Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 41
Filtrar
1.
PLoS Comput Biol ; 19(4): e1011019, 2023 04.
Artículo en Inglés | MEDLINE | ID: mdl-37036844

RESUMEN

Neurons, represented as a tree structure of morphology, have various distinguished branches of dendrites. Different types of synaptic receptors distributed over dendrites are responsible for receiving inputs from other neurons. NMDA receptors (NMDARs) are expressed as excitatory units, and play a key physiological role in synaptic function. Although NMDARs are widely expressed in most types of neurons, they play a different role in the cerebellar Purkinje cells (PCs). Utilizing a computational PC model with detailed dendritic morphology, we explored the role of NMDARs at different parts of dendritic branches and regions. We found somatic responses can switch from silent, to simple spikes and complex spikes, depending on specific dendritic branches. Detailed examination of the dendrites regarding their diameters and distance to soma revealed diverse response patterns, yet explain two firing modes, simple and complex spike. Taken together, these results suggest that NMDARs play an important role in controlling excitability sensitivity while taking into account the factor of dendritic properties. Given the complexity of neural morphology varying in cell types, our work suggests that the functional role of NMDARs is not stereotyped but highly interwoven with local properties of neuronal structure.


Asunto(s)
Dendritas , Receptores de N-Metil-D-Aspartato , Dendritas/fisiología , Neuronas/fisiología , Células de Purkinje/fisiología , Sinapsis/fisiología , Potenciales de Acción/fisiología
2.
PLoS Comput Biol ; 18(3): e1009925, 2022 03.
Artículo en Inglés | MEDLINE | ID: mdl-35259159

RESUMEN

A central goal in sensory neuroscience is to understand the neuronal signal processing involved in the encoding of natural stimuli. A critical step towards this goal is the development of successful computational encoding models. For ganglion cells in the vertebrate retina, the development of satisfactory models for responses to natural visual scenes is an ongoing challenge. Standard models typically apply linear integration of visual stimuli over space, yet many ganglion cells are known to show nonlinear spatial integration, in particular when stimulated with contrast-reversing gratings. We here study the influence of spatial nonlinearities in the encoding of natural images by ganglion cells, using multielectrode-array recordings from isolated salamander and mouse retinas. We assess how responses to natural images depend on first- and second-order statistics of spatial patterns inside the receptive field. This leads us to a simple extension of current standard ganglion cell models. We show that taking not only the weighted average of light intensity inside the receptive field into account but also its variance over space can partly account for nonlinear integration and substantially improve response predictions of responses to novel images. For salamander ganglion cells, we find that response predictions for cell classes with large receptive fields profit most from including spatial contrast information. Finally, we demonstrate how this model framework can be used to assess the spatial scale of nonlinear integration. Our results underscore that nonlinear spatial stimulus integration translates to stimulation with natural images. Furthermore, the introduced model framework provides a simple, yet powerful extension of standard models and may serve as a benchmark for the development of more detailed models of the nonlinear structure of receptive fields.


Asunto(s)
Retina , Células Ganglionares de la Retina , Animales , Luz , Ratones , Estimulación Luminosa/métodos , Retina/fisiología , Células Ganglionares de la Retina/fisiología , Urodelos
3.
Neural Comput ; 34(6): 1369-1397, 2022 05 19.
Artículo en Inglés | MEDLINE | ID: mdl-35534008

RESUMEN

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.


