Search bioRxiv⌕ Search

bioRxiv · 10.1101/2025.10.20.683584

Modelling Predictive Coding in the Primary Visual Cortex (V1): Layer 4 Receptive Field Properties in a Balanced Recurrent Spiking Neuronal Network

Abstract

Understanding how the cortex encodes sensory input in a biologically efficient and computationally robust manner remains a central question in neuroscience. Predictive coding offers a compelling theoretical framework for such cortical processing, but existing models lack the biological detail to fully explain the function of the cortical microcircuits. This study introduces a spiking neural network model of layer 4 of the primary visual cortex (V1), grounded in predictive coding principles, to clarify how the thalamorecipient layer transforms feedforward input into prediction-error-like signals under realistic excitatory-inhibitory constraints and to yield testable circuit-level predictions. The model integrates structured feedforward input, distinct excitatory and inhibitory populations, and balanced lateral connectivity to simulate spontaneous and stimulus-driven activity. Network responses are systematically examined under spatially unstructured noise input and structured grating stimuli. Neural membrane potentials encode real-time reconstruction errors between external input and internal estimates, with spikes dynamically correcting these mismatches. The network reproduces hallmark in vivo features, including irregular spontaneous activity, sparse and selective responses, and emergent orientation and phase tuning. Excitatory-Inhibitory (E-I) balance was maintained across conditions, with inhibitory neurons exhibiting tighter input coupling than excitatory neurons. Furthermore, the network exhibited contrast-dependent modulation of firing rates and E-I balance, dynamically adjusting its activity to changes in input strength. Decoding analyses demonstrates that structured inputs can be robustly reconstructed under moderate noise levels, although decoding fidelity declines sharply under severe corruption. Together, these results suggest that cortical layer 4 may serve as a structured sensory encoding stage in a hierarchical predictive coding system, providing a biologically grounded foundation for modeling prediction error computations in higher cortical areas. Author summaryIn this Study, we present a biologically grounded spiking neural network model of layer 4 of the primary visual cortex, built within the predictive coding framework. The aim is to better understand how this early cortical layer encodes sensory information while maintaining realistic neural dynamics. Many predictive coding models focus on higher cortical layers 2/3 and overlook layer 4s role. To address this, we develop here a network that integrates structured feedforward input via Gaborfiltered receptive fields, distinct excitatory and inhibitory populations, and fixed lateral connectivity, all adhering to Dales law. The model reproduces several in vivo features observed in layer 4 of the visual cortex, including sparse, irregular spiking, emergent orientation and phase tuning, and contrast-dependent firing. Notably, excitation and inhibition are dynamically balanced across input conditions without requiring synaptic learning. We also show that decoding performance remains robust under moderate noise levels, supporting that layer 4 provides a stable sensory foundation for higher-level prediction. This model offers a biologically realistic implementation of prediction error computation and sets the stage for hierarchical extensions that include feedback and learning. Overall, this work provides insights into how structured sensory representations and balance emerge in cortical microcircuits through architecture alone.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Nemati, E., Davey, C., Meffin, H. N., Burkitt, A. N.. 2025-10-21. Modelling Predictive Coding in the Primary Visual Cortex (V1): Layer 4 Receptive Field Properties in a Balanced Recurrent Spiking Neuronal Network. https://doi.org/10.1101/2025.10.20.683584

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

The Unreasonable Effectiveness of Cell Types in Describing Neuronal Physiological Features

Single-cell RNA sequencing (scRNA-seq) captures detailed gene expression profiles at scale, while patch-clamp recordings measure intrinsic neuronal electrophysiological properties. Modeling the relations between these two modalities remains a challenge. Here, we compare how well electrophysiological features can be predicted by traditional transcriptomic cell type classification, representations derived from a foundational model (scGPT) pretrained on large-scale scRNA-seq datasets, ion channel-coding genes, and highly variable genes. Using paired transcriptomic and electrophysiological patch-sequencing data from 495 human neurons from neurosurgical tissue, we find that cluster-level cell type representations consistently outperform highly variable gene selection, ion channel gene selection, and context-enriched scGPT embeddings. Notably, performance varies across model architectures and initializations, and the best results are obtained by combining the outputs of separate cell type and scGPT-based models. Together, these findings suggest that traditional discrete cellular classification is highly effective in predicting physiological features. For maximum performance it can be complemented by pretrained transformer models.

neuroscience↗

A nonlinear inhibition pathway underlying cortical responses to tuned holographic optogenetic perturbations

Optogenetics enables causal manipulation of cortical activity. Perturbation responses can be counterintuitive due to network interactions, making theory essential for predicting them. Existing approaches often rely on linear approximations, which fail for many biologically relevant perturbations. Here we develop a nonlinear theory of responses to holographic perturbations in cell-type-specific recurrent networks with structured connectivity. We fit a nonlinear model to mouse V1 data, which shows cotuned-ensemble suppression: perturbing spatially clustered neurons with similar preferred orientations yields markedly stronger short-range suppression than perturbing untuned ensembles. We show that cotuned-ensemble suppression arises from a feature-tuned, nonlinear inhibition pathway implicating somatostatin-positive (SST) interneurons. The theory predicts that cotuned ensembles suppress parvalbumin-positive (PV) neurons but facilitate SST neurons, and links the degree of cotuned-ensemble suppression or facilitation to the variance of the SST response. This framework identifies mechanisms by which nonlinear inhibition sculpts cortical dynamics and establishes a predictive basis for targeted optogenetic interventions.

neuroscience↗

Proteomic signatures of APOE ε4 across human tissues and cell types in Alzheimers disease

The apolipoprotein E {varepsilon}4 (APOE {varepsilon}4) allele is the strongest genetic risk factor for late-onset Alzheimers disease (AD). However, the underlying molecular mechanisms remain unclear. This study included 1691 participants from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP), 1226 participants from the Accelerating Medicines Partnership - Alzheimers Disease (AMP-AD) Diverse Cohorts Study, and 735 participants from the Alzheimers Disease Neuroimaging Initiative (ADNI). To characterise APOE {varepsilon}4 molecular effects, we analysed proteomic data from plasma, cerebrospinal fluid (CSF), and induced pluripotent stem cell (iPSC)-derived astrocytes and neurons, as well as transcriptomic and proteomic data from multiple brain regions. The association of APOE {varepsilon}4 with AD neuropathology was also examined. APOE {varepsilon}4 carriers shared a plasma proteomic signature enriched for immune processes, irrespective of AD diagnosis. A machine learning classifier trained on this signature discriminated APOE {varepsilon}4 carriers from non-carriers in an independent cohort using CSF proteomics. APOE {varepsilon}4 carriage was associated with higher Braak stages and Consortium to Establish a Registry for Alzheimers Disease (CERAD) score. However, only limited APOE {varepsilon}4-associated transcriptomic and proteomic changes were observed in bulk brain tissue, with poor cross-layer concordance. Proteomic analyses of iPSC-derived astrocytes and neurons further revealed cell-type-specific APOE {varepsilon}4-associated changes. APOE {varepsilon}4 is associated with a consistent proteomic signature across plasma and CSF. Its molecular effects in the brain differ across cell types, brain regions and molecular layers. These findings support the need for cell-type-resolved multi-omic studies to elucidate how APOE {varepsilon}4 confers AD risk.

neuroscience↗