Optimal Population Coding, Revisited

Cortical circuits perform the computations underlying rapid perceptual decisions within a few dozen milliseconds with each neuron emitting only a few spikes. Under these conditions, the theoretical analysis of neural population codes is challenging, as the most commonly used theoretical tool – Fisher information – can lead to erroneous conclusions about the optimality of different coding schemes. Here we revisit the effect of tuning function width and correlation structure on neural population codes based on ideal observer analysis in both a discrimination and reconstruction task. We show that the optimal tuning function width and the optimal correlation structure in both paradigms strongly depend on the available decoding time in a very similar way. In contrast, population codes optimized for Fisher information do not depend on decoding time and are severely suboptimal when only few spikes are available. In addition, we use the neurometric functions of the ideal observer in the classification task to investigate the differential coding properties of these Fisher-optimal codes for fine and coarse discrimination. We find that the discrimination error for these codes does not decrease to zero with increasing population size, even in simple coarse discrimination tasks. Our results suggest that quite different population codes may be optimal for rapid decoding in cortical computations than those inferred from the optimization of Fisher information

In All Likelihood, Deep Belief Is Not Enough

Statistical models of natural stimuli provide an important tool for researchers in the fields of machine learning and computational neuroscience. A canonical way to quantitatively assess and compare the performance of statistical models is given by the likelihood. One class of statistical models which has recently gained increasing popularity and has been applied to a variety of complex data are deep belief networks. Analyses of these models, however, have been typically limited to qualitative analyses based on samples due to the computationally intractable nature of the model likelihood. Motivated by these circumstances, the present article provides a consistent estimator for the likelihood that is both computationally tractable and simple to apply in practice. Using this estimator, a deep belief network which has been suggested for the modeling of natural image patches is quantitatively investigated and compared to other models of natural image patches. Contrary to earlier claims based on qualitative results, the results presented in this article provide evidence that the model under investigation is not a particularly good model for natural image

Inferring decoding strategy from choice probabilities in the presence of noise correlations

The activity of cortical neurons in sensory areas covaries with perceptual decisions, a relationship often quantified by choice probabilities. While choice probabilities have been measured extensively, their interpretation has remained fraught with difficulty. Here, we derive the mathematical relationship between choice probabilities, read-out weights and noise correlations within the standard neural decision making model. Our solution allows us to prove and generalize earlier observations based on numerical simulations, and to derive novel predictions. Importantly, we show how the read-out weight profile, or decoding strategy, can be inferred from experimentally measurable quantities. Furthermore, we present a test to decide whether the decoding weights of individual neurons are optimal, even without knowing the underlying noise correlations. We confirm the practical feasibility of our approach using simulated data from a realistic population model. Our work thus provides the theoretical foundation for a growing body of experimental results on choice probabilities and correlations

Bayesian estimation of orientation preference maps

Imaging techniques such as optical imaging of intrinsic signals, 2-photon calcium imaging and voltage sensitive dye imaging can be used to measure the functional organization of visual cortex across different spatial and temporal scales. Here, we present Bayesian methods based on Gaussian processes for extracting topographic maps from functional imaging data. In particular, we focus on the estimation of orientation preference maps (OPMs) from intrinsic signal imaging data. We model the underlying map as a bivariate Gaussian process, with a prior covariance function that reflects known properties of OPMs, and a noise covariance adjusted to the data. The posterior mean can be interpreted as an optimally smoothed estimate of the map, and can be used for model based interpolations of the map from sparse measurements. By sampling from the posterior distribution, we can get error bars on statistical properties such as preferred orientations, pinwheel locations or pinwheel counts. Finally, the use of an explicit probabilistic model facilitates interpretation of parameters and quantitative model comparisons. We demonstrate our model both on simulated data and on intrinsic signaling data from ferret visual cortex

