scholarly journals Computational biology: deep learning

2017 ◽  
Vol 1 (3) ◽  
pp. 257-274 ◽  
Author(s):  
William Jones ◽  
Kaur Alasoo ◽  
Dmytro Fishman ◽  
Leopold Parts
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Computational Biology ◽  
Medical Diagnostics ◽  
Network Architectures ◽  
Improve Performance ◽  
Prediction Problems ◽  
And Training ◽  
Abundant Data ◽  
Simple Network

Deep learning is the trendiest tool in a computational biologist's toolbox. This exciting class of methods, based on artificial neural networks, quickly became popular due to its competitive performance in prediction problems. In pioneering early work, applying simple network architectures to abundant data already provided gains over traditional counterparts in functional genomics, image analysis, and medical diagnostics. Now, ideas for constructing and training networks and even off-the-shelf models have been adapted from the rapidly developing machine learning subfield to improve performance in a range of computational biology tasks. Here, we review some of these advances in the last 2 years.

scholarly journals Artificial Intelligence in Thyroid Field. A Comprehensive Review

Cancers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 4740
Author(s):  
Fabiano Bini ◽  
Andrada Pica ◽  
Laura Azzimonti ◽  
Alessandro Giusti ◽  
Lorenzo Ruinelli ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Deep Learning ◽  
Cognitive Abilities ◽  
Medical Diagnostics ◽  
Critical Discussion ◽  
Research Field ◽  
Response To Treatment ◽  
Key Concepts ◽  
Mathematical Algorithms

Artificial intelligence (AI) uses mathematical algorithms to perform tasks that require human cognitive abilities. AI-based methodologies, e.g., machine learning and deep learning, as well as the recently developed research field of radiomics have noticeable potential to transform medical diagnostics. AI-based techniques applied to medical imaging allow to detect biological abnormalities, to diagnostic neoplasms or to predict the response to treatment. Nonetheless, the diagnostic accuracy of these methods is still a matter of debate. In this article, we first illustrate the key concepts and workflow characteristics of machine learning, deep learning and radiomics. We outline considerations regarding data input requirements, differences among these methodologies and their limitations. Subsequently, a concise overview is presented regarding the application of AI methods to the evaluation of thyroid images. We developed a critical discussion concerning limits and open challenges that should be addressed before the translation of AI techniques to the broad clinical use. Clarification of the pitfalls of AI-based techniques results crucial in order to ensure the optimal application for each patient.

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.

Deep Learning Applications in Medical Imaging

2021 ◽  
pp. 156-177
Author(s):  
Janani Viswanathan ◽  
N. Saranya ◽  
Abinaya Inbamani
Keyword(s):  
Machine Learning ◽  
Image Processing ◽  
Deep Learning ◽  
Medical Image ◽  
Medical Image Processing ◽  
Medical Diagnostics ◽  
Healthcare Sector ◽  
Computational Techniques ◽  
Healthcare Applications ◽  
Medical Sector

Deep learning (DL) and artificial intelligence (AI) are emerging tools in the healthcare sector for medical diagnostics. This chapter elaborates on general reasons for the popularity of computational techniques such as deep learning and machine learning (ML) applications in the medical image processing domain. The initial part of this chapter focuses on reviewing the fundamental concepts of DL algorithms, competence with machine learning, need in healthcare, applications, and challenges in medical image processing. Doing so allows understanding the reasons for the construction of all of them and offers a different view on various domains in the medical sector. The tools and technology required for DL, selection, implementation, optimization, and testing are discussed with respect to an application of cancer detection. Thus, this chapter gives an overall vision of deep learning concepts related to biomedical research.

Data processing using deep learning of the generative-adversarial neural network (GAN)

2021 ◽  
Author(s):  
V.Y. Ilichev ◽  
I.V. Chukhraev
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Effective Means ◽  
Network Models ◽  
Neural Network Models ◽  
High Quality ◽  
Python Language ◽  
And Training

The article is devoted to the consideration of one of the areas of application of modern and promising computer technology – machine learning. This direction is based on the creation of models consisting of neural networks and their deep learning. At present, there is a need to generate new, not yet existing, images of objects of different types. Most often, text files or images act as such objects. To achieve a high quality of results, a generation method based on the adversarial work of two neural networks (generator and discriminator) was once worked out. This class of neural network models is distinguished by the complexity of topography, since it is necessary to correctly organize the structure of neural layers in order to achieve maximum accuracy and minimal error. The described program is created using the Python language and special libraries that extend the set of commands for performing additional functions: working with neural networks Keras (main library), integrating with the operating system Os, outputting graphs Matplotlib, working with data arrays Numpy and others. A description is given of the type and features of each neural layer, as well as the use of library connection functions, input of initial data, compilation and training of the obtained model. Next, the implementation of the procedure for outputting the results of evaluating the errors of the generator and discriminator and the accuracy achieved by the model depending on the number of cycles (eras) of its training is considered. Based on the results of the work, conclusions were drawn and recommendations were made for the use and development of the considered methodology for creating and training generative and adversarial neural networks. Studies have demonstrated the procedure for operating with comparatively simple and accessible, but effective means of a universal Python language with the Keras library to create and teach a complex neural network model. In fact, it has been proved that the use of this method allows to achieve high-quality results of machine learning, previously achievable only when using special software systems for working with neural networks.

