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Radiology Radiology

Reactivation of Motor-Related Gamma Activity in Human NREM Sleep.

In Frontiers in neuroscience ; h5-index 72.0

Models of memory consolidation posit a central role for reactivation of brain activity patterns during sleep, especially in non-Rapid Eye Movement (NREM) sleep. While such "replay" of recent waking experiences has been well-demonstrated in rodents, electrophysiological evidence of reactivation in human sleep is still largely lacking. In this intracranial study in patients with epilepsy (N = 9) we explored the spontaneous electroencephalographic reactivation during sleep of spatial patterns of brain activity evoked by motor learning. We first extracted the gamma-band (60-140 Hz) patterns underlying finger movements during a tapping task and underlying no-movement during a short rest period just prior to the task, and trained a binary classifier to discriminate between motor movements vs. rest. We then used the trained model on NREM sleep data immediately after the task and on NREM sleep during a control sleep period preceding the task. Compared with the control sleep period, we found, at the subject level, an increase in the detection rate of motor-related patterns during sleep following the task, but without association with performance changes. These data provide electrophysiological support for the reoccurrence in NREM sleep of the neural activity related to previous waking experience, i.e. that a basic tenet of the reactivation theory does occur in human sleep.

Eichenlaub Jean-Baptiste, Biswal Siddharth, Peled Noam, Rivilis Nicole, Golby Alexandra J, Lee Jong Woo, Westover M Brandon, Halgren Eric, Cash Sydney S

2020

NREM sleep, human sleep, intracranial recordings, machine-learning, memory reactivation

General General

Synaptic Plasticity Dynamics for Deep Continuous Local Learning (DECOLLE).

In Frontiers in neuroscience ; h5-index 72.0

A growing body of work underlines striking similarities between biological neural networks and recurrent, binary neural networks. A relatively smaller body of work, however, addresses the similarities between learning dynamics employed in deep artificial neural networks and synaptic plasticity in spiking neural networks. The challenge preventing this is largely caused by the discrepancy between the dynamical properties of synaptic plasticity and the requirements for gradient backpropagation. Learning algorithms that approximate gradient backpropagation using local error functions can overcome this challenge. Here, we introduce Deep Continuous Local Learning (DECOLLE), a spiking neural network equipped with local error functions for online learning with no memory overhead for computing gradients. DECOLLE is capable of learning deep spatio temporal representations from spikes relying solely on local information, making it compatible with neurobiology and neuromorphic hardware. Synaptic plasticity rules are derived systematically from user-defined cost functions and neural dynamics by leveraging existing autodifferentiation methods of machine learning frameworks. We benchmark our approach on the event-based neuromorphic dataset N-MNIST and DvsGesture, on which DECOLLE performs comparably to the state-of-the-art. DECOLLE networks provide continuously learning machines that are relevant to biology and supportive of event-based, low-power computer vision architectures matching the accuracies of conventional computers on tasks where temporal precision and speed are essential.

Kaiser Jacques, Mostafa Hesham, Neftci Emre

2020

backpropagataon, embedded learning, neuromorphic hardware, spiking neural network, surrogate gradient algorithm

General General

Mixed-Precision Deep Learning Based on Computational Memory.

