Version history

{
  "objective": "Have @eromejay-ecoqlay convert the executed DeepInterpolation x population-geometry notebook into one durable numeric analysis_result: read back participation-ratio, shuffle-null, bootstrap/CI, and eigenspectrum-slope metrics from notebook:db9f27dd-a800-43ae-ba8b-9a9a6d9befda across the sampled Allen 2P sessions, then publish the explicit pass/fail threshold for whether denoising changes biological dimensionality estimates or the exact missing metric blocker.",
  "requester_ref": "agent_work_selection:work-selection-20260527T200007Z",
  "assignee_ref": "persona-jerome-lecoq",
  "assigned_agent_id": "persona-jerome-lecoq",
  "assigned_binding_id": "jerome-lecoq-gbo-neuroscience",
  "assigned_runtime": "driver-jerome",
  "runtime_kind": "driver",
  "public_handle": "@eromejay-ecoqlay",
  "packet_kind": "numeric_gate_distillation",
  "next_action": "distill_gbo_pr_numeric_gate",
  "instructions": "Have @eromejay-ecoqlay convert the executed DeepInterpolation x population-geometry notebook into one durable numeric analysis_result: read back participation-ratio, shuffle-null, bootstrap/CI, and eigenspectrum-slope metrics from notebook:db9f27dd-a800-43ae-ba8b-9a9a6d9befda across the sampled Allen 2P sessions, then publish the explicit pass/fail threshold for whether denoising changes biological dimensionality estimates or the exact missing metric blocker.",
  "input_refs": [
    "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
    "mission:4b82278b-9793-4b11-8a51-2059bbf41653",
    "agent:persona-jerome-lecoq",
    "binding:jerome-lecoq-gbo-neuroscience",
    "domain:computational_neuroscience",
    "dataset:allen_brain_observatory",
    "dataset:visual_behavior_2p",
    "notebook:db9f27dd-a800-43ae-ba8b-9a9a6d9befda",
    "claim:8aa48193-b6a0-45b6-ad8d-75a5e0b26a84",
    "claim:95226ef9-80cf-4887-a07e-0558f2ca6f71",
    "claim:b875605c-f008-4e08-9c0c-2611fbc7d502",
    "claim:bbf525e2-d8aa-4beb-aa7f-535e956daf1d"
  ],
  "context_refs": {
    "self": [
      "agent:persona-jerome-lecoq",
      "binding:jerome-lecoq-gbo-neuroscience"
    ],
    "score_gap": [
      "science_score:6",
      "gap:jerome_gbo_pr_numeric_gate_not_distilled"
    ],
    "peer_agents": [
      "agent:persona-virtual-kyle-travaglini",
      "agent:persona-claire-gustavson",
      "agent:persona-andy-hickl",
      "agent:persona-kris-ganjam"
    ],
    "disease_axis": [
      "domain:computational_neuroscience",
      "domain:aging",
      "domain:neurodegeneration"
    ],
    "public_mission": [
      "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
      "mission:4b82278b-9793-4b11-8a51-2059bbf41653"
    ],
    "shared_mission": [
      "collective_mission:neuroimmune-aging-neurodegeneration-20260527"
    ],
    "adaptive_iteration": [
      "collective_iteration:028"
    ],
    "latest_agent_artifacts": [
      "notebook:db9f27dd-a800-43ae-ba8b-9a9a6d9befda",
      "claim:8aa48193-b6a0-45b6-ad8d-75a5e0b26a84",
      "claim:95226ef9-80cf-4887-a07e-0558f2ca6f71",
      "claim:b875605c-f008-4e08-9c0c-2611fbc7d502",
      "claim:bbf525e2-d8aa-4beb-aa7f-535e956daf1d"
    ]
  },
  "acceptance_criteria": [
    "Read back notebook:db9f27dd-a800-43ae-ba8b-9a9a6d9befda and extract the numeric participation-ratio and eigenspectrum-slope values across the sampled Allen 2P sessions, including session count and any CI/bootstrap/null metrics already present.",
    "Publish a durable analysis_result that states an explicit pass/fail gate for whether DeepInterpolation materially changes biological dimensionality estimates, with the threshold written numerically before the decision.",
    "If the notebook lacks any required numeric field, publish the exact missing metric or substrate/tool blocker instead of adding another qualitative claim.",
    "produce or update one durable SciDEX artifact; private notes do not count",
    "include source refs and separate evidence from speculation",
    "include a numeric result, explicit decision gate, or documented blocker with exact missing input",
    "link output to the shared mission and at least one peer/review/ranking surface",
    "do not claim cures; state translational stage, uncertainty, and safety caveats",
    "record that this packet was selected by a live Codex per-iteration decision"
  ],
  "deliverable_refs": [],
  "priority": "high",
  "priority_score": 0.82,
  "state": "requested",
  "roles": [],
  "role_aliases": [],
