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There are two distinct classes of cells in the primary visual cortex (V1): simple cells and complex cells. One defining feature of complex cells is their spatial phase invariance; they respond strongly to oriented grating stimuli with a preferred orientation but with a wide range of spatial phases. A classical model of complete spatial phase invariance in complex cells is the energy model, in which the responses are the sum of the squared outputs of two linear spatially phase-shifted filters. However, recent experimental studies have shown that complex cells have a diverse range of spatial phase invariance and only a subset can be characterized by the energy model. While several models have been proposed to explain how complex cells could learn to be selective to orientation but invariant to spatial phase, most existing models overlook many biologically important details. We propose a biologically plausible model for complex cells that learns to pool inputs from simple cells based on the presentation of natural scene stimuli. The model is a three-layer network with rate-based neurons that describes the activities of LGN cells (layer 1), V1 simple cells (layer 2), and V1 complex cells (layer 3). The first two layers implement a recently proposed simple cell model that is biologically plausible and accounts for many experimental phenomena. The neural dynamics of the complex cells is modeled as the integration of simple cells inputs along with response normalization. Connections between LGN and simple cells are learned using Hebbian and anti-Hebbian plasticity. Connections between simple and complex cells are learned using a modified version of the Bienenstock, Cooper, and Munro (BCM) rule. Our results demonstrate that the learning rule can describe a diversity of complex cells, similar to those observed experimentally. Author summary: Many cortical functions originate from the learning ability of the brain. How the properties of cortical cells are learned is vital for understanding how the brain works. There are many models that explain how V1 simple cells can be learned. However, how V1 complex cells are learned still remains unclear. In this paper, we propose a model of learning in complex cells based on the Bienenstock, Cooper, and Munro (BCM) rule. We demonstrate that properties of receptive fields of complex cells can be learned using this biologically plausible learning rule. Quantitative comparisons between the model and experimental data are performed. Results show that model complex cells can account for the diversity of complex cells found in experimental studies. In summary, this study provides a plausible explanation for how complex cells can be learned using biologically plausible plasticity mechanisms. Our findings help us to better understand biological vision processing and provide us with insights into the general signal processing principles that the visual cortex employs to process visual information. [ABSTRACT FROM AUTHOR]

Neurons in the primary visual cortex respond selectively to simple features of visual stimuli, such as orientation and spatial frequency. Simple cells, which have phase-sensitive responses, can be modeled by a single receptive field filter in a linear-nonlinear model. However, it is challenging to analyze phase-invariant complex cells, which require more elaborate models having a combination of nonlinear subunits. Estimating parameters of these models is made additionally more difficult by cortical neurons' trial-to-trial response variability. We develop a simple convolutional neural network method to estimate receptive field models for both simple and complex visual cortex cells from their responses to natural images. The model consists of a spatiotemporal filter, a parameterized rectifier unit (PReLU), and a two-dimensional Gaussian "map" of the receptive field envelope. A single model parameter determines the simple vs. complex nature of the receptive field, capturing complex cell responses as a summation of homogeneous subunits, and collapsing to a linear-nonlinear model for simple type cells. The convolutional method predicts simple and complex cell responses to natural image stimuli as well as grating tuning curves. The fitted models yield a continuum of values for the PReLU parameter across the sampled neurons, showing that the simple/complex nature of cells can vary in a continuous manner. We demonstrate that complex-like cells respond less reliably than simple-like cells. However, compensation for this unreliability with noise ceiling analysis reveals predictive performance for complex cells proportionately closer to that for simple cells. Most spatial receptive field structures are well fit by Gabor functions, whose parameters confirm well-known properties of cat A17/18 receptive fields. Author summary: Methods for recording increasingly many visual cortex neurons are advancing rapidly, demanding new approaches to characterize diverse receptive fields. We present a compact convolutional neural network model of early cortical neurons, which is uniformly applicable to simple and complex cells, and whose parameters are straightforwardly interpretable and readily estimated from responses to natural image stimuli. This novel approach introduces a single estimated model parameter to capture the simple/complex nature of a neuron's receptive field, revealing a continuum of simple vs complex-like behaviour. We show that almost all complex-like cells exhibit a lower response reliability to repeated presentations of the same stimuli, compared to more reliable responses from simple-like cells. Accounting for this "noise ceiling" brings predictive performance for complex cells proportionately closer to that for simple cells. Using this model estimation approach with natural images, we evaluate findings from previous approaches that were restricted to simple-type cells and the use of grating or white noise stimuli, revealing a diversity of Gabor-like spatial receptive field shapes, which lie along a continuum of spatial bandwidths. [ABSTRACT FROM AUTHOR]

