release 6e71f00 · 8 sessions · DANDI:000021

cortexflow

what the stimulus explains

The movies repeat. A model that has learned what each neuron does at each frame can forecast well without capturing any dynamics of its own. These comparisons separate the two.

natural movie one

  • Classical
  • Neural
  • Stimulus-locked
−0.600−0.400−0.2000.0000.200AR (per unit) · history onlyAR (per unit) · history onlySmoothed persistence · history onlySmoothed persistence · history onlyGRU · history + stimulus + runningGRU · history + stimulus + runningGRU · history + stimulusGRU · history + stimulusGRU · history onlyGRU · history onlyVAR (ridge) · history + runningVAR (ridge) · history + runningVAR (ridge) · history onlyVAR (ridge) · history onlyTransformer · history onlyTransformer · history onlyVAR (ridge) · history + stimulus + runningVAR (ridge) · history + stimulus + runningTransformer · history + stimulusTransformer · history + stimulusVAR (ridge) · history + stimulusVAR (ridge) · history + stimulusTCN · history onlyTCN · history onlyTransformer · history + stimulus + runningTransformer · history + stimulus + runningRNN · history onlyRNN · history onlyLSTM · history onlyLSTM · history onlyPSTH + resid. VAR · stimulus + residual historyPSTH + resid. VAR · stimulus + residual historyPCA + VAR · history + stimulus + runningPCA + VAR · history + stimulus + runningLDS (Kalman) · history onlyLDS (Kalman) · history onlyPCA + VAR · history onlyPCA + VAR · history onlyPSTH · stimulus onlyPSTH · stimulus onlyMean rate · history onlyMean rate · history onlyPersistence · history onlyPersistence · history onlyone-step R² vs training-mean rate
One-step R² on this condition's test windows. Aqua rows are stimulus-locked references: the PSTH ignores neural history entirely.

natural movie three

  • Classical
  • Neural
  • Stimulus-locked
−0.600−0.400−0.2000.0000.200AR (per unit) · history onlyAR (per unit) · history onlyVAR (ridge) · history onlyVAR (ridge) · history onlyVAR (ridge) · history + runningVAR (ridge) · history + runningSmoothed persistence · history onlySmoothed persistence · history onlyGRU · history onlyGRU · history onlyTransformer · history onlyTransformer · history onlyVAR (ridge) · history + stimulusVAR (ridge) · history + stimulusVAR (ridge) · history + stimulus + runningVAR (ridge) · history + stimulus + runningGRU · history + stimulusGRU · history + stimulusGRU · history + stimulus + runningGRU · history + stimulus + runningTCN · history onlyTCN · history onlyTransformer · history + stimulusTransformer · history + stimulusLSTM · history onlyLSTM · history onlyRNN · history onlyRNN · history onlyTransformer · history + stimulus + runningTransformer · history + stimulus + runningPSTH + resid. VAR · stimulus + residual historyPSTH + resid. VAR · stimulus + residual historyPCA + VAR · history onlyPCA + VAR · history onlyPCA + VAR · history + stimulus + runningPCA + VAR · history + stimulus + runningLDS (Kalman) · history onlyLDS (Kalman) · history onlyPSTH · stimulus onlyPSTH · stimulus onlyMean rate · history onlyMean rate · history onlyPersistence · history onlyPersistence · history onlyone-step R² vs training-mean rate
One-step R² on this condition's test windows. Aqua rows are stimulus-locked references: the PSTH ignores neural history entirely.

grey screen (spontaneous)

  • Classical
  • Neural
  • Stimulus-locked
−0.600−0.400−0.2000.0000.200AR (per unit) · history onlyAR (per unit) · history onlySmoothed persistence · history onlySmoothed persistence · history onlyGRU · history + stimulusGRU · history + stimulusGRU · history + stimulus + runningGRU · history + stimulus + runningTransformer · history onlyTransformer · history onlyGRU · history onlyGRU · history onlyTransformer · history + stimulusTransformer · history + stimulusLSTM · history onlyLSTM · history onlyTransformer · history + stimulus + runningTransformer · history + stimulus + runningVAR (ridge) · history + stimulus + runningVAR (ridge) · history + stimulus + runningVAR (ridge) · history + runningVAR (ridge) · history + runningVAR (ridge) · history + stimulusVAR (ridge) · history + stimulusVAR (ridge) · history onlyVAR (ridge) · history onlyTCN · history onlyTCN · history onlyPSTH + resid. VAR · stimulus + residual historyPSTH + resid. VAR · stimulus + residual historyRNN · history onlyRNN · history onlyPCA + VAR · history + stimulus + runningPCA + VAR · history + stimulus + runningPCA + VAR · history onlyPCA + VAR · history onlyLDS (Kalman) · history onlyLDS (Kalman) · history onlyPSTH · stimulus onlyPSTH · stimulus onlyMean rate · history onlyMean rate · history onlyPersistence · history onlyPersistence · history onlyone-step R² vs training-mean rate
No stimulus is on screen, so stimulus covariates carry only the fact that the screen is grey. Whatever history-only models achieve here is predictability without a stimulus to lock to.

the stimulus gain

The same model with and without the stimulus code, paired by session. Positive means the stimulus helped. Running speed is tested separately; a gain from running is a statement about prediction, not evidence that locomotion causes the activity.

History + stimulus minus history only (ΔR²)
Model · conditionMean gain95% CISessions
VAR (ridge) · natural movie one−0.0064[−0.0126, −0.0009]8
VAR (ridge) · natural movie three−0.0098[−0.0140, −0.0067]8
VAR (ridge) · grey screen (spontaneous)+0.0001[−0.0009, +0.0010]8
GRU · natural movie one+0.0012[−0.0099, +0.0176]8
GRU · natural movie three−0.0100[−0.0146, −0.0053]8
GRU · grey screen (spontaneous)+0.0044[−0.0006, +0.0117]8
Transformer · natural movie one−0.0042[−0.0105, +0.0002]8
Transformer · natural movie three−0.0105[−0.0174, −0.0056]8
Transformer · grey screen (spontaneous)−0.0035[−0.0075, +0.0012]8

gain by horizon

  • Classical
  • Neural
−0.0050.0000.0050.0100.0150.0200.025125102050GRUTransformerVAR (ridge)horizon (bins of 50 ms)ΔR² from the stimulus code
Stimulus gain in free rollout as the horizon grows. A gain that widens with horizon is the signature of a model leaning on the stimulus schedule rather than on the population's own recent past.