Publish NeuroClaimBench v2.1

CITATION.cff

@@ -0,0 +1,33 @@
+cff-version: 1.2.0
+message: "Please cite the CONFIRM paper when using this benchmark."
+type: dataset
+title: "NeuroClaimBench"
+version: "2.1"
+url: "https://huggingface.co/datasets/stanjsx/NeuroClaimBench"
+license: CC-BY-4.0
+authors:
+  - family-names: Wei
+    given-names: Yuxiang
+  - family-names: Zhu
+    given-names: Lijing
+  - family-names: Lan
+    given-names: Qizhen
+  - family-names: Zhang
+    given-names: Yanteng
+  - family-names: Calhoun
+    given-names: Vince D.
+preferred-citation:
+  type: article
+  title: "CONFIRM: Governing Scientific Reporting for Trustworthy Agentic Neuroimaging"
+  authors:
+    - family-names: Wei
+      given-names: Yuxiang
+    - family-names: Zhu
+      given-names: Lijing
+    - family-names: Lan
+      given-names: Qizhen
+    - family-names: Zhang
+      given-names: Yanteng
+    - family-names: Calhoun
+      given-names: Vince D.
+  url: "https://openreview.net/forum?id=KYE1DzsxWc"

DATA_ACCESS.md

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+# Cohort data and task execution
+
+The metadata package supports inspection and scoring of reporting decisions.
+Executing a frozen task requires its prepared cohort files. Obtain source
+cohort data through the relevant provider or study team under their access
+terms. The CC BY 4.0 license covers this package's metadata and documentation.
+
+## Source cohorts
+
+The task inventory names ABIDE1, ABIDE2, ADHD200, ABCD, ADNI, ADNI_fMRI,
+BSNIP2, COBRE, ChineseSZ, FBIRN, GSP, HCP, HCP_Aging, JH, NACC, OASIS3,
+OASIS3_fMRI, UKB, and OpenNeuro ds000030. It also includes constructed stress
+datasets and evidence partitions derived from those sources.
+
+Use `dataset_id` in `tasks.jsonl` and `provenance` in `cases.jsonl` to identify
+the source of each task. The metadata contains no participant tables,
+participant-level control assignments, or preprocessing outputs.
+
+## Exact benchmark inputs
+
+Each task names its discovery and replication cohorts. Store their prepared
+tables as `<cohort>.parquet`. The runner verifies the file bytes against the
+published SHA-256 hashes before computing results.
+
+| Task type | Required prepared files | Hash field |
+|---|---|---|
+| Task with no `generator_spec`, including fixed stress datasets | Named discovery and replication cohorts | `tasks.jsonl`: `partition_hashes` |
+| Task with a `generator_spec`, including random-label controls | Frozen generated discovery and replication cohorts | `outcomes.jsonl`: `generated_cohort_hashes` |
+
+Place all cohorts for a task together in one directory and pass that
+directory as `--data-root`. Additional `--data-root` arguments search other
+directories. Generator specifications record the construction rules, seeds,
+and assignment hashes; executing these tasks requires the generated tables.
+
+Exact reruns require the original prepared artifacts, including partition
+membership and file serialization. Raw provider downloads require further
+preparation and do not supply those frozen files. Missing or mismatched
+inputs produce explicit error rows. The scorer counts errors as withheld
+and reports them separately in its coverage counts.
+
+## Analyze newly prepared data
+
+Use `confirm run` with a new analysis plan for newly prepared cohorts.
+Prepare one Parquet table per cohort with these columns:
+
+| Column | Content |
+|---|---|
+| `subject_id` | Participant identifier |
+| `cohort` | Cohort name matching the filename |
+| `site` | Acquisition site or scanner batch |
+| `age` | Numeric age |
+| `sex` | `M` or `F` |
+| Imaging measurements | Numeric columns with `smri_`, `pet_`, `fc_`, or `raw_` prefixes |
+
+Include all additional variables named in the plan, such as `eTIV`,
+diagnosis, or behavioral scores. Keep discovery, replication, and holdout
+participants separate. `confirm demo --out outputs/demo` creates complete
+synthetic tables and plans illustrating this format. The CONFIRM source
+package also includes a CSV mapping template and conversion guide.
+
+Report analyses of new cohorts with their own input identities and results.
+The frozen benchmark records describe the published task inputs and outcomes.

DATA_DICTIONARY.md

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+# NeuroClaimBench data dictionary
+
+JSONL files contain one JSON object per line. IDs are stable strings;
+SHA-256 fields identify file contents or serialized records.
+
+## Core records
+
+| File | Records | Contents |
+|---|---:|---|
+| `cases.jsonl` | 544 | Scientific questions, analysis plans, source identities, and record links |
+| `references.jsonl` | 544 | Reference labels, evidence basis, agreement, and scoring eligibility |
+| `tasks.jsonl` | 489 | Executable plans and identities of their prepared input cohorts |
+| `outcomes.jsonl` | 489 | Recorded CONFIRM gate results and execution status |
+
+### Cases
+
+- `benchmark_case_id` identifies the case; `claim_uid` identifies its claim.
+- `semantic_cluster_id` groups related claims for clustered analyses.
+- `benchmark_track` is `scientific`, `synthetic_stress`, or `external_transfer`.
+- `target_family`, `modality`, and `question` describe the scientific target.
+- `contract` contains the analysis plan. `reference_id` links to its reference;
+  `task_ids` lists its executable tasks and is empty for excluded cases.
+- `provenance`, `aliases`, and alignment fields identify source records and
+  the match between each question and its analysis plan.
+
+### References
+
+- `disposition` is `confirm` (reference supports the claim), `abstain`
+  (reference withholds support), or `unresolved` (insufficient evidence).
+- `basis` is `literature`, `constructed_control`, or `unresolved`.
+- `strength` separates literature references into `strict` and `provisional`
+  groups. The provisional group contains additional labels admitted under
+  two-model direct-evidence rules. Neuroimaging experts finalized the
+  literature labels. Controls use `constructed`; unresolved references use
+  `evidence_gap`.
+- `score_eligible` selects references for agreement metrics.
+- `evidence_ids`, `derivation_rule`, `agreeing_models`, `agreement_pattern`,
+  and `vote_counts` record the evidence and rule supporting each label.
+
+`confirm` in a reference is a literature or control label. CONFIRM's reporting
+decision is computed independently from the gate results in `outcomes.jsonl`.
+
+### Tasks
+
+- `task_id` identifies the task; `benchmark_case_id` links to its case.
+- `dataset_id`, `discovery_cohort`, and `replication_cohorts` identify inputs.
+- `contract` is the executable analysis plan; `contract_sha256` identifies it.
+- `partition_hashes` identifies the required prepared files for tasks without
+  a generator specification. `partition_paths` records their source paths.
+- `generator_spec` describes control construction; `generator_artifact_hashes`
+  identifies the associated construction artifacts.
+- `evidence_role` and `evidence_freshness` describe the evidence partition.
+- `code_sha`, `schema_version`, and `gate_policy_version` identify the
+  implementation and policy used to define the task.
+
+### Outcomes
+
+- `task_id` joins the outcome to its task; `status` records execution status.
+- `gate_verdict` contains the gate checks, diagnostic label, and rationale.
+- `confirm_outcome` and `raw_final_label` record the Full-standard result.
+- `error` describes a failed execution when present.
+- `cohort_content_hashes` identifies analyzed input files.
+  `generated_cohort_hashes` identifies generated files required by tasks
+  with a `generator_spec`.
+- `task_fingerprint` and `detailed_result_sha256` identify the task and its
+  detailed result artifact; the package distributes the compact outcome.
+
+## Results and supporting records
+
+| File | Contents |
+|---|---|
+| `benchmark_splits.json` | Track memberships, adjudication candidates, and excluded-case IDs |
+| `benchmark_results.csv` | Case-level references, outcomes, and evaluation coverage |
+| `benchmark_summary.json` | Metrics by track, target, reference basis, and strength |
+| `benchmark_strata_summary.csv` | Counts, rates, Wilson intervals, and cluster-bootstrap intervals by evaluation group |
+| `target_reference_summary.csv` | The same summaries grouped by target family |
+| `cluster_bootstrap_sensitivity.csv` | Wilson and semantic-cluster-bootstrap interval comparison |
+| `reference_agreement_audit.csv` | Counts by evidence basis, strength, and model-agreement pattern |
+| `unresolved_case_summary.csv` | Unresolved cases, agreement patterns, and recorded outcomes |
+| `alignment_policy.json` | Rules for question-plan alignment and execution eligibility |
+| `analysis_audit.json` | Alignment, evidence, execution-coverage, and result-consistency checks |
+| `analysis_manifest.json` | Analysis input/output hashes and bootstrap settings |
+| `v2_to_v2.1_crosswalk.csv` | Source-to-benchmark ID and contract-hash mappings |
+| `feedback_parent_crosswalk.csv` | Links from follow-up experiment parent claims to benchmark cases |
+| `feedback_reference_summary.csv` | Follow-up parent support grouped by reference category and search budget |
+| `feedback_crosswalk_manifest.json` | Hashes and matching counts for the follow-up parent links |
+
+Source paths and artifact hashes in these records describe the benchmark's
+scientific provenance. The files needed for scoring are included in this
+package. [Task execution](DATA_ACCESS.md) uses separately obtained prepared
+cohort files.
+
+## Package files
+
+| File | Contents |
+|---|---|
+| `README.md` | Installation and quickstart |
+| `USAGE.md` | Loading, metrics, scoring, and task execution |
+| `DATA_ACCESS.md` | Source cohorts, table format, and exact-input requirements |
+| `DATA_DICTIONARY.md` | File and field definitions |
+| `benchmark_manifest.json` | Record filenames, hashes, schema version, counts, and source identities |
+| `RELEASE_MANIFEST.json` | Benchmark identity, record counts, and distributed file inventory |
+| `PACKAGE_MANIFEST.json` | Version, license, framework dependency, and core record hashes |
+| `CITATION.cff` | Authors and paper citation |
+| `LICENSE` | CC BY 4.0 license text |
+| `SHA256SUMS` | Checksums of every distributed file except this checksum file |

