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arxiv: 2606.27386 · v1 · pith:W4ZJVY6Knew · submitted 2026-06-15 · 💻 cs.DL · cs.AI

Agentic Publication Protocol: An Attempt to Modernize Scientific Publication

Sirui Lu , Xiao-Liang Qi This is my paper

Pith reviewed 2026-06-29 01:54 UTC · model grok-4.3

classification 💻 cs.DL cs.AI
keywords agentic publicationscientific publishingLLM agentsreproducibilityrepository formatresearch agentstacit knowledgeversion control
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The pith

A protocol packages scientific papers as version-controlled repositories so AI agents can explain results, reproduce experiments, and guide follow-up research.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper outlines the Agentic Publication Protocol as a way to move beyond static manuscripts that omit much of the practical knowledge needed to work with a result. Under the protocol a repository becomes the published object and includes an AGENTS.md file that tells an AI agent how to describe the work, run the code, and suggest next steps. The authors argue this format can preserve tacit know-how such as implementation choices and failed paths that current papers leave out. If the approach works, readers could interact with published work through agents rather than reading alone, lowering the barrier to reproduction and extension.

Core claim

The Agentic Publication Protocol treats a version-controlled repository as the publication object and uses an AGENTS.md file together with optional skills to define a paper agent that can explain the work, reproduce key results when possible, and support follow-up research.

What carries the argument

The AGENTS.md file that defines the paper agent and its interaction skills for explanation and reproduction.

If this is right

  • Published work becomes executable by agents without requiring readers to reconstruct missing details from the text alone.
  • Tacit decisions about code, data handling, and edge cases get recorded in a form agents can use directly.
  • Follow-up experiments can start from the same agent instructions rather than from a fresh reading of the manuscript.
  • Reproducibility checks can be run by agents against the same repository format used for publication.
  • Evaluation of a paper can include measuring how well its defined agent performs the listed tasks.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • Preprint servers could automatically generate or validate AGENTS.md files for new submissions.
  • Citation practices might shift toward crediting both the original repository and successful agent reproductions.
  • Training data for future agents could be drawn from successful interactions recorded under this protocol.
  • Review processes could incorporate automated checks of whether an agent's reproduction matches the claimed results.

Load-bearing premise

Current large language model agents can interpret AGENTS.md files and associated artifacts well enough to perform explanation, reproduction, and research-support tasks with little extra human help.

What would settle it

A test in which independent agents given only an APP-formatted repository are asked to reproduce the paper's main results and either succeed at rates comparable to human readers or fail systematically on the same steps.

Figures

Figures reproduced from arXiv: 2606.27386 by Sirui Lu, Xiao-Liang Qi.

Figure 1
Figure 1. Figure 1: Repository structure of an APP publication. The repository contains the paper, human-facing [PITH_FULL_IMAGE:figures/full_fig_p004_1.png] view at source ↗
Figure 2
Figure 2. Figure 2: Publication workflow supported by APP skills. (a) Overall workflow from a working paper repository [PITH_FULL_IMAGE:figures/full_fig_p005_2.png] view at source ↗
Figure 3
Figure 3. Figure 3: Automatic APP evaluation and improvement workflow. Development skills first help find suitable [PITH_FULL_IMAGE:figures/full_fig_p008_3.png] view at source ↗
Figure 4
Figure 4. Figure 4: Average compare-app aspect scores over the 11 public papers. corresponding skills. For example, a researcher interested in publishing a paper in APP can build the paper agent by herself, or with the publish-paper workflow, and evaluate it using the development skills provided here. We expect researchers in different fields to develop different approaches to building APP publications that can explore the fu… view at source ↗
Figure 5
Figure 5. Figure 5: Schematic illustration of the qualitative change in the research network introduced by agentification. [PITH_FULL_IMAGE:figures/full_fig_p012_5.png] view at source ↗
read the original abstract

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 \texttt{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.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

2 major / 1 minor

Summary. The manuscript proposes the Agentic Publication Protocol (APP), a lightweight repository-based publication format that packages a paper with code, data, environment specifications, reproducibility instructions, and an AGENTS.md file (plus optional skills) so that LLM-based paper agents can explain the work, reproduce key results when feasible, and support follow-up research. It outlines design principles, protocol details, relevant agent skills, development tools for evaluating and improving the protocol, and a broader discussion of scientific research in the agent era.

