universal-physics-tensor 9.0.0 → 11.0.0

package/dist/atlas/link-prediction.js

@@ -13,7 +13,17 @@
  * - **structural predictor** — common neighbours in the remaining graph, ties
  *   broken by sharing the premise's family, then by id;
  * - **text baseline** — word-token overlap between the models' dynamics and
- *   state-space descriptions, ties broken by id.
+ *   state-space descriptions (`text-overlap.ts`), ties broken by id.
+ *
+ * **The recorded result stands.** The negative result (typed neighbourhood below text
+ * overlap on twenty trials; NOTES.md, "Link prediction is NEGATIVE") is reproduced by
+ * {@link runLinkPrediction} exactly as recorded and is not re-run for a better answer. What
+ * was added beside it, never inside it: a seeded percentile-bootstrap interval on every
+ * recall and MRR (MathTS `bootstrapCI`), a seeded permutation test on the two per-trial
+ * reciprocal-rank vectors (MathTS `permutationTest`, stated for what it is), and McNemar's
+ * exact p on the paired hits (`benchmark/stats.ts`). The Katz-index predictor
+ * ({@link runKatzLinkPrediction}) is a SEPARATE result: every record it returns carries
+ * `postHoc: true` and the label, and it is never a field of the recorded comparison.
  *
  * ⚠ **What this result cannot carry.** The graph is small (24 models, 22 pairs)
  * and was curated by the same agent that runs the test, in-distribution. It is a
@@ -21,50 +31,35 @@
  * discovery claim, not a hub or gap claim, and not evidence about physics the
  * atlas does not contain. ROADMAP Phase 6 asks for it as a hypothesis test, and
  * that is its whole scope. Product A (`src/composition/discovery.ts`) is not
- * touched: a test pins that nothing under `src/atlas/` imports it.
+ * touched: a test pins that nothing under `src/atlas/` imports it, and the Katz
+ * predictor is not wired into discovery, whose candidates are in different
+ * components by construction (every path score there is 0).
  *
  * @module atlas/link-prediction
  * @internal
  */
-const tokens = (text) => new Set(text.toLowerCase().split(/[^\p{L}\p{N}]+/u).filter((t) => t.length > 0));
-const jaccard = (a, b) => {
-    if (a.size === 0 && b.size === 0)
-        return 0;
-    let inter = 0;
-    for (const x of a)
-        if (b.has(x))
-            inter++;
-    return inter / (a.size + b.size - inter);
-};
-/** Rank candidates by descending score list (lexicographic), then ascending id. */
-function rank(candidates, score) {
-    return [...candidates].sort((x, y) => {
-        const sx = score(x);
-        const sy = score(y);
-        for (let i = 0; i < sx.length; i++)
-            if (sx[i] !== sy[i])
-                return sy[i] - sx[i];
-        return x < y ? -1 : x > y ? 1 : 0;
-    });
-}
-/**
- * Run leave-one-bridge-out link prediction over the families' model graph.
- *
- * @param families - the atlas families (normally `ATLAS_FAMILIES`).
- * @param k - the depth a hit must fall within (10, as pre-registered for recall).
- * @internal
- */
-export function runLinkPrediction(families, k = 10) {
+import { bootstrapCI, inv, permutationTest } from '@danielsimonjr/mathts-functions';
+import { jaccard, rankBy, tokens } from './text-overlap.js';
+import { mcnemar } from './benchmark/stats.js';
+import { meanOf } from '../numerical/statistics.js';
+/** The statement of the permutation test's kind, so no reader takes it for a paired test. @internal */
+export const PERMUTATION_KIND = 'two-sample permutation of the reciprocal-rank vectors (pooled re-split; the pairing is not kept)';
+/** The label every Katz record carries. @internal */
+export const POST_HOC_LABEL = 'post hoc: added after the negative result was recorded';
+/** The one seed every resample in this module uses, and the resample count. Stated, not hidden. */
+const RESAMPLE_SEED = 20260924;
+const RESAMPLES = 10000;
+/** Every held-out query of the families, and the pairs excluded as still connected. */
+function holdOuts(families) {
     const models = new Map();
     for (const f of families)
         for (const m of f.models)
             models.set(m.id, m);
     const bridges = families.flatMap((f) => f.bridges);
     const edgesOf = (b) => b.premises.map((p) => [p, b.conclusion]);
-    const trials = [];
+    const queries = [];
     let stillConnected = 0;
     for (const held of bridges) {
-        // The graph WITHOUT the held-out bridge.
         const adj = new Map();
         for (const id of models.keys())
             adj.set(id, new Set());
@@ -77,8 +72,8 @@ export function runLinkPrediction(families, k = 10) {
             }
         }
         for (const [premise, conclusion] of edgesOf(held)) {
-            const pModel = models.get(premise);
-            if (pModel === undefined)
+            const premiseModel = models.get(premise);
+            if (premiseModel === undefined)
                 continue;
             const neighbours = adj.get(premise) ?? new Set();
             if (neighbours.has(conclusion)) {
@@ -86,43 +81,194 @@ export function runLinkPrediction(families, k = 10) {
                 continue;
             }
             const candidates = [...models.keys()].filter((id) => id !== premise && !neighbours.has(id));
-            const common = (id) => {
-                let n = 0;
-                for (const x of adj.get(id) ?? [])
-                    if (neighbours.has(x))
-                        n++;
-                return n;
-            };
-            const structural = rank(candidates, (id) => [common(id), models.get(id).family === pModel.family ? 1 : 0]);
-            const pText = tokens(`${pModel.dynamics} ${pModel.stateSpace}`);
-            const text = rank(candidates, (id) => {
-                const m = models.get(id);
-                return [jaccard(pText, tokens(`${m.dynamics} ${m.stateSpace}`))];
-            });
-            const at = (list) => {
-                const i = list.indexOf(conclusion);
-                return i < 0 ? Number.POSITIVE_INFINITY : i + 1;
-            };
-            trials.push({
-                bridgeId: held.id,
-                premise,
-                conclusion,
-                structuralRank: at(structural),
-                textRank: at(text),
-                candidates: candidates.length,
-            });
+            queries.push({ held, premise, conclusion, premiseModel, adj, candidates });
         }
     }
-    const mean = (xs) => (xs.length === 0 ? Number.NaN : xs.reduce((a, b) => a + b, 0) / xs.length);
+    return { models, queries, stillConnected };
+}
+/** 1-based position of `id` in a ranking; Infinity when absent. */
+const rankOf = (list, id) => {
+    const i = list.indexOf(id);
+    return i < 0 ? Number.POSITIVE_INFINITY : i + 1;
+};
+/** Seeded percentile bootstrap of the mean of per-trial values (a 0/1 hit, or a reciprocal rank). */
+function bootstrapMean(values) {
+    const ci = bootstrapCI([...values], (sample) => meanOf(sample), {
+        confidence: 0.95,
+        resamples: RESAMPLES,
+        seed: RESAMPLE_SEED,
+    });
+    return { estimate: ci.estimate, lower: ci.lower, upper: ci.upper, confidence: ci.confidence };
+}
+/** The mean of a trial statistic; NaN with no trials, as the recorded result always read it. */
+const meanOrNaN = (xs) => (xs.length === 0 ? Number.NaN : meanOf(xs));
+/**
+ * Run leave-one-bridge-out link prediction over the families' model graph. The recorded
+ * comparison (structural against text), with its seeded intervals and paired statistics.
