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Senden, M.

Publications and source records attributed to Senden, M..

At least 19 recordsLinked to original sources

Predictive perception via simultaneous learning and inference

Perception has been proposed to involve an inferential process that combines noisy sensory evidence with prior expectations to estimate the latent states of the environment. Exact Bayesian inference is intractable in the continuous, high-dimensional state spaces of the natural world. Variational schemes address this by restricting the form of the posterior, whereas sampling schemes represent the posterior with a finite set of samples. In both cases the approximation concerns the posterior rather than the state space over which it is defined. Here we place the approximation elsewhere. Rather than restricting the form of the posterior, we restrict the state space, modeling environmental states as discrete and thereby making Bayesian filtering exact. Beliefs are then unconstrained in shape and what has to be learned can be reduced to a transition matrix updated online by a local rule. The cost is that the states, rather than the distribution, must be specified in advance. The Simultaneous Learning and Inference Model (SLIM) combines this exact filtering with a gated Hebbian rule that learns transitions from inferred rather than observed states. In simulations SLIM recovers environmental dynamics under sensory noise and adapts when those dynamics change, with error growing only once the sensor becomes uninformative. A hierarchical instantiation reproduces local and global prediction error effects. Applied to two auditory decision-making experiments under noise, SLIM reproduces behavioral signatures of expectation and supplies trial-level measures of expectation and surprise. Exact inference over a small discrete state space with a single local Hebbian rule is therefore sufficient to account for these phenomena, without an explicit optimization objective and without a parametric approximation to the posterior.

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The Evolving Landscape of Neuroscience

Understanding the evolution and structure of large scientific fields is crucial for optimizing knowledge production. Neuroscience is a rapidly expanding and diversifying field. To retain an overview of its cross-domain insights and research questions, this study leverages text-embedding and clustering techniques together with large language models for analyzing 461,316 articles published between 1999 and 2023 and reveals the fields structural organization and dominant research domains. Inter-cluster citation analysis uncovers a surprisingly integrated picture and key intellectual hubs that shape the broader landscape. The field further exhibits a strong experimental focus, widespread reliance on specific mechanistic explanations rather than unifying theoretical frameworks, and a growing emphasis on applied research. Fundamental research is at the risk of decline and cross-scale integration remains limited. This study provides a framework for understanding neurosciences trajectory and identifies potential avenues for strengthening the field, offering a model for understanding the trajectory of complex research communities.

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Gamma Synchrony Mediates Figure-Ground Perception

Gamma synchrony is ubiquitous in visual cortex, but whether it contributes to perceptual grouping remains contentious based on observations that gamma frequency is not consistent across stimulus features and that gamma synchrony depends on distances between image elements. These stimulus dependencies have been argued to challenge the idea that the visual system groups image elements by synchronizing the neural assemblies that encode them. Here we argue instead that these dependencies may shape synchrony in perceptually meaningful ways. Indeed, according to the theory of weakly coupled oscillators (TWCO), synchrony-based grouping mechanisms require stimulus dependence. Synchronization among coupled oscillators depends on frequency dissimilarity and coupling strength, which in early visual cortex relate to local feature dissimilarity and physical distance, respectively. We manipulated these factors in a texture segregation experiment wherein human observers identified the orientation of a figure defined by reduced contrast heterogeneity compared to the background. Human performance followed TWCO predictions both qualitatively and quantitatively, as formalized in a computational model. Moreover, we found that when enriched with a Hebbian learning rule, our model also predicted human learning effects: Increases in model gamma synchrony due to perceptual learning predicted improvements in texture segregation across sessions. Taken together, our data suggest that the stimulus-dependence of gamma synchrony captures local image statistics and is linked to the stimulus-dependence of texture segregation, and that the effect of visual experience on gamma synchrony provides a viable perceptual learning mechanism for training-induced improvements in texture segregation. Our results suggest that gamma synchrony with its inherent stimulus dependencies can provide a plausible mechanistic basis for perceptual grouping and visual scene segmentation.

