{
  "schema": "universal-informatics/experiment/v1",
  "experiment_id": "oxtr-qrc-01-qualification",
  "status": "completed",
  "source_sha256": "9fe40670c064ca9f3d2bc76f6b73a99311421b4939a885a178124e1e71881544",
  "question": "Do quantum responses generated from Fibonacci and M9 P24 representations improve our ability to predict transcription factor occupancy around OXTR?",
  "phase": "Measurement qualification: two DNA samples, eight numerical preparations per sample. This phase checks measurement delivery and comparison; it contains no binding prediction accuracy score.",
  "methods": {
    "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": {
      "id": "fibonacci-m9-p24",
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        "native_doubling": true,
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        "rotation_to_recognised": 4,
        "m9_doubling_cycle_present": true,
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        "start_interval_values": [
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        "endpoint_rule": "Exclude endpoints, include wraparound; raw residues used for sums. Empty interiors sum to zero."
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        "three_step_repeat": true,
        "formation_id": "6-nodes-offset-0",
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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."
    }
  },
  "measurements": {
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    "study_id": "oxtr-qrc-01",
    "study_version": "1.0.0",
    "model_version": "1.1.0-qualification",
    "updated_at": "2026-10-25T01:22:56.336442+00:00",
    "purpose": "Two-window measurement qualification. Occupancy prediction is not yet evaluated.",
    "input_sha256": "0a86b5247d1a8e950d525debeed806109f009f6c51c70555eafcef4199336b33",
    "positions_m": [
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    "windows": [
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    "records": [
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    "distinguishability": [
      {
        "window": "chr3-8752896-8753152",
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    "gpu_run_completed": false,
    "qpu_run_completed": false
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  "timing": {
    "source": "Recorded Amazon Braket task metadata",
    "definition": "Elapsed wall time from submission to completion, including queue and execution; not QPU processing duration.",
    "study_01": {
      "submitted_at": "2026-10-25T01:05:00.993000+00:00",
      "completed_at": "2026-10-25T01:21:52.327000+00:00",
      "elapsed_seconds": 1011.334,
      "first_result_seconds": 196.056,
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      "tasks": [
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        {
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        {
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        },
        {
          "case": "chr3-8745472-8745728-gamma",
          "task_id": "f30cda70-0079-41e9-aa40-72e24b51f15d",
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        {
          "case": "chr3-8745472-8745728-ordinary",
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        {
          "case": "chr3-8745472-8745728-phi",
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        {
          "case": "chr3-8745472-8745728-shuffled",
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        {
          "case": "chr3-8752896-8753152-alpha",
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        {
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        {
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          "completed_at": "2026-10-25T01:13:42.064000+00:00"
        },
        {
          "case": "chr3-8752896-8753152-fibonacci",
          "task_id": "4d690682-bbcd-471f-84fe-d7d29ab4f0f3",
          "state": "COMPLETED",
          "submitted_at": "2026-10-25T01:05:02.535000+00:00",
          "completed_at": "2026-10-25T01:09:11.173000+00:00"
        },
        {
          "case": "chr3-8752896-8753152-gamma",
          "task_id": "056c9488-bd07-469c-93e2-edf24e8fff9c",
          "state": "COMPLETED",
          "submitted_at": "2026-10-25T01:05:06.755000+00:00",
          "completed_at": "2026-10-25T01:12:47.788000+00:00"
        },
        {
          "case": "chr3-8752896-8753152-ordinary",
          "task_id": "92a97488-675a-4126-838a-75ff29e0c539",
          "state": "COMPLETED",
          "submitted_at": "2026-10-25T01:05:00.993000+00:00",
          "completed_at": "2026-10-25T01:08:17.049000+00:00"
        },
        {
          "case": "chr3-8752896-8753152-phi",
          "task_id": "fd03b07f-1c48-40a1-8510-05bcfa38987b",
          "state": "COMPLETED",
          "submitted_at": "2026-10-25T01:05:03.835000+00:00",
          "completed_at": "2026-10-25T01:10:05.401000+00:00"
        },
        {
          "case": "chr3-8752896-8753152-shuffled",
          "task_id": "f4bc57c5-2ab1-463e-8e3b-88c7c61e4eb0",
          "state": "COMPLETED",
          "submitted_at": "2026-10-25T01:05:08.657000+00:00",
          "completed_at": "2026-10-25T01:14:38.144000+00:00"
        }
      ]
    },
    "earlier_connection_test": {
      "task_id": "3ae0ec02-160e-45a0-8f37-c88c1bbccda7",
      "state": "COMPLETED",
      "submitted_at": "2026-10-24T04:07:26.498000+00:00",
      "completed_at": "2026-10-24T22:59:41.681000+00:00",
      "elapsed_seconds": 67935.183
    },
    "interpretation": "Both experiments completed. Timings depend on device availability and queue, and are not delivery guarantees."