+ *
+ * @param families - the atlas families (normally `ATLAS_FAMILIES`).
+ * @param k - the depth a hit must fall within (10, as pre-registered for recall).
+ * @internal
+ */
+export function runLinkPrediction(families, k = 10) {
+    const { models, queries, stillConnected } = holdOuts(families);
+    const trials = queries.map((q) => {
+        const neighbours = q.adj.get(q.premise) ?? new Set();
+        const common = (id) => {
+            let n = 0;
+            for (const x of q.adj.get(id) ?? [])
+                if (neighbours.has(x))
+                    n++;
+            return n;
+        };
+        const structural = rankBy(q.candidates, (id) => [common(id), models.get(id).family === q.premiseModel.family ? 1 : 0]);
+        const pText = tokens(`${q.premiseModel.dynamics} ${q.premiseModel.stateSpace}`);
+        const text = rankBy(q.candidates, (id) => {
+            const m = models.get(id);
+            return [jaccard(pText, tokens(`${m.dynamics} ${m.stateSpace}`))];
+        });
+        return {
+            bridgeId: q.held.id,
+            premise: q.premise,
+            conclusion: q.conclusion,
+            structuralRank: rankOf(structural, q.conclusion),
+            textRank: rankOf(text, q.conclusion),
+            candidates: q.candidates.length,
+        };
+    });
+    const structuralHit = trials.map((t) => (t.structuralRank <= k ? 1 : 0));
+    const textHit = trials.map((t) => (t.textRank <= k ? 1 : 0));
+    const structuralRR = trials.map((t) => 1 / t.structuralRank);
+    const textRR = trials.map((t) => 1 / t.textRank);
+    // The paired hit table: both, structural only, text only, neither.
+    let a = 0;
+    let b = 0;
+    let c = 0;
+    let d = 0;
+    trials.forEach((_, i) => {
+        if (structuralHit[i] && textHit[i])
+            a++;
+        else if (structuralHit[i])
+            b++;
+        else if (textHit[i])
+            c++;
+        else
+            d++;
+    });
+    const permuted = permutationTest(structuralRR, textRR, (x, y) => meanOrNaN(x) - meanOrNaN(y), {
+        resamples: RESAMPLES,
+        seed: RESAMPLE_SEED,
+    });
+    return {
+        k,
+        trials,
+        stillConnected,
+        structuralHits: structuralHit.reduce((acc, x) => acc + x, 0),
+        textHits: textHit.reduce((acc, x) => acc + x, 0),
+        chanceRecall: meanOrNaN(trials.map((t) => Math.min(k, t.candidates) / t.candidates)),
+        structuralMrr: meanOrNaN(structuralRR),
+        textMrr: meanOrNaN(textRR),
+        intervals: {
+            seed: RESAMPLE_SEED,
+            resamples: RESAMPLES,
+            structuralRecall: bootstrapMean(structuralHit),
+            textRecall: bootstrapMean(textHit),
+            structuralMrr: bootstrapMean(structuralRR),
+            textMrr: bootstrapMean(textRR),
+        },
+        permutation: {
+            statistic: permuted.statistic,
+            pValue: permuted.pValue,
+            seed: RESAMPLE_SEED,
+            resamples: RESAMPLES,
+            kind: PERMUTATION_KIND,
+        },
+        mcnemarExactP: mcnemar({ a, b, c, d }).exactP,
+    };
+}
+/** A square number matrix of order n, read back from MathTS `inv`, which types its result `unknown`. */
+function squareMatrix(value, n) {
+    if (!Array.isArray(value) || value.length !== n) {
+        throw new TypeError(`inv did not return a ${n}×${n} matrix`);
+    }
+    for (const row of value) {
+        if (!Array.isArray(row) || row.length !== n || !row.every((x) => typeof x === 'number' && Number.isFinite(x))) {
+            throw new TypeError(`inv did not return a ${n}×${n} matrix of finite numbers`);
+        }
+    }
+    return value;
+}
+/**
+ * The Katz index of the graph without the held-out bridge: K = (I − βA)⁻¹ − I through MathTS
+ * `inv`, with β = 1/(2·max degree). The largest eigenvalue of a 0/1 adjacency is at most the
+ * maximum degree, so β is below the spectral bound 1/λ_max and the series Σ βˡ Aˡ converges.
+ * A graph with no edge has K = 0 everywhere, and β is stated as 0.5 (there is nothing to attenuate).
+ */
+function katzIndex(adj, ids) {
+    const n = ids.length;
+    const index = new Map(ids.map((id, i) => [id, i]));
+    const A = Array.from({ length: n }, () => new Array(n).fill(0));
+    let maxDegree = 0;
+    for (const [u, neighbours] of adj) {
+        const i = index.get(u);
+        if (i === undefined)
+            continue;
+        maxDegree = Math.max(maxDegree, neighbours.size);
+        for (const v of neighbours) {
+            const j = index.get(v);
+            if (j !== undefined)
+                A[i][j] = 1;
+        }
+    }
+    const beta = maxDegree === 0 ? 0.5 : 1 / (2 * maxDegree);
+    const M = A.map((row, i) => row.map((x, j) => (i === j ? 1 : 0) - beta * x));
+    const inverse = squareMatrix(inv(M), n);
+    const K = inverse.map((row, i) => row.map((x, j) => (i === j ? x - 1 : x)));
+    return { K, beta };
+}
+/**
+ * The Katz-index predictor, SEPARATE from the recorded comparison and labelled post hoc: it was
+ * added after the negative result was recorded, so its numbers are exploratory and are never
+ * merged into that result. Ranks each candidate by K[premise][candidate] (paths of every length,
+ * attenuated by β per step), ties by id. Not wired into discovery (`src/composition/`): Product A
+ * candidates are in different components by construction, so every path score there is 0.
+ *
+ * @internal
+ */
+export function runKatzLinkPrediction(families, k = 10) {
+    const { models, queries, stillConnected } = holdOuts(families);
+    const ids = [...models.keys()];
+    const index = new Map(ids.map((id, i) => [id, i]));
+    const trials = queries.map((q) => {
+        const katz = katzIndex(q.adj, ids);
+        const p = index.get(q.premise);
+        const score = (id) => katz.K[p][index.get(id)];
+        const ranked = rankBy(q.candidates, (id) => [score(id)]);
+        return {
+            bridgeId: q.held.id,
+            premise: q.premise,
+            conclusion: q.conclusion,
+            katzRank: rankOf(ranked, q.conclusion),
+            katzScore: q.candidates.includes(q.conclusion) ? score(q.conclusion) : 0,
+            candidates: q.candidates.length,
+            beta: katz.beta,
+            postHoc: true,
+        };
+    });
+    const betas = trials.map((t) => t.beta);
+    const hit = trials.map((t) => (t.katzRank <= k ? 1 : 0));
+    const rr = trials.map((t) => 1 / t.katzRank);
     return {
+        postHoc: true,
+        label: POST_HOC_LABEL,
         k,
+        betaRange: betas.length === 0 ? [Number.NaN, Number.NaN] : [Math.min(...betas), Math.max(...betas)],
         trials,
         stillConnected,
-        structuralHits: trials.filter((t) => t.structuralRank <= k).length,
-        textHits: trials.filter((t) => t.textRank <= k).length,
-        chanceRecall: mean(trials.map((t) => Math.min(k, t.candidates) / t.candidates)),
-        structuralMrr: mean(trials.map((t) => 1 / t.structuralRank)),
-        textMrr: mean(trials.map((t) => 1 / t.textRank)),
+        katzHits: hit.reduce((acc, x) => acc + x, 0),
+        katzMrr: meanOrNaN(rr),
+        chanceRecall: meanOrNaN(trials.map((t) => Math.min(k, t.candidates) / t.candidates)),
+        intervals: { seed: RESAMPLE_SEED, resamples: RESAMPLES, recall: bootstrapMean(hit), mrr: bootstrapMean(rr) },
     };
 }
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package/dist/atlas/link-prediction.js.map

