digital-drosophila/models/male-cns-lif/apl-timing-lab-v1/PROTOCOL.md

Phase 4AJ: a single graded-APL timing hypothesis

Independent branch authorized by the human. All earlier models and data remain read-only. The learning goal remains unmet; neither an audit nor fixed-CAL PASS constitutes usable learning.

Fixed intervention

Use the exact sealed AG author-style float64 LIF and float32 legacy graded APL. Compare h applied at its generating tick with the identical generated operator applied 18 steps later. No other change: dt=0.1 ms, anatomical delay=18 steps, refractory=22 steps, tau_m=20 ms, tau_syn=5 ms, W_syn=0.275 mV, original signs, threshold/rest/reset, all canonical IDs/edges, legacy APL tau=20 ms and gain=0.01. The unchanged fast-APL zero mask includes 1,212 non-KC edges not replaced by the graded operator. The branch does not silently fix this limitation.

This is engineering scheduling parity, not evidence of a measured 1.8 ms graded APL delay. Whole h is delayed, including KC feedback; it is not a PN-only intervention. APL still subtracts unconditionally at end-of-step, including refractory KC, whereas ordinary synaptic arrivals are guarded by refractory. Equal arrival time is not equivalent biological action.

Stages and gates

1. Exact conditional reconstruction of all 420 metadata-defined ALLN in all 60 sealed CAL r0 records. Audit every simultaneous earliest non-design PN, before first KC, and duration-matched never-active PN controls. PN→ALLN→PN witnesses must be actual accepted timed edges; distinguish signed weights, reset windows and zeroed edges. No shortest paths, unique-cause or necessity claims. Unknown antecedents are retained and do not falsify numerical audit.
2. Fixed stored h trace shift audit: no loss, duplication, amplitude arithmetic or brain simulation. Initial +0 padding and chronological unconsumed tail explicitly retained. No extra brain/APL tail advance or future-decay claim.
3. Both arms: eight fixed real-edge fixtures, three fresh GPU repeats, independent Brian LIF/own spikes/own FIFO, legacy APL component audit. Delay0 must reproduce sealed AG scientific outputs bitwise.
4. Both arms: the same two fullgraph first-seed CAL probes, independent Brian comparison and APL component audit. Numerical failure stops later execution.
5. Both arms: every original six-odor × two-mode × five-seed CAL, plus first-seed repeat for each odor/mode. Exact source input files, not regenerated random inputs. All results retained. Known baseline representation failure does not skip treatment; no seed selection, threshold/gain search or gate relaxation.
6. Recompute comparisons from raw evidence, old checksums and five frozen reference regressions. Seal truthful outcome with SHA-256 and source version.

Interpretation limits

Generated h depends on changed closed-loop spikes, so branch inhibition integrals need not match. Fixed-trace conservation is a transport check, not proof of equal closed-loop dose. Accepted request counts can also change with refractory state, despite byte-identical requested input schedules.

Brian state integration is independent but APL arithmetic is intentionally a shared frozen component. Original operator AST replay and rounding audit remain separate; no universal CPU/GPU equivalence is claimed from sampled fixtures.

CAL gate retains original 3–9% mean KC fraction, all-run limits, within/between Jaccard and Euclidean gates, and minimum odor-pair count in both input modes. Passing fixed CAL is not heldout generalization or associative memory. Further progress requires independent seeds/novel odors, credit specificity, isolated and whole-brain functional readouts, then conditioning with proper controls.

No training, eta/threshold/sign tuning, plastic mask expansion, heldout dynamic access, visual input, decoder, RL, game, Web or new candidate in this experiment.

Literature scope

Shiu et al. 2024, DOI 10.1038/s41586-024-07763-9, supplies the spiking-LIF scheduling reference, not a measured MaleCNS graded-APL delay. Amin et al. 2020, DOI 10.7554/eLife.56954, and Prisco et al. 2021 (PMC8741211) motivate local graded APL/calyx interaction but do not determine this millisecond delay value. Prior sealed source/literature audits retain versions and provenance.