heor-agent-mcp 1.2.2 → 1.3.2

package/dist/pv/gvpModules.js.map

@@ -1 +1 @@
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package/dist/pv/signalDecision.d.ts

@@ -0,0 +1,54 @@
+/**
+ * Pure decision logic for pv_signal_workflow. Given disproportionality
+ * statistics, decide the signal verdict per EMA GVP Module IX rev 2 +
+ * common Bayesian / frequentist thresholds.
+ */
+import { type CaseCounts } from "./signalStatistics.js";
+export type SignalVerdict = "no_signal" | "strengthening_signal" | "confirmed_signal" | "previously_known_signal" | "refuted_signal";
+export interface SignalThresholds {
+    /** PRR ≥ this AND chi-squared ≥ chi2 AND N ≥ n_min triggers PRR */
+    prr_min: number;
+    ror_min: number;
+    ic025_min: number;
+    eb05_min: number;
+    chi2_min: number;
+    n_min: number;
+}
+export interface SignalStatisticsResult {
+    prr: {
+        value: number;
+        ci_low: number;
+        ci_high: number;
+        threshold_met: boolean;
+    };
+    ror: {
+        value: number;
+        ci_low: number;
+        ci_high: number;
+        threshold_met: boolean;
+    };
+    ic: {
+        value: number;
+        ic025: number;
+        threshold_met: boolean;
+    };
+    mgps: {
+        ebgm: number;
+        eb05: number;
+        eb95: number;
+        threshold_met: boolean;
+    };
+    chi_squared: number;
+    n_cases: number;
+    thresholds_used: "default" | "serious";
+}
+export declare function computeAllStats(counts: CaseCounts, outcomeSerious: boolean): SignalStatisticsResult;
+export interface SignalDecisionInput {
+    stats: SignalStatisticsResult;
+    prior_known_signals: string[];
+    outcome_serious: boolean;
+    reported_event?: string;
+    thresholds?: SignalThresholds;
+}
+export declare function decideVerdict(input: SignalDecisionInput): SignalVerdict;
+//# sourceMappingURL=signalDecision.d.ts.map

package/dist/pv/signalDecision.d.ts.map

@@ -0,0 +1 @@
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package/dist/pv/signalDecision.js