@@ -1 +1 @@
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* Atlas Phase 6, S6.3 — link prediction over the typed model graph: ONE result,\n * stated as a hypothesis about the representation.\n *\n * Design note: `docs/planning/Atlas-Phase-6-Design.md` §1.\n *\n * The graph: every model in every registered family is a node; every\n * premise→conclusion pair of every bridge is an undirected edge. The test is\n * leave-one-bridge-out: remove a bridge's edges, then ask each predictor to rank\n * the conclusion among every model not already adjacent to the premise. A hit is\n * the held-out conclusion inside the top k.\n *\n * - **structural predictor** — common neighbours in the remaining graph, ties\n *   broken by sharing the premise's family, then by id;\n * - **text baseline** — word-token overlap between the models' dynamics and\n *   state-space descriptions (`text-overlap.ts`), ties broken by id.\n *\n * **The recorded result stands.** The negative result (typed neighbourhood below text\n * overlap on twenty trials; NOTES.md, \"Link prediction is NEGATIVE\") is reproduced by\n * {@link runLinkPrediction} exactly as recorded and is not re-run for a better answer. What\n * was added beside it, never inside it: a seeded percentile-bootstrap interval on every\n * recall and MRR (MathTS `bootstrapCI`), a seeded permutation test on the two per-trial\n * reciprocal-rank vectors (MathTS `permutationTest`, stated for what it is), and McNemar's\n * exact p on the paired hits (`benchmark/stats.ts`). The Katz-index predictor\n * ({@link runKatzLinkPrediction}) is a SEPARATE result: every record it returns carries\n * `postHoc: true` and the label, and it is never a field of the recorded comparison.\n *\n * ⚠ **What this result cannot carry.** The graph is small (24 models, 22 pairs)\n * and was curated by the same agent that runs the test, in-distribution. It is a\n * statement about how this representation behaves on its own content — not a\n * discovery claim, not a hub or gap claim, and not evidence about physics the\n * atlas does not contain. ROADMAP Phase 6 asks for it as a hypothesis test, and\n * that is its whole scope. Product A (`src/composition/discovery.ts`) is not\n * touched: a test pins that nothing under `src/atlas/` imports it, and the Katz\n * predictor is not wired into discovery, whose candidates are in different\n * components by construction (every path score there is 0).\n *\n * @module atlas/link-prediction\n * @internal\n */\n\nimport { bootstrapCI, inv, permutationTest } from '@danielsimonjr/mathts-functions';\nimport type { AtlasFamily } from './family.js';\nimport type { AtlasModel } from './model.js';\nimport type { AtlasBridge } from './types.js';\nimport { jaccard, rankBy, tokens } from './text-overlap.js';\nimport { mcnemar } from './benchmark/stats.js';\nimport { meanOf } from '../numerical/statistics.js';\n\n/** One held-out pair and whether each predictor recovered it. @internal */\nexport interface LinkPredictionTrial {\n  readonly bridgeId: string;\n  readonly premise: string;\n  readonly conclusion: string;\n  /** 1-based rank of the held-out conclusion; Infinity when it was not a candidate. */\n  readonly structuralRank: number;\n  readonly textRank: number;\n  /** How many candidates the conclusion competed against. */\n  readonly candidates: number;\n}\n\n/** A percentile-bootstrap interval with the point estimate it brackets (MathTS `bootstrapCI`). @internal */\nexport interface BootstrapInterval {\n  readonly estimate: number;\n  readonly lower: number;\n  readonly upper: number;\n  /** The confidence level, 0.95. */\n  readonly confidence: number;\n}\n\n/** The seeded intervals of the recorded comparison. @internal */\nexport interface LinkPredictionIntervals {\n  /** The seed every resample used; stated so the interval is reproducible. */\n  readonly seed: number;\n  readonly resamples: number;\n  readonly structuralRecall: BootstrapInterval;\n  readonly textRecall: BootstrapInterval;\n  readonly structuralMrr: BootstrapInterval;\n  readonly textMrr: BootstrapInterval;\n}\n\n/** The seeded permutation test on the two per-trial reciprocal-rank vectors. @internal */\nexport interface ReciprocalRankPermutation {\n  /** Mean structural reciprocal rank minus mean text reciprocal rank (the observed MRR difference). */\n  readonly statistic: number;\n  /** Two-tailed p from MathTS `permutationTest`. */\n  readonly pValue: number;\n  readonly seed: number;\n  readonly resamples: number;\n  /**\n   * What the test is. MathTS has no paired permutation: `permutationTest` pools the two vectors\n   * and re-splits them, so the trial pairing is not kept and the null is looser than a sign-flip\n   * test's. The paired test on the hits is `mcnemarExactP`.\n   */\n  readonly kind: typeof PERMUTATION_KIND;\n}\n\n/** The statement of the permutation test's kind, so no reader takes it for a paired test. @internal */\nexport const PERMUTATION_KIND =\n  'two-sample permutation of the reciprocal-rank vectors (pooled re-split; the pairing is not kept)' as const;\n\n/** The whole leave-one-bridge-out run. @internal */\nexport interface LinkPredictionResult {\n  readonly k: number;\n  readonly trials: readonly LinkPredictionTrial[];\n  /**\n   * Held-out pairs whose endpoints stay adjacent through ANOTHER bridge. Such a\n   * pair is not a missing link — the conclusion cannot even be a candidate — so\n   * it is excluded from the trials and counted here instead of silently.\n   */\n  readonly stillConnected: number;\n  readonly structuralHits: number;\n  readonly textHits: number;\n  /**\n   * The hit rate a RANDOM ranking would get: the mean over trials of\n   * min(k, candidates)/candidates. On a small graph this is high, and a\n   * predictor's recall means nothing until it is read against it.\n   */\n  readonly chanceRecall: number;\n  /** Mean reciprocal rank of the held-out conclusion. */\n  readonly structuralMrr: number;\n  readonly textMrr: number;\n  /** Seeded bootstrap intervals on the four numbers above. */\n  readonly intervals: LinkPredictionIntervals;\n  /** The seeded permutation test on the per-trial reciprocal ranks. */\n  readonly permutation: ReciprocalRankPermutation;\n  /** McNemar's exact p on the paired hit table (both, structural only, text only, neither). */\n  readonly mcnemarExactP: number;\n}\n\n/** The label every Katz record carries. @internal */\nexport const POST_HOC_LABEL = 'post hoc: added after the negative result was recorded' as const;\n\n/** One held-out pair under the Katz-index predictor. @internal */\nexport interface KatzTrial {\n  readonly bridgeId: string;\n  readonly premise: string;\n  readonly conclusion: string;\n  /** 1-based rank of the held-out conclusion by Katz index; Infinity when it was not a candidate. */\n  readonly katzRank: number;\n  /** The Katz index K[premise][conclusion] = ((I − βA)⁻¹ − I)[premise][conclusion]; 0 when no path. */\n  readonly katzScore: number;\n  readonly candidates: number;\n  /** This trial's attenuation β = 1/(2·max degree) of its own held-out graph. */\n  readonly beta: number;\n  readonly postHoc: true;\n}\n\n/** The Katz-index run: a separate, post-hoc result, never merged into the recorded comparison. @internal */\nexport interface KatzLinkPredictionResult {\n  readonly postHoc: true;\n  readonly label: typeof POST_HOC_LABEL;\n  readonly k: number;\n  /**\n   * `[min, max]` of the trials' attenuations. Each held-out graph has its own maximum degree, so\n   * β = 1/(2·max degree) is per trial (`KatzTrial.beta`), each below its graph's spectral bound\n   * 1/λ_max since λ_max ≤ max degree. The result once reported one β, the last trial's.\n   */\n  readonly betaRange: readonly [number, number];\n  readonly trials: readonly KatzTrial[];\n  readonly stillConnected: number;\n  readonly katzHits: number;\n  readonly katzMrr: number;\n  readonly chanceRecall: number;\n  readonly intervals: {\n    readonly seed: number;\n    readonly resamples: number;\n    readonly recall: BootstrapInterval;\n    readonly mrr: BootstrapInterval;\n  };\n}\n\n/** The one seed every resample in this module uses, and the resample count. Stated, not hidden. */\nconst RESAMPLE_SEED = 20260924;\nconst RESAMPLES = 10000;\n\n/** One leave-one-bridge-out query: the graph without the bridge, and the candidates. */\ninterface HoldOut {\n  readonly held: AtlasBridge;\n  readonly premise: string;\n  readonly conclusion: string;\n  readonly premiseModel: AtlasModel;\n  /** The undirected graph WITHOUT the held-out bridge. */\n  readonly adj: ReadonlyMap<string, ReadonlySet<string>>;\n  readonly candidates: readonly string[];\n}\n\n/** Every held-out query of the families, and the pairs excluded as still connected. */\nfunction holdOuts(families: readonly AtlasFamily[]): {\n  readonly models: ReadonlyMap<string, AtlasModel>;\n  readonly queries: readonly HoldOut[];\n  readonly stillConnected: number;\n} {\n  const models = new Map<string, AtlasModel>();\n  for (const f of families) for (const m of f.models) models.set(m.id, m);\n  const bridges = families.flatMap((f) => f.bridges);\n  const edgesOf = (b: AtlasBridge): Array<readonly [string, string]> => b.premises.map((p) => [p, b.conclusion] as const);\n\n  const queries: HoldOut[] = [];\n  let stillConnected = 0;\n  for (const held of bridges) {\n    const adj = new Map<string, Set<string>>();\n    for (const id of models.keys()) adj.set(id, new Set());\n    for (const b of bridges) {\n      if (b === held) continue;\n      for (const [u, v] of edgesOf(b)) {\n        adj.get(u)?.add(v);\n        adj.get(v)?.add(u);\n      }\n    }\n    for (const [premise, conclusion] of edgesOf(held)) {\n      const premiseModel = models.get(premise);\n      if (premiseModel === undefined) continue;\n      const neighbours = adj.get(premise) ?? new Set<string>();\n      if (neighbours.has(conclusion)) {\n        stillConnected++;\n        continue;\n      }\n      const candidates = [...models.keys()].filter((id) => id !