Bret KerrBret Kerr · Franklin, MA
RA CAPITAL · QRS · HEALTHCARE AI ASSOCIATE
LIVE
workspace.racap_gold.semper_maior_metrics · 50 synthetic cos · 2 invalid quarantined · dashboard publishedOPEN DASHBOARD →
RA Capital · QRS · Healthcare AI Associate — POC by Bret Kerr, Franklin MA · Boston hybrid

Unstructured filings into governed, queryable signals the QRS team can trust.

●●●●●●●●Role signals mapped 8/8— every requirement has surface proof
5-minute Interview TourDatabricks live receipt
Built in Franklin, MA — Boston hybrid ready.
WHAT
QRS-shaped stack: 10 pipelines · KG · eval harness · governed skills
STATUS
Every claim graded — receipt / synthetic / spec (Honesty Ledger)
START
5-min Interview Tour · Coverage Board
BUILT
Solo, orchestrated with multi-model AI workflow
The Mandate · Role BriefingRequirements quoted from the posted role

QRS · Healthcare AI Associate — coverage board

Every requirement in the posting is mapped to something already rendered on this artifact — nothing aspirational. Read it the way QRS would brief a portfolio manager: source signal, transformation path, control surface, evidence, and where the evidence lives.

RA Capital ManagementQRS · Quantitative Research & StrategyBoston, MA · HybridUSD 120–150kPosted Apr 17, 2026Candidate: Franklin, MA · Boston-hybrid ready · US work-authorized

QRS information dashboard

From messy healthcare text to portfolio-manager action.

Dashboard posture: show the signal path, not just the final model score. That is the job: turn unstructured healthcare and financial data into reliable, decision-grade representations.
Role signals mapped
8 / 8

Every posted requirement has a proof surface on this artifact.

Unstructured sources
10-Q · 10-K · 14D-9

Filing text becomes entities, linked datasets, and scored features.

AI workflow span
KG · RAG · NER · Eval

Extraction, retrieval, relationship mapping, and limitations are explicit.

Decision surface
Portfolio brief

Signals resolve into ranked candidates and investor-readable narrative.

Signal transformation workflow

01

Corpus Intake

SEC filings, clinical readouts, ownership context, and market signals enter as messy source text.

02

Structuring Layer

NER, relationship mapping, Pydantic schemas, graph edges, and Delta-ready tables impose queryable shape.

03

Model + Retrieval Layer

Deterministic scoring, retrieval-aware summaries, and LLM-assisted extraction stay separated by risk level.

04

Investment Narrative

Portfolio managers get ranked targets, quality caveats, source provenance, and a human-readable thesis.

Coverage intensity

Unstructured-data systems ●●●●●
AI workflow design ●●●●●
Dashboard communication ●●●●●
Data integrity controls ●●●●○

Illustrative heuristic fit index for page navigation only, based on evidence density in this artifact — not a benchmark or measured score.

Portfolio Management

Ownership-tier classification (Peripheral / Core / Core+) and a ranked P(M&A) candidate table — Semper Maior implemented exactly.

Risk Management

Danger Zone conjunction flag (runway < 2y AND burn/cap > 0.25), a governed write perimeter, and tiered human-in-the-loop safeguards.

Data Science

PyTorch MLP scoring, ten pipelines re-expressed as governed Claude Code skills, and an expert-judgment fine-tuning layer.

Invest

Ranked target watchlist, tier rationale, M&A probability, and narrative brief.

Venture

Company-building signals, clinical/commercial anomalies, and whitespace hypotheses.

Legal / Compliance

Auditable source trails, claim-status tags, and controlled write boundaries.

TechAtlas / QRS

Reusable skills, graph-ready entities, Delta exports, and evaluation hooks.

Role RequirementProof on This ArtifactWhere
Unstructured data → structured representations (knowledge graphs, embeddings, linked datasets)Ten pipelines with a shared anatomy — input → representation → analyst query → decision; PY-01 renders as a queryable knowledge graph on this page.Pipeline Matrix ↓
AI-driven workflows: LLM pipelines, retrieval systems, entity extraction, relationship mappingAnthropic NER stage in the pipeline; ten downloadable skills covering extraction, retrieval, and relationship mapping across therapeutic areas.Skill Layer →
Evaluation frameworks — and an understanding of their limitations in high-stakes settingsA named eval harness (golden sets, verbatim substring verification, retrieval metrics, judged rubrics) plus a five-row failure-mode table; deterministic tensor math owns the scoring where LLMs hallucinate ($12–$289/share Cold-Start Triplet spread).Eval & Limits ↓
Spark (PySpark), SQL, and PythonA pandas → PySpark port shown as a real diff, a medallion Delta layout, and star-schema SQL with three analyst queries; the entire POC is Python.Scale Path ↓
Dashboards and visualizations that communicate findings effectivelyDanger-zone scatter and tier-rate charts below, the 9:16 exportable infographic board — and this coverage board itself.Live below
Data quality and integrity — best practices in collection, processing, and storageProvenance ledger, Pydantic validation, dedup checksums, drift alarms — and the Honesty Ledger that classifies every claim on this site.Honesty Ledger ↓
Cohesive stories and actionable narratives for the investing teamThe narrative pipeline below (corpus → dispatch → infographic → dashboard), with a worked synthetic analyst note.Narrative ↓
Sustained unstructured-data work in AI systems · MA-based, Boston hybrid, US work authorizationDemonstrated by volume, not asserted by tenure: the receipts strip below (1.4M-word verified RAG corpus, governed memory system, this stack). Based in Franklin, MA — no relocation needed; authorized without sponsorship.Receipts ↓

Source provenance

Requirement-to-proof rows point each claim to a rendered page surface or Skill Layer artifact.

Schema discipline

Pydantic, Delta table dry-runs, and generated SQL keep extraction outputs inspectable before writes.

Model limitation handling

LLMs assist extraction; tensor math owns high-stakes scoring where hallucinated prices would be costly.

Human review gates

Expert-judgment tags distinguish verified, background, and proposed claims before investor consumption.

Role description: “Quantitative Research and Strategy, Healthcare AI Associate,” RA Capital Management, posted Apr 17, 2026. Requirement text condensed from the posting; proof column references sections rendered on this page and the Skill Layer view.

Bret Kerr — candidate, QRS Healthcare AI Associate POC
The Candidate · Fit Brief

The candidate behind the POC

Bret Kerr — AI-native research and strategy operator. This is not a defense of a non-traditional background; it is an argument that the background is the prerequisite. A decade of creative and digital-strategy leadership inside a global email-security enterprise (Mimecast, through its IPO and PE take-private) is a decade of building trust-sensitive, compliance-bounded work for a company whose entire product is handling other people's confidential data. Layer on recent applied-AI and MCP-security consulting in the cybersecurity sector — including publicly predicting the $14B cybersecurity “haircut” before the market repriced it — and hackathon-winning multi-model orchestration, and you have the exact prerequisites for building secure, hallucination-resistant AI pipelines in regulated finance. This page is the credential: every requirement of the QRS Healthcare AI Associate role has a working demonstration above.

QRS NeedCareer ProofProof on This Page
Unstructured data → structured representationsBuilt ContextJamming.com — an AI-native research system turning long-form research into structured chapters, metadata, and search surfaces.SEC 10-Q / 10-K / 14D-9 text → NER → typed features → Databricks Delta tables.
RAG, embeddings & knowledge workflowsHands-on Claude, ChatGPT, Gemini, Codex Code; SQLite/FTS and vector-search retrieval; cross-model review as a code-review heuristic — verification stays deterministic.Retrieval-aware pipeline design — deterministic tensor math where LLMs hallucinate.
Entity & relationship mappingFounder profiles, technical dossiers, market maps, investment-style narratives.50-company universe, ownership-tier classification, Kolchinsky FounderFile.
Trust-sensitive / regulated complexityA decade inside a global email-security enterprise (Mimecast, IPO → PE take-private); recent applied-AI and MCP-security consulting in cybersecurity.Semper Maior implemented exactly — Danger Zone conjunction, Core/Peripheral tiers — plus MNPI-safe governance hooks.
Senior stakeholder collaborationA decade of creative and digital-strategy leadership at Mimecast, turning ambiguous executive inputs into polished, accurate outputs.This page — an executive-ready interview artifact, built and shipped solo.
Founder File · RA Capital
Peter Kolchinsky — a FounderFiles dossier on RA Capital's co-founder →
Entity and relationship mapping demonstrated on the firm itself — the same diligence method this POC applies to the 50-company universe.
Reference · Former Manager
“Bret sees around corners.”
Jeff Schumann · CEO & co-founder, Aware (acquired by Mimecast, 2024)
Bret's manager as SVP, Brand & AI Strategy at Mimecast, Spring 2025 — bonded over AI research.
The Compounding Math of Skills

A skill is a one-time encoding of a workflow — the trigger conditions, the governance, the failure modes — that every analyst then inherits for free. The math compounds: if one skill turns a 45-minute recurring task into a 5-minute reviewed run, and ten analysts hit that task twice a week, that single skill returns roughly 13 hours a week to the team. This page ships ten.

