nlm-memory 0.20.0 → 0.21.0

package/dist/core/embedding/pg-embed-backfill.js.map

@@ -0,0 +1 @@
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package/dist/core/entities/dedup-suggest.d.ts

@@ -0,0 +1,25 @@
+/**
+ * Conservative lexical dedup suggestion for the entity table.
+ *
+ * No embedding similarity in v1: the workstream matcher falsification showed
+ * lexical-adjacent-but-different entities are exactly where embeddings
+ * over-merge. Start conservative; tighten only after adjudication data exists.
+ */
+export interface EntityInput {
+    readonly canonical: string;
+    readonly sessionCount: number;
+    readonly status: string;
+}
+export interface MergeSuggestion {
+    readonly source: string;
+    readonly target: string;
+    readonly cls: "safe" | "likely";
+}
+/**
+ * Suggest merge pairs from a flat list of entities.
+ *
+ * Groups by fold key, then checks likely patterns within each group.
+ * Never suggests a pair twice; never chains (one target per group, all
+ * remaining members are sources into that target).
+ */
+export declare function suggestMerges(entities: ReadonlyArray<EntityInput>): ReadonlyArray<MergeSuggestion>;

package/dist/core/entities/dedup-suggest.js

@@ -0,0 +1,107 @@
+/**
+ * Conservative lexical dedup suggestion for the entity table.
+ *
+ * No embedding similarity in v1: the workstream matcher falsification showed
+ * lexical-adjacent-but-different entities are exactly where embeddings
+ * over-merge. Start conservative; tighten only after adjudication data exists.
+ */
+/**
+ * Fold for safe-class comparison: lowercase, strip spaces, hyphens,
+ * underscores, and dots.
+ */
+function safeFold(s) {
+    return s.toLowerCase().replace(/[\s\-_.]+/g, "");
+}
+// Checked against the already-folded form (hyphens stripped by safeFold).
+const REPO_SUFFIXES_FOLDED = ["ts", "js", "py", "rs", "go"];
+function stripRepoSuffix(folded) {
+    for (const suf of REPO_SUFFIXES_FOLDED) {
+        if (folded.endsWith(suf) && folded.length > suf.length) {
+            return folded.slice(0, -suf.length);
+        }
+    }
+    return folded;
+}
+function isSingularPlural(a, b) {
+    return b === a + "s" || a === b + "s";
+}
+function isRepoSuffixPair(a, b) {
+    const baseA = stripRepoSuffix(a);
+    const baseB = stripRepoSuffix(b);
+    if (a === baseA && b === baseB)
+        return false;
+    return baseA === baseB;
+}
+/**
+ * Pick the target: higher sessionCount wins; on tie, lexicographically smaller
+ * canonical is the target (deterministic).
+ */
+function pickTarget(a, b) {
+    if (a.sessionCount !== b.sessionCount) {
+        return a.sessionCount > b.sessionCount
+            ? { target: a, source: b }
+            : { target: b, source: a };
+    }
+    return a.canonical <= b.canonical
+        ? { target: a, source: b }
+        : { target: b, source: a };
+}
+/**
+ * Suggest merge pairs from a flat list of entities.
+ *
+ * Groups by fold key, then checks likely patterns within each group.
+ * Never suggests a pair twice; never chains (one target per group, all
+ * remaining members are sources into that target).
+ */
+export function suggestMerges(entities) {
+    const active = entities.filter((e) => e.status !== "retired");
+    const safeGroups = new Map();
+    for (const e of active) {
+        const key = safeFold(e.canonical);
+        if (!safeGroups.has(key))
+            safeGroups.set(key, []);
+        safeGroups.get(key).push(e);
+    }
+    // Emission-order invariant the CLI applier depends on: every pair that uses
+    // an entity as TARGET is emitted before the (single) pair that consumes it as
+    // SOURCE, so sequential application never merges into an already-retired row.
+    // Reordering emissions (or applying suggestions out of list order) breaks this.
+    const suggestions = [];
+    const consumedAsSource = new Set();
+    for (const group of safeGroups.values()) {
+        if (group.length < 2)
+            continue;
+        const sorted = [...group].sort((a, b) => {
+            if (b.sessionCount !== a.sessionCount)
+                return b.sessionCount - a.sessionCount;
+            return a.canonical <= b.canonical ? -1 : 1;
+        });
+        const target = sorted[0];
+        for (let i = 1; i < sorted.length; i++) {
+            const source = sorted[i];
+            if (consumedAsSource.has(source.canonical))
+                continue;
+            suggestions.push({ source: source.canonical, target: target.canonical, cls: "safe" });
+            consumedAsSource.add(source.canonical);
+        }
+    }
+    const activeNonSafe = active.filter((e) => !consumedAsSource.has(e.canonical));
+    for (let i = 0; i < activeNonSafe.length; i++) {
+        for (let j = i + 1; j < activeNonSafe.length; j++) {
+            const a = activeNonSafe[i];
+            const b = activeNonSafe[j];
+            if (consumedAsSource.has(a.canonical) || consumedAsSource.has(b.canonical))
+                continue;
+            const fa = safeFold(a.canonical);
+            const fb = safeFold(b.canonical);
+            const isLikely = isSingularPlural(fa, fb) || isRepoSuffixPair(fa, fb);
+            if (!isLikely)
+                continue;
+            const { target, source } = pickTarget(a, b);
+            suggestions.push({ source: source.canonical, target: target.canonical, cls: "likely" });
+            consumedAsSource.add(source.canonical);
+        }
+    }
+    return suggestions;
+}
+//# sourceMappingURL=dedup-suggest.js.map

