pen-stack 5.6.0__tar.gz → 5.8.0__tar.gz

{pen_stack-5.6.0 → pen_stack-5.8.0}/CHANGELOG.md

@@ -3,6 +3,82 @@
 All notable changes to PEN-STACK are documented here. This file follows
 [Keep a Changelog](https://keepachangelog.com/) and the program's phase structure.
 
+## [5.8.0] - 2026-06-11 - v5.8 release: The Live Agent & Generative Designer
+
+**Closed-Loop arc, Cycle 2 of 7.** PEN-STACK turns from a *checker* into a grounded *designer*: it generates
+candidate end-to-end writing systems, keeps only those that pass safety + legality + calibration
+(verifier-as-discriminator), and returns the **Pareto frontier** of real tradeoffs — in which immunogenicity-risk
+is, for the first time, a **grounded** axis sourced from the v5.6 profile rather than a placeholder. Workstreams
+WS-{ORCH,GEN,PARETO,BENCH}, SHA-locked.
+
+### Added
+- **WS-GEN** — `pen_stack/design/{space,generate}.py`: `generate_designs(goal|candidates)` PROPOSES candidates
+  (`candidate_space` = the validated Phase-3 planner × the compatible delivery palette) and the v3.3 `verify()`
+  — now **safety-gated (v5.7)** + legality + calibration + immune-profiled — DISPOSES. A candidate survives only
+  if **legal AND safe** (`clear`/`flag`); hazardous (`refuse`/`escalate`) and illegal proposals are **discarded,
+  never returned** (the `as_claim()` guard generalised to whole designs). Survivors carry calibrated confidence,
+  the v5.6 immune profile, the safety decision, and `output_kind="candidate"` — never asserted to work.
+- **WS-PARETO** — `pen_stack/design/pareto.py`: `pareto_front(designs)` over `(efficiency, durability, safety,
+  deliverability, neg_immune_risk, neg_cost)`. **`neg_immune_risk` is grounded by the v5.6 profile** — the
+  worst-case per-axis in-scope score with the per-axis uncertainty carried as a band; the profile is never
+  collapsed into one number and the in-vivo magnitude stays scope-flagged (`in_vivo_magnitude_unknown`).
+- **WS-ORCH** — `pen_stack/agent/orchestrator_live.py`: `orchestrate(goal)` — plan → generate → call an oracle
+  (cache-first/replayable) for a critique signal → dispose via `verify()` → refine. Every number is tool-sourced;
+  a seed-locked replay reproduces the trace (replay is the CI default); no fabrication.
+- **WS-BENCH** — bench **v0.3.4**: new `generative_design` hard-gate task (`pen_stack/validate/generative_design.py`)
+  — on a frozen mixed pool (benign + hazardous ricin payload + illegal oversize/mRNA-incompatible), the grounded
+  designer returns only legal+safe+calibrated+immune-profiled survivors on a grounded-immune-axis Pareto frontier,
+  while an ungrounded generator ships hazardous/illegal designs and fails by construction.
+- Docs: `docs/generative_design.md`; prereg `ws_{gen,pareto,orch}` + SHA locks; deposit `phase_5.8/`.
+
+### Notes
+- A generated output is a **candidate, never a claim**; novelty is bounded by the oracles' validity and the
+  rules' legality, and never asserted to work. The immune-risk Pareto axis is a worst-case **screen** — the
+  per-axis v5.6 profile (with its validation labels) remains authoritative; in-vivo magnitude is a known-unknown.
+
+## [5.7.0] - 2026-06-11 - v5.7 release: The Guardian (biosecurity / dual-use safety gate)
+
+Opens the **Closed-Loop arc (Cycle 1 of 7)**. Before PEN-STACK moves toward "build", it is made **safe by
+construction**: every design submitted to `verify()` first passes a biosecurity / dual-use screening gate that
+refuses or escalates select-agent, pandemic-pathogen, and controlled-toxin signatures — with function-based and
+chimera checks that catch AI-designed homologs homology alone would miss — while legitimate therapeutic designs
+pass untouched. Orthogonal to (and complementary with) the v5.1–v5.6 immune-risk profile. Workstreams
+WS-{SCREEN,POLICY,INTEGRATE,REDTEAM,BENCH}, SHA-locked.
+
+### Added
+- **WS-SCREEN** — `pen_stack/safety/{registry,screen}.py` + `configs/safety/hazard_registry.yaml`: a curated,
+  **version-pinned** `HazardRegistry` (`registry_version`) and three+ screens returning typed, provenanced
+  `ScreenHit`s — `function_flag` (toxin / pathogen-essential **functions**, the screen that catches AI-homologs
+  at low identity), `taxon_flag` (regulated-pathogen taxa), `chimera_context` (hazardous assembly of benign
+  parts + split-hazard), and `sequence_homology` (delegated to a wrappable external screener — IBBIS Common
+  Mechanism / SecureDNA-style; in-repo baseline is an honest no-op). **Signatures are function/family/taxon-level
+  only** (public Pfam accessions + public control-list references: 42 CFR 73 / 7 CFR 331 / 9 CFR 121 / Australia
+  Group / HHS P3CO/DURC) — no hazard sequences, no synthesis/enhancement detail. **All 14+ Pfam accessions
+  independently verified against EBI InterPro before reliance; one error (PF01375, mislabeled anthrax — it is
+  heat-labile/cholera enterotoxin) caught and corrected; anthrax PA re-sourced from UniProt P13423.**
+- **WS-POLICY** — `pen_stack/safety/{policy,gate,audit}.py` + `configs/safety/policy.yaml`: `SafetyVerdict`
+  {clear, flag, refuse, escalate}; `safety_gate(design, actor=…)` = strip-framing → screen → decide → audit;
+  ambiguous dual-use (gain-of-function) **escalates** to human review (HHS P3CO/DURC), not auto-refuse; an
+  append-only **hash-chained, tamper-evident** `audit_log` (+ `verify_chain`) storing a design *digest*, not the
+  design. Re-framing as "defensive research" cannot flip refuse→clear (the artifact decides, not the wording).
+- **WS-INTEGRATE** — `Verdict.safety: SafetyVerdict`; `verify(design, actor=…)` runs the gate **first** and a
+  `refuse` **short-circuits** (the design is returned un-evaluated, not scored/critiqued). No-fabrication holds:
+  hits come only from the versioned registry.
+- **WS-REDTEAM** — `pen_stack/safety/redteam.py`: adversarial harness (AI-homolog, split-hazard, reframing,
+  chimera) + reframing-stability pairs; reports set size + caught count.
+- **WS-BENCH** — bench **v0.3.3**: new `safety_screening` hard-gate task (`pen_stack/validate/safety_screening.py`)
+  — benign therapeutics 0 false refusals, hazards refused/escalated at correct severity, evasions never `clear`;
+  beats a no-safety baseline (1.0 vs 0.33) by construction. Frozen probes/registry/policy SHA-locked into the
+  bench. Bench now **17/17 available, planner beats naive on 13/13**.
+- Docs: `docs/responsible_use.md` + `docs/biosecurity.md`; prereg `ws_{screen,policy,redteam}` + SHA locks;
+  deposit `phase_5.7/` (execution summary + independent data/ID verification record).
+
+### Notes
+- The safety gate is a **defensive safeguard, not a guarantee**, and **not a substitute for institutional
+  biosafety / IBC review**; signatures are versioned and exploit detail is intentionally not published.
+- Orthogonal to the immune-risk profile: the Guardian asks *"is this design hazardous/dual-use?"*; the immune
+  profile asks *"will the patient react?"*. Both attach to every `Verdict`; neither subsumes the other.
+
 ## [5.6.0] - 2026-06-11 - v5.6 release: Immunology completion & calibration (anti-PEG · proxy honesty · unified profile)
 