LICENSE

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PACKAGE_MANIFEST.json

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+{
+  "name": "NeuroClaimBench",
+  "version": "2.1",
+  "schema_version": 2,
+  "license": "CC-BY-4.0",
+  "framework_version": "0.1.0",
+  "frozen_record_sha256": {
+    "cases": "57605904c124ecadbc9105d9b55e3bba58ee94aab0e68d6a5f93e587f6359c41",
+    "references": "90f6cf8595784c84afb80020b071ab6521931c6382365cd60da7f6452ec3e137",
+    "tasks": "ff775415fc63fc0f39483a6c53d5ee8750cf717d8ba44a39d4d460f2912aad53",
+    "outcomes": "1559acf53cbbcb6f09fe17710c4a854a4d6501b170df086535ac0c5bb1cc384b"
+  },
+  "raw_cohort_data_included": false,
+  "pubmed_abstracts_included": false,
+  "detailed_audit_archive_included": false,
+  "repository": "https://huggingface.co/datasets/stanjsx/NeuroClaimBench",
+  "code_repository": "https://github.com/yuxiangwei0808/CONFIRM"
+}

README.md

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+---
+pretty_name: NeuroClaimBench
+language:
+- en
+license: cc-by-4.0
+size_categories:
+- n<1K
+tags:
+- neuroimaging
+- scientific-reporting
+- benchmark
+- claim-validation
+configs:
+- config_name: cases
+  default: true
+  data_files:
+  - split: test
+    path: cases.jsonl
+- config_name: references
+  data_files:
+  - split: test
+    path: references.jsonl
+- config_name: tasks
+  data_files:
+  - split: test
+    path: tasks.jsonl
+- config_name: outcomes
+  data_files:
+  - split: test
+    path: outcomes.jsonl
+---
+
+# NeuroClaimBench v2.1
+
+NeuroClaimBench evaluates whether a system supports or withholds a
+neuroimaging claim. It accompanies
+[CONFIRM: Governing Scientific Reporting for Trustworthy Agentic Neuroimaging](https://openreview.net/forum?id=KYE1DzsxWc).
+
+The package contains 489 executable tasks: 279 scientific claims, 150
+constructed stress controls, and 60 external-transfer claims and controls.
+The inventory also includes 55 cases excluded from execution because of
+ambiguous question-plan alignment, unavailable analysis inputs, or invalid designs.
+Questions, analysis plans, reference labels, and recorded CONFIRM outcomes
+are provided as JSONL files.
+
+**Code:** [CONFIRM](https://github.com/yuxiangwei0808/CONFIRM) · **Dataset:** [Hugging Face](https://huggingface.co/datasets/stanjsx/NeuroClaimBench)
+
+## Load from Hugging Face
+
+Install the dataset library:
+
+```bash
+python -m pip install datasets
+```
+
+Load an individual record collection:
+
+```python
+from datasets import load_dataset
+
+tasks = load_dataset("stanjsx/NeuroClaimBench", "tasks", split="test", revision="v2.1")
+print(tasks[0]["task_id"])
+print(tasks[0]["contract"])
+```
+
+The configurations are `cases` (544 rows), `references` (544), `tasks` (489),
+and `outcomes` (489). Each uses a single `test` split. The default configuration
+is `cases`; these are record collections for evaluation, with links described
+in the [data dictionary](DATA_DICTIONARY.md).
+
+To download the complete benchmark for the command-line tools:
+
+```python
+from huggingface_hub import snapshot_download
+
+snapshot_download(
+    repo_id="stanjsx/NeuroClaimBench",
+    repo_type="dataset",
+    revision="v2.1",
+    local_dir="neuroclaimbench-v2.1",
+)
+```
+
+## Install the tools
+
+Use Python 3.10 or newer. CONFIRM supplies the `neuroclaimbench` command.
+Download `confirm-0.1.0-py3-none-any.whl` from the
+[CONFIRM v0.1.0 release](https://github.com/yuxiangwei0808/CONFIRM/releases/tag/v0.1.0)
+into the directory containing the extracted `neuroclaimbench-v2.1` folder.
+Run from that parent directory:
+
+```bash
+python -m venv .venv
+source .venv/bin/activate
+python -m pip install ./confirm-0.1.0-py3-none-any.whl
+```
+
+On Windows, activate with `.venv\Scripts\activate`. To install from source,
+extract `confirm-0.1.0.zip` and run `python -m pip install ./confirm-0.1.0`
+from its parent directory. An existing CONFIRM installation provides the
+same benchmark commands.
+
+## Verify and score
+
+Run from the directory containing the extracted benchmark folder:
+
+```bash
+neuroclaimbench verify --benchmark neuroclaimbench-v2.1
+neuroclaimbench predictions --benchmark neuroclaimbench-v2.1 \
+  --standard full --out outputs/confirm-full.jsonl
+neuroclaimbench score --benchmark neuroclaimbench-v2.1 \
+  --predictions outputs/confirm-full.jsonl
+```
+
+These commands verify all files, export 489 decisions from the recorded
+gate results, and score agreement with the reference labels. They require
+no cohort data or model calls. Choose a new output filename for each export.
+
+## Guides
+
+- [Python loading, metrics, and evaluation](USAGE.md)
+- [File and field definitions](DATA_DICTIONARY.md)
+- [Cohort data and exact-input requirements](DATA_ACCESS.md)
+- [Citation](CITATION.cff)
+
+Executing a task requires its corresponding prepared cohort files. The
+metadata package contains no participant tables, random-control assignment
+tables, or PubMed abstracts.
+
+## License
+
+The authors' benchmark metadata and documentation are licensed under
+[CC BY 4.0](LICENSE). Source datasets and referenced third-party works retain
+their own licenses and access terms. Cite the paper and this benchmark when
+using the release.

RELEASE_MANIFEST.json

@@ -0,0 +1,47 @@
+{
+  "name": "NeuroClaimBench",
+  "benchmark_version": "v2.1",
+  "release_schema_version": 2,
+  "license": "CC-BY-4.0",
+  "counts": {
+    "cases": 544,
+    "outcomes": 489,
+    "references": 544,
+    "tasks": 489
+  },
+  "release_file_count": 29,
+  "files": [
+    "CITATION.cff",
+    "DATA_ACCESS.md",
+    "DATA_DICTIONARY.md",
+    "LICENSE",
+    "PACKAGE_MANIFEST.json",
+    "README.md",
+    "RELEASE_MANIFEST.json",
+    "SHA256SUMS",
+    "USAGE.md",
+    "alignment_policy.json",
+    "analysis_audit.json",
+    "analysis_manifest.json",
+    "benchmark_manifest.json",
+    "benchmark_results.csv",
+    "benchmark_splits.json",
+    "benchmark_strata_summary.csv",
+    "benchmark_summary.json",
+    "cases.jsonl",
+    "cluster_bootstrap_sensitivity.csv",
+    "feedback_crosswalk_manifest.json",
+    "feedback_parent_crosswalk.csv",
+    "feedback_reference_summary.csv",
+    "outcomes.jsonl",
+    "reference_agreement_audit.csv",
+    "references.jsonl",
+    "target_reference_summary.csv",
+    "tasks.jsonl",
+    "unresolved_case_summary.csv",
+    "v2_to_v2.1_crosswalk.csv"
+  ],
+  "raw_cohort_data_included": false,
+  "pubmed_abstracts_included": false,
+  "detailed_audit_archive_included": false
+}