An influential account of neuronal responses in primary visual cortex is the normalized energy model. This model is often implemented as a multi-stage computation. The first stage is linear filtering. The second stage is the extraction of contrast energy, whereby a complex cell computes the squared and summed outputs of a pair of the linear filters in quadrature phase. The third stage is normalization, in which a local population of complex cells mutually inhibit one another. Because the population includes cells tuned to a range of orientations and spatial frequencies, the result is that the responses are effectively normalized by the local stimulus contrast. Here, using evidence from human functional MRI, we show that the classical model fails to account for the relative responses to two classes of stimuli: straight, parallel, band-passed contours (gratings), and curved, band-passed contours (snakes). The snakes elicit fMRI responses that are about twice as large as the gratings, yet a traditional divisive normalization model predicts responses that are about the same. Motivated by these observations and others from the literature, we implement a divisive normalization model in which cells matched in orientation tuning ("tuned normalization") preferentially inhibit each other. We first show that this model accounts for differential responses to these two classes of stimuli. We then show that the model successfully generalizes to other band-pass textures, both in V1 and in extrastriate cortex (V2 and V3). We conclude that even in primary visual cortex, complex features of images such as the degree of heterogeneity, can have large effects on neural responses. Author summary: How does the nervous system transform images into patterns of neural responses? A test of our understanding of this process is whether we can implement a computational model that takes digital images as input and accurately predicts responses in some part of the visual pathway. A widely used model of the transformation from image to neural response in primary visual cortex is the normalized energy model, in which image contrast drives neural activity, but the activity is self-limited because neural responses inhibit one another ("normalization"). We used functional MRI to measure the responses of human visual cortex while participants viewed a variety of images, and asked how accurately a normalized energy model could predict these responses. We find that if the model assumes that all neurons mutually inhibit one another ("untuned normalization") it is not accurate, but if it assumes that only neurons tuned to similar image features inhibit one another ("tuned normalization"), predictions are much more accurate. We speculate that feature-tuned normalization helps the brain extract meaningful information about higher-order image statistics that are prevalent in many natural images. [ABSTRACT FROM AUTHOR]

Many research questions in sensory neuroscience involve determining whether the neural representation of a stimulus property is invariant or specific to a particular stimulus context (e.g., Is object representation invariant to translation? Is the representation of a face feature specific to the context of other face features?). Between these two extremes, representations may also be context-tolerant or context-sensitive. Most neuroimaging studies have used operational tests in which a target property is inferred from a significant test against the null hypothesis of the opposite property. For example, the popular cross-classification test concludes that representations are invariant or tolerant when the null hypothesis of specificity is rejected. A recently developed neurocomputational theory suggests two insights regarding such tests. First, tests against the null of context-specificity, and for the alternative of context-invariance, are prone to false positives due to the way in which the underlying neural representations are transformed into indirect measurements in neuroimaging studies. Second, jointly performing tests against the nulls of invariance and specificity allows one to reach more precise and valid conclusions about the underlying representations, particularly when the null of invariance is tested using the fine-grained information from classifier decision variables rather than only accuracies (i.e., using the decoding separability test). Here, we provide empirical and computational evidence supporting both of these theoretical insights. In our empirical study, we use encoding of orientation and spatial position in primary visual cortex as a case study, as previous research has established that these properties are encoded in a context-sensitive way. Using fMRI decoding, we show that the cross-classification test produces false-positive conclusions of invariance, but that more valid conclusions can be reached by jointly performing tests against the null of invariance. The results of two simulations further support both of these conclusions. We conclude that more valid inferences about invariance or specificity of neural representations can be reached by jointly testing against both hypotheses, and using neurocomputational theory to guide the interpretation of results. Author summary: Many research questions in sensory neuroscience involve determining whether the representation of a stimulus property is invariant or specific to a change in stimulus context (e.g., translation-invariant object representation; configural representation of face features). Between these two extremes, representations may also be context-tolerant or context-sensitive. Most neuroimaging research has studied invariance using operational tests, among which the most widely used in recent years is cross-classification. We provide evidence from a functional MRI study, simulations, and theoretical results supporting two insights regarding such tests: (1) tests that seek to provide evidence for invariance (like cross-classification) have an inflated false positive rate, but (2) using complementary tests that seek evidence for context-specificity leads to more valid conclusions. [ABSTRACT FROM AUTHOR]

