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23 changes: 23 additions & 0 deletions CHANGELOG.md
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@@ -0,0 +1,23 @@
# Changelog

## v1.1.0 — Expanded research archive

Release date: 2026-08-26

- Added the exhaustive temperature-dependent tree-geometry supporting study, including its frozen protocol, source instances, compact canonical summaries, scientific report, and validation records.
- Recorded the negative operational result that retained target-state cooling power is not validated as a compressed-state tree-selection objective on the tested development corpus.
- Preserved the prospectively frozen weighted sparse-Ising `MAXJ` confirmation and its primary result tables unchanged.
- Improved the claim-to-evidence map, reader routes, classical graphical-model context, reproduction instructions, and study-level citation links.
- Clarified that the primary evidence is an internal confirmation on unseen, separately generated targets rather than an external replication.
- Updated package, citation, and machine-readable metadata to Version 1.1.0.

Published release: [`v1.1.0`](https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.1.0)

## v1.0.0 — Initial public release

Release date: 2026-08-25

- Published the prospectively frozen confirmation on 24 weighted sparse-Ising targets and 1,440 optimization trajectories.
- Included exact preparation-resource accounting, supporting geometry studies, raw and compact results, validation records, and the reproducible Python package.

Published release: [`v1.0.0`](https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.0.0)
4 changes: 2 additions & 2 deletions CITATION.cff
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@@ -1,13 +1,13 @@
cff-version: 1.2.0
message: "If you use the software, data, figures, protocols, or derived results, cite this repository and identify the release tag or commit; see CITATION.md for copy-ready formats."
message: "If you use the software, data, figures, protocols, or derived results, cite release v1.1.0 and identify any later commit used; see CITATION.md for copy-ready formats."
title: "Representation Alignment in Commuting Quantum Boltzmann Machines"
type: software
authors:
- family-names: Lin
given-names: Ruge
affiliation: "The Hong Kong University of Science and Technology (Guangzhou)"
version: 1.1.0
date-released: 2026-08-25
date-released: 2026-08-26
repository-code: "https://github.com/GoGoKo699/QBM-Representation-Alignment"
url: "https://github.com/GoGoKo699/QBM-Representation-Alignment"
license: BSD-3-Clause
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17 changes: 11 additions & 6 deletions CITATION.md
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@@ -1,10 +1,10 @@
# How to cite this repository

If you use the software, data, figures, protocols, or derived results, cite the repository and identify the exact version or commit used.
If you use the software, data, figures, protocols, or derived results, cite the repository and identify the exact release or commit used.

## Recommended citation

> Lin, R. (2026). *Representation Alignment in Commuting Quantum Boltzmann Machines* (Version 1.1.0) [Computer software]. GitHub. https://github.com/GoGoKo699/QBM-Representation-Alignment
> Lin, R. (2026). *Representation Alignment in Commuting Quantum Boltzmann Machines* (Version 1.1.0) [Computer software]. GitHub. https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.1.0

GitHub also displays a **Cite this repository** control generated from [`CITATION.cff`](CITATION.cff).