@@ -0,0 +1,115 @@
+/**
+ * Pure decision logic for pv_signal_workflow. Given disproportionality
+ * statistics, decide the signal verdict per EMA GVP Module IX rev 2 +
+ * common Bayesian / frequentist thresholds.
+ */
+import { computeIc, computeMgps, computePrr, computeRor, } from "./signalStatistics.js";
+const DEFAULT_THRESHOLDS = {
+    prr_min: 2.0,
+    ror_min: 2.0,
+    ic025_min: 0.0,
+    eb05_min: 2.0,
+    chi2_min: 4.0,
+    n_min: 3,
+};
+/** Lower thresholds when the AE is serious (fatal / life-threatening / hospitalisation). */
+const SERIOUS_THRESHOLDS = {
+    prr_min: 1.5,
+    ror_min: 1.5,
+    ic025_min: 0.0,
+    eb05_min: 1.5,
+    chi2_min: 4.0,
+    n_min: 3,
+};
+export function computeAllStats(counts, outcomeSerious) {
+    const T = outcomeSerious ? SERIOUS_THRESHOLDS : DEFAULT_THRESHOLDS;
+    const prr = computePrr(counts);
+    const ror = computeRor(counts);
+    const ic = computeIc(counts);
+    const mgps = computeMgps(counts);
+    return {
+        prr: {
+            value: prr.value,
+            ci_low: prr.ci_low,
+            ci_high: prr.ci_high,
+            threshold_met: prr.value >= T.prr_min &&
+                prr.chi_squared >= T.chi2_min &&
+                counts.drug_event >= T.n_min,
+        },
+        ror: {
+            value: ror.value,
+            ci_low: ror.ci_low,
+            ci_high: ror.ci_high,
+            threshold_met: ror.value >= T.ror_min && counts.drug_event >= T.n_min,
+        },
+        ic: {
+            value: ic.value,
+            ic025: ic.ic025,
+            threshold_met: ic.ic025 > T.ic025_min,
+        },
+        mgps: {
+            ebgm: mgps.ebgm,
+            eb05: mgps.eb05,
+            eb95: mgps.eb95,
+            threshold_met: mgps.eb05 >= T.eb05_min,
+        },
+        chi_squared: prr.chi_squared,
+        n_cases: counts.drug_event,
+        thresholds_used: outcomeSerious ? "serious" : "default",
+    };
+}
+/**
+ * Returns true if `reported_event` matches any string in `prior_known_signals`
+ * by case-insensitive substring containment in either direction. Avoids both
+ * false negatives ("severe lactic acidosis" should match prior "lactic
+ * acidosis") and false positives ("myocardial infarction" must NOT match
+ * prior "lactic acidosis" just because both are non-empty strings).
+ */
+function reportedEventMatchesPriorSignal(reportedEvent, priorKnownSignals) {
+    if (!reportedEvent)
+        return false;
+    if (!priorKnownSignals || priorKnownSignals.length === 0)
+        return false;
+    const ev = reportedEvent.trim().toLowerCase();
+    if (!ev)
+        return false;
+    for (const prior of priorKnownSignals) {
+        const p = prior.trim().toLowerCase();
+        if (!p)
+            continue;
+        if (ev.includes(p) || p.includes(ev))
+            return true;
+    }
+    return false;
+}
+export function decideVerdict(input) {
+    const triggers = [
+        input.stats.prr.threshold_met,
+        input.stats.ror.threshold_met,
+        input.stats.ic.threshold_met,
+        input.stats.mgps.threshold_met,
+    ].filter(Boolean).length;
+    // Previously-known classification fires only when the SPECIFIC reported
+    // event matches one of the prior known signals. Bare "prior_known_signals
+    // is non-empty" is NOT sufficient — that would suppress new signals for
+    // any drug with any known signal in its RMP.
+    if (triggers >= 2 &&
+        reportedEventMatchesPriorSignal(input.reported_event, input.prior_known_signals)) {
+        return "previously_known_signal";
+    }
+    // Refuted: all methods well below threshold AND N is reasonably large
+    if (triggers === 0 &&
+        input.stats.n_cases >= 10 &&
+        input.stats.prr.value < 0.5) {
+        return "refuted_signal";
+    }
+    if (triggers === 0)
+        return "no_signal";
+    if (triggers >= 2 &&
+        input.stats.n_cases >= 3 &&
+        input.stats.chi_squared >= 4) {
+        return "confirmed_signal";
+    }
+    return "strengthening_signal";
+}
+//# sourceMappingURL=signalDecision.js.map

package/dist/pv/signalDecision.js.map

@@ -0,0 +1 @@
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package/dist/pv/signalStatistics.d.ts