SHA256SUMS

@@ -0,0 +1,28 @@
+e8dd550275260f7c28d33e699b98138c31b34da2a221fb2a45f5985a3c92bceb  CITATION.cff
+b03098ab30c8723e556d3e6383b0df944b6c39cee8a543fa90d38986d131cbcc  DATA_ACCESS.md
+df33d3c7310630d8b7bad3a60dc547fe0675f3a8c59bf6345f5415f91f1497ce  DATA_DICTIONARY.md
+d557539df68e771cc1eedcc91d13f70fca930e508d11eedcafa4b15db49e3744  LICENSE
+769093a1e37b397552a5015ef8bf8029d95107b330658fb746a418854f585f9a  PACKAGE_MANIFEST.json
+dd20cdde2ccc8e64afb9623ef1e44b915acdb1d675c4689684ba5a0d1ba192bd  README.md
+119ae933b7959d1907fe0e97be724686d47f660e85feecd2a9b1f4b3c8286f1d  RELEASE_MANIFEST.json
+c60a681c5e3e6d019deb32b220b98edda8cbde497c902726a9e21f69f8b3998d  USAGE.md
+ac738bbcd45c44dc572202509af06445f81dafeb9a848df0142c1981489e58bd  alignment_policy.json
+5e8d88f2589f78d602d178b72ac6b01b9b77afff8e9b1bc5db1bcd31125c477d  analysis_audit.json
+3f8d5323bcabc00f9da07f05a1306b7225f35bfa379137005788a5b9badd7e89  analysis_manifest.json
+267771002a1587299ed584c315bf653faf3c6590b0c696ebf3935755c202925a  benchmark_manifest.json
+42264c47aef3283d939593b3619066d9533d49580fe487e37ddd80f1009a0c53  benchmark_results.csv
+b42e67d657db052faec1dbcfedc42b74b3ff0e6a6e136f0813d19b2c20808dea  benchmark_splits.json
+7c89a88dfa55e1f389e1215ff9ec78d556bbec414109b2d6b9daef2e793a660d  benchmark_strata_summary.csv
+8f3fc71a930c1f40b7907bb4e24b97783d850d2c1a3dc0b44c15a9636b5a898e  benchmark_summary.json
+57605904c124ecadbc9105d9b55e3bba58ee94aab0e68d6a5f93e587f6359c41  cases.jsonl
+5680f5851f1ce897760dddd83f1c9fa1674c9428bd326acf746698b3bb9a7f4d  cluster_bootstrap_sensitivity.csv
+878680e8292976766b5d99eeb37da5fbc69f96fa2e2b3f5b16dea2ce23673122  feedback_crosswalk_manifest.json
+50377442a008422d397215600a373f16edbe3ad4dad1e7455f65040c37f01ecb  feedback_parent_crosswalk.csv
+81f223e12bfac6f5f84ef27a20805ee86d420c88b205cb7e7bd1748f9e490ef4  feedback_reference_summary.csv
+1559acf53cbbcb6f09fe17710c4a854a4d6501b170df086535ac0c5bb1cc384b  outcomes.jsonl
+c32136a0fe38e2c429a7f4c4a16066bd7029b7578c729b5264f101bcc37a3c08  reference_agreement_audit.csv
+90f6cf8595784c84afb80020b071ab6521931c6382365cd60da7f6452ec3e137  references.jsonl
+c8b5272a9a10641b70eb687d81dc96ead022b4a113fabfd976b37f5bda1835e1  target_reference_summary.csv
+ff775415fc63fc0f39483a6c53d5ee8750cf717d8ba44a39d4d460f2912aad53  tasks.jsonl
+66402d994f880ceed0a69196c3ef9a8212e228e607c07610209e9bf87e03c9b1  unresolved_case_summary.csv
+fd2d98b99cd0802deacdbe9526e24246bb87e702c08b4905c140cd77121b2c1b  v2_to_v2.1_crosswalk.csv

USAGE.md

@@ -0,0 +1,164 @@
+# NeuroClaimBench evaluation guide
+
+Install CONFIRM using the [quickstart](README.md). Run the commands below
+from the benchmark directory containing `cases.jsonl`. In the CONFIRM source
+package, that directory is `benchmark/neuroclaimbench-v2.1/`.
+
+## Verify the benchmark
+
+```bash
+neuroclaimbench verify --benchmark .
+```
+
+Verification checks SHA-256 checksums, record schemas, unique IDs, links
+between records, and inventory counts. The `summary` command performs the
+same verification and prints the inventory.
+
+| Track | Inventory cases | Executable tasks |
+|---|---:|---:|
+| Scientific claims | 332 | 279 |
+| Constructed stress controls | 150 | 150 |
+| External-transfer claims and controls | 62 | 60 |
+| Total | 544 | 489 |
+
+Each executable case has one task. The 55 excluded cases comprise 40 with
+ambiguous question-plan alignment and 15 with unavailable analysis inputs
+or invalid designs. The benchmark has 268 score-eligible references:
+96 literature references and 172 constructed controls. The 221 executable
+tasks with unresolved references contribute to coverage counts and are
+excluded from reference-agreement metrics.
+
+## Load records in Python
+
+```python
+from bench.benchmark import BenchmarkDataset
+
+benchmark = BenchmarkDataset(".")
+cases = {case.benchmark_case_id: case for case in benchmark.cases}
+references = {ref.reference_id: ref for ref in benchmark.references}
+
+task = benchmark.tasks[0]
+case = cases[task.benchmark_case_id]
+reference = references[case.reference_id]
+print(case.question)
+print(task.contract.model_dump())
+print(reference.disposition, reference.score_eligible)
+```
+
+The loader validates record schemas. Use `neuroclaimbench verify` for
+checksum and cross-record checks. Join tasks and outcomes on `task_id`;
+join a task to its case through `benchmark_case_id`, then to its reference
+through `reference_id`. The [data dictionary](DATA_DICTIONARY.md) defines
+the files and fields.
+
+## Score recorded CONFIRM decisions
+
+```bash
+neuroclaimbench predictions --benchmark . \
+  --standard full --out ../outputs/confirm-full.jsonl
+neuroclaimbench score --benchmark . \
+  --predictions ../outputs/confirm-full.jsonl
+```
+
+Choose `screen`, `replicate`, or `full`. The predictions command applies the
+selected standard to the recorded gate vectors. It writes a new file and
+exports an error row for any outcome lacking a completed gate vector.
+
+## Score another system
+
+Give your system the question, frozen analysis plan, and required data.
+Reserve the reference labels and recorded CONFIRM outcomes for evaluation.
+Write one JSON object per task to a JSONL file:
+
+```json
+{"task_id": "<exact task_id from tasks.jsonl>", "status": "completed", "supported": false}
+```
+
+Use a JSON boolean for `supported`. For an execution failure or a missing
+verdict, use an error row:
+
+```json
+{"task_id": "<exact task_id from tasks.jsonl>", "status": "error", "error": "Input cohort unavailable"}
+```
+
+Pass the file to `neuroclaimbench score --benchmark . --predictions FILE`.
+The scorer requires unique, known task IDs and complete coverage by default.
+`--allow-partial` scores a subset and reports omitted tasks. Use complete
+predictions when comparing systems.
+
+### Metrics and error handling
+
+| Metric | Numerator | Denominator |
+|---|---|---|
+| Literature recall | Supported decisions | Evaluated literature references labeled `confirm` |
+| Literature false support | Supported decisions | Evaluated literature references labeled `abstain` |
+| Control false support | Supported decisions | Evaluated constructed controls |
+
+Under the paper's scoring rule, execution errors count as withheld and
+remain in the evaluated denominator. Output reports their count separately
+from completed decisions. Missing tasks are excluded from denominators
+when `--allow-partial` is specified.
+
+Metrics are grouped by track. Literature metrics are also grouped by
+reference strength: `strict`, `provisional`, and `combined`. Each metric
+reports `supported`, `evaluated`, `completed`, `eligible`, `errors`, and
+`missing` counts. `evaluated` includes submitted error rows; `completed`
+counts valid decisions. A rate is `null` when its denominator is zero.
+The output's `partial` flag indicates missing tasks or execution errors.
+
+The scorer returns point estimates. The distributed summary tables also
+provide the paper's Wilson and cluster-bootstrap intervals for recorded
+results.
+
+### Match the paper's scalar comparison
+
+The main scientific comparison uses 46 scalar literature claims: 31 labeled
+`confirm` and 15 labeled `abstain`. The default `all` scope also includes
+brain-wide claims, giving 51 and 19 scientific literature references,
+respectively. Select the scalar scope to match the main comparison:
+
+```bash
+neuroclaimbench score --benchmark . \
+  --predictions ../outputs/confirm-full.jsonl --literature-scope scalar
+```
+
+This filters literature metrics to scalar tasks and includes all constructed
+controls. Supply all 489 predictions; the scorer selects the metric subsets.
+Expected results for the scientific scalar set and the 150 stress controls:
+
+| Standard | Literature recall | Literature false support | Control false support |
+|---|---:|---:|---:|
+| Screen | 19/31 | 6/15 | 5/150 |
+| Replicate | 15/31 | 2/15 | 1/150 |
+| Full | 15/31 | 2/15 | 0/150 |
+
+Literature reference agreement and CONFIRM support measure different things:
+references summarize the adjudicated literature evidence, while CONFIRM
+support means the selected reporting checks passed.
+
+## Execute tasks
+
+Obtain the prepared inputs specified in the
+[data-access guide](DATA_ACCESS.md), then run:
+
+```bash
+neuroclaimbench run --benchmark . --data-root path/to/frozen-cohorts \
+  --standard full --out ../outputs/rerun
+```
+
+Supply additional `--data-root` arguments for separate directories. Each
+task's discovery and replication files must be together in one supplied
+directory. Repeat `--task-id` to select specific tasks. Use a new output
+directory for each run.
+
+The command verifies cohort hashes before execution and writes per-task
+results and `predictions.jsonl`. Unavailable or mismatched inputs produce
+error rows. Exit code 1 indicates at least one failed task. Score the output
+with the same `score` command; include `--allow-partial` when running a subset.
+
+## File integrity and provenance
+
+`SHA256SUMS` covers every distributed file except itself. The manifests
+identify the package contents, schema, and record hashes. Source paths and
+hashes inside scientific records identify the artifacts used to construct
+the benchmark. Runtime input files are located through `--data-root`.

