Unraveling neural coding of dynamic natural visual scenes via convolutional recurrent neural networks

A systematic analysis of the joint effects of ganglion cells, lagged LGN cells, and intercortical inhibition on spatiotemporal processing and direction selectivity

Simple cells in the visual cortex process spatial as well as temporal information of the visual stream and enable the perception of motion information. Previous work suggests different mechanisms associated with direction selectivity, such as a temporal offset in thalamocortical input stream through lagged and non-lagged cells of the lateral geniculate nucleus (LGN), or solely from intercortical inhibition, or through a baseline selectivity provided by the thalamocortical connection tuned by intercortical inhibition. While there exists a large corpus of models for spatiotemporal receptive fields, the majority of them built-in the spatiotemporal dynamics by utilizing a combination of spatial and temporal functions and thus, do not explain the emergence of spatiotemporal dynamics on basis of network dynamics emerging in the retina and the LGN. In order to better comprehend the emergence of spatiotemporal processing and direction selectivity, we used a spiking neural network to implement the visual pathway from the retina to the primary visual cortex. By varying different functional parts in our network, we demonstrate how the direction selectivity of simple cells emerges through the interplay between two components: tuned intercortical inhibition and a temporal offset in the feedforward path through lagged LGN cells. In contrast to previous findings, our model simulations suggest an alternative dynamic between these two mechanisms: While intercortical inhibition alone leads to bidirectional selectivity, a temporal shift in the thalamocortical pathway breaks this symmetry in favor of one direction, leading to unidirectional selectivity.

Robust Sensory Information Reconstruction and Classification With Augmented Spikes

Sensory information recognition is primarily processed through the ventral and dorsal visual pathways in the primate brain visual system, which exhibits layered feature representations bearing a strong resemblance to convolutional neural networks (CNNs), encompassing reconstruction and classification. However, existing studies often treat these pathways as distinct entities, focusing individually on pattern reconstruction or classification tasks, overlooking a key feature of biological neurons, the fundamental units for neural computation of visual sensory information. Addressing these limitations, we introduce a unified framework for sensory information recognition with augmented spikes. By integrating pattern reconstruction and classification within a single framework, our approach not only accurately reconstructs multimodal sensory information but also provides precise classification through definitive labeling. Experimental evaluations conducted on various datasets including video scenes, static images, dynamic auditory scenes, and functional magnetic resonance imaging (fMRI) brain activities demonstrate that our framework delivers state-of-the-art pattern reconstruction quality and classification accuracy. The proposed framework enhances the biological realism of multimodal pattern recognition models, offering insights into how the primate brain visual system effectively accomplishes the reconstruction and classification tasks through the integration of ventral and dorsal pathways.

Robust Decoding of Rich Dynamical Visual Scenes With Retinal Spikes

Sensory information transmitted to the brain activates neurons to create a series of coping behaviors. Understanding the mechanisms of neural computation and reverse engineering the brain to build intelligent machines requires establishing a robust relationship between stimuli and neural responses. Neural decoding aims to reconstruct the original stimuli that trigger neural responses. With the recent upsurge of artificial intelligence, neural decoding provides an insightful perspective for designing novel algorithms of brain-machine interface. For humans, vision is the dominant contributor to the interaction between the external environment and the brain. In this study, utilizing the retinal neural spike data collected over multi trials with visual stimuli of two movies with different levels of scene complexity, we used a neural network decoder to quantify the decoded visual stimuli with six different metrics for image quality assessment establishing comprehensive inspection of decoding. With the detailed and systematical study of the effect and single and multiple trials of data, different noise in spikes, and blurred images, our results provide an in-depth investigation of decoding dynamical visual scenes using retinal spikes. These results provide insights into the neural coding of visual scenes and services as a guideline for designing next-generation decoding algorithms of neuroprosthesis and other devices of brain-machine interface.