In Frontiers in neuroscience ; h5-index 72.0

Deep neural networks (DNNs) have revolutionized the field of artificial intelligence and have achieved unprecedented success in cognitive tasks such as image and speech recognition. Training of large DNNs, however, is computationally intensive and this has motivated the search for novel computing architectures targeting this application. A computational memory unit with nanoscale resistive memory devices organized in crossbar arrays could store the synaptic weights in their conductance states and perform the expensive weighted summations in place in a non-von Neumann manner. However, updating the conductance states in a reliable manner during the weight update process is a fundamental challenge that limits the training accuracy of such an implementation. Here, we propose a mixed-precision architecture that combines a computational memory unit performing the weighted summations and imprecise conductance updates with a digital processing unit that accumulates the weight updates in high precision. A combined hardware/software training experiment of a multilayer perceptron based on the proposed architecture using a phase-change memory (PCM) array achieves 97.73% test accuracy on the task of classifying handwritten digits (based on the MNIST dataset), within 0.6% of the software baseline. The architecture is further evaluated using accurate behavioral models of PCM on a wide class of networks, namely convolutional neural networks, long-short-term-memory networks, and generative-adversarial networks. Accuracies comparable to those of floating-point implementations are achieved without being constrained by the non-idealities associated with the PCM devices. A system-level study demonstrates 172 × improvement in energy efficiency of the architecture when used for training a multilayer perceptron compared with a dedicated fully digital 32-bit implementation.

Nandakumar S R, Le Gallo Manuel, Piveteau Christophe, Joshi Vinay, Mariani Giovanni, Boybat Irem, Karunaratne Geethan, Khaddam-Aljameh Riduan, Egger Urs, Petropoulos Anastasios, Antonakopoulos Theodore, Rajendran Bipin, Sebastian Abu, Eleftheriou Evangelos

2020

deep learning, in-memory computing, memristive devices, mixed-signal design, phase-change memory

General General

Early Detection of Alzheimer's Disease Using Magnetic Resonance Imaging: A Novel Approach Combining Convolutional Neural Networks and Ensemble Learning.

In Frontiers in neuroscience ; h5-index 72.0

Early detection is critical for effective management of Alzheimer's disease (AD) and screening for mild cognitive impairment (MCI) is common practice. Among several deep-learning techniques that have been applied to assessing structural brain changes on magnetic resonance imaging (MRI), convolutional neural network (CNN) has gained popularity due to its superb efficiency in automated feature learning with the use of a variety of multilayer perceptrons. Meanwhile, ensemble learning (EL) has shown to be beneficial in the robustness of learning-system performance via integrating multiple models. Here, we proposed a classifier ensemble developed by combining CNN and EL, i.e., the CNN-EL approach, to identify subjects with MCI or AD using MRI: i.e., classification between (1) AD and healthy cognition (HC), (2) MCIc (MCI patients who will convert to AD) and HC, and (3) MCIc and MCInc (MCI patients who will not convert to AD). For each binary classification task, a large number of CNN models were trained applying a set of sagittal, coronal, or transverse MRI slices; these CNN models were then integrated into a single ensemble. Performance of the ensemble was evaluated using stratified fivefold cross-validation method for 10 times. The number of the intersection points determined by the most discriminable slices separating two classes in a binary classification task among the sagittal, coronal, and transverse slice sets, transformed into the standard Montreal Neurological Institute (MNI) space, acted as an indicator to assess the ability of a brain region in which the points were located to classify AD. Thus, the brain regions with most intersection points were considered as those mostly contributing to the early diagnosis of AD. The result revealed an accuracy rate of 0.84 ± 0.05, 0.79 ± 0.04, and 0.62 ± 0.06, respectively, for classifying AD vs. HC, MCIc vs. HC, and MCIc vs. MCInc, comparable to previous reports and a 3D deep learning approach (3D-SENet) based on a more state-of-the-art and popular Squeeze-and-Excitation Networks model using channel attention mechanism. Notably, the intersection points accurately located the medial temporal lobe and several other structures of the limbic system, i.e., brain regions known to be struck early in AD. More interestingly, the classifiers disclosed multiple patterned MRI changes in the brain in AD and MCIc, involving these key regions. These results suggest that as a data-driven method, the combined CNN and EL approach can locate the most discriminable brain regions indicated by the trained ensemble model while the generalization ability of the ensemble model was maximized to successfully capture AD-related brain variations early in the disease process; it can also provide new insights into understanding the complex heterogeneity of whole-brain MRI changes in AD. Further research is needed to examine the clinical implication of the finding, capability of the advocated CNN-EL approach to help understand and evaluate an individual subject's disease status, symptom burden and progress, and the generalizability of the advocated CNN-EL approach to locate the most discriminable brain regions in the detection of other brain disorders such as schizophrenia, autism, and severe depression, in a data-driven way.

