We present a formal framework for modeling neural network dynamics using Category Theory, specifically through Markov categories. In this setting, neural states are represented as objects and state transitions as Markov kernels, i.e., morphisms in the category. This categorical perspective offers an algebraic alternative to traditional approaches based on stochastic differential equations, enabling a rigorous and structured approach to studying neural dynamics as a stochastic process with topological insights. By abstracting neural states as submeasurable spaces and transitions as kernels, our framework bridges biological complexity with formal mathematical structure, providing a foundation for analyzing emergent behavior. As part of this approach, we incorporate concepts from Interacting Particle Systems and employ mean-field approximations to construct Markov kernels, which are then used to simulate neural dynamics via the Ising model. Our simulations reveal a shift from unimodal to multimodal transition distributions near critical temperatures, reinforcing the connection between emergent behavior and abrupt changes in system dynamics.

Emergent effect is crucial to understanding the properties of complex systems that do not appear in their basic units, but there has been a lack of theories to measure and understand its mechanisms. In this letter, we consider emergence as a kind of structural nonlinearity, discuss a framework based on homological algebra that encodes emergence as the mathematical structure of cohomologies, and then apply it to network models to develop a computational measure of emergence. This framework ties the potential for emergent effects of a system to its network topology and local structures, paving the way to predict and understand the cause of emergent effects. We show in our numerical experiment that our measure of emergence correlates with the existing information-theoretic measure of emergence.