pen-stack 5.3.0__tar.gz → 5.4.0__tar.gz

{pen_stack-5.3.0 → pen_stack-5.4.0}/CHANGELOG.md

@@ -3,6 +3,36 @@
 All notable changes to PEN-STACK are documented here. This file follows
 [Keep a Changelog](https://keepachangelog.com/) and the program's phase structure.
 
+## [5.4.0] - 2026-06-10 - v5.4 release: Computed innate-sensing scorer (completes the computable immune axes)
+
+The third computed delivery-immunology signal, after v5.2 genotoxicity and v5.3 capsid epitope load. Innate
+sensing of a delivered nucleic acid is computed directly from the **cargo sequence** — CpG O/E for DNA (TLR9),
+U-richness + dsRNA for mRNA (TLR7/RIG-I) — covering every cargo form. Workstream WS-INNATE, SHA-locked.
+
+### Added
+- **WS-INNATE scorer** — `pen_stack/planner/innate_sensing.py`: `cpg_observed_expected()` (Gardiner-Garden &
+  Frommer) + `innate_sensing(seq, cargo_form)` → `OracleResult`. **DNA** → CpG O/E (vertebrate genome ~0.2
+  tolerated; non-depleted DNA → 1 TLR9-stimulatory), `innate_score = max(0, 1 − CpG_O/E)`. **mRNA** → uridine
+  fraction + ViennaRNA dsRNA pairing (graceful when ViennaRNA absent), flagged **partial/`extrapolating`**.
+  **RNP** → minimal/transient. Abstains on empty / unrecognised input (never fabricates). Pure sequence
+  computation — no external data, runs in CI.
+- **Surfaced in `verify()`** — when a design supplies `cargo_seq`, the computed innate load is attached as a
+  `cargo_innate_sensing` scope flag (cargo form from the writer output form, else the vehicle's first
+  compatible form) and added to `delivery_profile.cargo_innate`. No confidence added; the realized in-vivo
+  innate response stays a known-unknown.
+- Scope card `innate_sensing`; `prereg/ws_innate.yaml`. `cite.curated_dois()` ingests the innate provenance
+  DOIs (CpG-TLR9 10.1073/pnas.161293498, CpG-depleted AAV 10.1172/JCI68205, RNA modification
+  10.1016/j.immuni.2005.06.008, + Krieg 1995 / Hornung 2006).
+
+### Changed
+- Version 5.3.0 -> 5.4.0 (minor — additive computed scorer).
+
+### Honesty invariant (unchanged)
+- Sequence-intrinsic motif-**load** signal. The realized **in-vivo innate response** magnitude in a patient is
+  **not** modelled (known-unknown); the mRNA score is **partial** because the dominant evasion lever —
+  **nucleoside modification** (m1-pseudouridine) — is a manufacturing choice not derivable from sequence; DNA
+  methylation state is likewise out of scope. No magnitude predicted.
+
 ## [5.3.0] - 2026-06-10 - v5.3 release: Computed capsid epitope-load oracle (covers all vectors)
 
 v5.2 computed genotoxicity only meaningfully touches integrating vectors. v5.3 brings the **NetMHC-style

{pen_stack-5.3.0 → pen_stack-5.4.0}/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: 5.3.0
+version: 5.4.0
 date-released: 2026-06-10
 authors:
   - family-names: "Mahaboob Ali"