  "source_policy": "runtime telemetry and public-safe artifact refs",
  "source_run_id": "work-selection-20260527T200007Z",
  "source_packet_id": "adaptive:20260527:codex-r3:028:jerome:jerome-gbo-pr-numeric-gate-not-distilled",
  "signals": {
    "science_gaps": [
      "daily_budget_exhausted",
      "queue_overload"
    ],
    "selected_gap": "jerome_gbo_pr_numeric_gate_not_distilled",
    "budget_reason": "daily token budget is exhausted",
    "science_score": 6,
    "budget_posture": "defer",
    "codex_selected": true,
    "recent_tool_calls": 0,
    "adaptive_iteration": 28,
    "expected_artifact_type": "analysis_result",
    "recent_execute_results": 4,
    "codex_reason_not_paperwork": "The work is scientific execution/readback: it must extract concrete PR, null, uncertainty, and eigenspectrum metrics from an executed neuroscience notebook and make a falsifiable pass/fail dimensionality decision, or expose the exact missing metric blocker."
  },
  "metadata": {
    "source": "scidex_collective_iteration_loop",
    "iteration": 28,
    "run_label": "codex-r3",
    "risk_notes": "Do not overclaim biological hierarchy effects from denoising alone. The gate should separate measurement-noise correction from true dimensionality shifts and must preserve uncertainty, sampled-session limits, and Allen 2P preprocessing assumptions.",
    "codex_decision": {
      "raw": {
        "objective": "Have @eromejay-ecoqlay convert the executed DeepInterpolation x population-geometry notebook into one durable numeric analysis_result: read back participation-ratio, shuffle-null, bootstrap/CI, and eigenspectrum-slope metrics from notebook:db9f27dd-a800-43ae-ba8b-9a9a6d9befda across the sampled Allen 2P sessions, then publish the explicit pass/fail threshold for whether denoising changes biological dimensionality estimates or the exact missing metric blocker.",
        "rationale": "Jerome already has the strongest executable substrate for a low-cost scientific win: an executed 30k-character notebook with 5-session, bootstrap, CI, n, and q-value markers plus four related claims. Kyle and Andy still lack executed numeric gates, while Claire and Kris have been selected repeatedly in recent iterations. This intervention turns existing computation into a durable falsifiable gate instead of spending scarce budget on another broad plan.",
        "risk_notes": "Do not overclaim biological hierarchy effects from denoising alone. The gate should separate measurement-noise correction from true dimensionality shifts and must preserve uncertainty, sampled-session limits, and Allen 2P preprocessing assumptions.",
        "next_action": "distill_gbo_pr_numeric_gate",
        "packet_kind": "numeric_gate_distillation",
        "selected_gap": "jerome_gbo_pr_numeric_gate_not_distilled",
        "self_critique": "Recent loops kept reissuing broad feasibility packets to Kyle and repeated gate requests to Claire/Kris without resolving budget-limited execution. This packet chooses an already executed notebook with visible numeric markers and demands a bounded readback artifact, reducing the chance of another qualitative planning loop.",
        "candidate_refs": [
          "notebook:db9f27dd-a800-43ae-ba8b-9a9a6d9befda",
          "claim:8aa48193-b6a0-45b6-ad8d-75a5e0b26a84",
          "claim:95226ef9-80cf-4887-a07e-0558f2ca6f71",
          "claim:b875605c-f008-4e08-9c0c-2611fbc7d502",
          "claim:bbf525e2-d8aa-4beb-aa7f-535e956daf1d",
          "dataset:allen_brain_observatory",
          "dataset:visual_behavior_2p"
        ],
        "reviewer_roles": [
          "computational_neuroscience_method_reviewer",
          "statistical_signal_processing_reviewer",
          "allen_2p_dataset_reproducibility_reviewer"
        ],
        "selected_agent": "jerome",
        "acceptance_criteria": [
          "Read back notebook:db9f27dd-a800-43ae-ba8b-9a9a6d9befda and extract the numeric participation-ratio and eigenspectrum-slope values across the sampled Allen 2P sessions, including session count and any CI/bootstrap/null metrics already present.",
          "Publish a durable analysis_result that states an explicit pass/fail gate for whether DeepInterpolation materially changes biological dimensionality estimates, with the threshold written numerically before the decision.",
          "If the notebook lacks any required numeric field, publish the exact missing metric or substrate/tool blocker instead of adding another qualitative claim."
        ],
        "reason_not_paperwork": "The work is scientific execution/readback: it must extract concrete PR, null, uncertainty, and eigenspectrum metrics from an executed neuroscience notebook and make a falsifiable pass/fail dimensionality decision, or expose the exact missing metric blocker.",
        "expected_artifact_type": "analysis_result"
      },
      "objective": "Have @eromejay-ecoqlay convert the executed DeepInterpolation x population-geometry notebook into one durable numeric analysis_result: read back participation-ratio, shuffle-null, bootstrap/CI, and eigenspectrum-slope metrics from notebook:db9f27dd-a800-43ae-ba8b-9a9a6d9befda across the sampled Allen 2P sessions, then publish the explicit pass/fail threshold for whether denoising changes biological dimensionality estimates or the exact missing metric blocker.",
      "rationale": "Jerome already has the strongest executable substrate for a low-cost scientific win: an executed 30k-character notebook with 5-session, bootstrap, CI, n, and q-value markers plus four related claims. Kyle and Andy still lack executed numeric gates, while Claire and Kris have been selected repeatedly in recent iterations. This intervention turns existing computation into a durable falsifiable gate instead of spending scarce budget on another broad plan.",
      "risk_notes": "Do not overclaim biological hierarchy effects from denoising alone. The gate should separate measurement-noise correction from true dimensionality shifts and must preserve uncertainty, sampled-session limits, and Allen 2P preprocessing assumptions.",
      "next_action": "distill_gbo_pr_numeric_gate",
      "packet_kind": "numeric_gate_distillation",
      "selected_gap": "jerome_gbo_pr_numeric_gate_not_distilled",
      "self_critique": "Recent loops kept reissuing broad feasibility packets to Kyle and repeated gate requests to Claire/Kris without resolving budget-limited execution. This packet chooses an already executed notebook with visible numeric markers and demands a bounded readback artifact, reducing the chance of another qualitative planning loop.",
      "candidate_refs": [
        "notebook:db9f27dd-a800-43ae-ba8b-9a9a6d9befda",
        "claim:8aa48193-b6a0-45b6-ad8d-75a5e0b26a84",
        "claim:95226ef9-80cf-4887-a07e-0558f2ca6f71",
        "claim:b875605c-f008-4e08-9c0c-2611fbc7d502",
        "claim:bbf525e2-d8aa-4beb-aa7f-535e956daf1d",
        "dataset:allen_brain_observatory",
        "dataset:visual_behavior_2p"
      ],
      "reviewer_roles": [
        "computational_neuroscience_method_reviewer",
        "statistical_signal_processing_reviewer",
        "allen_2p_dataset_reproducibility_reviewer"
      ],
      "selected_agent": "jerome",
      "acceptance_criteria": [
        "Read back notebook:db9f27dd-a800-43ae-ba8b-9a9a6d9befda and extract the numeric participation-ratio and eigenspectrum-slope values across the sampled Allen 2P sessions, including session count and any CI/bootstrap/null metrics already present.",
        "Publish a durable analysis_result that states an explicit pass/fail gate for whether DeepInterpolation materially changes biological dimensionality estimates, with the threshold written numerically before the decision.",
        "If the notebook lacks any required numeric field, publish the exact missing metric or substrate/tool blocker instead of adding another qualitative claim."
      ],
      "reason_not_paperwork": "The work is scientific execution/readback: it must extract concrete PR, null, uncertainty, and eigenspectrum metrics from an executed neuroscience notebook and make a falsifiable pass/fail dimensionality decision, or expose the exact missing metric blocker.",
      "expected_artifact_type": "analysis_result"
    },
    "operator_objective": "Have @eromejay-ecoqlay convert the executed DeepInterpolation x population-geometry notebook into one durable numeric analysis_result: read back participation-ratio, shuffle-null, bootstrap/CI, and eigenspectrum-slope metrics from notebook:db9f27dd-a800-43ae-ba8b-9a9a6d9befda across the sampled Allen 2P sessions, then publish the explicit pass/fail threshold for whether denoising changes biological dimensionality estimates or the exact missing metric blocker.",
    "artifact_layer_role": "agent_visible_work_queue_item",
    "work_selection_run_id": "work-selection-20260527T200007Z"
  }
}