neurotcs 1.35.0__tar.gz

neurotcs-1.35.0/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for describing the origin of the Work and
+      reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright 2026 Marufjon Salokhiddinov, MD PhD
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

neurotcs-1.35.0/PKG-INFO

@@ -0,0 +1,271 @@
+Metadata-Version: 2.4
+Name: neurotcs
+Version: 1.35.0
+Summary: Citation-locked, fail-closed longitudinal medical AI audit framework (NeuroTCS / temporalmetric).
+Author-email: "Marufjon Salokhiddinov, MD PhD" <drmaruf1991@gmail.com>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/DrMaruf1991/NeuroTCS
+Project-URL: Repository, https://github.com/DrMaruf1991/NeuroTCS
+Project-URL: Issues, https://github.com/DrMaruf1991/NeuroTCS/issues
+Keywords: medical-ai,longitudinal,audit,clinical-trial,regulatory,neuroimaging,alzheimer,alzheimers-disease,dementia,amyloid,tau,cdr,mci,fda,fhir
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pydantic>=2.5
+Requires-Dist: PyYAML>=6.0
+Requires-Dist: pandas>=2.0
+Requires-Dist: pyarrow>=14.0
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: reportlab>=4.0
+Requires-Dist: jsonschema>=4.0
+Requires-Dist: pyreadr>=0.4.7
+Requires-Dist: numpy>=1.24
+Requires-Dist: scipy>=1.11
+Provides-Extra: dev
+Requires-Dist: pytest>=7.4; extra == "dev"
+Requires-Dist: pytest-cov>=4.1; extra == "dev"
+Requires-Dist: ruff>=0.1.0; extra == "dev"
+Provides-Extra: fhir
+Requires-Dist: fhir.resources>=7.0; extra == "fhir"
+Dynamic: license-file
+
+# NeuroTCS
+
+**Citation-locked, fail-closed longitudinal medical AI audit framework.**
+
+[![CI](https://github.com/DrMaruf1991/NeuroTCS/actions/workflows/ci.yml/badge.svg)](https://github.com/DrMaruf1991/NeuroTCS/actions/workflows/ci.yml)
+[![License: Apache-2.0](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![Version 1.33.1](https://img.shields.io/badge/version-1.33.1-success.svg)](CHANGELOG.md)
+[![Tests 1437](https://img.shields.io/badge/tests-1437%20passed-success.svg)](tests/)
+[![Spec v1.7 FINAL](https://img.shields.io/badge/spec-v1.7_FINAL-success.svg)](docs/spec/temporalmetric_v1.7_FINAL.md)
+
+NeuroTCS audits the temporal coherence of longitudinal medical AI predictions against internationally endorsed published clinical guidelines. It answers the question regulators, hospitals, and trialists ask first: *does this AI model's visit-to-visit prediction trajectory obey the clinical biology it claims to predict?*
+
+The framework is anchored on Dr. Marufjon Salokhiddinov's ASNR 2026 presentation (Austin, May 2026) and the temporalmetric v1.7 FINAL technical specification.
+
+## Hallmark result — four-cohort triangulation lock
+
+Five locked audit invariants reproduce byte-exactly across N=5 cold reruns, numpy 2.0.2↔2.4.4, pyreadr 0.5.0↔0.5.6, on Linux and Windows. Max pairwise ΔcTCS = 0.009206 (ADNI vs MIRIAD), all 6 pairwise comparisons ≤ 0.01 world-class threshold.
+
+| Cohort | n_scored / n_total | Transitions | Flagged | cTCS | audit_id |
+|---|---:|---:|---:|---:|---|
+| OASIS-3 (Aim 2 external replication) | 1,377 | 7,248 | 30 (0.41%) | **0.994191** | `92df5429...` |
+| ADNI-2/3/4 (Aim 1, canonical R-format) | 2,958 / 3,762 | 12,006 | 65 (0.54%) | **0.994575** | `7a973f7b...` |
+| NACC UDS v73 (added v1.8) | 39,361 / 56,529 | 158,423 | 1,217 (0.77%) | **0.991502** | `58329c65...` |
+| MIRIAD longitudinal (Aim 3 A) | 69 | 454 | 7 (1.54%) | **0.985369** | `abda26cb...` |
+| MIRIAD test-retest (Aim 3 B) | 69 (pairs) | 69 | 0 (0.00%) | **1.000000** | `4de7f711...` |
+
+Each cohort also locks an `audit_id_v2` (C6 collision-resistant variant). See `tests/audit_core/test_real_*.py` for full locked-invariant constants, and [`docs/datasheet/ad_neurotcs_datasheet.md`](docs/datasheet/ad_neurotcs_datasheet.md) Section A for full audit_ids and methodology.
