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Updated Saturday, 25 September 2021

2021 ◽  
Vol 15 ◽  
Author(s):  
Lukas Muttenthaler ◽  
Martin N. Hebart

Over the past decade, deep neural network (DNN) models have received a lot of attention due to their near-human object classification performance and their excellent prediction of signals recorded from biological visual systems. To better understand the function of these networks and relate them to hypotheses about brain activity and behavior, researchers need to extract the activations to images across different DNN layers. The abundance of different DNN variants, however, can often be unwieldy, and the task of extracting DNN activations from different layers may be non-trivial and error-prone for someone without a strong computational background. Thus, researchers in the fields of cognitive science and computational neuroscience would benefit from a library or package that supports a user in the extraction task. THINGSvision is a new Python module that aims at closing this gap by providing a simple and unified tool for extracting layer activations for a wide range of pretrained and randomly-initialized neural network architectures, even for users with little to no programming experience. We demonstrate the general utility of THINGsvision by relating extracted DNN activations to a number of functional MRI and behavioral datasets using representational similarity analysis, which can be performed as an integral part of the toolbox. Together, THINGSvision enables researchers across diverse fields to extract features in a streamlined manner for their custom image dataset, thereby improving the ease of relating DNNs, brain activity, and behavior, and improving the reproducibility of findings in these research fields.


2021 ◽  
Vol 15 ◽  
Author(s):  
Florian Porrmann ◽  
Sarah Pilz ◽  
Alessandra Stella ◽  
Alexander Kleinjohann ◽  
Michael Denker ◽  
...  

The SPADE (spatio-temporal Spike PAttern Detection and Evaluation) method was developed to find reoccurring spatio-temporal patterns in neuronal spike activity (parallel spike trains). However, depending on the number of spike trains and the length of recording, this method can exhibit long runtimes. Based on a realistic benchmark data set, we identified that the combination of pattern mining (using the FP-Growth algorithm) and the result filtering account for 85–90% of the method's total runtime. Therefore, in this paper, we propose a customized FP-Growth implementation tailored to the requirements of SPADE, which significantly accelerates pattern mining and result filtering. Our version allows for parallel and distributed execution, and due to the improvements made, an execution on heterogeneous and low-power embedded devices is now also possible. The implementation has been evaluated using a traditional workstation based on an Intel Broadwell Xeon E5-1650 v4 as a baseline. Furthermore, the heterogeneous microserver platform RECS|Box has been used for evaluating the implementation on two HiSilicon Hi1616 (Kunpeng 916), an Intel Coffee Lake-ER Xeon E-2276ME, an Intel Broadwell Xeon D-D1577, and three NVIDIA Tegra devices (Jetson AGX Xavier, Jetson Xavier NX, and Jetson TX2). Depending on the platform, our implementation is between 27 and 200 times faster than the original implementation. At the same time, the energy consumption was reduced by up to two orders of magnitude.


2021 ◽  
Vol 15 ◽  
Author(s):  
Seonghun Park ◽  
Do-Won Kim ◽  
Chang-Hee Han ◽  
Chang-Hwan Im

Neurocinematics is an emerging discipline in neuroscience, which aims to provide new filmmaking techniques by analyzing the brain activities of a group of audiences. Several neurocinematics studies attempted to track temporal changes in mental states during movie screening; however, it is still needed to develop efficient and robust electroencephalography (EEG) features for tracking brain states precisely over a long period. This study proposes a novel method for estimating emotional arousal changes in a group of individuals during movie screening by employing steady-state visual evoked potential (SSVEP), which is a widely used EEG response elicited by the presentation of periodic visual stimuli. Previous studies have reported that the emotional arousal of each individual modulates the strength of SSVEP responses. Based on this phenomenon, movie clips were superimposed on a background, eliciting an SSVEP response with a specific frequency. Two emotionally arousing movie clips were presented to six healthy male participants, while EEG signals were recorded from the occipital channels. We then investigated whether the movie scenes that elicited higher SSVEP responses coincided well with those rated as the most impressive scenes by 37 viewers in a separate experimental session. Our results showed that the SSVEP response averaged across six participants could accurately predict the overall impressiveness of each movie, evaluated with a much larger group of individuals.


2021 ◽  
Vol 15 ◽  
Author(s):  
Isaac Goicovich ◽  
Paulo Olivares ◽  
Claudio Román ◽  
Andrea Vázquez ◽  
Cyril Poupon ◽  
...  

Fiber clustering methods are typically used in brain research to study the organization of white matter bundles from large diffusion MRI tractography datasets. These methods enable exploratory bundle inspection using visualization and other methods that require identifying brain white matter structures in individuals or a population. Some applications, such as real-time visualization and inter-subject clustering, need fast and high-quality intra-subject clustering algorithms. This work proposes a parallel algorithm using a General Purpose Graphics Processing Unit (GPGPU) for fiber clustering based on the FFClust algorithm. The proposed GPGPU implementation exploits data parallelism using both multicore and GPU fine-grained parallelism present in commodity architectures, including current laptops and desktop computers. Our approach implements all FFClust steps in parallel, improving execution times in all of them. In addition, our parallel approach includes a parallel Kmeans++ algorithm implementation and defines a new variant of Kmeans++ to reduce the impact of choosing outliers as initial centroids. The results show that our approach provides clustering quality results very similar to FFClust, and it requires an execution time of 3.5 s for processing about a million fibers, achieving a speedup of 11.5 times compared to FFClust.


