scholarly journals Combining Deep Learning and Active Contours Opens The Way to Robust, Automated Analysis of Brain Cytoarchitectonics

2018 ◽  
Author(s):  
Konstantin Thierbach ◽  
Pierre-Louis Bazin ◽  
Walter De Back ◽  
Filippos Gavriilidis ◽  
Evgeniya Kirilina ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Active Contours ◽  
Feedforward Neural Networks ◽  
Automated Analysis ◽  
Light Sheet ◽  
Cell Detection ◽  
Light Sheet Microscopy ◽  
And Topology ◽  
High Level

AbstractDeep learning has thoroughly changed the field of image analysis yielding impressive results whenever enough annotated data can be gathered. While partial annotation can be very fast, manual segmentation of 3D biological structures is tedious and error-prone. Additionally, high-level shape concepts such as topology or boundary smoothness are hard if not impossible to encode in Feedforward Neural Networks. Here we present a modular strategy for the accurate segmentation of neural cell bodies from light-sheet microscopy combining mixed-scale convolutional neural networks and topology-preserving geometric deformable models. We show that the network can be trained efficiently from simple cell centroid annotations, and that the final segmentation provides accurate cell detection and smooth segmentations that do not introduce further cell splitting or merging.

scholarly journals Deep Learning Strategies for ProtoDUNE Raw Data Denoising

2022 ◽  
Vol 6 (1) ◽  
Author(s):  
Marco Rossi ◽  
Sofia Vallecorsa
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Learning Strategies ◽  
Simulation Data ◽  
Raw Data ◽  
Digital Detector ◽  
Speed Up ◽  
Neural Network Hardware ◽  
Graph Neural Networks ◽  
High Level

AbstractIn this work, we investigate different machine learning-based strategies for denoising raw simulation data from the ProtoDUNE experiment. The ProtoDUNE detector is hosted by CERN and it aims to test and calibrate the technologies for DUNE, a forthcoming experiment in neutrino physics. The reconstruction workchain consists of converting digital detector signals into physical high-level quantities. We address the first step in reconstruction, namely raw data denoising, leveraging deep learning algorithms. We design two architectures based on graph neural networks, aiming to enhance the receptive field of basic convolutional neural networks. We benchmark this approach against traditional algorithms implemented by the DUNE collaboration. We test the capabilities of graph neural network hardware accelerator setups to speed up training and inference processes.

scholarly journals Using Deep Learning to Predict Complex Systems: A Case Study in Wind Farm Generation

Complexity ◽  
2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
J. M. Torres ◽  
R. M. Aguilar
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Electricity Market ◽  
Power Plants ◽  
Wind Farm ◽  
Polynomial Regression ◽  
Supply And Demand ◽  
Feedforward Neural Networks ◽  
Activation Function ◽  
Renewable Energies

Making every component of an electrical system work in unison is being made more challenging by the increasing number of renewable energies used, the electrical output of which is difficult to determine beforehand. In Spain, the daily electricity market opens with a 12-hour lead time, where the supply and demand expected for the following 24 hours are presented. When estimating the generation, energy sources like nuclear are highly stable, while peaking power plants can be run as necessary. Renewable energies, however, which should eventually replace peakers insofar as possible, are reliant on meteorological conditions. In this paper we propose using different deep-learning techniques and architectures to solve the problem of predicting wind generation in order to participate in the daily market, by making predictions 12 and 36 hours in advance. We develop and compare various estimators based on feedforward, convolutional, and recurrent neural networks. These estimators were trained and validated with data from a wind farm located on the island of Tenerife. We show that the best candidates for each type are more precise than the reference estimator and the polynomial regression currently used at the wind farm. We also conduct a sensitivity analysis to determine which estimator type is most robust to perturbations. An analysis of our findings shows that the most accurate and robust estimators are those based on feedforward neural networks with a SELU activation function and convolutional neural networks.

Deep-learning on-chip light-sheet microscopy enabling video-rate volumetric imaging of dynamic biological specimens

Lab on a Chip ◽  
2021 ◽  
Author(s):  
Xiaopeng Chen ◽  
Junyu Ping ◽  
Yixuan Sun ◽  
Chengqiang Yi ◽  
Sijian Liu ◽  
...  
Keyword(s):  
Deep Learning ◽  
Light Scattering ◽  
Light Sheet ◽  
High Contrast ◽  
Spatiotemporal Resolution ◽  
Volumetric Imaging ◽  
Light Sheet Microscopy ◽  
High Spatiotemporal Resolution ◽  
On Chip

Volumetric imaging of dynamic signals in a large, moving, and light-scattering specimen is extremely challenging, owing to the requirement on high spatiotemporal resolution and difficulty in obtaining high-contrast signals. Here...