{pen_stack-5.3.0 → pen_stack-5.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 5.3.0
+Version: 5.4.0
 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
@@ -91,7 +91,7 @@ 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-5.3.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-5.4.0-blue.svg)](CHANGELOG.md)
 [![Tests](https://img.shields.io/badge/tests-240%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/)
@@ -135,6 +135,23 @@ 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 v5.4 — Computed innate-sensing scorer (completes the computable immune axes)
+
+The third computed delivery-immunology signal (after v5.2 genotoxicity and v5.3 capsid epitope load). Innate
+sensing of a delivered nucleic acid is computed directly from the **cargo sequence**, covering every cargo
+form. It is a sequence-intrinsic motif-*load* signal; the realized in-vivo innate response stays a
+known-unknown, and the mRNA score is honestly *partial* (the dominant lever — nucleoside modification — isn't
+derivable from sequence).
+
+| Cargo form | Pathway | Computed from sequence | Score |
+|---|---|---|---|
+| **DNA** (AAV / HDAd / HSV / plasmid) | TLR9 / cGAS | CpG observed/expected ratio | `max(0, 1 − CpG_O/E)` — vertebrate genome ~0.2 tolerated, non-depleted DNA → 1 stimulatory |
+| **mRNA** (LNP-mRNA / electroporation) | TLR7/8 + RIG-I/MDA5/PKR | U-fraction + ViennaRNA dsRNA pairing | partial / `extrapolating` (nucleoside modification out of scope) |
+| **RNP** (eVLP / electroporation) | minimal (transient gRNA) | — | ~0.9 by mechanism |
+
+`verify()` surfaces it as a `cargo_innate_sensing` flag whenever a `cargo_seq` is supplied. See
+`pen_stack/planner/innate_sensing.py`, `prereg/ws_innate.yaml`, and the `innate_sensing` scope card.
+
 ## What is new in v5.3 — Computed capsid epitope-load oracle (covers all vectors)
 
 v5.2 computed genotoxicity only touches integrating vectors. v5.3 brings the **NetMHC-style calculation** to the

{pen_stack-5.3.0 → pen_stack-5.4.0}/README.md

@@ -16,7 +16,7 @@ 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-5.3.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-5.4.0-blue.svg)](CHANGELOG.md)
 [![Tests](https://img.shields.io/badge/tests-240%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/)
@@ -60,6 +60,23 @@ 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 v5.4 — Computed innate-sensing scorer (completes the computable immune axes)
+
+The third computed delivery-immunology signal (after v5.2 genotoxicity and v5.3 capsid epitope load). Innate
+sensing of a delivered nucleic acid is computed directly from the **cargo sequence**, covering every cargo
+form. It is a sequence-intrinsic motif-*load* signal; the realized in-vivo innate response stays a
+known-unknown, and the mRNA score is honestly *partial* (the dominant lever — nucleoside modification — isn't
+derivable from sequence).
+
+| Cargo form | Pathway | Computed from sequence | Score |
+|---|---|---|---|
+| **DNA** (AAV / HDAd / HSV / plasmid) | TLR9 / cGAS | CpG observed/expected ratio | `max(0, 1 − CpG_O/E)` — vertebrate genome ~0.2 tolerated, non-depleted DNA → 1 stimulatory |
+| **mRNA** (LNP-mRNA / electroporation) | TLR7/8 + RIG-I/MDA5/PKR | U-fraction + ViennaRNA dsRNA pairing | partial / `extrapolating` (nucleoside modification out of scope) |
+| **RNP** (eVLP / electroporation) | minimal (transient gRNA) | — | ~0.9 by mechanism |
+
+`verify()` surfaces it as a `cargo_innate_sensing` flag whenever a `cargo_seq` is supplied. See
+`pen_stack/planner/innate_sensing.py`, `prereg/ws_innate.yaml`, and the `innate_sensing` scope card.
+
 ## What is new in v5.3 — Computed capsid epitope-load oracle (covers all vectors)
 
 v5.2 computed genotoxicity only touches integrating vectors. v5.3 brings the **NetMHC-style calculation** to the

