symphony-dt 2.0.0__tar.gz

symphony_dt-2.0.0/.gitignore

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+# environments and caches
+.venv/
+.cmdstan/
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.hypothesis/
+.coverage
+coverage.xml
+htmlcov/
+dist/
+build/
+site/
+*.egg-info/
+# Stan build products
+src/symphony_dt/models/**/model
+src/symphony_dt/models/**/forecast_gq
+src/symphony_dt/models/**/conditional
+src/symphony_dt/models/**/*.hpp
+*.o
+# run outputs
+runs/
+symphony_runs/
+.DS_Store
+
+# tutorial outputs
+docs/tutorials/tutorial_*/
+docs/coverage-badge.json

symphony_dt-2.0.0/CHANGELOG.md

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+# Changelog
+
+All notable changes are recorded here. The project follows semantic versioning.
+
+## [2.0.0] - 2026-11-06
+
+A complete rewrite. Version 1 is preserved on the `v1` branch and the `v1.0-preprint` tag.
+
+### Added
+- pd_v2, the SYMPHONY v2 model of record, byte-identical to the study and checked by sha256 at import.
+- `TwinDataset`, the canonical long-format data model, with coded validation errors and fingerprints.
+- Instrument registry, validity envelope, harmonisation hooks and unit conversion.
+- Readers and writers for CSV, TSV, Parquet, Excel, Arrow and polars; netCDF posteriors.
+- Adapters with YAML mappings: wide tables, a generic long layout, OMOP CDM, HL7 FHIR R4, CDISC SDTM and the
+  PPMI download layout.
+- The Stan data builder and the simulator, ported with golden tests against the study code.
+- `fit()` with chain-level checkpoint and resume, run manifests and ArviZ output.
+- The study's convergence gates with logged overrides.
+- Exact-route forecasting with a generated-quantities program, and an experimental fast route.
+- The scoring code of record (coverage, CRPS, LOCF, LMM by EM, events, bootstrap, strata), golden-tested.
+- SBC toolkit with Bonferroni and Benjamini-Hochberg judges; posterior predictive checks.
+- Governance: manifests, provenance, pre-registration freezes, deviation records, model and data cards,
+  TRIPOD+AI helper, reproduction command and HTML reports.
+- `symphony-dt` command line, documentation site, tutorials and logo.
+
+### Changed
+- Licence from Apache-2.0 (v1) to BSD-3-Clause.

symphony_dt-2.0.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: "symphony-dt: Bayesian digital twins of Parkinson's disease progression"
+abstract: >-
+  A toolkit for building, checking, calibrating, forecasting with and auditing Bayesian hierarchical
+  state-space digital twins on longitudinal clinical cohorts, with the frozen SYMPHONY v2 model of
+  Parkinson's disease progression.
+type: software
+authors:
+  - family-names: Hemedan
+    given-names: Ahmed
+version: 2.0.0
+date-released: 2026-11-06
+license: BSD-3-Clause
+repository-code: "https://github.com/a7med7emedan/symphony-dt"
+url: "https://a7med7emedan.github.io/symphony-dt/"
+keywords:
+  - bayesian
+  - digital-twin
+  - parkinsons-disease
+  - stan
+  - uncertainty-quantification
+  - clinical-prediction
+  - reproducibility

symphony_dt-2.0.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2026, Ahmed Hemedan
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