== premise && !neighbours.has(id));\n      queries.push({ held, premise, conclusion, premiseModel, adj, candidates });\n    }\n  }\n  return { models, queries, stillConnected };\n}\n\n/** 1-based position of `id` in a ranking; Infinity when absent. */\nconst rankOf = (list: readonly string[], id: string): number => {\n  const i = list.indexOf(id);\n  return i < 0 ? Number.POSITIVE_INFINITY : i + 1;\n};\n\n/** Seeded percentile bootstrap of the mean of per-trial values (a 0/1 hit, or a reciprocal rank). */\nfunction bootstrapMean(values: readonly number[]): BootstrapInterval {\n  const ci = bootstrapCI([...values], (sample) => meanOf(sample), {\n    confidence: 0.95,\n    resamples: RESAMPLES,\n    seed: RESAMPLE_SEED,\n  });\n  return { estimate: ci.estimate, lower: ci.lower, upper: ci.upper, confidence: ci.confidence };\n}\n\n/** The mean of a trial statistic; NaN with no trials, as the recorded result always read it. */\nconst meanOrNaN = (xs: readonly number[]): number => (xs.length === 0 ? Number.NaN : meanOf(xs));\n\n/**\n * Run leave-one-bridge-out link prediction over the families' model graph. The recorded\n * comparison (structural against text), with its seeded intervals and paired statistics.\n *\n * @param families - the atlas families (normally `ATLAS_FAMILIES`).\n * @param k - the depth a hit must fall within (10, as pre-registered for recall).\n * @internal\n */\nexport function runLinkPrediction(families: readonly AtlasFamily[], k = 10): LinkPredictionResult {\n  const { models, queries, stillConnected } = holdOuts(families);\n  const trials: LinkPredictionTrial[] = queries.map((q) => {\n    const neighbours = q.adj.get(q.premise) ?? new Set<string>();\n    const common = (id: string): number => {\n      let n = 0;\n      for (const x of q.adj.get(id) ?? []) if (neighbours.has(x)) n++;\n      return n;\n    };\n    const structural = rankBy(q.candidates, (id) => [common(id), models.get(id)!.family === q.premiseModel.family ? 1 : 0]);\n    const pText = tokens(`${q.premiseModel.dynamics} ${q.premiseModel.stateSpace}`);\n    const text = rankBy(q.candidates, (id) => {\n      const m = models.get(id)!;\n      return [jaccard(pText, tokens(`${m.dynamics} ${m.stateSpace}`))];\n    });\n    return {\n      bridgeId: q.held.id,\n      premise: q.premise,\n      conclusion: q.conclusion,\n      structuralRank: rankOf(structural, q.conclusion),\n      textRank: rankOf(text, q.conclusion),\n      candidates: q.candidates.length,\n    };\n  });\n\n  const structuralHit: number[] = trials.map((t) => (t.structuralRank <= k ? 1 : 0));\n  const textHit: number[] = trials.map((t) => (t.textRank <= k ? 1 : 0));\n  const structuralRR = trials.map((t) => 1 / t.structuralRank);\n  const textRR = trials.map((t) => 1 / t.textRank);\n\n  // The paired hit table: both, structural only, text only, neither.\n  let a = 0;\n  let b = 0;\n  let c = 0;\n  let d = 0;\n  trials.forEach((_, i) => {\n    if (structuralHit[i] && textHit[i]) a++;\n    else if (structuralHit[i]) b++;\n    else if (textHit[i]) c++;\n    else d++;\n  });\n\n  const permuted = permutationTest(structuralRR, textRR, (x, y) => meanOrNaN(x) - meanOrNaN(y), {\n    resamples: RESAMPLES,\n    seed: RESAMPLE_SEED,\n  });\n\n  return {\n    k,\n    trials,\n    stillConnected,\n    structuralHits: structuralHit.reduce((acc, x) => acc + x, 0),\n    textHits: textHit.reduce((acc, x) => acc + x, 0),\n    chanceRecall: meanOrNaN(trials.map((t) => Math.min(k, t.candidates) / t.candidates)),\n    structuralMrr: meanOrNaN(structuralRR),\n    textMrr: meanOrNaN(textRR),\n    intervals: {\n      seed: RESAMPLE_SEED,\n      resamples: RESAMPLES,\n      structuralRecall: bootstrapMean(structuralHit),\n      textRecall: bootstrapMean(textHit),\n      structuralMrr: bootstrapMean(structuralRR),\n      textMrr: bootstrapMean(textRR),\n    },\n    permutation: {\n      statistic: permuted.statistic,\n      pValue: permuted.pValue,\n      seed: RESAMPLE_SEED,\n      resamples: RESAMPLES,\n      kind: PERMUTATION_KIND,\n    },\n    mcnemarExactP: mcnemar({ a, b, c, d }).exactP,\n  };\n}\n\n/** A square number matrix of order n, read back from MathTS `inv`, which types its result `unknown`. */\nfunction squareMatrix(value: unknown, n: number): number[][] {\n  if (!Array.isArray(value) || value.length !== n) {\n    throw new TypeError(`inv did not return a ${n}×${n} matrix`);\n  }\n  for (const row of value) {\n    if (!Array.isArray(row) || row.length !== n || !row.every((x) => typeof x === 'number' && Number.isFinite(x))) {\n      throw new TypeError(`inv did not return a ${n}×${n} matrix of finite numbers`);\n    }\n  }\n  return value as number[][];\n}\n\n/**\n * The Katz index of the graph without the held-out bridge: K = (I − βA)⁻¹ − I through MathTS\n * `inv`, with β = 1/(2·max degree). The largest eigenvalue of a 0/1 adjacency is at most the\n * maximum degree, so β is below the spectral bound 1/λ_max and the series Σ βˡ Aˡ converges.\n * A graph with no edge has K = 0 everywhere, and β is stated as 0.5 (there is nothing to attenuate).\n */\nfunction katzIndex(adj: ReadonlyMap<string, ReadonlySet<string>>, ids: readonly string[]): { K: number[][]; beta: number } {\n  const n = ids.length;\n  const index = new Map(ids.map((id, i) => [id, i]));\n  const A: number[][] = Array.from({ length: n }, () => new Array<number>(n).fill(0));\n  let maxDegree = 0;\n  for (const [u, neighbours] of adj) {\n    const i = index.get(u);\n    if (i === undefined) continue;\n    maxDegree = Math.max(maxDegree, neighbours.size);\n    for (const v of neighbours) {\n      const j = index.get(v);\n      if (j !== undefined) A[i][j] = 1;\n    }\n  }\n  const beta = maxDegree === 0 ? 0.5 : 1 / (2 * maxDegree);\n  const M = A.map((row, i) => row.map((x, j) => (i === j ? 1 : 0) - beta * x));\n  const inverse = squareMatrix(inv(M), n);\n  const K = inverse.map((row, i) => row.map((x, j) => (i === j ? x - 1 : x)));\n  return { K, beta };\n}\n\n/**\n * The Katz-index predictor, SEPARATE from the recorded comparison and labelled post hoc: it was\n * added after the negative result was recorded, so its numbers are exploratory and are never\n * merged into that result. Ranks each candidate by K[premise][candidate] (paths of every length,\n * attenuated by β per step), ties by id. Not wired into discovery (`src/composition/`): Product A\n * candidates are in different components by construction, so every path score there is 0.\n *\n * @internal\n */\nexport function runKatzLinkPrediction(families: readonly AtlasFamily[], k = 10): KatzLinkPredictionResult {\n  const { models, queries, stillConnected } = holdOuts(families);\n  const ids = [...models.keys()];\n  const index = new Map(ids.map((id, i) => [id, i]));\n  const trials: KatzTrial[] = queries.map((q) => {\n    const katz = katzIndex(q.adj, ids);\n    const p = index.get(q.premise)!;\n    const score = (id: string): number => katz.K[p][index.get(id)!];\n    const ranked = rankBy(q.candidates, (id) => [score(id)]);\n    return {\n      bridgeId: q.held.id,\n      premise: q.premise,\n      conclusion: q.conclusion,\n      katzRank: rankOf(ranked, q.conclusion),\n      katzScore: q.candidates.includes(q.conclusion) ? score(q.conclusion) : 0,\n      candidates: q.candidates.length,\n      beta: katz.beta,\n      postHoc: true,\n    };\n  });\n  const betas = trials.map((t) => t.beta);\n  const hit: number[] = trials.map((t) => (t.katzRank <= k ? 1 : 0));\n  const rr = trials.map((t) => 1 / t.katzRank);\n  return {\n    postHoc: true,\n    label: POST_HOC_LABEL,\n    k,\n    betaRange: betas.length === 0 ? [Number.NaN, Number.NaN] : [Math.min(...betas), Math.max(...betas)],\n    trials,\n    stillConnected,\n    katzHits: hit.reduce((acc, x) => acc + x, 0),\n    katzMrr: meanOrNaN(rr),\n    chanceRecall: meanOrNaN(trials.map((t) => Math.min(k, t.candidates) / t.candidates)),\n    intervals: { seed: RESAMPLE_SEED, resamples: RESAMPLES, recall: bootstrapMean(hit), mrr: bootstrapMean(rr) },\n  };\n}\n"]}

