@inflexa-ai/harness 0.35.7 → 0.36.0

package/dist/workflows/target-assessment/synthesis-probes.js

@@ -1,320 +0,0 @@
-/**
- * Synthesis content probes — deterministic floor on Phase-5 LLM output
- * depth.
- *
- * Each per-section synthesis step runs its agent's structured output
- * through the relevant probe before accepting it. A failed probe
- * triggers one bounded retry with a critique appended; a second failure
- * marks the section `coverage: "queried_no_data"` with
- * `error.kind: "synthesis-too-shallow"` (the workflow proceeds — the
- * dossier still persists with the rest of the data intact).
- *
- * Probes are deliberately deterministic regex/length checks — not
- * LLM-as-judge. The prompts already require evidence citation; the
- * probes are a regression-prevention floor for the rare LLM regression
- * that produces fragment-length output anyway.
- *
- * Threshold tuning: the constants block at the top of this file is the
- * single source of truth. Adjust there, never inline.
- */
-import { buildVoiceCritique } from "../../prompts/target-assessment/tox-voice/index.js";
-// ── Tunable thresholds ───────────────────────────────────────────────
-export const PROBE_THRESHOLDS = {
-    recommendation: {
-        rationaleMinChars: 600,
-        rationaleMinCharsRelaxed: 200,
-        requiredSectionRefs: 3,
-        requiredKeyItems: 1,
-    },
-    liabilityBullet: {
-        rationaleMinChars: 80,
-        requiresSourceOrCounter: true,
-    },
-    safetyFlag: {
-        trailMinChars: 100,
-        requiredSourceRefs: 2,
-    },
-    translationalCommentary: {
-        commentaryMinChars: 120,
-    },
-};
-// ── Helpers: substring matching ──────────────────────────────────────
-const KNOWN_SECTION_NAMES = [
-    "safety_profile",
-    "tractability",
-    "indications",
-    "clinical_development",
-    "reference_biology.preclinical",
-    "reference_biology",
-    "analytics.translational_chain",
-    "off_target_panel",
-    "off_tissue_risk",
-    "drug_interactions",
-    "liability_summary",
-    "summary",
-];
-const KNOWN_SOURCE_NAMES = ["FAERS", "trial AEs", "off-target panel", "class precedent"];
-export function countSectionReferences(text) {
-    const lower = text.toLowerCase();
-    const matched = new Set();
-    for (const name of KNOWN_SECTION_NAMES) {
-        if (lower.includes(name.toLowerCase())) {
-            matched.add(name);
-        }
-    }
-    // Treat `reference_biology.preclinical` as more specific than
-    // `reference_biology`; if both match, only count the more specific.
-    if (matched.has("reference_biology.preclinical")) {
-        matched.delete("reference_biology");
-    }
-    return { matchedSections: [...matched] };
-}
-export function countSourceReferences(text) {
-    const lower = text.toLowerCase();
-    const matched = new Set();
-    for (const name of KNOWN_SOURCE_NAMES) {
-        if (lower.includes(name.toLowerCase()))
-            matched.add(name);
-    }
-    return { matchedSources: [...matched] };
-}
-const NUMERIC_COUNTER_RE = /\b\d+(?:\.\d+)?(?:\s*(?:%|µm|um|fold|drugs?|reports?|signals?|trials?|tissues?|sources?|years?))?/i;
-function hasNumericCounter(text) {
-    return NUMERIC_COUNTER_RE.test(text);
-}
-// ── Numeric-claim verifier ───────────────────────────────────────────
-// Matches a "≥/>= N nTPM in M (distinct) tissues" count claim. The GLP1R
-// dossier review found a bullet asserting "≥10 nTPM in 14 distinct tissues"
-// when normal_tissue_expression actually held 23 — a class of miscount the
-// length/source probes cannot catch.