symphony_dt-2.0.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: symphony-dt
+Version: 2.0.0
+Summary: Bayesian hierarchical state-space digital twins for longitudinal clinical cohorts, with the SYMPHONY v2 Parkinson's disease model.
+Project-URL: Homepage, https://a7med7emedan.github.io/symphony-dt/
+Project-URL: Documentation, https://a7med7emedan.github.io/symphony-dt/
+Project-URL: Repository, https://github.com/a7med7emedan/symphony-dt
+Project-URL: Issues, https://github.com/a7med7emedan/symphony-dt/issues
+Project-URL: Changelog, https://github.com/a7med7emedan/symphony-dt/blob/main/CHANGELOG.md
+Author: Ahmed Hemedan
+Maintainer: Ahmed Hemedan
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Keywords: bayesian,clinical-prediction,digital-twin,parkinsons-disease,reproducibility,stan,state-space-model,uncertainty-quantification
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Typing :: Typed
+Requires-Python: >=3.11
+Requires-Dist: arviz>=0.18
+Requires-Dist: cmdstanpy>=1.2
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: numpy>=1.26
+Requires-Dist: pandas>=2.1
+Requires-Dist: pydantic>=2.5
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: rich>=13.0
+Requires-Dist: scipy>=1.11
+Requires-Dist: typer>=0.12
+Requires-Dist: xarray>=2023.10
+Provides-Extra: dev
+Requires-Dist: build>=1.2; extra == 'dev'
+Requires-Dist: h5netcdf>=1.3; extra == 'dev'
+Requires-Dist: h5py>=3.10; extra == 'dev'
+Requires-Dist: hypothesis>=6.100; extra == 'dev'
+Requires-Dist: ipykernel>=6; extra == 'dev'
+Requires-Dist: mkdocs-jupyter>=0.24; extra == 'dev'
+Requires-Dist: mkdocs-material>=9.5; extra == 'dev'
+Requires-Dist: mkdocstrings[python]>=0.25; extra == 'dev'
+Requires-Dist: mypy>=1.10; extra == 'dev'
+Requires-Dist: nbconvert>=7; extra == 'dev'
+Requires-Dist: openpyxl>=3.1; extra == 'dev'
+Requires-Dist: pandas-stubs; extra == 'dev'
+Requires-Dist: polars>=0.20; extra == 'dev'
+Requires-Dist: pre-commit>=3.7; extra == 'dev'
+Requires-Dist: properscoring>=0.1; extra == 'dev'
+Requires-Dist: pyarrow>=14; extra == 'dev'
+Requires-Dist: pytest-cov>=5; extra == 'dev'
+Requires-Dist: pytest>=8; extra == 'dev'
+Requires-Dist: ruff>=0.6; extra == 'dev'
+Requires-Dist: twine>=5; extra == 'dev'
+Requires-Dist: types-pyyaml; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: ipykernel>=6; extra == 'docs'
+Requires-Dist: mkdocs-jupyter>=0.24; extra == 'docs'
+Requires-Dist: mkdocs-material>=9.5; extra == 'docs'
+Requires-Dist: mkdocstrings[python]>=0.25; extra == 'docs'
+Requires-Dist: nbconvert>=7; extra == 'docs'
+Provides-Extra: io
+Requires-Dist: h5netcdf>=1.3; extra == 'io'
+Requires-Dist: h5py>=3.10; extra == 'io'
+Requires-Dist: openpyxl>=3.1; extra == 'io'
+Requires-Dist: polars>=0.20; extra == 'io'
+Requires-Dist: pyarrow>=14; extra == 'io'
+Provides-Extra: test
+Requires-Dist: h5netcdf>=1.3; extra == 'test'
+Requires-Dist: h5py>=3.10; extra == 'test'
+Requires-Dist: hypothesis>=6.100; extra == 'test'
+Requires-Dist: openpyxl>=3.1; extra == 'test'
+Requires-Dist: polars>=0.20; extra == 'test'
+Requires-Dist: properscoring>=0.1; extra == 'test'
+Requires-Dist: pyarrow>=14; extra == 'test'
+Requires-Dist: pytest-cov>=5; extra == 'test'
+Requires-Dist: pytest>=8; extra == 'test'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="docs/assets/logo/symphony-dt-dark.svg">
+    <img src="docs/assets/logo/symphony-dt-light.svg" alt="symphony-dt logo" width="180">
+  </picture>
+</p>
+
+<h1 align="center">symphony-dt</h1>
+
+<p align="center">Bayesian hierarchical state-space digital twins for longitudinal clinical cohorts.</p>
+
+<p align="center">
+  <a href="https://pypi.org/project/symphony-dt/"><img src="https://img.shields.io/pypi/v/symphony-dt.svg" alt="PyPI"></a>
