arXiv subjects

Simone Carlo Surace

Publications and source records attributed to Simone Carlo Surace.

10 recordsLinked to original sources

arXiv2022

Efficient Sampling-Based Bayesian Active Learning for synaptic characterization

Bayesian Active Learning (BAL) is an efficient framework for learning the parameters of a model, in which input stimuli are selected to maximize the mutual information between the observations and the unknown parameters. However, the applicability of BAL to experiments is limited as it requires performing high-dimensional integrations and optimizations in real time: current methods are either too time consuming, or only applicable to specific models. Here, we propose an Efficient Sampling-Based Bayesian Active Learning (ESB-BAL) framework, which is efficient enough to be used in real-time biological experiments. We apply our method to the problem of estimating the parameters of a chemical synapse from the postsynaptic responses to evoked presynaptic action potentials. Using synthetic data and synaptic whole-cell patch-clamp recordings, we show that our method can improve the precision of model-based inferences, thereby paving the way towards more systematic and efficient experimental designs in physiology.

q-bio.QM↗

arXiv2022

A Unification of Weighted and Unweighted Particle Filters

Particle filters (PFs), which are successful methods for approximating the solution of the filtering problem, can be divided into two types: weighted and unweighted PFs. It is well known that weighted PFs suffer from the weight degeneracy and curse of dimensionality. To sidestep these issues, unweighted PFs have been gaining attention, though they have their own challenges. The existing literature on these types of PFs is based on distinct approaches. In order to establish a connection, we put forward a framework that unifies weighted and unweighted PFs in the continuous-time filtering problem. We show that the stochastic dynamics of a particle system described by a pair process, representing particles and their importance weights, should satisfy two necessary conditions in order for its distribution to match the solution of the Kushner--Stratonovich equation. In particular, we demonstrate that the bootstrap particle filter (BPF), which relies on importance sampling, and the feedback particle filter (FPF), which is an unweighted PF based on optimal control, arise as special cases from a broad class and that there is a smooth transition between the two. The freedom in designing the PF dynamics opens up potential ways to address the existing issues in the aforementioned algorithms, namely weight degeneracy in the BPF and gain estimation in the FPF.

math.OC↗

arXiv2019

The Hitchhiker's Guide to Nonlinear Filtering

Nonlinear filtering is the problem of online estimation of a dynamic hidden variable from incoming data and has vast applications in different fields, ranging from engineering, machine learning, economic science and natural sciences. We start our review of the theory on nonlinear filtering from the simplest `filtering' task we can think of, namely static Bayesian inference. From there we continue our journey through discrete-time models, which is usually encountered in machine learning, and generalize to and further emphasize continuous-time filtering theory. The idea of changing the probability measure connects and elucidates several aspects of the theory, such as the parallels between the discrete- and continuous-time problems and between different observation models. Furthermore, it gives insight into the construction of particle filtering algorithms. This tutorial is targeted at scientists and engineers and should serve as an introduction to the main ideas of nonlinear filtering, and as a segway to more advanced and specialized literature.

stat.ME↗

arXiv2019

Asymptotically exact unweighted particle filter for manifold-valued hidden states and point process observations

The filtering of a Markov diffusion process on a manifold from counting process observations leads to `large' changes in the conditional distribution upon an observed event, corresponding to a multiplication of the density by the intensity function of the observation process. If that distribution is represented by unweighted samples or particles, they need to be jointly transformed such that they sample from the modified distribution. In previous work, this transformation has been approximated by a translation of all the particles by a common vector. However, such an operation is ill-defined on a manifold, and on a vector space, a constant gain can lead to a wrong estimate of the uncertainty over the hidden state. Here, taking inspiration from the feedback particle filter (FPF), we derive an asymptotically exact filter (called ppFPF) for point process observations, whose particles evolve according to intrinsic (i.e. parametrization-invariant) dynamics that are composed of the dynamics of the hidden state plus additional control terms. While not sharing the gain-times-error structure of the FPF, the optimal control terms are expressed as solutions to partial differential equations analogous to the weighted Poisson equation for the gain of the FPF. The proposed filter can therefore make use of existing approximation algorithms for solutions of weighted Poisson equations.

math.OC↗

arXiv2019

Gauge Freedom within the Class of Linear Feedback Particle Filters

Feedback particle filters (FPFs) are Monte-Carlo approximations of the solution of the filtering problem in continuous time. The samples or particles evolve according to a feedback control law in order to track the posterior distribution. However, it is known that by itself, the requirement to track the posterior does not lead to a unique algorithm. Given a particle filter, another one can be constructed by applying a time-dependent transformation of the particles that keeps the posterior distribution invariant. Here, we characterize this gauge freedom within the class of FPFs for the linear-Gaussian filtering problem, and thereby extend previously known parametrized families of linear FPFs.