Recurring task, encoded once
45 → 5 min
One skill × 10 analysts (illustrative)
~13 hrs/wk
Distribution — commit & inherit
Day 1

Illustrative adoption model — same honesty standard as the synthetic universe above. The mechanism is real: skills committed to a repo are inherited by every teammate running Claude Code, no install step.

I am strongest where technical ambiguity, unstructured source material, AI workflow design, and executive-facing communication overlap. For RA Capital, that means transforming large bodies of text and research into structured evidence, useful retrieval surfaces, and clear analytical narratives that support investment teams operating in high-complexity healthcare AI markets.
↓ Resume (PDF)bret.kerr@gmail.comFounderFile → Kolchinsky
Semper Maior · I
"Ninety-eight percent of M&A premiums accrue to the Core set. Danger Zone is a structural necessity, not an opportunity."
From RA Capital's 1H23 Semper Maior report — the thesis this pipeline encodes.
Synthetic Universe · n=50 · seed=42
Universe
50
Danger Zone
9
Core+
15
Core
13
Peripheral
22
Mean P(M&A) Core+
0.203
Semper Maior Analytics · Live Visualization

Danger Zone Scatter + Ownership Tier M&A Rates

Cash Runway vs Burn-to-Cap · sized by market cap
DANGER ZONEBIOA | Runway: 1.96y | Burn/Cap: 0.366 | Cap: $223MONCO | Runway: 0.46y | Burn/Cap: 0.052 | Cap: $1976MGLXT | Runway: 7.96y | Burn/Cap: 0.131 | Cap: $230MCRVA | Runway: 5.31y | Burn/Cap: 0.056 | Cap: $952MNVLX | Runway: 0.44y | Burn/Cap: 0.442 | Cap: $108MPTHR | Runway: 0.88y | Burn/Cap: 0.153 | Cap: $279MIMMX | Runway: 2.48y | Burn/Cap: 0.518 | Cap: $106MRDGE | Runway: 0.48y | Burn/Cap: 0.808 | Cap: $235MBLTX | Runway: 3.29y | Burn/Cap: 0.033 | Cap: $1088MAPEX | Runway: 0.43y | Burn/Cap: 2.627 | Cap: $50MCYTX | Runway: 8.94y | Burn/Cap: 0.047 | Cap: $642MDLGN | Runway: 4.64y | Burn/Cap: 0.106 | Cap: $497MEMRX | Runway: 1.73y | Burn/Cap: 0.443 | Cap: $169MFXBT | Runway: 3.33y | Burn/Cap: 1.804 | Cap: $56MGNTX | Runway: 1.69y | Burn/Cap: 0.274 | Cap: $401MHLTT | Runway: 0.48y | Burn/Cap: 0.634 | Cap: $183MIMMU | Runway: 3.24y | Burn/Cap: 0.106 | Cap: $494MJMBY | Runway: 1.06y | Burn/Cap: 0.128 | Cap: $376MKLXT | Runway: 2.2y | Burn/Cap: 0.042 | Cap: $2929MLXBT | Runway: 1.99y | Burn/Cap: 0.218 | Cap: $267MMXBT | Runway: 3.43y | Burn/Cap: 0.311 | Cap: $96MNXBT | Runway: 2.18y | Burn/Cap: 0.065 | Cap: $461MOPXT | Runway: 10.42y | Burn/Cap: 0.072 | Cap: $486MPRXT | Runway: 1.12y | Burn/Cap: 0.044 | Cap: $2137MQRBT | Runway: 1.12y | Burn/Cap: 0.068 | Cap: $1081MRRXT | Runway: 0.82y | Burn/Cap: 0.186 | Cap: $581MSRBT | Runway: 3.97y | Burn/Cap: 0.02 | Cap: $2446MTRXT | Runway: 2.27y | Burn/Cap: 0.957 | Cap: $78MURBT | Runway: 1.7y | Burn/Cap: 0.65 | Cap: $159MVRBT | Runway: 3.33y | Burn/Cap: 0.491 | Cap: $109MATXT | Runway: 8.71y | Burn/Cap: 0.417 | Cap: $220MBTXT | Runway: 2.01y | Burn/Cap: 0.688 | Cap: $61MCTXT | Runway: 1.48y | Burn/Cap: 0.062 | Cap: $834MDTXT | Runway: 1.14y | Burn/Cap: 0.187 | Cap: $273METXT | Runway: 7.05y | Burn/Cap: 0.556 | Cap: $54MFTXT | Runway: 3.58y | Burn/Cap: 0.962 | Cap: $97MGTXT | Runway: 2.28y | Burn/Cap: 0.087 | Cap: $549MHTXT | Runway: 0.85y | Burn/Cap: 0.062 | Cap: $1085MITXT | Runway: 0.62y | Burn/Cap: 0.019 | Cap: $4894MRXMD | Runway: 2.39y | Burn/Cap: 0.01 | Cap: $9000MGCVR | Runway: 2.23y | Burn/Cap: 0.17 | Cap: $626MARZN | Runway: 3.18y | Burn/Cap: 0.617 | Cap: $101MNEUV | Runway: 1.35y | Burn/Cap: 0.992 | Cap: $50MRDSC | Runway: 2.37y | Burn/Cap: 0.122 | Cap: $517MBRCL | Runway: 4.5y | Burn/Cap: 0.236 | Cap: $127MGCVX | Runway: 4.93y | Burn/Cap: 0.141 | Cap: $213MNNBX | Runway: 8.87y | Burn/Cap: 0.182 | Cap: $165MXNBT | Runway: 4.48y | Burn/Cap: 0.109 | Cap: $304MZBIO | Runway: 2.54y | Burn/Cap: 0.06 | Cap: $1459MPLXT | Runway: 3.65y | Burn/Cap: 0.079 | Cap: $448M0y2y4y6y8y0.000.250.500.75Cash Runway (years)Burn / Cap RatioSafeDanger Zonesize = mkt cap

Danger Zone = runway < 2y ANDburn/cap > 0.25. The conjunction is what signals acute strategic necessity — a deal, dilutive financing, or cash exhaustion is imminent.

Historical M&A acquisition rate by ownership tier
5%Peripheraln=2215%Coren=1335%Core+n=150%10%20%30%40%50%Illustrative tier priors (synthetic labels)

Per RA's 1H23 Semper Maior report, 98% of H1'23 M&A premiums accrued to the Core set. The 5/15/35% tier rates shown here are illustrative priors used to generate synthetic training labels for this POC — not RA empirical acquisition rates.

Semper Maior Classification Engine · InteractiveIllustrative / synthetic data

Core / Peripheral / Danger Zone — the published framework, automated

This automates the Core/Peripheral and Danger Zone classifications published in RA Capital's RApport series. A synthetic 13F institutional-ownership extract is cross-referenced against a specialist-investor roster: at least one specialist biotech holder makes a company Core; none makes it Peripheral. The distinction is where the capital goes — per the RApport Semper Maior series, over 98% of biotech M&A capital has flowed into Core companies.

Every dataset in this module is synthetic — invented issuers, invented holders. No real fund's positions are shown or implied. There is no LLM anywhere in this classification path: set membership and threshold arithmetic, displayed in full below.

Step 1 · 13F extract × specialist roster
AXBI · Axiobright Therapeutics
Synthetic 13F institutional-ownership extract
Holder of recordPositionMatch
Beacon Biotech Specialists LP$24.1MSPECIALIST
Meridian Global Index$18.6Mgeneralist
Harborlight Capital$9.2Mgeneralist
specialist_holders = 1Core

Specialist roster (illustrative): Beacon Biotech Specialists LP · Foxglove Life Sciences Fund · Sable Point Biotech Partners. Production swaps this for a maintained registry of specialist biotech investors.

