From e1c93cf186a6423b581298261638ae38b2cafd0c Mon Sep 17 00:00:00 2001 From: YurenHao0426 Date: Mon, 10 Aug 2026 09:56:59 -0500 Subject: exp: freeze Larkum public innovation pilot --- LARKUM_PUBLIC_PILOT.md | 97 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 LARKUM_PUBLIC_PILOT.md (limited to 'LARKUM_PUBLIC_PILOT.md') diff --git a/LARKUM_PUBLIC_PILOT.md b/LARKUM_PUBLIC_PILOT.md new file mode 100644 index 0000000..883946d --- /dev/null +++ b/LARKUM_PUBLIC_PILOT.md @@ -0,0 +1,97 @@ +# Larkum public-data innovation pilot + +## Purpose and status + +This exploratory pilot asks whether subtracting the dendritic activity predicted +from local spine traffic exposes a direction-independent trial-outcome signal in +public neural recordings. It is an independent biological consistency test for +the innovation operation, not a test of network training or an exact +somato-dendritic residual. The data structure and class counts were inspected +before this protocol was fixed, so the result is not an untouched confirmation. + +The data are from Maristany de las Casas et al., *Science* (2026), “Tuft +dendrites in frontal motor cortex enable flexible learning,” DOI +`10.1126/science.adx4358`. The archived public data are released under CC BY +4.0 at `https://doi.gin.g-node.org/10.12751/g-node.etlk5k/`. + +## Fixed dataset + +Use the eleven `Figure2/Data/*_dff.mat` sessions in archive +`10.12751_g-node.etlk5k.zip`: + +- animals `DCO1`, `DCO2`, and `DCO4`; +- saline (`Sal`) and chemogenetic NDNF activation (`DCZ`) conditions; +- trial-aligned `spine_local`, `branch`, `TrialTypes`, `Choice`, and `DirOut`; +- omit trials with a non-finite choice or malformed neural arrays. + +No Figure 1, 3, 4, 5, or 6 endpoint enters this pilot. Those modules do not +provide the same trial-level pairing needed here. + +## Fixed innovation estimator + +For every session, subtract the first 30-frame mean from every spine and branch +ROI on each trial. The expected branch trace is a multi-output ridge regression +from all local-spine traces, frame identity, instruction identity, and their +interaction. The ridge coefficient is fixed at `1.0`. + +The predictor never receives choice, correctness, outcome, drug condition, or +future-session data. Saline trials are five-fold cross-fitted in contiguous +trial blocks. The DCZ predictor is fitted once on all saline trials from the +same session and then frozen. The innovation is + +```text +branch activity - predicted branch activity. +``` + +A simpler task-template residual subtracts the saline mean trace for the same +instruction without using spine activity. + +## Fixed endpoint + +The outcome window is 0 to 1 second after report onset, corresponding to the +public analysis time axis from -3 to 3 seconds over 180 frames. Split this +window into six bins. In each bin summarize the population by signed mean, +mean absolute activity, and RMS activity. This produces the same 18 features +for raw branch activity, task-template residual, spine-conditioned innovation, +and local-spine activity. + +The primary endpoint is cross-instruction, leave-one-animal-out decoding of +`DirOut`: + +1. hold out one animal; +2. train a balanced logistic decoder on one instruction direction from the + other two animals; +3. test it on the opposite instruction direction in the held-out animal; +4. repeat in the other direction and for all three held-out animals; +5. pool the out-of-fold predictions and report AUROC. + +This split is load-bearing. Correctness is determined by instruction and lick +direction, so ordinary random cross-validation can relabel sensory or movement +activity as an outcome signal. Under the cross-instruction split, a pure +choice-direction signal reverses sign. A choice-only decoder is retained as a +negative control. + +Report separately for saline and DCZ: + +- AUROC for raw branch, task-template residual, spine-conditioned innovation, + local spine, and choice-only control; +- per-animal AUROC and the number of correct/error trials; +- the paired AUROC difference between innovation and raw branch; +- the saline-minus-DCZ change in innovation AUROC; +- 95% descriptive intervals from 5,000 session-block bootstrap samples, + resampling sessions within animal. + +The bootstrap describes stability across the released sessions. With only +three animals, it is not treated as population-level animal inference. + +## Decision rule + +The pilot supports the narrow biological claim only if saline innovation has +AUROC above 0.5, exceeds raw branch activity, and the gain has the same sign in +all three held-out animals. A weaker DCZ innovation endpoint is a causal +consistency result, not a required pass condition because DCZ has few error +trials. Failure, sign inconsistency, or an advantage confined to ordinary +within-instruction decoding rejects this dataset as flagship evidence. + +Regardless of outcome, this pilot cannot establish improved learning, +scalability, or an exact Harnett-style soma-dendrite residual. -- cgit v1.2.3