Allele Frequency with Variance

# Blind Machine curated protocol bundle — MULTIPLICATION-SUPPORTING (depth 1).## 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 + 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 §5 for this protocol's definition.## This is the "money comparison" row of the paper: the SAME published coordinate# definition and the SAME contributor payload as the flagship (protocol 1), but# the server SQUARES an encrypted value (ct x ct, depth 1) to derive the second# moment. It isolates the cost of exactly one multiplicative level. The additive# client-precompute benchmark VARIANT (client pre-squares, server only sums) is# documented in BENCHMARK.md and is NOT a separate registry protocol.name: allele_frequency_with_varianceversion: 1.0.0builder:  type: uv  project: envcrypto: tenseal-bfv               # display hint; real deps live in env/uv.lockcomputation: multiplicative_bfv   # server squares under encryption (ct x ct, depth 1)min_contributors: 30# The published coordinate definition — IDENTICAL to the flagship (protocol 1),# which is exactly what makes protocol 5 the controlled multiplicative-depth# comparison. Every contributor MUST encode against the identical definition or# the blind aggregate is meaningless; that invariant is enforced by folding this# manifest into the bundle SHA-256. For the synthetic v1 demo the coordinate list# is generated deterministically from `seed` (see docs/protocol_structure.md).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]output:  shape: sum_and_sumsq_vectors    # sum_g in Z^L and sum_g2 in Z^L (+ append-1 sentinel -> N)  exactness: exact                # BFV is exact in Z_t; g^2 <= 4 so max sum_g2 = 4N < t  tolerance: 0  # Stage 30 writes ONE opaque result.bin FILE (the worker content-addresses a  # single artifact). Both moment ciphertexts (sum_g, sum_g2) are packed into a  # deterministic BMCT1 container (magic b"BMCT1\n"; shared verbatim with  # genotype_phenotype_covariance). max_ciphertext_mb below bounds the WHOLE  # packed container.release_policy:  aggregate_only: true            # only the two summed moment vectors are ever decrypted  allowed_runs_per_project: 1     # run cap (differencing mitigation, not a defense)# Bumped for the larger multiplication-supporting ring: poly_modulus_degree 16384# ciphertexts are ~2-4x the 8192 ones, and the square path holds a second# accumulator, so both memory and ciphertext size grow vs the flagship.resources:  max_memory_mb: 16384  max_wall_seconds: 7200  max_ciphertext_mb: 2048# 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