+  <a href="https://pypi.org/project/symphony-dt/"><img src="https://img.shields.io/pypi/pyversions/symphony-dt.svg" alt="Python versions"></a>
+  <a href="https://github.com/a7med7emedan/symphony-dt/actions/workflows/ci.yml"><img src="https://github.com/a7med7emedan/symphony-dt/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
+  <a href="https://a7med7emedan.github.io/symphony-dt/"><img src="https://img.shields.io/endpoint?url=https://a7med7emedan.github.io/symphony-dt/coverage-badge.json" alt="Coverage"></a>
+  <a href="https://a7med7emedan.github.io/symphony-dt/"><img src="https://github.com/a7med7emedan/symphony-dt/actions/workflows/docs.yml/badge.svg" alt="Docs"></a>
+  <a href="LICENSE"><img src="https://img.shields.io/badge/licence-BSD--3--Clause-blue.svg" alt="Licence"></a>
+</p>
+
+symphony-dt builds, checks, calibrates, forecasts with and audits Bayesian digital twins of longitudinal clinical
+cohorts. It ships **pd_v2**, the frozen model of the SYMPHONY v2 study of Parkinson's disease progression. pd_v2
+follows MDS-UPDRS Part III, MoCA and SCOPA-AUT over time, in Stan, driven from Python with cmdstanpy.
+
+**Developed by Ahmed Hemedan.** Validation manuscript in preparation.
+
+## Install
+
+```bash
+pip install "symphony-dt[io]"
+python -m cmdstanpy.install_cmdstan --version 2.39.0
+symphony-dt check --compile
+```
+
+## A ten-line example
+
+```python
+import numpy as np
+from symphony_dt.data import simulate_cohort
+from symphony_dt.fit import fit
+from symphony_dt.forecast import split_at_anchor, forecast_exact
+
+cohort = simulate_cohort(60, seed=1)                       # synthetic data only
+split = split_at_anchor(cohort.stan_data, list(range(0, 60, 4)), anchor_years=2.0)
+result = fit(split.fit, chains=4, iter_warmup=1000, iter_sampling=1000, output_dir="run")
+print("\n".join(result.gates().summary_lines()))           # the study's convergence gates
+forecast = forecast_exact(result, split, total_keep=400)
+print(forecast.interval(0.95).head())
+```
+
+## What it does
+
+- A validated, long-format data model with a design-envelope check. Adapters read wide tables, OMOP CDM, HL7 FHIR
+  R4, CDISC SDTM and the PPMI download layout.
+- The pd_v2 model of record, byte-identical to the study and checked by sha256 at import.
+- Fitting with chain-level resume, and the study's convergence gates fixed in one place.
+- Exact forecasts by the study's design, and an experimental fast route for new participants.
+- The scoring code of record: interval coverage, CRPS, LOCF and mixed-model baselines, events, bootstrap.
+- Simulation-based calibration with explicit multiplicity control, and posterior predictive checks.
+- Run manifests, data fingerprints, pre-registration freezes, PROV provenance, model and data cards.
+
+Every public function carries a validation label: VALIDATED, TESTED or EXPERIMENTAL. See the
+[documentation](https://a7med7emedan.github.io/symphony-dt/).
+
+## Governance
+
+> **No participant data ship with this package, and none may be added.** Tests, examples and tutorials use the
+> package's own simulator. A privacy gate runs before every commit and in CI. The model was developed on PPMI data
+> under the PPMI data use agreement; obtain PPMI data yourself from PPMI. No PPMI-derived result appears here until
+> the validation manuscript is published. The twin's forecasts are associational: no causal, treatment or
+> deployment claim is made. See [GOVERNANCE.md](GOVERNANCE.md).
+
+## Citation
+
+> Hemedan A. symphony-dt: Bayesian digital twins of Parkinson's disease progression, version 2.0.0.
+> https://github.com/a7med7emedan/symphony-dt
+
+See [CITATION.cff](CITATION.cff).
+
+## Licence
+
+BSD-3-Clause, copyright Ahmed Hemedan. Version 1 remains on the `v1` branch and the `v1.0-preprint` tag under its
+original Apache-2.0 licence.