scholarly journals DNNBrain: A Unifying Toolbox for Mapping Deep Neural Networks and Brains

2020 ◽  
Vol 14 ◽  
Author(s):  
Xiayu Chen ◽  
Ming Zhou ◽  
Zhengxin Gong ◽  
Wei Xu ◽  
Xingyu Liu ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Cognitive Neuroscience ◽  
Deep Neural Networks ◽  
Learning Strategy ◽  
Neural Systems ◽  
Levels Of Abstraction ◽  
Internal Representations ◽  
Internal Operations ◽  
High Level

Deep neural networks (DNNs) have attained human-level performance on dozens of challenging tasks via an end-to-end deep learning strategy. Deep learning allows data representations that have multiple levels of abstraction; however, it does not explicitly provide any insights into the internal operations of DNNs. Deep learning's success is appealing to neuroscientists not only as a method for applying DNNs to model biological neural systems but also as a means of adopting concepts and methods from cognitive neuroscience to understand the internal representations of DNNs. Although general deep learning frameworks, such as PyTorch and TensorFlow, could be used to allow such cross-disciplinary investigations, the use of these frameworks typically requires high-level programming expertise and comprehensive mathematical knowledge. A toolbox specifically designed as a mechanism for cognitive neuroscientists to map both DNNs and brains is urgently needed. Here, we present DNNBrain, a Python-based toolbox designed for exploring the internal representations of DNNs as well as brains. Through the integration of DNN software packages and well-established brain imaging tools, DNNBrain provides application programming and command line interfaces for a variety of research scenarios. These include extracting DNN activation, probing and visualizing DNN representations, and mapping DNN representations onto the brain. We expect that our toolbox will accelerate scientific research by both applying DNNs to model biological neural systems and utilizing paradigms of cognitive neuroscience to unveil the black box of DNNs.

scholarly journals An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data

2021 ◽  
Author(s):  
Sahar Iravani ◽  
Tim O.F. Conrad
Keyword(s):  
Mass Spectrometry ◽  
Neural Networks ◽  
Deep Learning ◽  
Clinical State ◽  
Biomarker Detection ◽  
Proteomics Data ◽  
Comparable Amount ◽  
Complex Protein ◽  
Propagation Technique ◽  
High Level

AbstractAnalyzing mass spectrometry-based proteomics data with deep learning (DL) approaches poses several challenges due to the high dimensionality, low sample size, and high level of noise. Besides, DL-based workflows are often hindered to be integrated into medical settings due to the lack of interpretable explanation. We present DLearnMS, a DL biomarker detection framework, to address these challenges on proteomics instances of liquid chromatography-mass spectrometry (LC-MS) - a well-established tool for quantifying complex protein mixtures. Our DLearnMS framework learns the clinical state of LC-MS data instances using convolutional neural networks. Next, based on the trained neural networks, biomarkers can be identified using the layer-wise relevance propagation technique. This enables detecting discriminating regions of the data and the design of more robust networks. We show that DLearnMS outperforms conventional LC-MS biomarker detection approaches in detecting fewer false positive peaks while maintaining a comparable amount of true positives peaks. Unlike other methods, no explicit preprocessing step is needed in DLearnMS.

scholarly journals Inference of Brain States under Anesthesia with Meta Learning Based Deep Learning Models

2021 ◽  
Author(s):  
Qihang Wang ◽  
Feng Liu ◽  
Guihong Wan ◽  
Ying Chen
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Short Term Memory ◽  
Signal To Noise Ratio ◽  
General Anesthetics ◽  
Learning Models ◽  
Multi Stage ◽  
Meta Learning ◽  
Brain States ◽  
High Level

AbstractMonitoring the depth of unconsciousness during anesthesia is useful in both clinical settings and neuroscience investigations to understand brain mechanisms. Electroencephalogram (EEG) has been used as an objective means of characterizing brain altered arousal and/or cognition states induced by anesthetics in real-time. Different general anesthetics affect cerebral electrical activities in different ways. However, the performance of conventional machine learning models on EEG data is unsatisfactory due to the low Signal to Noise Ratio (SNR) in the EEG signals, especially in the office-based anesthesia EEG setting. Deep learning models have been used widely in the field of Brain Computer Interface (BCI) to perform classification and pattern recognition tasks due to their capability of good generalization and handling noises. Compared to other BCI applications, where deep learning has demonstrated encouraging results, the deep learning approach for classifying different brain consciousness states under anesthesia has been much less investigated. In this paper, we propose a new framework based on meta-learning using deep neural networks, named Anes-MetaNet, to classify brain states under anesthetics. The Anes-MetaNet is composed of Convolutional Neural Networks (CNN) to extract power spectrum features, and a time consequence model based on Long Short-Term Memory (LSTM) Networks to capture the temporal dependencies, and a meta-learning framework to handle large cross-subject variability. We used a multi-stage training paradigm to improve the performance, which is justified by visualizing the high-level feature mapping. Experiments on the office-based anesthesia EEG dataset demonstrate the effectiveness of our proposed Anes-MetaNet by comparison of existing methods.