  },
  "biological_evidence": {
    "schema": "universal-informatics/next-test-evidence/v1",
    "checked_at": "2026-10-25T02:55:15.837983+00:00",
    "purpose": "Post-run data coverage audit; not a biological prediction result. No measurements or selected inputs changed.",
    "coordinates": "GRCh38 chr3, 0-based start, end-exclusive; UI displays start + 1 and end.",
    "locus": {
      "start": 8740380,
      "end": 8779628
    },
    "assay": {
      "accession": "ENCSR932ZMX",
      "factor": "CTCF",
      "cell": "GM23338",
      "cell_description": "induced pluripotent stem cells",
      "replicates": 2,
      "file": "ENCFF651DQL",
      "output_type": "conservative IDR thresholded peaks",
      "audit_warnings": [
        "antibody characterized with exemption",
        "low read depth",
        "mild to moderate bottlenecking",
        "moderate library complexity"
      ]
    },
    "peaks": [
      {
        "start": 8742928,
        "end": 8743128
      },
      {
        "start": 8755748,
        "end": 8755830
      },
      {
        "start": 8756915,
        "end": 8757115
      },
      {
        "start": 8767829,
        "end": 8768017
      },
      {
        "start": 8769391,
        "end": 8769649
      }
    ],
    "samples": [
      {
        "id": "chr3-8752896-8753152",
        "start": 8752896,
        "end": 8753152,
        "overlap_count": 0
      },
      {
        "id": "chr3-8745472-8745728",
        "start": 8745472,
        "end": 8745728,
        "overlap_count": 0
      }
    ],
    "sources": [
      {
        "file": "ENCSR932ZMX.json",
        "sha256": "673c18bf44b64c4a7a9da0e4508f89b31a757502927a03222cf12e80a123ac46"
      },
      {
        "file": "ENCFF651DQL.bed.gz",
        "sha256": "ee5624447f4852f48ddf34c03a7d41c5ec7ebf9e86e7c0b93888eb6ad483ec68"
      },
      {
        "file": "inputs.json",
        "sha256": "0a86b5247d1a8e950d525debeed806109f009f6c51c70555eafcef4199336b33"
      }
    ],
    "prediction_test_run": false,
    "hardware_jobs_submitted": 0
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  "field_guide": {
    "window": "A 256-base DNA sample in GRCh38 chromosome 3; start is zero-based and end is exclusive. DNA letters stay unchanged across numerical preparations.",
    "variant": "ordinary, fibonacci, phi, alpha, beta, gamma, epsilon or shuffled: eight ways to prepare numerical input from the same DNA sample.",
    "ideal_observables": "Noise-free mathematical calculation of the six-atom model; first six values are single-atom excitation probabilities, followed by all 15 pairs in physical_model.pairs order.",
    "gpu_observables": "Same 21 measurements estimated from the CUDA-Q program sampled on the NVIDIA GPU through qBraid.",
    "hardware_observables": "Same 21 measurements from Aquila after retaining successful shots with all six atoms present at the start.",
    "counts": "Histogram of six-bit excitation readings; 1 denotes an excited atom. The stored six positions use the study ordering convention. These are atom measurements, not protein-binding probabilities.",
    "shots": "Number of repeated measurements requested per program. hardware_valid_shots is the retained count used as denominator.",
    "provider_reference": "gpu_job_id and hardware_task_id link measurements to provider jobs; no credentials are included.",
    "units": "Probabilities range from 0 to 1. positions_m are metres. Physical-model units are included in physical_model.units.",
    "interpretation": "An increase in atom excitation is not automatically a better biological prediction. A biological gain requires more accurate predictions on separate DNA with laboratory binding measurements."
  },
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      "ended_at": "2026-10-25T01:10:05.401Z",
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      "ideal_observables": [
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