-const TISSUE_COUNT_CLAIM_RE = /(?:≥|>=)\s*(\d+(?:\.\d+)?)\s*ntpm\s+in\s+(\d+)\s+(?:distinct\s+)?tissues/i;
-/**
- * Verify a bullet's "≥N nTPM in M tissues" claim against
- * `reference_biology.normal_tissue_expression`. Returns a critique string
- * on mismatch, or `null` when there is no such claim, no dossier, or the
- * expression section is not available (nothing to verify against).
- */
-function verifyTissueCountClaim(text, dossier) {
-    if (!dossier)
-        return null;
-    const nte = dossier.reference_biology?.normal_tissue_expression;
-    if (!nte || nte.coverage !== "available")
-        return null;
-    // Raw GTEx `tpm` values are not on the normalized nTPM scale a "≥N nTPM"
-    // bullet claim refers to — comparing them would be meaningless. `ntpm` and
-    // `consensus_normalized` are both nTPM-scale and ARE verified.
-    if (nte.data.unit === "tpm")
-        return null;
-    const m = text.match(TISSUE_COUNT_CLAIM_RE);
-    if (!m)
-        return null;
-    const threshold = parseFloat(m[1]);
-    const claimed = parseInt(m[2], 10);
-    const actual = nte.data.rows.filter((r) => typeof r.value === "number" && r.value >= threshold).length;
-    if (claimed === actual)
-        return null;
-    return (`Bullet claims "${m[0]}" but normal_tissue_expression has ${actual} ` +
-        `tissue(s) with value ≥ ${threshold} nTPM, not ${claimed}. ` +
-        `Correct the count to ${actual}.`);
-}
-// ── Voice composition helper ─────────────────────────────────────────
-/**
- * Compose a base probe result with a voice check.
- *
- * Length fails are hard — a too-short output cannot be redeemed by
- * good voice. All other fails (source, section-refs, key-items) are
- * overridable: a banned-phrase violation is reported in preference to
- * an incomplete source citation, because voice is the narrower and
- * more actionable failure for the retry prompt.
- *
- * When the base is a clean pass, voice can still flip the verdict to
- * "fail-voice" (banned phrases / wrong register) or downgrade to
- * "relaxed" (borderline passive ratio).
- */
-function composeWithVoice(base, text, section) {
-    if (base.verdict === "fail-length") {
-        // A too-short output cannot be redeemed by good voice, so the verdict
-        // stays fail-length. But surface any voice issues in the critique too —
-        // the single bounded retry should be able to fix length AND voice in
-        // one pass, not discover the voice problem only on its final attempt.
-        const voice = buildVoiceCritique(text, section);
-        if (voice.verdict === "fail-voice" && voice.critique) {
-            return {
-                ...base,
-                critique: `${base.critique ?? ""}\n\nAdditionally: ${voice.critique}`,
-            };
-        }
-        return base;
-    }
-    const voice = buildVoiceCritique(text, section);
-    if (voice.verdict === "fail-voice") {
-        return {
-            verdict: "fail-voice",
-            critique: voice.critique,
-            output_chars: base.output_chars,
-        };
-    }
-    if (voice.verdict === "relaxed" && base.verdict === "pass") {
-        return {
-            verdict: "relaxed",
-            critique: voice.critique,
-            output_chars: base.output_chars,
-        };
-    }
-    return base;
-}
-// ── Recommendation probe ─────────────────────────────────────────────
-function recommendationCoverageRelaxed(dossier) {
-    // Relax probe rules when the dossier is genuinely thin — at least two
-    // of the three "primary" evidence streams must be unavailable.
-    const probes = [
-        dossier.safety_profile.organ_rollup.coverage !== "available",
-        dossier.clinical_development.trials.coverage !== "available",
-        dossier.reference_biology.preclinical.data_coverage.ko !== "available",
-    ];
-    return probes.filter(Boolean).length >= 2;
-}
-export function probeRecommendation(out, dossier) {
-    const t = PROBE_THRESHOLDS.recommendation;
-    const len = out.rationale.length;
-    const relaxed = recommendationCoverageRelaxed(dossier);
-    // Build the prose payload up-front so the voice probe runs on every
-    // path — including the fail-length branch. Banned phrases and
-    // colloquial organ-system references have no data-coverage dependency
-    // and must be caught regardless of how thin the upstream evidence is.