2021 ◽  
Vol 15 ◽  
Author(s):  
Jafar Tavoosi ◽  
Chunwei Zhang ◽  
Ardashir Mohammadzadeh ◽  
Saleh Mobayen ◽  
Amir H. Mosavi

Image interpolation is an essential process for image processing and computer graphics in wide applications to medical imaging. For image interpolation used in medical diagnosis, the two-dimensional (2D) to three-dimensional (3D) transformation can significantly reduce human error, leading to better decisions. This research proposes the type-2 fuzzy neural networks method which is a hybrid of the fuzzy logic and neural networks as well as recurrent type-2 fuzzy neural networks (RT2FNNs) for advancing a novel 2D to 3D strategy. The ability of the proposed methods in the approximation of the function for image interpolation is investigated. The results report that both proposed methods are reliable for medical diagnosis. However, the RT2FNN model outperforms the type-2 fuzzy neural networks model. The average squares error for the recurrent network and the typical network reported 0.016 and 0.025, respectively. On the other hand, the number of fuzzy rules for the recurrent network and the typical network reported 16 and 22, respectively.


2021 ◽  
Vol 15 ◽  
Author(s):  
Luca L. Bologna ◽  
Roberto Smiriglia ◽  
Dario Curreri ◽  
Michele Migliore

The description of neural dynamics, in terms of precise characterizations of action potential timings and shape and voltage related measures, is fundamental for a deeper understanding of the neural code and its information content. Not only such measures serve the scientific questions posed by experimentalists but are increasingly being used by computational neuroscientists for the construction of biophysically detailed data-driven models. Nonetheless, online resources enabling users to perform such feature extraction operation are lacking. To address this problem, in the framework of the Human Brain Project and the EBRAINS research infrastructure, we have developed and made available to the scientific community the NeuroFeatureExtract, an open-access online resource for the extraction of electrophysiological features from neural activity data. This tool allows to select electrophysiological traces of interest, fetched from public repositories or from users’ own data, and provides ad hoc functionalities to extract relevant features. The output files are properly formatted for further analysis, including data-driven neural model optimization.


2021 ◽  
Vol 15 ◽  
Author(s):  
Xin Chen ◽  
Yuanjie Zheng ◽  
Changxu Dong ◽  
Sutao Song

In terms of seizure prediction, how to fully mine relational data information among multiple channels of epileptic EEG? This is a scientific research subject worthy of further exploration. Recently, we propose a multi-dimensional enhanced seizure prediction framework, which mainly includes information reconstruction space, graph state encoder, and space-time predictor. It takes multi-channel spatial relationship as breakthrough point. At the same time, it reconstructs data unit from frequency band level, updates graph coding representation, and explores space-time relationship. Through experiments on CHB-MIT dataset, sensitivity of the model reaches 98.61%, which proves effectiveness of the proposed model.


2021 ◽  
Vol 15 ◽  
Author(s):  
Charly G. Lecomte ◽  
Johannie Audet ◽  
Jonathan Harnie ◽  
Alain Frigon

Gait analysis in cats and other animals is generally performed with custom-made or commercially developed software to track reflective markers placed on bony landmarks. This often involves costly motion tracking systems. However, deep learning, and in particular DeepLabCutTM (DLC), allows motion tracking without requiring placing reflective markers or an expensive system. The purpose of this study was to validate the accuracy of DLC for gait analysis in the adult cat by comparing results obtained with DLC and a custom-made software (Expresso) that has been used in several cat studies. Four intact adult cats performed tied-belt (both belts at same speed) and split-belt (belts operating at different speeds) locomotion at different speeds and left-right speed differences on a split-belt treadmill. We calculated several kinematic variables, such as step/stride lengths and joint angles from the estimates made by the two software and assessed the agreement between the two measurements using intraclass correlation coefficient or Lin’s concordance correlation coefficient as well as Pearson’s correlation coefficients. The results showed that DLC is at least as precise as Expresso with good to excellent agreement for all variables. Indeed, all 12 variables showed an agreement above 0.75, considered good, while nine showed an agreement above 0.9, considered excellent. Therefore, deep learning, specifically DLC, is valid for measuring kinematic variables during locomotion in cats, without requiring reflective markers and using a relatively low-cost system.


2021 ◽  
Vol 15 ◽  
Author(s):  
Alexandre Routier ◽  
Ninon Burgos ◽  
Mauricio Díaz ◽  
Michael Bacci ◽  
Simona Bottani ◽  
...  

We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to (i) spend less time on data management and processing, (ii) perform reproducible evaluations of their methods, and (iii) easily share data and results within their institution and with external collaborators. The core of Clinica is a set of automatic pipelines for processing and analysis of multimodal neuroimaging data (currently, T1-weighted MRI, diffusion MRI, and PET data), as well as tools for statistics, machine learning, and deep learning. It relies on the brain imaging data structure (BIDS) for the organization of raw neuroimaging datasets and on established tools written by the community to build its pipelines. It also provides converters of public neuroimaging datasets to BIDS (currently ADNI, AIBL, OASIS, and NIFD). Processed data include image-valued scalar fields (e.g., tissue probability maps), meshes, surface-based scalar fields (e.g., cortical thickness maps), or scalar outputs (e.g., regional averages). These data follow the ClinicA Processed Structure (CAPS) format which shares the same philosophy as BIDS. Consistent organization of raw and processed neuroimaging files facilitates the execution of single pipelines and of sequences of pipelines, as well as the integration of processed data into statistics or machine learning frameworks. The target audience of Clinica is neuroscientists or clinicians conducting clinical neuroscience studies involving multimodal imaging, and researchers developing advanced machine learning algorithms applied to neuroimaging data.


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