{pen_stack-5.3.0 → pen_stack-5.4.0}/configs/oracles/scope_cards.yaml

@@ -138,3 +138,17 @@ oracles:
       a viral vehicle whose antigen sequence is not committed (abstains)"
     generalizes_to_unseen_loci: false
     license: "open (this work; MHCflurry 10.1016/j.cels.2020.06.010, HLA-I supertypes 10.1186/1471-2172-9-1)"
+
+  innate_sensing:               # v5.4 WS-INNATE: computed nucleic-acid innate-sensing motif load
+    family: genome
+    version: "cpg-oe+dsrna-2026"
+    output_kind: baseline       # deterministic sequence statistic, not generative
+    valid_for: "sequence-intrinsic innate-sensing LOAD of a cargo sequence: CpG observed/expected (DNA ->
+      TLR9/cGAS; CpG-depleted DNA is tolerated, non-depleted is stimulatory) and U-richness + dsRNA pairing
+      (mRNA -> TLR7/8 + RIG-I/MDA5/PKR); a relative, computable proxy"
+    not_valid_for: "the realized IN-VIVO innate RESPONSE magnitude in a patient (a known-unknown); RNA
+      NUCLEOSIDE MODIFICATION (m1-pseudouridine), the dominant mRNA evasion lever - NOT sequence-derivable
+      (the mRNA score is PARTIAL / extrapolating); DNA methylation state of the delivered cargo"
+    generalizes_to_unseen_loci: false
+    license: "open (this work; CpG-TLR9 10.1073/pnas.161293498, CpG-depleted AAV 10.1172/JCI68205,
+      RNA modification 10.1016/j.immuni.2005.06.008)"

{pen_stack-5.3.0 → pen_stack-5.4.0}/pen_stack/__init__.py

@@ -1,2 +1,2 @@
 """PEN-STACK v3.0 - open infrastructure for genome writing."""
-__version__ = "5.3.0"
+__version__ = "5.4.0"

{pen_stack-5.3.0 → pen_stack-5.4.0}/pen_stack/agent/cite.py

@@ -36,6 +36,9 @@ def curated_dois() -> frozenset[str]:
             dois.update(a.get("provenance_dois", []) or [])
         except FileNotFoundError:
             pass
+    # v5.4 computed innate-sensing provenance (CpG-TLR9 / AAV CpG-depletion / RNA modification)
+    from pen_stack.planner.innate_sensing import PROVENANCE_DOIS as _innate_dois
+    dois.update(_innate_dois)
     gsh = yaml.safe_load(resource("configs/gsh_validated_heldout.yaml").read_text(encoding="utf-8"))["gsh"]
     for g in gsh:
         if g.get("doi"):