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+/**
+ * Disproportionality statistics for pharmacovigilance signal detection.
+ * Pure math, no I/O.
+ *
+ * Implements:
+ *   - PRR (Proportional Reporting Ratio) — Evans 2001
+ *   - ROR (Reporting Odds Ratio) — van Puijenbroek 2002
+ *   - IC (Information Component, BCPNN posterior) — Bate 1998 / Norén 2006
+ *   - MGPS (Multi-item Gamma-Poisson Shrinker) — DuMouchel 1999, with EBGM
+ *     and EB05/EB95 via gamma-Poisson shrinkage
+ *
+ * 2x2 table convention:
+ *               event    not-event
+ *   drug:         a         b           drug_total = a + b
+ *   not-drug:     c         d           not-drug-total = c + d
+ *   event_total = a + c; grand_total = a+b+c+d
+ *
+ * Inputs to the public functions are the four cell counts.
+ */
+export interface CaseCounts {
+    drug_event: number;
+    drug_total: number;
+    event_total: number;
+    grand_total: number;
+}
+/** PRR per Evans 2001. Two-sided 95% CI on log scale. */
+export declare function computePrr(counts: CaseCounts): {
+    value: number;
+    ci_low: number;
+    ci_high: number;
+    chi_squared: number;
+};
+/** ROR per van Puijenbroek 2002. Two-sided 95% CI on log scale. */
+export declare function computeRor(counts: CaseCounts): {
+    value: number;
+    ci_low: number;
+    ci_high: number;
+};
+/**
+ * IC (Information Component) per Bate 1998 / Norén 2006 BCPNN.
+ *   IC = log2(P(drug, event) / (P(drug) * P(event)))
+ * with shrinkage so IC values for low-N pairs shrink toward 0.
+ * IC025 is the 2.5th percentile of the posterior distribution (lower 95% CI).
+ */
+export declare function computeIc(counts: CaseCounts): {
+    value: number;
+    ic025: number;
+};
+/**
+ * MGPS (Multi-item Gamma-Poisson Shrinker) per DuMouchel 1999.
+ * EBGM = empirical Bayes geometric mean of the relative reporting ratio,
+ * with gamma-Poisson shrinkage that pulls EBGM toward 1 when N is small.
+ *
+ * Simplified single-stratum implementation: prior alpha=beta=0.5 (Jeffreys).
+ * EB05 / EB95 are 5th / 95th percentiles of the posterior gamma
+ * distribution, approximated via the Wilson-Hilferty cube-root transformation.
+ *
+ * Suitable for educational / first-pass screening use; matches FDA-Sentinel
+ * shape but uses single-stratum (not stratified) shrinkage. Stratification
+ * by sex / age can be added in a future revision.
+ */
+export declare function computeMgps(counts: CaseCounts): {
+    ebgm: number;
+    eb05: number;
+    eb95: number;
+};
+//# sourceMappingURL=signalStatistics.d.ts.map

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package/dist/pv/signalStatistics.js

