cs.NESep 30, 2026
SaveNull-model treatment of the sensory-motor boundary changes an evolutionary connectome comparison
Organizations: IonLabs
Abstract
Randomised copies of a connectome are the usual baseline for asking whether measured wiring matters, and the answer depends on what the randomisation preserves. We evolved embodied foraging agents whose brains are a compressed adult Drosophila connectome (FlyWire v783; 512 cell-type groups and 1,000 Kenyon cells) alongside agents built on randomised wiring, in pre-registered experiments with ten seeds, four ecologies and 600 generations. Two standard randomisations, a column shuffle and degree-preserving edge swaps, route 10.6 to 10.7 % of olfactory output directly onto descending motor groups, against 0.012 % in the connectome. On the registered primary endpoint, fitness averaged over the run, no difference was detected; at the last common-garden probe the connectome was behind both controls (-0.22 and -0.20 fitness units on seed means). Against controls that keep every sensory-output and motor-input edge and rewire only the interior, the seed-mean difference lay within a +/-0.10 equivalence bound (+0.002 and -0.074, unchanged under a calibration that also matches activity spread), although per ecology the interior column shuffle was ahead by 0.26 in one of four ecologies at ten seeds, a lead that ten further pre-registered seeds did not replicate. Rewiring the connectome so that it acquires the shortcut raised its fitness by 0.44 (10 of 10 seeds) and its dependence on olfaction from 0.15 to 0.99; graded doses raised both in step; at comparable swap counts the full dose was ahead of an interior-only sham by 0.53 (10 of 10 seeds); and a sham that rewired the same boundary edges without creating shortcuts matched the connectome (+0.007) while the full dose was ahead of it by 0.60. What a null preserves at the sensory-motor boundary can decide an evolutionary connectome comparison, and sensory-to-motor path statistics belong next to the degree statistics a null is said to preserve.
Figures & tables
Figure 1: What the null preserves at the sensory-motor boundary, and what it changes. (a) In the compressed connectome olfactory input reaches descending (motor) groups through several synapses; the standard column-shuffle and degree-preserving nulls route about a tenth of olfactory output directly onto them; the boundary-preserving nulls keep every sensory-output and motor-input edge and replace about nine in ten interior edges. (b) Differences in evolved fitness at the last common-garden probe with 90 % intervals: connectome minus each null on seed means over four ecologies (median), and the shortcut interventions over two ecologies (transplant: median; full dose minus sham and sham minus connectome: mean, as registered). The last two rows are the boundary-targeted sham (Section 4.5 ), from separate runs with their own connectome island. The grey band is the ±0.10 equivalence bound.
| code | operation | additionally preserved |
|---|---|---|
| N1 | column shuffle | out-degree, per-source weight multiset |
| N2 | degree-preserving target swaps | in- and out-degree |
| N4 | N2 on interior edges only | as N2, plus every sensory-output and motor-input edge |
| N5 | N1 on interior edges only | as N1, plus every sensory-output and motor-input edge |
Table 1: Randomised controls. All keep edge counts and Dale signs.
| condition | smell: direct | smell: hops | vision: direct | taste: direct |
|---|---|---|---|---|
| connectome | 0.00012 | 3 | 0.381 | 0.121 |
| N1 column shuffle | 0.107 | 1 | 0.108 | 0.113 |
| N2 degree-preserving | 0.106 | 1 | 0.128 | 0.093 |
| N4 interior swaps | 0.00010 | 3 | 0.340 | 0.125 |
| N5 interior shuffle | 0.00011 | 3 | 0.369 | 0.123 |
Table 2: Sensory-to-motor structure of the calibrated networks (medians over 10 seeds). “Direct”: share of that sense’s output weight landing on descending groups; “hops”: median shortest path from that sense to a descending group.
| control | seed means | P0T0 | P1T0 | P0T1 | P1T1 |
|---|---|---|---|---|---|
| N1 (shortcut) | −0.224 | −0.621 | −0.312 | −0.159 | +0.054 |
| [−0.34, −0.10] | [−0.66, −0.47] | [−0.44, −0.22] | [−0.21, +0.01] | [−0.05, +0.13] | |
| N2 (shortcut) | −0.199 | −0.403 | −0.338 | −0.017 | +0.015 |
| [−0.32, −0.13] | [−0.42, −0.31] | [−0.53, −0.07] | [−0.33, +0.01] | [−0.13, +0.14] | |
| N4 (boundary) | +0.002 | −0.064 | +0.021 | −0.031 | +0.120 |
| [−0.026, +0.045] | [−0.26, +0.00] | [−0.03, +0.04] | [−0.12, +0.09] | [−0.06, +0.28] |
Table 3: Corrected grid, last probe (generation 550), connectome minus control: median over 10 seeds, with the 90 % interval below. Equivalence is assessed only on seed means across ecologies.
Figure 2: Intervention. Left and middle: fitness trajectories in the two ecologies (median and interquartile range over 10 seeds). Right: differences from the connectome at the last probe, seed means over both ecologies, with 90 % intervals. Adding shortcut-creating rewiring (AS) reproduces the control’s advantage; removing it from the degree-preserving control (N2R) removes the advantage where it was clear.
