proposed question inspectable before downstream execution. On ten LLM-agent research topics, FirstResearch outperforms controlled prompt-level baselines inspired by AI co-scientist, Agent Laboratory, and AI Scientist-v2 under a primary DeepSeek-blind-judge protocol. A Gemini-2.5-Flash independent-judge rescore of the same 40 baseline packages preserves the system-level ranking, with FirstResearch scoring 4.86/5 versus 4.38/5 for the strongest baseline and Pearson agreement of 0.865 on average score. A one-repeat ablation checkpoint further suggests that the certificate-centered core is the strongest component: certificate-only scoring reaches 4.90/5 under DeepSeek and 4.88/5 under Gemini, while removing certificates drops below 1/5 under both judges. These results are preliminary and use LLM judges rather than human domain experts, but they support a narrow scientific-discovery claim: explicit derivation constraints are a promising mechanism for making LLM-generated scientific questions more auditable. Code, prompts, saved outputs, and reproduction scripts are available at https://github.com/louiswang524/FirstResearch.