neurojax-biophysics

name: neurojax_biophysics description: Guidelines for implementing biophysical neural mass models in NeuroJAX.

NeuroJAX (OSL-JAX) Biophysics

Goal

To implement differentiable biophysical models (Neural Masses) that can be fitted to data using diffrax and optimistix.

Physics Kernels

All models should inherit from a common base and solve ODEs/SDEs.

Wong-Wang (Reduced)

• Use Case: Whole-brain functional connectivity fitting.
• Complexity: Low (2 variables).
• Implementation: See vbjax for reference equations. Wraps in equinox.Module.

Canonical Microcircuit (CMC)

• Use Case: Layer-specific inference (Laminar Dynamics).
• Complexity: High (4 populations: SS, SP, II, DP).
• Origin: SPM Dynamic Causal Modelling (DCM).
• Implementation: Needs diffrax ODE solver.

Implementation Pattern

class AbstractNeuralMass(eqx.Module):
    def vector_field(self, t, y, args):
        raise NotImplementedError

class WongWang(AbstractNeuralMass):
    coupling: float
    def vector_field(self, t, y, args):
        # dx/dt = ...
        return dS