Expand All @@ -16,16 +16,17 @@ GitHub also displays a **Cite this repository** control generated from [`CITATIO
title = {Representation Alignment in Commuting Quantum Boltzmann Machines},
year = {2026},
version = {1.1.0},
url = {https://github.com/GoGoKo699/QBM-Representation-Alignment},
url = {https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.1.0},
license = {BSD-3-Clause}
}
```

## Which version to cite

- **Primary confirmed `MAXJ` result:** cite the preserved [`v1.0.0`](https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.0.0) release. It contains the prospectively frozen weighted sparse-Ising confirmation and its complete evidence chain.
- **Expanded archive:** cite Version 1.1.0 together with a matching release tag when available. Otherwise include the full commit SHA so the cited state is unambiguous.
- **Complete research archive:** cite the published [`v1.1.0`](https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.1.0) release. It includes the prospectively frozen weighted sparse-Ising confirmation, all supporting studies, the later temperature-dependent tree boundary study, and the reviewer-facing citation and navigation improvements.
- **Primary confirmed `MAXJ` result in its original release state:** cite [`v1.0.0`](https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.0.0).
- **Pre-boundary-study state:** the branch `archive/confirmed-result-2026-08-25` preserves the repository immediately before the temperature-dependent supporting study was added.
- **A later unreleased state:** cite the most recent release and include the full commit SHA used.

To record the exact commit of a local checkout, run:

Expand All @@ -37,7 +38,11 @@ git rev-parse HEAD

- The primary confirmation is under [`experiments/sparse_ising_confirmation/`](experiments/sparse_ising_confirmation/), with canonical tables in [`results/confirmatory/`](results/confirmatory/).
- The later exhaustive graph-selection boundary study is under [`studies/temperature_tree_geometry/`](studies/temperature_tree_geometry/), with compact tables in [`results/temperature_tree_geometry/`](results/temperature_tree_geometry/).
- For a particular table or figure, cite the repository and name the file path, release tag, or full commit SHA used.
- For a particular table or figure, cite the release and name the file path. Include a full commit SHA only when the cited state differs from the tagged release.

## Release history

See [`CHANGELOG.md`](CHANGELOG.md) for the scientific and repository-level contents of each release.

## Future paper citation

Expand Down
9 changes: 5 additions & 4 deletions README.md
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@@ -1,11 +1,12 @@
# Representation Alignment in Commuting Quantum Boltzmann Machines

[![tests](https://github.com/GoGoKo699/QBM-Representation-Alignment/actions/workflows/tests.yml/badge.svg)](https://github.com/GoGoKo699/QBM-Representation-Alignment/actions/workflows/tests.yml)
[![Release: v1.1.0](https://img.shields.io/badge/release-v1.1.0-blue.svg)](https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.1.0)
[![License: BSD 3-Clause](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](LICENSE)
[![Python 3.10-3.13](https://img.shields.io/badge/Python-3.10--3.13-blue.svg)](pyproject.toml)
[![Cite](https://img.shields.io/badge/Cite-CITATION.cff-blue.svg)](CITATION.md)

**Reader routes:** [confirmed result](#confirmed-result) · [claim-to-evidence map](docs/evidence_map.md) · [scope and nonclaims](docs/scientific_claims.md) · [research context](docs/research_context.md) · [reproduce](docs/reproducibility.md) · [cite](CITATION.md)
**Reader routes:** [confirmed result](#confirmed-result) · [claim-to-evidence map](docs/evidence_map.md) · [scope and nonclaims](docs/scientific_claims.md) · [research context](docs/research_context.md) · [reproduce](docs/reproducibility.md) · [release notes](CHANGELOG.md) · [cite](CITATION.md)

This repository studies a concrete ansatz-design question:

Expand Down Expand Up @@ -65,9 +66,9 @@ conditional angles: 31
CNOT upper count: 30
```

The full target graphs have treewidth 3 - 5 and require 75–159 conditional angles, with median 131.
The full target graphs have treewidth between 3 and 5 and require 75–159 conditional angles, with median 131.

In source code and CSV files, `problem_tree` denotes the deterministic maximum- $|J|$ target-supported spanning tree, abbreviated `MAXJ` in the documentation.
In source code and CSV files, `problem_tree` denotes the deterministic target-supported spanning tree obtained by maximizing edge weight $|J|$, abbreviated `MAXJ` in the documentation.

- [Primary effects](results/confirmatory/primary_effects.csv)
- [Aggregate outcomes](results/confirmatory/aggregate.csv)
Expand All @@ -93,7 +94,7 @@ GitHub reads [`CITATION.cff`](CITATION.cff) and exposes a **Cite this repository

> Lin, R. (2026). *Representation Alignment in Commuting Quantum Boltzmann Machines* (Version 1.1.0) [Computer software]. GitHub. https://github.com/GoGoKo699/QBM-Representation-Alignment

For the primary confirmed `MAXJ` result alone, the preserved GitHub release is [`v1.0.0`](https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.0.0). For the expanded Version 1.1.0 archive, cite a matching release tag when available; otherwise include the full commit SHA. See [`CITATION.md`](CITATION.md) for the exact choice.
For the complete archive, cite the published [`v1.1.0`](https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.1.0) release. For the primary confirmed `MAXJ` result in its original release state, cite [`v1.0.0`](https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.0.0). See [`CITATION.md`](CITATION.md) for copy-ready formats and exact-result guidance.

## Geometry

Expand Down
4 changes: 2 additions & 2 deletions docs/evidence_map.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ This page gives reviewers, reusers, and first-time readers the shortest path fro

**Claim.** At fixed treewidth, interaction count, and parameter count, a target-supported spanning-tree Gibbs representation trains better than a generic chain; selecting the spanning tree by maximum absolute target-coupling weight improves further over a prespecified random target-supported tree.

