AstroRAG -- A Pagerank-Based Retrieval-Augmented Generation Pipeline for Question Answering in Astronomy

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.

Retrieval-Augmented Generation (RAG) has become the standard way to ground large language models in external knowledge, yet most systems retrieve a fixed number of passages for every question regardless of its difficulty. This wastes computation on easy questions, starves hard ones, and gives no signal for when a generated answer can be trusted. With a growing share of question answering systems built on top of commercial language model APIs, a method that can decide how much to retrieve, and how far to trust its own answers, without retraining the underlying model, is of clear practical value. This paper presents AB-RAG (Adaptive Budgeted Retrieval-Augmented Generation), a training-free and backbone-agnostic framework that generates an answer, estimates its confidence from a combination of three signals, and then decides whether to stop or to retrieve more evidence, subject to a fixed retrieval budget. The estimator combines the model's own certainty, the agreement between the answer and the evidence, and the variance of the retrieval scores. For models that expose token probabilities the certainty signal is read directly; for closed APIs it is approximated by self-consistency, so the method works without access to model internals. Across three backbones and two datasets, the central result is that the confidence estimate reliably separates correct from incorrect answers on every backbone, reaching a clean split of 57.6% against 0% Exact Match between high- and low-confidence answers on a factoid dataset. The adaptive policy improves accuracy on capable backbones, and the study reports its negative and nuanced findings honestly, including a confidence signal that proved unsuitable for short answers and a retrieval signal whose sign was found and corrected through measurement. The entire study was carried out on a single consumer laptop with only a few dollars of API spend.

Retrieval-augmented generation (RAG) improves question answering by grounding large language models (LLMs) in external knowledge such as text corpora. However, its reasoning process remains largely opaque: intermediate reasoning steps are difficult to verify and cannot be reliably attributed to specific evidence. Moreover, missing user-specific context is rarely detected systematically, often leading to incomplete or incorrect output. We propose NeSy-RAG, a modular neuro-symbolic RAG framework that synthesizes attributable Prolog modules from retrieved text chunks. For each chunk, the system generates semantically meaningful predicates that encode Boolean claims, which may depend on user facts. Using joint natural language-code embeddings, predicates are retrieved and composed into Prolog queries. To address incomplete user context, we introduce a symbolic knowledge-gap detection mechanism that identifies missing user facts whose truth values affect the query outcome and automatically triggers follow-up interactions. Executing the resulting Prolog queries yields deterministic answers together with transparent execution traces that link each reasoning step to its originating source. On the ShARC benchmark, without domain-specific training, NeSy-RAG achieves 61.1% accuracy, outperforming a same-model RAG baseline that achieves 42.8% accuracy.