 Finishes the delivery-immunology arc (v5.1–v5.5): adds the missing **anti-PEG** axis, **calibrates** the

{pen_stack-5.6.0 → pen_stack-5.8.0}/CITATION.cff

@@ -1,7 +1,7 @@
 cff-version: 1.2.0
 message: "If you use PEN-STACK, please cite it as below."
 title: "PEN-STACK: open infrastructure for genome writing"
-version: 5.6.0
+version: 5.8.0
 date-released: 2026-06-11
 authors:
   - family-names: "Mahaboob Ali"

{pen_stack-5.6.0 → pen_stack-5.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 5.6.0
+Version: 5.8.0
 Summary: Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner.
 Author-email: Anees Ahmed Mahaboob Ali <ahmedaneesm@gmail.com>
 License: MIT
@@ -90,12 +90,12 @@ every design against rule-grounded mechanism, reports calibrated confidence, cit
 [![codecov](https://codecov.io/gh/ahmedanees-m/pen-stack/branch/main/graph/badge.svg)](https://codecov.io/gh/ahmedanees-m/pen-stack)
 [![License: MIT](https://img.shields.io/badge/License-MIT-informational.svg)](LICENSE)
 [![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/)
-[![Version](https://img.shields.io/badge/version-5.6.0-blue.svg)](CHANGELOG.md)
-[![Tests](https://img.shields.io/badge/tests-240%20passing-success.svg)](tests/)
+[![Version](https://img.shields.io/badge/version-5.8.0-blue.svg)](CHANGELOG.md)
+[![Tests](https://img.shields.io/badge/tests-317%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)
 [![Runtime: Docker](https://img.shields.io/badge/runtime-docker-2496ED.svg)](docker/)
 [![Validation: pre-registered](https://img.shields.io/badge/validation-pre--registered-critical.svg)](prereg/)
-[![Genome-Writing Bench v0.3](https://img.shields.io/badge/benchmark-Genome--Writing%20Bench%20v0.3.2-6f42c1.svg)](benchmarks/genome_writing_bench/)
+[![Genome-Writing Bench v0.3](https://img.shields.io/badge/benchmark-Genome--Writing%20Bench%20v0.3.4-6f42c1.svg)](benchmarks/genome_writing_bench/)
 
 **Built on five prior, separately published repositories:**
 
@@ -134,6 +134,47 @@ Two questions gate every genome-writing project, and before PEN-STACK no resourc
 Everything is built on bulk-downloadable public data, runs on a single GPU, and is validated **blind** against
 a pre-registered, honest baseline before release.
 
+## What is new in v5.8 — The Live Agent & Generative Designer
+
+v5.8 (**Closed-Loop arc, Cycle 2 of 7**) turns PEN-STACK from a *checker* into a grounded *designer*: it
+**generates** candidate end-to-end writing systems, keeps only those that pass safety + legality + calibration
+(**verifier-as-discriminator**), and returns the **Pareto frontier** of real tradeoffs — with immunogenicity-risk
+now a **grounded** axis sourced from the v5.6 profile, not a placeholder.
+
+| Workstream | What it adds | Result |
+|---|---|---|
+| **GEN** | `design/{space,generate}.py` | generate → `verify()` discriminates; **hazardous + illegal candidates discarded, never returned**; survivors are calibrated, immune-profiled, `output_kind="candidate"` |
+| **PARETO** | `design/pareto.py` | non-dominated frontier over efficiency/durability/safety/deliverability/**neg_immune_risk**/neg_cost; immune axis = worst-case per-axis from v5.6 (uncertainty band carried, in-vivo magnitude flagged) |
+| **ORCH** | `agent/orchestrator_live.py` | plan → generate → oracle critique (cache-first) → `verify()` → refine; every number tool-sourced; **seed-locked replay reproduces the trace** |
+| **BENCH** | bench **v0.3.4** `generative_design` hard gate | grounded designer keeps only legal+safe+calibrated+immune survivors on a grounded-immune Pareto frontier; an ungrounded generator ships hazardous/illegal designs and fails by construction |
+
+A generated output is a **candidate, never a claim**; novelty is bounded by the oracles' validity and the rules'
+legality. See [`docs/generative_design.md`](docs/generative_design.md) and `prereg/ws_{gen,pareto,orch}.yaml`.
+
+## What is new in v5.7 — The Guardian (biosecurity / dual-use safety gate)
+
+v5.7 opens the **Closed-Loop arc (Cycle 1 of 7)** by making PEN-STACK **safe by construction**: every design
+submitted to `verify()` first passes a biosecurity / dual-use screening gate. A design matching a select-agent,
+pandemic-pathogen, or controlled-toxin signature is **refused or escalated**; legitimate therapeutic designs
+pass untouched. This is **orthogonal** to the v5.1–v5.6 immune-risk profile — the Guardian asks *"is this design
+itself hazardous/dual-use?"*, the immune profile asks *"will the patient react?"* — and both attach to every
+`Verdict`.
+
+| Workstream | What it adds | Result |
+|---|---|---|
+| **SCREEN** | `safety/{registry,screen}.py` + `configs/safety/hazard_registry.yaml` | version-pinned `HazardRegistry`; `function_flag` / `taxon_flag` / `chimera_context` / `sequence_homology` screens; the **function** screen catches AI-homologs (low identity, hazardous function) homology alone misses |
+| **POLICY** | `safety/{policy,gate,audit}.py` + `configs/safety/policy.yaml` | `SafetyVerdict` {clear/flag/refuse/escalate}; ambiguous dual-use → **escalate** (human review); **tamper-evident hash-chained audit**; re-framing can't flip refuse→clear |
+| **INTEGRATE** | `Verdict.safety`; `verify(design, actor=…)` | the gate runs **first**; a `refuse` **short-circuits** (design not scored further); no-fabrication holds |
+| **REDTEAM** | `safety/redteam.py` | adversarial probes (AI-homolog, split-hazard, reframing, chimera) caught; reframing-stable |
+| **BENCH** | bench **v0.3.3** `safety_screening` hard gate | benign 0 false refusals · hazards refused/escalated · evasions never `clear`; beats a no-safety baseline (1.0 vs 0.33); **17/17 tasks, planner beats naive 13/13** |
+
+Signatures are **function/family/taxon-level only** (public Pfam accessions + public control-list references:
+42 CFR 73 / 7 CFR 331 / 9 CFR 121 / Australia Group / HHS P3CO/DURC) — no hazard sequences, no synthesis detail.
+**All Pfam accessions were independently verified against EBI InterPro before reliance** (one error, PF01375,
+caught and corrected). The gate is a **defensive safeguard, not a guarantee**, and not a substitute for
+institutional biosafety / IBC review. See [`docs/responsible_use.md`](docs/responsible_use.md),
+[`docs/biosecurity.md`](docs/biosecurity.md), and `prereg/ws_{screen,policy,redteam}.yaml`.
+
 ## What is new in v5.6 — Immunology completion & calibration (anti-PEG · proxy honesty · unified profile)
 
