arXiv subjects

Matthew Chalk

Publications and source records attributed to Matthew Chalk.

7 recordsLinked to original sources

arXiv2026

A multi-scale information geometry reveals the structure of mutual information in neural populations

Understanding how neural population responses represent sensory information is a central problem in systems neuroscience. One approach is to define a representational geometry on stimulus space in which distances reflect how reliably stimuli can be distinguished from neural activity. However, different constructions of these distances can lead to qualitatively different conclusions about the neural code. Here, we show that a unique Riemannian representational geometry emerges from first principles governing how distances contract as stimulus resolution is lost through coarse-graining. This results in a multi-scale extension of the Fisher information metric, capturing encoding structure from fine stimulus details to coarse global distinctions. The resulting geometry is exactly related to the mutual information encoded by the population: well encoded stimulus directions - those contributing more to mutual information - are expanded, whereas poorly encoded directions are contracted. The metric tensor can be estimated using diffusion models, making the framework practical for large neural populations and high-dimensional stimuli. Applied to visual cortical responses to natural images, the eigenvectors of the metric tensor identify stimulus variations that contribute most to information transmission, yielding interpretable features that are robust to modelling choices. Together, these results provide a principled, information-theoretic framework for characterising neural population codes.

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arXiv2025

Decomposing stimulus-specific sensory neural information via diffusion models

To understand sensory coding, we must ask not only how much information neurons encode, but also what that information is about. This requires decomposing mutual information into contributions from individual stimuli and stimulus features: a fundamentally ill-posed problem with infinitely many possible solutions. We address this by introducing three core axioms, additivity, positivity, and locality that any meaningful stimulus-wise decomposition should satisfy. We then derive a decomposition that meets all three criteria and remains tractable for high-dimensional stimuli. Our decomposition can be efficiently estimated using diffusion models, allowing for scaling up to complex, structured and naturalistic stimuli. Applied to a model of visual neurons, our method quantifies how specific stimuli and features contribute to encoded information. Our approach provides a scalable, interpretable tool for probing representations in both biological and artificial neural systems.

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arXiv2023

Human-in-the-Loop Optimization for Deep Stimulus Encoding in Visual Prostheses

Neuroprostheses show potential in restoring lost sensory function and enhancing human capabilities, but the sensations produced by current devices often seem unnatural or distorted. Exact placement of implants and differences in individual perception lead to significant variations in stimulus response, making personalized stimulus optimization a key challenge. Bayesian optimization could be used to optimize patient-specific stimulation parameters with limited noisy observations, but is not feasible for high-dimensional stimuli. Alternatively, deep learning models can optimize stimulus encoding strategies, but typically assume perfect knowledge of patient-specific variations. Here we propose a novel, practically feasible approach that overcomes both of these fundamental limitations. First, a deep encoder network is trained to produce optimal stimuli for any individual patient by inverting a forward model mapping electrical stimuli to visual percepts. Second, a preferential Bayesian optimization strategy utilizes this encoder to optimize patient-specific parameters for a new patient, using a minimal number of pairwise comparisons between candidate stimuli. We demonstrate the viability of this approach on a novel, state-of-the-art visual prosthesis model. We show that our approach quickly learns a personalized stimulus encoder, leads to dramatic improvements in the quality of restored vision, and is robust to noisy patient feedback and misspecifications in the underlying forward model. Overall, our results suggest that combining the strengths of deep learning and Bayesian optimization could significantly improve the perceptual experience of patients fitted with visual prostheses and may prove a viable solution for a range of neuroprosthetic technologies.

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arXiv2021

Contextual Bayesian optimization with binary outputs

Bayesian optimization (BO) is an efficient method to optimize expensive black-box functions. It has been generalized to scenarios where objective function evaluations return stochastic binary feedback, such as success/failure in a given test, or preference between different parameter settings. In many real-world situations, the objective function can be evaluated in controlled 'contexts' or 'environments' that directly influence the observations. For example, one could directly alter the 'difficulty' of the test that is used to evaluate a system's performance. With binary feedback, the context determines the information obtained from each observation. For example, if the test is too easy/hard, the system will always succeed/fail, yielding uninformative binary outputs. Here we combine ideas from Bayesian active learning and optimization to efficiently choose the best context and optimization parameter on each iteration. We demonstrate the performance of our algorithm and illustrate how it can be used to tackle a concrete application in visual psychophysics: efficiently improving patients' vision via corrective lenses, using psychophysics measurements.

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arXiv2021

Efficient Exploration in Binary and Preferential Bayesian Optimization

Bayesian optimization (BO) is an effective approach to optimize expensive black-box functions, that seeks to trade-off between exploitation (selecting parameters where the maximum is likely) and exploration (selecting parameters where we are uncertain about the objective function). In many real-world situations, direct measurements of the objective function are not possible, and only binary measurements such as success/failure or pairwise comparisons are available. To perform efficient exploration in this setting, we show that it is important for BO algorithms to distinguish between different types of uncertainty: epistemic uncertainty, about the unknown objective function, and aleatoric uncertainty, which comes from noisy observations and cannot be reduced. In effect, only the former is important for efficient exploration. Based on this, we propose several new acquisition functions that outperform state-of-the-art heuristics in binary and preferential BO, while being fast to compute and easy to implement. We then generalize these acquisition rules to batch learning, where multiple queries are performed simultaneously.

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arXiv2018

Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons

Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network, and thus depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expected to be robust to changes of the stimulus ensemble. Despite the importance of this distinction for understanding how sensory networks encode information collectively, no method exists to reliably separate intrinsic interactions from extrinsic correlations in neural activity data, limiting our ability to build predictive models of the network response. In this paper we introduce a general strategy to infer {population models of interacting neurons that collectively encode stimulus information}. The key to disentangling intrinsic from extrinsic correlations is to infer the {couplings between neurons} separately from the encoding model, and to combine the two using corrections calculated in a mean-field approximation. We demonstrate the effectiveness of this approach on retinal recordings. The same coupling network is inferred from responses to radically different stimulus ensembles, showing that these couplings indeed reflect stimulus-independent interactions between neurons. The inferred model predicts accurately the collective response of retinal ganglion cell populations as a function of the stimulus.

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arXiv2016

Relevant sparse codes with variational information bottleneck

In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximizes information about a 'relevance' variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximizing a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelized versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y.

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