Significance. If the protocol can be shown to work reliably, it would offer a concrete mechanism for publishing operational scientific know-how alongside static manuscripts, potentially improving reproducibility and enabling automated agents to build directly on published artifacts. The design is timely and provides a structured approach to agent-paper interaction that could influence future standards in digital libraries and reproducible research.

major comments (2)
  1. [Abstract] Abstract: The central claim that APP enables a paper agent to 'explain the work, reproduce key results when possible, and support follow-up research' with the AGENTS.md format rests on the untested assumption that current or near-future LLM agents can interpret these artifacts and execute the tasks with minimal additional human effort; no implementation, benchmark, or error analysis is supplied to support this.
  2. [Section describing development tools] Section describing development tools: Although the manuscript states that it describes 'development tools for evaluating and improving the protocol and associated agent skills,' no actual evaluation results, benchmarks, or demonstrations of agent performance on APP-formatted repositories are reported, leaving the feasibility of the protocol unverified.
minor comments (1)
  1. Including a concrete example of an AGENTS.md file (perhaps in an appendix) would make the protocol specification more actionable for readers.

Simulated Author's Rebuttal

2 responses · 0 unresolved

We thank the referee for the constructive comments on our manuscript proposing the Agentic Publication Protocol. The report correctly identifies that the work is a conceptual proposal without accompanying empirical evaluations. We address each major comment below and indicate the revisions we will make.

read point-by-point responses

  1. Referee: [Abstract] The central claim that APP enables a paper agent to 'explain the work, reproduce key results when possible, and support follow-up research' with the AGENTS.md format rests on the untested assumption that current or near-future LLM agents can interpret these artifacts and execute the tasks with minimal additional human effort; no implementation, benchmark, or error analysis is supplied to support this.

    Authors: We agree that the manuscript advances a proposed format whose practical effectiveness with LLM agents remains untested. The abstract describes intended capabilities rather than demonstrated performance. We will revise the abstract to state explicitly that APP is a proposed protocol and that validation through implementations and benchmarks is left for future work. revision: yes

  2. Referee: [Section describing development tools] Although the manuscript states that it describes 'development tools for evaluating and improving the protocol and associated agent skills,' no actual evaluation results, benchmarks, or demonstrations of agent performance on APP-formatted repositories are reported, leaving the feasibility of the protocol unverified.

    Authors: The section outlines the intended design of evaluation tools but does not report results, as the paper's scope is the definition of the protocol rather than its empirical assessment. We will revise the section to clarify that the tools are proposed for subsequent evaluation efforts and that no performance data or demonstrations are included in the current manuscript. revision: yes

Circularity Check

0 steps flagged

No circularity: standalone design proposal with no derivations or self-referential claims

full rationale

The manuscript is a design document proposing the Agentic Publication Protocol (APP) as a repository format using AGENTS.md and skills. It contains no equations, fitted parameters, predictions, or load-bearing self-citations. The central claim is a definitional proposal whose utility depends on external assumptions about future LLM agents, but this is not circularity within the paper's own chain. No steps reduce to inputs by construction.

Axiom & Free-Parameter Ledger

0 free parameters · 1 axioms · 2 invented entities

The proposal rests on the untested assumption that LLM agents can reliably act on the provided files and introduces new entities without independent evidence of their effectiveness.

axioms (1)
  • domain assumption LLM agents can be effectively instructed via structured files to perform scientific tasks such as result explanation and reproduction.
    This capability is presupposed for the protocol to deliver its intended benefits.
invented entities (2)
  • AGENTS.md file no independent evidence
    purpose: Define instructions for a paper-specific agent
    New file format and convention introduced by the protocol.
  • Agentic Publication Protocol (APP) no independent evidence
    purpose: Standardized repository format for agent-accessible publications
    Core new construct proposed in the paper.

pith-pipeline@v0.9.1-grok · 5717 in / 1184 out tokens · 25788 ms · 2026-06-29T01:54:52.810153+00:00 · methodology

discussion (0)

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Reference graph

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