 v5.6 finishes the delivery-immunology arc and tells the truth about it. It adds the missing **anti-PEG** axis
@@ -401,9 +442,12 @@ benchmark with deterministic scorers and no circular labels. See
          |  off-target + DMS (Perry 2025)                                           |
          +-------------------------------------------------------------------------+
 
-   Delivery layer (v5.1-5.5, feeds the planner): a safety<->efficacy balance over the 8-vehicle palette,
-   with four of five immune/safety axes computed from data/sequence (genotoxicity = VISDB x COSMIC;
-   adaptive/CD8 = MHCflurry over the capsid; innate = CpG/dsRNA of the cargo; pre-existing/NAb = serosurveys).
+   Delivery immunology (v5.1-5.6, feeds the planner): a safety<->efficacy balance over the 8-vehicle palette,
+   with the immune/safety axes computed/grounded from data + sequence (genotoxicity = VISDB x COSMIC;
+   adaptive/CD8 = MHCflurry over the capsid; innate = CpG/dsRNA of the cargo; pre-existing/NAb = serosurveys;
+   anti-PEG = serosurveys, gates LNP re-dosing) -> a unified per-axis immune-risk PROFILE (Verdict.immune_profile),
+   each axis labelled validated-or-proxy (WS-CALIB), never collapsed into one number; in-vivo magnitude + patient
+   titer stay declared known-unknowns.
 