Bayesian Evidential Deep Learning with PAC Regularization

We propose a novel method for closed-form predictive distribution modeling with neural nets. In quantifying prediction uncertainty, we build on Evidential Deep Learning, which has been impactful as being both simple to implement and giving closed-form access to predictive uncertainty. We employ it to model aleatoric uncertainty and extend it to account also for epistemic uncertainty by converting it to a Bayesian Neural Net. While extending its uncertainty quantification capabilities, we maintain its analytically accessible predictive distribution model by performing progressive moment matching for the first time for approximate weight marginalization. The eventual model introduces a prohibitively large number of hyperparameters for stable training. We overcome this drawback by deriving a vacuous PAC bound that comprises the marginal likelihood of the predictor and a complexity penalty. We observe on regression, classification, and out-of-domain detection benchmarks that our method improves model fit and uncertainty quantification

Counterfactual-based Root Cause Analysis for Dynamical Systems

Identifying the underlying reason for a failing dynamic process or otherwise anomalous observation is a fundamental challenge, yet has numerous industrial applications. Identifying the failure-causing sub-system using causal inference, one can ask the question: "Would the observed failure also occur, if we had replaced the behaviour of a sub-system at a certain point in time with its normal behaviour?" To this end, a formal description of behaviour of the full system is needed in which such counterfactual questions can be answered. However, existing causal methods for root cause identification are typically limited to static settings and focusing on additive external influences causing failures rather than structural influences. In this paper, we address these problems by modelling the dynamic causal system using a Residual Neural Network and deriving corresponding counterfactual distributions over trajectories. We show quantitatively that more root causes are identified when an intervention is performed on the structural equation and the external influence, compared to an intervention on the external influence only. By employing an efficient approximation to a corresponding Shapley value, we also obtain a ranking between the different subsystems at different points in time being responsible for an observed failure, which is applicable in settings with large number of variables. We illustrate the effectiveness of the proposed method on a benchmark dynamic system as well as on a real world river dataset

Bayesian Evidential Deep Learning with PAC Regularization

We propose a novel method for closed-form predictive distribution modeling with neural nets. In quantifying prediction uncertainty, we build on Evidential Deep Learning, which has been impactful as being both simple to implement and giving closed-form access to predictive uncertainty. We employ it to model aleatoric uncertainty and extend it to account also for epistemic uncertainty by converting it to a Bayesian Neural Net. While extending its uncertainty quantification capabilities, we maintain its analytically accessible predictive distribution model by performing progressive moment matching for the first time for approximate weight marginalization. The eventual model introduces a prohibitively large number of hyperparameters for stable training. We overcome this drawback by deriving a vacuous PAC bound that comprises the marginal likelihood of the predictor and a complexity penalty. We observe on regression, classification, and out-of-domain detection benchmarks that our method improves model fit and uncertainty quantification

Inferring the Structure of Ordinary Differential Equations

Understanding physical phenomena oftentimes means understanding the underlying dynamical system that governs observational measurements. While accurate prediction can be achieved with black box systems, they often lack interpretability and are less amenable for further expert investigation. Alternatively, the dynamics can be analysed via symbolic regression. In this paper, we extend the approach by (Udrescu et al., 2020) called AIFeynman to the dynamic setting to perform symbolic regression on ODE systems based on observations from the resulting trajectories. We compare this extension to state-of-the-art approaches for symbolic regression empirically on several dynamical systems for which the ground truth equations of increasing complexity are available. Although the proposed approach performs best on this benchmark, we observed difficulties of all the compared symbolic regression approaches on more complex systems, such as Cart-Pole

Bayesian Inference for Generalized Linear Models for Spiking Neurons

Generalized Linear Models (GLMs) are commonly used statistical methods for modelling the relationship between neural population activity and presented stimuli. When the dimension of the parameter space is large, strong regularization has to be used in order to fit GLMs to datasets of realistic size without overfitting. By imposing properly chosen priors over parameters, Bayesian inference provides an effective and principled approach for achieving regularization. Here we show how the posterior distribution over model parameters of GLMs can be approximated by a Gaussian using the Expectation Propagation algorithm. In this way, we obtain an estimate of the posterior mean and posterior covariance, allowing us to calculate Bayesian confidence intervals that characterize the uncertainty about the optimal solution. From the posterior we also obtain a different point estimate, namely the posterior mean as opposed to the commonly used maximum a posteriori estimate. We systematically compare the different inference techniques on simulated as well as on multi-electrode recordings of retinal ganglion cells, and explore the effects of the chosen prior and the performance measure used. We find that good performance can be achieved by choosing an Laplace prior together with the posterior mean estimate