Agentic Publication Protocol: An Attempt to Modernize Scientific Publication

Scientific publication compresses a branching, iterative research process into a linear narrative, discarding the majority of what was discovered along the way. This compilation imposes two structural costs: a Storytelling Tax, where failed experiments, rejected hypotheses, and the branching exploration process are discarded to fit a linear narrative; and an Engineering Tax, where the gap between reviewer-sufficient prose and agent-sufficient specification leaves critical implementation details unwritten. Tolerable for human readers, these costs become critical when AI agents must understand, reproduce, and extend published work. We introduce the Agent-Native Research Artifact (ARA), a protocol that replaces the narrative paper with a machine-executable research package structured around four layers: scientific logic, executable code with full specifications, an exploration graph that preserves the failures compilation discards, and evidence grounding every claim in raw outputs. Three mechanisms support the ecosystem: a Live Research Manager that captures decisions and dead ends during ordinary development; an ARA Compiler that translates legacy PDFs and repos into ARAs; and an ARA-native review system that automates objective checks so human reviewers can focus on significance, novelty, and taste. On PaperBench and RE-Bench, ARA raises question-answering accuracy from 72.4% to 93.7% and reproduction success from 57.4% to 64.4%. On RE-Bench's five open-ended extension tasks, preserved failure traces in ARA accelerate progress, but can also constrain a capable agent from stepping outside the prior-run box depending on the agent's capabilities. Our code is open-sourced at https://github.com/Orchestra-Research/Agent-Native-Research-Artifact.

Verifiability, attribution, and reproducibility are foundational requirements of scientific knowledge, yet current publishing infrastructure does not enforce them at scale. We introduce Traxia, an agent-native scientific publishing framework in which AI research agents publish verifiable papers, build reputational identities, peer-review one another, and collaborate with humans in a shared provenance model. Traxia treats agents as first-class epistemic participants: every paper carries a reasoning trace, every claim a confidence interval, every agent a cryptographically signed identity, and every collaboration an immutable contribution log. We formalise five components: Agent Identity and Registry, Verifiable Publishing Layer, four-tier Peer Review Protocol, Reputation and Staking Engine, and a Knowledge Graph with contradiction detection. The framework targets reproducibility failure, provenance opacity, and exclusion of Global South research capacity. This paper presents architectural foundations and formal specifications only; it does not report empirical results. Evaluation and deeper component studies will follow in subsequent papers. A prototype partially implements core formalisms; the full system remains under active development.

Recent work has used LLM agents to reproduce empirical social science results with access to both the data and code. We broaden this scope by asking: Can they reproduce results given only a paper's methods description and original data? We develop an agentic reproduction system that extracts structured methods descriptions from papers, runs reimplementations under strict information isolation -- agents never see the original code, results, or paper -- and enables deterministic, cell-level comparison of reproduced outputs to the original results. An error attribution step traces discrepancies through the system chain to identify root causes. Evaluating four agent scaffolds and four LLMs on 48 papers with human-verified reproducibility, we find that agents can largely recover published results, but performance varies substantially between models, scaffolds, and papers. Root cause analysis reveals that failures stem both from agent errors and from underspecification in the papers themselves.