Upload dataset

.gitattributes

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+*.pdf filter=lfs diff=lfs merge=lfs -text
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+*.npz filter=lfs diff=lfs merge=lfs -text

ARTIFACT_AUDIT.md

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+# Artifact Audit
+
+Audit date: 2026-05-04
+
+## Scope
+
+Artifact folder: SparseWake anonymous release tree.
+
+The manuscript source was not edited for this artifact-preparation task.
+
+## Checks
+
+| Check | Status | Notes |
+|---|---|---|
+| No absolute local paths | Pass | Text scan found no drive prefixes or Unix home paths. |
+| No usernames, institution names, machine names, or personal emails | Pass | Text scan found no known local identifiers. |
+| No WakeSchool ABM source code or DNS solver files | Pass | Artifact contains processed HDF5 datasets, Python benchmark utilities, result CSVs, figures, tables, and documentation only. |
+| No unrelated data | Pass | Included full processed benchmark HDF5 files, sample HDF5, result CSVs, configs, documentation, and generated verification outputs. |
+| All included HDF5 files have checksums | Pass | See `data/checksums.sha256`. |
+| `verify_dataset.py` runs on sample data | Pass | Verified `data/sample/sparsewake_sample.h5`. |
+| Table-generation script runs from stored CSVs | Pass | `scripts/reproduce_tables.py` wrote CSV tables to `tables/`. |
+| Main figure-generation script runs from stored CSVs | Pass | `scripts/make_main_figures.py` wrote PDF/SVG figures. |
+| Supplement figure-generation script runs from stored CSVs | Pass | `scripts/make_supp_figures.py` wrote PDF/SVG figures. |
+| Quick training smoke test runs on sample data | Pass | `scripts/train_temporal_mlp.py --quick` completed and wrote quick metrics. |
+| README, dataset card, evaluation card, provenance, and Croissant metadata exist | Pass | Required documentation files are present. |
+| Manuscript numbers traceable to CSV or result summary | Pass | Clean summaries are in `data/results/`; source traceability is documented in the cards and manifest. |
+
+## Tested Commands
+
+```bash
+python scripts/verify_dataset.py --data data/sample/sparsewake_sample.h5
+python scripts/train_temporal_mlp.py --config configs/main_v04.yaml --data data/sample/sparsewake_sample.h5 --quick
+python scripts/reproduce_tables.py --results data/results --out tables
+python scripts/make_main_figures.py --results data/results --out figures
+python scripts/make_supp_figures.py --results data/results --out figures
+```
+
+## Manual Items Before Upload
+
+- Confirm `data/processed/download_manifest.json` uses relative paths or anonymous hosted paths.
+- Run a formal Croissant validator if required by the final artifact platform.
+- Confirm final license wording is CC BY 4.0.