Motion feature extraction using magnocellular-inspired spiking neural networks for drone detection

Traditional object detection methods usually underperform when locating tiny or small drones against complex backgrounds, since the appearance features of the targets and the backgrounds are highly similar. To address this, inspired by the magnocellular motion processing mechanisms, we proposed to utilize the spatial-temporal characteristics of the flying drones based on spiking neural networks, thereby developing the Magno-Spiking Neural Network (MG-SNN) for drone detection. The MG-SNN can learn to identify potential regions of moving targets through motion saliency estimation and subsequently integrates the information into the popular object detection algorithms to design the retinal-inspired spiking neural network module for drone motion extraction and object detection architecture, which integrates motion and spatial features before object detection to enhance detection accuracy. To design and train the MG-SNN, we propose a new backpropagation method called Dynamic Threshold Multi-frame Spike Time Sequence (DT-MSTS), and establish a dataset for the training and validation of MG-SNN, effectively extracting and updating visual motion features. Experimental results in terms of drone detection performance indicate that the incorporation of MG-SNN significantly improves the accuracy of low-altitude drone detection tasks compared to popular small object detection algorithms, acting as a cheap plug-and-play module in detecting small flying targets against complex backgrounds.

Decoding dynamic visual scenes across the brain hierarchy

Understanding the computational mechanisms that underlie the encoding and decoding of environmental stimuli is a crucial investigation in neuroscience. Central to this pursuit is the exploration of how the brain represents visual information across its hierarchical architecture. A prominent challenge resides in discerning the neural underpinnings of the processing of dynamic natural visual scenes. Although considerable research efforts have been made to characterize individual components of the visual pathway, a systematic understanding of the distinctive neural coding associated with visual stimuli, as they traverse this hierarchical landscape, remains elusive. In this study, we leverage the comprehensive Allen Visual Coding-Neuropixels dataset and utilize the capabilities of deep learning neural network models to study neural coding in response to dynamic natural visual scenes across an expansive array of brain regions. Our study reveals that our decoding model adeptly deciphers visual scenes from neural spiking patterns exhibited within each distinct brain area. A compelling observation arises from the comparative analysis of decoding performances, which manifests as a notable encoding proficiency within the visual cortex and subcortical nuclei, in contrast to a relatively reduced encoding activity within hippocampal neurons. Strikingly, our results unveil a robust correlation between our decoding metrics and well-established anatomical and functional hierarchy indexes. These findings corroborate existing knowledge in visual coding related to artificial visual stimuli and illuminate the functional role of these deeper brain regions using dynamic stimuli. Consequently, our results suggest a novel perspective on the utility of decoding neural network models as a metric for quantifying the encoding quality of dynamic natural visual scenes represented by neural responses, thereby advancing our comprehension of visual coding within the complex hierarchy of the brain.

Retrospective for the Dynamic Sensorium Competition for predicting large-scale mouse primary visual cortex activity from videos

Understanding how biological visual systems process information is challenging because of the nonlinear relationship between visual input and neuronal responses. Artificial neural networks allow computational neuroscientists to create predictive models that connect biological and machine vision. Machine learning has benefited tremendously from benchmarks that compare different model on the same task under standardized conditions. However, there was no standardized benchmark to identify state-of-the-art dynamic models of the mouse visual system. To address this gap, we established the SENSORIUM 2023 Benchmark Competition with dynamic input, featuring a new large-scale dataset from the primary visual cortex of ten mice. This dataset includes responses from 78,853 neurons to 2 hours of dynamic stimuli per neuron, together with the behavioral measurements such as running speed, pupil dilation, and eye movements. The competition ranked models in two tracks based on predictive performance for neuronal responses on a held-out test set: one focusing on predicting in-domain natural stimuli and another on out-of-distribution (OOD) stimuli to assess model generalization. As part of the NeurIPS 2023 competition track, we received more than 160 model submissions from 22 teams. Several new architectures for predictive models were proposed, and the winning teams improved the previous state-of-the-art model by 50%. Access to the dataset as well as the benchmarking infrastructure will remain online at www.sensorium-competition.net.