Asunto(s)
Calcio , Corteza Visual , Animales , Encéfalo , Macaca , Redes Neurales de la Computación , Estimulación Luminosa , Corteza Visual/fisiología , Percepción Visual/fisiología
4.
PLoS Comput Biol ; 17(6): e1009163, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-34181653

RESUMEN

Synchronous oscillations in neural populations are considered being controlled by inhibitory neurons. In the granular layer of the cerebellum, two major types of cells are excitatory granular cells (GCs) and inhibitory Golgi cells (GoCs). GC spatiotemporal dynamics, as the output of the granular layer, is highly regulated by GoCs. However, there are various types of inhibition implemented by GoCs. With inputs from mossy fibers, GCs and GoCs are reciprocally connected to exhibit different network motifs of synaptic connections. From the view of GCs, feedforward inhibition is expressed as the direct input from GoCs excited by mossy fibers, whereas feedback inhibition is from GoCs via GCs themselves. In addition, there are abundant gap junctions between GoCs showing another form of inhibition. It remains unclear how these diverse copies of inhibition regulate neural population oscillation changes. Leveraging a computational model of the granular layer network, we addressed this question to examine the emergence and modulation of network oscillation using different types of inhibition. We show that at the network level, feedback inhibition is crucial to generate neural oscillation. When short-term plasticity was equipped on GoC-GC synapses, oscillations were largely diminished. Robust oscillations can only appear with additional gap junctions. Moreover, there was a substantial level of cross-frequency coupling in oscillation dynamics. Such a coupling was adjusted and strengthened by GoCs through feedback inhibition. Taken together, our results suggest that the cooperation of distinct types of GoC inhibition plays an essential role in regulating synchronous oscillations of the GC population. With GCs as the sole output of the granular network, their oscillation dynamics could potentially enhance the computational capability of downstream neurons.


Asunto(s)
Corteza Cerebelosa/citología , Corteza Cerebelosa/fisiología , Modelos Neurológicos , Animales , Biología Computacional , Sinapsis Eléctricas/fisiología , Potenciales Postsinápticos Excitadores/fisiología , Retroalimentación Fisiológica , Humanos , Potenciales Postsinápticos Inhibidores/fisiología , Fibras Nerviosas/fisiología , Red Nerviosa/citología , Red Nerviosa/fisiología , Vías Nerviosas/fisiología , Plasticidad Neuronal/fisiología , Neuronas/fisiología , Análisis de la Célula Individual/estadística & datos numéricos , Sinapsis/fisiología
5.
PLoS Comput Biol ; 17(11): e1009640, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34843460

RESUMEN

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.


Asunto(s)
Potenciales de Acción , Biología Computacional/métodos , Modelos Neurológicos , Red Nerviosa , Neuronas/fisiología , Algoritmos , Terminales Presinápticos/fisiología , Corteza Visual Primaria/fisiología
6.
PLoS Comput Biol ; 17(2): e1008670, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33566820

RESUMEN

The dynamics of cerebellar neuronal networks is controlled by the underlying building blocks of neurons and synapses between them. For which, the computation of Purkinje cells (PCs), the only output cells of the cerebellar cortex, is implemented through various types of neural pathways interactively routing excitation and inhibition converged to PCs. Such tuning of excitation and inhibition, coming from the gating of specific pathways as well as short-term plasticity (STP) of the synapses, plays a dominant role in controlling the PC dynamics in terms of firing rate and spike timing. PCs receive cascade feedforward inputs from two major neural pathways: the first one is the feedforward excitatory pathway from granule cells (GCs) to PCs; the second one is the feedforward inhibition pathway from GCs, via molecular layer interneurons (MLIs), to PCs. The GC-PC pathway, together with short-term dynamics of excitatory synapses, has been a focus over past decades, whereas recent experimental evidence shows that MLIs also greatly contribute to controlling PC activity. Therefore, it is expected that the diversity of excitation gated by STP of GC-PC synapses, modulated by strong inhibition from MLI-PC synapses, can promote the computation performed by PCs. However, it remains unclear how these two neural pathways are interacted to modulate PC dynamics. Here using a computational model of PC network installed with these two neural pathways, we addressed this question to investigate the change of PC firing dynamics at the level of single cell and network. We show that the nonlinear characteristics of excitatory STP dynamics can significantly modulate PC spiking dynamics mediated by inhibition. The changes in PC firing rate, firing phase, and temporal spike pattern, are strongly modulated by these two factors in different ways. MLIs mainly contribute to variable delays in the postsynaptic action potentials of PCs while modulated by excitation STP. Notably, the diversity of synchronization and pause response in the PC network is governed not only by the balance of excitation and inhibition, but also by the synaptic STP, depending on input burst patterns. Especially, the pause response shown in the PC network can only emerge with the interaction of both pathways. Together with other recent findings, our results show that the interaction of feedforward pathways of excitation and inhibition, incorporated with synaptic short-term dynamics, can dramatically regulate the PC activities that consequently change the network dynamics of the cerebellar circuit.