Connectomes represent comprehensive descriptions of neural connections in a nervous system to better understand and model central brain function and peripheral processing of afferent and efferent neural signals. Connectomes can be considered as a distinctive and necessary structural component alongside glial, vascular, neurochemical, and metabolic networks of the nervous systems of higher organisms that are required for the control of body functions and interaction with the environment. They are carriers of functional epiphenomena such as planning behavior and cognition, which are based on the processing of highly dynamic neural signaling patterns. In this study, we examine more detailed connectomes with edge weighting and orientation properties, in which reciprocal neuronal connections are also considered. Diffusion processes are a further necessary condition for generating dynamic bioelectric patterns in connectomes. Based on our high-precision connectome data, we investigate different diffusion-reaction models to study the propagation of dynamic concentration patterns in control and lesioned connectomes. Therefore, differential equations for modeling diffusion were combined with well-known reaction terms to allow the use of connection weights, connectivity orientation and spatial distances. Three reaction-diffusion systems Gray-Scott, Gierer-Meinhardt and Mimura-Murray were investigated. For this purpose, implicit solvers were implemented in a numerically stable reaction-diffusion system within the framework of neuroVIISAS. The implemented reaction-diffusion systems were applied to a subconnectome which shapes the mechanosensitive pathway that is strongly affected in the multiple sclerosis demyelination disease. It was found that demyelination modeling by connectivity weight modulation changes the oscillations of the target region, i.e. the primary somatosensory cortex, of the mechanosensitive pathway. In conclusion, a new application of reaction-diffusion systems to weighted and directed connectomes has been realized. Because the implementation were performed in the neuroVIISAS framework many possibilities for the study of dynamic reaction-diffusion processes in empirical connectomes as well as specific randomized network models are available now. Author summary: Reaction-diffusion systems were adapted and analyzed in weighted and directed connectomes. The systems were applied to a multiple sclerosis model by modulating connectivity weights within the reaction-diffusion process. This leads to changes in the oscillation patterns of a target region of the mechanosensitive pathway. [ABSTRACT FROM AUTHOR]

Construction of chromosomes 3D models based on single cell Hi-C data constitute an important challenge. We present a reconstruction approach, DPDchrom, that incorporates basic knowledge whether the reconstructed conformation should be coil-like or globular and spring relaxation at contact sites. In contrast to previously published protocols, DPDchrom can naturally form globular conformation due to the presence of explicit solvent. Benchmarking of this and several other methods on artificial polymer models reveals similar reconstruction accuracy at high contact density and DPDchrom advantage at low contact density. To compare 3D structures insensitively to spatial orientation and scale, we propose the Modified Jaccard Index. We analyzed two sources of the contact dropout: contact radius change and random contact sampling. We found that the reconstruction accuracy exponentially depends on the number of contacts per genomic bin allowing to estimate the reconstruction accuracy in advance. We applied DPDchrom to model chromosome configurations based on single-cell Hi-C data of mouse oocytes and found that these configurations differ significantly from a random one, that is consistent with other studies. Author summary: Reconstruction of 3D configuration of chromosomes based on single cell Hi-C data (contact matrix) constitutes an important way to understand the specific features of genome packaging in individual cells. For this purpose, we develop method DPDchrom based on dissipative particle dynamics. Two sources of the contact dropout, contact radius change and random contact sampling, have different impact to the reconstruction accuracy suggesting unequal value of contacts. We found the exponential dependence of the reconstruction accuracy on the number of contacts per genomic bin. We reconstructed entire nucleus of mouse using single cell Hi-C data and found significant dissimilarity of conformations reconstructed using experimental and shuffled data. These findings open perspectives to study 3D arrangement of cis-regulatory elements orchestrating transcription program. [ABSTRACT FROM AUTHOR]