AUDIT_REPORT.md

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+# SparseWake Artifact Audit Report
+
+Audit date: 2026-05-06
+
+Scope: anonymous SparseWake dataset release. The manuscript source checked for consistency was `main_v11.tex`; it was read but not compiled or edited.
+
+## Overall Status
+
+| Requirement | Status | Notes |
+|---|---|---|
+| Anonymous release contents | PASS WITH ACTION | Release tree text scan found no author names, private emails, private repository URLs, local paths, usernames, machine names, or institution names. The parent repository `.git` history is not anonymous and must not be included in the review ZIP. |
+| Manuscript-to-artifact coverage | PASS WITH NOTES | Manuscript datasets, tables, result summaries, and referenced figure PDFs are present. Main and supplement figure PDFs are included under manuscript-compatible paths. |
+| HDF5 benchmark data | PASS | Three full processed HDF5 files and one sample HDF5 are present. HDF5 root/dataset attributes contain no identity metadata. |
+| Reproducible benchmark code | PASS | Sample verification, table reproduction, figure reproduction, and quick training smoke test run from the release tree. |
+| Data integrity | PASS | Checksums are listed in `data/checksums.sha256`; `scripts/verify_dataset.py` can verify sample structure and checksum entries. |
+| Documentation | PASS | README, dataset card, evaluation card, provenance, field documentation, limitations, license, CITATION.cff, Croissant metadata, audit report, manifest, and release checklist are present. |
+| Double-blind packaging | PASS WITH ACTION | Package the release-tree contents only. Do not package the parent repository `.git` directory or development logs outside the release tree. |
+
+## Manuscript-to-Artifact Manifest
+
+| Manuscript item | Expected artifact file | Status | Notes |
+|---|---|---|---|
+| Benchmark overview figure, `figures/main/Fig1.pdf` | `figures/main/Fig1.pdf` | PASS | PDF included; embedded local source reference was anonymized. |
+| Main localization figure, `figures/main/Fig2.pdf` | `figures/main/Fig2.pdf`; reproducible summary figure `figures/fig02_main_results.*` | PASS | Main PDF included; script-generated PDF/SVG also present. |
+| Self-signal figure, `figures/main/Fig3.pdf` | `figures/main/Fig3.pdf`; reproducible summary figure `figures/fig03_self_signal_control.*` | PASS | Main PDF included; script-generated PDF/SVG also present. |
+| Architecture screen figure, `figures/supp/Fig4.pdf` | `figures/supp/Fig4.pdf`; `figures/figS4_architecture_screen.*` | PASS | CSV source: `data/results/model_screen.csv`. |
+| Noise/SNR diagnostics, `figures/supp/Fig5.pdf` | `figures/supp/Fig5.pdf`; CSV source `data/results/noise_snr_diagnostics.csv` | PASS | Figure PDF included. |
+| Orientation diagnostics, `figures/supp/Fig6.pdf` | `figures/supp/Fig6.pdf`; CSV source `data/results/orientation_metrics.csv` | PASS | Figure PDF included. |
+| Sample-size convergence, `figures/supp/Fig7.pdf` | `figures/supp/Fig7.pdf`; `figures/figS5_sample_size_convergence.*` | PASS | CSV source: `data/results/sample_size_convergence.csv`. |
+| Dataset validation, `figures/supp/Fig8.pdf` | `figures/supp/Fig8.pdf` | PASS | Figure PDF included. |
+| Spatial error heatmap, `figures/supp/Fig9.pdf` | `figures/supp/Fig9.pdf` | PASS | Figure PDF included. |
+| Benchmark specification table | `README.md`, `docs/benchmark_protocol.md`, `docs/data_fields.md` | PASS | Protocol, fields, sensors, labels, metrics, and split are documented. |
+| Dataset roles table | `data/processed/README.md`, `data/processed/download_manifest.json` | PASS | Role names map to release HDF5 files. |
+| Architecture-screen pilot | `data/results/model_screen.csv`, `configs/model_screen.yaml` | PASS | Result summary included; pilot HDF5 is not released as a separate full dataset because it is auxiliary. |
+| External component benchmark | `data/processed/abm_sensing_dataset_v04_close_orient30_potential_160k.h5` | PASS | Contains wake-only, potential-only, wake-plus-potential, labels, poses, regions, and sensor world positions. |
+| Paired self-signal controls, aligned | `data/processed/abm_sensing_dataset_v05_self_external_paired_160k_compressed.h5` | PASS | Contains external-only, self-only, and total-like arrays. |
+| Paired self-signal controls, randomized orientation | `data/processed/abm_sensing_dataset_v05_self_external_orient30_160k.h5` | PASS | Contains external/self/total arrays for randomized follower orientation. |
+| History sweep H=1,4,8,16,24 | `data/results/main_numbers.csv`, `data/results/v04_h_sweep_summary_table.csv` | PASS | Values match manuscript prose within rounding. |
+| Full-state `location_theta` | `data/results/orientation_metrics.csv`, `configs/main_v04.yaml` | PASS | Close-wake position RMSE `0.040` and heading MAE `0.53 deg` trace to CSV. |
+| Sensor ablation 6,4,3,2 sensors | `data/results/sensor_ablation.csv`, `data/results/v04_sensor_subset_summary_table.csv` | PASS | All counts referenced in the manuscript are present. |
+| Common raw-noise stress test | `data/results/component_noise.csv`, `data/results/v04_component_common_noise_summary_table.csv` | PASS | Potential-only, wake-only, and wake-plus-potential rows are present. |
+| Self-signal controls | `data/results/aligned_self_signal_control.csv`, `data/results/self_signal_randomized.csv`, `data/results/v05_self_control_table.csv` | PASS | Aligned and randomized-orientation controls are present. |
+| Total-like noise robustness | `data/results/v05_total_noise_table.csv`, `data/results/main_numbers.csv` | PASS | Noise multipliers through 0.05 are present. |
+| Sample-size convergence | `data/results/sample_size_convergence.csv`, `configs/sample_size.yaml` | PASS | 500, 1000, 2500, and 4000 training-pose conditions are present. |
+| Compute report | `data/results/compute_resources.csv`, this report | PASS WITH UNCERTAINTY | Exact CPU/GPU/RAM were not logged in the frozen run and are marked unresolved below. |
+
+## Data and Code Checks
+
+HDF5 files checked:
+
+| File | Status | Notes |
+|---|---|---|
+| `data/processed/abm_sensing_dataset_v04_close_orient30_potential_160k.h5` | PASS | `160000` samples; fields include `X_raw`, `X_wake_raw`, `X_potential_raw`, `y`, `groups`, `region_id`, `follower_pose`, `leader_pose`, and `sensor_world_positions`. |
+| `data/processed/abm_sensing_dataset_v05_self_external_orient30_160k.h5` | PASS | `160000` samples; includes external, self, and total-like component arrays. |
+| `data/processed/abm_sensing_dataset_v05_self_external_paired_160k_compressed.h5` | PASS | `160000` samples; includes aligned paired self-signal component arrays. |
+| `data/sample/sparsewake_sample.h5` | PASS | `2048` samples and explicit `pose_id`; used for smoke tests. |
+
+Implementation checks:
+
+| Check | Status | Notes |
+|---|---|---|
+| Global follower coordinates excluded from model inputs | PASS | Training code loads only selected `X_*` component arrays as `input`; `follower_pose` and `sensor_world_positions` remain metadata. |
+| Held-out-pose test logic | PASS | `src/sparsewake/splits.py` matches the experiment driver: `default_rng(seed).choice` selects held-out test poses, then sklearn `train_test_split(..., test_size=0.15, random_state=seed)` splits the remaining samples into train/validation. |
+| Train-set-only standardization | PASS | `src/sparsewake/train.py` fits input mean/std only on `train_idx`. |
+| `raw_norm` feature dimension | PASS | `src/sparsewake/features.py` produces `37` features per time step for six sensors and `888` dimensions for H=24. |
+| Main metric implementation | PASS | Position RMSE and circular `theta_rel` MAE are implemented in `src/sparsewake/metrics.py`. |
+
+## Anonymity Scan
+
+Text files scanned: Markdown, Python, YAML, JSON, CSV, CFF, SVG, checksum, and text files in the release tree.
+
+Binary/metadata checked: HDF5 root and dataset attributes; PDF/SVG metadata and raw byte search for known local identifiers and path patterns.
+
+Findings:
+
+- Release tree text scan: PASS.
+- Croissant metadata: PASS. It uses anonymous creator/citation fields and contains no creator email, publisher institution, private URL, or local path.
+- HDF5 attributes: PASS. Full HDF5 files have no root or dataset attributes; sample HDF5 attributes are generic.
+- PDF/SVG metadata: PASS after sanitizing one embedded local source-file reference in `figures/main/Fig1.pdf`. Remaining creator/producer metadata names software only, such as Matplotlib or Adobe PDF library.
+- Git history: FAIL FOR PARENT REPOSITORY. The parent repository history contains author names, emails, and a private remote path. Do not include `.git` in the anonymous ZIP.
+
+## Commands Tested
+
+These commands were run from the release-tree root:
+
+```bash
+python scripts/verify_dataset.py --data data/sample/sparsewake_sample.h5
+..\.venv\Scripts\python.exe scripts/train_temporal_mlp.py --config configs/main_v04.yaml --data data/sample/sparsewake_sample.h5 --quick
+python scripts/reproduce_tables.py --results data/results --out tables
+python scripts/make_main_figures.py --results data/results --out figures
+python scripts/make_supp_figures.py --results data/results --out figures
+```
+
+Additional structural checks:
+
+```bash
+..\.venv\Scripts\python.exe -c "import sys; sys.path.insert(0,'src'); from sparsewake.data import load_h5; from sparsewake.features import raw_norm_features, build_design_matrix; d=load_h5('data/sample/sparsewake_sample.h5'); print(raw_norm_features(d['input']).shape); print(build_design_matrix(d, history=24)[0].shape)"
+git log --all --format="%H %an %ae %s" -n 40
+```
+
+The default system `python` environment did not include `torch`; the repository virtual environment did. A fresh reviewer environment should install `requirements.txt` or `environment.yml`.
+
+## Files Changed During Audit
+
+| File | Change |
+|---|---|
+| `src/sparsewake/features.py` | Corrected `raw_norm` to match `abm_sensing_dataset/experiments/sensing_v2/feature_builders.py`: raw channels, normalized raw channels, and one denominator per time step. |
+| `src/sparsewake/splits.py` | Corrected split helper to match `run_sensing_v2_experiments.py::make_pose_holdout`: held-out test poses via `default_rng(seed).choice`, then sklearn train/validation split within non-test samples. |
+| `requirements.txt`, `environment.yml` | Added `scikit-learn` because the actual experiment split uses `sklearn.model_selection.train_test_split`. |
+| `scripts/verify_dataset.py` | Added checksum verification option. |
+| `README.md` | Added checksum verification to the sample verification command. |
+| `dataset_card.md` | Corrected train/validation/test protocol wording. |
+| `docs/benchmark_protocol.md` | Corrected split protocol wording. |
+| `evaluation_card.md` | Corrected split protocol wording. |
+| `figures/main/Fig1.pdf`, `figures/main/Fig2.pdf`, `figures/main/Fig3.pdf` | Added manuscript-compatible main figure PDFs; sanitized embedded source path in Fig1. |
+| `figures/supp/Fig4.pdf` through `figures/supp/Fig9.pdf` | Added manuscript-compatible supplement figure PDFs. |
+| `tables/quick_train_metrics.json` | Updated by smoke-test training. |
+| `AUDIT_REPORT.md` | Added this report. |
+| `RELEASE_CHECKLIST.md` | Added final upload checklist. |
+| `MANIFEST.json` | Added generated file manifest. |
+| `data/checksums.sha256` | Updated final checksums. |
+
+## Unresolved Issues Before Upload
+
+1. `data/processed/download_manifest.json` should contain relative paths or anonymous hosted paths for the full HDF5 files.
+2. The parent repository `.git` history is not anonymous. The final review upload must contain only release-tree contents and must not include `.git`.
+3. Exact CPU/GPU model, RAM, MATLAB version, and dataset-generation wall time were not logged in the frozen run. The artifact reports conservative wall-clock times for representative three-seed runs and marks hardware details as unknown.
+4. The architecture-screen pilot is represented by summary CSV/config rather than a separate pilot HDF5 release. This is consistent with the manuscript role because the pilot is auxiliary; reviewers can reproduce benchmark evaluation from the released full processed HDF5 files.
+
+## Manuscript Statements Needing Revision
+
+No numeric scientific result needed revision based on this audit.
+
+Recommended non-scientific wording if the artifact is hosted outside the review system: state that the full processed HDF5 files are included directly in the anonymous dataset repository.