Asunto(s)
Corteza Cerebelosa/metabolismo , Redes Neurales de la Computación , Células de Purkinje/citología , Potenciales de Acción/fisiología , Animales , Cerebelo/fisiología , Simulación por Computador , Potenciales Postsinápticos Excitadores/fisiología , Humanos , Interneuronas/fisiología , Modelos Neurológicos , Vías Nerviosas , Plasticidad Neuronal/fisiología , Neuronas/metabolismo , Distribución Normal , Transducción de Señal , Sinapsis/fisiología , Transmisión Sináptica/fisiología
7.
Neural Comput ; 33(11): 2971-2995, 2021 10 12.
Artículo en Inglés | MEDLINE | ID: mdl-34474470

RESUMEN

Our real-time actions in everyday life reflect a range of spatiotemporal dynamic brain activity patterns, the consequence of neuronal computation with spikes in the brain. Most existing models with spiking neurons aim at solving static pattern recognition tasks such as image classification. Compared with static features, spatiotemporal patterns are more complex due to their dynamics in both space and time domains. Spatiotemporal pattern recognition based on learning algorithms with spiking neurons therefore remains challenging. We propose an end-to-end recurrent spiking neural network model trained with an algorithm based on spike latency and temporal difference backpropagation. Our model is a cascaded network with three layers of spiking neurons where the input and output layers are the encoder and decoder, respectively. In the hidden layer, the recurrently connected neurons with transmission delays carry out high-dimensional computation to incorporate the spatiotemporal dynamics of the inputs. The test results based on the data sets of spiking activities of the retinal neurons show that the proposed framework can recognize dynamic spatiotemporal patterns much better than using spike counts. Moreover, for 3D trajectories of a human action data set, the proposed framework achieves a test accuracy of 83.6% on average. Rapid recognition is achieved through the learning methodology-based on spike latency and the decoding process using the first spike of the output neurons. Taken together, these results highlight a new model to extract information from activity patterns of neural computation in the brain and provide a novel approach for spike-based neuromorphic computing.


Asunto(s)
Modelos Neurológicos , Redes Neurales de la Computación , Potenciales de Acción , Algoritmos , Humanos , Neuronas
8.
PLoS Comput Biol ; 12(11): e1005189, 2016 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-27814363

RESUMEN

Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations), in their temporal dimension (temporal neural response variations), or in their combination (temporally coordinated neural population firing). Here we investigate the utility of tensor factorizations of population spike trains along space and time. These factorizations decompose a dataset of single-trial population spike trains into spatial firing patterns (combinations of neurons firing together), temporal firing patterns (temporal activation of these groups of neurons) and trial-dependent activation coefficients (strength of recruitment of such neural patterns on each trial). We validated various factorization methods on simulated data and on populations of ganglion cells simultaneously recorded in the salamander retina. We found that single-trial tensor space-by-time decompositions provided low-dimensional data-robust representations of spike trains that capture efficiently both their spatial and temporal information about sensory stimuli. Tensor decompositions with orthogonality constraints were the most efficient in extracting sensory information, whereas non-negative tensor decompositions worked well even on non-independent and overlapping spike patterns, and retrieved informative firing patterns expressed by the same population in response to novel stimuli. Our method showed that populations of retinal ganglion cells carried information in their spike timing on the ten-milliseconds-scale about spatial details of natural images. This information could not be recovered from the spike counts of these cells. First-spike latencies carried the majority of information provided by the whole spike train about fine-scale image features, and supplied almost as much information about coarse natural image features as firing rates. Together, these results highlight the importance of spike timing, and particularly of first-spike latencies, in retinal coding.