package/dist/atlas/model.js.map

@@ -1 +1 @@
-{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/atlas/model.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG"}
+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/atlas/model.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG","sourcesContent":["/**\n * The `Model` record — Phase 3's promotion of the Phase 0 `AtlasModel`.\n *\n * ROADMAP Phase 3 makes the MODEL the unit rather than the equation: state\n * space, dynamics, observables, parameters, boundary/initial data, symmetry\n * group where known, regime. This module is the record's new home; the nine\n * Phase 0 fields are carried over unchanged and three are added.\n *\n * **`boundaryData`, `initialData` and `symmetryGroup` are all OPTIONAL**\n * (`docs/planning/Atlas-Phase-3-Design.md` §4, which supersedes the\n * implementation plan's wording on the first two). No boundary or initial\n * data is recorded for the nine oscillator models, so a required field would\n * force either fabricated values or empty ones asserting \"there are none\".\n * `oscillators/models.ts` refuses exactly that fabrication for `inequalities`.\n * **An absent field says \"not recorded\"; a present empty one says \"there are\n * none\", and only one of those is true here** — so the nine literals stay\n * byte-identical and record nothing they do not have a source for.\n *\n * `src/atlas/serialize.ts` enumerates model fields explicitly, so a model\n * carrying none of the three serializes byte-identically to Phase 0's\n * committed `data/atlas/oscillators.json`.\n *\n * @module atlas/model\n */\n\nimport type { DimensionalVariable } from '../dimensional/buckingham.js';\nimport type { Regime } from './types.js';\n\n/**\n * One model in the atlas.\n *\n * The first nine fields are Phase 0's `AtlasModel` verbatim. The last three\n * are the Phase 3 additions and are omitted, never emptied, when unrecorded.\n *\n * @public\n */\nexport interface AtlasModel {\n  /** `'model-spring'`, `'model-lc'`, … */\n  readonly id: string;\n  readonly family: string;\n  readonly stateSpace: string;\n  /** Display form of the ODE. */\n  readonly dynamics: string;\n  readonly observables: readonly string[];\n  /** Dimensioned parameters. */\n  readonly parameters: readonly DimensionalVariable[];\n  /** `'theta0'`, `'qa'` — declared with the zero dimension. */\n  readonly dimensionlessInputs: readonly string[];\n  /** `'CE-simple-harmonic-frequency'`, … — must resolve in `CANONICAL_EQUATIONS`. */\n  readonly canonicalRefs: readonly string[];\n  readonly regime: Regime;\n\n  // ── Phase 3 additions (OPTIONAL; a model without them is unchanged) ─────\n  /**\n   * Boundary conditions the model is posed with, each as its stated display\n   * form (`'u(0, t) = u(L, t) = 0'`). **Omit when none is recorded** — an\n   * empty array would claim the model has no boundary conditions.\n   */\n  readonly boundaryData?: readonly string[];\n  /**\n   * Initial conditions the model is posed with (`'x(0) = x₀'`). Omit when\n   * none is recorded; see `boundaryData`.\n   */\n  readonly initialData?: readonly string[];\n  /**\n   * The symmetry group where it is known, as stated (`'SO(2)'`,\n   * `'time translation'`). Omit when unknown — Phase 3 records only\n   * symmetries a source states.\n   */\n  readonly symmetryGroup?: string;\n}\n\n/** A `Model`'s id, as `CanonicalEquation.model` references it. @internal */\nexport type ModelId = string;\n"]}

package/dist/atlas/oscillators/bridges-coarse.d.ts.map

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package/dist/atlas/oscillators/bridges-coarse.js