package/dist/core/entities/dedup-suggest.js.map

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package/dist/core/eval/classifier-fixture-eval.d.ts

@@ -0,0 +1,29 @@
+import type { ClassifyResult } from "../../ports/llm-client.js";
+export interface FixtureEvalResult {
+    readonly perTranscript: ReadonlyArray<{
+        readonly id: string;
+        readonly schemaValid: boolean;
+        readonly timedOutOrUnreachable: boolean;
+        readonly labelMatch: boolean;
+        readonly entityPrecision: number;
+        readonly entityRecall: number;
+        readonly decisionPrecision: number;
+        readonly decisionRecall: number;
+        readonly confidence: number;
+        readonly confidenceCalibrated: boolean;
+        readonly elapsedMs: number;
+    }>;
+    readonly aggregate: {
+        readonly schemaValidRate: number;
+        readonly labelAccuracy: number;
+        readonly entityF1: number;
+        readonly decisionF1: number;
+        readonly confidenceCalibrationRate: number;
+        readonly p50LatencyMs: number;
+        readonly p95LatencyMs: number;
+        readonly timedOutOrUnreachable: number;
+    };
+}
+export declare function runClassifierFixtureEval(classify: (transcript: string) => Promise<ClassifyResult>, fixturesDir: string, opts?: {
+    readonly limit?: number;
+}): Promise<FixtureEvalResult>;