Asunto(s)
Potenciales de Acción/fisiología , Algoritmos , Modelos Neurológicos , Modelos Estadísticos , Red Nerviosa/fisiología , Células Ganglionares de la Retina/fisiología , Animales , Simulación por Computador , Análisis Factorial , Humanos , Urodelos
9.
PLoS Comput Biol ; 11(7): e1004425, 2015 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-26230927

RESUMEN

When visual contrast changes, retinal ganglion cells adapt by adjusting their sensitivity as well as their temporal filtering characteristics. The latter has classically been described by contrast-induced gain changes that depend on temporal frequency. Here, we explored a new perspective on contrast-induced changes in temporal filtering by using spike-triggered covariance analysis to extract multiple parallel temporal filters for individual ganglion cells. Based on multielectrode-array recordings from ganglion cells in the isolated salamander retina, we found that contrast adaptation of temporal filtering can largely be captured by contrast-invariant sets of filters with contrast-dependent weights. Moreover, differences among the ganglion cells in the filter sets and their contrast-dependent contributions allowed us to phenomenologically distinguish three types of filter changes. The first type is characterized by newly emerging features at higher contrast, which can be reproduced by computational models that contain response-triggered gain-control mechanisms. The second type follows from stronger adaptation in the Off pathway as compared to the On pathway in On-Off-type ganglion cells. Finally, we found that, in a subset of neurons, contrast-induced filter changes are governed by particularly strong spike-timing dynamics, in particular by pronounced stimulus-dependent latency shifts that can be observed in these cells. Together, our results show that the contrast dependence of temporal filtering in retinal ganglion cells has a multifaceted phenomenology and that a multi-filter analysis can provide a useful basis for capturing the underlying signal-processing dynamics.


Asunto(s)
Potenciales de Acción/fisiología , Adaptación Ocular/fisiología , Sensibilidad de Contraste/fisiología , Modelos Neurológicos , Red Nerviosa/fisiología , Células Ganglionares de la Retina/fisiología , Animales , Simulación por Computador , Inhibición Neural/fisiología , Urodelos
10.
J Neural Eng ; 21(2)2024 Apr 25.
Artículo en Inglés | MEDLINE | ID: mdl-38621378

RESUMEN

Objective: Epilepsy is a complex disease spanning across multiple scales, from ion channels in neurons to neuronal circuits across the entire brain. Over the past decades, computational models have been used to describe the pathophysiological activity of the epileptic brain from different aspects. Traditionally, each computational model can aid in optimizing therapeutic interventions, therefore, providing a particular view to design strategies for treating epilepsy. As a result, most studies are concerned with generating specific models of the epileptic brain that can help us understand the certain machinery of the pathological state. Those specific models vary in complexity and biological accuracy, with system-level models often lacking biological details.Approach: Here, we review various types of computational model of epilepsy and discuss their potential for different therapeutic approaches and scenarios, including drug discovery, surgical strategies, brain stimulation, and seizure prediction. We propose that we need to consider an integrated approach with a unified modelling framework across multiple scales to understand the epileptic brain. Our proposal is based on the recent increase in computational power, which has opened up the possibility of unifying those specific epileptic models into simulations with an unprecedented level of detail.Main results: A multi-scale epilepsy model can bridge the gap between biologically detailed models, used to address molecular and cellular questions, and brain-wide models based on abstract models which can account for complex neurological and behavioural observations.Significance: With these efforts, we move toward the next generation of epileptic brain models capable of connecting cellular features, such as ion channel properties, with standard clinical measures such as seizure severity.


