Computation-through-Dynamics Toolkit: Simulated datasets and quality metrics for dynamical models of neural activity

Abstract

A primary goal of systems neuroscience is to discover how ensembles of neurons transform inputs into goal-directed behavior, a process known as neural computation. A powerful framework for understanding neural computation uses neural dynamics – the rules that govern how neural activity evolves over time – to explain how goal-directed input-output transformations occur. As dynamical rules are not directly observable, we need computational models that can infer neural dynamics from recorded neural activity. We typically validate such models using synthetic datasets with known ground-truth dynamics, but unfortunately existing synthetic datasets don’t reflect fundamental features of neural computation and may therefore be poor proxies for neural systems. Further, the field lacks validated metrics for quantifying the accuracy of the dynamics inferred by models. The Computation-through-Dynamics Toolkit (CtDToolkit) addresses these critical gaps by providing: 1) synthetic datasets that reflect computational properties of biological neural circuits, 2) interpretable metrics for quantifying model performance, and 3) a standardized pipeline for training and evaluating models with or without known external inputs. In this manuscript, we demonstrate how CtDToolkit can help guide the development, tuning, and troubleshooting of neural dynamics models. In summary, CtDToolkit provides a necessary framework for model developers to better understand and characterize neural computation through the lens of dynamics.