Texture regularity, such as the repeating pattern in a carpet, brickwork or tree bark, is a ubiquitous feature of the visual world. The perception of regularity has generally been studied using multi-element textures in which the degree of regularity has been manipulated by adding random jitter to the elements' positions. Here we used three-factor Maximum Likelihood Conjoint Measurement (MLCM) for the first time to investigate the encoding of regularity information under more complex conditions in which element spacing and size, in addition to positional jitter, were manipulated. Human observers were presented with large numbers of pairs of multi-element stimuli with varying levels of the three factors, and indicated on each trial which stimulus appeared more regular. All three factors contributed to regularity perception. Jitter, as expected, strongly affected regularity perception. This effect of jitter on regularity perception is strongest at small element spacing and large texture element size, suggesting that the visual system utilizes the edge-to-edge distance between elements as the basis for regularity judgments. We then examined how the responses of a bank of Gabor wavelet spatial filters might account for our results. Our analysis indicates that the peakedness of the spatial frequency (SF) distribution, a previously favored proposal, is insufficient for regularity encoding since it varied more with element spacing and size than with jitter. Instead, our results support the idea that the visual system may extract texture regularity information from the moments of the SF-distribution across orientation. In our best-performing model, the variance of SF-distribution skew across orientations can explain 70% of the variance of estimated texture regularity from our data, suggesting that it could provide a candidate read-out for perceived regularity. Author summary: We investigated human perception of texture regularity, in which subjects made comparative judgements of regularity in pairs of texture stimuli with differing levels of three parameters of texture construction—spacing and size of texture elements, and their positional jitter. We analyzed the data using a novel approach involving three-factor Maximum Likelihood Conjoint Measurement (MLCM). We utilized a novel three-way approach in MLCM to evaluate the effect size and significance of the three factors as well as their interactions. We found that all three factors contributed to perceived regularity, with significant main effects and interactions between factors, in a manner suggesting edge-to-edge distances between elements might contribute importantly to regularity judgments. Using a bank of Gabor wavelet spatial filters to model the response of the human visual system to our textures, we compared four types of ways that the distribution of wavelet responses could account for our measured data on perceived regularity. Our results suggest that the orientation as well as spatial frequency (SF) information from the wavelet filters also contributes importantly—in particular, the skew of the variance of the SF-distribution across orientation provides a candidate basis for perceived texture regularity. [ABSTRACT FROM AUTHOR]

Local excitatory connections in mouse primary visual cortex (V1) are stronger and more prevalent between neurons that share similar functional response features. However, the details of how functional rules for local connectivity shape neuronal responses in V1 remain unknown. We hypothesised that complex responses to visual stimuli may arise as a consequence of rules for selective excitatory connectivity within the local network in the superficial layers of mouse V1. In mouse V1 many neurons respond to overlapping grating stimuli (plaid stimuli) with highly selective and facilitatory responses, which are not simply predicted by responses to single gratings presented alone. This complexity is surprising, since excitatory neurons in V1 are considered to be mainly tuned to single preferred orientations. Here we examined the consequences for visual processing of two alternative connectivity schemes: in the first case, local connections are aligned with visual properties inherited from feedforward input (a ‘like-to-like’ scheme specifically connecting neurons that share similar preferred orientations); in the second case, local connections group neurons into excitatory subnetworks that combine and amplify multiple feedforward visual properties (a ‘feature binding’ scheme). By comparing predictions from large scale computational models with in vivo recordings of visual representations in mouse V1, we found that responses to plaid stimuli were best explained by assuming ‘feature binding’ connectivity. Unlike under the ‘like-to-like’ scheme, selective amplification within feature-binding excitatory subnetworks replicated experimentally observed facilitatory responses to plaid stimuli; explained selective plaid responses not predicted by grating selectivity; and was consistent with broad anatomical selectivity observed in mouse V1. Our results show that visual feature binding can occur through local recurrent mechanisms without requiring feedforward convergence, and that such a mechanism is consistent with visual responses and cortical anatomy in mouse V1. [ABSTRACT FROM AUTHOR]