{
  "schema": "universal-informatics/oxtr-qrc-study/v1",
  "id": "oxtr-qrc-01",
  "version": "1.0.0",
  "status": "measurement_qualification_complete",
  "question": "Do quantum responses generated from Fibonacci and M9 P24 representations improve our ability to predict transcription factor occupancy around OXTR?",
  "gene": "OXTR",
  "method": "Quantum reservoir computing",
  "created_on": "2026-10-25",
  "scope": "The first measurement phase has completed CPU and GPU checks and all 16 Aquila programs. Held-out occupancy prediction remains to be evaluated.",
  "atlas": {
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      "rotation_degrees": 0.0,
      "status": "Proposed geometric traversal; physical interpretation not assessed."
    },
    "orientation": "clockwise from north",
    "grids": "Alpha/Gamma/Epsilon: 24 period positions; Beta: 9 residue positions"
  },
  "reference": {
    "species": "Homo sapiens",
    "assembly": "GRCh38 / hg38",
    "chromosome": "chr3",
    "start_0based": 8740380,
    "end_exclusive": 8779628,
    "length_bp": 39248,
    "gene_id": "ENSG00000180914",
    "canonical_transcript": "ENST00000316793.8",
    "gene_start_1based": 8750381,
    "gene_end_1based": 8769628,
    "gene_strand": -1,
    "selection": "Ensembl OXTR gene body plus 10,000 bases on each genomic side",
    "scope": "A defined locus window; distal regulatory elements outside it are not captured. Overlapping records may extend beyond its boundaries.",
    "origin_genomic_base_0based": 8779627,
    "direction": "OXTR minus strand; descending genomic coordinates",
    "clockwise_from": "north",
    "coordinate_convention": "0-based, end-exclusive"
  },
  "template": {
    "id": "rydberg-reservoir-global-pulse-v1",
    "qubits": 6,
    "geometry": "Six sites on a regular hexagon; ring radius and nearest-neighbour separation 9 micrometres, with one vertex at north. Positions are fixed throughout each run.",
    "radius_m": 9e-06,
    "omega_rad_s": 2000000,
    "detuning_bound_rad_s": 4000000,
    "duration_s": 4e-06,
    "input_slots": 24,
    "edge_ramp_s": 2e-07,
    "input": "A 24-slot vector of motif/spacing descriptors. Each encoding uses the same source features and identical normalization fitted on training data only.",
    "encoding": "Global detuning varies with the input; fixed nonzero drive permits noncommuting evolution. Canonical representation weights/order define registered alternatives. No local detuning access is assumed.",
    "output": "Six excitation probabilities and fifteen labelled pair probabilities at the final time; additional times require distinct tasks and a new frozen version.",
    "model": "H(t)/hbar = Omega(t)/2 sum_i X_i - Delta_x(t) sum_i n_i + sum_i<j C6/r_ij^6 n_i n_j",
    "c6_source": "Read and freeze Aquila device capabilities at compilation; never infer a molecular interaction from this Hamiltonian.",
    "symmetry": "Global driving of this symmetric array can produce redundant single-site and pair features. Measure effective feature rank on training data and retain the same symmetry treatment across all encodings; six atoms do not imply 21 independent features."
  },
  "variants": [
    {
      "id": "ordinary",
      "label": "Ordinary representation",
      "role": "Same biological descriptors in their original genomic order."
    },
    {
      "id": "fibonacci",
      "label": "Native Fibonacci",
      "role": "Predeclared distance features from native Fibonacci gaps, with the physical base-pair range fixed before labels are inspected."
    },
    {
      "id": "phi",
      "label": "Phi Ratio",
      "role": "Ratios of neighbouring motif gaps; retain physical gaps and distinguish native ratios from modular residues."
    },
    {
      "id": "alpha",
      "label": "Alpha \u00b7 M9 P24",
      "role": "Full canonical residue order; never equate 24 period positions with 24 hours or a universal 24-base spacing."
    },
    {
      "id": "beta",
      "label": "Beta \u00b7 M9 P24",
      "role": "Canonical 4,8,7,5,1,2 cycle. Six-of-nine membership alone is a broad divisibility feature."
    },
    {
      "id": "gamma",
      "label": "Gamma \u00b7 M9 P24",
      "role": "Canonical two-triangle order encoded in time. Shared positions alone do not distinguish Epsilon."
    },
    {
      "id": "epsilon",
      "label": "Epsilon \u00b7 M9 P24",
      "role": "Canonical seven-visit path, with the repeated closing point retained. A timed encoding must pass a distinguishability check."
    },
    {
      "id": "shuffled",
      "label": "Matched shuffled representations",
      "role": "Seeded controls preserve feature distributions, pulse duration, energy-scale bounds and input information."