@@ -11,7 +11,7 @@
  * @module atlas/oscillators/bridges-coarse
  */
 import { LENGTH, MASS, VELOCITY } from '../../dimensional/types.js';
-import { deriveRegimeGroups } from '../regime.js';
+import { makeRegime } from '../regime.js';
 import { relationContractOf } from './bridges-exact.js';
 import { SPRING_CONSTANT } from './dimensions.js';
 const FAMILY = 'oscillators';
@@ -82,16 +82,12 @@ export const BRIDGE_CHAIN_WAVE = {
         'the discrete lattice spacing a as an independent scale',
     ],
     sideConditions: ['long-wavelength, qa ≪ 1'],
-    regime: {
-        family: FAMILY,
-        inequalities: [{ group: 'qa', op: '<', bound: 1, alias: 'qa ≪ 1' }],
-        groupDefinitions: deriveRegimeGroups(FAMILY, [
-            { name: 'm', dim: MASS },
-            { name: 'kappa', dim: SPRING_CONSTANT },
-            { name: 'a', dim: LENGTH },
-            { name: 'c', dim: VELOCITY },
-        ], ['qa']),
-    },
+    regime: makeRegime(FAMILY, [
+        { name: 'm', dim: MASS },
+        { name: 'kappa', dim: SPRING_CONSTANT },
+        { name: 'a', dim: LENGTH },
+        { name: 'c', dim: VELOCITY },
+    ], ['qa'], [{ group: 'qa', op: '<', bound: 1, alias: 'qa ≪ 1' }]),
     counterexamples: [
         {
             description: 'A mode at the band edge qa = π has ω = 2√(κ/m) on the lattice, while the ' +
@@ -100,7 +96,6 @@ export const BRIDGE_CHAIN_WAVE = {
             witness: 'W9',
         },
     ],
-    evidence: new Set(['proposed', 'dimension-checked', 'numerically-supported']),
     witnesses: [
         {
             id: 'W9',

package/dist/atlas/oscillators/bridges-coarse.js.map

@@ -1 +1 @@
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The information loss is therefore recorded in\n * `doesNotPreserve` and witnessed numerically by `W9`.\n *\n * @module atlas/oscillators/bridges-coarse\n */\n\nimport { LENGTH, MASS, VELOCITY } from '../../dimensional/types.js';\nimport { makeRegime } from '../regime.js';\nimport type { AtlasBridge, RelationContract } from '../types.js';\nimport { relationContractOf } from './bridges-exact.js';\nimport { SPRING_CONSTANT } from './dimensions.js';\n\nconst FAMILY = 'oscillators';\n\n/**\n * The lattice dispersion relation of `m u_n″ = κ(u_{n+1} − 2u_n + u_{n−1})`:\n * `ω(q) = 2 √(κ/m) |sin(qa/2)|`.\n *\n * @internal\n */\nexport function latticeDispersion(q: number, a: number, kappa: number, m: number): number {\n  return 2 * Math.sqrt(kappa / m) * Math.abs(Math.sin((q * a) / 2));\n}\n\n/**\n * The continuum dispersion relation of `u_tt = c² u_xx` with `c² = κ a² / m`:\n * `ω = c q`.\n *\n * @internal\n */\nexport function continuumDispersion(q: number, a: number, kappa: number, m: number): number {\n  return Math.sqrt((kappa * a * a) / m) * Math.abs(q);\n}\n\n/** The long-wavelength wave speed `c = a √(κ/m)`. @internal */\nexport function chainWaveSpeed(a: number, kappa: number, m: number): number {\n  return a * Math.sqrt(kappa / m);\n}\n\n/**\n * The band edge of the lattice, at `qa = π`: `ω_max = 2 √(κ/m)`.\n * The continuum relation `ω = c q` is unbounded and has no counterpart —\n * that absence IS the information the coarse-graining discards.\n *\n * @internal\n */\nexport function latticeBandEdge(kappa: number, m: number): number {\n  return 2 * Math.sqrt(kappa / m);\n}\n\n/**\n * Leading-order relative dispersion error `1 − ω_lattice/ω_continuum`,\n * approximated as `(qa)²/24`.\n *\n * Convention note (fixed for the whole sprint): with `x = qa/2`,\n * `1 − sin x / x = x²/6 − x⁴/120 + …`, so the true relative error is\n * `(qa)²/24 − (qa)⁴/1920`. The quartic term makes `(qa)²/24` an\n * OVERESTIMATE; the signed deviation `(true − approx)/approx` is therefore\n * NEGATIVE and equals `−(qa)²/80` to leading order. The W9 assertion is on\n * the MAGNITUDE, so the sign convention does not change the test — it is\n * stated here so the next reader does not rederive it.\n *\n * @internal\n */\nexport function dispersionErrorApproximation(qa: number): number {\n  return (qa * qa) / 24;\n}\n\n/** Bridge 5: chain → wave equation by coarse-graining. @internal */\nexport const BRIDGE_CHAIN_WAVE: AtlasBridge = {\n  id: 'ab-chain-wave',\n  relation: 'coarse-graining',\n  premises: ['model-chain'],\n  conclusion: 'model-wave-1d',\n  transformation: 'u_n(t) ↦ u(x = n a, t), with c² = κ a² / m',\n  preserves: [\n    'long-wavelength dispersion ω ≈ c q',\n    'wave speed c = a √(κ/m)',\n    'linearity',\n  ],\n  doesNotPreserve: [\n    'modes with q > π/a',\n    'the band edge ω_max = 2 √(κ/m) at qa = π',\n    'the discrete lattice spacing a as an independent scale',\n  ],\n  sideConditions: ['long-wavelength, qa ≪ 1'],\n  regime: makeRegime(\n    FAMILY,\n    [\n      { name: 'm', dim: MASS },\n      { name: 'kappa', dim: SPRING_CONSTANT },\n      { name: 'a', dim: LENGTH },\n      { name: 'c', dim: VELOCITY },\n    ],\n    ['qa'],\n    [{ group: 'qa', op: '<', bound: 1, alias: 'qa ≪ 1' }],\n  ),\n  counterexamples: [\n    {\n      description:\n        'A mode at the band edge qa = π has ω = 2√(κ/m) on the lattice, while the ' +\n        'continuum relation ω = c q is unbounded: the coarse-grained model has no ' +\n        'band edge at all.',\n      witness: 'W9',\n    },\n  ],\n  witnesses: [\n    {\n      id: 'W9',\n      kind: 'numeric',\n      test: 'tests/atlas/oscillators-coarse.test.ts',\n      tolerance: 'relative dispersion error matches (qa)²/24 within 0.5% of itself',\n    },\n    {\n      id: 'W9b',\n      kind: 'numeric',\n      test: 'tests/atlas/oscillators-coarse.test.ts',\n      tolerance:\n        'ring of 64 masses integrated: ω matches the lattice dispersion within 1e-9 and the coarse error ' +\n        '(qa)²/24 within 1%; superposition within 1e-10 (linearity); a 10% wrong κ and a cubic on-site force each fail',\n    },\n  ],\n  // The monatomic-chain dispersion omega(q) = 2 sqrt(kappa/m) |sin(qa/2)| and its\n  // long-wavelength continuum limit are standard solid-state results. Work and topic are\n  // cited rather than a precise section number, which would be fabrication in a more\n  // confident costume. This array was EMPTY, which is honest but leaves a textbook result\n  // looking unsourced.\n  citations: [\n    'Kittel, Introduction to Solid State Physics - Phonons I: the monatomic linear chain, its dispersion relation and the qa << 1 continuum limit',\n    'Ashcroft & Mermin, Solid State Physics - the one-dimensional monatomic Bravais lattice and the first Brillouin zone band edge at qa = pi',\n  ],\n  reviewStatus: 'proposed',\n};\n\n/**\n * Bridge 5 re-registered through `RelationContract`.\n *\n * `coarse-graining` leaves `bound` OPTIONAL, and this record carries none: the\n * `qa²/24` dispersion residual is a per-mode series term, not a Lipschitz\n * constant with a uniform offset in a stated norm. The union permits the\n * absence rather than forcing an invented `K` and `delta`.\n *\n * No `deltaAt` either, for the same reason and by the same rule: `deltaAt` is\n * the machine form OF a `delta`, so a record with no `delta` has nothing for\n * it to be the machine form of. `admitApproximation` requires `deltaAt` only\n * of an `approximation`, so this record passes admission unchanged.\n *\n * @internal\n */\nexport const CONTRACT_CHAIN_WAVE: RelationContract = relationContractOf(BRIDGE_CHAIN_WAVE);\n"]}