alignment_policy.json

@@ -0,0 +1,35 @@
+{
+  "allowed_repairs": [
+    "restore an explicitly stated ADHD subtype contrast using raw dx labels",
+    "restore a question-stated executable outcome",
+    "add required measured confounds as safety_covariate_augmentation"
+  ],
+  "canonical_question": "The original scientific question is canonical.",
+  "gemini_role": "Advisory semantic audit only; deterministic rules authorize repairs.",
+  "immutable_fields": [
+    "predictor",
+    "group_contrast",
+    "population",
+    "outcome",
+    "modality",
+    "direction"
+  ],
+  "low_power_policy": "Low sample size alone is not an exclusion; the unchanged power gate adjudicates it.",
+  "non_executable_only_when": [
+    "requested group is absent",
+    "requested outcome is absent",
+    "required columns are unavailable",
+    "design is rank deficient",
+    "residual degrees of freedom are nonpositive"
+  ],
+  "policy_sha256": "ec29615ad0f3a814162c0ae1dd84448ea57b08fa5e2dcc165dfbc0fa05ab30ad",
+  "prohibited_inputs": [
+    "CONFIRM verdicts",
+    "p-values",
+    "effect estimates",
+    "benchmark labels",
+    "adjudication votes",
+    "feedback-search results"
+  ],
+  "version": "neuroclaimbench-v2.1-alignment-20260723"
+}

analysis_audit.json

@@ -0,0 +1,1804 @@
+{
+  "acceptance": {
+    "benchmark_items": 544,
+    "evaluation_tasks": 489,
+    "execution_error_count": 0,
+    "missing_partition_hash_count": 0,
+    "scored_alignment_mismatch_count": 0,
+    "task_outcomes": 489,
+    "task_result_reconciled": true
+  },
+  "alignment_audit": {
+    "forbidden_inputs_used": [],
+    "gemini_parsed_assessment_only_count": 362,
+    "gemini_raw_response_trace_count": 0,
+    "gemini_trace_count": 362,
+    "literature_advisory_count": 362,
+    "outcome_blind": true,
+    "output_sha256": {
+      "alignment_policy.json": "ac738bbcd45c44dc572202509af06445f81dafeb9a848df0142c1981489e58bd",
+      "alignment_records.jsonl": "bcc588ba4bc5d9d93121d0e039e54cc97e0914bbda2e21ccbc5a7013744b91e4",
+      "gemini_alignment_prompts.jsonl": "4ec728040b27dcdc0978a116286dcd386ba0d1960115615ad568fbe7862bfb05",
+      "gemini_alignment_responses.jsonl": "380e292a3953ed850f808b2793e8757529fa7d1fbfffe987dc1480970bd89a55"
+    },
+    "policy_sha256": "ec29615ad0f3a814162c0ae1dd84448ea57b08fa5e2dcc165dfbc0fa05ab30ad",
+    "policy_version": "neuroclaimbench-v2.1-alignment-20260723",
+    "record_count": 562,
+    "repair_count": 7,
+    "resolution_counts": {
+      "aligned": 81,
+      "aligned_with_safety_augmentation": 422,
+      "ambiguous_unresolved": 40,
+      "non_executable": 15,
+      "repairable_contract": 4
+    },
+    "source_benchmark_items_sha256": "bc2203dd134007d9fc3a4b02c098cf6064d83d02a0c6b3d43debd42e5e11e7ec",
+    "source_executable_count": 552,
+    "source_package": "data/neuroclaimbench/v2.1-source",
+    "version": "2.1.0"
+  },
+  "benchmark_metrics": {
+    "external_constructed_controls_by_dataset": {
+      "NACC": {
+        "cluster_bootstrap_resamples": 2000,
+        "cluster_bootstrap_seed": 20260723,
+        "confirmable_claim_recall": null,
+        "confirmable_claim_recall_cluster_bootstrap_95": null,
+        "confirmable_claim_recall_count": 0,
+        "confirmable_claim_recall_denominator": 0,
+        "confirmable_claim_recall_wilson_95": null,
+        "n_claims": 14,
+        "n_errors": 0,
+        "n_evaluated": 14,
+        "n_not_evaluated": 0,
+        "n_score_eligible": 14,
+        "unsafe_confirmation_cluster_bootstrap_95": [
+          0.0,
+          0.0
+        ],
+        "unsafe_confirmation_count": 0,
+        "unsafe_confirmation_denominator": 14,
+        "unsafe_confirmation_rate": 0.0,
+        "unsafe_confirmation_wilson_95": [
+          0.0,
+          0.2153108027376358
+        ]
+      },
+      "ds000030": {
+        "cluster_bootstrap_resamples": 2000,
+        "cluster_bootstrap_seed": 20260723,
+        "confirmable_claim_recall": null,
+        "confirmable_claim_recall_cluster_bootstrap_95": null,
+        "confirmable_claim_recall_count": 0,
+        "confirmable_claim_recall_denominator": 0,
+        "confirmable_claim_recall_wilson_95": null,
+        "n_claims": 8,
+        "n_errors": 0,
+        "n_evaluated": 8,
+        "n_not_evaluated": 0,
+        "n_score_eligible": 8,
+        "unsafe_confirmation_cluster_bootstrap_95": [
+          0.0,
+          0.0
+        ],
+        "unsafe_confirmation_count": 0,
+        "unsafe_confirmation_denominator": 8,
+        "unsafe_confirmation_rate": 0.0,
+        "unsafe_confirmation_wilson_95": [
+          0.0,
+          0.32440756488388023
+        ]
+      }
+    },
+    "external_literature_by_dataset": {
+      "NACC": {
+        "combined_primary": {
+          "cluster_bootstrap_resamples": 2000,
+          "cluster_bootstrap_seed": 20260723,
+          "confirmable_claim_recall": 0.0,
+          "confirmable_claim_recall_cluster_bootstrap_95": [
+            0.0,
+            0.0
+          ],
+          "confirmable_claim_recall_count": 0,
+          "confirmable_claim_recall_denominator": 7,
+          "confirmable_claim_recall_wilson_95": [
+            0.0,
+            0.35433043506668743
+          ],
+          "n_claims": 7,
+          "n_errors": 0,
+          "n_evaluated": 7,
+          "n_not_evaluated": 0,
+          "n_score_eligible": 7,
+          "unsafe_confirmation_cluster_bootstrap_95": null,
+          "unsafe_confirmation_count": 0,
+          "unsafe_confirmation_denominator": 0,
+          "unsafe_confirmation_rate": null,
+          "unsafe_confirmation_wilson_95": null
+        },
+        "provisional": {
+          "cluster_bootstrap_resamples": 2000,
+          "cluster_bootstrap_seed": 20260723,
+          "confirmable_claim_recall": 0.0,
+          "confirmable_claim_recall_cluster_bootstrap_95": [
+            0.0,
+            0.0
+          ],
+          "confirmable_claim_recall_count": 0,
+          "confirmable_claim_recall_denominator": 2,
+          "confirmable_claim_recall_wilson_95": [
+            0.0,
+            0.6576197724933469
+          ],
+          "n_claims": 2,
+          "n_errors": 0,
+          "n_evaluated": 2,
+          "n_not_evaluated": 0,
+          "n_score_eligible": 2,
+          "unsafe_confirmation_cluster_bootstrap_95": null,
+          "unsafe_confirmation_count": 0,
+          "unsafe_confirmation_denominator": 0,
+          "unsafe_confirmation_rate": null,
+          "unsafe_confirmation_wilson_95": null
+        },
+        "strict": {
+          "cluster_bootstrap_resamples": 2000,
+          "cluster_bootstrap_seed": 20260723,
+          "confirmable_claim_recall": 0.0,
+          "confirmable_claim_recall_cluster_bootstrap_95": [
+            0.0,
+            0.0
+          ],
+          "confirmable_claim_recall_count": 0,
+          "confirmable_claim_recall_denominator": 5,
+          "confirmable_claim_recall_wilson_95": [
+            0.0,
+            0.43448246478317476
+          ],
+          "n_claims": 5,
+          "n_errors": 0,
+          "n_evaluated": 5,
+          "n_not_evaluated": 0,
+          "n_score_eligible": 5,
+          "unsafe_confirmation_cluster_bootstrap_95": null,
+          "unsafe_confirmation_count": 0,
+          "unsafe_confirmation_denominator": 0,
+          "unsafe_confirmation_rate": null,
+          "unsafe_confirmation_wilson_95": null
+        }
+      },
+      "ds000030": {
+        "combined_primary": {
+          "cluster_bootstrap_resamples": 2000,
+          "cluster_bootstrap_seed": 20260723,
+          "confirmable_claim_recall": 0.0,
+          "confirmable_claim_recall_cluster_bootstrap_95": [
+            0.0,
+            0.0
+          ],
+          "confirmable_claim_recall_count": 0,
+          "confirmable_claim_recall_denominator": 11,
+          "confirmable_claim_recall_wilson_95": [
+            0.0,
+            0.2588329669680317
+          ],
+          "n_claims": 19,
+          "n_errors": 0,
+          "n_evaluated": 19,
+          "n_not_evaluated": 0,
+          "n_score_eligible": 19,
+          "unsafe_confirmation_cluster_bootstrap_95": [
+            0.0,
+            0.0
+          ],
+          "unsafe_confirmation_count": 0,
+          "unsafe_confirmation_denominator": 8,
+          "unsafe_confirmation_rate": 0.0,
+          "unsafe_confirmation_wilson_95": [
+            0.0,
+            0.32440756488388023
+          ]
+        },
+        "provisional": {
+          "cluster_bootstrap_resamples": 2000,
+          "cluster_bootstrap_seed": 20260723,
+          "confirmable_claim_recall": null,
+          "confirmable_claim_recall_cluster_bootstrap_95": null,
+          "confirmable_claim_recall_count": 0,
+          "confirmable_claim_recall_denominator": 0,
+          "confirmable_claim_recall_wilson_95": null,
+          "n_claims": 3,
+          "n_errors": 0,
+          "n_evaluated": 3,
+          "n_not_evaluated": 0,
+          "n_score_eligible": 3,
+          "unsafe_confirmation_cluster_bootstrap_95": [
+            0.0,
+            0.0
+          ],
+          "unsafe_confirmation_count": 0,
+          "unsafe_confirmation_denominator": 3,
+          "unsafe_confirmation_rate": 0.0,
+          "unsafe_confirmation_wilson_95": [
+            0.0,
+            0.5614970317550454
+          ]
+        },
+        "strict": {
+          "cluster_bootstrap_resamples": 2000,
+          "cluster_bootstrap_seed": 20260723,
+          "confirmable_claim_recall": 0.0,
+          "confirmable_claim_recall_cluster_bootstrap_95": [
+            0.0,
+            0.0
+          ],
+          "confirmable_claim_recall_count": 0,
+          "confirmable_claim_recall_denominator": 11,
+          "confirmable_claim_recall_wilson_95": [
+            0.0,
+            0.2588329669680317
+          ],
+          "n_claims": 16,
+          "n_errors": 0,
+          "n_evaluated": 16,
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+      "ncb-synthetic-stress-b06c112fe652826c",
+      "ncb-synthetic-stress-b0ad25a9bd80f5a9",
+      "ncb-synthetic-stress-b0c5075602b380ed",
+      "ncb-synthetic-stress-b3381266246ed676",
+      "ncb-synthetic-stress-b6e37ce62a4f72f8",
+      "ncb-synthetic-stress-bbf85b6c044b210f",
+      "ncb-synthetic-stress-bc7a72687a803144",
+      "ncb-synthetic-stress-bd117704d246d32d",
+      "ncb-synthetic-stress-be65950958048714",
+      "ncb-synthetic-stress-bfbbfbb8d1be3254",
+      "ncb-synthetic-stress-c0127a06d407afa7",
+      "ncb-synthetic-stress-c0dc3336ffe218d2",
+      "ncb-synthetic-stress-c1154a14cd1e8ef3",
+      "ncb-synthetic-stress-c20a3d5f8e9e123f",
+      "ncb-synthetic-stress-c220a093f814e539",
+      "ncb-synthetic-stress-c2d028849e27a38a",
+      "ncb-synthetic-stress-c752b6285a527e82",
+      "ncb-synthetic-stress-c7fc286c99cc66c6",
+      "ncb-synthetic-stress-c93f76e6f75aeaeb",
+      "ncb-synthetic-stress-ca59e7bcf2e17f7b",
+      "ncb-synthetic-stress-cb1ea057a92edbc7",
+      "ncb-synthetic-stress-cc6a8be21390c788",
+      "ncb-synthetic-stress-cc868c07af008306",
+      "ncb-synthetic-stress-ce1212b806f25235",
+      "ncb-synthetic-stress-cfc8fee426568090",
+      "ncb-synthetic-stress-d240bf163611d308",
+      "ncb-synthetic-stress-d7791ed71415a487",
+      "ncb-synthetic-stress-d85043ecf72b62d3",
+      "ncb-synthetic-stress-d916964e92a59eb0",
+      "ncb-synthetic-stress-dd4beff29754d17d",
+      "ncb-synthetic-stress-ddef0966bc3b9b24",
+      "ncb-synthetic-stress-df080a369be8d182",
+      "ncb-synthetic-stress-dfbe62737d4d8555",
+      "ncb-synthetic-stress-e1ef0d8ef65b2b01",
+      "ncb-synthetic-stress-e23fddfb3f829797",
+      "ncb-synthetic-stress-e2684641edc8c6e6",
+      "ncb-synthetic-stress-e2967e8bdd4698b5",
+      "ncb-synthetic-stress-e781a1d10147abaa",
+      "ncb-synthetic-stress-e99377ceac8e5d23",
+      "ncb-synthetic-stress-e9fb3c58c1aaf079",
+      "ncb-synthetic-stress-ec601d06e6ff6b54",
+      "ncb-synthetic-stress-ecf6d32180cfff58",
+      "ncb-synthetic-stress-ee7abc3b89d1d4cc",
+      "ncb-synthetic-stress-effa2f259eb5a69f",
+      "ncb-synthetic-stress-f034e20c6a6bc7f8",
+      "ncb-synthetic-stress-f091755e09ca7583",
+      "ncb-synthetic-stress-f2d4eb788a04c639",
+      "ncb-synthetic-stress-f377cad3c090b549",
+      "ncb-synthetic-stress-f5dbfb11e9ef72d0",
+      "ncb-synthetic-stress-f8423e8ba6d67c54",
+      "ncb-synthetic-stress-f8fa9003aa7c9d3b",
+      "ncb-synthetic-stress-f91a2cdb84ef6798",
+      "ncb-synthetic-stress-f936b668e13706b3",
+      "ncb-synthetic-stress-f9b3b69c40a65738",
+      "ncb-synthetic-stress-fcd62e593092700b",
+      "ncb-synthetic-stress-feb2bcefb03564db"
+    ]
+  },
+  "version": "2.1.0"
+}