The Dynamic Sensorium competition for predicting large-scale mouse visual cortex activity from videos

Understanding how biological visual systems process information is challenging due to the complex nonlinear relationship between neuronal responses and high-dimensional visual input. Artificial neural networks have already improved our understanding of this system by allowing computational neuroscientists to create predictive models and bridge biological and machine vision. During the Sensorium 2022 competition, we introduced benchmarks for vision models with static input (i.e. images). However, animals operate and excel in dynamic environments, making it crucial to study and understand how the brain functions under these conditions. Moreover, many biological theories, such as predictive coding, suggest that previous input is crucial for current input processing. Currently, there is no standardized benchmark to identify state-of-the-art dynamic models of the mouse visual system. To address this gap, we propose the Sensorium 2023 Benchmark Competition with dynamic input (https://www.sensorium-competition.net/). This competition includes the collection of a new large-scale dataset from the primary visual cortex of ten mice, containing responses from over 78,000 neurons to over 2 hours of dynamic stimuli per neuron. Participants in the main benchmark track will compete to identify the best predictive models of neuronal responses for dynamic input (i.e. video). We will also host a bonus track in which submission performance will be evaluated on out-of-domain input, using withheld neuronal responses to dynamic input stimuli whose statistics differ from the training set. Both tracks will offer behavioral data along with video stimuli. As before, we will provide code, tutorials, and strong pre-trained baseline models to encourage participation. We hope this competition will continue to strengthen the accompanying Sensorium benchmarks collection as a standard tool to measure progress in large-scale neural system identification models of the entire mouse visual hierarchy and beyond.

Exploiting noise as a resource for computation and learning in spiking neural networks

Networks of spiking neurons underpin the extraordinary information-processing capabilities of the brain and have become pillar models in neuromorphic artificial intelligence. Despite extensive research on spiking neural networks (SNNs), most studies are established on deterministic models, overlooking the inherent non-deterministic, noisy nature of neural computations. This study introduces the noisy SNN (NSNN) and the noise-driven learning (NDL) rule by incorporating noisy neuronal dynamics to exploit the computational advantages of noisy neural processing. The NSNN provides a theoretical framework that yields scalable, flexible, and reliable computation and learning. We demonstrate that this framework leads to spiking neural models with competitive performance, improved robustness against challenging perturbations compared with deterministic SNNs, and better reproducing probabilistic computation in neural coding. Generally, this study offers a powerful and easy-to-use tool for machine learning, neuromorphic intelligence practitioners, and computational neuroscience researchers.

SpikeSEE: An energy-efficient dynamic scenes processing framework for retinal prostheses

Intelligent and low-power retinal prostheses are highly demanded in this era, where wearable and implantable devices are used for numerous healthcare applications. In this paper, we propose an energy-efficient dynamic scenes processing framework (SpikeSEE) that combines a spike representation encoding technique and a bio-inspired spiking recurrent neural network (SRNN) model to achieve intelligent processing and extreme low-power computation for retinal prostheses. The spike representation encoding technique could interpret dynamic scenes with sparse spike trains, decreasing the data volume. The SRNN model, inspired by the human retina's special structure and spike processing method, is adopted to predict the response of ganglion cells to dynamic scenes. Experimental results show that the Pearson correlation coefficient of the proposed SRNN model achieves 0.93, which outperforms the state-of-the-art processing framework for retinal prostheses. Thanks to the spike representation and SRNN processing, the model can extract visual features in a multiplication-free fashion. The framework achieves 8 times power reduction compared with the convolutional recurrent neural network (CRNN) processing-based framework. Our proposed SpikeSEE predicts the response of ganglion cells more accurately with lower energy consumption, which alleviates the precision and power issues of retinal prostheses and provides a potential solution for wearable or implantable prostheses.

Artificial intelligence techniques for retinal prostheses: a comprehensive review and future direction

Objective. Retinal prostheses are promising devices to restore vision for patients with severe age-related macular degeneration or retinitis pigmentosa disease. The visual processing mechanism embodied in retinal prostheses play an important role in the restoration effect. Its performance depends on our understanding of the retina's working mechanism and the evolvement of computer vision models. Recently, remarkable progress has been made in the field of processing algorithm for retinal prostheses where the new discovery of the retina's working principle and state-of-the-arts computer vision models are combined together.Approach. We investigated the related research on artificial intelligence techniques for retinal prostheses. The processing algorithm in these studies could be attributed to three types: computer vision-related methods, biophysical models, and deep learning models.Main results. In this review, we first illustrate the structure and function of the normal and degenerated retina, then demonstrate the vision rehabilitation mechanism of three representative retinal prostheses. It is necessary to summarize the computational frameworks abstracted from the normal retina. In addition, the development and feature of three types of different processing algorithms are summarized. Finally, we analyze the bottleneck in existing algorithms and propose our prospect about the future directions to improve the restoration effect.Significance. This review systematically summarizes existing processing models for predicting the response of the retina to external stimuli. What's more, the suggestions for future direction may inspire researchers in this field to design better algorithms for retinal prostheses.