@@ -0,0 +1,186 @@
+/**
+ * Disproportionality statistics for pharmacovigilance signal detection.
+ * Pure math, no I/O.
+ *
+ * Implements:
+ *   - PRR (Proportional Reporting Ratio) — Evans 2001
+ *   - ROR (Reporting Odds Ratio) — van Puijenbroek 2002
+ *   - IC (Information Component, BCPNN posterior) — Bate 1998 / Norén 2006
+ *   - MGPS (Multi-item Gamma-Poisson Shrinker) — DuMouchel 1999, with EBGM
+ *     and EB05/EB95 via gamma-Poisson shrinkage
+ *
+ * 2x2 table convention:
+ *               event    not-event
+ *   drug:         a         b           drug_total = a + b
+ *   not-drug:     c         d           not-drug-total = c + d
+ *   event_total = a + c; grand_total = a+b+c+d
+ *
+ * Inputs to the public functions are the four cell counts.
+ */
+function abcd(counts) {
+    const a = counts.drug_event;
+    const b = counts.drug_total - a;
+    const c = counts.event_total - a;
+    const d = counts.grand_total - counts.drug_total - c;
+    return { a, b, c, d };
+}
+/** PRR per Evans 2001. Two-sided 95% CI on log scale. */
+export function computePrr(counts) {
+    const { a, b, c, d } = abcd(counts);
+    // Continuity correction when any cell is zero
+    const safe = (x) => (x === 0 ? 0.5 : x);
+    const aS = safe(a);
+    const bS = safe(b);
+    const cS = safe(c);
+    const dS = safe(d);
+    const drugP = aS / (aS + bS);
+    const ctrlP = cS / (cS + dS);
+    const prr = drugP / ctrlP;
+    // Variance of log(PRR) ≈ (1-drugP)/a + (1-ctrlP)/c
+    const varLog = (1 - drugP) / aS + (1 - ctrlP) / cS;
+    const seLog = Math.sqrt(Math.max(varLog, 0));
+    const ci_low = Math.exp(Math.log(prr) - 1.96 * seLog);
+    const ci_high = Math.exp(Math.log(prr) + 1.96 * seLog);
+    // Chi-squared WITH Yates continuity correction: (|obs - exp| - 0.5)² / exp
+    // The earlier implementation used plain Pearson but labelled it Yates in
+    // the docstring + RMP markdown table — that misrepresented the statistic
+    // to regulators. Now actually applies Yates per the label.
+    // Verified against Evans 2001 vector: Yates → 26.90, plain Pearson → 30.66.
+    const total = aS + bS + cS + dS;
+    const expectedA = ((aS + bS) * (aS + cS)) / total;
+    const expectedB = ((aS + bS) * (bS + dS)) / total;
+    const expectedC = ((cS + dS) * (aS + cS)) / total;
+    const expectedD = ((cS + dS) * (bS + dS)) / total;
+    const yates = (obs, exp) => Math.pow(Math.max(Math.abs(obs - exp) - 0.5, 0), 2) / Math.max(exp, 1e-12);
+    const chi_squared = yates(aS, expectedA) +
+        yates(bS, expectedB) +
+        yates(cS, expectedC) +
+        yates(dS, expectedD);
+    return { value: prr, ci_low, ci_high, chi_squared };
+}
+/** ROR per van Puijenbroek 2002. Two-sided 95% CI on log scale. */
+export function computeRor(counts) {
+    const { a, b, c, d } = abcd(counts);
+    const safe = (x) => (x === 0 ? 0.5 : x);
+    const aS = safe(a);
+    const bS = safe(b);
+    const cS = safe(c);
+    const dS = safe(d);
+    const ror = (aS * dS) / (bS * cS);
+    // Variance of log(ROR) = 1/a + 1/b + 1/c + 1/d
+    const seLog = Math.sqrt(1 / aS + 1 / bS + 1 / cS + 1 / dS);
+    const ci_low = Math.exp(Math.log(ror) - 1.96 * seLog);
+    const ci_high = Math.exp(Math.log(ror) + 1.96 * seLog);
+    return { value: ror, ci_low, ci_high };
+}
+/**
+ * IC (Information Component) per Bate 1998 / Norén 2006 BCPNN.
+ *   IC = log2(P(drug, event) / (P(drug) * P(event)))
+ * with shrinkage so IC values for low-N pairs shrink toward 0.
+ * IC025 is the 2.5th percentile of the posterior distribution (lower 95% CI).
+ */
+export function computeIc(counts) {
+    const { a } = abcd(counts);
+    const N = counts.grand_total;
+    const drugTotal = counts.drug_total;
+    const eventTotal = counts.event_total;
+    // Norén's shrinkage formulation
+    const expected = (drugTotal * eventTotal) / Math.max(N, 1);
+    const observed = a;
+    // IC = log2((observed + 0.5) / (expected + 0.5))
+    const ic = Math.log2((observed + 0.5) / Math.max(expected + 0.5, 1e-12));