pen_stack-5.4.0/pen_stack/planner/innate_sensing.py

@@ -0,0 +1,135 @@
+"""Computed innate-immune-sensing scorer for nucleic-acid cargo (v5.4, WS-INNATE).
+
+Innate sensing of a delivered nucleic acid is a property of the CARGO SEQUENCE (and its form), computed here
+directly from sequence - the third computed delivery-immunology signal (after v5.2 genotoxicity and v5.3 capsid
+epitope load). It covers every cargo form the palette carries:
+
+  * DNA  (AAV / HDAd / HSV / electroporated plasmid) -> TLR9 / cGAS sensing of unmethylated CpG. The standard
+    sequence statistic is the CpG observed/expected ratio (Gardiner-Garden & Frommer): vertebrate genomes are
+    CpG-DEPLETED (O/E ~ 0.2) and tolerated, while non-depleted plasmid/viral DNA (O/E -> 1) is TLR9-stimulatory;
+    CpG-DEPLETED vectors evade detection. innate_score = max(0, 1 - CpG_O/E).
+  * mRNA (LNP-mRNA / electroporated mRNA) -> TLR7/8 (U-rich ssRNA) + RIG-I / MDA5 / PKR (dsRNA). Computed from
+    uridine fraction + ViennaRNA base-pairing. This signal is PARTIAL and flagged `extrapolating`: the dominant
+    innate-evasion lever for mRNA is NUCLEOSIDE MODIFICATION (m1-pseudouridine), which is NOT derivable from the
+    nucleotide sequence (a manufacturing choice) - a stated known-limitation.
+  * RNP / protein -> minimal, transient nucleic-acid exposure (no DNA; short-lived gRNA): score ~ high.
+
+Answers through the v4.0 OracleResult contract (output_kind="baseline"). HONESTY: this is a sequence-intrinsic
+motif-LOAD signal; the realized in-vivo innate RESPONSE magnitude in a patient is NOT modelled and stays a
+known-unknown; DNA methylation state and RNA nucleoside modification are out of sequence scope.
+"""
+from __future__ import annotations
+
+from pen_stack.oracles.schema import OracleResult, Provenance
+
+_SCOPE_CARD = "innate_sensing"
+_DNA = set("ACGT")
+_RNA = set("ACGU")
+# CpG-TLR9 (Krieg 1995 / Bauer 2001), CpG-depleted AAV evasion (Faust 2013), RNA nucleoside modification
+# (Kariko 2005), 5'ppp dsRNA RIG-I (Hornung 2006).
+PROVENANCE_DOIS = ["10.1038/374546a0", "10.1073/pnas.161293498", "10.1172/JCI68205",
+                   "10.1016/j.immuni.2005.06.008", "10.1126/science.1132505"]
+
+
+def _clean(seq: str) -> str:
+    return "".join(c for c in (seq or "").upper() if c.isalpha())
+
+
+def cpg_observed_expected(dna: str) -> dict:
+    """CpG observed/expected ratio (Gardiner-Garden & Frommer): (n_CpG / (n_C * n_G)) * length. Vertebrate
+    genome ~0.2 (depleted); non-depleted plasmid/viral DNA approaches 1; engineered CpG-free -> 0."""
+    s = _clean(dna).replace("U", "T")
+    L = len(s)
+    nC, nG = s.count("C"), s.count("G")
+    n_cpg = s.count("CG")
+    oe = (n_cpg / (nC * nG) * L) if (nC and nG) else 0.0
+    gc = (nC + nG) / L if L else 0.0
+    return {"length": L, "cpg_count": n_cpg, "cpg_oe": round(oe, 4), "gc": round(gc, 4)}
+
+
+def _dsrna_paired_fraction(rna: str) -> float | None:
+    """Fraction of bases paired in the ViennaRNA MFE structure (dsRNA -> RIG-I/MDA5/PKR). None if ViennaRNA
+    absent (graceful degradation, as in bridge/fold_qc.py)."""
+    try:
+        import RNA
+    except Exception:  # noqa: BLE001
+        return None
+    s = _clean(rna).replace("T", "U")
+    if not s:
+        return None
+    struct, _ = RNA.fold_compound(s).mfe()
+    paired = sum(1 for c in struct if c in "()")
+    return round(paired / len(struct), 4) if struct else None
+
+
+def _prov() -> Provenance:
+    return Provenance(model="cargo_innate_sensing", version="1.0", source="adapter",
+                      extra={"provenance_dois": PROVENANCE_DOIS})
+
+
+def innate_sensing(seq: str, cargo_form: str) -> OracleResult:
+    """Computed innate-sensing score for a cargo sequence + form, as an OracleResult (v4.0 contract).
+
+    `cargo_form` in {DNA, mRNA, RNP}. Returns innate_score in [0,1] (1 = least innate-stimulatory). Abstains
+    (available=False) on an empty sequence or an unrecognised/uncomputable form. Never fabricates."""
+    s = _clean(seq)
+    form = (cargo_form or "").strip()
+    if not s:
+        return OracleResult(oracle="genome", value=None, provenance=_prov(), scope_card=_SCOPE_CARD,
+                            in_scope=False, available=False, output_kind="baseline",
+                            note="no cargo sequence supplied")
+
+    if form == "DNA":
+        c = cpg_observed_expected(s)
+        score = max(0.0, min(1.0, 1.0 - c["cpg_oe"]))
+        return OracleResult(
+            oracle="genome",
+            value={"innate_score": round(score, 3), "pathway": "TLR9/cGAS (unmethylated CpG)",
+                   "cpg_oe": c["cpg_oe"], "cpg_count": c["cpg_count"], "gc": c["gc"], "length": c["length"]},
+            provenance=_prov(), native_uncertainty=None, scope_card=_SCOPE_CARD, in_scope=True,
+            extrapolating=False, output_kind="baseline", available=True,
+            note=(f"CpG O/E={c['cpg_oe']} ({c['cpg_count']} CpG, {c['length']} bp); innate_score=max(0,1-O/E). "
+                  "Vertebrate genome O/E~0.2 (tolerated), non-depleted DNA ->1 (TLR9-stimulatory). DNA "
+                  "methylation state and the realized in-vivo innate RESPONSE are known-unknowns (not modelled)."))
+
+    if form == "mRNA":
+        u_frac = s.replace("T", "U").count("U") / len(s)
+        paired = _dsrna_paired_fraction(s)
+        # partial sequence-only signal: U-richness (TLR7/8) + dsRNA pairing (RIG-I/PKR). The dominant evasion
+        # lever (nucleoside modification, m1-pseudouridine) is NOT sequence-derivable -> flagged extrapolating.
+        if paired is None:
+            score = max(0.0, min(1.0, 1.0 - u_frac))
+            note_ds = "ViennaRNA absent: dsRNA term omitted; score from U-fraction only."
+        else:
+            score = max(0.0, min(1.0, 1.0 - 0.5 * u_frac - 0.5 * paired))
+            note_ds = f"dsRNA paired_fraction={paired} (RIG-I/MDA5/PKR)."
+        return OracleResult(
+            oracle="rna",
+            value={"innate_score": round(score, 3), "pathway": "TLR7/8 (U-rich ssRNA) + RIG-I/MDA5/PKR (dsRNA)",
+                   "u_fraction": round(u_frac, 4), "dsrna_paired_fraction": paired, "length": len(s)},
+            provenance=_prov(), native_uncertainty=None, scope_card=_SCOPE_CARD, in_scope=True,
+            extrapolating=True, output_kind="baseline", available=True,
+            note=("PARTIAL sequence-only signal. " + note_ds + " The dominant mRNA innate-evasion lever - "
+                  "NUCLEOSIDE MODIFICATION (m1-pseudouridine) - is NOT sequence-derivable and is out of scope; "
+                  "the realized in-vivo innate response is a known-unknown."))
+
+    if form == "RNP":
+        return OracleResult(
+            oracle="rna",
+            value={"innate_score": 0.9, "pathway": "minimal (transient gRNA; no DNA)", "length": len(s)},
+            provenance=_prov(), native_uncertainty=None, scope_card=_SCOPE_CARD, in_scope=True,
+            extrapolating=True, output_kind="baseline", available=True,
+            note=("RNP cargo: transient, no DNA -> minimal nucleic-acid innate sensing (synthetic gRNA may "
+                  "trigger RIG-I via 5'-triphosphate; modification mitigates - not sequence-derivable). "
+                  "Realized response is a known-unknown."))
+
+    return OracleResult(oracle="genome", value=None, provenance=_prov(), scope_card=_SCOPE_CARD,
+                        in_scope=False, available=False, output_kind="baseline",
+                        note=f"unrecognised cargo_form {cargo_form!r} (expected DNA / mRNA / RNP)")
+
+
+def computed_innate_score(seq: str, cargo_form: str) -> tuple[float | None, OracleResult]:
+    """Convenience: (innate_score or None, full OracleResult). None when the scorer abstains. Never fabricates."""
+    r = innate_sensing(seq, cargo_form)
+    val = (r.value or {}).get("innate_score") if (r.available and r.value) else None
+    return val, r