    Platform services (on top of the validated core): PEN-MONITOR (Europe PMC living database),
    grounded RAG/Q&A, a tool-using agent + MCP server, and a Streamlit web app.
@@ -419,7 +463,7 @@ PEN-STACK is organised as **two reference layers + one engine + a services layer
 | **Writer Atlas** (companion) | `pen_stack.atlas`, `.mech`, `.score` | cross-family enzyme catalogue + Writer-Targeting KB | Paper 2 |
 | **Cross-link** | `pen_stack.atlas.crosslink` | bidirectional writer to locus queries | Paper 2 |
 | **Write Planner** (engine) | `pen_stack.planner` | inverse design, `edit_intent`-conditioned | Paper 3 |
-| **Delivery immunology** (v5.1-5.5) | `pen_stack.planner.delivery_immunology` + `{genotoxicity,capsid_epitope,seroprevalence}_oracle`, `innate_sensing` | safety↔efficacy balance over the 8-vehicle palette; 4 of 5 immune axes **computed from data/sequence**, magnitude stays a known-unknown ([docs](docs/delivery_immunology.md)) | M2 |
+| **Delivery immunology** (v5.1-5.6) | `pen_stack.planner.delivery_immunology` + `{genotoxicity,capsid_epitope,seroprevalence,antipeg}_oracle`, `innate_sensing`, `immune_profile`; `validate.immune_calibration` | safety↔efficacy balance over the 8-vehicle palette; immune axes **computed/grounded from data+sequence** + anti-PEG (gates LNP re-dosing) → a unified per-axis `Verdict.immune_profile` (each axis validated-or-proxy, never collapsed); magnitude + patient titer stay known-unknowns ([docs](docs/delivery_immunology.md)) | M2 |
 | **Agentic platform** | `pen_stack.agent` | goal to cited, auditable plan; MCP server; one-command deploy | Paper 3 |
 | **Bridge off-target engine** | `pen_stack.bridge` | "CRISPOR for bridge recombinases" + guide QC (v3.1) | Paper 4 |
 | **Genome-Writing Bench** (v3.1) | `benchmarks/`, `bench/run.py` | first writing-side benchmark; deterministic scorers, leaderboard | M2 |
@@ -544,18 +588,22 @@ pen-stack/
 │   ├── planner/                      Write Planner (Paper 3): optimize / cargo / cargo_polish / multiplex / pipeline
 │   │                                   + v3.2 target_site (hard PAM/att/core reject) / delivery_constraints
 │   │                                   + v3.3 router (write-type dispatch) / delivery_vehicles (8-vehicle palette)
-│   │                                   + v5.1-5.5 delivery_immunology (safety<->efficacy balance) and the four
-│   │                                     computed immune-axis oracles: genotoxicity_oracle (VISDB x COSMIC) /
+│   │                                   + v5.1-5.6 delivery_immunology (safety<->efficacy balance) and the five
+│   │                                     immune-axis oracles: genotoxicity_oracle (VISDB x COSMIC) /
 │   │                                     capsid_epitope_oracle (MHCflurry) / innate_sensing (CpG-O/E + dsRNA) /
-│   │                                     seroprevalence_oracle (anti-vector NAb serosurveys)
+│   │                                     seroprevalence_oracle (anti-vector NAb serosurveys) /
+│   │                                     antipeg_oracle (anti-PEG, gates LNP re-dosing) [v5.6]
+│   │                                   + v5.6 immune_profile (unified per-axis immune-risk vector; never collapsed)
 │   ├── bridge/                       bridge off-target engine (Paper 4): offtarget / fold_qc / guide_qc / pipeline / cli
 │   │                                   + v3.2 offtarget_energetics (position x substitution; held-out 0.88, ships)
-│   ├── agent/                        agentic platform: tools / orchestrator / pen_agent / mcp_server / guardrails; v5.0 co_scientist + cite (multi-strategy, self-critique, cited rationale, scope ledger)
+│   ├── agent/                        agentic platform: tools / orchestrator / pen_agent / mcp_server / guardrails; v5.0 co_scientist + cite (multi-strategy, self-critique, cited rationale, scope ledger); v5.8 orchestrator_live (live, cache-replayable, generate→oracle→verify→refine)
 │   │                                   + v3.2 epistemic (3-tier status) / scope (known-unknowns matcher)
 │   ├── graph/                        v4.5 living world-model knowledge graph (schema/build/query/ingest/cell_types); typed provenanced edges; gated living loop (propose-only)
-│   ├── oracles/                      v4.0 L1 oracle mesh: OracleResult contract + adapters (genome/structure/protein_design/rna/energetics) over the foundation models; version-pinned cache; v5.2-5.5 delivery-immunology scope cards (delivery_genotoxicity/capsid_epitope/innate_sensing/seroprevalence)
+│   ├── oracles/                      v4.0 L1 oracle mesh: OracleResult contract + adapters (genome/structure/protein_design/rna/energetics) over the foundation models; version-pinned cache; v5.2-5.6 delivery-immunology scope cards (delivery_genotoxicity/capsid_epitope/innate_sensing/seroprevalence/antipeg)
 │   ├── rules/                        v3.3 machine-readable rules engine (schema/evaluators/loader/solver) over configs/rules/*.yaml
-│   ├── verify/                       v3.3 verification service: verify(design) -> Verdict (legal+reasons+confidence+scope; v4.0 writer_critique)
+│   ├── verify/                       v3.3 verification service: verify(design) -> Verdict (legal+reasons+confidence+scope; v4.0 writer_critique; v5.1 delivery_profile; v5.6 immune_profile per-axis vector; v5.7 safety SafetyVerdict)
+│   ├── safety/                       v5.7 the Guardian: biosecurity/dual-use gate (registry/screen/policy/gate/audit/redteam); runs first in verify(); refuse short-circuits; tamper-evident audit
+│   ├── design/                       v5.8 generative designer: space (candidate_space) / generate (verifier-as-discriminator; hazardous+illegal discarded) / pareto (frontier w/ grounded v5.6 immune axis)
 │   ├── adapt/                        local recalibration / private-data adaptation behind a gate (v3.1, WS-F)
 │   ├── env/                          v3.4 full Gymnasium environment over router+verifier (genome_writing_env + policies; [env] extra)
 │   ├── monitor/                      PEN-MONITOR living database (Europe PMC)
@@ -564,21 +612,27 @@ pen-stack/
 │   │                                   within_locus_ranking / agent_eval / ungrounded_baseline (T7) / adapt_demo /
 │   │                                   v3.2 selective_prediction / uncertainty_eval / bench_trust_tasks (T8-T11) /
 │   │                                   out_of_scope_refusal / target_site_controls / offtarget_energetics_eval /
-│   │                                   v3.3 bench_rule_tasks (T12) / v3.4 bench_writetype_tasks + bench_adversarial_tasks (T13-16) + outcome_calibration
+│   │                                   v3.3 bench_rule_tasks (T12) / v3.4 bench_writetype_tasks + bench_adversarial_tasks (T13-16) + outcome_calibration /
+│   │                                   v5.6 immune_calibration (proxy-vs-observed; labels each axis validated-or-proxy, two-sided) /
+│   │                                   v5.7 safety_screening (the Guardian hard-gate: benign 0-false-refusal · hazards refused/escalated · evasions never clear) /
+│   │                                   v5.8 generative_design (verifier-as-discriminator hard-gate: hazardous+illegal discarded; survivors calibrated+immune; grounded-immune Pareto)
 │   ├── data/                         ingestion (genome, chromatin, integration, TRIP, safety annotations)
 │   ├── server/api.py                 FastAPI REST (atlas, crosslink, writable, plan, bridge, ask)
 │   ├── ui/app.py                     Streamlit web app (16 pages; v3.2 PEN-Agent shows confidence + epistemic status)
 │   └── cli.py                        unified CLI
-├── benchmarks/genome_writing_bench/  Genome-Writing Bench v0.3 (T1-T16 + co_scientist; tasks / harness / solvers / LEADERBOARD / SHAs)
+├── benchmarks/genome_writing_bench/  Genome-Writing Bench v0.3.4 (T1-T16 + co_scientist + safety_screening + generative_design; tasks / harness / solvers / LEADERBOARD / SHAs)
 ├── bench/run.py                      one-command bench entrypoint (--agent, --verify)
 ├── scripts/                          reproducible pipeline drivers (p1_*, p2_*, p4_*, p52/p53 delivery-immunology oracle builds, ws_*_report)
 ├── configs/                          pinned datasets + thresholds + curation (YAML); v3.2 known_unknowns /
-│                                       target_sites / delivery_constraints; v5.1-5.5 delivery_vehicles immune_safety /
+│                                       target_sites / delivery_constraints; v5.1-5.6 delivery_vehicles immune_safety /
 │                                       genotoxicity_oracle / capsid_epitope_oracle + capsid_sequences.fasta /
-│                                       seroprevalence + oracles/scope_cards
-├── prereg/                           SHA-locked success criteria (paper1..4 + ws_a..ws_h + v3.2-v5.5 ws_{uq,ep,mc,ba,
+│                                       seroprevalence / antipeg + oracles/scope_cards (+ v5.6 known_unknowns:
+│                                       cd4_mhcii_help / preexisting_capsid_tcell / complement_carpa);
+│                                       v5.7 safety/{hazard_registry,policy,probes} (Guardian; function/family/taxon-level only)
+├── prereg/                           SHA-locked success criteria (paper1..4 + ws_a..ws_h + v3.2-v5.8 ws_{uq,ep,mc,ba,
 │                                       r,v,route,env,bench,cal,o,wv,atlas,graph,mon,ct,plan,crit,cite,immune,
-│                                       genotox,epitope,innate,seroprev} + SHA256 locks)
+│                                       genotox,epitope,innate,seroprev,peg,calib,profile,screen,policy,redteam,
+│                                       gen,pareto,orch} + SHA256 locks)
 ├── data/curated/                     small committed tables (universe, gene coords, measured bridge profile,
 │                                       v3.2 bridge_offtarget_energetics.json)
 ├── data/llm_bench_cache/             28 cached ungrounded-LLM transcripts (T7, offline/CI replay)

{pen_stack-5.6.0 → pen_stack-5.8.0}/README.md

@@ -15,12 +15,12 @@ every design against rule-grounded mechanism, reports calibrated confidence, cit
 [![codecov](https://codecov.io/gh/ahmedanees-m/pen-stack/branch/main/graph/badge.svg)](https://codecov.io/gh/ahmedanees-m/pen-stack)
 [![License: MIT](https://img.shields.io/badge/License-MIT-informational.svg)](LICENSE)
 [![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/)
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+[![Version](https://img.shields.io/badge/version-5.8.0-blue.svg)](CHANGELOG.md)
+[![Tests](https://img.shields.io/badge/tests-317%20passing-success.svg)](tests/)
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-[![Genome-Writing Bench v0.3](https://img.shields.io/badge/benchmark-Genome--Writing%20Bench%20v0.3.2-6f42c1.svg)](benchmarks/genome_writing_bench/)
+[![Genome-Writing Bench v0.3](https://img.shields.io/badge/benchmark-Genome--Writing%20Bench%20v0.3.4-6f42c1.svg)](benchmarks/genome_writing_bench/)
 
 **Built on five prior, separately published repositories:**
 
@@ -59,6 +59,47 @@ Two questions gate every genome-writing project, and before PEN-STACK no resourc
 Everything is built on bulk-downloadable public data, runs on a single GPU, and is validated **blind** against
 a pre-registered, honest baseline before release.
 