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PrediRep: Modelling hierarchical predictive coding with an unsupervised deep learning network

Hierarchical predictive coding (hPC) proposes that the cortex continuously generates predictions of incoming sensory stimuli. Deep neural networks inspired by hPC are frequently used to probe the neurocomputational mechanisms suggested by the theory in silico and to generate hypotheses for experimental investigations. However, these networks often deviate from hPC by prioritizing computational efficiency over alignment with its principles. To remedy this, we introduce PrediRep, a deep learning model explicitly designed to emphasize alignment with the theory. PrediRep incorporates the principles of hPC found in the other networks, while avoiding their deviations from it. We evaluate the performance of PrediRep on a next-frame prediction task and its functional alignment with hPC, comparing it to other contemporary deep learning networks inspired by the theory. Our findings demonstrate that PrediRep achieves the closest functional alignment with hierarchical predictive coding without sacrificing computational performance.

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AngoraPy: A Python Toolkit For Modelling Anthropomorphic Goal-Driven Sensorimotor Systems

AO_SCPLOWBSTRACTC_SCPLOWGoal-driven deep learning is increasingly used to supplement classical modeling approaches in computational neuroscience. The strength of deep neural networks lies in their ability to autonomously learn the connectivity required to solve complex and ecologically valid tasks, obviating the need for hand-engineered or hypothesis-driven connectivity patterns. Consequently, goal-driven models can generate hypotheses about the neurocomputations underlying cortical processing. Whereas goal-driven modeling is becoming increasingly common in perception neuroscience, its application to sensorimotor control is currently hampered by the complexity of the methods required to train models comprising the closed sensation-action loop. To mitigate this hurdle, we introduce AngoraPy, a modeling library that provides researchers with the tools to train complex recurrent convolutional neural networks that model sensorimotor systems.

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Layered Structure of Cortex Explains Reversal Dynamics in Bistable Perception

Bistable perception involves the spontaneous alternation between two exclusive interpretations of a single stimulus. Previous research has suggested that this perceptual phenomenon results from winnerless dynamics in the cortex. Indeed, winnerless dynamics can explain many key behavioral characteristics of bistable perception. However, it fails to explain an increase in alternation rate that is typically observed in response to increased stimulus drive and instead predicts a decline in alternation rate. To reconcile this discrepancy, several lines of work have augmented winnerless dynamics with additional processes such as global gain control, input suppression, and release mechanisms. These offer potential explanations at an algorithmic level. But it remains unclear which, if any, of these mechanisms are implemented in the cortex and what their biological substrates might be. We show that the answers to these questions lie within the architecture of the cortical microcircuit. Utilizing a dynamic mean field approach, we implement a laminar columnar circuit with empirically derived interlaminar connectivity. By coupling two such circuits such that they exhibit competition, we are able to produce winnerless dynamics reflective of bistable perception. Within our model, we identify two mechanisms through which the layered structure of the cortex gives rise to increased alternation rate in response to increased stimulus drive. First, deep layers act to inhibit the upper layers, thereby reducing the attractor depth and increasing the alternation rate. Second, recurrent connections between superficial and granular layers implement an input suppression mechanism which again reduces the attractor depth of the winnerless competition. These findings demonstrate the functional significance of the layered cortical architecture as they showcase perceptual implications of neuroatomical properties such as interlaminar connectivity and layer-specific activation. Author summaryIn our study, we explore the mechanistic underpinnings of bistable perception, a phenomenon where a single visual stimulus can be perceived in two distinct ways, and where our percept alternates spontaneously between interpretations. Although winnerless competition mechanisms have been widely recognized to govern this, they fall short in explaining why we observe more perceptual alternations with a stronger stimulus. To uncover the cortexs role in this discrepancy, we constructed a detailed model that mirrors the layered structure and interlaminar connections of the cortex. Remarkably, the architecture of these layers emerged as instrumental players. We discovered that the deeper layers of the cortex seem to inhibit the upper layers, facilitating a quicker alternation between perceptions when stimulated. Additionally, the interlaminar recurrent connections between the upper output layer and middle input layer appeared to destabilize the prevailing interpretation of the stimulus, leading to faster alternations. Our research illuminates how the complex architecture of the cortex, particularly the interconnections between its layers, plays a pivotal role in influencing our perception. The layered structure of the cortex goes beyond mere anatomy; it influences our perceptual experiences.