+
+The cTCS metric generalises across institution, decade, recruitment criteria, AND staging instrument. Three of the four cohorts use CDR-anchored staging; MIRIAD uses MMSE-anchored staging. The 4-cohort agreement at ≤0.01 ΔcTCS is the strongest cross-cohort evidence to date that the framework measures what it claims to measure.
+
+## What's in this repo
+
+NeuroTCS is the umbrella for seven engineering pieces plus five v1.7.0 methodological modules. Pieces 1–4 + 6 are production-shipped; Pieces 5 and 7 are roadmap items planned for v1.9.x (importing them raises a helpful `ImportError` pointing to the roadmap).
+
+| Piece | Subpackage | Status | Description |
+|---|---|---|---|
+| 1 | `neurotcs.input_contract.v1_0` | ✅ shipped | Categorical input contract (8-step validation, fail-closed) |
+| 2 | `neurotcs.input_contract.v1_1` | ✅ shipped | Continuous-biomarker contract with UCUM unit enforcement |
+| 3 | `neurotcs.rulepack` | ✅ shipped | **3 production AD rule packs** (NIA-AA 2018, AA 2024, AA 2024 TRAC) |
+| 4 | `neurotcs.audit_core` | ✅ shipped | cTCS / pTCS / uTCS engine + cluster bootstrap + BCa + Huber |
+| 5 | `neurotcs.output_schema` | 🗺️ roadmap v1.9.x | FHIR Observation emitter (importing raises ImportError) |
+| 6a | `neurotcs.input_contract.v1_1.adapters` | ✅ shipped | OASIS-3, ADNI (canonical R-format), NACC, MIRIAD trajectory loaders |
+| 6b | `neurotcs.reference_adapters` | ✅ shipped | Reference submission-builders for vendor onboarding (ADNI categorical + volumetric) |
+| 7 | `neurotcs.validation_harness` | 🗺️ roadmap v1.9.x | Synthetic-trajectory self-tests (importing raises ImportError) |
+
+Plus five methodological modules (all shipped in v1.7.0+, all with tests):
+
+- `neurotcs.sample_size` — external-validation precision per Riley 2024
+- `neurotcs.fairness` — FUTURE-AI Fairness + Robustness panels per Lekadir 2025 BMJ
+- `neurotcs.silent_deployment` — Kwong 2022 silent-trial methodology
+- `neurotcs.scanner_factorial` — Scanner × vendor × interval factorial robustness
+- `neurotcs.threshold_derivation` — Larson 2025 empirical operational thresholds
+
+## Rule packs shipped
+
+NeuroTCS v1.x is scope-narrowed to **Alzheimer's disease** in preparation for FDA Q-Submission (target Q1 2027). The 3 AD rule packs encode the dominant diagnostic and trajectory frameworks. See [docs/SCOPE.md](docs/SCOPE.md) for the scope-decision rationale; non-AD packs that previously shipped in v1.7.x (PD/Hoehn-Yahr, MS/McDonald, oncology RECIST + iRECIST, stroke mRS, lung-nodule Fleischner) have been extracted to seed future per-disease repositories post-FDA-clearance.
+
+| Pack | Disease | Anchor publication | PMID | Transitions |
+|---|---|---|---|---|
+| `ad/niaaa_2018@1.3.0` | Alzheimer's | Jack 2018 NIA-AA Framework | 29653606 | 4 + 2 inadmissible |
+| `ad/aa_2024@2.1.0` | Alzheimer's | Jack 2024 AA Revised Criteria | 38934362 | 28 + 17 inadmissible (Table 7 integrated staging, 17 states) |
+| `ad/aa_2024_trac@1.1.0` | Alzheimer's (anti-Aβ) | La Joie 2025 TRAC framework | 41298245 | 6 + 3 inadmissible (5 require `treatment_status`) |
+
+Each rule pack is:
+
+- **Citation-locked** — every transition requires `citation_pmid` or `citation_doi` AND `guideline_section` (exact section/table/figure pointer).
+- **Version-stamped** — canonical JSON SHA-256 hash computed at load time.
+- **Fail-closed** — Pydantic v2 strict mode rejects unknown fields, missing citations, inconsistent state spaces.
+
+**Schema v1.3.0** adds backward-compatible support for **context-conditional admissibility** (the TRAC pack uses this to encode that A+ → A− amyloid clearance is admissible *only* under anti-Aβ therapy) and `attribution_type` (clinical_inference vs guideline_quote, per ERRATA E-2026-003).