CITATION.cff

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+cff-version: 1.2.0
+title: "SparseWake: Processed Benchmark Artifact"
+message: "If you use this benchmark, cite the SparseWake dataset release and the upstream simulator source paper where applicable."
+type: dataset
+authors:
+  - name: "Anonymous Authors"
+    affiliation: "Anonymous"
+date-released: 2026-05-04
+version: "0.1.0"
+keywords:
+  - hydrodynamic sensing
+  - fish schooling
+  - benchmark
+  - temporal learning
+  - pose holdout

LICENSE

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+Creative Commons Attribution 4.0 International (CC BY 4.0)
+
+This SparseWake dataset release is licensed under the Creative Commons
+Attribution 4.0 International license.
+
+You are free to share and adapt the released processed datasets, metadata,
+summary tables, documentation, and release utilities for any purpose, provided
+that appropriate credit is given, a link to the license is provided, and changes
+are indicated.
+
+License text: https://creativecommons.org/licenses/by/4.0/
+
+The upstream fish-schooling simulator source code, high-fidelity solver assets,
+MATLAB simulator-query code, and simulator internals are not redistributed in
+this dataset release and are not covered by this license.

MANIFEST.json

@@ -0,0 +1,596 @@
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+  "generated_date": "2026-05-06",
+  "file_count": 98,
+  "notes": "The MANIFEST.json self-checksum is intentionally null. data/checksums.sha256 contains the checksum for MANIFEST.json and all other listed files except itself.",
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+      "sha256": "b8fea3d44907ebbbeb239e0f87def362bd6d44926adffd92d3d0ceaf0738f7de",
+      "purpose": "reproduced table output copied from stored summaries"
+    },
+    {
+      "path": "tables/v05_self_control_table.csv",
+      "size_bytes": 3558,
+      "sha256": "3dff6ff8dfc60fac223793a0ad09b75e0d05b58c1d323947ec7c1fe6d09d13cb",
+      "purpose": "reproduced table output copied from stored summaries"
+    },
+    {
+      "path": "tables/v05_total_noise_table.csv",
+      "size_bytes": 6477,
+      "sha256": "e5b2055b4b68b36ecb144357f08a284cf4a76d36a344b27d0e866d2f2bb46123",
+      "purpose": "reproduced table output copied from stored summaries"
+    }
+  ]
+}

README.md

@@ -8,62 +8,114 @@ tags:
 - time-series
 - regression
 - physical-sensing
+- hdf5
+- fish-schooling
 ---
 
-# Dataset Name
-SparseWake
+# SparseWake
 
-## Dataset summary
+SparseWake is an anonymous benchmark artifact for sparse temporal hydrodynamic sensing. It contains processed HDF5 datasets, metadata, summary CSV files, figures, checksums, and lightweight Python scripts for inspecting the data and reproducing benchmark-level evaluation outputs.
 