symphony_dt-2.0.0/README.md

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+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="docs/assets/logo/symphony-dt-dark.svg">
+    <img src="docs/assets/logo/symphony-dt-light.svg" alt="symphony-dt logo" width="180">
+  </picture>
+</p>
+
+<h1 align="center">symphony-dt</h1>
+
+<p align="center">Bayesian hierarchical state-space digital twins for longitudinal clinical cohorts.</p>
+
+<p align="center">
+  <a href="https://pypi.org/project/symphony-dt/"><img src="https://img.shields.io/pypi/v/symphony-dt.svg" alt="PyPI"></a>
+  <a href="https://pypi.org/project/symphony-dt/"><img src="https://img.shields.io/pypi/pyversions/symphony-dt.svg" alt="Python versions"></a>
+  <a href="https://github.com/a7med7emedan/symphony-dt/actions/workflows/ci.yml"><img src="https://github.com/a7med7emedan/symphony-dt/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
+  <a href="https://a7med7emedan.github.io/symphony-dt/"><img src="https://img.shields.io/endpoint?url=https://a7med7emedan.github.io/symphony-dt/coverage-badge.json" alt="Coverage"></a>
+  <a href="https://a7med7emedan.github.io/symphony-dt/"><img src="https://github.com/a7med7emedan/symphony-dt/actions/workflows/docs.yml/badge.svg" alt="Docs"></a>
+  <a href="LICENSE"><img src="https://img.shields.io/badge/licence-BSD--3--Clause-blue.svg" alt="Licence"></a>
+</p>
+
+symphony-dt builds, checks, calibrates, forecasts with and audits Bayesian digital twins of longitudinal clinical
+cohorts. It ships **pd_v2**, the frozen model of the SYMPHONY v2 study of Parkinson's disease progression. pd_v2
+follows MDS-UPDRS Part III, MoCA and SCOPA-AUT over time, in Stan, driven from Python with cmdstanpy.
+
+**Developed by Ahmed Hemedan.** Validation manuscript in preparation.
+
+## Install
+
+```bash
+pip install "symphony-dt[io]"
+python -m cmdstanpy.install_cmdstan --version 2.39.0
+symphony-dt check --compile
+```
+
+## A ten-line example
+
+```python
+import numpy as np
+from symphony_dt.data import simulate_cohort
+from symphony_dt.fit import fit
+from symphony_dt.forecast import split_at_anchor, forecast_exact
+
+cohort = simulate_cohort(60, seed=1)                       # synthetic data only
+split = split_at_anchor(cohort.stan_data, list(range(0, 60, 4)), anchor_years=2.0)
+result = fit(split.fit, chains=4, iter_warmup=1000, iter_sampling=1000, output_dir="run")
+print("\n".join(result.gates().summary_lines()))           # the study's convergence gates
+forecast = forecast_exact(result, split, total_keep=400)
+print(forecast.interval(0.95).head())
+```
+
+## What it does
+
+- A validated, long-format data model with a design-envelope check. Adapters read wide tables, OMOP CDM, HL7 FHIR
+  R4, CDISC SDTM and the PPMI download layout.
+- The pd_v2 model of record, byte-identical to the study and checked by sha256 at import.
+- Fitting with chain-level resume, and the study's convergence gates fixed in one place.
+- Exact forecasts by the study's design, and an experimental fast route for new participants.
+- The scoring code of record: interval coverage, CRPS, LOCF and mixed-model baselines, events, bootstrap.
+- Simulation-based calibration with explicit multiplicity control, and posterior predictive checks.
+- Run manifests, data fingerprints, pre-registration freezes, PROV provenance, model and data cards.
+
+Every public function carries a validation label: VALIDATED, TESTED or EXPERIMENTAL. See the
+[documentation](https://a7med7emedan.github.io/symphony-dt/).
+
+## Governance
+
+> **No participant data ship with this package, and none may be added.** Tests, examples and tutorials use the
+> package's own simulator. A privacy gate runs before every commit and in CI. The model was developed on PPMI data
+> under the PPMI data use agreement; obtain PPMI data yourself from PPMI. No PPMI-derived result appears here until
+> the validation manuscript is published. The twin's forecasts are associational: no causal, treatment or
+> deployment claim is made. See [GOVERNANCE.md](GOVERNANCE.md).
+
+## Citation
+
+> Hemedan A. symphony-dt: Bayesian digital twins of Parkinson's disease progression, version 2.0.0.
+> https://github.com/a7med7emedan/symphony-dt
+
+See [CITATION.cff](CITATION.cff).
+
+## Licence
+
+BSD-3-Clause, copyright Ahmed Hemedan. Version 1 remains on the `v1` branch and the `v1.0-preprint` tag under its
+original Apache-2.0 licence.