Asunto(s)
Encéfalo , Simulación por Computador , Epilepsia , Modelos Neurológicos , Humanos , Epilepsia/fisiopatología , Epilepsia/terapia , Encéfalo/fisiopatología , Animales , Red Nerviosa/fisiopatología
11.
Neural Netw ; 176: 106346, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38713970

RESUMEN

Spiking neural networks (SNNs) provide necessary models and algorithms for neuromorphic computing. A popular way of building high-performance deep SNNs is to convert ANNs to SNNs, taking advantage of advanced and well-trained ANNs. Here we propose an ANN to SNN conversion methodology that uses a time-based coding scheme, named At-most-two-spike Exponential Coding (AEC), and a corresponding AEC spiking neuron model for ANN-SNN conversion. AEC neurons employ quantization-compensating spikes to improve coding accuracy and capacity, with each neuron generating up to two spikes within the time window. Two exponential decay functions with tunable parameters are proposed to represent the dynamic encoding thresholds, based on which pixel intensities are encoded into spike times and spike times are decoded into pixel intensities. The hyper-parameters of AEC neurons are fine-tuned based on the loss function of SNN-decoded values and ANN-activation values. In addition, we design two regularization terms for the number of spikes, providing the possibility to achieve the best trade-off between accuracy, latency and power consumption. The experimental results show that, compared to other similar methods, the proposed scheme not only obtains deep SNNs with higher accuracy, but also has more significant advantages in terms of energy efficiency and inference latency. More details can be found at https://github.com/RPDS2020/AEC.git.


Asunto(s)
Potenciales de Acción , Algoritmos , Redes Neurales de la Computación , Neuronas , Potenciales de Acción/fisiología , Neuronas/fisiología , Modelos Neurológicos , Humanos
12.
Commun Biol ; 7(1): 487, 2024 Apr 22.
Artículo en Inglés | MEDLINE | ID: mdl-38649503

RESUMEN

The phenomenon of semantic satiation, which refers to the loss of meaning of a word or phrase after being repeated many times, is a well-known psychological phenomenon. However, the microscopic neural computational principles responsible for these mechanisms remain unknown. In this study, we use a deep learning model of continuous coupled neural networks to investigate the mechanism underlying semantic satiation and precisely describe this process with neuronal components. Our results suggest that, from a mesoscopic perspective, semantic satiation may be a bottom-up process. Unlike existing macroscopic psychological studies that suggest that semantic satiation is a top-down process, our simulations use a similar experimental paradigm as classical psychology experiments and observe similar results. Satiation of semantic objectives, similar to the learning process of our network model used for object recognition, relies on continuous learning and switching between objects. The underlying neural coupling strengthens or weakens satiation. Taken together, both neural and network mechanisms play a role in controlling semantic satiation.


Asunto(s)
Aprendizaje Profundo , Semántica , Humanos , Redes Neurales de la Computación , Modelos Neurológicos
13.
Artículo en Inglés | MEDLINE | ID: mdl-38265909

RESUMEN

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.

14.
Artículo en Inglés | MEDLINE | ID: mdl-38833393

RESUMEN

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.

15.
IEEE Trans Neural Netw Learn Syst ; 34(9): 5841-5855, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-34890341

RESUMEN

Spiking neural networks (SNNs), inspired by the neuronal network in the brain, provide biologically relevant and low-power consuming models for information processing. Existing studies either mimic the learning mechanism of brain neural networks as closely as possible, for example, the temporally local learning rule of spike-timing-dependent plasticity (STDP), or apply the gradient descent rule to optimize a multilayer SNN with fixed structure. However, the learning rule used in the former is local and how the real brain might do the global-scale credit assignment is still not clear, which means that those shallow SNNs are robust but deep SNNs are difficult to be trained globally and could not work so well. For the latter, the nondifferentiable problem caused by the discrete spike trains leads to inaccuracy in gradient computing and difficulties in effective deep SNNs. Hence, a hybrid solution is interesting to combine shallow SNNs with an appropriate machine learning (ML) technique not requiring the gradient computing, which is able to provide both energy-saving and high-performance advantages. In this article, we propose a HybridSNN, a deep and strong SNN composed of multiple simple SNNs, in which data-driven greedy optimization is used to build powerful classifiers, avoiding the derivative problem in gradient descent. During the training process, the output features (spikes) of selected weak classifiers are fed back to the pool for the subsequent weak SNN training and selection. This guarantees HybridSNN not only represents the linear combination of simple SNNs, as what regular AdaBoost algorithm generates, but also contains neuron connection information, thus closely resembling the neural networks of a brain. HybridSNN has the benefits of both low power consumption in weak units and overall data-driven optimizing strength. The network structure in HybridSNN is learned from training samples, which is more flexible and effective compared with existing fixed multilayer SNNs. Moreover, the topological tree of HybridSNN resembles the neural system in the brain, where pyramidal neurons receive thousands of synaptic input signals through their dendrites. Experimental results show that the proposed HybridSNN is highly competitive among the state-of-the-art SNNs.