Systematic reduction of the dimensionality of natural scenes allows accurate predictions of retinal ganglion cell spike outputs

The mammalian retina engages a broad array of linear and nonlinear circuit mechanisms to convert natural scenes into retinal ganglion cell (RGC) spike outputs. Although many individual integration mechanisms are well understood, we know less about how multiple mechanisms interact to encode the complex spatial features present in natural inputs. Here, we identified key spatial features in natural scenes that shape encoding by primate parasol RGCs. Our approach identified simplifications in the spatial structure of natural scenes that minimally altered RGC spike responses. We observed that reducing natural movies into 16 linearly integrated regions described ∼80% of the structure of parasol RGC spike responses; this performance depended on the number of regions but not their precise spatial locations. We used simplified stimuli to design high-dimensional metamers that recapitulated responses to naturalistic movies. Finally, we modeled the retinal computations that convert flashed natural images into one-dimensional spike counts.

Neural Decoding of Visual Information Across Different Neural Recording Modalities and Approaches

Vision plays a peculiar role in intelligence. Visual information, forming a large part of the sensory information, is fed into the human brain to formulate various types of cognition and behaviours that make humans become intelligent agents. Recent advances have led to the development of brain-inspired algorithms and models for machine vision. One of the key components of these methods is the utilization of the computational principles underlying biological neurons. Additionally, advanced experimental neuroscience techniques have generated different types of neural signals that carry essential visual information. Thus, there is a high demand for mapping out functional models for reading out visual information from neural signals. Here, we briefly review recent progress on this issue with a focus on how machine learning techniques can help in the development of models for contending various types of neural signals, from fine-scale neural spikes and single-cell calcium imaging to coarse-scale electroencephalography (EEG) and functional magnetic resonance imaging recordings of brain signals.

Decoding Pixel-Level Image Features from Two-Photon Calcium Signals of Macaque Visual Cortex

Images of visual scenes comprise essential features important for visual cognition of the brain. The complexity of visual features lies at different levels, from simple artificial patterns to natural images with different scenes. It has been a focus of using stimulus images to predict neural responses. However, it remains unclear how to extract features from neuronal responses. Here we address this question by leveraging two-photon calcium neural data recorded from the visual cortex of awake macaque monkeys. With stimuli including various categories of artificial patterns and diverse scenes of natural images, we employed a deep neural network decoder inspired by image segmentation technique. Consistent with the notation of sparse coding for natural images, a few neurons with stronger responses dominated the decoding performance, whereas decoding of ar tificial patterns needs a large number of neurons. When natural images using the model pretrained on artificial patterns are decoded, salient features of natural scenes can be extracted, as well as the conventional category information. Altogether, our results give a new perspective on studying neural encoding principles using reverse-engineering decoding strategies.

Representing the dynamics of high-dimensional data with non-redundant wavelets

A crucial question in data science is to extract meaningful information embedded in high-dimensional data into a low-dimensional set of features that can represent the original data at different levels. Wavelet analysis is a pervasive method for decomposing time-series signals into a few levels with detailed temporal resolution. However, obtained wavelets are intertwined and over-represented across levels for each sample and across different samples within one population. Here, using neuroscience data of simulated spikes, experimental spikes, calcium imaging signals, and human electrocorticography signals, we leveraged conditional mutual information between wavelets for feature selection. The meaningfulness of selected features was verified to decode stimulus or condition with high accuracy yet using only a small set of features. These results provide a new way of wavelet analysis for extracting essential features of the dynamics of spatiotemporal neural data, which then enables to support novel model design of machine learning with representative features.

