Positioning manuscripts in the scientific landscape with agentic AI

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.

Scientific publication is still organized primarily around static manuscripts, even though much of scientific progress depends on tacit know-how: how to run code, reproduce figures, interpret edge cases, choose useful follow-up directions, and avoid failed paths. Large language model agents create an opportunity to publish not only knowledge, but also operational know-how in a form that future readers and researchers can directly use. This paper outlines the Agentic Publication Protocol (APP), a lightweight repository format for packaging a paper together with code, data, environment information, reproducibility instructions, and an agent-facing instruction file. APP treats a version-controlled repository as the publication object and uses AGENTS.md and optional skills to define a paper agent that can explain the work, reproduce key results when possible, and support follow-up research. We describe the design principles and details of the protocol, as well as the agent skills useful for publishing papers under the protocol. We also describe development tools for evaluating and improving the protocol and associated agent skills. Finally, we provide a broader discussion of the future of scientific research in the agent era.

While recent advances in large language models have enabled end-to-end automated manuscript generation, existing systems suffer from three critical deficiencies: (i) generated claims are not deterministically grounded in verifiable literature, (ii) experimental results are frequently fabricated rather than executed, and (iii) there exists no standardized, multi-dimensional framework to assess whether AI-generated manuscripts meet the quality and rigor required for real-world publication. We present Prompt-to-Paper, a multi-agent framework that directly addresses this evaluation gap through three integrated innovations. First, a deterministic retrieval-augmented generation pipeline with section-aware relevance scoring and snowball citation expansion grounds every claim in a verifiable corpus of 60--100 papers. Second, an autonomous coding agent executes real computational biology experiments replacing synthetic outputs with genuine numerical results. Third, an eight-dimensional automated quality scorer, benchmarked with approximate reference statistics from published papers and augmented with explicit hallucination penalties, provides standardized, reproducible quality assessments. The quality-driven improvement loop uses a context-rich reviser that routes each iteration to one of three researcher actions and fires a deep research cycle every ten iterations to re-run experiments and re-manuscript from stronger outputs. We validate the system on five bioinformatics case studies; all five cases compiled submission-formatted PDFs with zero out-of-range citations. The improvement loop raises manuscript quality by an average of +17.96 points on a 0--100 scale (maximum +26.04. As partial external checks, a human reviewer scored the five manuscripts at an average of 7.0 out of 10. Complete manuscripts are produced at approximately 0.31 USD per paper.