How Do LLMs Encode Scientific Quality? An Empirical Study Using Monosemantic Features from Sparse Autoencoders

Advances in large language models (LLMs) are rapidly transforming scientific work, yet empirical evidence on how these systems reshape research activities remains limited. We report a mixed-methods pilot evaluation of an AI-orchestrated research workflow in which a human researcher coordinated multiple LLM-based agents to perform data extraction, corpus construction, artifact generation, and artifact evaluation. Using the generation and assessment of multiple-choice questions (MCQs) as a testbed, we collected 1,071 SAT Math MCQs and employed LLM agents to extract questions from PDFs, retrieve and convert open textbooks into structured representations, align each MCQ with relevant textbook content, generate new MCQs under specified difficulty and cognitive levels, and evaluate both original and generated MCQs using a 24-criterion quality framework. Across all evaluations, average MCQ quality was high. However, criterion-level analysis and equivalence testing show that generated MCQs are not fully comparable to expert-vetted baseline questions. Strict similarity (24/24 criteria equivalent) was never achieved. Persistent gaps concentrated in skill\ depth, cognitive engagement, difficulty calibration, and metadata alignment, while surface-level qualities, such as {grammar fluency}, {clarity options}, {no duplicates}, were consistently strong. Beyond MCQ outcomes, the study documents a labor shift. The researcher's work moved from authoring items'' toward {specification, orchestration, verification}, and {governance}. Formalizing constraints, designing rubrics, building validation loops, recovering from tool failures, and auditing provenance constituted the primary activities. We discuss implications for the future of scientific work, including emerging AI research operations'' skills required for AI-empowered research pipelines.

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.

Large Language Models (LLMs) are increasingly used to brainstorm and evaluate research ideas, yet assessing such judgments is fundamentally difficult because the true impact of a new idea may take years to emerge. We address this challenge by using the impact forecasting of human-authored manuscripts as a verifiable proxy task. In a prospective forecasting study, we find that frontier LLMs fail to reliably distinguish high-impact papers from ordinary publications, suggesting that static text-based judging is insufficient for scientific evaluation. To address this limitation, we propose $\textbf{FAME}$ ($\underline{\text{F}}$orecasting $\underline{\text{A}}$cademic Impact via Continuous-Time $\underline{\text{M}}$anifold $\underline{\text{E}}$volution), a spatiotemporal framework for modeling the dynamic trajectories of scientific topics. FAME projects papers into a dynamic latent space informed by textual features and a verified knowledge-flow graph, learning geometric constraints that align impactful manuscripts with the forward momentum of their fields. Experiments on 3,200 arXiv papers across three fast-evolving subfields show that FAME consistently and substantially outperforms state-of-the-art LLM evaluators in prospective multidimensional impact forecasting. Furthermore, integrating FAME's dynamic geometric signals into LLMs significantly improves their forecasting performance. These results support manuscript impact forecasting as a useful, measurable proxy benchmark and position FAME as a strong, trajectory-aware foundation for automated scientific evaluation.