| # 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`. |
|
|