Pan Dan, Zeng An, Jia Longfei, Huang Yin, Frizzell Tory, Song Xiaowei

2020

Alzheimer’s Disease Neuroimaging Initiative, Alzheimer’s disease, MCI-to-AD conversion, MRI biomarkers, convolutional neural networks, ensemble learning, magnetic resonance imaging, mild cognitive impairment

General General

Computational Prediction of Ubiquitination Proteins Using Evolutionary Profiles and Functional Domain Annotation.

In Current genomics

Background : Ubiquitination, as a post-translational modification, is a crucial biological process in cell signaling, apoptosis, and localization. Identification of ubiquitination proteins is of fundamental importance for understanding the molecular mechanisms in biological systems and diseases. Although high-throughput experimental studies using mass spectrometry have identified many ubiquitination proteins and ubiquitination sites, the vast majority of ubiquitination proteins remain undiscovered, even in well-studied model organisms.

Objective : To reduce experimental costs, computational methods have been introduced to predict ubiquitination sites, but the accuracy is unsatisfactory. If it can be predicted whether a protein can be ubiquitinated or not, it will help in predicting ubiquitination sites. However, all the computational methods so far can only predict ubiquitination sites.

Methods : In this study, the first computational method for predicting ubiquitination proteins without relying on ubiquitination site prediction has been developed. The method extracts features from sequence conservation information through a grey system model, as well as functional domain annotation and subcellular localization.

Results : Together with the feature analysis and application of the relief feature selection algorithm, the results of 5-fold cross-validation on three datasets achieved a high accuracy of 90.13%, with Matthew's correlation coefficient of 80.34%. The predicted results on an independent test data achieved 87.71% as accuracy and 75.43% of Matthew's correlation coefficient, better than the prediction from the best ubiquitination site prediction tool available.

Conclusion : Our study may guide experimental design and provide useful insights for studying the mechanisms and modulation of ubiquitination pathways. The code is available at: https://github.com/Chunhuixu/UBIPredic_QWRCHX.

Qiu Wangren, Xu Chunhui, Xiao Xuan, Xu Dong

2019-Aug

Ubiquitination, functional domain, machine learning, protein annotation, random forest, subcellular localization

Radiology Radiology

Hyperspectral Microscopic Imaging for Automatic Detection of Head and Neck Squamous Cell Carcinoma Using Histologic Image and Machine Learning.

In Proceedings of SPIE--the International Society for Optical Engineering

The purpose of this study is to develop hyperspectral imaging (HSI) for automatic detection of head and neck cancer cells on histologic slides. A compact hyperspectral microscopic system is developed in this study. Histologic slides from 15 patients with squamous cell carcinoma (SCC) of the larynx and hypopharynx are imaged with the system. The proposed nuclei segmentation method based on principle component analysis (PCA) can extract most nuclei in the hyperspectral image without extracting other sub-cellular components. Both spectra-based support vector machine (SVM) and patch-based convolutional neural network (CNN) are used for nuclei classification. CNNs were trained with both hyperspectral images and pseudo RGB images of extracted nuclei, in order to evaluate the usefulness of extra information provided by hyperspectral imaging. The average accuracy of spectra-based SVM classification is 68%. The average AUC and average accuracy of the HSI patch-based CNN classification is 0.94 and 82.4%, respectively. The hyperspectral microscopic imaging and classification methods provide an automatic tool to aid pathologists in detecting SCC on histologic slides.

Ma Ling, Halicek Martin, Zhou Ximing, Dormer James, Fei Baowei

2020-Feb

Hyperspectral imaging, convolutional neural network, histology, nuclei extraction, support vector machine