symphony_dt-2.0.0/STALE_20261106T074328Z_v1/CHANGELOG.md

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+# Changelog
+
+## Unreleased
+
+### Fixed
+- The NumPyro scaffold and conditioning models now use the truncated Gaussian likelihood of the Methods. Before, they scored clipped scores under an untruncated Normal, which understated the density near each scale's floor and ceiling. Posterior draws change as a result.
+- Missing endpoints are replaced by a safe value before scoring and then masked, so they contribute neither log density nor NaN gradients.
+- Conditioning used `log1p(exp(z))` for the softplus drive, which overflows for large `z`. It now uses the stable form, matching the scaffold.
+- `symphony_dt.__version__` reported 0.1.0 while the package was 0.2.0. It is now read from the installed package metadata.
+- README equations used `\operatorname`, which GitHub's maths renderer rejects, so they showed as red error boxes. They now use `\mathrm`.
+- `select_tau_conf` targeted 95% coverage while every engine produces central 90% intervals. The target is now 0.90. Missing target scores are skipped rather than counted as misses.
+
+### Changed
+- Coverage columns are renamed to `cov90_updrs3`, `cov90_moca`, `cov90_scopa` and `cov90_overall`, matching the central 90% interval (5th to 95th percentile) they score. The values are unchanged: numbers reported as `cov95_*` by 0.2.0 and earlier are 90% coverage.
+- **Deprecated:** `cov95_*` is still written alongside `cov90_*`, with identical values, for one release and will then be removed. The `evaluation_coverage` contract, `parity-check`, `aggregate-all` and `aggregate-evaluation` accept either name, so old and new run directories can be merged. `parity-check` warns when a table or notebook uses only the old names.
+- `nuts forecast --tau-conf` has no silent default any more. Without it or `--tau-conf-json`, 1.0 is used and a warning says that gating rule 3 is inactive.
+- The `tau_conf` grid diagnostics are keyed `cov90_le_*` (were `cov95_le_*`).
+
+### Added
+- `symphony-dt nuts select-tau-conf`: computes Delta and the one-step 90% interval for each training-fold anchor from the conditioning outputs, selects `tau_conf`, and writes it with the coverage and fraction kept at every grid point to JSON.
+- `nuts forecast --tau-conf-json` reads that file. Posterior forecasts gain a `delta_iqr` column with the latent uncertainty that rule 3 compares with `tau_conf`.
+- `ColumnRule.aliases` in the schema contracts, an `evaluation_coverage` contract checked by `parity-check`, and coverage column references in notebook introspection.
+- Tests for the coverage aliases, and for `select-tau-conf` and `--tau-conf-json` on quickstart data.
+- `symphony-dt --version`, and help text for the top-level command and the `nuts` group.
+- Chains run in parallel only when JAX has one device per chain, otherwise sequentially, without a warning.
+- Tests for the bounded likelihood against the closed-form truncated normal density, and for the version flag.
+- Logo, wordmark and method figure under `docs/assets/`. The logo is a tulip, the Parkinson's disease symbol, whose right half is a digital twin drawn as posterior samples. Logo and wordmark adapt to dark mode.
+- `codemeta.json`, a richer `CITATION.cff` abstract, and expanded package keywords and project links.
+
+## 0.2.0
+
+### Fixed
+- `nuts forecast` no longer crashes on every conditioned run. NumPyro only records divergences by default, so `accept_prob` was never collected, its mean was `None`, and the gate raised `TypeError`. Conditioning now requests `accept_prob` (draws are unchanged), and the gate treats any missing or non-finite diagnostic as a failed run instead of crashing.
+- Conditioning `diagnostics.json` could contain bare `NaN`, which is not valid JSON. Non-finite values are now written as `null`.
+- Removed three unused patch modules and a hard-coded local input path from `configs/config.demo.yaml`.
+
+### Added
+- `symphony-dt synth`: synthetic, PPMI-shaped input tables. Every value is invented.
+- `symphony-dt quickstart`: synthetic data, demo run and parity check in one command.
+- `symphony-dt run --input-dir`: override the configured input directory per run.
+- `aggregate-all` warns when shard runs are mixed with demo or full runs.
+- Dockerfile (non-root, code only, optional NumPyro/JAX), `.dockerignore`.
+- GitHub Actions CI: lint, tests on Python 3.10 to 3.12, inference extras, synthetic end-to-end, Docker build and run.
+- End-to-end NUTS test on synthetic data, quickstart and diagnostics tests.
+- Results explorer notebook unpacked into `notebooks/explorer/`. The results bundle is opt-in via `SYMPHONY_BUNDLE_GDRIVE_ID` instead of a hard-coded file ID.
+
+## 0.1.0
+- Initial pipeline: demo, full and shard modes, aggregation, parity checks, optional NumPyro inference.