{pen_stack-5.3.0 → pen_stack-5.4.0}/pen_stack/verify/service.py

@@ -107,6 +107,27 @@ def verify(design: Design | dict, question: str | None = None) -> Verdict:
                                 "reason": "documented ordinal immune/safety priors surfaced; the in-vivo immune "
                                           "MAGNITUDE remains a known-unknown (not predicted)"})
 
+    # v5.4 WS-INNATE: if a cargo SEQUENCE is supplied, compute its innate-sensing load from sequence
+    # (CpG/TLR9 for DNA, U/dsRNA for mRNA). Surfaced as a scope flag; the realized innate RESPONSE magnitude
+    # is a known-unknown. Cargo form = the writer output form, else the vehicle's first compatible form.
+    if design.cargo_seq:
+        form = design.writer_output_form
+        if not form and design.delivery_vehicle:
+            from pen_stack.planner.delivery_vehicles import vehicle as _veh
+            forms = (_veh(design.delivery_vehicle) or {}).get("compatible_cargo_form") or []
+            form = forms[0] if forms else None
+        if form:
+            from pen_stack.planner.innate_sensing import innate_sensing
+            inr = innate_sensing(design.cargo_seq, form)
+            if inr.available:
+                scope_flags.append({"kind": "cargo_innate_sensing", "cargo_form": form,
+                                    "innate_score": inr.value["innate_score"], "pathway": inr.value["pathway"],
+                                    "reason": "computed sequence-intrinsic innate-sensing load; the realized "
+                                              "in-vivo innate RESPONSE magnitude is a known-unknown"})
+                if delivery_profile is not None:
+                    delivery_profile = dict(delivery_profile)
+                    delivery_profile["cargo_innate"] = inr.value
+
     return Verdict(
         legal=routed["legal"], deferred=False, write_type=design.write_type, routing=routing,
         rule_results=results,

