| # Bio-Semantics Integration Contract — Gate 1 |
|
|
| **Version:** bio-semantics/1.0.0 |
| **Status:** Gate 1 candidate — contract specification only. Not implemented or tested. |
|
|
| --- |
|
|
| ## Integration Pipeline |
|
|
| ``` |
| Python → Validation → Normalization → Model Inputs → Stan → MiniZinc → Quipper → Artifact Validation → Visualization/Reporting |
| ``` |
|
|
| Each stage result carries: |
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|
| | Field | Type | |
| |-------|------| |
| | run_id, stage_id, semantic_stage | identifiers | |
| | status | blocked / not_run / running / succeeded / failed / timeout | |
| | reason | string | |
| | input_artifact_ids[], output_artifact_ids[] | references | |
| | tool_name, tool_version, command_arguments[], working_directory | execution | |
| | started_at, ended_at, exit_code | timing | |
| | stdout_artifact_id, stderr_artifact_id | logs | |
| | random_seed | value / not_applicable / unavailable | |
| |
| Solver outcome is separate from process status: |
| |
| ``` |
| solver_outcome: feasible | optimal | infeasible | unknown | timeout | failed | not_run |
| ``` |
| |
| A successful process exit is insufficient evidence of successful inference, a feasible solution, convergence, or quantum execution. |
| |
| --- |
| |
| ## Quantity Kinds |
| |
| | Kind | Meaning | |
| |------|---------| |
| | observed | Measurement with source record locator | |
| | inferred | Posterior quantity with model/run references and uncertainty | |
| | derived | Deterministic transformation with algorithm and input references | |
| | predicted | Unobserved modeled quantity with model/run references | |
| | constrained | Declared permitted relation or solver result | |
| | encoded | Representation with semantic source, codec identifier, and bit length | |
| | executed | Actual execution event with run evidence | |
| |
| --- |
| |
| ## Validator Rules (10) |
| |
| 1. Reject unsupported versions, unknown discriminants, contradictory variants, empty identifiers, duplicate observation IDs |
| 2. Require exactly one of present value or missing reason |
| 3. Raw counts: canonical unsigned decimal only (no negatives, fractions, exponents, whitespace) |
| 4. Decimal quantities: reject NaN/infinity, require declared units |
| 5. Require sample/gene references to resolve |
| 6. Reject inferred/predicted/constrained quantities labeled observed |
| 7. Preserve excluded rows with explicit inclusion map |
| 8. Missing source bytes block verified-ingestion claims |
| 9. Synthetic-origin propagation through every descendant artifact |
| 10. Never create model-result objects merely because a process was scheduled |
| |
| --- |
| |
| ## Binary Semantics Profiles |
| |
| - **u32-checked/1**: unsigned 32-bit, big-endian, range 0..4294967295; overflow traps |
| - **i32-checked/1**: signed two's-complement, big-endian; overflow traps; MIN_INT/-1 traps |
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|
| --- |
|
|
| ## PTM: ptm-bit-parity/1 |
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| Input alphabet: {0,1}. Tape alphabet: {0,1,_}. States: {q_even, q_odd, q_accept, q_reject}. |
| |
| | State | Read | Write | Move | Next | |
| |-------|------|-------|------|------| |
| | q_even | 0 | 0 | R | q_even | |
| | q_even | 1 | 1 | R | q_odd | |
| | q_odd | 0 | 0 | R | q_odd | |
| | q_odd | 1 | 1 | R | q_even | |
| | q_even | _ | 0 | Stay | q_accept | |
| | q_odd | _ | 1 | Stay | q_accept | |
| |
| For input length n: exactly n+1 transitions, n+1 tape cells, constant auxiliary storage. |
| |
| --- |
| |
| ## Gated Phases |
| |
| 1. **Contract gate**: Contracts and validators accepted; encodings/arithmetic/PTM documented; provenance validated |
| 2. **Engine gate**: Stan/MiniZinc/Quipper sources exist; native validation evidence recorded; failures preserved |
| 3. **Integration/release gate**: All panels rendered with lineage; WORM loaded first; governance checks preserved |
| |
| --- |
| |
| ## Acceptance Tests (specified, not run) |
| |
| | Case | Expected | |
| |------|----------| |
| | Present raw count "0" | Valid observed zero | |
| | Missing count with not_measured | Valid missing; never zero-filled | |
| | Missing variant also contains value | Invalid | |
| | Raw count "-1", "1.5", "1e3" | Invalid | |
| | Count above native backend range | Adapter rejects conversion | |
| | Normalized measurement labeled observed | Invalid | |
| | Posterior relabeled observed | Invalid | |
| | Missing source/hash | Provenance incomplete | |
| | Synthetic input -> posterior -> report | Synthetic marker propagated | |
| | Two records with duplicate identity | Invalid | |
| | u32 maximum plus one | Overflow fault | |
| | Integer divide by zero | Arithmetic fault | |
| | Encode/decode present zero versus missing | Distinct round trips | |
| | PTM "", "0", "1", "1011" | Output 0, 0, 1, 1; transitions 1, 2, 2, 5 | |
| | Fortran summation | Expected sum=5050 | |
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