Polygenic Score Aggregate

# Blind Machine curated protocol bundle — polygenic_score_aggregate.## This manifest is the ONLY file the Rails platform parses. The author's pure# functions in server.py / local_project_owner.py / local_data_owner.py own the# computation; the numbered stage files are kit-owned shims that call them (see# docs/rfcs/0002). This file owns the governance + review surface (display# metadata + coordinate/weight definition + the gate values that let compute be# authorized without unpacking the tarball). See docs/protocol_structure.md for# the schema and docs/protocol_catalog.md §4 for this protocol's definition.## The "looks multiplicative, remains additive" protocol: the statistic is a# weighted sum sum_j w_j * g_j, but every weight is PUBLIC, so the server applies# them as a plaintext-scalar multiply (ciphertext x plaintext), never a# ciphertext x ciphertext multiply. It therefore stays on minimal, additive-tier# BFV params with no relinearization or Galois keys.name: polygenic_score_aggregateversion: 1.0.0builder:  type: uv  project: envcrypto: tenseal-bfv             # display hint; real deps live in env/uv.lockcomputation: additive_bfv       # additive fold + public plaintext-scalar multiplymin_contributors: 20# The published coordinate definition. Every contributor MUST encode against the# identical definition (dosage g in {0,1,2}^L) or the blind weighted sum is# meaningless — that invariant is what folding this manifest into the bundle# SHA-256 enforces. For the synthetic v1 demo the coordinate list is generated# deterministically from `seed` rather than enumerated inline (see# docs/protocol_structure.md: "The manifest may use generated coordinates for# synthetic v1 protocols.").input:  type: integer_vector  length: 1000  value_domain: [0, 1, 2]       # alt-allele dosage per coordinate; missing -> 0  coordinates:    kind: synthetic_variants    seed: blind-v1-demo-coordinates    fields: [chrom, pos, ref, alt]# The published PUBLIC effect weights — part of the protocol identity, folded into# the digest. Integer-scaled by the fixed-point factor `scale` (S): the server# multiplies the summed cohort ciphertext by these integer weights (with weight 1# on the append-1 sentinel slot). Generated deterministically from `seed` by# 30_compute_encrypted.py's `scaled_weights(length)`; a reviewer regenerates the# exact vector from (seed, scale, length). Real-domain effect weight[j] =# w_scaled[j] / S, in (0, 2.0] for this demo.weights:  scale: 1000                   # fixed-point factor S; real rounding error <= 1/S  values:    kind: synthetic_weights    seed: blind-v1-pgs-weights    range: [1, 2000]            # integer-scaled weight bounds (real (0, 2.0])output:  shape: weighted_aggregate_vector  # w_scaled[j] * sum_i g_ij (+ sentinel -> N)  exactness: exact                  # exact in the integer-scaled domain (BFV, Z_t)  tolerance: 0                      # integer aggregate is bit-exact; real <= 1/Srelease_policy:  aggregate_only: true          # only the summed, weighted vector is ever decrypted  allowed_runs_per_project: 1   # run cap (differencing mitigation, not a defense)# Params unchanged from the flagship (poly 8192), so the flagship compute budget# holds; only the plaintext modulus grows (30-bit, for the weight-inflated value# envelope). See 00_keygen.py.resources:  max_memory_mb: 8192  max_wall_seconds: 3600  max_ciphertext_mb: 512# Collaboration scenario (docs/rfcs/0002 §4.1): who runs which role's functions.# The author writes pure functions grouped BY ROLE into the files below; the# numbered stage shims that call them are kit-owned framework code, materialized# at run time (never signed into the bundle). `aggregate` = 1 project owner + N# data owners.scenario:  name: aggregate  roles:    project_owner: { file: local_project_owner.py, functions: [ keygen, decrypt, decode ] }    data_owner:    { file: local_data_owner.py,    functions: [ encode, encrypt ] }    server:        { file: server.py,              functions: [ compute ] }# Content-addressing digests. Computed at registry ingest — `bundle` by# protocols/hash_bundle.py, `env_lock` over env/uv.lock + env/.python-version +# pinned runner metadata. Left null in the committed bundle ON PURPOSE: the# canonical bundle digest is computed over the raw bytes of every signed file# INCLUDING this manifest, so a computed `bundle` value here would be# self-referential (its own input). The authoritative digest instead NAMES the# bundle (protocol-<name>@<digest>) and is recorded out-of-band# (.blind-signature / DB), never inside the file it would have to hash. See# protocols/README.md § "Why the manifest ships null hash placeholders".hashes:  bundle: null  env_lock: null