Figure 3: Graded shortcut transplant. Left and middle: fitness at the last probe against the share of olfactory output landing directly on descending groups, per ecology; grey lines are seeds, purple the mean with standard error, and the green square the interior-only sham (101 swaps) plotted at the connectome’s own share. Right: fitness lost when olfaction is blocked, against the same axis.
Appendix figures & tables17 assets
Supplementary material from the paper’s appendix.
Appendix
| code | operation | preserved |
|---|---|---|
| N1 | permute the row positions of each presynaptic column’s non-zeros | out-degree, Dale sign, per-source weight multiset |
| N2 | Maslov–Sneppen target swaps (Maslov & Sneppen, 2002), 10·|E| attempts | in- and out-degree, weight–source pairing, sign |
| N3 | permute entries within each (super-class × hemisphere) block pair | connections between block pairs, block-level laterality |
| N4 | Maslov–Sneppen swaps restricted to interior edges | as N2, plus every edge leaving a sensory group and every edge entering a descending group |
| N5 | column shuffle restricted to interior edges | as N1, plus the same boundary edges |
| when | what | effect on reported results |
|---|---|---|
| exploratory phase, before PROTOCOL.md | 27 changes to brain construction, calibration and world code (for example: mandatory inclusion of the gustatory-to-dopaminergic path groups; replacement of clustered Kenyon cells by individually wired ones; removal of an energy loophole that let agents survive without eating; a retracted learning-specificity result traced to a numerically unstable calibration) | none of the frozen experiments were run before these changes |
| after PROTOCOL_ECO.md was frozen, before any run | the setting meant to remove the predator instead enabled an adaptive predator; fixed and re-frozen before the first grid | none |
| after the first grid | stored genomes were population samples rather than elites, by an indexing error | affects only the post hoc assays of Appendix H , as stated there |
| after the first grid (AI-assisted review of draft 1) | one-sided heading noise, Appendix D | the first grid’s generation-0 result is not used; all later experiments corrected |
| after the first grid | the standard nulls carry olfactory-to-motor shortcuts, Section 4.1 | motivated the corrected grid and the intervention |
Figure 4: First grid: common-garden fitness over 600 generations in the four ecologies, median and interquartile range over 10 seeds. This experiment was run before the noise correction (Appendix D ) and uses controls that carry sensory-to-motor shortcuts.
Figure 5: Corrected grid: connectome, shortcut-carrying controls (N1, N2) and boundary-preserving controls (N4, N5).
| cell | control | median | 90 % CI | smallest bound | δ = 0.05 | 0.075 | 0.10 | 0.15 | 0.20 |
|---|---|---|---|---|---|---|---|---|---|
| seed mean | N4 | +0.002 | [−0.026, +0.045] | 0.045 | yes | yes | yes | yes | yes |
| seed mean | N5 | −0.074 | [−0.096, +0.002] | 0.096 | no | no | yes | yes | yes |
| P0T0 | N4 | −0.064 | [−0.255, +0.002] | 0.255 | no | no | no | no | no |
| P0T0 | N5 | −0.264 | [−0.368, −0.179] | 0.368 | no | no | no | no | no |
| P1T0 | N4 | +0.021 | [−0.026, +0.038] | 0.038 | yes | yes | yes | yes | yes |
| P1T0 | N5 | +0.067 | [−0.067, +0.090] | 0.090 | no | no | yes | yes | yes |
| condition | between-group SD | silent groups | Kenyon-cell mean |
|---|---|---|---|
| A | 0.118 | 7 | 0.050 |
| N1 | 0.118 | 3 | 0.050 |
| N2 | 0.118 | 6.5 | 0.050 |
| N4 | 0.118 | 4.5 | 0.050 |
| N5 | 0.118 | 4.5 | 0.050 |
| contrast | global (registered grid) | distribution-matched | verdict |
|---|---|---|---|
| A − N4 | +0.002 [−0.026, +0.045] | +0.055 [+0.035, +0.097] | EQUIVALENT |
| A − N5 | −0.074 [−0.096, +0.002] | −0.009 [−0.076, +0.046] | EQUIVALENT |