{pen_stack-5.3.0 → pen_stack-5.4.0}/pen_stack.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 5.3.0
+Version: 5.4.0
 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
@@ -91,7 +91,7 @@ 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-5.3.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-5.4.0-blue.svg)](CHANGELOG.md)
 [![Tests](https://img.shields.io/badge/tests-240%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/)
@@ -135,6 +135,23 @@ 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 v5.4 — Computed innate-sensing scorer (completes the computable immune axes)
+
+The third computed delivery-immunology signal (after v5.2 genotoxicity and v5.3 capsid epitope load). Innate
+sensing of a delivered nucleic acid is computed directly from the **cargo sequence**, covering every cargo
+form. It is a sequence-intrinsic motif-*load* signal; the realized in-vivo innate response stays a
+known-unknown, and the mRNA score is honestly *partial* (the dominant lever — nucleoside modification — isn't
+derivable from sequence).
+
+| Cargo form | Pathway | Computed from sequence | Score |
+|---|---|---|---|
+| **DNA** (AAV / HDAd / HSV / plasmid) | TLR9 / cGAS | CpG observed/expected ratio | `max(0, 1 − CpG_O/E)` — vertebrate genome ~0.2 tolerated, non-depleted DNA → 1 stimulatory |
+| **mRNA** (LNP-mRNA / electroporation) | TLR7/8 + RIG-I/MDA5/PKR | U-fraction + ViennaRNA dsRNA pairing | partial / `extrapolating` (nucleoside modification out of scope) |
+| **RNP** (eVLP / electroporation) | minimal (transient gRNA) | — | ~0.9 by mechanism |
+
+`verify()` surfaces it as a `cargo_innate_sensing` flag whenever a `cargo_seq` is supplied. See
+`pen_stack/planner/innate_sensing.py`, `prereg/ws_innate.yaml`, and the `innate_sensing` scope card.
+
 ## What is new in v5.3 — Computed capsid epitope-load oracle (covers all vectors)
 
 v5.2 computed genotoxicity only touches integrating vectors. v5.3 brings the **NetMHC-style calculation** to the

{pen_stack-5.3.0 → pen_stack-5.4.0}/pen_stack.egg-info/SOURCES.txt

@@ -160,6 +160,7 @@ pen_stack/planner/delivery_constraints.py
 pen_stack/planner/delivery_immunology.py
 pen_stack/planner/delivery_vehicles.py
 pen_stack/planner/genotoxicity_oracle.py
+pen_stack/planner/innate_sensing.py
 pen_stack/planner/multiplex.py
 pen_stack/planner/optimize.py
 pen_stack/planner/pipeline.py
@@ -253,6 +254,7 @@ prereg/SHA256_LOCK_ws_genotox.json
 prereg/SHA256_LOCK_ws_graph.json
 prereg/SHA256_LOCK_ws_h.json
 prereg/SHA256_LOCK_ws_immune.json
+prereg/SHA256_LOCK_ws_innate.json
 prereg/SHA256_LOCK_ws_mc.json
 prereg/SHA256_LOCK_ws_mon.json
 prereg/SHA256_LOCK_ws_o.json
@@ -290,6 +292,7 @@ prereg/ws_genotox.yaml
 prereg/ws_graph.yaml
 prereg/ws_h.yaml
 prereg/ws_immune.yaml
+prereg/ws_innate.yaml
 prereg/ws_mc.yaml
 prereg/ws_mon.yaml
 prereg/ws_o.yaml