scholarly journals Investigating Deep Feedforward Neural Networks for Classification of Transposon-Derived piRNAs

2020 ◽  
Author(s):  
Alisson Hayasi da Costa ◽  
Renato Augusto C. dos Santos ◽  
Ricardo Cerri
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
State Of The Art ◽  
Feedforward Neural Networks ◽  
The State ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Advantages And Disadvantages ◽  
Large Application

AbstractPIWI-Interacting RNAs (piRNAs) form an important class of non-coding RNAs that play a key role in the genome integrity through the silencing of transposable elements. However, despite their importance and the large application of deep learning in computational biology for classification tasks, there are few studies of deep learning and neural networks for piRNAs prediction. Therefore, this paper presents an investigation on deep feedforward networks models for classification of transposon-derived piRNAs. We analyze and compare the results of the neural networks in different hyperparameters choices, such as number of layers, activation functions and optimizers, clarifying the advantages and disadvantages of each configuration. From this analysis, we propose a model for human piRNAs classification and compare our method with the state-of-the-art deep neural network for piRNA prediction in the literature and also traditional machine learning algorithms, such as Support Vector Machines and Random Forests, showing that our model has achieved a great performance with an F-measure value of 0.872, outperforming the state-of-the-art method in the literature.

scholarly journals Stress Field Prediction in Cantilevered Structures Using Convolutional Neural Networks

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhenguo Nie ◽  
Haoliang Jiang ◽  
Levent Burak Kara
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Topology Optimization ◽  
Structural Analysis ◽  
Stress Field ◽  
Convolutional Neural Networks ◽  
Von Mises Stress ◽  
Channel Network ◽  
Promising Alternative ◽  
And Topology

Abstract The demand for fast and accurate structural analysis is becoming increasingly more prevalent with the advance of generative design and topology optimization technologies. As one step toward accelerating structural analysis, this work explores a deep learning-based approach for predicting the stress fields in 2D linear elastic cantilevered structures subjected to external static loads at its free end using convolutional neural networks (CNNs). Two different architectures are implemented that take as input the structure geometry, external loads, and displacement boundary conditions, and output the predicted von Mises stress field. The first is a single input channel network called SCSNet as the baseline architecture, and the second is the multichannel input network called StressNet. Accuracy analysis shows that StressNet results in significantly lower prediction errors than SCSNet on three loss functions, with a mean relative error of 2.04% for testing. These results suggest that deep learning models may offer a promising alternative to classical methods in structural design and topology optimization. Code and dataset are available.2

scholarly journals Application of a Convolutional Neural Network for image classification for the analysis of collisions in High Energy Physics

2019 ◽  
Vol 214 ◽  
pp. 06017 ◽  
Author(s):  
Celia Fernández Madrazo ◽  
Ignacio Heredia ◽  
Lara Lloret ◽  
Jesús Marco de Lucas
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
High Energy Physics ◽  
Open Data ◽  
Feedforward Neural Networks ◽  
Relevant Information ◽  
High Energy ◽  
Particle Collisions ◽  
Learning Framework ◽  
Energy Physics

The application of deep learning techniques using convolutional neural networks for the classification of particle collisions in High Energy Physics is explored. An intuitive approach to transform physical variables, like momenta of particles and jets, into a single image that captures the relevant information, is proposed. The idea is tested using a well-known deep learning framework on a simulation dataset, including leptonic ttbar events and the corresponding background at 7 TeV from the CMS experiment at LHC, available as Open Data. This initial test shows competitive results when compared to more classical approaches, like those using feedforward neural networks.

Deep Learning

2016 ◽  
Vol 10 (03) ◽  
pp. 417-439 ◽  
Author(s):  
Xing Hao ◽  
Guigang Zhang ◽  
Shang Ma
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Complex Structures ◽  
Training Algorithms ◽  
High Level ◽  
And Training

Deep learning is a branch of machine learning that tries to model high-level abstractions of data using multiple layers of neurons consisting of complex structures or non-liner transformations. With the increase of the amount of data and the power of computation, neural networks with more complex structures have attracted widespread attention and been applied to various fields. This paper provides an overview of deep learning in neural networks including popular architecture models and training algorithms.

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