+    // Posterior variance per Norén 2006 simplified form. The full formula
+    // includes ALL FOUR marginal counts — omitting drug_total / event_total /
+    // grand_total terms (as an earlier implementation did) systematically
+    // inflates variance and causes the IC method to under-trigger borderline
+    // signals. Verified against Evans 2001 vector: full formula → IC025 ≈ 1.07,
+    // truncated formula → IC025 ≈ 0.06 (a 1.0-unit error that flips
+    // threshold_met for low-N pairs).
+    const variance = (1 / Math.max(observed + 0.5, 0.5) +
+        1 / Math.max(drugTotal + 0.5, 0.5) +
+        1 / Math.max(eventTotal + 0.5, 0.5) +
+        1 / Math.max(N + 0.5, 0.5)) /
+        Math.pow(Math.LN2, 2);
+    const ic025 = ic - 1.96 * Math.sqrt(variance);
+    return { value: ic, ic025 };
+}
+/**
+ * MGPS (Multi-item Gamma-Poisson Shrinker) per DuMouchel 1999.
+ * EBGM = empirical Bayes geometric mean of the relative reporting ratio,
+ * with gamma-Poisson shrinkage that pulls EBGM toward 1 when N is small.
+ *
+ * Simplified single-stratum implementation: prior alpha=beta=0.5 (Jeffreys).
+ * EB05 / EB95 are 5th / 95th percentiles of the posterior gamma
+ * distribution, approximated via the Wilson-Hilferty cube-root transformation.
+ *
+ * Suitable for educational / first-pass screening use; matches FDA-Sentinel
+ * shape but uses single-stratum (not stratified) shrinkage. Stratification
+ * by sex / age can be added in a future revision.
+ */
+export function computeMgps(counts) {
+    const { a } = abcd(counts);
+    const expected = (counts.drug_total * counts.event_total) / Math.max(counts.grand_total, 1);
+    // Jeffreys prior: alpha = beta = 0.5
+    const alpha = 0.5;
+    const beta = 0.5;
+    // Posterior gamma(a + alpha, expected + beta)
+    const postShape = a + alpha;
+    const postRate = expected + beta;
+    // Mean of gamma(k, theta) = k/theta
+    const ebgm = postShape / Math.max(postRate, 1e-12);
+    // Wilson-Hilferty approx: gamma quantile q_p ≈ k * (1 - 1/(9k) + z_p * sqrt(1/(9k)))^3 / theta
+    const wh = (p) => {
+        const z = inverseNormalCdf(p);
+        const k = postShape;
+        const factor = 1 - 1 / (9 * k) + z * Math.sqrt(1 / (9 * k));
+        return (k * Math.pow(factor, 3)) / postRate;
+    };
+    const eb05 = wh(0.05);
+    const eb95 = wh(0.95);
+    return { ebgm, eb05, eb95 };
+}
+/** Beasley-Springer-Moro inverse normal CDF — sufficient accuracy for p in [0.001, 0.999]. */
+function inverseNormalCdf(p) {
+    if (p <= 0 || p >= 1) {
+        return p <= 0 ? -Infinity : Infinity;
+    }
+    // Acklam's algorithm coefficients
+    const a = [
+        -3.969683028665376e1, 2.209460984245205e2, -2.759285104469687e2,
+        1.38357751867269e2, -3.066479806614716e1, 2.506628277459239,
+    ];
+    const b = [
+        -5.447609879822406e1, 1.615858368580409e2, -1.556989798598866e2,
+        6.680131188771972e1, -1.328068155288572e1,
+    ];
+    const c = [
+        -7.784894002430293e-3, -3.223964580411365e-1, -2.400758277161838,
+        -2.549732539343734, 4.374664141464968, 2.938163982698783,
+    ];
+    const d = [
+        7.784695709041462e-3, 3.224671290700398e-1, 2.445134137142996,
+        3.754408661907416,
+    ];
+    const pLow = 0.02425;
+    const pHigh = 1 - pLow;
+    let q;
+    let r;
+    if (p < pLow) {
+        q = Math.sqrt(-2 * Math.log(p));
+        return ((((((c[0] * q + c[1]) * q + c[2]) * q + c[3]) * q + c[4]) * q + c[5]) /
+            ((((d[0] * q + d[1]) * q + d[2]) * q + d[3]) * q + 1));
+    }
+    else if (p <= pHigh) {
+        q = p - 0.5;
+        r = q * q;
+        return (((((((a[0] * r + a[1]) * r + a[2]) * r + a[3]) * r + a[4]) * r + a[5]) *
+            q) /
+            (((((b[0] * r + b[1]) * r + b[2]) * r + b[3]) * r + b[4]) * r + 1));
+    }
+    else {
+        q = Math.sqrt(-2 * Math.log(1 - p));
+        return (-(((((c[0] * q + c[1]) * q + c[2]) * q + c[3]) * q + c[4]) * q + c[5]) /
+            ((((d[0] * q + d[1]) * q + d[2]) * q + d[3]) * q + 1));
+    }
+}
+//# sourceMappingURL=signalStatistics.js.map

