universal-physics-tensor 0.45.1 → 0.46.0

package/dist/atlas/export.js

@@ -0,0 +1,106 @@
+/**
+ * Atlas Phase 6, S6.4 — the versioned export: one combined JSON artifact for
+ * every family, and a JSON-LD projection with stable ids, QUDT quantity kinds
+ * where they genuinely resolve, and PROV-O-shaped provenance.
+ *
+ * Design note: `docs/planning/Atlas-Phase-6-Design.md` §2.
+ *
+ * Pure: no I/O. The QUDT resolution table (`data/atlas/qudt-resolution.json`) is
+ * passed IN by the emitter, so this module cannot drift from the table it was
+ * given and never reads the tree.
+ *
+ * ## Why the QUDT table is keyed by (model, parameter), never by name
+ *
+ * `kappa` is a SPRING CONSTANT in `model-chain` and a THERMAL CONDUCTIVITY in
+ * `model-heat`. A name-keyed table would assign one of them the other's
+ * quantity kind — a notation collision in the atlas's own data.
+ *
+ * ## Schema version
+ *
+ * The combined artifact keeps `schemaVersion: '0'`. Phase 4 added one OPTIONAL
+ * field (`formalRef`); an additive optional field is not a breaking change, and
+ * the plan bumps to `v1` only on one.
+ *
+ * @module atlas/export
+ * @internal
+ */
+import { toAtlasJson } from './serialize.js';
+/** The stable id namespace. A URN, so no id depends on a host that could move. @internal */
+export const ATLAS_ID_PREFIX = 'urn:upt:atlas:';
+const modelIri = (id) => `${ATLAS_ID_PREFIX}model:${id}`;
+const bridgeIri = (id) => `${ATLAS_ID_PREFIX}bridge:${id}`;
+/** The combined artifact: every family's record under one version stamp. @internal */
+export function toCombinedAtlasJson(families, packageVersion) {
+    return {
+        schemaVersion: '0',
+        packageVersion,
+        families: families.map((f) => {
+            const { packageVersion: _dropped, ...record } = toAtlasJson(f, packageVersion);
+            return record;
+        }),
+    };
+}
+/**
+ * The JSON-LD projection.
+ *
+ * @throws Error when a model parameter has NO entry in the resolution table — an
+ * unlisted parameter is a gap in the table, and exporting it silently blank
+ * would be indistinguishable from a deliberate "no QUDT kind resolves".
+ * @internal
+ */
+export function toAtlasJsonLd(families, packageVersion, qudt) {
+    const graph = [];
+    for (const family of families) {
+        for (const m of family.models) {
+            graph.push({
+                '@id': modelIri(m.id),
+                '@type': 'upt:Model',
+                'upt:family': family.family,
+                'upt:dynamics': m.dynamics,
+                'upt:parameter': m.parameters.map((p) => {
+                    const key = `${m.id}/${p.name}`;
+                    if (!(key in qudt.entries)) {
+                        throw new Error(`toAtlasJsonLd: no QUDT resolution entry for ${key}`);
+                    }
+                    const kind = qudt.entries[key];
+                    return {
+                        'upt:symbol': p.name,
+                        'upt:dimension': [p.dim.L, p.dim.M, p.dim.T, p.dim.I, p.dim.Theta, p.dim.N, p.dim.J],
+                        ...(kind === null ? {} : { 'qudt:hasQuantityKind': { '@id': kind } }),
+                    };
+                }),
+                ...(m.canonicalRefs.length === 0 ? {} : { 'upt:canonicalRef': [...m.canonicalRefs] }),
+            });
+        }
+        for (const b of family.bridges) {
+            graph.push({
+                '@id': bridgeIri(b.id),
+                '@type': ['upt:Bridge', 'prov:Entity'],
+                'upt:relation': b.relation,
+                'upt:premise': b.premises.map((p) => ({ '@id': modelIri(p) })),
+                'upt:conclusion': { '@id': modelIri(b.conclusion) },
+                // PROV-O shape: the bridge's claim is derived from its premises, and
+                // its sources are the citations it states.
+                'prov:wasDerivedFrom': b.premises.map((p) => ({ '@id': modelIri(p) })),
+                'dcterms:source': [...b.citations],
+                'upt:reviewStatus': b.reviewStatus,
+                'upt:witness': b.witnesses.map((w) => ({ 'upt:id': w.id, 'upt:kind': w.kind, 'upt:test': w.test })),
+                ...(b.formalRef === undefined
+                    ? {}
+                    : { 'upt:formalRef': { 'upt:statement': b.formalRef.statement, 'upt:fidelity': b.formalRef.fidelity } }),
+            });
+        }
+    }
+    return {
+        '@context': {
+            upt: `${ATLAS_ID_PREFIX}vocab:`,
+            prov: 'http://www.w3.org/ns/prov#',
+            qudt: 'http://qudt.org/schema/qudt/',
+            dcterms: 'http://purl.org/dc/terms/',
+        },
+        '@id': `${ATLAS_ID_PREFIX}release:${packageVersion}`,
+        'upt:qudtProbedAt': qudt.probedAt,
+        '@graph': graph,
+    };
+}
+//# sourceMappingURL=export.js.map