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WCMI can extract meaningful information from high-dimensional data

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Extracted features from neural signals are non-redundant

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Simple decoders can read out these features with superb accuracy

One of the essential questions in data science is to extract meaningful information from high-dimensional data. A useful approach is to represent data using a few features that maintain the crucial information. The leading property of spatiotemporal data is foremost ever-changing dynamics in time. Wavelet analysis, as a classical method for disentangling time series, can capture temporal dynamics with detail. Here, we leveraged conditional mutual information between wavelets to select a small subset of non-redundant features. We demonstrated the efficiency and effectiveness of features using various types of neuroscience data with different sampling frequencies at the level of the single cell, cell population, and coarse-scale brain activity. Our results shed new insights into representing the dynamics of spatiotemporal data using a few fundamental features extracted by wavelet analysis, which may have wide implications to other types of data with rich temporal dynamics.

Retinal Processing: Insights from Mathematical Modelling

The retina is the entrance of the visual system. Although based on common biophysical principles, the dynamics of retinal neurons are quite different from their cortical counterparts, raising interesting problems for modellers. In this paper, I address some mathematically stated questions in this spirit, discussing, in particular: (1) How could lateral amacrine cell connectivity shape the spatio-temporal spike response of retinal ganglion cells? (2) How could spatio-temporal stimuli correlations and retinal network dynamics shape the spike train correlations at the output of the retina? These questions are addressed, first, introducing a mathematically tractable model of the layered retina, integrating amacrine cells' lateral connectivity and piecewise linear rectification, allowing for computing the retinal ganglion cells receptive field together with the voltage and spike correlations of retinal ganglion cells resulting from the amacrine cells networks. Then, I review some recent results showing how the concept of spatio-temporal Gibbs distributions and linear response theory can be used to characterize the collective spike response to a spatio-temporal stimulus of a set of retinal ganglion cells, coupled via effective interactions corresponding to the amacrine cells network. On these bases, I briefly discuss several potential consequences of these results at the cortical level.

Dissecting cascade computational components in spiking neural networks

Finding out the physical structure of neuronal circuits that governs neuronal responses is an important goal for brain research. With fast advances for large-scale recording techniques, identification of a neuronal circuit with multiple neurons and stages or layers becomes possible and highly demanding. Although methods for mapping the connection structure of circuits have been greatly developed in recent years, they are mostly limited to simple scenarios of a few neurons in a pairwise fashion; and dissecting dynamical circuits, particularly mapping out a complete functional circuit that converges to a single neuron, is still a challenging question. Here, we show that a recent method, termed spike-triggered non-negative matrix factorization (STNMF), can address these issues. By simulating different scenarios of spiking neural networks with various connections between neurons and stages, we demonstrate that STNMF is a persuasive method to dissect functional connections within a circuit. Using spiking activities recorded at neurons of the output layer, STNMF can obtain a complete circuit consisting of all cascade computational components of presynaptic neurons, as well as their spiking activities. For simulated simple and complex cells of the primary visual cortex, STNMF allows us to dissect the pathway of visual computation. Taken together, these results suggest that STNMF could provide a useful approach for investigating neuronal systems leveraging recorded functional neuronal activity.

It is well known that the computation of neuronal circuits is carried out through the staged and cascade structure of different types of neurons. Nevertheless, the information, particularly sensory information, is processed in a network primarily with feedforward connections through different pathways. A peculiar example is the early visual system, where light is transcoded by the retinal cells, routed by the lateral geniculate nucleus, and reached the primary visual cortex. One meticulous interest in recent years is to map out these physical structures of neuronal pathways. However, most methods so far are limited to taking snapshots of a static view of connections between neurons. It remains unclear how to obtain a functional and dynamical neuronal circuit beyond the simple scenarios of a few randomly sampled neurons. Using simulated spiking neural networks of visual pathways with different scenarios of multiple stages, mixed cell types, and natural image stimuli, we demonstrate that a recent computational tool, named spike-triggered non-negative matrix factorization, can resolve these issues. It enables us to recover the entire structural components of neural networks underlying the computation, together with the functional components of each individual neuron. Utilizing it for complex cells of the primary visual cortex allows us to reveal every underpinning of the nonlinear computation. Our results, together with other recent experimental and computational efforts, show that it is possible to systematically dissect neural circuitry with detailed structural and functional components.