-SparseWake evaluates whether sparse body-fixed temporal flow measurements can recover the relative state of a neighboring wake-producing fish in a controlled single-leader setting. The benchmark contains processed synthetic data generated from a DNS-parameterized fish-schooling agent-based model.
+## Dataset Summary
 
-The released data support the evaluation protocol described in the anonymous submission: held-out follower poses, temporal-history sweeps, sensor-count ablations, component-separated flow inputs, common raw-noise stress tests, and self-signal controls.
+SparseWake evaluates whether sparse body-fixed temporal flow measurements can recover the relative state of a neighboring wake-producing fish in a controlled single-leader setting. The benchmark data are synthetic and were generated from a DNS-parameterized fish-schooling agent-based model. The artifact starts from processed HDF5 files and does not require the upstream simulator or high-fidelity solver.
 
-## What is included
+The released data support held-out-pose evaluation, temporal-history sweeps, sensor-count ablations, component-separated flow inputs, common raw-noise stress tests, sample-size convergence checks, architecture screening summaries, and paired self-signal controls.
 
-- Processed HDF5 benchmark files.
-- Dataset metadata and sensor coordinates.
-- Held-out-pose split protocol.
-- Summary CSV files for reported tables and figures.
-- Lightweight loading and verification scripts.
-- Checksums and file manifest.
+## What Is Included
 
-## What is not included
+- Full processed HDF5 benchmark datasets in `data/processed/`.
+- A small sample HDF5 file in `data/sample/` for inspection and smoke tests.
+- Dataset metadata, schema documentation, split protocol, provenance notes, and limitations in `docs/`.
+- Summary CSV files for reported tables and figures in `data/results/`.
+- Reproduced table CSVs in `tables/`.
+- Manuscript-compatible figure PDFs and script-generated figure outputs in `figures/`.
+- Lightweight loading, verification, plotting, and smoke-test training scripts in `scripts/`.
+- Minimal reusable Python utilities in `src/sparsewake/`.
+- Checksums in `data/checksums.sha256` and a full file manifest in `MANIFEST.json`.
+- Croissant-style metadata in `croissant_metadata.json`.
 
-The upstream fish-schooling ABM source code and the underlying high-fidelity CFD solver are not redistributed. The release is intended to reproduce benchmark evaluations from the processed HDF5 files, not to regenerate the DNS-parameterized wake library from first principles.
+## Main Files
 
-## Intended use
+| Path | Purpose |
+|---|---|
+| `data/processed/abm_sensing_dataset_v04_close_orient30_potential_160k.h5` | Main external component benchmark with wake-only, potential-only, and wake-plus-potential signals. |
+| `data/processed/abm_sensing_dataset_v05_self_external_paired_160k_compressed.h5` | Paired aligned-orientation self-signal control with external-only, self-only, and total-like external-plus-self arrays. |
+| `data/processed/abm_sensing_dataset_v05_self_external_orient30_160k.h5` | Randomized-orientation self-signal control with external-only, self-only, and total-like arrays. |
+| `data/sample/sparsewake_sample.h5` | Small sample file for quick inspection and smoke tests. |
+| `docs/data_fields.md` | HDF5 fields, shapes, and label definitions. |
+| `docs/benchmark_protocol.md` | Evaluation split, feature construction, standardization, and metrics. |
+| `docs/provenance.md` | Data-generation provenance and non-redistributed upstream components. |
+| `dataset_card.md` | Dataset-card details beyond this landing page. |
+| `evaluation_card.md` | Benchmark task, metrics, ablations, and expected summary numbers. |
+| `scripts/verify_dataset.py` | HDF5 structure and checksum verifier. |
+| `scripts/train_temporal_mlp.py` | Small temporal-MLP smoke test and rerun utility. |
+| `scripts/reproduce_tables.py` | Copies stored summary CSVs into `tables/`. |
+| `scripts/make_main_figures.py`, `scripts/make_supp_figures.py` | Recreate lightweight figures from stored CSV summaries. |
 
-This dataset is intended for evaluating sparse temporal physical sensing, hydrodynamic neighbor-state estimation, and reproducibility of the reported benchmark protocol.
+## What Is Not Included
 
-## Not Intended Use
+The upstream fish-schooling ABM source code, DNS solver files, MATLAB simulator-query code, and simulator internals are not redistributed. This release is intended to reproduce benchmark evaluations from processed HDF5 files, not to regenerate the DNS-parameterized wake library from first principles.
 
-SparseWake is not a full biological lateral-line pressure model, a multi-neighbor schooling model, or a replacement for direct CFD solvers.
+## Intended Use
 
-## Data Source
+SparseWake is intended for evaluating sparse temporal physical sensing, hydrodynamic neighbor-state estimation, robustness under controlled flow-component and noise protocols, and reproducibility of benchmark-level evaluation summaries.
 
-The processed data were generated from WakeSchool, an external fish-schooling simulator with DNS-parameterized wake and body-flow components. The artifact starts from processed HDF5 benchmark datasets and does not redistribute simulator source code.
+## Out-of-Scope Use
 
-## Released Fields
+SparseWake should not be treated as a complete biological lateral-line model, a full natural fish-schooling simulator, a pressure/shear sensing dataset, a direct CFD replacement, or a validation dataset for multi-neighbor closed-loop schooling behavior.
 