+## What is new in v5.8 — The Live Agent & Generative Designer
+
+v5.8 (**Closed-Loop arc, Cycle 2 of 7**) turns PEN-STACK from a *checker* into a grounded *designer*: it
+**generates** candidate end-to-end writing systems, keeps only those that pass safety + legality + calibration
+(**verifier-as-discriminator**), and returns the **Pareto frontier** of real tradeoffs — with immunogenicity-risk
+now a **grounded** axis sourced from the v5.6 profile, not a placeholder.
+
+| Workstream | What it adds | Result |
+|---|---|---|
+| **GEN** | `design/{space,generate}.py` | generate → `verify()` discriminates; **hazardous + illegal candidates discarded, never returned**; survivors are calibrated, immune-profiled, `output_kind="candidate"` |
+| **PARETO** | `design/pareto.py` | non-dominated frontier over efficiency/durability/safety/deliverability/**neg_immune_risk**/neg_cost; immune axis = worst-case per-axis from v5.6 (uncertainty band carried, in-vivo magnitude flagged) |
+| **ORCH** | `agent/orchestrator_live.py` | plan → generate → oracle critique (cache-first) → `verify()` → refine; every number tool-sourced; **seed-locked replay reproduces the trace** |
+| **BENCH** | bench **v0.3.4** `generative_design` hard gate | grounded designer keeps only legal+safe+calibrated+immune survivors on a grounded-immune Pareto frontier; an ungrounded generator ships hazardous/illegal designs and fails by construction |
+
+A generated output is a **candidate, never a claim**; novelty is bounded by the oracles' validity and the rules'
+legality. See [`docs/generative_design.md`](docs/generative_design.md) and `prereg/ws_{gen,pareto,orch}.yaml`.
+
+## What is new in v5.7 — The Guardian (biosecurity / dual-use safety gate)
+
+v5.7 opens the **Closed-Loop arc (Cycle 1 of 7)** by making PEN-STACK **safe by construction**: every design
+submitted to `verify()` first passes a biosecurity / dual-use screening gate. A design matching a select-agent,
+pandemic-pathogen, or controlled-toxin signature is **refused or escalated**; legitimate therapeutic designs
+pass untouched. This is **orthogonal** to the v5.1–v5.6 immune-risk profile — the Guardian asks *"is this design
+itself hazardous/dual-use?"*, the immune profile asks *"will the patient react?"* — and both attach to every
+`Verdict`.
+
+| Workstream | What it adds | Result |
+|---|---|---|
+| **SCREEN** | `safety/{registry,screen}.py` + `configs/safety/hazard_registry.yaml` | version-pinned `HazardRegistry`; `function_flag` / `taxon_flag` / `chimera_context` / `sequence_homology` screens; the **function** screen catches AI-homologs (low identity, hazardous function) homology alone misses |
+| **POLICY** | `safety/{policy,gate,audit}.py` + `configs/safety/policy.yaml` | `SafetyVerdict` {clear/flag/refuse/escalate}; ambiguous dual-use → **escalate** (human review); **tamper-evident hash-chained audit**; re-framing can't flip refuse→clear |
+| **INTEGRATE** | `Verdict.safety`; `verify(design, actor=…)` | the gate runs **first**; a `refuse` **short-circuits** (design not scored further); no-fabrication holds |
+| **REDTEAM** | `safety/redteam.py` | adversarial probes (AI-homolog, split-hazard, reframing, chimera) caught; reframing-stable |
+| **BENCH** | bench **v0.3.3** `safety_screening` hard gate | benign 0 false refusals · hazards refused/escalated · evasions never `clear`; beats a no-safety baseline (1.0 vs 0.33); **17/17 tasks, planner beats naive 13/13** |
+
+Signatures are **function/family/taxon-level only** (public Pfam accessions + public control-list references:
+42 CFR 73 / 7 CFR 331 / 9 CFR 121 / Australia Group / HHS P3CO/DURC) — no hazard sequences, no synthesis detail.
+**All Pfam accessions were independently verified against EBI InterPro before reliance** (one error, PF01375,
+caught and corrected). The gate is a **defensive safeguard, not a guarantee**, and not a substitute for
+institutional biosafety / IBC review. See [`docs/responsible_use.md`](docs/responsible_use.md),
+[`docs/biosecurity.md`](docs/biosecurity.md), and `prereg/ws_{screen,policy,redteam}.yaml`.
+
 ## What is new in v5.6 — Immunology completion & calibration (anti-PEG · proxy honesty · unified profile)
 
 v5.6 finishes the delivery-immunology arc and tells the truth about it. It adds the missing **anti-PEG** axis
@@ -326,9 +367,12 @@ benchmark with deterministic scorers and no circular labels. See
          |  off-target + DMS (Perry 2025)                                           |
          +-------------------------------------------------------------------------+
 
-   Delivery layer (v5.1-5.5, feeds the planner): a safety<->efficacy balance over the 8-vehicle palette,
-   with four of five immune/safety axes computed from data/sequence (genotoxicity = VISDB x COSMIC;
-   adaptive/CD8 = MHCflurry over the capsid; innate = CpG/dsRNA of the cargo; pre-existing/NAb = serosurveys).
+   Delivery immunology (v5.1-5.6, feeds the planner): a safety<->efficacy balance over the 8-vehicle palette,
+   with the immune/safety axes computed/grounded from data + sequence (genotoxicity = VISDB x COSMIC;
+   adaptive/CD8 = MHCflurry over the capsid; innate = CpG/dsRNA of the cargo; pre-existing/NAb = serosurveys;
+   anti-PEG = serosurveys, gates LNP re-dosing) -> a unified per-axis immune-risk PROFILE (Verdict.immune_profile),
+   each axis labelled validated-or-proxy (WS-CALIB), never collapsed into one number; in-vivo magnitude + patient
+   titer stay declared known-unknowns.
 