math.OC↗

arXiv2018

On the choice of metric in gradient-based theories of brain function

The idea that the brain functions so as to minimize certain costs pervades theoretical neuroscience. Since a cost function by itself does not predict how the brain finds its minima, additional assumptions about the optimization method need to be made to predict the dynamics of physiological quantities. In this context, steepest descent (also called gradient descent) is often suggested as an algorithmic principle of optimization potentially implemented by the brain. In practice, researchers often consider the vector of partial derivatives as the gradient. However, the definition of the gradient and the notion of a steepest direction depend on the choice of a metric. Since the choice of the metric involves a large number of degrees of freedom, the predictive power of models that are based on gradient descent must be called into question, unless there are strong constraints on the choice of the metric. Here we provide a didactic review of the mathematics of gradient descent, illustrate common pitfalls of using gradient descent as a principle of brain function with examples from the literature and propose ways forward to constrain the metric.

q-bio.NC↗

arXiv2018

Online Maximum Likelihood Estimation of the Parameters of Partially Observed Diffusion Processes

We revisit the problem of estimating the parameters of a partially observed diffusion process, consisting of a hidden state process and an observed process, with a continuous time parameter. The estimation is to be done online, i.e. the parameter estimate should be updated recursively based on the observation filtration. We provide a theoretical analysis of the stochastic gradient ascent algorithm on the incomplete-data log-likelihood. The convergence of the algorithm is proved under suitable conditions regarding the ergodicity of the process consisting of state, filter, and tangent filter. Additionally, our parameter estimation is shown numerically to have the potential of improving suboptimal filters, and can be applied even when the system is not identifiable due to parameter redundancies. Online parameter estimation is a challenging problem that is ubiquitous in fields such as robotics, neuroscience, or finance in order to design adaptive filters and optimal controllers for unknown or changing systems. Despite this, theoretical analysis of convergence is currently lacking for most of these algorithms. This article sheds new light on the theory of convergence in continuous time.

math.OC↗

arXiv2017

How to avoid the curse of dimensionality: scalability of particle filters with and without importance weights

Particle filters are a popular and flexible class of numerical algorithms to solve a large class of nonlinear filtering problems. However, standard particle filters with importance weights have been shown to require a sample size that increases exponentially with the dimension D of the state space in order to achieve a certain performance, which precludes their use in very high-dimensional filtering problems. Here, we focus on the dynamic aspect of this curse of dimensionality (COD) in continuous time filtering, which is caused by the degeneracy of importance weights over time. We show that the degeneracy occurs on a time-scale that decreases with increasing D. In order to soften the effects of weight degeneracy, most particle filters use particle resampling and improved proposal functions for the particle motion. We explain why neither of the two can prevent the COD in general. In order to address this fundamental problem, we investigate an existing filtering algorithm based on optimal feedback control that sidesteps the use of importance weights. We use numerical experiments to show that this Feedback Particle Filter (FPF) by Yang et al. (2013) does not exhibit a COD.

math.OC↗

arXiv2016

The Neural Particle Filter

The robust estimation of dynamically changing features, such as the position of prey, is one of the hallmarks of perception. On an abstract, algorithmic level, nonlinear Bayesian filtering, i.e. the estimation of temporally changing signals based on the history of observations, provides a mathematical framework for dynamic perception in real time. Since the general, nonlinear filtering problem is analytically intractable, particle filters are considered among the most powerful approaches to approximating the solution numerically. Yet, these algorithms prevalently rely on importance weights, and thus it remains an unresolved question how the brain could implement such an inference strategy with a neuronal population. Here, we propose the Neural Particle Filter (NPF), a weight-less particle filter that can be interpreted as the neuronal dynamics of a recurrently connected neural network that receives feed-forward input from sensory neurons and represents the posterior probability distribution in terms of samples. Specifically, this algorithm bridges the gap between the computational task of online state estimation and an implementation that allows networks of neurons in the brain to perform nonlinear Bayesian filtering. The model captures not only the properties of temporal and multisensory integration according to Bayesian statistics, but also allows online learning with a maximum likelihood approach. With an example from multisensory integration, we demonstrate that the numerical performance of the model is adequate to account for both filtering and identification problems. Due to the weightless approach, our algorithm alleviates the 'curse of dimensionality' and thus outperforms conventional, weighted particle filters in higher dimensions for a limited number of particles.

q-bio.NC↗

arXiv2015

A statistical model for in vivo neuronal dynamics

Single neuron models have a long tradition in computational neuroscience. Detailed biophysical models such as the Hodgkin-Huxley model as well as simplified neuron models such as the class of integrate-and-fire models relate the input current to the membrane potential of the neuron. Those types of models have been extensively fitted to in vitro data where the input current is controlled. Those models are however of little use when it comes to characterize intracellular in vivo recordings since the input to the neuron is not known. Here we propose a novel single neuron model that characterizes the statistical properties of in vivo recordings. More specifically, we propose a stochastic process where the subthreshold membrane potential follows a Gaussian process and the spike emission intensity depends nonlinearly on the membrane potential as well as the spiking history. We first show that the model has a rich dynamical repertoire since it can capture arbitrary subthreshold autocovariance functions, firing-rate adaptations as well as arbitrary shapes of the action potential. We then show that this model can be efficiently fitted to data without overfitting. Finally, we show that this model can be used to characterize and therefore precisely compare various intracellular in vivo recordings from different animals and experimental conditions.

q-bio.NC↗