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Neural Correlates of High-Level Visual Saliency Models

Visual saliency highlights regions in a scene that are most relevant to an observer. The process by which a saliency map is formed has been a crucial subject of investigation in both machine vision and neuroscience. Deep learning-based approaches incorporate high-level information and have achieved accurate predictions of eye movement patterns, the overt behavioral analogue of a saliency map. As such, they may constitute a suitable surrogate of cortical saliency computations. In this study, we leveraged recent advances in computational saliency modeling and the Natural Scenes Dataset (NSD) to examine the relationship between model-based representations and the brain. Our aim was to uncover the neural correlates of high-level saliency and compare them with low-level saliency as well as emergent features from neural networks trained on different tasks. The results identified hV4 as a key region for saliency computations, informed by semantic processing in ventral visual areas. During natural scene viewing, hV4 appears to serve a transformative role linking low- and high-level features to attentional selection. Moreover, we observed spatial biases in ventral and parietal areas for saliency-based receptive fields, shedding light on the interplay between attention and oculomotor behavior.

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The global communication architecture of the human brain transcends the subcortical - cortical - cerebellar subdivisions

The white matter is made of anatomical fibres that constitute the highway of long-range connections between different parts of the brain. This network is referred to as the brains structural connectivity and lays the foundation of network interaction between brain areas. When analysing the architectural principles of this global network most studies have mainly focused on cortico-cortical and partly on cortico-subcortical connections. Here we show, for the first time, how the integrated cortical, subcortical, and cerebellar brain areas shape the structural architecture of the whole brain. We find that dense clusters vertically transverse cortical, subcortical, and cerebellar brain areas, which are themselves centralised by a global rich-club consisting similarly of cortical and subcortical brain areas. Notably, the most prominent hubs can be found in subcortical brain regions, and their targeted in-silico lesions proved to be most harmful for global signal propagation. Individually, the cortical, subcortical, and cerebellar sub-networks manifest distinct network features despite some similarities, which underline their unique structural fingerprints. Our results, exposing the heterogeneity of internal organisation across cortex, subcortex, and cerebellum, and the crucial role of the subcortex for the integration of the global anatomical pathways, highlight the need to overcome the prevalent cortex-centric focus towards a global consideration of the structural connectivity.

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Unlocking the Secrets of the Primate Visual Cortex: A CNN-Based Approach Traces the Origins of Major Organizational Principles to Retinal Sampling

Primate visual cortex exhibits key organizational principles: Cortical magnification, eccentricity-dependent receptive field size and spatial frequency tuning as well as radial bias. We provide compelling evidence that these principles arise from the interplay of the non-uniform distribution of retinal ganglion cells (RGCs), and a quasi-uniform convergence rate from the retina to the cortex. We show that convolutional neural networks (CNNs) outfitted with a retinal sampling layer, which resamples images according to retinal ganglion cell density, develop these organizational principles. Surprisingly, our results indicate that radial bias is spatial-frequency dependent and only manifests for high spatial frequencies. For low spatial frequencies, the bias shifts towards orthogonal orientations. These findings introduce a novel hypothesis about the origin of radial bias. Quasi-uniform convergence limits the range of spatial frequencies (in retinal space) that can be resolved, while retinal sampling determines the spatial frequency content throughout the retina.

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Multi-Scale Spiking Network Model of Human Cerebral Cortex

Although the structure of cortical networks provides the necessary substrate for their neuronal activity, the structure alone does not suffice to understand it. Leveraging the increasing availability of human data, we developed a multi-scale, spiking network model of human cortex to investigate the relationship between structure and dynamics. In this model, each area in one hemisphere of the Desikan-Killiany parcellation is represented by a 1 mm2 column with a layered structure. The model aggregates data across multiple modalities, including electron microscopy, electrophysiology, morphological reconstructions, and DTI, into a coherent framework. It predicts activity on all scales from the single-neuron spiking activity to the area-level functional connectivity. We compared the model activity against human electrophysiological data and human resting-state fMRI data. This comparison reveals that the model can reproduce aspects of both spiking statistics and fMRI correlations if the cortico-cortical connections are sufficiently strong. Furthermore, we show that a single-spike perturbation propagates through the network within a time close to the limit imposed by the delays.

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ConvNets Develop Organizational Principles of the Visual Cortex when using Ganglion Cell-Based Sampling

AO_SCPLOWBSTRACTC_SCPLOWThe distribution of retinal ganglion cells in primate visual systems portrays a densely distributed central region, with an incrementally decreasing cell density as the angle of visual eccentricity increases. This results in a non-uniform sampling of the retinal image that resembles a wheelbarrow distortion. We propose that this sampling gives rise to several organizational properties of the primate visual system, including cortical magnification, linear relationship between eccentricity and receptive field sizes, eccentricity-dependent drop-off in spatial-frequency preference, and radial bias. We test this hypothesis by training a convolutional neural network to classify the orientation of sine gratings and Gabor stimuli, resampled according to retinal ganglion cell distributions. Our simulations show that introducing this sampling step gives rise to the aforementioned organizational principles in convolutional layers while only minimally affecting their classification performance. This lends credence to the notion that the retinal ganglion cell distribution is an important factor for the emergence of these organizational principles in visual systems.