+
+## Authority model
+
+NeuroTCS rule packs do NOT require disease-specialist co-authorship to be authoritative. They require provenance to internationally endorsed published guidelines. The schema makes this explicit:
+
+- `clinical_source_authority` — names the peer-reviewed publication + endorsing professional society where clinical authority resides.
+- `transcribed_by` — names the board-certified physician who attests the YAML faithfully encodes the cited guideline.
+- `guideline_section` per transition — exact pointer so any reviewer can verify the transcription.
+- `reviewers` — additive specialist sign-off (non-blocking).
+
+This mirrors how FHIR / SNOMED / LOINC terminology encodings work. Authority lives in the cited publication, not in a co-author's signature.
+
+See [`docs/transcription_audit/`](docs/transcription_audit/) for side-by-side YAML ↔ source-paragraph audits.
+
+## Quick start
+
+```bash
+git clone https://github.com/DrMaruf1991/NeuroTCS.git
+cd NeuroTCS
+pip install -e .
+
+# Framework-only tests (no cohort data required) — expect 1437 passed, 13 skipped (v1.33.1)
+python -m pytest tests/ -q \
+    --ignore=tests/audit_core/test_real_adni_audit.py \
+    --ignore=tests/audit_core/test_real_oasis3_audit.py \
+    --ignore=tests/audit_core/test_real_nacc_audit.py \
+    --ignore=tests/audit_core/test_real_miriad_audit.py \
+    --ignore=tests/audit_core/test_real_miriad_fairness_audit.py \
+    --ignore=tests/audit_core/test_four_cohort_triangulation.py
+
+# Full suite with cohort data (set env vars first; expect 1437+cohort tests passed, cohort-version-dependent)
+export NEUROTCS_OASIS3_CDR=/path/to/OASIS3_UDSb4_cdr.csv
+export NEUROTCS_ADNI_DXSUM_RDA=/path/to/ADNIMERGE2/data/DXSUM.rda
+export NEUROTCS_NACC_CSV=/path/to/investigator_nacc73_slim.csv
+export NEUROTCS_MIRIAD_DIR=/path/to/MIRIAD_directory
+python -m pytest tests/ -q
+```
+
+The test count is environment-dependent: **1437 passed / 13 skipped** without cohort env vars (cohort tests skip; current as of v1.33.1). With all four cohort env vars pointing at valid files, the cohort tests additionally execute and pass; the exact pass count is cohort-version-dependent. Both outcomes are correct behavior.
+
+### Rule pack only
+
+```python
+from neurotcs import load_rulepack
+
+pack = load_rulepack("ad/niaaa_2018")
+ok, rule = pack.rulepack.is_admissible("CN", "AD", delta_t_days=200)
+print(ok)  # False — CN->AD requires >=365 days (Jack 2018)
+```
+
+### Full audit pipeline (canonical pattern)
+
+```python
+from neurotcs import audit, load_rulepack
+from neurotcs.input_contract.v1_1.adapters.adapter_adni_canonical import (
+    load_adni_trajectories,
+)
+
+pack = load_rulepack("ad/niaaa_2018")
+trajectories, report = load_adni_trajectories(
+    dxsum_rda_path="/path/to/ADNIMERGE2/data/DXSUM.rda",
+    hash_ids=False, skip_invalid=True,
+)
+result = audit(trajectories, pack, bootstrap_B=10_000, seed=42, ci_method="bca")
+
+print(f"cTCS:        {result.ctcs.ci.point:.6f}")   # 0.994575 (v1.20.0 locked)
+print(f"audit_id:    {result.audit_id}")            # 7a973f7b... (v1.20.0 locked)
+print(f"audit_id_v2: {result.audit_id_v2}")         # dda642ff... (v1.20.0 locked)
+result.to_json("report.json")
+```
+
+Worked examples for all four cohorts: see [`tests/audit_core/test_real_*.py`](tests/audit_core/) (each test reproduces a locked invariant) and [`examples/`](examples/) (runnable demos).
+
+### CLI
+
+```bash
+neurotcs-audit audit \
+  --predictions predictions.csv \
+  --rulepack ad/niaaa_2018 \
+  --output report.json \
+  --bootstrap 10000 --seed 42 \
+  --patient-col RID --date-col EXAMDATE --state-col DIAGNOSIS \
+  --state-label-map Dementia=AD
+```
+
+## Reviewer verification
+
+For third-party reviewers (FDA technical staff, pharma diligence, academic peer reviewers, hospital AI governance):
+
+- **v2 canonical protocol**: [`docs/reviewer_package/reviewer_verification_prompt.md`](docs/reviewer_package/reviewer_verification_prompt.md) — 8-step manual reproduction (~90 min). Produces signed YAML attestation.