| A − N1 | −0.224 [−0.337, −0.103] | −0.274 [−0.306, −0.123] | BEHIND |
| A − N2 | −0.199 [−0.321, −0.133] | −0.146 [−0.231, −0.037] | BEHIND |
| control | change | verdict |
|---|---|---|
| N1 | +0.010 [−0.112, +0.072] | UNDETERMINED |
| N2 | +0.101 [+0.016, +0.133] | CHANGED |
| N4 | +0.062 [−0.002, +0.117] | UNDETERMINED |
| N5 | +0.076 [−0.017, +0.128] | UNDETERMINED |
| ecology | control | global | distribution-matched |
|---|---|---|---|
| P0T0 | N1 | −0.621 [−0.661, −0.469] | −0.437 [−0.563, −0.235] |
| P0T0 | N2 | −0.403 [−0.421, −0.308] | −0.478 [−0.677, −0.052] |
| P0T0 | N4 | −0.064 [−0.255, +0.002] | +0.139 [−0.128, +0.230] |
| P0T0 | N5 | −0.264 [−0.368, −0.179] | −0.066 [−0.320, +0.124] |
| P1T0 | N1 | −0.312 [−0.441, −0.197] | −0.489 [−0.664, −0.275] |
| P1T0 | N2 | −0.338 [−0.530, −0.074] | −0.164 [−0.483, −0.013] |
| ecology | control | seeds 0–9 | seeds 10–19 | n = 20 | p_holm (n = 20) | inside ±0.10 (R1) |
|---|---|---|---|---|---|---|
| P0T0 | N1 | −0.621 [−0.661, −0.469] | −0.304 [−0.513, −0.161] | −0.491 [−0.624, −0.298] | 0.001 | no |
| P0T0 | N2 | −0.403 [−0.421, −0.308] | +0.100 [−0.068, +0.332] | −0.214 [−0.375, +0.042] | 0.248 | no |
| P0T0 | N4 | −0.064 [−0.255, +0.002] | +0.090 [−0.109, +0.217] | −0.011 [−0.114, +0.080] | 0.841 | no |
| P0T0 | N5 | −0.264 [−0.368, −0.179] | +0.031 [−0.068, +0.152] | −0.104 [−0.208, +0.016] | 0.265 | no |
| P1T0 | N1 | −0.312 [−0.441, −0.197] | −0.417 [−0.522, +0.067] | −0.333 [−0.482, −0.197] | 0.004 | no |
| P1T0 | N2 | −0.338 [−0.530, −0.074] | −0.101 [−0.335, +0.103] | −0.203 [−0.430, −0.032] | 0.046 | no |
| control | median [90 % CI] | seeds with connectome ahead | inside ±0.10 |
|---|---|---|---|
| N1 | −0.401 [−0.497, −0.241] | 3/20 | no |
| N2 | −0.155 [−0.273, −0.060] | 4/20 | no |
| N4 | 0.000 [−0.087, +0.083] | 10/20 | yes |
| N5 | −0.059 [−0.093, +0.018] | 7/20 | yes |
| quantity (seed mean over P0T0 and P1T0, n = 10) | mean | 90 % CI | registered rule |
|---|---|---|---|
| P: AS10 − BS10, last probe | +0.600 | [+0.414, +0.797] | lower bound > +0.10 → shortcut-specific |
| R: AS10 − BS10, fresh worlds (4 × 8 lives, generation-599 elites) | +0.639 | [+0.490, +0.792] | same category as P → robust |
| S2: AS10 − BS10, P0T0 / P1T0 | +0.568 / +0.631 | [+0.315, +0.832] / [+0.428, +0.831] | descriptive |
| S3: BS10 − A | +0.007 | [−0.070, +0.086] | ±0.10 reference: inside |
| S4: olfaction-ablation cost AS10 / BS10 | 1.175 / 0.354 | difference +0.821 [+0.563, +1.079] | descriptive |
| S5: AS10 − A | +0.606 | [+0.435, +0.798] | lower bound > 0 → replicated |
| endpoint | global | pergroup | distmatch (post hoc) |
|---|---|---|---|
| generation 0 | A > N1, N2, N3 (10/10, 10/10, 10/10), p_holm 0.006 | A > all (9/10, 10/10, 10/10), p_holm 0.006–0.008 | A > all (10/10, 9/10, 10/10), p_holm 0.006 |
| olfaction ablation | A −0.03 vs +0.31 / +0.34 / +0.30; p_holm 0.006–0.014 | A −0.08 vs +0.16 / +0.18 / +0.22; p_holm 0.006–0.008 | A −0.10 vs +0.25 / +0.32 / +0.28; p_holm 0.006–0.008 |
| vision ablation | A +0.30 vs +0.13 / +0.14 / +0.07; p_holm 0.06–0.11 | A +0.33 vs +0.09 / +0.13 / +0.17; p_holm 0.041 | A +0.47 vs +0.17 / +0.13 / +0.05; p_holm 0.012 |
| generation 275 | no difference vs N1, N2 (p_holm 1.0); vs N3 p_holm 0.059 | no difference vs N1, N2; vs N3 p_holm 0.111 | no difference vs N1, N2; vs N3 p_holm 0.252 |
| AUC (primary) | A > N1, N3 (p_holm 0.006); N2 n.s. | A > N3 only (p_holm 0.012) | A > N3 only (p_holm 0.012) |
Figure 6: Common-garden fitness over 300 generations in paper-v1, per calibration scheme (median and interquartile range over 10 seeds).
Figure 7: Paper-v1 endpoints per seed: generation 0, AUC (primary), generation 275, and ablation costs.
Figure 8: Circuit metrics before evolution under three calibration schemes.
Figure 9: Generation-250 samples of paper-v1 tested in harder worlds without further evolution.