Asunto(s)
Algoritmos , Redes Neurales de la Computación , Aprendizaje Automático , Neuronas/fisiología , Encéfalo/fisiología
16.
Artículo en Inglés | MEDLINE | ID: mdl-37227906

RESUMEN

Representation learning in heterogeneous graphs with massive unlabeled data has aroused great interest. The heterogeneity of graphs not only contains rich information, but also raises difficult barriers to designing unsupervised or self-supervised learning (SSL) strategies. Existing methods such as random walk-based approaches are mainly dependent on the proximity information of neighbors and lack the ability to integrate node features into a higher-level representation. Furthermore, previous self-supervised or unsupervised frameworks are usually designed for node-level tasks, which are commonly short of capturing global graph properties and may not perform well in graph-level tasks. Therefore, a label-free framework that can better capture the global properties of heterogeneous graphs is urgently required. In this article, we propose a self-supervised heterogeneous graph neural network (GNN) based on cross-view contrastive learning (HeGCL). The HeGCL presents two views for encoding heterogeneous graphs: the meta-path view and the outline view. Compared with the meta-path view that provides semantic information, the outline view encodes the complex edge relations and captures graph-level properties by using a nonlocal block. Thus, the HeGCL learns node embeddings through maximizing mutual information (MI) between global and semantic representations coming from the outline and meta-path view, respectively. Experiments on both node-level and graph-level tasks show the superiority of the proposed model over other methods, and further exploration studies also show that the introduction of nonlocal block brings a significant contribution to graph-level tasks.

17.
STAR Protoc ; 4(4): 102722, 2023 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-37976152

RESUMEN

Finding the complete functional circuits of neurons is a challenging problem in brain research. Here, we present a protocol, based on visual stimuli and spikes, for obtaining the complete circuit of recorded neurons using spike-triggered nonnegative matrix factorization. We describe steps for data preprocessing, inferring the spatial receptive field of the subunits, and analyzing the module matrix. This approach identifies computational components of the feedforward network of retinal ganglion cells and dissects the network structure based on natural image stimuli. For complete details on the use and execution of this protocol, please refer to Jia et al. (2021).1.


Asunto(s)
Modelos Neurológicos , Células Ganglionares de la Retina , Redes Neurales de la Computación , Algoritmos , Encéfalo
18.
J Cheminform ; 15(1): 118, 2023 Dec 08.
Artículo en Inglés | MEDLINE | ID: mdl-38066570