benchmark_strata_summary.csv

@@ -0,0 +1,13 @@
+stratum,benchmark_split,reference_basis,reference_strength,dataset_id,n_claims,n_score_eligible,n_evaluated,n_errors,confirmable_count,confirmable_denominator,confirmable_recall,confirmable_wilson_95,confirmable_cluster_bootstrap_95,unsafe_count,unsafe_denominator,unsafe_rate,unsafe_wilson_95,unsafe_cluster_bootstrap_95
+scientific_literature_combined,scientific,literature,strict+provisional,,70,70,70,0,21,51,0.4117647058823529,"[0.2875439520458094, 0.5483466279362843]","[0.28, 0.5714285714285714]",2,19,0.10526315789473684,"[0.02935856029887013, 0.31394082711109006]","[0.0, 0.2777777777777778]"
+scientific_literature_provisional,scientific,literature,provisional,,44,44,44,0,10,28,0.35714285714285715,"[0.2070582950773768, 0.5416969348557219]","[0.18518518518518517, 0.5333333333333333]",2,16,0.125,"[0.03497748774324047, 0.36022827265758695]","[0.0, 0.3333333333333333]"
+scientific_literature_strict,scientific,literature,strict,,26,26,26,0,11,23,0.4782608695652174,"[0.29237157416646653, 0.6703726266357259]","[0.2608695652173913, 0.7083333333333334]",0,3,0.0,"[0.0, 0.5614970317550454]","[0.0, 0.0]"
+external_literature_NACC_combined_primary,external_transfer,literature,strict+provisional,NACC,7,7,7,0,0,7,0.0,"[0.0, 0.35433043506668743]","[0.0, 0.0]",0,0,,null,null
+external_literature_NACC_provisional,external_transfer,literature,provisional,NACC,2,2,2,0,0,2,0.0,"[0.0, 0.6576197724933469]","[0.0, 0.0]",0,0,,null,null
+external_literature_NACC_strict,external_transfer,literature,strict,NACC,5,5,5,0,0,5,0.0,"[0.0, 0.43448246478317476]","[0.0, 0.0]",0,0,,null,null
+external_literature_ds000030_combined_primary,external_transfer,literature,strict+provisional,ds000030,19,19,19,0,0,11,0.0,"[0.0, 0.2588329669680317]","[0.0, 0.0]",0,8,0.0,"[0.0, 0.32440756488388023]","[0.0, 0.0]"
+external_literature_ds000030_provisional,external_transfer,literature,provisional,ds000030,3,3,3,0,0,0,,null,null,0,3,0.0,"[0.0, 0.5614970317550454]","[0.0, 0.0]"
+external_literature_ds000030_strict,external_transfer,literature,strict,ds000030,16,16,16,0,0,11,0.0,"[0.0, 0.2588329669680317]","[0.0, 0.0]",0,5,0.0,"[0.0, 0.43448246478317476]","[0.0, 0.0]"
+external_constructed_NACC,external_transfer,constructed_control,constructed,NACC,14,14,14,0,0,0,,null,null,0,14,0.0,"[0.0, 0.2153108027376358]","[0.0, 0.0]"
+external_constructed_ds000030,external_transfer,constructed_control,constructed,ds000030,8,8,8,0,0,0,,null,null,0,8,0.0,"[0.0, 0.32440756488388023]","[0.0, 0.0]"
+synthetic_constructed,synthetic_safety,constructed_control,constructed,,150,150,150,0,0,0,,null,null,0,150,0.0,"[0.0, 0.0249702443680766]","[0.0, 0.0]"

benchmark_summary.json

@@ -0,0 +1,1461 @@
+{
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+      "confirmable_claim_recall_wilson_95": null,
+      "n_claims": 14,
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+      "unsafe_confirmation_denominator": 14,
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+        0.2153108027376358
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+      "confirmable_claim_recall_wilson_95": null,
+      "n_claims": 8,
+      "n_errors": 0,
+      "n_evaluated": 8,
+      "n_not_evaluated": 0,
+      "n_score_eligible": 8,
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+      "unsafe_confirmation_denominator": 8,
+      "unsafe_confirmation_rate": 0.0,
+      "unsafe_confirmation_wilson_95": [
+        0.0,
+        0.32440756488388023
+      ]
+    }
+  },
+  "external_literature_by_dataset": {
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+        "confirmable_claim_recall_denominator": 7,
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+          0.35433043506668743
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+        "n_claims": 7,
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+  },
+  "interpretation_restrictions": [
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+    "external literature references and random controls are never pooled",
+    "unresolved references are retained but excluded from scored performance",
+    "strict plus provisional literature references are the retrospective primary operational result",
+    "constructed-control cluster intervals are conditional stress-test uncertainty, not population FCR",
+    "multi-model literature references are not human expert ground truth",
+    "v2.1 policy was frozen before the v2.1 rerun but after v2 outcomes were visible"
+  ],
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+      "scientific": 279,
+      "synthetic_safety": 150
+    },
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+  },
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+    }
+  },
+  "metrics_by_split_target_and_reference_basis": {
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+      },
+      "psychosis": {
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+            "cluster_bootstrap_resamples": 2000,
+            "cluster_bootstrap_seed": 20260723,
+            "confirmable_claim_recall": 0.0,
+            "confirmable_claim_recall_cluster_bootstrap_95": [
+              0.0,
+              0.0
+            ],
+            "confirmable_claim_recall_count": 0,
+            "confirmable_claim_recall_denominator": 3,
+            "confirmable_claim_recall_wilson_95": [
+              0.0,
+              0.5614970317550454
+            ],
+            "n_claims": 5,
+            "n_errors": 0,
+            "n_evaluated": 5,
+            "n_not_evaluated": 0,
+            "n_score_eligible": 5,
+            "unsafe_confirmation_cluster_bootstrap_95": [
+              0.0,
+              0.0
+            ],
+            "unsafe_confirmation_count": 0,
+            "unsafe_confirmation_denominator": 2,
+            "unsafe_confirmation_rate": 0.0,
+            "unsafe_confirmation_wilson_95": [
+              0.0,
+              0.6576197724933469
+            ]
+          }
+        }
+      },
+      "normative_fmri": {
+        "literature": {
+          "evidence_gap": {
+            "cluster_bootstrap_resamples": 2000,
+            "cluster_bootstrap_seed": 20260723,
+            "confirmable_claim_recall": null,
+            "confirmable_claim_recall_cluster_bootstrap_95": null,
+            "confirmable_claim_recall_count": 0,
+            "confirmable_claim_recall_denominator": 0,
+            "confirmable_claim_recall_wilson_95": null,
+            "n_claims": 49,
+            "n_errors": 0,
+            "n_evaluated": 0,
+            "n_not_evaluated": 0,
+            "n_score_eligible": 0,
+            "unsafe_confirmation_cluster_bootstrap_95": null,
+            "unsafe_confirmation_count": 0,
+            "unsafe_confirmation_denominator": 0,
+            "unsafe_confirmation_rate": null,
+            "unsafe_confirmation_wilson_95": null
+          },
+          "provisional": {
+            "cluster_bootstrap_resamples": 2000,
+            "cluster_bootstrap_seed": 20260723,
+            "confirmable_claim_recall": 0.0,
+            "confirmable_claim_recall_cluster_bootstrap_95": [
+              0.0,
+              0.0
+            ],
+            "confirmable_claim_recall_count": 0,
+            "confirmable_claim_recall_denominator": 1,
+            "confirmable_claim_recall_wilson_95": [
+              0.0,
+              0.7934506856227626
+            ],
+            "n_claims": 1,
+            "n_errors": 0,
+            "n_evaluated": 1,
+            "n_not_evaluated": 0,
+            "n_score_eligible": 1,
+            "unsafe_confirmation_cluster_bootstrap_95": null,
+            "unsafe_confirmation_count": 0,
+            "unsafe_confirmation_denominator": 0,
+            "unsafe_confirmation_rate": null,
+            "unsafe_confirmation_wilson_95": null
+          },
+          "strict": {
+            "cluster_bootstrap_resamples": 2000,
+            "cluster_bootstrap_seed": 20260723,
+            "confirmable_claim_recall": 1.0,
+            "confirmable_claim_recall_cluster_bootstrap_95": [
+              1.0,
+              1.0
+            ],
+            "confirmable_claim_recall_count": 1,
+            "confirmable_claim_recall_denominator": 1,
+            "confirmable_claim_recall_wilson_95": [
+              0.20654931437723745,
+              1.0
+            ],
+            "n_claims": 1,
+            "n_errors": 0,
+            "n_evaluated": 1,
+            "n_not_evaluated": 0,
+            "n_score_eligible": 1,
+            "unsafe_confirmation_cluster_bootstrap_95": null,
+            "unsafe_confirmation_count": 0,
+            "unsafe_confirmation_denominator": 0,
+            "unsafe_confirmation_rate": null,
+            "unsafe_confirmation_wilson_95": null
+          }
+        }
+      },
+      "psychosis": {
+        "literature": {
+          "evidence_gap": {
+            "cluster_bootstrap_resamples": 2000,
+            "cluster_bootstrap_seed": 20260723,
+            "confirmable_claim_recall": null,
+            "confirmable_claim_recall_cluster_bootstrap_95": null,
+            "confirmable_claim_recall_count": 0,
+            "confirmable_claim_recall_denominator": 0,
+            "confirmable_claim_recall_wilson_95": null,
+            "n_claims": 39,
+            "n_errors": 0,
+            "n_evaluated": 0,
+            "n_not_evaluated": 0,
+            "n_score_eligible": 0,
+            "unsafe_confirmation_cluster_bootstrap_95": null,
+            "unsafe_confirmation_count": 0,
+            "unsafe_confirmation_denominator": 0,
+            "unsafe_confirmation_rate": null,
+            "unsafe_confirmation_wilson_95": null
+          },
+          "provisional": {
+            "cluster_bootstrap_resamples": 2000,
+            "cluster_bootstrap_seed": 20260723,
+            "confirmable_claim_recall": 0.1111111111111111,
+            "confirmable_claim_recall_cluster_bootstrap_95": [
+              0.0,
+              0.25
+            ],
+            "confirmable_claim_recall_count": 1,
+            "confirmable_claim_recall_denominator": 9,
+            "confirmable_claim_recall_wilson_95": [
+              0.019890887638544907,
+              0.434999705576656
+            ],
+            "n_claims": 12,
+            "n_errors": 0,
+            "n_evaluated": 12,
+            "n_not_evaluated": 0,
+            "n_score_eligible": 12,
+            "unsafe_confirmation_cluster_bootstrap_95": [
+              0.0,
+              0.0
+            ],
+            "unsafe_confirmation_count": 0,
+            "unsafe_confirmation_denominator": 3,
+            "unsafe_confirmation_rate": 0.0,
+            "unsafe_confirmation_wilson_95": [
+              0.0,
+              0.5614970317550454
+            ]
+          },
+          "strict": {
+            "cluster_bootstrap_resamples": 2000,
+            "cluster_bootstrap_seed": 20260723,
+            "confirmable_claim_recall": 0.0,
+            "confirmable_claim_recall_cluster_bootstrap_95": [
+              0.0,
+              0.0
+            ],
+            "confirmable_claim_recall_count": 0,
+            "confirmable_claim_recall_denominator": 7,
+            "confirmable_claim_recall_wilson_95": [
+              0.0,
+              0.35433043506668743
+            ],
+            "n_claims": 7,
+            "n_errors": 0,
+            "n_evaluated": 7,
+            "n_not_evaluated": 0,
+            "n_score_eligible": 7,
+            "unsafe_confirmation_cluster_bootstrap_95": null,
+            "unsafe_confirmation_count": 0,
+            "unsafe_confirmation_denominator": 0,
+            "unsafe_confirmation_rate": null,
+            "unsafe_confirmation_wilson_95": null
+          }
+        }
+      }
+    },
+    "synthetic_safety": {
+      "synthetic_stress": {
+        "constructed_control": {
+          "constructed": {
+            "cluster_bootstrap_resamples": 2000,
+            "cluster_bootstrap_seed": 20260723,
+            "confirmable_claim_recall": null,
+            "confirmable_claim_recall_cluster_bootstrap_95": null,
+            "confirmable_claim_recall_count": 0,
+            "confirmable_claim_recall_denominator": 0,
+            "confirmable_claim_recall_wilson_95": null,
+            "n_claims": 150,
+            "n_errors": 0,
+            "n_evaluated": 150,
+            "n_not_evaluated": 0,
+            "n_score_eligible": 150,
+            "unsafe_confirmation_cluster_bootstrap_95": [
+              0.0,
+              0.0
+            ],
+            "unsafe_confirmation_count": 0,
+            "unsafe_confirmation_denominator": 150,
+            "unsafe_confirmation_rate": 0.0,
+            "unsafe_confirmation_wilson_95": [
+              0.0,
+              0.0249702443680766
+            ]
+          }
+        }
+      }
+    }
+  },
+  "outcome_coverage": {
+    "completed_claim_count": 489,
+    "confirm_outcome_counts": {
+      "abstained": 424,
+      "confirmed": 65
+    },
+    "error_claim_count": 0,
+    "not_evaluated_claim_count": 0
+  },
+  "primary_scientific_literature": {
+    "cluster_bootstrap_resamples": 2000,
+    "cluster_bootstrap_seed": 20260723,
+    "confirmable_claim_recall": 0.4117647058823529,
+    "confirmable_claim_recall_cluster_bootstrap_95": [
+      0.28,
+      0.5714285714285714
+    ],
+    "confirmable_claim_recall_count": 21,
+    "confirmable_claim_recall_denominator": 51,
+    "confirmable_claim_recall_wilson_95": [
+      0.2875439520458094,
+      0.5483466279362843
+    ],
+    "n_claims": 70,
+    "n_errors": 0,
+    "n_evaluated": 70,
+    "n_not_evaluated": 0,
+    "n_score_eligible": 70,
+    "unsafe_confirmation_cluster_bootstrap_95": [
+      0.0,
+      0.2777777777777778
+    ],
+    "unsafe_confirmation_count": 2,
+    "unsafe_confirmation_denominator": 19,
+    "unsafe_confirmation_rate": 0.10526315789473684,
+    "unsafe_confirmation_wilson_95": [
+      0.02935856029887013,
+      0.31394082711109006
+    ]
+  },
+  "provenance": {
+    "benchmark_claims_payload_sha256": "4ecf76cef32508d44057c7e91821ba5be1cbc77d50c34130c6e9533a10f16b78",
+    "task_outcomes_payload_sha256": "3e9e782766f60ea04e2180ec9af42cdc5b479bff6506f0671e91116a0e8a0925"
+  },
+  "scientific_literature_sensitivity": {
+    "provisional": {
+      "cluster_bootstrap_resamples": 2000,
+      "cluster_bootstrap_seed": 20260723,
+      "confirmable_claim_recall": 0.35714285714285715,
+      "confirmable_claim_recall_cluster_bootstrap_95": [
+        0.18518518518518517,
+        0.5333333333333333
+      ],
+      "confirmable_claim_recall_count": 10,
+      "confirmable_claim_recall_denominator": 28,
+      "confirmable_claim_recall_wilson_95": [
+        0.2070582950773768,
+        0.5416969348557219
+      ],
+      "n_claims": 44,
+      "n_errors": 0,
+      "n_evaluated": 44,
+      "n_not_evaluated": 0,
+      "n_score_eligible": 44,
+      "unsafe_confirmation_cluster_bootstrap_95": [
+        0.0,
+        0.3333333333333333
+      ],
+      "unsafe_confirmation_count": 2,
+      "unsafe_confirmation_denominator": 16,
+      "unsafe_confirmation_rate": 0.125,
+      "unsafe_confirmation_wilson_95": [
+        0.03497748774324047,
+        0.36022827265758695
+      ]
+    },
+    "strict": {
+      "cluster_bootstrap_resamples": 2000,
+      "cluster_bootstrap_seed": 20260723,
+      "confirmable_claim_recall": 0.4782608695652174,
+      "confirmable_claim_recall_cluster_bootstrap_95": [
+        0.2608695652173913,
+        0.7083333333333334
+      ],
+      "confirmable_claim_recall_count": 11,
+      "confirmable_claim_recall_denominator": 23,
+      "confirmable_claim_recall_wilson_95": [
+        0.29237157416646653,
+        0.6703726266357259
+      ],
+      "n_claims": 26,
+      "n_errors": 0,
+      "n_evaluated": 26,
+      "n_not_evaluated": 0,
+      "n_score_eligible": 26,
+      "unsafe_confirmation_cluster_bootstrap_95": [
+        0.0,
+        0.0
+      ],
+      "unsafe_confirmation_count": 0,
+      "unsafe_confirmation_denominator": 3,
+      "unsafe_confirmation_rate": 0.0,
+      "unsafe_confirmation_wilson_95": [
+        0.0,
+        0.5614970317550454
+      ]
+    }
+  },
+  "synthetic_constructed_controls": {
+    "cluster_bootstrap_resamples": 2000,
+    "cluster_bootstrap_seed": 20260723,
+    "confirmable_claim_recall": null,
+    "confirmable_claim_recall_cluster_bootstrap_95": null,
+    "confirmable_claim_recall_count": 0,
+    "confirmable_claim_recall_denominator": 0,
+    "confirmable_claim_recall_wilson_95": null,
+    "n_claims": 150,
+    "n_errors": 0,
+    "n_evaluated": 150,
+    "n_not_evaluated": 0,
+    "n_score_eligible": 150,
+    "unsafe_confirmation_cluster_bootstrap_95": [
+      0.0,
+      0.0
+    ],
+    "unsafe_confirmation_count": 0,
+    "unsafe_confirmation_denominator": 150,
+    "unsafe_confirmation_rate": 0.0,
+    "unsafe_confirmation_wilson_95": [
+      0.0,
+      0.0249702443680766
+    ]
+  },
+  "unresolved_verdict_distribution": {
+    "external_transfer": {
+      "abstained": 12
+    },
+    "scientific": {
+      "abstained": 167,
+      "confirmed": 42
+    },
+    "synthetic_safety": {}
+  }
+}

cluster_bootstrap_sensitivity.csv

@@ -0,0 +1,25 @@
+stratum,endpoint,count,denominator,rate,wilson_95,semantic_cluster_bootstrap_95,bootstrap_resamples,bootstrap_seed
+scientific_literature_combined,confirmable_claim_recall,21,51,0.4117647058823529,"[0.2875439520458094, 0.5483466279362843]","[0.28, 0.5714285714285714]",2000,20260723
+scientific_literature_combined,unsafe_confirmation,2,19,,"[0.02935856029887013, 0.31394082711109006]","[0.0, 0.2777777777777778]",2000,20260723
+scientific_literature_strict,confirmable_claim_recall,11,23,0.4782608695652174,"[0.29237157416646653, 0.6703726266357259]","[0.2608695652173913, 0.7083333333333334]",2000,20260723
+scientific_literature_strict,unsafe_confirmation,0,3,,"[0.0, 0.5614970317550454]","[0.0, 0.0]",2000,20260723
+scientific_literature_provisional,confirmable_claim_recall,10,28,0.35714285714285715,"[0.2070582950773768, 0.5416969348557219]","[0.18518518518518517, 0.5333333333333333]",2000,20260723
+scientific_literature_provisional,unsafe_confirmation,2,16,,"[0.03497748774324047, 0.36022827265758695]","[0.0, 0.3333333333333333]",2000,20260723
+external_literature_NACC_combined_primary,confirmable_claim_recall,0,7,0.0,"[0.0, 0.35433043506668743]","[0.0, 0.0]",2000,20260723
+external_literature_NACC_combined_primary,unsafe_confirmation,0,0,,null,null,2000,20260723
+external_literature_NACC_strict,confirmable_claim_recall,0,5,0.0,"[0.0, 0.43448246478317476]","[0.0, 0.0]",2000,20260723
+external_literature_NACC_strict,unsafe_confirmation,0,0,,null,null,2000,20260723
+external_literature_NACC_provisional,confirmable_claim_recall,0,2,0.0,"[0.0, 0.6576197724933469]","[0.0, 0.0]",2000,20260723
+external_literature_NACC_provisional,unsafe_confirmation,0,0,,null,null,2000,20260723
+external_literature_ds000030_combined_primary,confirmable_claim_recall,0,11,0.0,"[0.0, 0.2588329669680317]","[0.0, 0.0]",2000,20260723
+external_literature_ds000030_combined_primary,unsafe_confirmation,0,8,,"[0.0, 0.32440756488388023]","[0.0, 0.0]",2000,20260723
+external_literature_ds000030_strict,confirmable_claim_recall,0,11,0.0,"[0.0, 0.2588329669680317]","[0.0, 0.0]",2000,20260723
+external_literature_ds000030_strict,unsafe_confirmation,0,5,,"[0.0, 0.43448246478317476]","[0.0, 0.0]",2000,20260723
+external_literature_ds000030_provisional,confirmable_claim_recall,0,0,,null,null,2000,20260723
+external_literature_ds000030_provisional,unsafe_confirmation,0,3,,"[0.0, 0.5614970317550454]","[0.0, 0.0]",2000,20260723
+external_constructed_NACC,confirmable_claim_recall,0,0,,null,null,2000,20260723
+external_constructed_NACC,unsafe_confirmation,0,14,,"[0.0, 0.2153108027376358]","[0.0, 0.0]",2000,20260723
+external_constructed_ds000030,confirmable_claim_recall,0,0,,null,null,2000,20260723
+external_constructed_ds000030,unsafe_confirmation,0,8,,"[0.0, 0.32440756488388023]","[0.0, 0.0]",2000,20260723
+synthetic_constructed,confirmable_claim_recall,0,0,,null,null,2000,20260723
+synthetic_constructed,unsafe_confirmation,0,150,,"[0.0, 0.0249702443680766]","[0.0, 0.0]",2000,20260723