package/dist/atlas/export.js.map

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package/dist/atlas/families.d.ts

@@ -0,0 +1,14 @@
+/**
+ * Every registered atlas family, in the order they were built.
+ *
+ * Gates that must cover the WHOLE atlas (the evidence rule, admission, the
+ * JSON artifacts) iterate this list rather than naming one family, so a new
+ * family is checked the moment it is registered here. A gate that named
+ * `OSCILLATOR_FAMILY` directly would pass forever over a family it never read.
+ *
+ * @module atlas/families
+ */
+import type { AtlasFamily } from './oscillators/index.js';
+/** All atlas families. @internal */
+export declare const ATLAS_FAMILIES: readonly AtlasFamily[];
+//# sourceMappingURL=families.d.ts.map

package/dist/atlas/families.d.ts.map

@@ -0,0 +1 @@
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package/dist/atlas/families.js

@@ -0,0 +1,20 @@
+/**
+ * Every registered atlas family, in the order they were built.
+ *
+ * Gates that must cover the WHOLE atlas (the evidence rule, admission, the
+ * JSON artifacts) iterate this list rather than naming one family, so a new
+ * family is checked the moment it is registered here. A gate that named
+ * `OSCILLATOR_FAMILY` directly would pass forever over a family it never read.
+ *
+ * @module atlas/families
+ */
+import { DIFFUSION_FAMILY } from './diffusion/index.js';
+import { OSCILLATOR_FAMILY } from './oscillators/index.js';
+import { WAVES_FAMILY } from './waves/index.js';
+/** All atlas families. @internal */
+export const ATLAS_FAMILIES = [
+    OSCILLATOR_FAMILY,
+    DIFFUSION_FAMILY,
+    WAVES_FAMILY,
+];
+//# sourceMappingURL=families.js.map

package/dist/atlas/families.js.map

@@ -0,0 +1 @@
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package/dist/atlas/index.d.ts