-    const recommendationText = [out.rationale, out.key_strengths.join(" "), out.key_risks.join(" "), out.modality_choice.rationale].join("\n");
-    // Length floor (minimum applies even when relaxed).
-    const minLen = relaxed ? t.rationaleMinCharsRelaxed : t.rationaleMinChars;
-    if (len < minLen) {
-        return composeWithVoice({
-            verdict: "fail-length",
-            critique: `Your prior rationale was ${len} characters; rewrite to ≥ ${minLen} characters integrating the dossier's evidence.`,
-            output_chars: len,
-        }, recommendationText, "executive-recommendation");
-    }
-    if (relaxed) {
-        // Coverage is thin: do not require section-reference count or
-        // key-strengths/risks. Voice probe still applies. Returns "relaxed"
-        // when voice is clean so diagnostics reflect that the strict rules
-        // were not applied.
-        return composeWithVoice({ verdict: "relaxed", critique: null, output_chars: len }, recommendationText, "executive-recommendation");
-    }
-    // Section-reference and key-item content fails are routed through
-    // composeWithVoice so a banned-phrase / colloquial-organ violation can
-    // override them. Voice fails are narrower and more actionable for the
-    // single retry budget — getting both issues into one critique is the
-    // difference between a recoverable section and a permanent
-    // queried_no_data drop.
-    const { matchedSections } = countSectionReferences(out.rationale);
-    if (matchedSections.length < t.requiredSectionRefs) {
-        return composeWithVoice({
-            verdict: "fail-section-references",
-            critique: `Your rationale referenced ${matchedSections.length} dossier section(s) (${matchedSections.join(", ") || "none"}); rewrite to cite ≥ ${t.requiredSectionRefs} of: safety_profile, tractability, indications, clinical_development, reference_biology.preclinical, analytics.translational_chain, off_target_panel.`,
-            output_chars: len,
-        }, recommendationText, "executive-recommendation");
-    }
-    if (out.key_strengths.length < t.requiredKeyItems || out.key_risks.length < t.requiredKeyItems) {
-        return composeWithVoice({
-            verdict: "fail-key-strengths-risks",
-            critique: `key_strengths (${out.key_strengths.length}) and key_risks (${out.key_risks.length}) must each have ≥ ${t.requiredKeyItems} entry when overall data coverage allows it.`,
-            output_chars: len,
-        }, recommendationText, "executive-recommendation");
-    }
-    return composeWithVoice({ verdict: "pass", critique: null, output_chars: len }, recommendationText, "executive-recommendation");
-}
-// ── Liability bullet probe ───────────────────────────────────────────
-export function probeLiabilityBullets(out, dossier) {
-    const t = PROBE_THRESHOLDS.liabilityBullet;
-    if (out.bullets.length === 0) {
-        // An empty bullets array is acceptable when `notes` discloses why.