feedback_crosswalk_manifest.json

@@ -0,0 +1,58 @@
+{
+  "arm_count": 12,
+  "arm_parent_checkpoint_tree_sha256": {
+    "R10C10": "62edb890e3b5248600b8f2ddf69f08bfd07574668e0ea3149b2d8b1410abc772",
+    "R10C2": "9086b60648dfa7563ab8a6be6a4ecc77b8e05c89222316047f43c4cccc58146f",
+    "R10C5": "7038f48e80ba60a58f80249f9758f0b94ef4a4c9851d087425d00a31002957e7",
+    "R1C10": "5344b5a8412eea41a811d32c8aaf4436108d14be7ab1e0fcca41a615b5932ea1",
+    "R1C2": "5e7cb5c21b4b24b494256fcd87fdc4a20f6571f8d6bd9ee15d262d4510594a58",
+    "R1C5": "96cdefd58e523194f68f01b02a2c9029823e20f8522dd63c1a14bb25a3b47ef5",
+    "R3C10": "dd59630680e4b1d51403b078f7cdb1e266c76bb54157b5d3133d75bb23b7f64c",
+    "R3C2": "c6db1554ea6dea3f15886c8d338366b293f956413949c17e1fd5f25615403513",
+    "R3C5": "590688f470c253fba5f185636956a875a55967f4d17422816b744eab3e158be9",
+    "R5C10": "7add95ac36495687b433d69560d93fa7e4bd1f59653d2b936006b90f760697a9",
+    "R5C2": "dc8702af4fa52dd869e8747c22128c0369ff061b0d8e92223b3006e243c8fbee",
+    "R5C5": "d439bbfee40410041501d8cce5eb4913af367b879198278375fa11a13cfa537a"
+  },
+  "arm_run_provenance_sha256": {
+    "R10C10": "5ca237ed104d2e2f4ba2296ef64d1d0ae9bc8ae1155a8bf9e5aae45a7ba001ca",
+    "R10C2": "ca3672feeb7f91069156de87b7fc5032f05d4335241a1af445aa5f5f5e5e5956",
+    "R10C5": "9cbdcfa880ebfa671c9a2b50fe6e1b4e8dc6a9a0b07f8fac0c229fa296055d5b",
+    "R1C10": "0124bab67801201c1c67d13d125382979d290928df043cae441da7dcad0adce5",
+    "R1C2": "9a8482a7b84025784bebc11947a4a1e299eeba2eef7186ff56089b2e15ee83c3",
+    "R1C5": "1b97a8102a43f72bc186160663ce382c466c68be66ab2b399aeafec8d8cc8ab8",
+    "R3C10": "011134b9a58ee19e6cef75bea7c8a62c8ddfd957913c005169161d57f8d77318",
+    "R3C2": "ba5ed056c81147ca24cebb61e97183479dd2602b56046844b7228d04aa8df452",
+    "R3C5": "f64a381747e905d9bb8f8e879dbb553282645479a480d9bc03d06253db9e8cb5",
+    "R5C10": "77d44152d7722429dc3e1948e6a420a3ba3c29d50496e1ee10b538ecf19cb564",
+    "R5C2": "9dfe6c6586de5273e1a1638fe043c99954695c53f51a2837fb866cfc76ff62cb",
+    "R5C5": "09825c56ca0aedbd6f6d8886b4146c115f47b68280b5c8ad665bcedf16efb2fd"
+  },
+  "input_sha256": {
+    "cases.jsonl": "57605904c124ecadbc9105d9b55e3bba58ee94aab0e68d6a5f93e587f6359c41",
+    "claim_search_source.json": "e94e3db9cb0d91325e91af4dcd34a2b82910cce00c5254f0c2d3e6a2d42a03d6",
+    "matrix_summary.json": "58eec1313414ebcfa83c8f1c8abaa60c3ba940093036e5e1e0b1a31dac9da3bb",
+    "references.jsonl": "90f6cf8595784c84afb80020b071ab6521931c6382365cd60da7f6452ec3e137"
+  },
+  "interpretation_restrictions": [
+    "repaired or semantically changed parents are pre_v2_contract_only",
+    "only exact_v2.1_reference rows enter reference-stratified summaries",
+    "the frozen feedback sweep was not rerun or modified"
+  ],
+  "match_status_counts": {
+    "exact_v2.1_reference": 2292,
+    "pre_v2_contract_only": 288
+  },
+  "matching_rule": "source claim ID plus exact pre-v2 executable contract hash",
+  "output_sha256": {
+    "feedback_parent_crosswalk.csv": "50377442a008422d397215600a373f16edbe3ad4dad1e7455f65040c37f01ecb",
+    "feedback_reference_summary.csv": "81f223e12bfac6f5f84ef27a20805ee86d420c88b205cb7e7bd1748f9e490ef4"
+  },
+  "parent_checkpoint_count": 2580,
+  "parent_checkpoint_tree_sha256": "5e1498b45d5233d57922139a8f855e10ebd49d5810d20312c7dab3f6032a27ff",
+  "parent_lineage_count": 215,
+  "row_count": 2580,
+  "source_code_sha256": "2b97a50c6ccacf14bbc496f256427fd44be9799437056f1e1af433aca5c47fb0",
+  "uses_feedback_outcomes_for_matching": false,
+  "version": "neuroclaimbench-v2.1-feedback-crosswalk-v2"
+}

feedback_reference_summary.csv

@@ -0,0 +1,397 @@
+rounds,candidates,match_status,target_family,source_mode,reference_basis,reference_strength,reference_disposition,parent_count,supported_parent_count,supported_parent_rate
+1,2,exact_v2.1_reference,ad_aging,literature_grounded,literature,strict,confirm,2,2,1.0
+1,2,exact_v2.1_reference,ad_aging,llm_proposed,literature,evidence_gap,unresolved,19,4,0.21052631578947367
+1,2,exact_v2.1_reference,ad_aging,llm_proposed,literature,provisional,confirm,1,0,0.0
+1,2,exact_v2.1_reference,ad_aging,llm_proposed,literature,strict,confirm,1,1,1.0
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reference_agreement_audit.csv

@@ -0,0 +1,8 @@
+reference_basis,reference_strength,agreement_pattern,claim_count
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+literature,evidence_gap,not_applicable,276
+literature,provisional,adjudicator_plus_assessor,7
+literature,provisional,all_three_models,5
+literature,provisional,assessors_only,37
+literature,strict,adjudicator_plus_assessor,8
+literature,strict,all_three_models,39

target_reference_summary.csv

@@ -0,0 +1,25 @@
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+external_transfer:ad_aging:literature:evidence_gap,external_transfer,ad_aging,literature,evidence_gap,10,0,0,0,0,0,,null,null,0,0,,null,null
+external_transfer:ad_aging:literature:provisional,external_transfer,ad_aging,literature,provisional,2,2,2,0,0,2,0.0,"[0.0, 0.6576197724933469]","[0.0, 0.0]",0,0,,null,null
+external_transfer:ad_aging:literature:strict,external_transfer,ad_aging,literature,strict,5,5,5,0,0,5,0.0,"[0.0, 0.43448246478317476]","[0.0, 0.0]",0,0,,null,null
+external_transfer:psychosis:constructed_control:constructed,external_transfer,psychosis,constructed_control,constructed,8,8,8,0,0,0,,null,null,0,8,0.0,"[0.0, 0.32440756488388023]","[0.0, 0.0]"
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+external_transfer:psychosis:literature:provisional,external_transfer,psychosis,literature,provisional,3,3,3,0,0,0,,null,null,0,3,0.0,"[0.0, 0.5614970317550454]","[0.0, 0.0]"
+external_transfer:psychosis:literature:strict,external_transfer,psychosis,literature,strict,16,16,16,0,0,11,0.0,"[0.0, 0.2588329669680317]","[0.0, 0.0]",0,5,0.0,"[0.0, 0.43448246478317476]","[0.0, 0.0]"
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unresolved_case_summary.csv

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