hh model
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Diffusion Tempering Improves Parameter Estimation with Probabilistic Integrators for Ordinary Differential Equations
Beck, Jonas, Bosch, Nathanael, Deistler, Michael, Kadhim, Kyra L., Macke, Jakob H., Hennig, Philipp, Berens, Philipp
Ordinary differential equations (ODEs) are widely used to describe dynamical systems in science, but identifying parameters that explain experimental measurements is challenging. In particular, although ODEs are differentiable and would allow for gradient-based parameter optimization, the nonlinear dynamics of ODEs often lead to many local minima and extreme sensitivity to initial conditions. We therefore propose diffusion tempering, a novel regularization technique for probabilistic numerical methods which improves convergence of gradient-based parameter optimization in ODEs. By iteratively reducing a noise parameter of the probabilistic integrator, the proposed method converges more reliably to the true parameters. We demonstrate that our method is effective for dynamical systems of different complexity and show that it obtains reliable parameter estimates for a Hodgkin-Huxley model with a practically relevant number of parameters.
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Splitting physics-informed neural networks for inferring the dynamics of integer- and fractional-order neuron models
Shekarpaz, Simin, Zeng, Fanhai, Karniadakis, George
We introduce a new approach for solving forward systems of differential equations using a combination of splitting methods and physics-informed neural networks (PINNs). The proposed method, splitting PINN, effectively addresses the challenge of applying PINNs to forward dynamical systems and demonstrates improved accuracy through its application to neuron models. Specifically, we apply operator splitting to decompose the original neuron model into sub-problems that are then solved using PINNs. Moreover, we develop an $L^1$ scheme for discretizing fractional derivatives in fractional neuron models, leading to improved accuracy and efficiency. The results of this study highlight the potential of splitting PINNs in solving both integer- and fractional-order neuron models, as well as other similar systems in computational science and engineering.
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Efficient identification of informative features in simulation-based inference
Beck, Jonas, Deistler, Michael, Bernaerts, Yves, Macke, Jakob, Berens, Philipp
Simulation-based Bayesian inference (SBI) can be used to estimate the parameters of complex mechanistic models given observed model outputs without requiring access to explicit likelihood evaluations. A prime example for the application of SBI in neuroscience involves estimating the parameters governing the response dynamics of Hodgkin-Huxley (HH) models from electrophysiological measurements, by inferring a posterior over the parameters that is consistent with a set of observations. To this end, many SBI methods employ a set of summary statistics or scientifically interpretable features to estimate a surrogate likelihood or posterior. However, currently, there is no way to identify how much each summary statistic or feature contributes to reducing posterior uncertainty. To address this challenge, one could simply compare the posteriors with and without a given feature included in the inference process. However, for large or nested feature sets, this would necessitate repeatedly estimating the posterior, which is computationally expensive or even prohibitive. Here, we provide a more efficient approach based on the SBI method neural likelihood estimation (NLE): We show that one can marginalize the trained surrogate likelihood post-hoc before inferring the posterior to assess the contribution of a feature. We demonstrate the usefulness of our method by identifying the most important features for inferring parameters of an example HH neuron model. Beyond neuroscience, our method is generally applicable to SBI workflows that rely on data features for inference used in other scientific fields.
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