run-research

name	run-research
description	Multi-session research workflow: compose logbooks, experiment issues, documentation updates, and snapshot discipline for long-running investigations.

Skill: Agent-Directed Research

Use this for long-running research where an agent iterates on benchmarks, experiments, and hypotheses over multiple sessions. Domain skills such as add-pallas-kernel may add constraints.

General Principle: Open Development

Long-lived work should leave a durable record: a logbook, coordinating issue updates, and enough commands/config to reproduce results. Do not publish secrets or private work the user asks to hold back.

Subskills

• .agents/skills/background-research/SKILL.md for prior-work foraging, source ledgers, contradiction passes, and ranked hypothesis candidates.
• .agents/skills/task-logbook/SKILL.md for logbooks and issue updates.
• .agents/skills/wandb-reporting/SKILL.md for W&B project selection, run naming, report links, and artifact hygiene.
• .agents/skills/task-snapshot/SKILL.md for commit/tag snapshots and stable artifact links.
• .agents/skills/update-docs/SKILL.md for updating durable docs, runbooks, reports, or skill guidance when research changes behavior or practice.

Layer domain skills on top for task-specific constraints.

Core Artifacts

1. A GitHub experiment issue. Agent-created experiment issues use the experiment and agent-generated labels.
2. A logbook at .agents/logbooks/<topic>.md.
3. A living hypothesis queue in the logbook, derived from append-only entries and updated as hypotheses are proposed, blocked, falsified, or promoted.
4. A long-lived branch, for example research/<topic> or research/<user>/<issue>-<topic>, with the logbook, research code, configs, small artifacts, and test harnesses needed to reproduce results.
5. One or more commit or tag snapshots for meaningful milestones.
6. Often a "production" branch that gets PR'd and merged.

Research Logbook

Use the term logbook consistently. Follow .agents/skills/task-logbook for formatting and issue-update rules.

Branches

Use a research branch for the logbook, one-off scripts, harnesses, and small artifacts. Extract a clean production branch only when the final code/docs shape is clear.

Standard Workflow

1. Prologue

1. Create or switch to a long-lived research branch. You may already be on one, or the user may have requested a specific branch name. Otherwise, pick a descriptive name like research/<topic> or research/<user>/<issue>-<topic>.
2. Create an experiment issue with file-issue unless scope or visibility needs human confirmation. If the user provides one, use it.
3. Start the logbook and link both ways: logbook to issue URL, issue body to logbook path. See the skill.
4. Pick a short experiment ID prefix for the series, for example MOE-HC-001, and use IDs like MOE-HC-001 in logbook entries, run names, and issue comments.
5. Pick a set of tags to use for all experiments, to be used with W&B, etc. Typically this is the ID prefix (without the number), the issue number, and anything else reasonable. Try to keep to 2-4 shared tags. You may use more tags to distinguish runs within a project as useful.
6. Record, as applicable: motivation, problem statement, context, success metrics, the initial hypothesis queue, first experiment matrix, relevant code paths, references, stop criteria, and the fixed baseline case for repeated comparison.

2. Research Loop

1. Forage: gather prior work and local context.
2. Propose: update the living hypothesis queue and pick the next test.
3. Run: implement the smallest useful experiment and collect evidence.
4. Interpret: compare against baseline, decide confidence, and update the logbook.
5. Promote: move only interesting, decision-relevant claims up the issue funnel.
6. Seal: snapshot durable results or extract production work.

Every cycle should leave the durable record better than it found it.

2.1 Forage: Background Research

Use background-research at the beginning, after a significant change of direction, or whenever you hit a wall. Assume medium or low effort unless the decision is expensive.

Use the background-research output to update the logbook's hypothesis queue: add new candidates, revise weak ones, mark known dead ends, and promote well-supported ideas into the next experiment matrix. Let background-research and task-logbook decide what belongs in the issue versus the logbook.

2.2 Propose / Run / Interpret: Dev Work and Experiments

For research-branch dev work, optimize for learning speed while preserving operational security and cost controls. Ad-hoc scripts, temporary config knobs, and copy/paste are acceptable there. Production-facing code keeps the usual AGENTS.md quality bar.

For each non-trivial experiment:

1. Do the dev work needed for the experiment.
2. Run the benchmark or experiment. Use babysit-job for long-lived runs.
3. Append exact commands, config, key outputs, interpretation, and next decision to the logbook. Follow task-logbook for issue updates.
4. Push dense scalar series, plots, or raw artifacts to W&B or another store when they are too large for issue comments.

3. Epilogue: Seal

Sealing should ordinarily only happen if the user requests it or the research has reached the defined goal.

1. Update the issue body with the final TL;DR, conclusion, decision log, and negative-results index. Again, follow the task-logbook skill.
2. Add a final issue comment covering what worked, what did not, confidence level, limitations, and ordered next steps.
3. Use update-docs when behavior, operational practice, reusable guidance, or durable research findings changed.
4. Ensure the final logbook entry and snapshot links are present.
5. Close the issue when the research thread is complete.

If the research produced useful production changes, extract them into a clean branch that can link to the logbook but does not include it. Follow standard Marin development practices on that branch.

Before closing the issue:

• Final TL;DR is current.
• Issue body includes a clear Conclusion.
• Next steps are listed.
• Final snapshot is linked.
• If there's a final production PR, link to it from the issue summary.

Practical Rules

• Prefer short-lived code changes unless a persistent harness is clearly useful.
• Keep benchmark harnesses configurable and minimal.
• Record exact command lines for every headline number.
• Treat failures and negative results as first-class data. Record dead ends and excessive hyperparameter sensitivity; skip routine bugs or undertuning.

See Also

• .agents/skills/organize-experiments/
• .agents/skills/add-pallas-kernel/
• .agents/skills/task-logbook/
• .agents/skills/update-docs/