Step 2 · Danger Zone — the math, in full
Cash & equivalents (10-Q)$151.0M
Quarterly net burn$23.5M
Market cap$310.0M
annualized_burn = $23.5M × 4        = $94.0M
cash_runway     = $151.0M ÷ $94.0M = 1.61y
burn_to_cap     = $94.0M ÷ $310.0M = 30.3%

runway  < 2.0y ? TRUE    ◄ condition met
burn/cap > 25% ? TRUE    ◄ condition met
BOTH required  → DANGER ZONE
⚠ Danger ZoneUnder 2 years of cash at a burn rate the market cap cannot absorb — acute strategic necessity.
Classified universe · all eight synthetic issuers
TickerSpecialistsTierRunwayBurn/CapFlag
AXBI1Core1.61y30.3%⚠ DZ
CYTR2Core3.75y6.1%
NMDL0Peripheral1.38y26.7%⚠ DZ
VLTX1Core4.01y7.7%
ORPH1Core1.45y29.3%⚠ DZ
TRBN0Peripheral2.71y6.7%
HLXP1Core2.86y31.7%
SLNT0Peripheral2.64y5.9%

Framework attribution: Core/Peripheral specialist-ownership classification and the Danger Zone conjunction (<2y runway AND burn-to-cap >25%) as published in RA Capital's RApport Semper Maior series. All issuers, holders, and figures above are synthetic — the framework is real; the data is not.

VERDICT GREEN· 42 checks / 0 failedMONITOR
Semantic Firewall · Deterministic VerificationImplemented on synthetic data

You can't debug the black box with the black box

The strongest objection to AI-built pipelines: if two models share a structural blind spot, cross-model consensus won't catch it — it will confidently log the failure as a success. The answer is not a better reviewer. It is a wall.

Agents propose, gates dispose. LLMs write and refactor pipeline code. Whether that code's output is trusted is decided exclusively by deterministic, non-LLM machinery: schema contracts, mathematical invariants, golden oracles, reconciliation checks, statistical process control with hard thresholds, and a circuit breaker.

Zero LLM calls in the verification path — grep-checkable: nothing under verification/ imports a model client or the network.

Generation layer · agents

Claude / Codex write pipeline code

Refactors, features, fixes

GemClaw cross-model review — a code-review heuristic, nothing more

PROPOSES →
Verification layer · deterministic gates dispose
G1 · Data contractsPASS

Schema contracts, nullability, ranges, key uniqueness, row-count reconciliation, sequence-gap detection on the ordered feed. (21 checks, 0 failed)

G2 · Mathematical invariantsPASS

Property-based invariants (Hypothesis, derandomized): probability axioms, conjunction semantics, monotonicity, MC estimator vs closed-form oracle, KG referential integrity. (12 checks, 0 failed)

G3 · Golden oraclesPASS

Frozen fixtures with expected outputs at explicit tolerances. Regeneration only via a human-flagged, logged command. (9 checks, 0 failed)

G4 · Dual-path reconciliationSTUBBED · P1

Each critical aggregate recomputed by an independent second implementation; |Δ| < ε asserted. Spec-design only — labeled, not faked.

G5 · Drift SPC (PSI / KS / CUSUM)STUBBED · P1

PSI / KS distance vs stored baselines + CUSUM, hard thresholds pinned in thresholds.yaml. Spec-design only — labeled, not faked.

G6 · Circuit breaker + quarantineARMED

Any failure halts downstream writes (page JSON, Delta export), quarantines the batch, and emits a structured failure record. No silent retries.

Latest gate run · verify_20260704T184010Z_a92961cd · verdict GREEN · 42 checks / 0 failed · git a92961cd
PipelineG1 contractsG2 invariantsG3 goldens
sec_ingestion✓ 9/9
universe.json✓ 11/11✓ 4/4
sec_ingestion → universe.json✓ 1/1
ma_predictor✓ 2/2
ra_metrics✓ 3/3✓ 5/5
ma_predictor (MC engine)✓ 3/3
kg-triples.json✓ 3/3
verification/tests✓ 1/1
Red-team harness · make redteam · redteam_20260704T184015Z_a92961cdCATCH RATE 2/2 — 100%, zero model involvement
fault_a✓ caught by Gate 1 (Data contracts)DATA-01 · DATA-02

Silently dropped row 17/50 (JMBY) from a copy of universe.json — 2% loss, no error raisedquarantine/redteam_20260704T184015Z_a92961cd_fault_a/failure_record_00_DATA-01.json

fault_b✓ caught by Gate 3 (Golden oracles)MATH-10

Sign flip injected into ra_metrics.compute_burn_to_cap_ratio (in-memory monkeypatch; source untouched) — lints, types, runs greenquarantine/redteam_20260704T184015Z_a92961cd_fault_b/failure_record_00_MATH-10.json

Sample failure record — emitted by the harness when fault_a dropped row 17 (structured, machine-readable, quarantined)
{
  "taxonomy": "DATA-01",
  "gate": 1,
  "gate_name": "Data contracts",
  "pipeline": "sec_ingestion → universe.json",
  "check": "row-count reconciliation: source == sink",
  "expected": "50",
  "observed": "49",
  "run_id": "redteam_20260704T184015Z_a92961cd_fault_a",
  "context": "make redteam — injected fault_a: Silently dropped row 17/50 (JMBY) from a copy of universe.json — 2% loss, no error raised",
  "input_hashes": {
    "app/RACap-POC/universe.json": "359719e563ae4a885909c9260a29235c1ff49cc114da9c6f31d0f5caa97ba8dc",
    "public/racap-poc/kg-triples.json": "70073d4cb85b7403f3f4d0e67204c8a734b4c3d3eccc1e4dbd2c559d5089a0e1",
    "verification/thresholds.yaml": "3c7b755da3708ac909961cc8d45865ac448ee5889acda94ca90ab71005dbed8d",
    "verification/golden/raw_universe.json": "9ba05c50437d383df57656107e35641c47c407b20d30e1090c58199e97a0488a",
    "verification/golden/metrics_golden.json": "9f3523dcb8fc08cf42815c0e8461da92d208f42052fec19e5885a3f9c3e4f171",
    "verification/golden/universe_golden.json": "359719e563ae4a885909c9260a29235c1ff49cc114da9c6f31d0f5caa97ba8dc",
    "ra-danger-zone/src/ra_metrics.py": "99a44e397daa189d57d2efd3609d8a76c0bbf9febf23c8d4ad7ba3f7fa616ce8",
    "ra-danger-zone/src/sec_ingestion.py": "7b991add893a4e48370cb98ca275d6e5c8001c16d41503dacc7d7918f27d09ec",
    "ra-danger-zone/src/ma_predictor.py": "0e5c0763597155438eb8e777647126ae4dc2951f35f9bf90606af7e38a124a57",
    "ra-danger-zone/src/db_export.py": "9f56a4971c0288a45865c365d6f9d86ffcd71eba0271e97f9727900595336d49"
  },
  "git_sha": "a92961cd5ca5ff4ed793419358ad217e90dd5255",
  "blocked_actions": [
    "app/RACap-POC/universe.json regeneration (page data)",
    "Databricks Delta export (db_export.export_to_databricks)"
  ],
  "timestamp": "2026-07-04T18:40:15+00:00"
}

Stated plainly: cross-model consensus (GemClaw) stays in this repo as a code-review heuristic — useful for catching smells, never counted as verification. Gates 4–5 (dual-path reconciliation, drift SPC) are spec-design only and labeled STUBBED above; their hard thresholds are already pinned in verification/thresholds.yamlso implementing them can't silently invent tolerances. Everything green on this panel is the committed output of make verify and make redteam against synthetic seed=42 data.

Governance layer · MNPI-safe by construction

The Skill Layer

All ten pipelines below, re-expressed as downloadable Claude Code skills — governance, failure modes, and orchestration baked into each artifact. 10 skills · 9 orchestration mechanisms · one-click install.

Governance & Lifecycle Hooks · Compliance Posture

Inherently safe infrastructure, not just capable infrastructure

A fund handling material non-public information needs an AI pipeline whose safety is structural, not prompted. Claude Code's PreToolUse / PostToolUsehooks are deterministic enforcement: an external script inspects every tool call and returns allow / deny / ask before the call executes. Prompt injection can rewrite a model's instructions; it cannot rewrite an external hook.