package/dist/core/eval/classifier-fixture-eval.js

@@ -0,0 +1,217 @@
+import { readFileSync, readdirSync } from "node:fs";
+import { join, basename } from "node:path";
+import { ClassifierSchemaError, LLMUnreachableError } from "../../ports/llm-client.js";
+import { rate } from "../eval/extraction-scoring.js";
+function loadReference(fixturesDir) {
+    const raw = readFileSync(join(fixturesDir, "reference.json"), "utf-8");
+    return JSON.parse(raw);
+}
+function loadTranscript(fixturesDir, id) {
+    return readFileSync(join(fixturesDir, "transcripts", `${id}.txt`), "utf-8");
+}
+function listTranscriptIds(fixturesDir) {
+    const dir = join(fixturesDir, "transcripts");
+    return readdirSync(dir)
+        .filter((f) => f.endsWith(".txt"))
+        .map((f) => basename(f, ".txt"))
+        .sort();
+}
+function normalizeStr(s) {
+    return s.toLowerCase().trim();
+}
+function labelMatches(extracted, ref) {
+    const e = normalizeStr(extracted);
+    const candidates = [ref.label, ...ref.labelAlternates].map(normalizeStr);
+    for (const c of candidates) {
+        if (e === c)
+            return true;
+        if (e.includes(c) || c.includes(e))
+            return true;
+        if (keyTokenOverlap(e, c) >= 0.5)
+            return true;
+    }
+    return false;
+}
+function keyTokenOverlap(a, b) {
+    const tokA = keyTokens(a);
+    const tokB = keyTokens(b);
+    if (tokA.size === 0 || tokB.size === 0)
+        return 0;
+    let hits = 0;
+    for (const t of tokA)
+        if (tokB.has(t))
+            hits++;
+    return hits / Math.max(tokA.size, tokB.size);
+}
+function keyTokens(s) {
+    const STOPWORDS = new Set([
+        "a", "an", "the", "and", "or", "for", "to", "of", "in", "on", "with",
+        "at", "by", "from", "up", "as", "is", "it", "its", "into", "that",
+        "this", "be", "are", "was", "were", "has", "have", "had",
+    ]);
+    return new Set(s
+        .replace(/[^a-z0-9\s]/g, " ")
+        .split(/\s+/)
+        .filter((t) => t.length >= 3 && !STOPWORDS.has(t)));
+}
+function entityMatchesAny(refEntity, extracted) {
+    const rn = normalizeStr(refEntity);
+    for (const e of extracted) {
+        const en = normalizeStr(e);
+        if (en === rn || en.includes(rn) || rn.includes(en))
+            return true;
+    }
+    return false;
+}
+function decisionMatchesAny(refDecision, extracted) {
+    const refToks = keyTokens(normalizeStr(refDecision));
+    if (refToks.size === 0)
+        return extracted.length > 0;
+    for (const e of extracted) {
+        const eToks = keyTokens(normalizeStr(e));
+        let hits = 0;
+        for (const t of refToks)
+            if (eToks.has(t))
+                hits++;
+        if (refToks.size > 0 && hits / refToks.size >= 0.5)
+            return true;
+    }
+    return false;
+}
+function scoreEntityPrecision(extracted, reference) {
+    if (extracted.length === 0)
+        return reference.length === 0 ? 1 : 0;
+    const hits = extracted.filter((e) => entityMatchesAny(e, reference));
+    return hits.length / extracted.length;
+}
+function scoreEntityRecall(extracted, reference) {
+    if (reference.length === 0)
+        return 1;
+    const verdicts = reference.map((r) => entityMatchesAny(r, extracted));
+    return (rate(verdicts, Boolean) ?? 0);
+}
+function scoreDecisionPrecision(extracted, reference) {
+    if (extracted.length === 0)
+        return reference.length === 0 ? 1 : 0;
+    const hits = extracted.filter((e) => decisionMatchesAny(e, reference));
+    return hits.length / extracted.length;
+}
+function scoreDecisionRecall(extracted, reference) {
+    if (reference.length === 0)
+        return 1;
+    const verdicts = reference.map((r) => decisionMatchesAny(r, extracted));
+    return (rate(verdicts, Boolean) ?? 0);
+}
+function percentile(sorted, p) {
+    if (sorted.length === 0)
+        return 0;
+    const idx = Math.floor((p / 100) * (sorted.length - 1));
+    return sorted[idx] ?? 0;
+}
+function f1(precision, recall) {
+    const denom = precision + recall;
+    if (denom === 0)
