AIPOCH Open-Science: An Open-Source AI Research Workbench with Reproducible .science Packages

AI co-scientists could accelerate computational research, but over a long-running study the workflow also has to stay inspectable, resumable and reproducible, which requires persistent computational state and provenance. Here we present OpenAI4S, an open-source scientific research agent built around the principle of Code as Action, Science as Sessions. OpenAI4S combines a persistent computing runtime with research-session management: orchestration is handled through structured tool calls, while scientific actions are represented as complete code cells executed in persistent Python and R kernels. An append-only Action Ledger, per-cell execution records, versioned artifacts, environment records, and workspace checkpoints preserve how results were produced and support session recovery, branching, and extension. Configurable sandboxing, permission controls, and code and trajectory screening provide complementary safeguards. We evaluate OpenAI4S on 36 research scenarios spanning retrosynthesis, molecular dynamics, protein binder design, protein mutation, catalyst screening, and mineral spectroscopy, measuring scientific task accuracy, workflow completeness, and reproducibility of the resulting repositories. OpenAI4S achieves an overall score of 7.83, compared with 5.7--6.4 for a general-purpose coding harness evaluated with three frontier models, with the largest gains on long-horizon and computation-intensive workflows. These results suggest that integrating persistent execution with session-level provenance can improve the reliability of AI-assisted scientific workflows. Environment specification and full rerunnability remain weak for every evaluated system, ours included, so reproducibility is still an open problem for scientific agents. The system is available under the MIT license at github.com/PKU-YuanGroup/OpenAI4S.

F(AI)2R is FAIR research with AI in the loop, twice: an AI-assisted authoring pass and a machine-readable audit pass over every artefact. AI systems now draft, refactor, and verify research artefacts, yet their contributions are rarely recorded in a form a later human or machine can audit. Building on the original F(AI)2R experiment, we generalize its provenance model beyond scholarly writing into aiprov, a PROV-O extension covering any AI-in-the-loop artefact, and we package the method as an executable skill that an AI agent operates itself: setup asks the human operator for their ORCID ID, resolves their identity from the public registry, and scaffolds continuous integration that gates every push on graph conformance and publishes the current build of this very paper. The paper is its own case study. Every activity, claim, and source in its production is recorded in the repository's provenance graph under two invariants: no parentless claim, and verification rungs that only humans may grant.

AI-assisted research compresses ideation, implementation, evaluation, and manuscript writing into a single interactive loop. This compression is useful, but it also creates a publication risk: paper claims can become easier to state than to audit. We present ResearchLoop, an evidence-gated control plane for AI-assisted computational research. ResearchLoop treats research questions, task contracts, evidence objects, claim ledgers, closeouts, and paper bindings as durable project state, realized here as a repository-backed runtime. This technical report provides the complete protocol specification, state model, transition rules, claim-admission algorithm, and insight-compounding mechanism. It also reports the full experimental record spanning nine versions (V0--V9), including a self-hosting case study, a controlled task-suite study with component ablations, a mathematical olympiad evaluation, and a supplementary SciCode boundary experiment evaluated with the official generated-code harness. All artifacts, manifests, and verification reports are preserved in the project repository.