@@ -0,0 +1,90 @@
+/**
+ * Atlas Phase 0 barrel — the oscillator pilot.
+ *
+ * Reachable only through the `universal-physics-tensor/atlas` subpath. Not
+ * re-exported from the root `universal-physics-tensor` entry before Phase 6.
+ *
+ * All symbols are `@internal`: these are throwaway pilot types (design note
+ * §4), not a stability contract.
+ *
+ * ⚠ **THE INVARIANT IS: NEVER THE BARREL.** `src/bridges/` and
+ * `src/composition/` must not import THIS FILE — `src/atlas/` imports
+ * `bridges/*` and `composition/*`, so a barrel import closes a cycle that
+ * `bun run docs:deps` reports. Importing a leaf module (`./types.js`,
+ * `./regime.js`, `./composition-table.js`, …) is fine and the tree has always
+ * done it, VALUES INCLUDED: `bridges/index.ts:40`, `composition/compose.ts`,
+ * `composition/graph-viz.ts`.
+ *
+ * This comment used to say "TYPES ONLY, and only from `src/atlas/types.js`",
+ * which the tree HAS NEVER SATISFIED while `docs:deps` reported 0 cycles.
+ * A rule stricter than the invariant it protects gets silently violated by
+ * correct code, and the next reader either believes a false description of
+ * the tree or "fixes" code that was right. Corrected 2026-09-22 against the
+ * same measurement that corrected `CLAUDE.md`.
+ *
+ * @module atlas
+ */
+export type { RelationType, EvidenceTag, LimitCharacter, RegimeInequality, Regime, ApproximationBound, Witness, Counterexample, AtlasBridge, AtlasRejection, FormalFidelity, FormalRef, } from './types.js';
+export { MissingHorizonError, MissingLipschitzError } from './types.js';
+export { ALL_EVIDENCE_TAGS } from './types.js';
+export { deriveEvidence, deriveEvidenceForVerdict, NO_PASSING_WITNESSES } from './derive-evidence.js';
+export type { CounterexampleLike, EvidenceInput, MembershipVerdict, RejectionLike, WitnessLike, } from './derive-evidence.js';
+export { composeRelation, COMPOSITION_TABLE, NO_COMPOSITE_CLAIM } from './composition-table.js';
+export type { CompositionResult, NoCompositeClaim } from './composition-table.js';
+export { boundPath, findPath } from './path-bound.js';
+export type { NoClaimReason, PathBoundClaim, PathBoundResult, PathNoClaim } from './path-bound.js';
+export type { AtlasModel, ModelId } from './model.js';
+export { composeBounds, composeBoundPath, IDENTITY_BOUND } from './error-algebra.js';
+export type { BoundPair, ComposedPath } from './error-algebra.js';
+export { deriveRegimeGroups, regimeHolds } from './regime.js';
+export type { RegimeCheck } from './regime.js';
+export { CAPACITANCE, CUBIC_STIFFNESS, DAMPING, INDUCTANCE, RESISTANCE, SPRING_CONSTANT, } from './oscillators/dimensions.js';
+export { ATLAS_MODELS, getAtlasModel } from './oscillators/models.js';
+export { OSCILLATOR_FAMILY } from './oscillators/index.js';
+export type { AtlasFamily } from './oscillators/index.js';
+export { toAtlasJson, ATLAS_RECORD_SCHEMA_VERSION } from './serialize.js';
+export type { AtlasRecordJson, JsonValue } from './serialize.js';
+export { blockingFindings, checkApplicability, } from './applicability.js';
+export type { ApplicabilityFinding, ApplicabilityFindingKind, ApplicabilityInput, ApplicabilitySeverity, } from './applicability.js';
+export { passingWitnessIds } from './witness-result.js';
+export type { UnresolvedReason, WitnessRunResult, WitnessStatus, } from './witness-result.js';
+export { ATLAS_FAMILIES } from './families.js';
+export { runLinkPrediction } from './link-prediction.js';
+export { ATLAS_ID_PREFIX, toAtlasJsonLd, toCombinedAtlasJson } from './export.js';