.claude/hooks/pretooluse-sql-guard.shPreToolUse
#!/usr/bin/env bash
# .claude/hooks/pretooluse-sql-guard.sh
# Wired to PreToolUse — fires on every Bash/SQL tool call
# BEFORE it reaches any database. Blocks on exit code 2.

payload="$(cat)"                       # hook receives tool input on stdin
sql="$(jq -r '.tool_input.command // empty' <<<"$payload")"

# Case-insensitive scan for destructive DDL/DML
if grep -iqE '\b(DROP|DELETE|TRUNCATE|ALTER)\b' <<<"$sql"; then
  echo "BLOCKED: destructive statement rejected by SQL guard." >&2
  echo "  matched: $(grep -ioE '\b(DROP|DELETE|TRUNCATE|ALTER)\b' <<<"$sql" | head -1)" >&2
  printf '%s\t%s\t%s\n' "$(date -u +%FT%TZ)" "DENY" "$sql" \
    >> .claude/audit/sql-guard.log     # append-only audit trail
  exit 2                               # exit 2 = block the command
fi

exit 0                                 # SELECT / read-only → allow
Why a hook beats a prompt rule
  • Prompt injection can override a system prompt; it cannot override an external exit code.
  • Adherence to prompted rules decays under long-context load — a hook fires every single call.
  • Subagents that never saw the system prompt still hit the same perimeter.
.claude/audit/sql-guard.logappend-only
2026-07-03T14:22:07Z DENY DROP TABLE gold.fact_catalyst; ◄ blocked, exit 2
2026-07-03T14:22:07Z ALLOW SELECT ticker, runway FROM gold.semper_maior_metrics …
2026-07-03T14:24:51Z ASK INSERT INTO gold.dim_company … ◄ write → routed to human approval
Blocked command — hook firing, verbatim
$ claude ▸ Bash("psql -c 'DROP TABLE gold.fact_catalyst;'")
  BLOCKED: destructive statement rejected by SQL guard.
    matched: DROP
  ↳ PreToolUse hook exited 2 — command never reached the database.
  ↳ appended: 2026-07-03T14:22:07Z  DENY  DROP TABLE gold.fact_catalyst;
Governed memory that never leaves the machine

The same governance posture extends to memory. The SkillMemoryBank lineage — Lane 2 Best in Show at the Red Hat OpenAccelerator Agent Build Day, Boston, June 2026 — runs a local IBM Granite model to compress interaction traces into a governed MEMORY.md. That compaction stage has zero network egress: raw traces are summarized on the machine, never shipped to a cloud API. Combined with the hook perimeter above, the result is an auditable pipeline with MNPI-safe defaults — destructive writes blocked deterministically, and sensitive memory compressed locally rather than transmitted.

Pipeline Architecture
SEC EDGAR10-Q · 10-K · 14D-9Anthropic NEREntity extractionRA MetricsDanger Zone · TiersPyTorch MLPP(M&A) scoringDatabricksDelta table export

* Anthropic NER replaces synthetic data in production — 10-Q/10-K/14D-9 parsing via sec-edgar-downloader + Claude API entity extraction

01–06 · SIX PILLARS · Pipeline Matrix

Portfolio · Risk · Data Science · Evals · Scale Path · Governance

Each pipeline follows the same anatomy: an unstructured source, the structured representation it becomes — knowledge graph, embeddings, or linked dataset — one query an analyst would actually ask of it, and the decision it supports. The paired Claude Code skill (footer of each card) carries the governance; the workflow is the point.

Status chips grade what this page can demonstrate, not what was built elsewhere — the conservative reading. All chips resolve to the Honesty Ledger.

01Data Science01 · Biomedical Knowledge Graph · ~75 secImplemented · synthetic data
Biomedical Knowledge Graph Extractor
Typed entities — company / target / indication / trial / mechanism — with typed relations
Input — unstructured source
Trial readouts, PubMed abstracts, company pipeline pages
Structured representation
knowledge graphTyped entities — company / target / indication / trial / mechanism — with typed relations see it on this page ↓
How the investment team queries it
Which private companies share a mechanism with our top-quartile holdings?
Decision it supports
Landscape mapping for new-territory theses; competitive-crowding checks
Data ScienceTechAtlasQRSskill: biomedical-kg-extractor
02Portfolio Mgmt02 · Three-Signal Market Scraper · ~60 secSpec
Three-Signal Market Scraper
Entity-resolved company signals joined across the three feeds, timestamped
Input — unstructured source
News wires, job postings, patent filings
Structured representation
linked datasetEntity-resolved company signals joined across the three feeds, timestamped
How the investment team queries it
Which seed-stage water-tech companies show hiring, patent, and coverage inflections this quarter?
Decision it supports
Sourcing screen for the venture pipeline
Portfolio MgmtVenturePlanetary Healthskill: three-signal-market-scraper
03Data Science03 · Next.js Dashboard API · ~50 secSpec
Next.js Dashboard API Automator
A typed, versioned API surface over the gold-layer marts
Input — unstructured source
Pipeline outputs — Delta marts, scored JSON artifacts
Structured representation
linked datasetA typed, versioned API surface over the gold-layer marts
How the investment team queries it
Give the invest team a live endpoint for the danger-zone screen, with provenance fields intact.
Decision it supports
Distribution — dashboards and visualizations that communicate findings
Data ScienceOperationsQRSskill: dashboard-api-automator
04Risk Mgmt04 · Clinical Trial Probability-of-Success · ~85 secSpec
Clinical Trial Probability-of-Success Classifier
Trial-level features joined to evidence flags and historical base rates
Input — unstructured source
ClinicalTrials.gov registries, genetic-evidence literature
Structured representation
linked datasetTrial-level features joined to evidence flags and historical base rates
How the investment team queries it
Rank our Phase 2 exposure by probability-of-success delta versus indication base rate.
Decision it supports
Position sizing around binary readout events
05Risk Mgmt05 · Commercial Volume Anomaly · ~55 secSpec
Commercial Volume Anomaly Detector
Product-region volume series with anomaly scores and consensus deltas
Input — unstructured source
Prescription/claims volume feeds, distributor inventory data
Structured representation
linked datasetProduct-region volume series with anomaly scores and consensus deltas see it on this page ↓
How the investment team queries it
Flag products whose script trends diverge more than 2σ from consensus-implied trajectories.
Decision it supports
Early warning on commercial underperformance in holdings
06Portfolio Mgmt06 · Structured Capital Monte · ~70 secSpec
Structured Capital Monte Carlo Engine
Simulated payoff distributions per capital structure, seedable and rerunnable
Input — unstructured source
Deal terms, royalty schedules, indication revenue forecasts
Structured representation
linked datasetSimulated payoff distributions per capital structure, seedable and rerunnable
How the investment team queries it
Which royalty step-down structure survives a 30% peak-sales miss at the P10 outcome?
Decision it supports
Structure pricing and downside protection in structured deals
Portfolio MgmtStructured Capitalskill: structured-capital-monte-carlo
07Data Science07 · Translational NLP Grant · ~65 secSpec
Translational NLP Grant Parser
Semantic vectors over translational research, clustered by mechanism adjacency
Input — unstructured source
NIH / SBIR grant abstracts, academic publications
Structured representation
embeddingsSemantic vectors over translational research, clustered by mechanism adjacency
How the investment team queries it
Surface grant clusters adjacent to our antibody-platform theses that no fund has priced yet.
Decision it supports
Early scientific sourcing ahead of company formation
Data ScienceBlackbirdRavenskill: translational-grant-parser
08Risk Mgmt08 · Standard-of-Care Price Compression · ~80 secSpec
Standard-of-Care Price Compression Modeler
Erosion curves per therapeutic class with entry-event triggers
Input — unstructured source
Payer policy documents, LOE calendars, pricing disclosures
Structured representation
linked datasetErosion curves per therapeutic class with entry-event triggers
How the investment team queries it
Model standard-of-care price compression when two biosimilars enter within 18 months.
Decision it supports
TAM haircuts and terminal-value discipline in valuation models
09Data Science09 · Planetary Health LCA · ~45 secSpec
Planetary Health LCA Parser
CO₂e / water / energy metrics aligned to a strict taxonomy with unit normalization
Input — unstructured source
Sustainability reports, life-cycle-assessment PDFs
Structured representation
linked datasetCO₂e / water / energy metrics aligned to a strict taxonomy with unit normalization
How the investment team queries it
Compare kg-CO₂e per functional unit across competing process routes in the portfolio.
Decision it supports
Planetary Health diligence and portfolio-level resource accounting
Data SciencePlanetary Healthskill: planetary-health-lca-parser
10Portfolio Mgmt10 · DTC/P Digital Media · ~55 secSpec
DTC/P Digital Media A/B Segment Analyzer
An experiment ledger with guardrail metrics and segment lineage
Input — unstructured source
Campaign event streams, segment exposure logs
Structured representation
linked datasetAn experiment ledger with guardrail metrics and segment lineage
How the investment team queries it
Which patient-acquisition segments hold up after Simpson’s-paradox and p-hacking checks?
Decision it supports
DTC/P spend allocation across segments
Portfolio MgmtDTC/P Analyticsskill: dtcp-ab-segment-analyzer
Source Code · Key Snippets

Four-module pipeline

src/sec_ingestion.pygenerate_universe() — synthetic SEC data
def generate_universe(seed: int = 42) -> pd.DataFrame:
    rng = np.random.default_rng(seed)

    # Cash: log-normal skewed toward lower balances
    cash_raw = rng.lognormal(mean=4.8, sigma=0.9, size=50) * 1e6
    cash_equivalents = np.clip(cash_raw, 20e6, 800e6)

    # Specialist ownership: bimodal (40% zeros, rest Poisson(3))
    zero_mask = rng.random(50) < 0.40
    counts = rng.poisson(lam=3.0, size=50).clip(1, 8)
    specialist_ownership_count = np.where(zero_mask, 0, counts)

    # has_cvr / has_mae from simulated 14D-9 NER pass
    has_cvr = rng.random(50) < 0.28
    has_mae = rng.random(50) < 0.62
src/ra_metrics.pyclassify_danger_zone() — Semper Maior classification
def classify_danger_zone(
    cash_runway_years: pd.Series,
    burn_to_cap_ratio: pd.Series,
    runway_threshold: float = 2.0,
    burn_cap_threshold: float = 0.25,
) -> pd.Series:
    """Flag Semper Maior Danger Zone — BOTH conditions required.