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Extremely Fast pRF Mapping for Real-Time Applications

Population receptive field (pRF) mapping is a popular tool in computational neuroimaging that allows for the investigation of receptive field properties, their topography and interrelations in health and disease. Furthermore, the possibility to invert population receptive fields provides a decoding model for constructing stimuli from observed cortical activation patterns. This has been suggested to pave the road towards pRF-based brain-computer interface (BCI) communication systems, which would be able to directly decode internally visualized letters from topographically organized brain activity. A major stumbling block for such an application is, however, that the pRF mapping procedure is computationally heavy and time consuming. To address this, we propose a novel and fast pRF mapping procedure that is suitable for real-time applications. The method is build upon hashed-Gaussian encoding of the stimulus, which significantly reduces computational resources. After the stimulus is encoded, mapping can be performed using either ridge regression for fast offline analyses or gradient descent for real-time applications. We validate our model-agnostic approach in silico, as well as on empirical fMRI data obtained from 3T and 7T MRI scanners. Our approach is capable of estimating receptive fields and their parameters for millions of voxels in mere seconds. This method thus facilitates real-time applications of population receptive field mapping.

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Interfering with a memory without erasing its trace

Previous research has shown that performance of a novice skill can be easily interfered with by subsequent training of another skill. We address the open questions whether extensively trained skills show the same vulnerability to interference as novice skills and which memory mechanism regulates interference between expert skills. We developed a recurrent neural network model of V1 able to learn from feedback experienced over the course of a long-term orientation discrimination experiment. After first exposing the model to one discrimination task for 3480 consecutive trials, we assessed how its performance was affected by subsequent training in a second, similar task. Training the second task strongly interfered with the first (highly trained) discrimination skill. The magnitude of interference depended on the relative amounts of training devoted to the different tasks. We used these and other model outcomes as predictions for a perceptual learning experiment in which human participants underwent the same training protocol as our model. Specifically, over the course of three months participants underwent baseline training in one orientation discrimination task for 15 sessions before being trained for 15 sessions on a similar task and finally undergoing another 15 sessions of training on the first task (to assess interference). Across all conditions, the pattern of interference observed empirically closely matched model predictions. According to our model, behavioral interference can be explained by antagonistic changes in neuronal tuning induced by the two tasks. Remarkably, this did not stem from erasing connections due to earlier learning but rather from a reweighting of lateral inhibition.

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MOU-EC: model-based whole-brain effective connectivity to extract biomarkers for brain dynamics from fMRI data and study distributed cognition

Neuroimaging techniques are increasingly used to study brain cognition in humans. Beyond their individual activation, the functional associations between brain areas have become a standard proxy to describe how information is distributed across the brain network. Among the many analysis tools available, dynamic models of brain activity have been developed to overcome the limitations of original connectivity measures such as functional connectivity. In particular, much effort has been devoted to the assessment of directional interactions between brain areas from their observed activity. This paper summarizes our recent approach to analyze fMRI data based on our whole-brain effective connectivity referred to as MOU-EC, while discussing the pros and cons of its underlying assumptions with respect to other established approaches. Once tuned, the model provides a connectivity measure that reflects the dynamical state of BOLD activity obtained using fMRI, which can be used to explore the brain cognition. We focus on two important applications. First, as a connectivity measure, MOU-EC can be used to extract biomarkers for task-specific brain coordination, understood as the patterns of areas exchanging information. The multivariate nature of connectivity measures raises several challenges for whole-brain analysis, for which machine-learning tools presents some advantages over statistical testing. Second, we show how to interpret changes in MOU-EC connections in a collective and model-based manner, bridging with network analysis. To illustrate our framework, we use a dataset where subjects were recorded in two conditions, watching a movie and a black screen (referred to as rest). Our framework provides a comprehensive set of tools that open exciting perspectives for the study of distributed cognition, as well as neuropathologies.