-- `X_raw`: wake-plus-potential induced velocity features, sample shape `[N, 6, 3]` after loading.
-- `X_wake_raw`: wake-only induced velocity features where available.
-- `X_potential_raw`: potential-only induced velocity features where available.
-- `X_external_raw`, `X_self_raw`, `X_total_raw`: self-signal controls where available.
+## Data Structure
+
+HDF5 arrays are stored in MATLAB-style or sample-first layouts depending on source export; `src/sparsewake/data.py` loads them sample-first. Core fields include:
+
+- `X_raw`: wake-plus-potential body-frame induced-velocity features.
+- `X_wake_raw`: wake-only component where available.
+- `X_potential_raw`: potential-only component where available.
+- `X_external_raw`, `X_self_raw`, `X_total_raw`: paired self-signal controls where available.
 - `y`: labels with columns `delta_x`, `delta_y`, `theta_rel`, `sin_phi`, `cos_phi`, `phi`.
 - `groups`: wake phase index.
-- `pose_id`: pose index for pose-holdout splitting in the sample dataset; full datasets can derive it from phase blocks.
-- `region_id`: region code for close wake, near side, and mid wake.
+- `region_id`: sampling region code.
 - `sensor_world_positions`: sensor coordinates for each sample.
 
-## Units and Conventions
+See `docs/data_fields.md` for the full schema and `docs/benchmark_protocol.md` for the split and feature protocol.
+
+## Quick Start
+
+```bash
+python -m venv .venv
+.venv/Scripts/pip install -r requirements.txt
+python scripts/verify_dataset.py --data data/sample/sparsewake_sample.h5 --checksums data/checksums.sha256
+python scripts/train_temporal_mlp.py --config configs/main_v04.yaml --data data/sample/sparsewake_sample.h5 --quick
+python scripts/reproduce_tables.py --results data/results --out tables
+```
+
+On Unix-like systems, use `.venv/bin/pip` and `.venv/bin/python`.
+
+## Reproduce Stored Tables and Figures
+
+```bash
+python scripts/reproduce_tables.py --results data/results --out tables
+python scripts/make_main_figures.py --results data/results --out figures
+python scripts/make_supp_figures.py --results data/results --out figures
+```
+
+These commands use stored summary CSV files and are intended for fast verification. Full training reruns are supported by `scripts/train_temporal_mlp.py` and `scripts/run_main_evaluation.py` when the full processed HDF5 files are present.
+
+## License
 
-Lengths are nondimensionalized by fish body length. Angles are stored in radians. Reported orientation metrics use degrees. The fish body is represented with semi-axes `a = 0.5 L` and `b = 0.075 L`.
+The SparseWake processed datasets, metadata, result summaries, documentation, and release utilities are made available under the Creative Commons Attribution 4.0 International license (CC BY 4.0). Upstream simulator source code and solver assets are not redistributed and are not covered by this dataset release.
 
-## Sensor Layout
+## Citation
 
-Six body-fixed sensors are arranged as anterior, midbody, and posterior left/right pairs. Sensor names are stored in documentation and sample HDF5 attributes.
+During anonymous review, cite this dataset as:
 
-## Ethical Considerations
+```bibtex
+@dataset{sparsewake_anonymous,
+  title = {SparseWake: A Temporal Hydrodynamic Sensing Benchmark},
+  author = {{Anonymous Authors}},
+  year = {2026}
+}
+```
 
-The dataset is synthetic fluid-dynamics data. It contains no human subjects, no animal measurements, and no personal data.
+Author-identifying contact information is intentionally omitted during anonymous review.

RELEASE_CHECKLIST.md

@@ -0,0 +1,34 @@
+# SparseWake Anonymous Release Checklist
+
+## Required Before Upload
+
+- [ ] Upload only the release-tree contents; do not include the parent `.git` directory.
+- [ ] Confirm the three full HDF5 files are present in `data/processed/`.
+- [ ] Run `python scripts/verify_dataset.py --data data/sample/sparsewake_sample.h5 --checksums data/checksums.sha256` after final packaging contents are fixed.
+- [ ] Confirm `MANIFEST.json` and `data/checksums.sha256` match the final upload contents.
+- [ ] Inspect the uploaded file list for hidden files, notebooks, local logs, cache folders, and OS metadata.
+- [ ] Do not include development directories outside the artifact tree.
+- [ ] Confirm Croissant metadata remains anonymous and does not contain creator email, institution, publisher, non-anonymous URL, or local path.
+- [ ] Confirm the license is listed as `cc-by-4.0` in the dataset card.
+
+## Reviewer Smoke-Test Commands
+
+```bash
+python -m venv .venv
+.venv/Scripts/pip install -r requirements.txt
+python scripts/verify_dataset.py --data data/sample/sparsewake_sample.h5 --checksums data/checksums.sha256
+python scripts/train_temporal_mlp.py --config configs/main_v04.yaml --data data/sample/sparsewake_sample.h5 --quick
+python scripts/reproduce_tables.py --results data/results --out tables
+python scripts/make_main_figures.py --results data/results --out figures
+python scripts/make_supp_figures.py --results data/results --out figures
+```
+
+Use `.venv/bin/pip` and `.venv/bin/python` on Unix-like systems.
+
+## Final Manual Review
+
+- [ ] README states benchmark purpose, dataset structure, HDF5 fields, targets, sensors, splits, metrics, reproduction commands, compute expectations, limitations, license, and citation.
+- [ ] Dataset card states synthetic/simulated origin, intended and out-of-scope use, limitations, no human or private data, and why upstream simulator/source code is not redistributed.
+- [ ] Referenced figures exist at `figures/main/Fig1.pdf` through `Fig3.pdf` and `figures/supp/Fig4.pdf` through `Fig9.pdf`.
+- [ ] Stored summary CSVs in `data/results/` match manuscript tables and figures within rounding tolerance.
+- [ ] `AUDIT_REPORT.md` lists unresolved issues, changed files, tested commands, and revision notes.