+        return 0;
+    return (2 * precision * recall) / denom;
+}
+function macroF1(perRow) {
+    if (perRow.length === 0)
+        return 0;
+    const sum = perRow.reduce((acc, x) => acc + f1(x.p, x.r), 0);
+    return sum / perRow.length;
+}
+export async function runClassifierFixtureEval(classify, fixturesDir, opts) {
+    const allRefs = loadReference(fixturesDir);
+    const allIds = listTranscriptIds(fixturesDir);
+    const refById = new Map(allRefs.map((r) => [r.id, r]));
+    const ids = opts?.limit != null ? allIds.slice(0, opts.limit) : allIds;
+    const perTranscript = [];
+    for (const id of ids) {
+        const ref = refById.get(id);
+        if (ref === undefined)
+            continue;
+        const transcript = loadTranscript(fixturesDir, id);
+        const start = Date.now();
+        let result = null;
+        let schemaValid = true;
+        let timedOutOrUnreachable = false;
+        try {
+            result = await classify(transcript);
+        }
+        catch (err) {
+            if (err instanceof ClassifierSchemaError) {
+                schemaValid = false;
+            }
+            else if (err instanceof LLMUnreachableError) {
+                schemaValid = false;
+                timedOutOrUnreachable = true;
+            }
+            else {
+                throw err;
+            }
+        }
+        const elapsedMs = Date.now() - start;
+        if (!schemaValid || result === null) {
+            perTranscript.push({
+                id,
+                schemaValid: false,
+                timedOutOrUnreachable,
+                labelMatch: false,
+                entityPrecision: 0,
+                entityRecall: 0,
+                decisionPrecision: 0,
+                decisionRecall: 0,
+                confidence: 0,
+                confidenceCalibrated: false,
+                elapsedMs,
+            });
+            continue;
+        }
+        const lm = labelMatches(result.label, ref);
+        const ep = scoreEntityPrecision(result.entities, ref.entities);
+        const er = scoreEntityRecall(result.entities, ref.entities);
+        const dp = scoreDecisionPrecision(result.decisions, ref.decisions);
+        const dr = scoreDecisionRecall(result.decisions, ref.decisions);
+        const confidence = result.confidence;
+        const confidenceCalibrated = ref.expectLowConfidence
+            ? confidence <= 0.4
+            : confidence > 0.4;
+        perTranscript.push({
+            id,
+            schemaValid: true,
+            timedOutOrUnreachable: false,
+            labelMatch: lm,
+            entityPrecision: ep,
+            entityRecall: er,
+            decisionPrecision: dp,
+            decisionRecall: dr,
+            confidence,
+            confidenceCalibrated,
+            elapsedMs,
+        });
+    }
+    const n = perTranscript.length;
+    const schemaValidRate = n === 0 ? 0 : perTranscript.filter((r) => r.schemaValid).length / n;
+    const labelAccuracy = n === 0 ? 0 : perTranscript.filter((r) => r.labelMatch).length / n;
+    const confidenceCalibrationRate = n === 0 ? 0 : perTranscript.filter((r) => r.confidenceCalibrated).length / n;
+    const timedOutOrUnreachable = perTranscript.filter((r) => r.timedOutOrUnreachable).length;
+    const entityF1 = macroF1(perTranscript.map((r) => ({ p: r.entityPrecision, r: r.entityRecall })));
+    const decisionF1 = macroF1(perTranscript.map((r) => ({ p: r.decisionPrecision, r: r.decisionRecall })));
+    const sortedLatency = [...perTranscript.map((r) => r.elapsedMs)].sort((a, b) => a - b);
+    const p50LatencyMs = percentile(sortedLatency, 50);
+    const p95LatencyMs = percentile(sortedLatency, 95);
+    return {
+        perTranscript,
+        aggregate: {
+            schemaValidRate,
+            labelAccuracy,
+            entityF1,
+            decisionF1,
+            confidenceCalibrationRate,
+            p50LatencyMs,
+            p95LatencyMs,
+            timedOutOrUnreachable,
+        },
+    };
+}
+//# sourceMappingURL=classifier-fixture-eval.js.map