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Configural properties underlie the perceived faceness of a stimulus

The global geometrical arrangement of face parts (eyes over nose over mouth), commonly referred to as first order configural (FOC) properties, is believed to constitute a fundamental aspect of face detection. Indeed, several brain regions in the face processing network have been shown to display increased activity in response to abstract stimuli for face-like as compared to random spatial arrangements. However, the absence of a mathematical formalization of FOC properties makes it difficult to systematically study their contribution to face perception. To fill this gap, we used analytical geometry to define a set of 19 FOC features. In two psychophysical studies, a 2-alternative forced choice task assessing difference in perceived faceness between two stimuli and a Likert test assessing measuring perceived faceness of individual stimuli, we evaluated the contribution of each feature to the perceived faceness of abstract stimuli consisting of four black rectangular shapes reflecting the two eyes, the nose and the mouth. From the two experiments two subsets of features relevant for face detection were selected, including 10 and 11 features, respectively. Interestingly, 7 features are shared between the two sets. The difference between the subsets reflects processing of individual FOC features in the first study and holistic processing in the second study. The partial superimposition, on the other hand, is reflective of a shared basic mechanism in the perception of first order configural properties.

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Comparing Task-Relevant Information Across Different Methods of Extracting Functional Connectivity

The concept of brain states, functionally relevant large-scale activity patterns, has become popular in neuroimaging. Not all components of such patterns are equally characteristic for each brain state, but machine learning provides a possibility for extracting and comparing the structure of brain states from functional data. However, their characterization in terms of functional connectivity measures varies widely, from cross-correlation to phase coherence, and the idea that different measures provide similar or coherent information is a common assumption made in neuroimaging. Here, we compare the brain state signatures extracted from of phase coherence, pairwise covariance, correlation, regularized covariance and regularized precision for a dataset of subjects performing five different cognitive tasks. In addition, we compare the classification performance in identifying the tasks for each connectivity measure. The measures are evaluated in their ability to discriminate the five tasks with two types of cross-validation: within-subject cross-validation, which reflects the stability of the signature over time; and between-subject cross-validation, which aims at extracting signatures that generalize across subjects. Secondly, we compare the informative features (connections or links between brain regions/areas) across measures to test the assumption that similar information is obtained about brain state signatures from different connectivity measures. In our results, the different types of cross-validation give different classification performance and emphasize that functional connectivity measures on fMRI require observation windows of sufficient duration. Furthermore, we find that informative links for the classification, meaning changes between tasks that are consistent across subjects, are entirely uncorrelated between BOLD correlations and covariances. These results indicate that the corresponding FC signature can strongly differ across FC methods used and that interpretation is subject to caution in terms of subnetworks related to a task.

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Reconstructing and decoding imagined letters from early visual cortex using ultra-high field fMRI

Visual mental imagery is the quasi-perceptual experience of \"seeing in the minds eye\". While a tight correspondence between imagery and perception in terms of subjective experience is well established, their correspondence in terms of neural representations remains insufficiently understood. In the present study, we exploit the high spatial resolution of functional magnetic resonance imaging (fMRI) at 7T, the retinotopic organization of early visual cortex, and machine learning techniques to investigate whether visual imagery of letter shapes preserves the topographic organization of perceived shapes. Sub-millimeter resolution fMRI images were obtained from early visual cortex in six subjects performing visual imagery of four different letter shapes. Predictions of imagery voxel activation patterns based on a population receptive field encoding model and physical letter stimuli provided first evidence in favor of detailed topographic organization. Subsequent visual field reconstructions of imagery data based on the inversion of the encoding model further showed that visual imagery preserves the geometric profile of letter shapes. These results open new avenues for decoding as we show that a denoising autoencoder can be used to pretrain a classifier purely based on perceptual data before fine-tuning it on imagery data. Finally, we show that the autoencoder can project imagery-related voxel activations onto their perceptual counterpart allowing for visually recognizable reconstructions even at the single-trial level. The latter may eventually be utilized for the development of content-based BCI letter-speller systems.

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Real Time Estimation of Population Receptive Fields Using Gradient Descent

A real-time population receptive field mapping procedure based on gradient descent is proposed. Model-free receptive fields produced by the algorithm are evaluated in context of simulated data exhibiting different levels of temporally autocorrelated noise and spatial point spread. As with any model-free approach, the exact shape of receptive fields produced by the real-time algorithm depends on the stimulus. Nevertheless, estimated receptive fields show good correspondence with ground-truth receptive fields in terms of both position and size. Furthermore, fitting a parametric model to the previously obtained estimates approximates the exact shape of the true underlying receptive fields well.

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