configs/main_v04.yaml

@@ -0,0 +1,10 @@
+name: main_v04
+data: data/processed/abm_sensing_dataset_v04_close_orient30_potential_160k.h5
+input_key: X_raw
+target: location_theta
+feature_set: raw_norm
+history: 24
+seed: 1
+epochs: 50
+batch_size: 1024
+

configs/model_screen.yaml

@@ -0,0 +1,16 @@
+name: model_screen
+data: data/processed/abm_sensing_dataset_v04_close_orient30_potential_160k.h5
+input_key: X_raw
+target: location
+feature_set: raw_norm
+history: 16
+seed: 1
+models:
+  - mean
+  - ridge
+  - random_forest
+  - single_frame_mlp
+  - temporal_mlp
+  - residual_tcn
+  - transformer
+

configs/sample_size.yaml

@@ -0,0 +1,15 @@
+name: sample_size
+data: data/processed/abm_sensing_dataset_v04_close_orient30_potential_160k.h5
+input_key: X_raw
+target: location
+feature_set: raw_norm
+history: 24
+seed: 1
+epochs: 50
+batch_size: 1024
+training_poses:
+  - 500
+  - 1000
+  - 2500
+  - 4000
+

configs/self_signal_randomized.yaml

@@ -0,0 +1,10 @@
+name: self_signal_randomized
+data: data/processed/abm_sensing_dataset_v05_self_external_orient30_160k.h5
+input_key: X_total_raw
+target: location_theta
+feature_set: raw_norm
+history: 24
+seed: 1
+epochs: 50
+batch_size: 1024
+

croissant_metadata.json

@@ -0,0 +1,95 @@
+{
+  "@context": {
+    "@language": "en",
+    "@vocab": "https://schema.org/",
+    "cr": "http://mlcommons.org/croissant/"
+  },
+  "@type": "cr:Dataset",
+  "name": "SparseWake",
+  "description": "Processed benchmark data for sparse temporal hydrodynamic relative-state estimation from body-fixed induced-flow histories.",
+  "license": "https://creativecommons.org/licenses/by/4.0/",
+  "version": "0.1.0",
+  "datePublished": "2026-05-04",
+  "creator": [
+    {
+      "@type": "Person",
+      "name": "Anonymous Authors"
+    }
+  ],
+  "citeAs": "Anonymous Authors. SparseWake: Processed Benchmark Artifact. 2026.",
+  "keywords": [
+    "hydrodynamic sensing",
+    "fish schooling",
+    "temporal learning",
+    "benchmark",
+    "pose holdout"
+  ],
+  "isAccessibleForFree": true,
+  "distribution": [
+    {
+      "@type": "cr:FileObject",
+      "@id": "sample_h5",
+      "name": "sparsewake_sample.h5",
+      "contentUrl": "data/sample/sparsewake_sample.h5",
+      "encodingFormat": "application/x-hdf5"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "main_external_component_h5",
+      "name": "abm_sensing_dataset_v04_close_orient30_potential_160k.h5",
+      "contentUrl": "data/processed/abm_sensing_dataset_v04_close_orient30_potential_160k.h5",
+      "encodingFormat": "application/x-hdf5"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "self_signal_randomized_h5",
+      "name": "abm_sensing_dataset_v05_self_external_orient30_160k.h5",
+      "contentUrl": "data/processed/abm_sensing_dataset_v05_self_external_orient30_160k.h5",
+      "encodingFormat": "application/x-hdf5"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "self_signal_paired_h5",
+      "name": "abm_sensing_dataset_v05_self_external_paired_160k_compressed.h5",
+      "contentUrl": "data/processed/abm_sensing_dataset_v05_self_external_paired_160k_compressed.h5",
+      "encodingFormat": "application/x-hdf5"
+    }
+  ],
+  "recordSet": [
+    {
+      "@type": "cr:RecordSet",
+      "name": "sensor_samples",
+      "description": "Per-sample sparse induced-flow measurements and relative-state labels.",
+      "field": [
+        {
+          "@type": "cr:Field",
+          "name": "X_raw",
+          "description": "Six-sensor wake-plus-potential induced velocity features."
+        },
+        {
+          "@type": "cr:Field",
+          "name": "y",
+          "description": "Labels: delta_x, delta_y, theta_rel, sin_phi, cos_phi, phi."
+        },
+        {
+          "@type": "cr:Field",
+          "name": "region_id",
+          "description": "Sampling region code."
+        },
+        {
+          "@type": "cr:Field",
+          "name": "pose_id",
+          "description": "Pose identifier for pose-holdout evaluation."
+        }
+      ]
+    }
+  ],
+  "responsibleAI": {
+    "dataType": "Synthetic fluid-dynamics benchmark data",
+    "containsPersonalData": false,
+    "humanSubjects": false,
+    "intendedUse": "Evaluation of sparse temporal hydrodynamic state estimation",
+    "outOfScopeUses": "Biological pressure-sensing claims, direct CFD replacement, or multi-neighbor schooling claims"
+  },
+  "notes": "Full processed HDF5 files are included in the dataset repository."
+}

data/README.md

@@ -0,0 +1,8 @@
+# Data Directory
+
+`sample/` contains a small HDF5 subset for inspection and smoke tests.
+
+`processed/` contains the processed HDF5 benchmark datasets when archive size allows. If full datasets are hosted separately in the final submission, `processed/download_manifest.json` lists the expected files, sizes, checksums, and placeholder hosted URLs.
+
+`results/` contains cleaned CSV summaries used to reproduce tables and figures.
+

data/checksums.sha256

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data/processed/README.md

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+# Processed Datasets
+
+This directory contains processed HDF5 benchmark datasets when they are included in the archive.
+
+Expected full datasets:
+
+- `abm_sensing_dataset_v04_close_orient30_potential_160k.h5`: main component-separated benchmark with wake-only, potential-only, wake-plus-potential input arrays and full-state labels.
+- `abm_sensing_dataset_v05_self_external_paired_160k_compressed.h5`: aligned self-signal paired dataset used for aligned external/self controls.
+- `abm_sensing_dataset_v05_self_external_orient30_160k.h5`: randomized-orientation self-signal dataset used for full-state self-signal controls.
+
+The `download_manifest.json` file lists file sizes, checksums, and relative paths for the full processed HDF5 files.