package/dist/atlas/oscillators/bridges-exact.d.ts.map

@@ -1 +1 @@
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package/dist/atlas/oscillators/bridges-exact.js

@@ -21,7 +21,7 @@
  * @module atlas/oscillators/bridges-exact
  */
 import { physjsFormalRef } from '../physjs-ref.js';
-import { deriveRegimeGroups } from '../regime.js';
+import { makeRegime } from '../regime.js';
 import { getAtlasModel } from './models.js';
 import { SPRING_LC_RELATIVE_PERIOD_TRANSPORT } from './norm-transport.js';
 const FAMILY = 'oscillators';
@@ -40,7 +40,10 @@ const WITNESS_RESULTS_TEST = 'tests/atlas/witness-results.test.ts';
  *
  * Work and topic are cited rather than precise section numbers, because a section number
  * stated without checking the edition in hand is the same fabrication in a more confident
- * costume. `reviewStatus` stays 'proposed' until the independent physicist review lands.
+ * costume. `reviewStatus` is the record's declared review state and derives no evidence
+ * tag (`deriveEvidence` never reads it). It is 'proposed' here because no independent
+ * physicist review of these records exists; the atlas no longer gates on one (the ruling
+ * is recorded in `ACTIVE.md` and `NOTES.md`).
  */
 const CITATIONS = [
     'Olson, Dynamical Analogies - the force-voltage (impedance) analogy between a mass-spring–damper and a series RLC circuit',
@@ -57,13 +60,8 @@ function bridgeRegime(premiseId, conclusionId) {
         ...getAtlasModel(premiseId).parameters,
         ...getAtlasModel(conclusionId).parameters,
     ];
-    return {
-        family: FAMILY,
-        inequalities: [],
-        groupDefinitions: deriveRegimeGroups(FAMILY, parameters, []),
-    };
+    return makeRegime(FAMILY, parameters, [], []);
 }
-const evidence = (...tags) => new Set(tags);
 /**
  * Bridge 1 — the lossless spring ↔ LC dictionary.
  *
@@ -104,7 +102,6 @@ export const BRIDGE_SPRING_LC = {
     // DERIVED from `data/atlas/witness-results.json`, where W1s records the CAS
     // check of this bridge's dictionary. A stored copy would be a second source
     // of truth that no run could falsify.
-    evidence: evidence('proposed', 'numerically-supported'),
     witnesses: [
         {
             id: 'W1',
@@ -166,7 +163,6 @@ export const BRIDGE_DAMPED_RLC = {
     ],
     regime: bridgeRegime('model-damped-spring', 'model-rlc'),
     counterexamples: [],
-    evidence: evidence('proposed', 'numerically-supported'),
     witnesses: [
         {
             id: 'W2',