-        if (out.notes.length >= 60) {
-            return { verdict: "pass", critique: null, output_chars: out.notes.length };
-        }
-        return {
-            verdict: "fail-length",
-            critique: `Empty bullets array with insufficient disclosure note (${out.notes.length} chars). Either populate at least one bullet or expand notes to ≥ 60 chars explaining the data picture.`,
-            output_chars: out.notes.length,
-        };
-    }
-    const totalChars = out.bullets.reduce((acc, b) => acc + b.rationale.length, 0);
-    const bulletText = out.bullets.map((b) => `${b.text}\n${b.rationale}`).join("\n");
-    for (const b of out.bullets) {
-        if (b.rationale.length < t.rationaleMinChars) {
-            return composeWithVoice({
-                verdict: "fail-length",
-                critique: `Bullet "${b.organ_or_axis}" rationale is ${b.rationale.length} chars; rewrite to ≥ ${t.rationaleMinChars} chars citing a numeric counter or a source by name.`,
-                output_chars: totalChars,
-            }, bulletText, "liability-bullets");
-        }
-        if (t.requiresSourceOrCounter) {
-            const { matchedSources } = countSourceReferences(b.rationale);
-            const counter = hasNumericCounter(b.rationale);
-            if (matchedSources.length === 0 && !counter) {
-                const sourceFailBase = {
-                    verdict: "fail-source-references",
-                    critique: `Bullet "${b.organ_or_axis}" rationale cites no source (FAERS, trial AEs, off-target panel, class precedent) and no numeric counter; rewrite citing one or both.`,
-                    output_chars: totalChars,
-                };
-                return composeWithVoice(sourceFailBase, bulletText, "liability-bullets");
-            }
-        }
-    }
-    for (const b of out.bullets) {
-        const numericCritique = verifyTissueCountClaim(b.text, dossier);
-        if (numericCritique) {
-            return {
-                verdict: "fail-numeric-claim",
-                critique: numericCritique,
-                output_chars: totalChars,
-            };
-        }
-    }
-    return composeWithVoice({ verdict: "pass", critique: null, output_chars: totalChars }, bulletText, "liability-bullets");
-}
-// ── Safety flag probe ────────────────────────────────────────────────
-export function probeSafetyFlags(out) {
-    const t = PROBE_THRESHOLDS.safetyFlag;
-    if (out.flags.length === 0) {
-        return { verdict: "pass", critique: null, output_chars: 0 };
-    }
-    const totalChars = out.flags.reduce((acc, f) => acc + f.trail.length, 0);
-    const flagText = out.flags.map((f) => `${f.organ}: ${f.trail} ${f.mechanism_hypothesis ?? ""}`).join("\n");
-    for (const f of out.flags) {
-        if (f.trail.length < t.trailMinChars) {
-            return composeWithVoice({
-                verdict: "fail-length",
-                critique: `Flag for "${f.organ}" trail is ${f.trail.length} chars; rewrite to ≥ ${t.trailMinChars} chars citing specific source counts.`,
-                output_chars: totalChars,
-            }, flagText, "target-organ-liabilities");
-        }
-        const { matchedSources } = countSourceReferences(f.trail);
-        if (matchedSources.length < t.requiredSourceRefs) {
-            const sourceFailBase = {
-                verdict: "fail-source-references",
-                critique: `Flag for "${f.organ}" cites ${matchedSources.length} source(s) (${matchedSources.join(", ") || "none"}); rewrite citing ≥ ${t.requiredSourceRefs} of: FAERS, trial AEs, off-target panel, class precedent.`,
-                output_chars: totalChars,
-            };
-            return composeWithVoice(sourceFailBase, flagText, "target-organ-liabilities");
-        }
-    }
-    return composeWithVoice({ verdict: "pass", critique: null, output_chars: totalChars }, flagText, "target-organ-liabilities");
-}
-// ── Translational commentary probe ───────────────────────────────────
-export function probeTranslationalCommentary(out) {
-    const t = PROBE_THRESHOLDS.translationalCommentary;
-    if (out.rows.length === 0) {
-        return { verdict: "pass", critique: null, output_chars: 0 };
-    }
-    const totalChars = out.rows.reduce((acc, r) => acc + r.commentary.length, 0);
-    const commentaryText = out.rows.map((r) => `${r.predicate} ${r.commentary}`).join("\n");
-    for (const r of out.rows) {
-        if (r.commentary.length < t.commentaryMinChars) {
-            return composeWithVoice({
-                verdict: "fail-length",
-                critique: `Row "${r.topic}" commentary is ${r.commentary.length} chars; rewrite to ≥ ${t.commentaryMinChars} chars bridging preclinical observation to human prediction.`,
-                output_chars: totalChars,
-            }, commentaryText, "translational-commentary");
-        }
-    }
-    return composeWithVoice({ verdict: "pass", critique: null, output_chars: totalChars }, commentaryText, "translational-commentary");
-}