RESUMEN

The solubility of proteins stands as a pivotal factor in the realm of pharmaceutical research and production. Addressing the imperative to enhance production efficiency and curtail experimental costs, the demand arises for computational models adept at accurately predicting solubility based on provided datasets. Prior investigations have leveraged deep learning models and feature engineering techniques to distill features from raw protein sequences for solubility prediction. However, these methodologies have not thoroughly delved into the interdependencies among features or their respective magnitudes of significance. This study introduces HybridGCN, a pioneering Hybrid Graph Convolutional Network that elevates solubility prediction accuracy through the combination of diverse features, encompassing sophisticated deep-learning features and classical biophysical features. An exploration into the intricate interplay between deep-learning features and biophysical features revealed that specific biophysical attributes, notably evolutionary features, complement features extracted by advanced deep-learning models. Augmenting the model's capability for feature representation, we employed ESM, a substantial protein language model, to derive a zero-shot learning feature capturing comprehensive and pertinent information concerning protein functions and structures. Furthermore, we proposed a novel feature fusion module termed Adaptive Feature Re-weighting (AFR) to integrate multiple features, thereby enabling the fine-tuning of feature importance. Ablation experiments and comparative analyses attest to the efficacy of the HybridGCN approach, culminating in state-of-the-art performances on the public eSOL and S. cerevisiae datasets.

19.
Front Neurosci ; 17: 1291051, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-38249589

RESUMEN

Spiking neural networks (SNNs), as brain-inspired neural network models based on spikes, have the advantage of processing information with low complexity and efficient energy consumption. Currently, there is a growing trend to design hardware accelerators for dedicated SNNs to overcome the limitation of running under the traditional von Neumann architecture. Probabilistic sampling is an effective modeling approach for implementing SNNs to simulate the brain to achieve Bayesian inference. However, sampling consumes considerable time. It is highly demanding for specific hardware implementation of SNN sampling models to accelerate inference operations. Hereby, we design a hardware accelerator based on FPGA to speed up the execution of SNN algorithms by parallelization. We use streaming pipelining and array partitioning operations to achieve model operation acceleration with the least possible resource consumption, and combine the Python productivity for Zynq (PYNQ) framework to implement the model migration to the FPGA while increasing the speed of model operations. We verify the functionality and performance of the hardware architecture on the Xilinx Zynq ZCU104. The experimental results show that the hardware accelerator of the SNN sampling model proposed can significantly improve the computing speed while ensuring the accuracy of inference. In addition, Bayesian inference for spiking neural networks through the PYNQ framework can fully optimize the high performance and low power consumption of FPGAs in embedded applications. Taken together, our proposed FPGA implementation of Bayesian inference with SNNs has great potential for a wide range of applications, it can be ideal for implementing complex probabilistic model inference in embedded systems.

20.
Neural Netw ; 165: 135-149, 2023 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-37285730

RESUMEN

Depression, as a global mental health problem, is lacking effective screening methods that can help with early detection and treatment. This paper aims to facilitate the large-scale screening of depression by focusing on the speech depression detection (SDD) task. Currently, direct modeling on the raw signal yields a large number of parameters, and the existing deep learning-based SDD models mainly use the fixed Mel-scale spectral features as input. However, these features are not designed for depression detection, and the manual settings limit the exploration of fine-grained feature representations. In this paper, we learn the effective representations of the raw signals from an interpretable perspective. Specifically, we present a joint learning framework with attention-guided learnable time-domain filterbanks for depression classification (DALF), which collaborates with the depression filterbanks features learning (DFBL) module and multi-scale spectral attention learning (MSSA) module. DFBL is capable of producing biologically meaningful acoustic features by employing learnable time-domain filters, and MSSA is used to guide the learnable filters to better retain the useful frequency sub-bands. We collect a new dataset, the Neutral Reading-based Audio Corpus (NRAC), to facilitate the research in depression analysis, and we evaluate the performance of DALF on the NRAC and the public DAIC-woz datasets. The experimental results demonstrate that our method outperforms the state-of-the-art SDD methods with an F1 of 78.4% on the DAIC-woz dataset. In particular, DALF achieves F1 scores of 87.3% and 81.7% on two parts of the NRAC dataset. By analyzing the filter coefficients, we find that the most important frequency range identified by our method is 600-700Hz, which corresponds to the Mandarin vowels /e/ and /eˆ/ and can be considered as an effective biomarker for the SDD task. Taken together, our DALF model provides a promising approach to depression detection.


Asunto(s)
Depresión , Metil Paratión , Depresión/diagnóstico , Habla , Acústica
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA