Automated MCQA Benchmarking at Scale: Evaluating Reasoning Traces as Retrieval Sources for Domain Adaptation of Small Language Models

As scientific knowledge grows at an unprecedented pace, evaluation benchmarks must evolve to reflect new discoveries and ensure language models are tested on current, diverse literature. We propose a scalable, modular framework for generating multiple-choice question-answering (MCQA) benchmarks directly from large corpora of scientific papers. Our pipeline automates every stage of MCQA creation, including PDF parsing, semantic chunking, question generation, and model evaluation. As a case study, we generate more than 16,000 MCQs from 22,000 open-access articles in radiation and cancer biology. We then evaluate a suite of small language models (1.1B-14B parameters) on these questions, comparing baseline accuracy with retrieval-augmented generation (RAG) from paper-derived semantic chunks and from reasoning traces distilled from GPT-4.1. We find that reasoning-trace retrieval consistently improves performance on both synthetic and expert-annotated benchmarks, enabling several small models to surpass GPT-4 on the 2023 Astro Radiation and Cancer Biology exam.