matter-embryogenesis / DATA_DICTIONARY.md
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Data dictionary and statistical units

All numerical records are synthetic simulations, not microscopy, laboratory measurements, or training examples. Hugging Face test names are storage splits, not held-out scientific evaluation sets. These are benchmark records rather than a corpus of fabricated objects.

Configuration Records Unit Canonical source
v3_manufacturing 512 One method × dimension × seed results/gauge/runs.json
v2_manufacturing 512 One method × dimension × seed results/runs.json
reserve_phase 155 One module count × reserve, aggregating 5,000 arrays results/gauge/phase.json
claims 20 One scoped claim group; some group multiple labels CLAIMS.json and THEOREM_INDEX.json

JSONL exports flatten nested dictionaries using underscore-separated field names; variable-length traces remain in the canonical JSON. Missing values are JSON null. No number is rounded in these exports. record_id is an export identifier. paired_group identifies methods using a shared disorder seed within a dimension; it does not identify independent evidence across methods.

Manufacturing fields

Field Meaning / units
dimension, nodes, modules Spatial dimension, network vertices, scalar conductance edge modules
seed, method Reproduction seed and controller/ablation label
complete Controller completed the fabrication procedure; not by itself functional success
termination_reason Recorded stopping cause, including infeasibility or lost reference
projective_function_pass Complete object passed the declared projective/voltage specification
projective_error Half-log generalized-eigenvalue condition number of grounded four-port responses; dimensionless
local_certificate_valid, false_local_certificate Ground-truth audit of the local certificate, not an additional controller measurement
voltage_max_absolute_error Maximum internal voltage-map discrepancy under the specified normalized drive
absolute_conductance_ratio Actual-to-target absolute conductance; projective success does not require this to be 1
chosen_relative_scale, physical_common_scale Chosen representative in witness units and simulated physical scale
reserve_capacity, max_reserve_used Conductance reserve in the simulator's normalized module units
additional_material_proxy, initial_material_proxy Conductance-weighted material proxies, not measured mass or chemical yield
samples_per_pair, pair_edges, ratio_samples Measurement allocation and total ratio sample count
diagnostic_radius Simultaneous log-estimation radius used by the controller
maximum_numerical_log_error_bound Checked inference numerical-error budget; ordinary floating-point implementation
growth_time, service_and_acquisition_time_subtotal Abstract simulator time, not seconds
inference_latency_excluded_from_subtotal Always true in this ensemble; inference and some hardware costs are not included
mean_cycle_residual_energy Cycle residual diagnostic; gradient differential bias may remain invisible
guard_certificate_* Flattened robust feasibility interval and stopping reason
config_* Flattened v2 configuration, preserving its different objective and disorder model

Remaining scalar names match their canonical JSON counterparts. See source comments and the manuscript for formulas. Automated field-type inventories are in schemas/data_schema.json.

Dependence and negative results

The v3 study has 32 seeds per condition, two dimensions and eight methods. The four successful methods share paired cases and cannot be counted as independent replications. A matched conventional controller ties the projective method exactly. Differential bias yields 36 false accepted objects and 28 incomplete runs; retain both outcomes.

The phase study uses 5,000 independent arrays for each of five module counts: 25,000 sampled arrays total. Each array batch is reused at 31 reserve values. Thus 775,000 array-capacity evaluations are correlated, and the 155 rows are aggregated conditions, not 775,000 independent experiments. The curve is exact only in its ideal bounded uniform disorder model.

The preserved v2 data use a different absolute-response objective and disturbance process. Do not pool v2/v3 outcomes as a single efficacy estimate. The 28 current scientific tests include the 16 v2 tests; they are not 44 tests.