package/dist/atlas/oscillators/bridges-exact.js.map

@@ -1 +1 @@
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It is carried in\n * `sideConditions` as prose instead, and the equality is what witness W2\n * executes. Writing an inequality that merely resembles it would be a\n * fabricated constraint, so none is written. `groupDefinitions` is derived\n * from the premise and conclusion parameters by `deriveRegimeGroups`, exactly\n * as the models do; nothing there is hand-authored.\n *\n * **Evidence tags are witness-gated.** A tag appears only because a witness in\n * `tests/atlas/oscillators-exact.test.ts` passes and shows it.\n *\n * @module atlas/oscillators/bridges-exact\n */\n\nimport { physjsFormalRef } from '../physjs-ref.js';\nimport { makeRegime } from '../regime.js';\nimport { getAtlasModel } from './models.js';\nimport type { AtlasBridge, Regime, RelationContract } from '../types.js';\nimport { SPRING_LC_RELATIVE_PERIOD_TRANSPORT } from './norm-transport.js';\n\nconst FAMILY = 'oscillators';\n\n/** The witness test file every witness below runs in. */\nconst TEST = 'tests/atlas/oscillators-exact.test.ts';\n/** Where the CAS witnesses W1s and W2s are named; the artifact pin runs them. */\nconst WITNESS_RESULTS_TEST = 'tests/atlas/witness-results.test.ts';\n\n/**\n * Literature for the electromechanical analogy, NOT a pointer at our own plan.\n *\n * The previous value here was `docs/planning/Atlas-Phase-0-Design.md §3, §6` - a citation\n * naming the document that ASSERTED the claim. That is circular, and it is worse than an\n * empty array because it LOOKS sourced and would satisfy any check that only asks whether\n * `citations[]` is non-empty. Same failure class as the evidence-tag theatre that\n * `tests/atlas/evidence-rule.test.ts` exists to catch.\n *\n * Work and topic are cited rather than precise section numbers, because a section number\n * stated without checking the edition in hand is the same fabrication in a more confident\n * costume. `reviewStatus` is the record's declared review state and derives no evidence\n * tag (`deriveEvidence` never reads it). It is 'proposed' here because no independent\n * physicist review of these records exists; the atlas no longer gates on one (the ruling\n * is recorded in `ACTIVE.md` and `NOTES.md`).\n */\nconst CITATIONS: readonly string[] = [\n  'Olson, Dynamical Analogies - the force-voltage (impedance) analogy between a mass-spring–damper and a series RLC circuit',\n  'Feynman, Lectures on Physics Vol. II, chapter on resonance - the LC oscillator and its mechanical counterpart',\n];\n\n/**\n * Regime coordinates spanning a bridge's premise and conclusion parameters.\n *\n * The two models' parameter names are disjoint in both bridges, so the union\n * is a legal `deriveRegimeGroups` input.\n */\nfunction bridgeRegime(premiseId: string, conclusionId: string): Regime {\n  const parameters = [\n    ...getAtlasModel(premiseId).parameters,\n    ...getAtlasModel(conclusionId).parameters,\n  ];\n  return makeRegime(FAMILY, parameters, [], []);\n}\n\n/**\n * Bridge 1 — the lossless spring ↔ LC dictionary.\n *\n * `m ↔ L`, `k ↔ 1/C`, `x ↔ q`. Under `u = x/x0` (or `q/q0`) and `τ = ω0 t`\n * both systems become `u'' + u = 0`, so the equivalence is exact and\n * invertible.\n *\n * Its counterexample is W2b, which lives on THIS bridge: it shows that adding\n * a resistor to the LC side breaks the equivalence, so bridge 1 is a statement\n * about the LOSSLESS pair only.\n *\n * @internal\n */\nexport const BRIDGE_SPRING_LC: AtlasBridge = {\n  id: 'ab-spring-lc',\n  relation: 'exact-equivalence',\n  premises: ['model-spring'],\n  conclusion: 'model-lc',\n  // Two nondimensionalizations, each with its own ω0; composed, the spring→LC map is\n  // q(t) = (q0/x0)·x(ω_LC t / ω_s). The dimensioned frequencies differ (W1a: ω_s = 2,\n  // ω_LC = 2√2); what is preserved is the frequency in units of ω0.\n  transformation:\n    'force–voltage analogy m ↔ L, k ↔ 1/C, x ↔ q (so ω0² = k/m ↔ 1/(LC)); ' +\n    'u = x/x0 or q/q0, τ = ω0 t; composed, q(t) = (q0/x0)·x(ω_LC t / ω_s)',\n  inverse: 'x = x0 u, t = τ/ω0',\n  preserves: ['the natural frequency in units of ω0 (ω = 1 in τ = ω0 t)', 'energy up to scale', 'phase portrait'],\n  doesNotPreserve: ['physical interpretation', 'units'],\n  sideConditions: ['m, k, L, C > 0', 'lossless', 'unforced', 'x0, q0 nonzero'],\n  regime: bridgeRegime('model-spring', 'model-lc'),\n  counterexamples: [\n    {\n      description:\n        'adding R to bridge 1 breaks it: the circuit L = 2, C = 0.125 of witness W2b with R = 4 has ' +\n        'ζ_RLC = (R/2)√(C/L) = 0.5, ' +\n        'which no lossless spring matches — the trajectories separate by more than 1e-2 at τ = π',\n      witness: 'W2b',\n    },\n  ],\n  // `symbolically-checked` is NOT stored here any more (Phase 4 S4.3): it is\n  // DERIVED from `data/atlas/witness-results.json`, where W1s records the CAS\n  // check of this bridge's dictionary. A stored copy would be a second source\n  // of truth that no run could falsify.\n  witnesses: [\n    {\n      id: 'W1',\n      kind: 'symbolic',\n      test: TEST,\n      tolerance: 'exact — rational exponent arithmetic, no floating point',\n    },\n    {\n      id: 'W1a',\n      kind: 'numeric',\n      test: TEST,\n      tolerance: '|u_spring − u_lc| < 1e-8; each within 1e-8 of cos τ',\n    },\n    {\n      id: 'W1b',\n      kind: 'numeric',\n      test: TEST,\n      tolerance: 'inverse-mapped trajectory solves m x″ + k x = 0 within 1e-8; a 1% wrong ω0 fails',\n    },\n    { id: 'W2b', kind: 'numeric', test: TEST, tolerance: 'separation > 1e-2 at τ = π' },\n    {\n      id: 'W1s',\n      kind: 'symbolic',\n      test: WITNESS_RESULTS_TEST,\n      tolerance: 'CAS: k/m under m ↔ L, k ↔ 1/C minus 1/(LC) simplifies to literal 0',\n    },\n  ],\n  citations: CITATIONS,\n  reviewStatus: 'proposed',\n  // spring → LC in relative period error only; see ./norm-transport.ts for what is not declared.\n  normTransports: [SPRING_LC_RELATIVE_PERIOD_TRANSPORT],\n  formalRef: physjsFormalRef('ab-spring-lc'),\n};\n\n/**\n * Bridge 2 — damped spring ↔ RLC, exact ON a side condition.\n *\n * The undamped dictionary of bridge 1 does not extend for free: `b` and `R`\n * are independent parameters, and the nondimensional systems coincide only\n * when the damping ratios match. The side condition is that equality, and W2\n * DERIVES `R` from it rather than assuming a value.\n *\n * @internal\n */\nexport const BRIDGE_DAMPED_RLC: AtlasBridge = {\n  id: 'ab-damped-rlc',\n  relation: 'exact-equivalence',\n  premises: ['model-damped-spring'],\n  conclusion: 'model-rlc',\n  transformation:\n    'force–voltage analogy m ↔ L, k ↔ 1/C, b ↔ R, x ↔ q; ' +\n    'u = x/x0 or q/q0, τ = ω0 t; composed, q(t) = (q0/x0)·x(ω_RLC t / ω_mech)',\n  inverse: 'x = x0 u, t = τ/ω0',\n  preserves: ['the natural frequency in units of ω0 (ω = 1 in τ = ω0 t)', 'damping ratio', 'phase portrait'],\n  doesNotPreserve: ['physical interpretation', 'units'],\n  sideConditions: [\n    'b/√(mk) = R√(C/L), equivalently ζ_mech = b/(2√(mk)) equals ζ_RLC = (R/2)√(C/L)',\n    'm, b, k, L, R, C > 0',\n    'unforced',\n    'x0, q0 nonzero',\n  ],\n  regime: bridgeRegime('model-damped-spring', 'model-rlc'),\n  counterexamples: [],\n  witnesses: [\n    {\n      id: 'W2',\n      kind: 'numeric',\n      test: TEST,\n      tolerance: 'R derived exactly; |u_mech − u_rlc| < 1e-8 at four τ',\n    },\n    {\n      id: 'W2s',\n      kind: 'symbolic',\n      test: WITNESS_RESULTS_TEST,\n      tolerance: 'CAS: b²/(4mk) under m ↔ L, k ↔ 1/C, b ↔ R minus R²C/(4L) simplifies to literal 0',\n    },\n  ],\n  citations: CITATIONS,\n  reviewStatus: 'proposed',\n  formalRef: physjsFormalRef('ab-damped-rlc'),\n};\n\n// ─────────────────────────────────────────────────────────────────────────────\n// Phase 1 re-registration: the Sprint 0 bridges through `RelationContract`\n// ─────────────────────────────────────────────────────────────────────────────\n\n/**\n * Re-register an `AtlasBridge` through the Phase 1 `RelationContract` union.\n *\n * `AtlasBridge` states its two conditional requirements — `exact-equivalence`\n * needs `inverse`, `approximation` needs `bound` — only in doc comments, so a\n * record that breaks them type-checks. `RelationContract` states them in the\n * type system. This function is the one place the Sprint 0 records cross from\n * the weaker shape to the stronger one, and it THROWS on the two cases the\n * doc comments could only describe.\n *\n * It copies rather than restates: every field comes off the bridge, so a\n * contract cannot drift from the record it re-registers.\n *\n * @throws TypeError when the bridge omits the field its relation requires.\n * @internal\n */\nexport function relationContractOf(bridge: AtlasBridge): RelationContract {\n  const { relation, transformation } = bridge;\n  switch (relation) {\n    case 'exact-equivalence': {\n      if (bridge.inverse === undefined) {\n        throw new TypeError(`${bridge.id}: exact-equivalence without an inverse`);\n      }\n      return { type: relation, transformation, inverse: bridge.inverse };\n    }\n    case 'approximation': {\n      if (bridge.bound === undefined) {\n        throw new TypeError(`${bridge.id}: approximation without a bound`);\n      }\n      return { type: relation, transformation, bound: bridge.bound };\n    }\n    case 'coarse-graining':\n      // `bound` is OPTIONAL here: the chain/wave bridge carries none, and the\n      // union allows that rather than forcing an invented one.\n      return bridge.bound === undefined\n        ? { type: relation, transformation }\n        : { type: relation, transformation, bound: bridge.bound };\n    default:\n      return { type: relation, transformation };\n  }\n}\n\n/** Bridge 1 re-registered through the Phase 1 contract. @internal */\nexport const CONTRACT_SPRING_LC: RelationContract = relationContractOf(BRIDGE_SPRING_LC);\n\n/** Bridge 2 re-registered through the Phase 1 contract. @internal */\nexport const CONTRACT_DAMPED_RLC: RelationContract = relationContractOf(BRIDGE_DAMPED_RLC);\n"]}