The protocol and seed commitments were frozen before the separately generated target ensemble was evaluated. This is an internal confirmation on unseen targets, not an external replication. In code and result files, `problem_tree` denotes the maximum- $|J|$ spanning tree (`MAXJ`).
The protocol and seed commitments were frozen before the separately generated target ensemble was evaluated. This is an internal confirmation on unseen targets, not an external replication. In code and result files, `problem_tree` denotes the target-supported spanning tree that maximizes edge weight $|J|$ (`MAXJ`).

| Evidence layer | Canonical location |
|---|---|
Expand Down Expand Up @@ -95,4 +95,4 @@ See [`docs/reproducibility.md`](reproducibility.md) for the complete workflow.

## Citation

Use [`CITATION.md`](../CITATION.md) for copy-ready APA-style and BibTeX entries and for choosing between release `v1.0.0`, a later release tag, or a full commit SHA. Machine-readable metadata are in [`CITATION.cff`](../CITATION.cff).
Use [`CITATION.md`](../CITATION.md) for copy-ready APA-style and BibTeX entries. Cite release `v1.1.0` for the complete archive or `v1.0.0` for the primary confirmed `MAXJ` result in its original release state. Machine-readable metadata are in [`CITATION.cff`](../CITATION.cff).
6 changes: 4 additions & 2 deletions docs/reproducibility.md
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@ The maintained dependencies are listed in `pyproject.toml` and `requirements.txt

## Record the exact version

Before running a calculation, record the checked-out commit:
The complete archive is published as GitHub release [`v1.1.0`](https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.1.0). The primary confirmed `MAXJ` result in its original release state is preserved as [`v1.0.0`](https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.0.0).

Before running a calculation from a later checkout, record its commit:

```bash
git rev-parse HEAD
```

The primary confirmed `MAXJ` result is preserved in GitHub release `v1.0.0`. For the expanded Version 1.1.0 archive, use a matching release tag when available or record the full commit SHA. Citation formats and version-selection guidance are in [`CITATION.md`](../CITATION.md).
Citation formats and version-selection guidance are in [`CITATION.md`](../CITATION.md). Release contents are summarized in [`CHANGELOG.md`](../CHANGELOG.md).

## Fast validation

Expand Down
13 changes: 8 additions & 5 deletions llms.txt
Original file line number Diff line number Diff line change
Expand Up @@ -3,15 +3,17 @@
Repository URL:
https://github.com/GoGoKo699/QBM-Representation-Alignment

Release metadata:
1.1.0 (2026-08-25), BSD-3-Clause
Published release:
v1.1.0 (2026-08-26), BSD-3-Clause
https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.1.0

Primary question:
How does the interaction graph of a commuting QBM affect finite-budget
trainability and exact Gibbs/q-sample preparation?

Canonical entry points:
- README.md: confirmed result, commands, repository map, and citation route.
- README.md: confirmed result, commands, repository map, release notes, and citation route.
- CHANGELOG.md: release contents and scientific scope changes.
- docs/evidence_map.md: claim-to-protocol/data/code/validation navigation.
- docs/scientific_claims.md: claim hierarchy and evidence boundaries.
- docs/research_context.md: established literature, classical tree comparison, and novelty boundary.
Expand Down Expand Up @@ -52,5 +54,6 @@ Important boundaries:
Citation:
- CITATION.md: copy-ready citation, BibTeX, and version-selection guidance.
- CITATION.cff: machine-readable GitHub citation metadata.
- use release v1.0.0 for the primary confirmed MAXJ result;
- for a later repository state, identify the matching release tag or full commit SHA.
- cite release v1.1.0 for the complete archive.
- cite release v1.0.0 for the primary confirmed MAXJ result in its original release state.
- identify the full commit SHA only when using a later unreleased state.
4 changes: 3 additions & 1 deletion results/repository_validation.json
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"layout": {
"container_local_paths": 0,
"file_count": 425,
"file_count": 426,
"oversized_files": 0,
"zero_byte_files": 0
},
Expand Down Expand Up @@ -103,6 +103,8 @@
"release_metadata": {
"license": "BSD-3-Clause",
"package_name": "qbm-representation-alignment",
"release_date": "2026-08-26",
"release_url": "https://github.com/GoGoKo699/QBM-Representation-Alignment/releases/tag/v1.1.0",
"repository_url": "https://github.com/GoGoKo699/QBM-Representation-Alignment",
"version": "1.1.0"
},
Expand Down
11 changes: 11 additions & 0 deletions scripts/validate_repository.py
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,9 @@
ROOT = Path(__file__).resolve().parents[1]
EXPECTED_NAME = "qbm-representation-alignment"
EXPECTED_VERSION = "1.1.0"
EXPECTED_RELEASE_DATE = "2026-08-26"
EXPECTED_URL = "https://github.com/GoGoKo699/QBM-Representation-Alignment"
EXPECTED_RELEASE_URL = f"{EXPECTED_URL}/releases/tag/v{EXPECTED_VERSION}"
EXPECTED_LICENSE = "BSD-3-Clause"
VALIDATION_RECORDS = {
"confirmatory": ROOT / "results" / "confirmatory" / "validation.json",
Expand All @@ -28,6 +30,7 @@
".gitattributes",
".github/workflows/tests.yml",
".gitignore",
"CHANGELOG.md",
"CITATION.cff",
"CITATION.md",
"CONTRIBUTING.md",
Expand Down Expand Up @@ -91,6 +94,7 @@ def _validate_release_metadata() -> dict[str, object]:

citation = (ROOT / "CITATION.cff").read_text(encoding="utf-8")
assert _yaml_scalar(citation, "version") == EXPECTED_VERSION
assert _yaml_scalar(citation, "date-released") == EXPECTED_RELEASE_DATE
assert _yaml_scalar(citation, "repository-code") == EXPECTED_URL
assert _yaml_scalar(citation, "url") == EXPECTED_URL
assert _yaml_scalar(citation, "license") == EXPECTED_LICENSE
Expand All @@ -100,12 +104,19 @@ def _validate_release_metadata() -> dict[str, object]:
assert "Copyright (c) 2026, Ruge Lin" in license_text

readme = (ROOT / "README.md").read_text(encoding="utf-8")
citation_guide = (ROOT / "CITATION.md").read_text(encoding="utf-8")
changelog = (ROOT / "CHANGELOG.md").read_text(encoding="utf-8")
assert EXPECTED_URL in readme
assert EXPECTED_RELEASE_URL in readme
assert EXPECTED_RELEASE_URL in citation_guide
assert f"## v{EXPECTED_VERSION}" in changelog
assert "BSD 3-Clause License" in readme

return {
"package_name": EXPECTED_NAME,
"version": EXPECTED_VERSION,
"release_date": EXPECTED_RELEASE_DATE,
"release_url": EXPECTED_RELEASE_URL,
"repository_url": EXPECTED_URL,
"license": EXPECTED_LICENSE,
}
Expand Down
8 changes: 8 additions & 0 deletions tests/test_repository_layout.py
Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,16 @@

ROOT = Path(__file__).resolve().parents[1]
EXPECTED_VERSION = "1.1.0"
EXPECTED_RELEASE_DATE = "2026-08-26"
EXPECTED_URL = "https://github.com/GoGoKo699/QBM-Representation-Alignment"
EXPECTED_RELEASE_URL = f"{EXPECTED_URL}/releases/tag/v{EXPECTED_VERSION}"


def test_canonical_public_files_exist():
required = [
".gitattributes",
".github/workflows/tests.yml",
"CHANGELOG.md",
"README.md",
"CITATION.cff",
"CITATION.md",
Expand Down Expand Up @@ -58,6 +61,7 @@ def test_release_metadata_is_consistent():

citation = (ROOT / "CITATION.cff").read_text(encoding="utf-8")
assert f"version: {EXPECTED_VERSION}" in citation
assert f"date-released: {EXPECTED_RELEASE_DATE}" in citation
assert f'repository-code: "{EXPECTED_URL}"' in citation
assert "license: BSD-3-Clause" in citation

Expand All @@ -72,13 +76,17 @@ def test_citation_is_easy_to_find_and_versioned():
readme = (ROOT / "README.md").read_text(encoding="utf-8")
citation = (ROOT / "CITATION.md").read_text(encoding="utf-8")
cff = (ROOT / "CITATION.cff").read_text(encoding="utf-8")
changelog = (ROOT / "CHANGELOG.md").read_text(encoding="utf-8")
assert "## How to cite" in readme
assert "Cite this repository" in readme
assert EXPECTED_RELEASE_URL in readme
assert f"Version {EXPECTED_VERSION}" in citation
assert EXPECTED_RELEASE_URL in citation
assert "@software" in citation
assert "v1.0.0" in citation
assert "full commit SHA" in citation
assert "see CITATION.md" in cff
assert f"## v{EXPECTED_VERSION}" in changelog


def test_deep_entry_points_link_back_to_citation():
Expand Down