cDNA Observations
OBSERVED| GENE | SAMPLE | COUNT | NORM |
|---|---|---|---|
| BRCA1 | S001 | 4,892 | 8.24 |
| TP53 | S001 | 12,340 | 11.02 |
| MYC | S002 | 891 | 6.15 |
| EGFR | S002 | MISSING | MISSING |
| KRAS | S003 | 2,107 | 7.89 |
| PTEN | S003 | 6,723 | 9.41 |
6 observations · 3 samples · 6 genes · 1 missing cell
Gene Expression Matrix
GENE
S001
S002
S003
BRCA1
8.24
5.12
7.01
TP53
11.02
9.88
10.45
MYC
4.21
6.15
3.89
Data Validation
semantics.py · 10 VALIDATOR RULES
01Version and discriminant check
02Value XOR missing reason
03Canonical unsigned decimal counts
04Finite decimals with units
05Sample/gene reference resolution
06Quantity kind integrity
07Exclusion map preservation
08Source byte completeness
09Synthetic origin propagation
10No phantom model results
Architecture Pipeline
BIOLOGICAL OBSERVATIONS
↓
cDNA EXPRESSION DATA
↓
DATA VALIDATION
↓
GENE EXPRESSION
↓
STAN MODEL
↓
POSTERIOR STATE
↓
MINIZINC MODEL
↓
COMPUTATIONAL RESULT
↓
VISUALIZER
↓
HUMAN-READABLE MODEL
Semantic Quantity Classification
OBSERVED — measurement
INFERRED — posterior
DERIVED — transformation
PREDICTED — model output
CONSTRAINED — solver
ENCODED — representation
EXECUTED — run evidence
Observed measurements ≠ inferred posteriors.
Inferred posteriors ≠ deterministic derivations.
Derivations ≠ binary representations.
Representations ≠ execution evidence.
Inferred posteriors ≠ deterministic derivations.
Derivations ≠ binary representations.
Representations ≠ execution evidence.
PTM — Bit Parity / 1
q_even
q_odd
q_accept
1
0
1
1
0
1
0
_
| 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 |
n INPUT SYMBOLS · n+1 TRANSITIONS · O(1) AUXILIARY STORAGE
Stan — Bayesian Inference
INFERREDPrior → Likelihood → Posterior
| PARAM | MEAN | SD | 95% CI | R-HAT | ESS |
|---|---|---|---|---|---|
| baseline | 6.84 | 0.42 | [6.02, 7.66] | 1.00 | 4200 |
| cond_eff | 1.23 | 0.31 | [0.63, 1.84] | 1.00 | 3800 |
| time_eff | 0.47 | 0.18 | [0.12, 0.82] | 1.01 | 2900 |
| sigma | 2.11 | 0.15 | [1.82, 2.41] | 1.00 | 4100 |
0 divergences · run_id: not_run
MiniZinc — Constraints
CONSTRAINED| VARIABLE | DOMAIN | CONSTRAINT | STATUS |
|---|---|---|---|
| sample_assign | {0,1} | balanced groups | feasible |
| batch_block | 1..4 | no confounding | feasible |
| gene_select | {0,1} | top-k variance | not_run |
solver_outcome: not_run
Quipper — Quantum Circuit
q0: ─── H ──── ● ──── M ───
q1: ──────── X ──── M ───
q2: ─── H ──────── M ───
DEPTH: 3 QUBITS: 3 GATES: 4
MEASUREMENTS: 3 ANCILLAS: 0
generation: specified · validation: not_run · execution: not_run
Binary Semantics
ENCODEDPROFILE: u32-checked/1
unsigned 32-bit · big-endian · 0..4294967295
overflow: trap · div-by-zero: trap
State Transition
SEMANTIC VALUE → ENCODING → BITS → STATE → TRANSITION
00000000 00000000 00010011 10110010
present zero ≠ missing · distinct encodings