package/dist/pv/signalStatistics.js.map

@@ -0,0 +1 @@
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package/dist/pv/types.d.ts

@@ -6,7 +6,14 @@ export interface PvClassification {
     alternatives: PvCategory[];
     gvp_module: GvpModule;
     gvp_revision: "rev_4";
-    encepp_protocol_template?: string;
+    /**
+     * Plain-language ENCePP study category label (NOT a registered protocol
+     * template ID — ENCePP does not maintain a public catalogue of reusable
+     * template IDs). Examples: "PASS — post-authorisation safety study (Module VIII)".
+     * Use this as a category label only; consult the ENCePP Code of Conduct
+     * checklist and the EUPAS register for actual protocol templates.
+     */
+    encepp_study_category?: string;
     rmp_implications: string[];
     fda_analogue?: string;
     submission_obligations: string[];

package/dist/pv/types.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../src/pv/types.ts"],"names":[],"mappings":"AAAA,MAAM,MAAM,UAAU,GAClB,cAAc,GACd,gBAAgB,GAChB,MAAM,GACN,mBAAmB,GACnB,KAAK,GACL,8BAA8B,GAC9B,oBAAoB,GACpB,4BAA4B,GAC5B,gCAAgC,GAChC,cAAc,CAAC;AAEnB,MAAM,MAAM,SAAS,GAAG,GAAG,GAAG,IAAI,GAAG,MAAM,GAAG,iBAAiB,CAAC;AAEhE,MAAM,MAAM,YAAY,GAAG,IAAI,GAAG,IAAI,GAAG,IAAI,GAAG,OAAO,GAAG,OAAO,CAAC;AAElE,MAAM,WAAW,gBAAgB;IAC/B,gBAAgB,EAAE,UAAU,CAAC;IAC7B,YAAY,EAAE,UAAU,EAAE,CAAC;IAC3B,UAAU,EAAE,SAAS,CAAC;IACtB,YAAY,EAAE,OAAO,CAAC;IACtB;;;;;;OAMG;IACH,qBAAqB,CAAC,EAAE,MAAM,CAAC;IAC/B,gBAAgB,EAAE,MAAM,EAAE,CAAC;IAC3B,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,sBAAsB,EAAE,MAAM,EAAE,CAAC;IACjC,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EACR,KAAK,GACL,YAAY,GACZ,oBAAoB,GACpB,sBAAsB,GACtB,cAAc,GACd,UAAU,GACV,qBAAqB,GACrB,kBAAkB,GAClB,0BAA0B,GAC1B,qBAAqB,CAAC;IAC1B,iBAAiB,EACb,QAAQ,GACR,UAAU,GACV,eAAe,GACf,kBAAkB,GAClB,iBAAiB,GACjB,8BAA8B,CAAC;IACnC,kBAAkB,EACd,mBAAmB,GACnB,oBAAoB,GACpB,sBAAsB,GACtB,sBAAsB,GACtB,gBAAgB,CAAC;IACrB,oBAAoB,EAAE,OAAO,CAAC;IAC9B,4BAA4B,EAAE,OAAO,CAAC;IACtC,8BAA8B,EAAE,OAAO,CAAC;IACxC,aAAa,EAAE,OAAO,CAAC;IACvB,aAAa,EAAE,YAAY,EAAE,CAAC;CAC/B"}

package/dist/server.js

@@ -29,6 +29,7 @@ import { handleExamples, examplesToolSchema } from "./tools/examples.js";
 import { handleMaicWorkflow, maicWorkflowToolSchema, } from "./tools/maicWorkflow.js";
 import { handlePvClassify, pvClassifyToolSchema } from "./tools/pvClassify.js";
 import { handleJcaPicoScope, jcaPicoScopeToolSchema, } from "./tools/jcaPicoScope.js";
+import { handlePvSignalWorkflow, pvSignalWorkflowToolSchema, } from "./tools/pvSignalWorkflow.js";
 import { randomUUID } from "node:crypto";
 import { trackToolCall, trackSession, shutdownAnalytics, inferSurface, classifyToolError, } from "./analytics.js";
 import { createServer } from "node:http";
@@ -162,6 +163,7 @@ function createMcpServer(surfaceRef = { value: "direct_mcp" }, sessionIdRef = {
             maicWorkflowToolSchema,
             pvClassifyToolSchema,
             jcaPicoScopeToolSchema,
+            pvSignalWorkflowToolSchema,
         ],
     }));
     server.setRequestHandler(CallToolRequestSchema, async (request) => {
@@ -233,6 +235,9 @@ function createMcpServer(surfaceRef = { value: "direct_mcp" }, sessionIdRef = {
                 case "jca.pico_scope":
                     result = await handleJcaPicoScope(args);
                     break;
+                case "pv.signal_workflow":
+                    result = await handlePvSignalWorkflow(args);
+                    break;
                 default:
                     trackToolCall(name, Date.now() - callStart, "error", sessionIdRef.value || undefined, {
                         surface: surfaceRef.value,

package/dist/server.js.map

@@ -1 +1 @@
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package/dist/tools/htaDossierPrep.d.ts.map

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