+export type { QudtResolution } from './export.js';
+export type { LinkPredictionResult, LinkPredictionTrial } from './link-prediction.js';
+export { DIFFUSION_FAMILY } from './diffusion/index.js';
+export { BRIDGE_HEAT_DIFFUSION, BRIDGE_SCHRODINGER_DIFFUSION, BRIDGE_WALK_DIFFUSION, DIFFUSION_BRIDGES, } from './diffusion/bridges.js';
+export { DIFFUSION_MODELS, getDiffusionModel } from './diffusion/models.js';
+export { WAVES_FAMILY } from './waves/index.js';
+export { BRIDGE_KLEIN_GORDON_WAVE, BRIDGE_SOUND_SPEED, BRIDGE_STRING_WAVE, BRIDGE_WAVE_DALEMBERT, WAVE_BRIDGES, } from './waves/bridges.js';
+export { WAVE_MODELS } from './waves/models.js';
+export { DIFFUSION_CLOSURE_BRIDGES } from './diffusion/bridges-closure.js';
+export { WAVE_CLOSURE_BRIDGES } from './waves/bridges-closure.js';
+export { FAILURE_KINDS, HELD_OUT_FAMILY, HELD_OUT_MARKERS } from './benchmark/types.js';
+export type { Authorship, BenchmarkItem, BenchmarkSplit, FailureKind } from './benchmark/types.js';
+export { checkRenamedVariants, findCrossSplitLeakage, leakageKey } from './benchmark/leakage.js';
+export type { LeakageCollision, VariantProblem } from './benchmark/leakage.js';
+export { ABLATION_CONFIGS, FULL_CONFIG, runAtlasCondition, runAtlasOnItem, } from './benchmark/run-atlas.js';
+export type { AtlasRunConfig, AtlasVerdict } from './benchmark/run-atlas.js';
+export { rankBySymbolOverlap, rankByStructure, rankByTextOverlap, recallAtK, } from './benchmark/baselines.js';
+export type { CorpusRecord, Ranking, RetrievalQuery } from './benchmark/baselines.js';
+export { parseBackendResponse } from './benchmark/backend-shapes.js';
+export { cohensKappa, mcnemar, pairedDifferenceInterval, powerReport, wilsonInterval, Z95, } from './benchmark/stats.js';
+export type { Interval, McNemarResult, PairedTable, PowerReport } from './benchmark/stats.js';
+export { pairedRejection, scoreAblation, scoreCondition } from './benchmark/study.js';
+export type { AblationRow, ConditionAnswer, ConditionMetrics, ItemLabel, PairedRejection, } from './benchmark/study.js';
+export type { BackendShapeError, BenchmarkBackendRequest, BenchmarkBackendResponse, } from './benchmark/backend-shapes.js';
+export { runWitnessRegistry, artifactPassingWitnessIds } from './witness-artifact.js';
+export type { WitnessResultRecord, WitnessResultsArtifact } from './witness-artifact.js';
+export { WITNESS_REGISTRY } from './witness-specs.js';
+export type { RegisteredNumericWitness, RegisteredSymbolicWitness, RegisteredWitness, } from './witness-specs.js';
+export { runSymbolicWitness } from './witness-symbolic.js';
+export type { SymbolicSimplifier, SymbolicWitnessSpec } from './witness-symbolic.js';
+export { runNumericWitness } from './witness-numeric.js';
+export type { Convergence, NumericWitnessRunResult, NumericWitnessSpec, } from './witness-numeric.js';
+export { contextUnion, statementContextUnion } from './statement.js';
+export type { Context, ContextUnionFormed, ContextUnionRefused, ContextUnionResult, NoUnionReason, Statement, StatementId, } from './statement.js';
+export { composeDerivations, composeDerivationsOrThrow, DerivationCompositionError, makeDerivation, } from './derivation.js';
+export type { CompositeFormed, CompositeRefused, Derivation, DerivationCompositionResult, DerivationId, DerivationSpec, NoCompositeReason, } from './derivation.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/atlas/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/atlas/index.js