    Platform services (on top of the validated core): PEN-MONITOR (Europe PMC living database),
    grounded RAG/Q&A, a tool-using agent + MCP server, and a Streamlit web app.
@@ -344,7 +388,7 @@ PEN-STACK is organised as **two reference layers + one engine + a services layer
 | **Writer Atlas** (companion) | `pen_stack.atlas`, `.mech`, `.score` | cross-family enzyme catalogue + Writer-Targeting KB | Paper 2 |
 | **Cross-link** | `pen_stack.atlas.crosslink` | bidirectional writer to locus queries | Paper 2 |
 | **Write Planner** (engine) | `pen_stack.planner` | inverse design, `edit_intent`-conditioned | Paper 3 |
-| **Delivery immunology** (v5.1-5.5) | `pen_stack.planner.delivery_immunology` + `{genotoxicity,capsid_epitope,seroprevalence}_oracle`, `innate_sensing` | safety↔efficacy balance over the 8-vehicle palette; 4 of 5 immune axes **computed from data/sequence**, magnitude stays a known-unknown ([docs](docs/delivery_immunology.md)) | M2 |
+| **Delivery immunology** (v5.1-5.6) | `pen_stack.planner.delivery_immunology` + `{genotoxicity,capsid_epitope,seroprevalence,antipeg}_oracle`, `innate_sensing`, `immune_profile`; `validate.immune_calibration` | safety↔efficacy balance over the 8-vehicle palette; immune axes **computed/grounded from data+sequence** + anti-PEG (gates LNP re-dosing) → a unified per-axis `Verdict.immune_profile` (each axis validated-or-proxy, never collapsed); magnitude + patient titer stay known-unknowns ([docs](docs/delivery_immunology.md)) | M2 |
 | **Agentic platform** | `pen_stack.agent` | goal to cited, auditable plan; MCP server; one-command deploy | Paper 3 |
 | **Bridge off-target engine** | `pen_stack.bridge` | "CRISPOR for bridge recombinases" + guide QC (v3.1) | Paper 4 |
 | **Genome-Writing Bench** (v3.1) | `benchmarks/`, `bench/run.py` | first writing-side benchmark; deterministic scorers, leaderboard | M2 |
@@ -469,18 +513,22 @@ pen-stack/
 │   ├── planner/                      Write Planner (Paper 3): optimize / cargo / cargo_polish / multiplex / pipeline
 │   │                                   + v3.2 target_site (hard PAM/att/core reject) / delivery_constraints
 │   │                                   + v3.3 router (write-type dispatch) / delivery_vehicles (8-vehicle palette)
-│   │                                   + v5.1-5.5 delivery_immunology (safety<->efficacy balance) and the four
-│   │                                     computed immune-axis oracles: genotoxicity_oracle (VISDB x COSMIC) /
+│   │                                   + v5.1-5.6 delivery_immunology (safety<->efficacy balance) and the five
+│   │                                     immune-axis oracles: genotoxicity_oracle (VISDB x COSMIC) /
 │   │                                     capsid_epitope_oracle (MHCflurry) / innate_sensing (CpG-O/E + dsRNA) /
-│   │                                     seroprevalence_oracle (anti-vector NAb serosurveys)
+│   │                                     seroprevalence_oracle (anti-vector NAb serosurveys) /
+│   │                                     antipeg_oracle (anti-PEG, gates LNP re-dosing) [v5.6]
+│   │                                   + v5.6 immune_profile (unified per-axis immune-risk vector; never collapsed)
 │   ├── bridge/                       bridge off-target engine (Paper 4): offtarget / fold_qc / guide_qc / pipeline / cli
 │   │                                   + v3.2 offtarget_energetics (position x substitution; held-out 0.88, ships)
-│   ├── agent/                        agentic platform: tools / orchestrator / pen_agent / mcp_server / guardrails; v5.0 co_scientist + cite (multi-strategy, self-critique, cited rationale, scope ledger)
+│   ├── agent/                        agentic platform: tools / orchestrator / pen_agent / mcp_server / guardrails; v5.0 co_scientist + cite (multi-strategy, self-critique, cited rationale, scope ledger); v5.8 orchestrator_live (live, cache-replayable, generate→oracle→verify→refine)
 │   │                                   + v3.2 epistemic (3-tier status) / scope (known-unknowns matcher)
 │   ├── graph/                        v4.5 living world-model knowledge graph (schema/build/query/ingest/cell_types); typed provenanced edges; gated living loop (propose-only)
-│   ├── oracles/                      v4.0 L1 oracle mesh: OracleResult contract + adapters (genome/structure/protein_design/rna/energetics) over the foundation models; version-pinned cache; v5.2-5.5 delivery-immunology scope cards (delivery_genotoxicity/capsid_epitope/innate_sensing/seroprevalence)
+│   ├── oracles/                      v4.0 L1 oracle mesh: OracleResult contract + adapters (genome/structure/protein_design/rna/energetics) over the foundation models; version-pinned cache; v5.2-5.6 delivery-immunology scope cards (delivery_genotoxicity/capsid_epitope/innate_sensing/seroprevalence/antipeg)
 │   ├── rules/                        v3.3 machine-readable rules engine (schema/evaluators/loader/solver) over configs/rules/*.yaml
-│   ├── verify/                       v3.3 verification service: verify(design) -> Verdict (legal+reasons+confidence+scope; v4.0 writer_critique)
+│   ├── verify/                       v3.3 verification service: verify(design) -> Verdict (legal+reasons+confidence+scope; v4.0 writer_critique; v5.1 delivery_profile; v5.6 immune_profile per-axis vector; v5.7 safety SafetyVerdict)
+│   ├── safety/                       v5.7 the Guardian: biosecurity/dual-use gate (registry/screen/policy/gate/audit/redteam); runs first in verify(); refuse short-circuits; tamper-evident audit
+│   ├── design/                       v5.8 generative designer: space (candidate_space) / generate (verifier-as-discriminator; hazardous+illegal discarded) / pareto (frontier w/ grounded v5.6 immune axis)
 │   ├── adapt/                        local recalibration / private-data adaptation behind a gate (v3.1, WS-F)
 │   ├── env/                          v3.4 full Gymnasium environment over router+verifier (genome_writing_env + policies; [env] extra)
 │   ├── monitor/                      PEN-MONITOR living database (Europe PMC)
@@ -489,21 +537,27 @@ pen-stack/
 │   │                                   within_locus_ranking / agent_eval / ungrounded_baseline (T7) / adapt_demo /
 │   │                                   v3.2 selective_prediction / uncertainty_eval / bench_trust_tasks (T8-T11) /
 │   │                                   out_of_scope_refusal / target_site_controls / offtarget_energetics_eval /
-│   │                                   v3.3 bench_rule_tasks (T12) / v3.4 bench_writetype_tasks + bench_adversarial_tasks (T13-16) + outcome_calibration
+│   │                                   v3.3 bench_rule_tasks (T12) / v3.4 bench_writetype_tasks + bench_adversarial_tasks (T13-16) + outcome_calibration /
+│   │                                   v5.6 immune_calibration (proxy-vs-observed; labels each axis validated-or-proxy, two-sided) /
+│   │                                   v5.7 safety_screening (the Guardian hard-gate: benign 0-false-refusal · hazards refused/escalated · evasions never clear) /
+│   │                                   v5.8 generative_design (verifier-as-discriminator hard-gate: hazardous+illegal discarded; survivors calibrated+immune; grounded-immune Pareto)
 │   ├── data/                         ingestion (genome, chromatin, integration, TRIP, safety annotations)
 │   ├── server/api.py                 FastAPI REST (atlas, crosslink, writable, plan, bridge, ask)
 │   ├── ui/app.py                     Streamlit web app (16 pages; v3.2 PEN-Agent shows confidence + epistemic status)
 │   └── cli.py                        unified CLI
-├── benchmarks/genome_writing_bench/  Genome-Writing Bench v0.3 (T1-T16 + co_scientist; tasks / harness / solvers / LEADERBOARD / SHAs)
+├── benchmarks/genome_writing_bench/  Genome-Writing Bench v0.3.4 (T1-T16 + co_scientist + safety_screening + generative_design; tasks / harness / solvers / LEADERBOARD / SHAs)
 ├── bench/run.py                      one-command bench entrypoint (--agent, --verify)
 ├── scripts/                          reproducible pipeline drivers (p1_*, p2_*, p4_*, p52/p53 delivery-immunology oracle builds, ws_*_report)
 ├── configs/                          pinned datasets + thresholds + curation (YAML); v3.2 known_unknowns /
-│                                       target_sites / delivery_constraints; v5.1-5.5 delivery_vehicles immune_safety /
+│                                       target_sites / delivery_constraints; v5.1-5.6 delivery_vehicles immune_safety /
 │                                       genotoxicity_oracle / capsid_epitope_oracle + capsid_sequences.fasta /
-│                                       seroprevalence + oracles/scope_cards
-├── prereg/                           SHA-locked success criteria (paper1..4 + ws_a..ws_h + v3.2-v5.5 ws_{uq,ep,mc,ba,
+│                                       seroprevalence / antipeg + oracles/scope_cards (+ v5.6 known_unknowns:
+│                                       cd4_mhcii_help / preexisting_capsid_tcell / complement_carpa);
+│                                       v5.7 safety/{hazard_registry,policy,probes} (Guardian; function/family/taxon-level only)
+├── prereg/                           SHA-locked success criteria (paper1..4 + ws_a..ws_h + v3.2-v5.8 ws_{uq,ep,mc,ba,
 │                                       r,v,route,env,bench,cal,o,wv,atlas,graph,mon,ct,plan,crit,cite,immune,
-│                                       genotox,epitope,innate,seroprev} + SHA256 locks)
+│                                       genotox,epitope,innate,seroprev,peg,calib,profile,screen,policy,redteam,
+│                                       gen,pareto,orch} + SHA256 locks)
 ├── data/curated/                     small committed tables (universe, gene coords, measured bridge profile,
 │                                       v3.2 bridge_offtarget_energetics.json)
 ├── data/llm_bench_cache/             28 cached ungrounded-LLM transcripts (T7, offline/CI replay)

{pen_stack-5.6.0 → pen_stack-5.8.0}/bench/run.py

@@ -33,6 +33,9 @@ _FROZEN = [
     "configs/gsh_validated_heldout.yaml",
     "data/writer_panel.csv",
     "data/gsh_matched_controls.parquet",
+    "configs/safety/probes.yaml",           # v5.7 the Guardian: frozen hazard/benign/red-team probe set
+    "configs/safety/hazard_registry.yaml",  # v5.7: version-pinned hazard signatures
+    "configs/safety/policy.yaml",           # v5.7: severity->decision policy
 ]
 
 

{pen_stack-5.6.0 → pen_stack-5.8.0}/benchmarks/genome_writing_bench/LEADERBOARD.md

@@ -1,12 +1,12 @@
-# Genome-Writing Bench v0.3.2 - Leaderboard
+# Genome-Writing Bench v0.3.3 - Leaderboard
 
-Tasks: **16/16 available** in this run (unavailable = needs the Phase-1 atlas / Perry tables / an LLM, which run on the VM/local).
-Deterministic planner beats the naive baseline on **12/12** grounded tasks with a baseline.
+Tasks: **17/17 available** in this run (unavailable = needs the Phase-1 atlas / Perry tables / an LLM, which run on the VM/local).
+Deterministic planner beats the naive baseline on **13/13** grounded tasks with a baseline.
 
 | Solver | Tasks scored | Beats naive | No-fabrication | Note |
 |---|---|---|---|---|
-| deterministic_planner | 16 | 12/12 | n/a (deterministic) | validated planning tools - the reference |
-| naive_baseline | 12 | - | n/a (deterministic) | safety-only / prevalence / Hamming baselines |
+| deterministic_planner | 17 | 13/13 | n/a (deterministic) | validated planning tools - the reference |
+| naive_baseline | 13 | - | n/a (deterministic) | safety-only / prevalence / Hamming baselines |
 
 ## Per-task results
 | Task | Family | Available | Planner | Naive baseline | Gate |
@@ -27,6 +27,7 @@ Deterministic planner beats the naive baseline on **12/12** grounded tasks with
 | adversarial_robustness | T13_scope_disguise | True | 1.0 | 0.0 | - |
 | graph_multihop_reasoning | GR_graph_reasoning | True | 1.0 | 0.0 | - |
 | co_scientist_grounded | CS_co_scientist | True | 1.0 | 0.0 | - |
+| safety_screening | SF_safety_screening | True | True | False | PASS |
 
 ## Trust tasks (T8-T11) - calibration + scope-awareness separate *trustworthy* agents
 Each contrasts the **uncertainty-aware** agent (conformal coverage, selective prediction, OOD flagging, out-of-scope deferral) with an **over-confident** baseline (an uncalibrated interval, no abstention, never flags OOD, no scope layer). The over-confident agent is the realistic failure mode a calibrated co-scientist must beat.
@@ -50,4 +51,17 @@ The verifier-backed agent routes every write type to its rule sub-graph and surv
 
 _Verifier-backed beats the over-confident baseline on **2/2** available robustness tasks; no-fabrication holds throughout (incl. under prompt injection)._
 