data/processed/abm_sensing_dataset_v04_close_orient30_potential_160k.h5

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+version https://git-lfs.github.com/spec/v1
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+size 62085330

data/processed/abm_sensing_dataset_v05_self_external_orient30_160k.h5

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+size 142727282

data/processed/abm_sensing_dataset_v05_self_external_paired_160k_compressed.h5

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+oid sha256:42429c4e0bc676761c1340d4862e6054207fdaaca970b2210179862683d858ed
+size 73066310

data/processed/download_manifest.json

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+{
+  "datasets": [
+    {
+      "file": "abm_sensing_dataset_v04_close_orient30_potential_160k.h5",
+      "size_bytes": 62085330,
+      "sha256": "8c28e39b42881f16d93294a9c76c919e51ed417e26b01d7a03e101ceef772b5c",
+      "path": "data/processed/abm_sensing_dataset_v04_close_orient30_potential_160k.h5"
+    },
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+      "sha256": "85752a2464a504efc1d6536fe53b50ab3093da407fcd375d71ae09c532cc675a",
+      "path": "data/processed/abm_sensing_dataset_v05_self_external_orient30_160k.h5"
+    },
+    {
+      "file": "abm_sensing_dataset_v05_self_external_paired_160k_compressed.h5",
+      "size_bytes": 73066310,
+      "sha256": "42429c4e0bc676761c1340d4862e6054207fdaaca970b2210179862683d858ed",
+      "path": "data/processed/abm_sensing_dataset_v05_self_external_paired_160k_compressed.h5"
+    }
+  ]
+}

data/results/aligned_self_signal_control.csv

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data/results/component_noise.csv

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data/results/compute_resources.csv

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+item,wall_clock_minutes,environment,note
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+randomized self-signal external-only full-state H24,10.7,project Python environment,three-seed run from submission-freeze audit
+randomized self-signal external+self full-state H24,12.1,project Python environment,three-seed run from submission-freeze audit
+randomized self-signal self-only full-state H24,5.5,project Python environment,three-seed run from submission-freeze audit

data/results/main_numbers.csv

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data/results/model_screen.csv

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data/results/noise_snr_diagnostics.csv

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data/results/orientation_metrics.csv

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data/results/sample_size_convergence.csv

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data/results/self_signal_randomized.csv

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data/results/sensor_ablation.csv

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data/results/v04_component_common_noise_summary_table.csv

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data/results/v04_h_sweep_summary_table.csv

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data/results/v04_sensor_subset_summary_table.csv

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data/results/v05_history_sweep_table.csv

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data/results/v05_self_control_table.csv

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data/results/v05_total_noise_table.csv

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data/sample/README.md

@@ -0,0 +1,6 @@
+# Sample Dataset
+
+`sparsewake_sample.h5` is a small subset of the processed SparseWake HDF5 data. It preserves full wake phases for a limited set of poses so pose-holdout splitting and temporal-history construction can be checked quickly.
+
+This sample is for artifact inspection and smoke testing. It is not the source of manuscript numbers.
+

data/sample/sparsewake_sample.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0579020b85545717e25c880f676f9d9bb7b76a168c331f44391f5f86619ab4a1
+size 986951

dataset_card.md

@@ -0,0 +1,49 @@
+# Dataset Card: SparseWake
+
+## Dataset Name
+
+SparseWake
+
+## Intended Use
+
+Evaluation of sparse temporal hydrodynamic state estimation from body-fixed induced-flow histories.
+
+## Not Intended Use
+
+SparseWake is not a full biological lateral-line pressure model, a multi-neighbor schooling model, or a replacement for direct CFD solvers.
+
+## Data Source
+
+The processed data were generated from WakeSchool, an external fish-schooling simulator with DNS-parameterized wake and body-flow components. The artifact starts from processed HDF5 benchmark datasets and does not redistribute simulator source code.
+
+## Released Fields
+
+- `X_raw`: wake-plus-potential induced velocity features, sample shape `[N, 6, 3]` after loading.
+- `X_wake_raw`: wake-only induced velocity features where available.
+- `X_potential_raw`: potential-only induced velocity features where available.
+- `X_external_raw`, `X_self_raw`, `X_total_raw`: self-signal controls where available.
+- `y`: labels with columns `delta_x`, `delta_y`, `theta_rel`, `sin_phi`, `cos_phi`, `phi`.
+- `groups`: wake phase index.
+- `pose_id`: pose index for pose-holdout splitting in the sample dataset; full datasets can derive it from phase blocks.
+- `region_id`: region code for close wake, near side, and mid wake.
+- `sensor_world_positions`: sensor coordinates for each sample.
+
+## Units and Conventions
+
+Lengths are nondimensionalized by fish body length. Angles are stored in radians. Reported orientation metrics use degrees. The fish body is represented with semi-axes `a = 0.5 L` and `b = 0.075 L`.
+
+## Sensor Layout
+
+Six body-fixed sensors are arranged as anterior, midbody, and posterior left/right pairs. Sensor names are stored in documentation and sample HDF5 attributes.
+
+## Train/Validation/Test Protocol
+
+Main results use a held-out-pose test protocol. For each seed, 20% of follower pose identities are assigned to the test set, and all saved wake phases for those poses are withheld from training. The remaining non-test samples are split into training and validation with a 15% validation fraction. Thus the test set is pose-disjoint from training, while training and validation may contain different phases of the same non-test pose.
+
+## Known Limitations
+
+The current benchmark uses induced velocity rather than pressure, pressure gradients, or wall shear. It is single-neighbor unless explicitly stated. Multi-neighbor assignment, closed-loop control, and biological self-filtering are outside the released benchmark.
+
+## Ethical Considerations
+
+The dataset is synthetic fluid-dynamics data. It contains no human subjects, no animal measurements, and no personal data.