@@ -0,0 +1,69 @@
+/**
+ * Atlas Phase 0 barrel — the oscillator pilot.
+ *
+ * Reachable only through the `universal-physics-tensor/atlas` subpath. Not
+ * re-exported from the root `universal-physics-tensor` entry before Phase 6.
+ *
+ * All symbols are `@internal`: these are throwaway pilot types (design note
+ * §4), not a stability contract.
+ *
+ * ⚠ **THE INVARIANT IS: NEVER THE BARREL.** `src/bridges/` and
+ * `src/composition/` must not import THIS FILE — `src/atlas/` imports
+ * `bridges/*` and `composition/*`, so a barrel import closes a cycle that
+ * `bun run docs:deps` reports. Importing a leaf module (`./types.js`,
+ * `./regime.js`, `./composition-table.js`, …) is fine and the tree has always
+ * done it, VALUES INCLUDED: `bridges/index.ts:40`, `composition/compose.ts`,
+ * `composition/graph-viz.ts`.
+ *
+ * This comment used to say "TYPES ONLY, and only from `src/atlas/types.js`",
+ * which the tree HAS NEVER SATISFIED while `docs:deps` reported 0 cycles.
+ * A rule stricter than the invariant it protects gets silently violated by
+ * correct code, and the next reader either believes a false description of
+ * the tree or "fixes" code that was right. Corrected 2026-09-22 against the
+ * same measurement that corrected `CLAUDE.md`.
+ *
+ * @module atlas
+ */
+export { MissingHorizonError, MissingLipschitzError } from './types.js';
+export { ALL_EVIDENCE_TAGS } from './types.js';
+// The Phase 1–3 core. Absent from this barrel until the S6.7 API review found
+// the gap: subpath users could not reach evidence derivation, the composition
+// table or path bounding at all (tests/atlas/barrel-completeness.test.ts).
+export { deriveEvidence, deriveEvidenceForVerdict, NO_PASSING_WITNESSES } from './derive-evidence.js';
+export { composeRelation, COMPOSITION_TABLE, NO_COMPOSITE_CLAIM } from './composition-table.js';
+export { boundPath, findPath } from './path-bound.js';
+export { composeBounds, composeBoundPath, IDENTITY_BOUND } from './error-algebra.js';
+export { deriveRegimeGroups, regimeHolds } from './regime.js';
+export { CAPACITANCE, CUBIC_STIFFNESS, DAMPING, INDUCTANCE, RESISTANCE, SPRING_CONSTANT, } from './oscillators/dimensions.js';
+export { ATLAS_MODELS, getAtlasModel } from './oscillators/models.js';
+export { OSCILLATOR_FAMILY } from './oscillators/index.js';
+export { toAtlasJson, ATLAS_RECORD_SCHEMA_VERSION } from './serialize.js';
+export { blockingFindings, checkApplicability, } from './applicability.js';
+export { passingWitnessIds } from './witness-result.js';
+export { ATLAS_FAMILIES } from './families.js';
+export { runLinkPrediction } from './link-prediction.js';
+export { ATLAS_ID_PREFIX, toAtlasJsonLd, toCombinedAtlasJson } from './export.js';
+export { DIFFUSION_FAMILY } from './diffusion/index.js';
+export { BRIDGE_HEAT_DIFFUSION, BRIDGE_SCHRODINGER_DIFFUSION, BRIDGE_WALK_DIFFUSION, DIFFUSION_BRIDGES, } from './diffusion/bridges.js';
+export { DIFFUSION_MODELS, getDiffusionModel } from './diffusion/models.js';
+export { WAVES_FAMILY } from './waves/index.js';
+export { BRIDGE_KLEIN_GORDON_WAVE, BRIDGE_SOUND_SPEED, BRIDGE_STRING_WAVE, BRIDGE_WAVE_DALEMBERT, WAVE_BRIDGES, } from './waves/bridges.js';
+export { WAVE_MODELS } from './waves/models.js';
+export { DIFFUSION_CLOSURE_BRIDGES } from './diffusion/bridges-closure.js';
+export { WAVE_CLOSURE_BRIDGES } from './waves/bridges-closure.js';
+// Phase 5 benchmark: the PURE parts only. `benchmark/loader.ts` reads files and is
+// deliberately not re-exported, so importing this barrel never pulls in file I/O.
+export { FAILURE_KINDS, HELD_OUT_FAMILY, HELD_OUT_MARKERS } from './benchmark/types.js';
+export { checkRenamedVariants, findCrossSplitLeakage, leakageKey } from './benchmark/leakage.js';
+export { ABLATION_CONFIGS, FULL_CONFIG, runAtlasCondition, runAtlasOnItem, } from './benchmark/run-atlas.js';
+export { rankBySymbolOverlap, rankByStructure, rankByTextOverlap, recallAtK, } from './benchmark/baselines.js';
+export { parseBackendResponse } from './benchmark/backend-shapes.js';
+export { cohensKappa, mcnemar, pairedDifferenceInterval, powerReport, wilsonInterval, Z95, } from './benchmark/stats.js';
+export { pairedRejection, scoreAblation, scoreCondition } from './benchmark/study.js';
+export { runWitnessRegistry, artifactPassingWitnessIds } from './witness-artifact.js';
+export { WITNESS_REGISTRY } from './witness-specs.js';
+export { runSymbolicWitness } from './witness-symbolic.js';
+export { runNumericWitness } from './witness-numeric.js';
+export { contextUnion, statementContextUnion } from './statement.js';
+export { composeDerivations, composeDerivationsOrThrow, DerivationCompositionError, makeDerivation, } from './derivation.js';
+//# sourceMappingURL=index.js.map