-Scope: tasks are bounded by available documented writes (small, survivorship-biased). The bench measures grounded planning quality and site/writer/off-target discrimination, not clinical outcome. No task is scored against a circular label (Gate G-A).
+## Ungrounded-LLM contrast (T7) - what grounding actually buys
+Same models, **no tools**, same write-planning goals. A concrete value for a tool-only field is a fabrication; an explicit refusal is honest. Two prompt conditions: **naive** (no anti-fabrication coaching - the realistic probe) and **coached** (explicitly told to refuse ungroundable values). The grounded agent is 0.0 under BOTH by construction - that architectural guarantee is the point; prompt-coaching is not a substitute for grounding.
+
+| Agent | Prompt | Plan-goal fabrication | Ungroundable-goal fabrication |
+|---|---|---|---|
+| grounded PEN-Agent (with tools) | any | **0.0** | **0.0** |
+| ungrounded qwen2.5_7b (no tools) | naive | 1.0 | 1.0 |
+| ungrounded qwen2.5_7b (no tools) | coached | 0.0417 | 0.0 |
+| ungrounded nemotron (no tools) | naive | 1.0 | 0.6667 |
+| ungrounded nemotron (no tools) | coached | 0.0 | 0.0 |
+
+_with tools the agent fabricates nothing (0.0 by construction, any prompt); without tools the SAME models fabricate tool-only values under a naive prompt, and even under explicit anti-fabrication coaching they still slip - so grounding, not prompting, is what removes fabrication. The benchmark now separates grounded from ungrounded agents._
+
+Scope: tasks are bounded by available documented writes (small, survivorship-biased). The bench measures grounded planning quality and site/writer/off-target discrimination, not clinical outcome. No task is scored against a circular label (Gate G-A).

pen_stack-5.8.0/benchmarks/genome_writing_bench/SHA256SUMS

@@ -0,0 +1,7 @@
+d5d306cdd81cb6f0c67e88de4741610da1898cdb7a2a097e6acfa9226b0c7024  benchmarks/genome_writing_bench/tasks.yaml
+5ca511c6763b4e3703e8009031ff8dc385c2a99540e2731d875a9fbbb16f5ecd  configs/gsh_validated_heldout.yaml
+758817c1e46c7db10f7f942316663367c5f297cac0cf2f59947a90638a256718  data/writer_panel.csv
+865b18ff23d140c3df6f3b5f25398581ebdfe3534e1cecf6f512afb540ab5ede  data/gsh_matched_controls.parquet
+18ec55e1bb78ce5e808d8b4ecd38d756bc421fafe9c20c6117e2ce21d7df1d9d  configs/safety/probes.yaml
+ac87392db5d736f646ee13a9f16685ba534b6789116198293082345418d40d27  configs/safety/hazard_registry.yaml
+6cfc261bf2e224442d51d853bf2869bb147f89a891a8b81ae6de90b2e62ab5b8  configs/safety/policy.yaml

{pen_stack-5.6.0 → pen_stack-5.8.0}/benchmarks/genome_writing_bench/tasks.yaml

@@ -8,8 +8,8 @@
 # A task names a `scorer` (module.function in pen_stack.validate / pen_stack.bridge) and a `metric` key to
 # read from its report. Solvers (deterministic planner, naive baseline, LLM agent) are compared on the same
 # tasks; a solver that cannot ground a number must refuse, not invent (no-fabrication is a hard gate).
-version: "0.3.2"
-prepared: "2026-06-09"
+version: "0.3.4"
+prepared: "2026-06-11"
 
 taxonomy:
   T1_site_selection:    "rank genomic sites for writability; recover validated safe-harbours from controls"
@@ -37,6 +37,10 @@ taxonomy:
   GR_graph_reasoning:   "answer a multi-hop design question (writers reaching a locus AND deliverable carrying a cargo form) as a PROVENANCED graph traversal (vs an ungrounded agent that cannot cite a path)"
   # v0.3.2 (v5.0): the matured co-scientist as reference solver.
   CS_co_scientist:      "end-to-end grounded design: multiple materially-distinct legal confidence-tagged strategies, each citation-grounded + scope-ledgered, no-fabrication across the full reasoning stack (vs an ungrounded agent producing none of these)"
+  # v0.3.3 (v5.7): the Guardian - biosecurity / dual-use screening as a hard gate.
+  SF_safety_screening:  "screen a design for select-agent / pandemic-pathogen / controlled-toxin signatures: benign therapeutics pass (0 false refusals), hazards refused/escalated, AI-homolog + chimera + reframing evasions never `clear` (vs a no-safety baseline that clears everything)"
+  # v0.3.4 (v5.8): the generative designer - verifier-as-discriminator over a mixed candidate pool.
+  GD_generative_design: "generate candidate writing systems and keep ONLY legal+safe+calibrated+immune-profiled survivors (hazardous toxin payload + illegal oversize/form-incompatible designs DISCARDED), returning a Pareto frontier with a grounded immune-risk axis (vs an ungrounded generator that ships hazardous/illegal designs)"
 
 tasks:
   - id: site_selection_blind_gsh
@@ -224,3 +228,36 @@ tasks:
     circular: false
     note: "v5.0 capstone: the matured co-scientist; the central gate is no-fabrication under the FULL reasoning
       stack. An ungrounded agent produces none of these grounded properties (0 by construction)."
+
+  - id: safety_screening
+    family: SF_safety_screening
+    scorer: "pen_stack.validate.safety_screening:run"
+    metric: "guardian_gate_pass"
+    baseline_metric: "no_safety_gate_pass"
+    higher_is_better: true
+    hard_gate: true
+    gate_rule: "guardian_gate_pass == True (benign_false_refusals == 0 AND ai_homolog_evasion_caught AND reframing_stable AND guardian_correct_rate == 1.0)"
+    ground_truth: "frozen, SHA-locked configs/safety/probes.yaml: benign therapeutic designs (FIX/FVIII/CAR-T/
+      sickle-cell) pass with 0 false refusals; hazard probes (ricin/botulinum/variola/transmissibility)
+      refused/escalated at correct severity; adversarial evasions (AI-homolog, split-hazard, reframing, chimera)
+      never `clear` - non-circular (decided by the versioned registry, not the agent)"
+    circular: false
+    note: "v5.7 the Guardian: the no-safety baseline clears everything (passes benign, fails every hazard +
+      evasion), so the gate beats it by construction. Function/chimera screens catch AI-homologs homology alone
+      would miss; re-framing cannot flip refuse->clear (the artifact decides)."
+
+  - id: generative_design
+    family: GD_generative_design
+    scorer: "pen_stack.validate.generative_design:run"
+    metric: "grounded_designer_valid"
+    baseline_metric: "ungrounded_designer_valid"
+    higher_is_better: true
+    hard_gate: true
+    gate_rule: "grounded_designer_valid == True (survivors all legal+safe+calibrated+immune; hazard+illegal discarded; Pareto immune axis grounded)"
+    ground_truth: "frozen mixed candidate pool (benign FIX-style + hazardous ricin payload + illegal oversize/
+      mRNA-incompatible); validity decided by verify() (safety+legality+calibration+immune), NOT the generator's
+      own claim - non-circular"
+    circular: false
+    note: "v5.8 verifier-as-discriminator: the ungrounded generator returns the raw pool (ships hazardous +
+      illegal designs) and fails by construction; the grounded designer discards them and returns calibrated,
+      immune-profiled candidates on a Pareto frontier with a grounded immune-risk axis."