    }
  ],
  "evaluation": {
    "target": "Presence of reproducible TF occupancy in a defined assay and cell context; no claim of exact contact bases, affinity or causal regulation.",
    "factor": null,
    "cell_context": null,
    "assay_accessions": [],
    "selection_rule": "Choose one human GRCh38 TF assay with replicates, appropriate controls, adequate locus coverage and no dependence on Fibonacci fit. Record accession, factor, cell, QC and label rules before fitting.",
    "inputs": [
      "DNA sequence and motif scores",
      "Motif positions, orientation and gaps",
      "Predefined Fibonacci, Phi Ratio and M9 P24 descriptors"
    ],
    "not_inputs": [
      "Experimental occupancy labels or ChIP signal",
      "Assay-specific labels used to choose encodings",
      "Test-set scores or feature rankings"
    ],
    "splits": "Chromosome/block-separated training and validation, with chr3/OXTR withheld from all fitting. Keep overlapping windows and biological replicates together.",
    "primary_metric": "Difference in average precision on the frozen independent test set, QRC versus the strongest validation-selected classical model on identical inputs.",
    "controls": [
      "Classical motif/sequence baseline",
      "Classical nonlinear model with identical representation features",
      "CUDA-Q simulated reservoir using the same physical program",
      "Aquila reservoir with ordinary encoding",
      "Matched shuffled encoding and label-permutation checks"
    ],
    "secondary": [
      "Calibration and precision at a fixed recall",
      "Per-representation effects with multiple-comparison correction",
      "Sensitivity to window origin, strand and measurement uncertainty"
    ],
    "success": "Positive held-out improvement with a prespecified uncertainty interval; report inconclusive or negative results without selecting a favourable encoding after testing. No speedup or aromatic mechanism follows from classification alone.",
    "uncertainty": "Bootstrap independent genomic blocks, keep repeat shots within their sample, report intervals. A locus with too few labels receives a ranking with uncertainty, not a predictive-performance claim."
  },
  "execution": {
    "current_stage": "qualification_complete",
    "submission_enabled": false,
    "simulation_backend": "NVIDIA CUDA-Q",
    "simulation_route": "Compile a checked time-evolution circuit, validate locally, then use the existing qBraid GPU route for supported compiled programs. Native CUDA-Q dynamics is an alternative only after runtime capability checks.",
    "hardware_backend": "QuEra Aquila via Amazon Braket",
    "parity": "Identical coordinates, C6, pulse schedule, basis/readout convention and observation times. Freeze the discretized AHS program before compiling the matched simulation.",
    "stages": [
      "design_review",
      "data_admission",
      "model_validation",
      "simulation",
      "hardware",
      "evaluation",
      "complete"
    ],
    "planned_shots_per_input": 100,
    "budget_rule": "No dispatch until the complete task count, provider quotes and shared budget reservation are recorded and approved for the run. Existing one-task approval is not reused.",
    "task_formula": "number of frozen input windows \u00d7 encoding variants \u00d7 readout times \u00d7 hardware repeats",
    "job_records": [
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    ],
    "results": null
  },
  "cache": {
    "key_fields": [
      "template_version",
      "dataset_hash",
      "split_hash",
      "feature_hash",
      "normalization_hash",
      "encoding_id",
      "device_capabilities_hash",
      "program_hash",
      "backend_version",
      "shots",
      "seed",
      "calibration_timestamp"
    ],
    "rule": "Show cache provenance and run date. A replay of saved results never creates a new hardware receipt. A changed input or model invalidates its dependent result."
  },
  "review": {
    "status": "First measurement phase complete",
    "next": "Evaluate the prespecified prediction benchmark against held-out biological observations.",
    "methods_url": "data/oxtr-qrc-qualification.md"
  },
  "sources": [
    "https://github.com/QuEraComputing/QRC-tutorials",
    "https://arxiv.org/abs/2407.02553",
    "https://arxiv.org/abs/2605.04737",
    "https://arxiv.org/abs/2602.14641",
    "https://docs.aws.amazon.com/braket/latest/developerguide/braket-quera-submitting-analog-program-aquila.html"
  ],
  "delivery": {
    "phase": "measurement_qualification",
    "return_url": "https://staging.universalmind.tv/informatics/?entry=research&area=quantum#study",
    "simulation": "Approximately 5\u201310 minutes from processing start, including the classical calculation and CUDA-Q simulation. Planning estimate; queue and workload can extend it.",
    "hardware": "Timing varies with device availability and the quantum queue. The 25 October 2026 qualification batch completed in 16 minutes 51 seconds from first submission to final completion; the earlier two-atom test took 18 hours 52 minutes. Observed timings are not delivery guarantees.",
    "report": "Publish simulation findings first, then the combined report after hardware completion and evaluation. Clearly identify each version.",
    "notification": "Optional email with verified consent at study launch; send a private return link without biological data in the message. Email delivery is not active in this design review.",
    "persistence": "The review interface saves an optional study record and delivery preference on this device. Execution requires a durable study record independent of browser lifetime.",
    "source": "https://docs.aws.amazon.com/braket/latest/developerguide/braket-task-when.html",
    "classical": "Approximately 5\u201310 minutes from processing start, including the classical calculation and CUDA-Q simulation. Planning estimate; queue and workload can extend it."
  },
  "roadmap": {
    "stage": 5,
    "title": "Drug Discovery Network & Open Source Genomic Insights",
    "status": "future_feature",
    "flow": [
      "Recorded classical and quantum results",
      "Preliminary AI insights",
      "Human review and sharing approval",
      "External research collaboration",
      "Open Source Genomic Insights"
    ],
    "sharing": "No active external submission or publishing connection. Future automation retains human oversight."
  },
  "qualification": {
    "version": "1.1.0-qualification",
    "status": "complete",
    "report": "oxtr-qrc-qualification.json",
    "methods": "oxtr-qrc-qualification.md",
    "windows": 2,
    "representations": 8,
    "shots_per_program": 100,
    "scope": "Execution and numerical qualification; no biological prediction result."
  }
}