package/dist/atlas/index.js.map

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package/dist/atlas/link-prediction.d.ts

@@ -0,0 +1,71 @@
+/**
+ * Atlas Phase 6, S6.3 — link prediction over the typed model graph: ONE result,
+ * stated as a hypothesis about the representation.
+ *
+ * Design note: `docs/planning/Atlas-Phase-6-Design.md` §1.
+ *
+ * The graph: every model in every registered family is a node; every
+ * premise→conclusion pair of every bridge is an undirected edge. The test is
+ * leave-one-bridge-out: remove a bridge's edges, then ask each predictor to rank
+ * the conclusion among every model not already adjacent to the premise. A hit is
+ * the held-out conclusion inside the top k.
+ *
+ * - **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.
+ *
+ * ⚠ **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
+ * statement about how this representation behaves on its own content — not a
+ * 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.
+ *
+ * @module atlas/link-prediction
+ * @internal
+ */
+import type { AtlasFamily } from './oscillators/index.js';
+/** One held-out pair and whether each predictor recovered it. @internal */
+export interface LinkPredictionTrial {
+    readonly bridgeId: string;
+    readonly premise: string;
+    readonly conclusion: string;
+    /** 1-based rank of the held-out conclusion; Infinity when it was not a candidate. */
+    readonly structuralRank: number;
+    readonly textRank: number;
+    /** How many candidates the conclusion competed against. */
+    readonly candidates: number;
+}
+/** The whole leave-one-bridge-out run. @internal */
+export interface LinkPredictionResult {
+    readonly k: number;
+    readonly trials: readonly LinkPredictionTrial[];
+    /**
+     * Held-out pairs whose endpoints stay adjacent through ANOTHER bridge. Such a
+     * pair is not a missing link — the conclusion cannot even be a candidate — so
+     * it is excluded from the trials and counted here instead of silently.
+     */
+    readonly stillConnected: number;
+    readonly structuralHits: number;
+    readonly textHits: number;
+    /**
+     * The hit rate a RANDOM ranking would get: the mean over trials of
+     * min(k, candidates)/candidates. On a small graph this is high, and a
+     * predictor's recall means nothing until it is read against it.
+     */
+    readonly chanceRecall: number;
+    /** Mean reciprocal rank of the held-out conclusion. */
+    readonly structuralMrr: number;
+    readonly textMrr: number;
+}
+/**
+ * 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 declare function runLinkPrediction(families: readonly AtlasFamily[], k?: number): LinkPredictionResult;
+//# sourceMappingURL=link-prediction.d.ts.map

package/dist/atlas/link-prediction.d.ts.map

@@ -0,0 +1 @@
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package/dist/atlas/link-prediction.js

@@ -0,0 +1,128 @@
+/**
+ * Atlas Phase 6, S6.3 — link prediction over the typed model graph: ONE result,
+ * stated as a hypothesis about the representation.
+ *
+ * Design note: `docs/planning/Atlas-Phase-6-Design.md` §1.
+ *
+ * The graph: every model in every registered family is a node; every
+ * premise→conclusion pair of every bridge is an undirected edge. The test is
+ * leave-one-bridge-out: remove a bridge's edges, then ask each predictor to rank
+ * the conclusion among every model not already adjacent to the premise. A hit is
+ * the held-out conclusion inside the top k.
+ *
+ * - **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.
+ *
+ * ⚠ **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
+ * statement about how this representation behaves on its own content — not a
+ * 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.
+ *
+ * @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) {
+    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 = [];
+    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());
+        for (const b of bridges) {
+            if (b === held)
+                continue;
+            for (const [u, v] of edgesOf(b)) {
+                adj.get(u)?.add(v);
+                adj.get(v)?.add(u);
+            }
+        }
+        for (const [premise, conclusion] of edgesOf(held)) {
+            const pModel = models.get(premise);
+            if (pModel === undefined)
+                continue;
+            const neighbours = adj.get(premise) ?? new Set();
+            if (neighbours.has(conclusion)) {
+                stillConnected++;
+                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,
+            });
+        }
+    }
+    const mean = (xs) => (xs.length === 0 ? Number.NaN : xs.reduce((a, b) => a + b, 0) / xs.length);
+    return {
+        k,
+        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)),
+    };
+}
+//# sourceMappingURL=link-prediction.js.map