    98% of M&A premiums flow to Core set companies.
    Danger Zone = structural necessity, not opportunity.
    """
    return (
        (cash_runway_years < runway_threshold) &
        (burn_to_cap_ratio > burn_cap_threshold)
    ).rename("danger_zone")
src/ma_predictor.pyMAPredictor — PyTorch MLP with BCELoss + Adam
class MAPredictor(nn.Module):
    """Two-layer MLP for M&A probability scoring.

    Why PyTorch, not an LLM?
    RA Capital's tests showed LLM "Cold-Start Triplet" hallucinations
    ranging from $12–$289/share on identical assets. Deterministic
    tensor math owns the scoring; LLMs handle SEC text extraction.
    """
    def __init__(self) -> None:
        super().__init__()
        self.net = nn.Sequential(
            nn.Linear(5, 32), nn.ReLU(), nn.Dropout(0.3),
            nn.Linear(32, 16), nn.ReLU(), nn.Dropout(0.3),
            nn.Linear(16, 1),  nn.Sigmoid(),
        )

    def forward(self, x: torch.Tensor) -> torch.Tensor:
        return self.net(x)
src/db_export.pyexport_to_databricks() — Delta table with dry-run
def export_to_databricks(df: pd.DataFrame, dry_run: bool = True) -> None:
    """Export scored universe to Databricks Delta table.

    Free Edition constraints:
    - No persistent clusters → local PyTorch, push result set only
    - 15GB storage limit → sufficient for rolling snapshot history
    - No Databricks Jobs → schedule externally (Airflow / Claude Code CLI)
    """
    if dry_run or not _check_env():
        print(_CREATE_DDL)
        print(f"INSERT INTO {_TABLE} ...")
        return

    with dbsql.connect(hostname, http_path, access_token) as conn:
        cursor.execute(_CREATE_DDL)
        cursor.execute(f"TRUNCATE TABLE {_TABLE}")
        cursor.execute(f"INSERT INTO {_TABLE} ...")
Module Reference
sec_ingestion.pyEDGAR-ready
SEC Filing Data Simulator
Generates 50 synthetic biotech companies with realistic distributions. Production: sec-edgar-downloader + Anthropic API NER on 10-Q/10-K/14D-9 filings.
ra_metrics.py
Semper Maior Transformation Engine
Exact RA Capital classification logic: Danger Zone flag, ownership tier (Peripheral/Core/Core+), below-cash flag with investment rationale in every docstring.
ma_predictor.pyPyTorch
PyTorch M&A Probability Model
Two-layer MLP (5→32→16→1), BCELoss, Adam, StandardScaler. CUDA→MPS→CPU device chain. MC-Dropout ready. Deterministic scoring avoids LLM Cold-Start Triplet hallucinations.
db_export.pyDelta Lake
Databricks Delta Connector
CREATE TABLE IF NOT EXISTS semper_maior_analytics + batch INSERT. Dry-run mode prints SQL without connecting — safe for local dev under Free Edition constraints.
visualize.py
Four-Panel Analysis Dashboard
matplotlib + seaborn: danger zone scatter, ownership tier boxplot, M&A probability histogram, and a formatted summary stats panel. Dark professional style.
main.py
Pipeline Orchestrator
argparse with --epochs, --output-dir, --no-dry-run. Sequential logging. End-to-end runtime under 60 seconds on CPU. Prints ranked Core+ candidate table.
Production Scaling Path

POC → QRS production infrastructure

ComponentThis POCProduction (QRS)
Data ingestionNumPy syntheticsec-edgar-downloader + Anthropic NER
StorageLocal DataFramesDatabricks Delta Lake (paid tier)
ML trainingLocal PyTorchMLflow on Databricks + hyperparameter sweep
Schedulingpython main.pyAirflow DAG or Claude Code CLI cron
Model versioningNoneMLflow Model Registry
GovernanceDry-run SQL logsUnity Catalog + lineage tracking
Install & Run
TERMINAL
pip install -r requirements.txt
python main.py

# Options
python main.py --epochs 200 --output-dir ./results
python main.py --no-dry-run  # requires Databricks env vars
Semper Maior · II
"Deterministic tensor math owns the scoring; LLMs handle SEC text extraction."
The division of labor that keeps a governed pipeline honest.
Queryable Knowledge Graph · PY-01Implemented · synthetic data

A structured representation the investment team can query

PY-01 turns biomedical text into typed entities and relationships: company, target, indication, trial, and mechanism. This demo ships as a static JSON graph and renders entirely in the browser. It has no live Neo4j dependency and carries the conservative label the page promises: implemented on synthetic data.

Loading graph module...

Static asset: /racap-poc/kg-triples.json · node color by entity type · click a node for its triples · filters run client-side.

Insight -> NarrativeImplemented · synthetic data

From corpus to cohesive stories: the narrative pipeline

The JD asks for cohesive stories and actionable narratives for the investing team. The Semantic Triple Transformation pattern is the communication layer: research is structured once, then rendered into the right artifact for the decision. In a fund setting, benchmark deltas matter only when they change a workflow, a screen, or a risk posture.

01

Research corpus

Public filings, trial registries, literature, market notes, and analyst questions enter as source material.

02

Semantic triples

Entities and relationships become portable claims: company, target, indication, trial, mechanism, evidence.

03

Narrative outputs

The same structured payload can become an analyst note, longform dispatch, infographic JSON, dashboard, or briefing memo.

04

Distribution surface

The final artifact is tuned to the decision venue: investment meeting, diligence dashboard, partner update, or public proof.

Worked exampleAgentic Content Marketing / STT pipelineExisting on-domain example of research ingestion, schema, narrative outputs, crawler-facing mirror content, and distribution copy. For QRS, the same transformation becomes analyst-facing communication.Open receipt ->
Synthetic analyst noteImplemented · synthetic data

A synthetic complement-biology readout moved from “interesting” to “position-review required” after the graph linked the sponsor, C5aR1 mechanism, and PNH indication to a near-term trial node. The structured data does not make the investment call; it narrows the question. The uncertainty band remains wide because the evidence is registry-level and lacks validated efficacy deltas. The action is therefore not “buy” or “sell.” It is a diligence queue: verify freshness, compare mechanism neighbors, inspect ownership tier, and decide whether the event belongs on the risk calendar.

Deterministic Grounding · Split-ViewIllustrative / synthetic data

The LLM proposes; the deterministic layer disposes

A VC financial model cannot run on stochastic outputs. This architecture visibly decouples the two: a probabilistic model extracts entities and relationships from unstructured filings, and a deterministic rule layer — not a model — adjusts the Probability-of-Success score by explicit, auditable percentages. The extraction is allowed to be fuzzy; the calculus is not.

Left · Probabilistic extraction (Claude)
Source span · mock 14D-9 excerpt (verbatim)
“…the tender offer values each share at $47.00 in cash, plus one non-tradeable contingent value rightper share. The Company's lead asset, zavolimab, did not meet its Phase II primary endpointin the ORION-2 study, though a pre-specified secondary showed…”
Extracted relationship triple
(sponsor: Corvex Bio)
   ──[acquires_via_tender]──▶ (target: Halcyon Rx)
(target: Halcyon Rx)
   ──[develops]──▶ (drug: zavolimab)
(drug: zavolimab)
   ──[failed_endpoint]──▶ (Phase II primary)
(deal: 14D-9)
   ──[includes]──▶ (structure: CVR)

Fuzzy by design — the model reads text. Its output is a proposal, not a number the model is trusted to compute.

Right · Deterministic grounding (rule layer)
PoS adjustment ledger · fixed rules, no model
Phase II primary endpoint miss−18%
CVR (contingent value right) present in 14D-9+6%
Material Adverse Effect clause flagged
Specialist-investor Core holder on register
base_PoS      = 0.41
  endpoint miss   −0.18
  CVR present     +0.06
─────────────────────────
grounded_PoS  = 0.29
0.410.29Same inputs, same output, every time. The triggering rule is shown, not inferred — an analyst can audit the delta.
Ingest14D-9 excerptLLM extractionNER + tripleDeterministic validationrule layerGrounded scorePoS adjustedDelta Lake exportprovenance kept

The failure this prevents: an LLM asked to “score” the deal directly can hallucinate a Probability-of-Success anywhere in a wide band on identical text. Here the model never touches the arithmetic — it proposes structured facts, and a deterministic layer disposes the score. Excerpt, drug, and sponsor are all synthetic.

The Differentiator · Evals

Evaluation frameworks — and their limitations in high-stakes settings

An AI workflow an investment team can trust is an evaluated workflow. This is the harness around every pipeline on this page — each component graded honestly: implemented with a receipt, implemented on synthetic data, or spec.

Citation faithfulness — verbatim substring verification

Implemented

Every generated claim must substring-match its source document verbatim, or it gets flagged before a reader ever sees it. This is not a spec: the mechanism is built and deployed in the Anthropic Book corpus project on this domain — 727 source documents, a ~1.4M-word corpus, embedding-based retrieval, and the verifier gating every citation. The RACap-POC adopts the same verifier as its faithfulness gate: a generated insight that cannot point to its exact source text does not ship to an analyst.

Golden-set regression

Spec

A curated set of question → expected-answer pairs per pipeline, versioned alongside the code. Deploys gate on passing — a retrieval change that silently breaks the danger-zone screen fails CI before it reaches the investment team. Spec, honestly labeled: the sets are designed but not yet curated.

Retrieval quality metrics

Spec

Recall@k and MRR against the golden set, reported per pipeline — because a RAG system that retrieves the wrong filings answers confidently from the wrong world. Depends on the golden sets above, so it inherits their spec status.

LLM-as-judge with rubric + human spot-check ratio

Spec

Rubric-scored judge models for qualities substring checks cannot catch — coherence, completeness, tone. Known limitation, stated up front: judge-model bias and rubric drift are real; that is exactly why a fixed human spot-check ratio exists rather than trusting the judge unsupervised.

Deterministic governance — Claude Code lifecycle hooks

Implemented

PreToolUse/PostToolUse hooks as enforcement, not suggestion: allow / deny / ask decisions with full audit logging, built into the skill layer's governance rail and the SkillMemoryBank governance layer. Deterministic hooks beat prompt-only guardrails for financial and clinical data for three reasons: prompt injection can rewrite a model's instructions but not an external hook; adherence to prompted rules degrades under long-context load while a hook fires every time; and subagents that never saw the system prompt still hit the same perimeter.

Known failure modes · and what this stack does about them
Failure modeWhy it matters at an investment firmMitigation in this stack
Hallucination under sparse retrievalFalse confidence exactly where evidence is thinnest — early-stage assets, rare indicationsVerbatim substring verifier + abstention threshold: no matched source, no claim
Temporal drift / knowledge cutoffA stale catalyst date or superseded trial status quietly poisons an event calendarPer-record provenance timestamps + freshness alarms (data-quality section below)
Entity-linking ambiguity — ticker vs. molecule vs. program nameInsights attributed to the wrong company or asset; the worst kind of confident errorLinked-dataset IDs + a disambiguation pass in the knowledge-graph pipeline
Silent schema drift in upstream sourcesA renamed field corrupts every downstream mart without a single loud failurePydantic validation at ingestion + drift alarms before writes reach silver/gold
Overconfident point estimatesA single P(M&A) number invites mis-sized positionsUncertainty surfacing — MC-Dropout std bands in ra-danger-zone — and a decision-support, not advice, posture

Calibration humility: the METR 2025 randomized controlled trial found experienced developers using AI tools were 19% slower on familiar codebases — which is why this stack measures its productivity and quality claims instead of assuming them.

And the intellectual anchor: the Expert Judgment Layer on this page covers the Thinking Machines Lab / Bridgewater result — the strongest public evidence that replicating expert judgment is an evaluation problem before it is a modeling problem. The fine-tune won because the team could measure expert agreement precisely enough to train against it.

Scale Path · Spark + SQLIllustrative schema — synthetic data

Spark (PySpark), SQL, and Python — the same logic at universe scale

Python is everywhere on this page. This section shows the other two-thirds of the JD's stack line: the danger-zone feature computation ported pandas → PySpark as a real diff, the Delta storage layout it would run against, and the SQL an analyst would put on top. The point is fluency, not a claim of production deployment.

Before · pandas (in-memory, n=50)
# src/ra_metrics.py — pandas
# (this is what scores the universe on this page)
result["cash_runway_years"] = (
    result["cash_equivalents"] / result["annual_burn_rate"]
)
result["burn_to_cap_ratio"] = (
    result["annual_burn_rate"] / result["market_cap"]
)
result["danger_zone"] = (
    (result["cash_runway_years"] < 2.0) &
    (result["burn_to_cap_ratio"] > 0.25)
)
result["ownership_tier"] = result[
    "specialist_ownership_count"
].map(_tier)
result["below_cash"] = (
    result["market_cap"] < result["cash_equivalents"]
)
After · PySpark (partitioned, lazy)
# src/ra_metrics_spark.py — PySpark
# (same logic, declared for a full-universe Delta lake)
df = (
    df.withColumn("cash_runway_years",
        F.col("cash_equivalents") / F.col("annual_burn_rate"))
      .withColumn("burn_to_cap_ratio",
        F.col("annual_burn_rate") / F.col("market_cap"))
      .withColumn("danger_zone",
        (F.col("cash_runway_years") < F.lit(2.0)) &
        (F.col("burn_to_cap_ratio") > F.lit(0.25)))
      .withColumn("ownership_tier",
        F.when(F.col("specialist_ownership_count") == 0, F.lit(0))
         .when(F.col("specialist_ownership_count") <= 2, F.lit(1))
         .otherwise(F.lit(2)))
      .withColumn("below_cash",
        F.col("market_cap") < F.col("cash_equivalents"))
)

# spark-submit --master 'local[2]' src/ra_metrics_spark.py

What actually changes at scale: the pandas version makes five sequential in-memory passes; the Spark version declares five narrow, partition-local transformations that Catalyst fuses into one code-generated stage, executed lazily at the first action — and the only shuffle in the whole job is the final tier aggregate. Partitioning and shuffle placement, not syntax, are the real port.

SpecPort shipped as runnable code + command in the repo; not executed in the environment that built this page (no JVM available) — stated plainly rather than implied.
Target storage layout · medallion on Databricks Delta
BRONZEraw, as-landed, immutable· Filings· trial registries· literature dumps· transcriptsSILVERconformed and trustworthy· Parsed· deduplicated· Pydantic-validated· provenance-stampedGOLDanalyst-queryable marts· Star-schema marts feeding the pipelines and dashboards

Target production layout, consistent with the existing Delta export in ra-danger-zone (db_export.py) — bronze keeps the evidence, silver earns the trust, gold answers the questions.

SQL evidence · star schema + three analyst queries
DDL · gold.fact_catalyst + dimensions
-- illustrative star schema — synthetic data
CREATE TABLE IF NOT EXISTS gold.fact_catalyst (
  catalyst_id    BIGINT,
  company_key    BIGINT,     -- -> gold.dim_company
  trial_key      BIGINT,     -- -> gold.dim_trial
  program_key    BIGINT,     -- -> gold.dim_program
  mechanism_key  BIGINT,     -- -> gold.dim_mechanism
  event_type     STRING,     -- readout | pdufa | adcom | loe
  expected_date  DATE,
  confidence     DOUBLE,     -- provenance-weighted
  source_url     STRING,     -- per-record provenance
  retrieved_at   TIMESTAMP,
  content_hash   STRING
) USING DELTA;
-- dim_company / dim_trial / dim_program / dim_mechanism
-- follow the same pattern: surrogate key, natural ids,
-- slowly-changing attributes, provenance columns.
Q1 · Event-risk calendar across a holdings list
SELECT c.ticker, f.event_type, f.expected_date
FROM gold.fact_catalyst f
JOIN gold.dim_company c USING (company_key)
JOIN holdings h ON h.ticker = c.ticker
WHERE f.expected_date
  BETWEEN current_date() AND date_add(current_date(), 90)
ORDER BY f.expected_date;

What an analyst learns: The next 90 days of binary-event exposure across the book, in one pass — the trial-readout calendar builds itself.

Q2 · Cash-runway screen surfacing below_cash names
SELECT c.ticker, m.cash_runway_years,
       m.below_cash, m.ownership_tier
FROM gold.semper_maior_metrics m
JOIN gold.dim_company c USING (company_key)
WHERE m.below_cash AND m.ownership_tier = 2  -- Core+
ORDER BY m.cash_runway_years;

What an analyst learns: Core+ names the market prices below their own cash — the mispriced-optionality screen. Reuses the ra-danger-zone below_cash flag scored on this page.

Q3 · Mechanism-cluster concentration
SELECT mech.mechanism,
       COUNT(DISTINCT p.company_key) AS names,
       SUM(c.market_cap)             AS cluster_cap
FROM gold.dim_mechanism mech
JOIN gold.dim_program  p USING (mechanism_key)
JOIN gold.dim_company  c USING (company_key)
GROUP BY mech.mechanism
HAVING COUNT(DISTINCT p.company_key) >= 5
ORDER BY cluster_cap DESC;

What an analyst learns: Where the (synthetic) universe crowds into the same mechanism — a correlation and crowding lens before adding a correlated name.

Warehouse Export · Databricks Delta

The QRS team lives in Databricks, PySpark, and Snowflake. The top-of-page receipt links to a real Free Edition Delta table and published dashboard; the terminal below remains a SIMULATED stream showing how the production export would report schema checks, parquet writes, and Delta commits.

Live receipt table: workspace.racap_gold.semper_maior_metricsPublished dashboard →Notebook →
db_export.py · workspace.racap_gold.semper_maior_metricsSimulated

The scored universe writes to a Databricks Delta table with schema enforcement and tier partitioning. Open the export to watch the (simulated) PySpark job stream its logs — schema check, JSON → Parquet, partition write, and the version commit. This log is illustrative — the same medallion path now runs live on Databricks Free Edition (see receipt above).

Live Scenario Dashboard · Plotly Dash

A self-service PM tool built on the pipeline's gold-layer output.

Embedded preview — falls back to the button above if the host blocks framing

If the embed above stays blank, the host is blocking iframe embedding — use the button instead.

Receipts

Verifiable artifacts mapped to the JD

This strip carries the unstructured-data requirement through proof volume and inspectable artifacts. No tenure claim, no inflated numbers, no private-client details.

RAG + eval727-document / ~1.4M-word corpusVoyage AI retrieval, 21.2k chunks, and verbatim substring verification for citation faithfulness.Maps to: Vector retrieval systems; evaluation frameworks.OPEN ->GovernanceSkillMemoryBankLane 2 Best in Show at The Open Accelerator Agent Build Day, Boston, June 27, 2026.Maps to: Limitations in high-stakes settings; governed memory compression.OPEN ->Remediationra-danger-zone audit trailThe POC was corrected toward real pipeline output, MC-Dropout uncertainty, and explicit synthetic labels.Maps to: Data quality and integrity; limitations surfaced before claims.OPEN ->Research writingArchitectural DeterminismPublic preprint and research artifact connecting technical architecture to institutional behavior.Maps to: Cross-domain synthesis; executive-ready narrative.OPEN ->DeliveryRecurring enterprise consultingCybersecurity-sector engagement, described without confidential client details or dollar figures.Maps to: Enterprise delivery under constraints.OPEN ->
Data Quality

Data quality and integrity: collection, processing, and storage

The stack is designed around a simple discipline: the analyst should know where a claim came from, when it was retrieved, how it was transformed, and whether it is production-real, synthetic, or design-only.

Partial-schema-tolerant Pydantic validation

PY-01 tolerates missing fields without silently accepting malformed records; invalid edges stay out of the graph.

Deduplication + content checksums

Every bronze record carries a SHA-256 content hash; silver deduplicates on it before validation.

Per-record provenance ledger

Source URL, retrieval timestamp, parser version, content hash, and claim lineage travel with the record.

Schema-drift alarms

Unexpected field loss, type changes, or enum expansion should stop writes before silver/gold tables update.

Medallion storage layout

Live on Free Edition: bronze keeps raw + provenance, silver enforces five CHECK expectations with a quarantine sibling, gold feeds the published dashboard.

Golden-set regression check

A SQL assertion verifies gold-layer counts and tier means against the published seed=42 summary before anything ships.

Human review gates

The current page separates verified, background, synthetic, and spec claims before a reader consumes them.

Storage note

The storage layout references the medallion diagram in Scale Path: bronze for raw public sources, silver for parsed and validated records, gold for analyst-queryable marts feeding dashboards and retrieval workflows.

If Hired

The first 90 days on QRS

The plan is deliberately institutional. A useful QRS workflow is not just a good demo; it is a governed system that matches how the investing team actually works.

Days 1-30

Map the institution before shipping

Learn RA's actual data estate, compliance perimeter, and the investment team's real query patterns. Inventory tooling, source systems, and current dashboards. Ship nothing broad; map everything carefully.

Days 31-60

Ship one narrow eval-gated workflow

Choose one retrieval workflow with the investment team, wire provenance from day one, and add the substring-verifier faithfulness gate before anyone treats the output as decision support.

Days 61-90

Operationalize and hand off

Move golden-set regression into CI, bring the provenance ledger live, document the workflow, and make sure the system survives without its author sitting next to it.

Semper Maior · III
"One pipeline is a demo. Three interlocking systems are a practice."
The rest of the page is the practice.
The Systems Layer · Beyond This POC

One pipeline is a demo. Three interlocking systems are a practice.

ra-danger-zone is one output of a larger research architecture I build and operate in public. The same discipline on this page — typed classification logic, validation gates, honest synthetic labels — runs at system scale across three live builds: a recursive research orchestrator, a preference-data labeling harness, and the open-source skill arsenal that powers both.

01 · ORCHESTRATIONMoEA LoopA typed rewrite system that drives research skills into a self-extending, auditable research tree. Seven fork primitives, a novelty ledger that terminates saturated branches, and an in-loop → on-loop → out-of-loop autonomy ladder gated by verification.contextjamming.com/moea-loop →02 · DATA ECONOMICSMoEA LabelerA preference-data pipeline attacking the 50–500× cost gap between expert labels and the compute they train. Ships with a validation backbone — κ ≥ 0.60 against human gold sets, bias audits, and a cited "what this cannot do" section. Same honesty standard as the synthetic universe above.contextjamming.com/MoEA-labeler →03 · DISTRIBUTIONClaude Code SkillsThe open-source arsenal both systems run on: anchored deep-research prompting, semantic triple transformation, self-gating dev docs. Apache 2.0 downloads plus paid perpetual licenses — a working build-to-product motion, not just a repo.contextjamming.com/book/skills →

Why it matters for RA Capital: the loop is the research throughput engine, the labeler is the data-quality economics, and the skills are the distribution mechanism. Each one gates its own output before a human sees it — the same posture an investment team needs from any AI system it trusts.

Independent Academic Research Case Study

Architectural Determinism: from expert-agent orchestration to a formal AI/physics thesis.

A second proof point for RA Capital is not another web artifact; it is the research method behind it. I conducted an independent academic research program that connected theoretical physics, cognitive neuroscience, and frontier AI architecture, then turned that work into a LaTeX-orchestrated preprint, public explainer, diagrams, and audio overview.

Research claim under test

The project asks whether the doctoral priors behind frontier AI labs reappear as system architecture: Hassabis's UCL work on scene construction as a bottom-up simulation engine for DeepMind, and the AdS/CFT/holography lineage around Constitutional AI as a boundary-condition model for Anthropic-style alignment. The claim is framed as an isomorphism to test and qualify, not a loose metaphor to admire.

External signal

The work received endorsement from Dr. Herbert Roitblat, Chief Data Scientist Emeritus at Mimecast. I treat that as a serious expert signal, while keeping the artifact labeled as independent research rather than peer-reviewed publication.

01 · ORCHESTRATIONExpert-agent research deskUsed Gemini Deep Research, Claude Opus Deep Research, GPT, and Grok as adversarial specialist agents: source discovery, thesis pressure-testing, counterargument generation, and synthesis.
02 · FORMALIZATIONLaTeX as the control planeLearned enough LaTeX to move from conversational research into a structured academic artifact: equations, citations, diagrams, claims, caveats, and revision discipline.
03 · DOMAIN TRANSFERPhysics-to-AI mappingBuilt enough theoretical-physics fluency to identify and formalize the AdS/CFT-to-Constitutional-AI boundary analogy, then separated rigorous structure from conjecture.
04 · BIOLOGICAL PRIORSHassabis scene constructionConnected Hassabis's PhD work on episodic memory and scene construction to DeepMind-style world modeling: reconstruct scenes, bind fragments, simulate futures, then search.

RA Capital relevance: this is the same muscle the QRS role needs — convert unfamiliar technical domains into explicit claims, audit the evidence, use frontier models as research instruments, and ship the result in a form experts can challenge.

Read the case study →

Field report · AI biology · July 2026

The Silicon Synthesis

A field report on the moment biology stopped behaving like a descriptive archive and started behaving like an engineering surface.

I. The Hit Rate

Spring arrived in a 96-well plate.

Chai Discovery's spring 2026 demonstration had the grammar of a small lab note and the consequence of a new operating system. One 96-well plate. A target with no prior functional binder. A set of proposed antibodies sent into the wet lab. Then the result: 20% bound. In a field where historical computational baselines treated de novo antibody binding as a near-miracle, the signal read like a discontinuity.

The number is the story because the plate was not a visualization. It was a physical adjudicator. The proposed leap was about 100× over the historical baseline, and the crucial word is over. The model did not merely summarize literature. It made a bet about molecular reality, then reality answered.

Biology is no longer only a body of descriptions. It is becoming a medium engineers can compile against.

II. The Engineering Turn

The limiting factor moved.

The old biology was a descriptive science because its deepest objects were too small, too dynamic, and too interdependent to command. The question was whether a mechanism existed at all. Now the question has shifted. The limiting factor is less often biological risk in the old sense and more often data quality, computational fidelity, and whether the model has seen enough of life's state space to generalize.

That is why the AI biology story belongs on an RA Capital proof artifact. It is a market-structure story disguised as a lab story. When biology becomes data plus compute, the moat moves: from owning a hypothesis to owning the feedback loop that tells the hypothesis when it is wrong.

III. The Bitter Lesson

Anton lost to the general machine.

David Shaw's Anton represented one theory of biological computation: hand-coded molecular dynamics burned into specialized silicon, a machine built to simulate physical motion from first principles. AlphaFold 3 represented the other theory: diffusion plus Pairformer, running on commodity GPUs, learning from the shape of biological data itself.

hand-coded physicsAntonspecialized silicon
scaled transformerscommodity GPUsevolutionary data

The Bitter Lesson in the wet lab is not that physics stopped mattering. It is that scalable learning systems learned to carry more of the physics than the hand-built machinery could encode. Boltz-1/2 from MIT Jameel Clinic delivered open-source AF3-class performance. Isomorphic's IsoDDE pushed further by modeling induced fit, outperforming AF3 by 2.3× on antibody-antigen prediction. The center of gravity moved from specialized machines to general systems trained against enough biology.

IV. Scaling Laws Meet Metagenomics

The training set became the planet.

Evolutionary Scale's ESMC models were trained on 2.8–6.8B raw environmental sequences. The ESM Atlas now holds more than 1.1B predicted structures. The importance of the metagenomic turn is not just volume. It is distribution. Raw environmental sequence pulls the model out of curated human databases and into the grammar produced by evolution itself.

Then the black box started giving up recognizable parts. Sparse autoencoders applied to the 6B-parameter ESMC, expanding a 2,560-dimensional hidden state into a 16,384-dimensional codebook at layer 60, spontaneously isolated the nucleophilic elbow, catalytic triads, Rossmann folds, and P-loops. On 4,868 SwissProt microbial enzymes, the result was 78.9% top-1 enzyme function accuracy, 37.6% over sequence-ML baselines and approaching BLASTp.

The model did not memorize the protein universe. It found handles inside it.

V. The Virtual Cell

From protein maps to cellular weather.

The Chan Zuckerberg Initiative's Virtual Biology Initiative is the systems-level version of the same bet: build models that can reason across cells, perturbations, and species instead of stopping at single proteins. Its commitment is $500M toward the data foundation for AI-accelerated biology.

TranscriptFormer trained on 112M cells across 12 species and 1.53B years of evolution, then showed zero-shot behavior on rhesus and marmoset. rBio adds a reasoning layer trained with reinforcement learning and soft biological-accuracy rewards. This is the Virtual Cell idea in miniature: not a single model, but a stack where simulated perturbation, cellular state, and natural-language explanation begin to share a common surface.

VI. Agentic Science and the Taste Bottleneck

The agents can read. Taste is harder.

DeepMind's Co-Scientist uses an Elo tournament to rank and refine hypotheses. Future House and Edison Scientific's Kosmos has read 1,500 papers, executed 42,000 lines of code, and produced a fully cited report in a single run. The direction is unmistakable: the scientific method is being unbundled into search, critique, experiment design, execution, and synthesis.

But interpretation remains stubborn. Experts agree only about ~70% of the time on complex biological interpretation. That is the taste bottleneck. RLHF can reward a plausible answer, but the frontier question is whether a system can learn the judgment that distinguishes an elegant dead end from a program of work.

VII. The Data Wall and Wet-Lab Moats

Data quality becomes strategy.

The strongest AI biology companies are not only model companies. They are data-loop companies. Edison and Incyte point toward a compounding feedback loop, where proprietary experiments improve the system that chooses the next experiment. AbInitio's proprietary biomanufacturing data suggests a different moat, closer to process intelligence than target discovery. CZI's Billion Cells effort with 10x, Ultima, and Scale Bio pushes the public-data side of the same thesis.

Focused Research Organizations fill the middle. Cultivarium, Parallel Squared, and E11 Bio are not merely philanthropic curiosities. They are infrastructure repairs: tools and datasets that academia struggles to maintain, venture capital struggles to justify, and the next generation of biological models may require.

VIII. Programmable Biology in the Clinic

The proof has to leave the screen.

The clinic is where programmable biology stops being a metaphor. Four rows matter because they are not concept art. They are named assets, named targets, and named stages moving through the slow machinery of medicine.

AbsciABS-201anti-PRLRPh 1/2a
Generate BiomedicinesGB-0895anti-TSLPPh 3
RelayRLY-2608pan-mutant PI3KαFDA Breakthrough · 43% ORR at Ph 3 dose
RecursionREC-617 / REC-4881CDK7 / MEKstage not specified in dispatch

The lesson for investors is not that every computational molecule works. The lesson is that the translation surface is now visible: design, bind, validate, manufacture, dose, measure, and feed the result back into the system.

IX. Coda

The failure rate becomes a systems problem.

The 90% clinical failure rate does not vanish because a model can generate a binder. It becomes, in principle, a computational problem: toxicity, off-target effects, developability, patient stratification, trial design, and manufacturing constraints all become surfaces to model, test, and improve.

The institutions that treat biology as data plus compute will define the next era of medicine. The institutions that treat it as a prettier literature search will miss the turn. The Silicon Synthesis is the moment the laboratory, the model, and the capital stack begin to share one grammar.

Field report compiled from the Silicon Synthesis dispatch · Context Jamming · ACRA Insight · July 4, 2026
Collaborative Architect · Open Questions

Three questions for the QRS team

A POC is a set of answers; the better signal is the quality of the questions behind it. These are the three I would want to work through with the team in the first weeks — each one is a real fork in the architecture, not a rhetorical flourish.

Q1Parsing reliability

What accuracy bar does the team hold extraction to on the hardest documents — 14D-9 deal terms and binary trial readouts — and how is that measured today? The deterministic-grounding split-view on this page assumes the extraction is fuzzy and the calculus is not; I want to calibrate that threshold to how QRS already grades it.

Q2Static → dynamic

Where does a static TechAtlas landscape map stop earning its keep and a dynamic, queryable knowledge graph start? The PY-01 graph here is one answer; I want to understand which questions the team wishes it could ask of the map but currently cannot.

Q3Open weights vs. APIs

For high-stakes triage, where does the team draw the line between a fine-tuned open-weight model (the CISPO / Tinker path above) and a commercial API — on cost, on MNPI containment, on the ability to preserve minority-token reasoning signal? This is the most consequential architecture decision and I would rather debate it than assume it.

Explainer · NotebookLM

Biotech M&A 2026 Playbook

An AI-generated video walkthrough (NotebookLM) built from RA Capital's Semper Maior 2026 report — the same thesis this pipeline encodes into Danger Zone and ownership-tier signals.

Read the Semper Maior 2026 report →
Compliance Posture

Public-data decision-support artifact

All data shown is synthetic or from public sources; no material non-public information is used or sought. Outputs are decision-support infrastructure, not investment advice or recommendations. Built independently; no RA Capital confidential information was used. RA Capital and division names are referenced for illustrative mapping only; trademarks belong to their owners.

In memory of Dr. Bret Ratner (1893–1957), immunologist and pioneer of pediatric allergy research — proof that betting on rigorous science to improve human health runs in the family. → founder-files/ratner

Filed by Bret Kerr · ACRA Insight LLC · Franklin, MA
RA Capital · QRS Healthcare AI Associate · Interview Artifact
No external APIs run on this page · All data is synthetic (seed=42)