package/dist/core/eval/classifier-fixture-eval.js.map

@@ -0,0 +1 @@
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package/dist/core/eval/extraction-scoring.d.ts

@@ -0,0 +1,63 @@
+/**
+ * Pure scoring + aggregation for the classifier extraction-quality eval.
+ *
+ * The scoring model is precision/recall over three extraction surfaces:
+ *  - DECISION PRECISION: of the decisions a candidate extracted, what fraction
+ *    a judge ruled `supported` against the TRANSCRIPT (not the reference -- a
+ *    candidate may legitimately surface a true decision the reference missed).
+ *  - DECISION RECALL: of the REFERENCE decisions, what fraction the judge ruled
+ *    semantically matched by some candidate decision.
+ *  - ENTITY PRECISION: of the entities a candidate extracted, what fraction the
+ *    judge ruled actually present/relevant in the transcript.
+ *
+ * These functions are deterministic and dependency-free. The live judge work
+ * (LLM verdicts) happens in the harness; this module only turns verdict arrays
+ * into rates so the math is unit-testable without an LLM.
+ */
+export type Verdict = "supported" | "unsupported";
+export type MatchVerdict = "matched" | "unmatched";
+export interface ExtractionVerdicts {
+    /** One per candidate-extracted decision: faithful to transcript? */
+    readonly decisionPrecision: ReadonlyArray<Verdict>;
+    /** One per reference decision: matched by any candidate decision? */
+    readonly decisionRecall: ReadonlyArray<MatchVerdict>;
+    /** One per candidate-extracted entity: present/relevant in transcript? */
+    readonly entityPrecision: ReadonlyArray<Verdict>;
+    /** Distinct transcript decisions captured by no extracted decision (judge count). */
+    readonly missedDecisions: number;
+}
+export interface SessionScore {
+    readonly decisionPrecision: number | null;
+    /** Reference-based recall: fraction of reference decisions matched. Position-biased. */
+    readonly decisionRecall: number | null;
+    /** Transcript-grounded recall: supported / (supported + missedDecisions). Reference-free. */
+    readonly decisionRecallTranscript: number | null;
+    readonly entityPrecision: number | null;
+    /** True when the candidate produced no usable ClassifyResult for this session. */
+    readonly schemaFailed: boolean;
+}
+/**
+ * Per-session rates. A surface with zero items yields `null` (not 0): a session
+ * with no extracted decisions has undefined precision, not 0% precision, and
+ * must not drag the mean down. nulls are dropped at aggregation time.
+ */
+export declare function scoreSession(verdicts: ExtractionVerdicts, schemaFailed: boolean): SessionScore;
+export declare function rate<T>(items: ReadonlyArray<T>, hit: (x: T) => boolean): number | null;
+export interface AggregateExtraction {
+    readonly n: number;
+    /** Sessions that produced a usable extraction (n - schema failures). */
+    readonly scored: number;
+    readonly schemaFailures: number;
+    /** Macro-average across sessions that had >= 1 item on the surface. */
+    readonly decisionPrecision: number | null;
+    readonly decisionRecall: number | null;
+    readonly decisionRecallTranscript: number | null;
+    readonly entityPrecision: number | null;
+    /** How many sessions contributed to each surface mean (had >= 1 item). */
+    readonly decisionPrecisionN: number;
+    readonly decisionRecallN: number;
+    readonly decisionRecallTranscriptN: number;
+    readonly entityPrecisionN: number;
+}
+/** Macro-average per-session rates, dropping nulls (surfaces with no items). */
+export declare function aggregateExtraction(scores: ReadonlyArray<SessionScore>): AggregateExtraction;

package/dist/core/eval/extraction-scoring.js

@@ -0,0 +1,79 @@
+/**
+ * Pure scoring + aggregation for the classifier extraction-quality eval.
+ *
+ * The scoring model is precision/recall over three extraction surfaces:
+ *  - DECISION PRECISION: of the decisions a candidate extracted, what fraction
+ *    a judge ruled `supported` against the TRANSCRIPT (not the reference -- a
+ *    candidate may legitimately surface a true decision the reference missed).
+ *  - DECISION RECALL: of the REFERENCE decisions, what fraction the judge ruled
+ *    semantically matched by some candidate decision.
+ *  - ENTITY PRECISION: of the entities a candidate extracted, what fraction the
+ *    judge ruled actually present/relevant in the transcript.
+ *
+ * These functions are deterministic and dependency-free. The live judge work
+ * (LLM verdicts) happens in the harness; this module only turns verdict arrays
+ * into rates so the math is unit-testable without an LLM.
+ */
+/**
+ * Per-session rates. A surface with zero items yields `null` (not 0): a session
+ * with no extracted decisions has undefined precision, not 0% precision, and
+ * must not drag the mean down. nulls are dropped at aggregation time.
+ */
+export function scoreSession(verdicts, schemaFailed) {
+    if (schemaFailed) {
+        return {
+            decisionPrecision: null,
+            decisionRecall: null,
+            decisionRecallTranscript: null,
+            entityPrecision: null,
+            schemaFailed: true,
+        };
+    }
+    const supported = verdicts.decisionPrecision.filter((v) => v === "supported").length;
+    const recallDenom = supported + verdicts.missedDecisions;
+    return {
+        decisionPrecision: rate(verdicts.decisionPrecision, (v) => v === "supported"),
+        decisionRecall: rate(verdicts.decisionRecall, (v) => v === "matched"),
+        decisionRecallTranscript: recallDenom === 0 ? null : supported / recallDenom,
+        entityPrecision: rate(verdicts.entityPrecision, (v) => v === "supported"),
+        schemaFailed: false,
+    };
+}
+export function rate(items, hit) {
+    if (items.length === 0)
+        return null;
+    let n = 0;
+    for (const x of items)
+        if (hit(x))
+            n++;
+    return n / items.length;
+}
+/** Macro-average per-session rates, dropping nulls (surfaces with no items). */
+export function aggregateExtraction(scores) {
+    const schemaFailures = scores.filter((s) => s.schemaFailed).length;
+    const dp = meanOfDefined(scores.map((s) => s.decisionPrecision));
+    const dr = meanOfDefined(scores.map((s) => s.decisionRecall));
+    const drt = meanOfDefined(scores.map((s) => s.decisionRecallTranscript));
+    const ep = meanOfDefined(scores.map((s) => s.entityPrecision));
+    return {
+        n: scores.length,
+        scored: scores.length - schemaFailures,
+        schemaFailures,
+        decisionPrecision: dp.mean,
+        decisionRecall: dr.mean,
+        decisionRecallTranscript: drt.mean,
+        entityPrecision: ep.mean,
+        decisionPrecisionN: dp.count,
+        decisionRecallN: dr.count,
+        decisionRecallTranscriptN: drt.count,
+        entityPrecisionN: ep.count,
+    };
+}
+function meanOfDefined(values) {
+    const defined = values.filter((v) => v !== null);
+    if (defined.length === 0)
+        return { mean: null, count: 0 };
+    const sum = defined.reduce((a, b) => a + b, 0);
+    return { mean: sum / defined.length, count: defined.length };
+}
+//# sourceMappingURL=extraction-scoring.js.map