docs/benchmark_protocol.md

@@ -0,0 +1,11 @@
+# Benchmark Protocol
+
+1. Load a processed HDF5 dataset.
+2. Select an input component, such as `X_raw`, `X_wake_raw`, `X_potential_raw`, `X_external_raw`, `X_self_raw`, or `X_total_raw`.
+3. Construct temporal windows of length `H` using saved wake phases for each pose.
+4. Split by held-out test pose: all phases of each test pose are withheld. Split the remaining non-test samples into training and validation.
+5. Standardize inputs using training-set statistics only.
+6. Train the temporal MLP baseline or another model.
+7. Report global and close-wake position RMSE; report circular `theta_rel` MAE for full-state runs.
+
+The quick training command is for functionality testing only. Manuscript numbers come from stored summaries in `data/results/`.

docs/data_fields.md

@@ -0,0 +1,20 @@
+# Data Fields
+
+HDF5 arrays are loaded sample-first by `src/sparsewake/data.py`.
+
+| Field | Loaded shape | Description |
+|---|---:|---|
+| `X_raw` | `[N, 6, 3]` | Wake-plus-potential per-sensor induced velocity features. |
+| `X_wake_raw` | `[N, 6, 3]` | Wake-only component where available. |
+| `X_potential_raw` | `[N, 6, 3]` | Potential-only component where available. |
+| `X_external_raw` | `[N, 6, 3]` | External neighbor signal in self-signal datasets. |
+| `X_self_raw` | `[N, 6, 3]` | Self-generated signal in self-signal datasets. |
+| `X_total_raw` | `[N, 6, 3]` | External-plus-self signal in self-signal datasets. |
+| `y` | `[N, 6]` | `delta_x`, `delta_y`, `theta_rel`, `sin_phi`, `cos_phi`, `phi`. |
+| `groups` | `[N]` | Wake phase index. |
+| `pose_id` | `[N]` | Pose index for pose-holdout when present; otherwise derived from phase blocks. |
+| `region_id` | `[N]` | Region code: 1 close wake, 2 near side, 3 mid wake. |
+| `sensor_world_positions` | `[N, 6, 2]` | Sensor coordinates for each sample. |
+
+Raw velocity feature channels are body-frame `u`, body-frame `v`, and speed magnitude.
+

docs/known_limitations.md

@@ -0,0 +1,8 @@
+# Known Limitations
+
+- The released benchmark starts from processed HDF5 datasets and does not include simulator source code.
+- Signals are induced velocity, not biological lateral-line pressure, pressure-gradient, or shear measurements.
+- Main tasks are single-neighbor relative-state estimation.
+- Multi-neighbor ambiguity, closed-loop control, posture variation, and direct pressure sensing are not resolved by this artifact.
+- Quick-mode training is a smoke test and should not be compared to manuscript metrics.
+

docs/provenance.md

@@ -0,0 +1,10 @@
+# Provenance
+
+Generation chain:
+
+```text
+WakeSchool simulator (external cited model) -> processed HDF5 benchmark datasets -> feature construction -> pose-holdout training/evaluation -> figures/tables.
+```
+
+This artifact starts from processed HDF5 benchmark datasets. It does not redistribute the WakeSchool simulator source, DNS solver files, MATLAB simulator-query code, or simulator internals.
+

environment.yml

@@ -0,0 +1,12 @@
+name: sparsewake-artifact
+channels:
+  - conda-forge
+dependencies:
+  - python>=3.10
+  - numpy
+  - pandas
+  - h5py
+  - matplotlib
+  - pyyaml
+  - pytorch
+  - scikit-learn

evaluation_card.md

@@ -0,0 +1,50 @@
+# Evaluation Card
+
+## Benchmark Task
+
+Given a temporal history of six body-fixed induced-flow sensors, predict the leader-centered relative state of a nearby fish.
+
+## Inputs
+
+Inputs are sparse velocity histories from processed HDF5 arrays. The main feature sets are:
+
+- `raw`: raw per-sensor induced velocity features.
+- `raw_norm`: raw features plus amplitude-normalized velocity features and the local scale.
+
+## Targets
+
+Location-only runs predict `(delta_x, delta_y)`. Full-state runs predict `(delta_x, delta_y, theta_rel)`.
+
+## Metrics
+
+Position error is reported as `sqrt(RMSE_delta_x^2 + RMSE_delta_y^2)` in body lengths. Relative-orientation error is circular mean absolute error for `theta_rel`, reported in degrees.
+
+## Pose-Holdout Split
+
+All wake phases for each held-out test pose are assigned to the test partition. Training and validation are drawn from the remaining non-test samples, so training and validation may contain different phases of the same non-test pose. This matches the experiment driver and prevents repeated-pose leakage into the test set.
+
+## Main Ablations
+
+- History length.
+- Sensor ablation.
+- Flow component: wake-only, potential-only, wake-plus-potential.
+- Common raw-noise stress test.
+- Architecture screen.
+- Sample-size convergence.
+- Self-signal controls.
+
+## Noise Protocol
+
+Noise is added to raw `u/v` channels before feature construction and standardization. The component/noise sweep uses a common absolute raw-sensor noise scale across flow components.
+
+## Self-Signal Controls
+
+Aligned and randomized-orientation datasets separate external-only, self-only, and total-like external-plus-self signals. Self-only is a negative control for leakage.
+
+## Expected Manuscript Numbers
+
+Stored CSVs in `data/results/` contain the manuscript numbers. The main full-state close-wake result is approximately `0.040 L` position RMSE and `0.53 deg` `theta_rel` MAE. Randomized-orientation external-plus-self full-state control is approximately `0.087 L` close-wake position RMSE and `1.08 deg` close-wake `theta_rel` MAE.
+
+## Failure Modes and Limitations
+
+Potential-only inputs can be accurate without noise but fail under the common absolute noise stress test. Farther wake regions are harder than close-wake regions. The artifact does not evaluate full biological pressure sensing, multi-neighbor assignment, or closed-loop control.

figures/README.md

@@ -0,0 +1,6 @@
+# Figures
+
+Figure scripts write PDF and SVG outputs here from the CSV summaries in `data/results/`.
+
+The generated quick figures are for artifact verification. Manuscript figures may use additional layout polish but are traceable to the same stored result summaries.
+

figures/main/Fig1.pdf

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