VNC walking CPG
Pugliese et al. firing-rate VNC simulations that identify a walking CPG (DNg100 / DNb08 screens).
Neurons are simulated — leaky integrate-and-fire or better — with documented, tuned parameters.
Dispute this rating →The evidence
No evidence, no level.The model predicted that DNb08 drives rhythmic leg movement; the authors then activated DNg100 and DNb08 optogenetically in real tethered flies, tracked leg joint kinematics with Anipose, and scored those real recordings with the same autocorrelation rhythmicity metric they apply to simulated neurons — so prediction and measurement sit on one axis.
https://www.biorxiv.org/content/10.1101/2025.09.12.675944v2Neuron state follows a documented leaky firing-rate ODE with threshold, gain and a saturating firing-rate cap - the dynamics that earn L1.
https://github.com/smpuglie/Pugliese_2026/blob/faee4b06869855ae0164cbf217fb6ec28ef3521b/src/simulation/vnc_sim.py#L35-L44Neuron parameters (membrane time constant, threshold, gain, firing-rate cap) are specified as distributions in the config, not fitted.
https://github.com/smpuglie/Pugliese_2026/blob/faee4b06869855ae0164cbf217fb6ec28ef3521b/configs/neuron_params/default.yaml#L1-L11The connectivity matrix is only rescaled by fixed excitatory/inhibitory multipliers at setup and never updated during a run - no synaptic plasticity anywhere, which rules out L2.
https://github.com/smpuglie/Pugliese_2026/blob/faee4b06869855ae0164cbf217fb6ec28ef3521b/src/simulation/vnc_sim.py#L47-L61Real flies are compared to the model with the same metric: Anipose-tracked leg joint angles from headless flies under DNg100 and DNb08 CsChrimson activation are scored with `neuron_oscillation_score`, the identical rhythmicity score used on simulated neurons, so behavioural and simulated rhythmicity are directly comparable.
https://github.com/smpuglie/Pugliese_2026/blob/faee4b06869855ae0164cbf217fb6ec28ef3521b/notebooks/Anipose%20data%20figures.ipynbThe accompanying preprint states that a simulation prediction about the DNb08 pathway driving rhythmic leg movements was confirmed experimentally with optogenetics in behaving flies.
https://www.biorxiv.org/content/10.1101/2025.09.12.675944v2
The most rigorously validated project in this batch, and the rating is capped by the scale's own definition rather than by the work's quality. The model is a firing-rate ODE over the VNC connectome - dR/dt = (half-tanh(a/fr_cap * (input - threshold)) * fr_cap - R) / tau, per-neuron tau, threshold, gain and firing-rate cap drawn from a stated distribution, integrated with an adaptive-step Dopri5 solver - so neuron state changes under a documented model: L1. Not L2, and this is the decisive point: no synapse is ever updated. The connectivity matrix is scaled once at setup by fixed excitatory/inhibitory multipliers, optionally perturbed with static noise or pruned for a robustness sweep, and then held constant for the whole integration; a grep for plasticity, STDP, dopamine, learning rate or eligibility across every .py and .yaml in the repo returns nothing. The preprint's own abstract states that the simulation predicted a DNb08 rhythmic-walking pathway that was then confirmed experimentally. If the site wants to recognise validated non-plastic circuit models, this project is the case that forces the question. It carries the validation mark, and it is the project that forced the scale to change: the authors activated DNg100 and DNb08 optogenetically in real tethered flies, tracked leg kinematics with Anipose, and scored those recordings with the same rhythmicity metric they apply to simulated neurons — with the simulation predicting the result before the experiment confirmed it. A cumulative scale filed that at L1 next to a sandbox.
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All projects →Research code for the Shiu et al. connectome-based leaky integrate-and-fire model, including activation/silencing experiments, notebooks, and FlyWire data configuration.
FlyWire whole-brain LIF implementation based on Shiu et al., with multiple simulation backends and benchmarking tools. This repository supplies the neural model; it is not a complete embodied demo package.
Ratings on thelearningfly.com are proposals, not verdicts. Every one of them is arguable in public.