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package/dist/atlas/model.d.ts

@@ -0,0 +1,70 @@
+/**
+ * The `Model` record — Phase 3's promotion of the Phase 0 `AtlasModel`.
+ *
+ * ROADMAP Phase 3 makes the MODEL the unit rather than the equation: state
+ * space, dynamics, observables, parameters, boundary/initial data, symmetry
+ * group where known, regime. This module is the record's new home; the nine
+ * Phase 0 fields are carried over unchanged and three are added.
+ *
+ * **`boundaryData`, `initialData` and `symmetryGroup` are all OPTIONAL**
+ * (`docs/planning/Atlas-Phase-3-Design.md` §4, which supersedes the
+ * implementation plan's wording on the first two). No boundary or initial
+ * data is recorded for the nine oscillator models, so a required field would
+ * force either fabricated values or empty ones asserting "there are none".
+ * `oscillators/models.ts` refuses exactly that fabrication for `inequalities`.
+ * **An absent field says "not recorded"; a present empty one says "there are
+ * none", and only one of those is true here** — so the nine literals stay
+ * byte-identical and record nothing they do not have a source for.
+ *
+ * `src/atlas/serialize.ts` enumerates model fields explicitly, so a model
+ * carrying none of the three serializes byte-identically to Phase 0's
+ * committed `data/atlas/oscillators.json`.
+ *
+ * @module atlas/model
+ */
+import type { DimensionalVariable } from '../dimensional/buckingham.js';
+import type { Regime } from './types.js';
+/**
+ * One model in the atlas.
+ *
+ * The first nine fields are Phase 0's `AtlasModel` verbatim. The last three
+ * are the Phase 3 additions and are omitted, never emptied, when unrecorded.
+ *
+ * @public
+ */
+export interface AtlasModel {
+    /** `'model-spring'`, `'model-lc'`, … */
+    readonly id: string;
+    readonly family: string;
+    readonly stateSpace: string;
+    /** Display form of the ODE. */
+    readonly dynamics: string;
+    readonly observables: readonly string[];
+    /** Dimensioned parameters. */
+    readonly parameters: readonly DimensionalVariable[];
+    /** `'theta0'`, `'qa'` — declared with the zero dimension. */
+    readonly dimensionlessInputs: readonly string[];
+    /** `'CE-simple-harmonic-frequency'`, … — must resolve in `CANONICAL_EQUATIONS`. */
+    readonly canonicalRefs: readonly string[];
+    readonly regime: Regime;
+    /**
+     * Boundary conditions the model is posed with, each as its stated display
+     * form (`'u(0, t) = u(L, t) = 0'`). **Omit when none is recorded** — an
+     * empty array would claim the model has no boundary conditions.
+     */
+    readonly boundaryData?: readonly string[];
+    /**
+     * Initial conditions the model is posed with (`'x(0) = x₀'`). Omit when
+     * none is recorded; see `boundaryData`.
+     */
+    readonly initialData?: readonly string[];
+    /**
+     * The symmetry group where it is known, as stated (`'SO(2)'`,
+     * `'time translation'`). Omit when unknown — Phase 3 records only
+     * symmetries a source states.
+     */
+    readonly symmetryGroup?: string;
+}
+/** A `Model`'s id, as `CanonicalEquation.model` references it. @internal */
+export type ModelId = string;
+//# sourceMappingURL=model.d.ts.map

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