+- **Cursor IDE prompt**: [`docs/reviewer_package/cursor_verification_prompt.md`](docs/reviewer_package/cursor_verification_prompt.md) — AI-guided execution (~30 min).
+- **Colab notebook**: [`docs/reviewer_package/NeuroTCS_v1.8.0_Reviewer_Verification.ipynb`](docs/reviewer_package/NeuroTCS_v1.8.0_Reviewer_Verification.ipynb) — browser-only zero-install preview (~10 min, synthetic-data demo).
+
+All three surfaces produce the same YAML attestation schema and reference the same locked invariants. The Colab path can only achieve `FRAMEWORK_INSTALL_VERIFIED` (DUA-controlled data cannot be uploaded to third-party cloud); local paths can achieve `FULL_REPRODUCED`.
+
+## Specification
+
+The canonical spec is [`docs/spec/temporalmetric_v1.7_FINAL.md`](docs/spec/temporalmetric_v1.7_FINAL.md). Read this to understand:
+
+- §A.2 — Coherence Temporal Consistency Score (cTCS) definition
+- §A.3 — Probabilistic TCS with matrix exponential M(Δτ) = exp(Q · Δτ / 365)
+- §A.4 — Unified TCS (weighted ensemble)
+- §A.5 — Cluster bootstrap (B = 10,000) + Huber M-estimation (c = 1.345)
+- §B.1 — Aims 1–6 validation plan
+- §B.2 — Required datasets (ADNI, OASIS-3, NACC, MIRIAD; ALZ-NET planned)
+- §B.6 — Rule pack registry and engineering discipline
+- §C — Library architecture
+
+## Roadmap to v0.2 / v1.0 / Q-Sub
+
+- **v1.8.0** (May 2026) — Four-cohort triangulation lock + ADNI canonical source. ✅ shipped.
+- **v1.8.1** (May 2026) — Documentation, test hygiene, CI matrix, reference-adapter reorganization, citation backfill. ✅ shipped.
+- **v1.9.0** (May 2026) — **AD-only scope contraction**: non-AD rule packs (PD, MS, oncology, stroke, lung nodule) extracted to seed future per-disease repositories post-FDA-clearance. ✅ shipped.
+- **v1.9.x** (Q3 2026) — Piece 5 (FHIR output) + Piece 7 (validation harness) + cohort-specific transition priors.
+- **W22 (~Sept 2026)** — Nature Medicine submission with AD validation across ADNI + OASIS-3 + NACC + MIRIAD.
+- **Oct 2026** — ASFNR Newport Beach workshop demo.
+- **Q1 2027** — FDA Q-Submission with v1.0.0 release.
+
+## Citation
+
+```bibtex
+@software{salokhiddinov2026neurotcs,
+  author    = {Salokhiddinov, Marufjon},
+  title     = {NeuroTCS: Citation-locked, fail-closed longitudinal medical AI audit framework},
+  version   = {1.20.0},
+  year      = {2026},
+  url       = {https://github.com/DrMaruf1991/NeuroTCS},
+  note      = {temporalmetric v1.7 FINAL specification, 3 AD production rule packs, four-cohort triangulation lock; v1.9.0+ AD-only scope}
+}
+```
+
+See [`CITATION.cff`](CITATION.cff) for GitHub's citation widget.
+
+## Known limitations (honestly disclosed)
+
+NeuroTCS publicly documents what is NOT yet covered so reviewers can assess
+fitness for purpose. The complete, current gap disclosure — spanning
+methodological, validation, fairness, and regulatory-status gaps — is
+maintained as a single source of truth in
+[`docs/datasheet/ad_neurotcs_datasheet.md`](docs/datasheet/ad_neurotcs_datasheet.md)
+**Section F — Honest gaps acknowledged**.
+
+To avoid drift, the README does not duplicate the list here; Section F is
+authoritative (enforced by `tests/docs/test_gap_disclosure_single_source.py`).
+These gaps do not invalidate the reproducibility evidence — they define the
+scope within which it is interpretable.
+
+## License
+
+Apache 2.0 — see [`LICENSE`](LICENSE). The cited published guidelines remain © their respective publishers; this package transcribes them into machine-readable form for academic / regulatory audit purposes under fair-use interpretation. NeuroTCS does NOT redistribute the publications themselves.
+
+## Contact
+
+**Dr. Marufjon Salokhiddinov, MD PhD**
+ESOR-BRACCO-ESNR Neuroimaging Fellow
+Kimyo International University in Tashkent (KIUT), Uzbekistan
+
+Issues and contributions via GitHub.