pen_stack-5.4.0/prereg/SHA256_LOCK_ws_innate.json

@@ -0,0 +1,8 @@
+{
+  "cycle": "v5.4",
+  "workstream": "WS-INNATE",
+  "prepared": "2026-06-10",
+  "sha256": {
+    "prereg/ws_innate.yaml": "732ed00254b8caf2f0edca0eb3e1dc697e480c1a9f59556d5fea654e39ee5b09"
+  }
+}

pen_stack-5.4.0/prereg/ws_innate.yaml

@@ -0,0 +1,39 @@
+# PEN-STACK v5.4 - WS-INNATE (computed nucleic-acid innate-sensing scorer). Directional.
+cycle: "v5.4"
+workstream: "WS-INNATE"
+prepared: "2026-06-10"
+
+motivation: >
+  Third computed delivery-immunology signal (after v5.2 genotoxicity, v5.3 capsid epitope load), completing the
+  computable immune axes. Innate sensing of a delivered nucleic acid is a property of the CARGO SEQUENCE + form,
+  computable directly from sequence - covering every cargo form the palette carries.
+
+deliverable: >
+  pen_stack/planner/innate_sensing.py: cpg_observed_expected() + innate_sensing(seq, cargo_form) -> OracleResult;
+  surfaced in verify() when a design supplies cargo_seq; scope card `innate_sensing`.
+
+method: >
+  DNA (TLR9/cGAS): CpG observed/expected ratio (Gardiner-Garden & Frommer) = (n_CpG/(nC*nG))*L. Vertebrate
+  genome ~0.2 (CpG-depleted, tolerated); non-depleted plasmid/viral DNA -> 1 (stimulatory); CpG-depleted
+  vectors evade TLR9. innate_score = max(0, 1 - CpG_O/E). mRNA (TLR7/8 + RIG-I/MDA5/PKR): uridine fraction +
+  ViennaRNA dsRNA base-pairing; innate_score = 1 - 0.5*U_frac - 0.5*paired_frac (U-only if ViennaRNA absent).
+  RNP: minimal/transient (score ~0.9). v4.0 OracleResult (output_kind="baseline"). Refs: CpG-TLR9 Krieg 1995
+  [10.1038/374546a0] / Bauer 2001 [10.1073/pnas.161293498]; CpG-depleted AAV Faust 2013 [10.1172/JCI68205];
+  RNA nucleoside modification Kariko 2005 [10.1016/j.immuni.2005.06.008]; 5'ppp dsRNA RIG-I Hornung 2006
+  [10.1126/science.1132505].
+
+acceptance: >
+  (1) CpG O/E computed correctly (CGCGCG -> 2.0) and mapped to a TLR9 score (CpG-free DNA -> 1.0, CpG-rich ->
+  0.0). (2) DNA / mRNA / RNP forms handled; mRNA flagged PARTIAL (extrapolating) with the nucleoside-
+  modification limitation declared. (3) the scorer ABSTAINS on empty / unrecognised input (never fabricates).
+  (4) verify() surfaces a cargo_innate_sensing scope flag when cargo_seq is supplied, none otherwise. (5)
+  provenance DOIs curated / Crossref-verified.
+
+honesty_invariant: >
+  Sequence-intrinsic motif-LOAD signal. The realized IN-VIVO innate RESPONSE magnitude in a patient is NOT
+  modelled (known-unknown); the mRNA score is PARTIAL because the dominant evasion lever - nucleoside
+  modification (m1-pseudouridine) - is a manufacturing choice NOT derivable from sequence; DNA methylation state
+  is likewise out of scope. No magnitude predicted.
+
+gate: "CpG O/E correct + TLR9 mapping; DNA/mRNA/RNP handled; mRNA flagged partial; abstains not fabricates; verify surfaces it; provenance curated; no-fabrication intact."
+locked_files: [prereg/ws_innate.yaml]

{pen_stack-5.3.0 → pen_stack-5.4.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pen-stack"
-version = "5.3.0"
+version = "5.4.0"
 description = "Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner."
 readme = "README.md"
 requires-python = ">=3.11"