package/dist/core/eval/extraction-scoring.js.map

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package/dist/core/eval/run-eval.d.ts

@@ -0,0 +1,40 @@
+/**
+ * Corpus-agnostic R@k / MRR runner shared by `nlm eval` and the regression
+ * gate. Takes a query set with expected ids and a recall searcher, returns a
+ * per-mode report. The query set is supplied by the caller and never bundled.
+ */
+import type { RecallMode } from "../../shared/types.js";
+export interface EvalQuery {
+    readonly query: string;
+    readonly expectedIds: ReadonlyArray<string>;
+}
+export interface EvalReport {
+    readonly mode: RecallMode;
+    readonly n: number;
+    readonly rAt1: number;
+    readonly rAt5: number;
+    readonly mrr: number;
+    readonly misses: ReadonlyArray<{
+        query: string;
+        expected: ReadonlyArray<string>;
+        got: ReadonlyArray<string>;
+    }>;
+}
+interface Searcher {
+    search(q: {
+        query: string;
+        mode: RecallMode;
+        limit: number;
+    }): Promise<{
+        results: ReadonlyArray<{
+            id: string;
+        }>;
+    }>;
+}
+export declare function runEval(deps: {
+    recall: Searcher;
+}, queries: ReadonlyArray<EvalQuery>, opts: {
+    mode: RecallMode;
+    k: number;
+}): Promise<EvalReport>;
+export {};

package/dist/core/eval/run-eval.js

@@ -0,0 +1,34 @@
+/**
+ * Corpus-agnostic R@k / MRR runner shared by `nlm eval` and the regression
+ * gate. Takes a query set with expected ids and a recall searcher, returns a
+ * per-mode report. The query set is supplied by the caller and never bundled.
+ */
+export async function runEval(deps, queries, opts) {
+    let hit1 = 0;
+    let hit5 = 0;
+    let rrSum = 0;
+    const misses = [];
+    for (const q of queries) {
+        const { results } = await deps.recall.search({ query: q.query, mode: opts.mode, limit: opts.k });
+        const ids = results.map((r) => r.id);
+        const rank = ids.findIndex((id) => q.expectedIds.includes(id)) + 1; // 0 => miss
+        if (rank === 1)
+            hit1++;
+        if (rank >= 1 && rank <= 5)
+            hit5++;
+        if (rank >= 1)
+            rrSum += 1 / rank;
+        else
+            misses.push({ query: q.query, expected: q.expectedIds, got: ids });
+    }
+    const n = queries.length || 1;
+    return {
+        mode: opts.mode,
+        n: queries.length,
+        rAt1: hit1 / n,
+        rAt5: hit5 / n,
+        mrr: rrSum / n,
+        misses,
+    };
+}
+//# sourceMappingURL=run-eval.js.map