A central challenge in sensory neuroscience is to understand neural computations and circuit mechanisms that underlie the encoding of ethologically relevant, natural stimuli. In multilayered neural circuits, nonlinear processes such as synaptic transmission and spiking dynamics present a significant obstacle to the creation of accurate computational models of responses to natural stimuli. Here we demonstrate that deep convolutional neural networks (CNNs) capture retinal responses to natural scenes nearly to within the variability of a cell's response, and are markedly more accurate than linear-nonlinear (LN) models and Generalized Linear Models (GLMs). Moreover, we find two additional surprising properties of CNNs: they are less susceptible to overfitting than their LN counterparts when trained on small amounts of data, and generalize better when tested on stimuli drawn from a different distribution (e.g. between natural scenes and white noise). An examination of the learned CNNs reveals several properties.

In these frameworks, templates are constructed using an iterative process of template estimation and alignment, which is often computationally very expensive. Due in part to this shortcoming, most methods compute asingle template for the entire population of images, or a few templates for specific sub-groups of the data.

We develop a finite-sample, design-based theory for random forests in which each tree is a randomized conditional predictor acting on fixed covariates and the forest is their Monte Carlo average. An exact variance identity separates Monte Carlo error from a covariance floor that persists under infinite aggregation. The floor arises through two mechanisms: observation reuse, where the same training outcomes receive weight across multiple trees, and partition alignment, where independently generated trees discover similar conditional prediction rules. We prove the floor is strictly positive under minimal conditions and show that alignment persists even when sample splitting eliminates observation overlap entirely. We introduce procedure-aligned synthetic resampling (PASR) to estimate the covariance floor, decomposing the total prediction uncertainty of a deployed forest into interpretable components. For continuous outcomes, resulting prediction intervals achieve nominal coverage with a theoretically guaranteed conservative bias direction. For classification forests, the PASR estimator is asymptotically unbiased, providing the first pointwise confidence intervals for predicted conditional probabilities from a deployed forest. Nominal coverage is maintained across a range of design configurations for both outcome types, including high-dimensional settings. The underlying theory extends to any tree-based ensemble with an exchangeable tree-generating mechanism.

In healthcare, predictive models increasingly inform patient-level decisions, yet little attention is paid to the variability in individual risk estimates and its impact on treatment decisions. For overparameterized models, now standard in machine learning, a substantial source of variability often goes undetected. Even when the data and model architecture are held fixed, randomness introduced by optimization and initialization can lead to materially different risk estimates for the same patient. This problem is largely obscured by standard evaluation practices, which rely on aggregate performance metrics (e.g., log-loss, accuracy) that are agnostic to individual-level stability. As a result, models with indistinguishable aggregate performance can nonetheless exhibit substantial procedural arbitrariness, which can undermine clinical trust. We propose an evaluation framework that quantifies individual-level prediction instability by using two complementary diagnostics: empirical prediction interval width (ePIW), which captures variability in continuous risk estimates, and empirical decision flip rate (eDFR), which measures instability in threshold-based clinical decisions. We apply these diagnostics to simulated data and GUSTO-I clinical dataset. Across observed settings, we find that for flexible machine-learning models, randomness arising solely from optimization and initialization can induce individual-level variability comparable to that produced by resampling the entire training dataset. Neural networks exhibit substantially greater instability in individual risk predictions compared to logistic regression models. Risk estimate instability near clinically relevant decision thresholds can alter treatment recommendations. These findings that stability diagnostics should be incorporated into routine model validation for assessing clinical reliability.

Withoutrequiring repeatable trials, itcanflexibly capture covariate-dependent jointSCDs, andprovide interpretable latent causes underlying the statistical dependencies between neurons.

Simultaneous behavioral and electrophysiological recordings call for new methods to reveal the interactions between neural activity and behavior. A milestone would be an interpretable model of the co-variability of spiking activity and behavior across trials. Here, we model a mouse cortical sensory-motor pathway in a tactile detection task reported by licking with a large recurrent spiking neural network (RSNN), fitted to the recordings via gradient-based optimization. We focus specifically on the difficulty to match the trial-to-trial variability in the data. Our solution relies on optimal transport to define a distance between the distributions of generated and recorded trials. The technique is applied to artificial data and neural recordings covering six cortical areas. We find that the resulting RSNN can generate realistic cortical activity and predict jaw movements across the main modes of trial-to-trial variability. Our analysis also identifies an unexpected mode of variability in the data corresponding to task-irrelevant movements of the mouse.

Proceedings of the International Conference on Machine Learning 2024