symphony_dt-2.0.0/STALE_20261106T074328Z_v1/CITATION.cff

@@ -0,0 +1,35 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: "symphony-dt: SYMPHONY clinic-updated digital twin for Parkinson's disease"
+type: software
+authors:
+  - family-names: Hemedan
+    given-names: Ahmed
+version: 0.2.0
+license: Apache-2.0
+repository-code: "https://github.com/a7med7emedan/symphony-dt"
+abstract: >-
+  symphony-dt is a reproducible Python package for a clinic-updated Bayesian
+  digital twin of Parkinson's disease. Three latent domain states (motor,
+  cognitive, autonomic) evolve under monotone stochastic dynamics with a sparse
+  cross-domain coupling and a hierarchical per-patient progression drive. A
+  bounded, truncated Gaussian observation model links them to MDS-UPDRS Part III,
+  MoCA and SCOPA-AUT. A global posterior is fitted by NUTS, conditioned per
+  patient, and propagated into multi-horizon forecasts and clinical event risk
+  curves behind confidence gating rules.
+keywords:
+  - digital twin
+  - Parkinson's disease
+  - Bayesian inference
+  - hierarchical model
+  - state space model
+  - stochastic dynamics
+  - NUTS
+  - NumPyro
+  - JAX
+  - posterior predictive
+  - uncertainty quantification
+  - calibration
+  - clinical forecasting
+  - PPMI
+  - reproducibility

symphony_dt-2.0.0/STALE_20261106T074328Z_v1/LICENSE

@@ -0,0 +1,177 @@
+                                 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,
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