scholarly journals Convolutional Networks Used to Classify Video and Audio Data

2019 ◽  
Vol 27 (45) ◽  
pp. 113-120
Author(s):  
Marcel Nikmon ◽  
Roman Budjač ◽  
Daniel Kuchár ◽  
Peter Schreiber ◽  
Dagmar Janáčová
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Data Classification ◽  
Current Data ◽  
Video Data ◽  
Batch Size ◽  
Network Architectures ◽  
Convolutional Networks ◽  
Audio Data ◽  
Video And Audio

Abstract Deep learning is a kind of machine learning, and machine learning is a kind of artificial intelligence. Machine learning depicts groups of various technologies, and deep learning is one of them. The use of deep learning is an integral part of the current data classification practice in today’s world. This paper introduces the possibilities of classification using convolutional networks. Experiments focused on audio and video data show different approaches to data classification. Most experiments use the well-known pre-trained AlexNet network with various pre-processing types of input data. However, there are also comparisons of other neural network architectures, and we also show the results of training on small and larger datasets. The paper comprises description of eight different kinds of experiments. Several training sessions were conducted in each experiment with different aspects that were monitored. The focus was put on the effect of batch size on the accuracy of deep learning, including many other parameters that affect deep learning [1].

scholarly journals Bringing TrackMate in the era of machine-learning and deep-learning.

2021 ◽  
Author(s):  
Dmitry Ershov ◽  
Minh-Son Phan ◽  
Joanna W. Pylvänäinen ◽  
Stéphane U Rigaud ◽  
Laure Le Blanc ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Fluorescence Microscopy ◽  
Learning Algorithms ◽  
Improve Performance ◽  
Automated Tracking ◽  
Wide Range ◽  
Bio Imaging ◽  
Microscopy Images

TrackMate is an automated tracking software used to analyze bioimages and distributed as a Fiji plugin. Here we introduce a new version of TrackMate rewritten to improve performance and usability, and integrating several popular machine and deep learning algorithms to improve versatility. We illustrate how these new components can be used to efficiently track objects from brightfield and fluorescence microscopy images across a wide range of bio-imaging experiments.

scholarly journals Common Bamboo Species Identification using Machine Learning and Deep Learning Algorithms

2020 ◽  
Vol 9 (4) ◽  
pp. 3012-3017
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
North India ◽  
Bambusa Vulgaris ◽  
Phyllostachys Nigra ◽  
Bambusa Tulda ◽  
Bambusa Ventricosa ◽  
And Training

Due to its growth rate and strength, bamboo's versatility is huge. Bamboo has been developed to replace hardwood naturally. But it can be difficult to recognize a bamboo as many appear in a cluster or singular. Each bamboo type has its applications. Because of the utility of bamboo, we have worked in Random Forest, naive bays, logistic regression, the SVM-kernel, CNN, and ResNET, amongst several machine-learning algorithms. A similar test was carried out and delineated using graphs based on uncertainty matrix parameters and training accuracy. In this paper, we have used the data of following five species such as Phyllostachys nigra, Bambusa vulgaris ‘Striata‘, Dendrocalamus giganteu, Bambusa ventricosa, and Bambusa tulda which are generally found in north India. We trained, tested and validated the species from datasets using different machine learning and deep learning algorithms.

scholarly journals SURVEY ON EVOLVING DEEP LEARNING NEURAL NETWORK ARCHITECTURES

2019 ◽  
Vol 2019 (2) ◽  
pp. 73-82 ◽  
Author(s):  
Dr. Abul Bashar
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
Feature Extraction ◽  
Deep Learning ◽  
Human Performance ◽  
Deep Neural Networks ◽  
Network Architectures ◽  
Neural Network Architectures ◽  
Deep Learning Neural Network

The deep learning being a subcategory of the machine learning follows the human instincts of learning by example to produce accurate results. The deep learning performs training to the computer frame work to directly classify the tasks from the documents available either in the form of the text, image, or the sound. Most often the deep learning utilizes the neural network to perform the accurate classification and is referred as the deep neural networks; one of the most common deep neural networks used in a broader range of applications is the convolution neural network that provides an automated way of feature extraction by learning the features directly from the images or the text unlike the machine learning that extracts the features manually. This enables the deep learning neural networks to have a state of art accuracy that mostly expels even the human performance. So the paper is to present the survey on the deep learning neural network architectures utilized in various applications for having an accurate classification with an automated feature extraction.

scholarly journals Graph-Based Deep Learning for Medical Diagnosis and Analysis: Past, Present and Future

Sensors ◽  
2021 ◽  
Vol 21 (14) ◽  
pp. 4758
Author(s):  
David Ahmedt-Aristizabal ◽  
Mohammad Ali Armin ◽  
Simon Denman ◽  
Clinton Fookes ◽  
Lars Petersson
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Data Driven ◽  
Future Research ◽  
Healthcare Data ◽  
Implicit Information ◽  
Different Types ◽  
Graph Neural Networks ◽  
Prediction Problems ◽  
Significant Attention

With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered, which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interacting nodes connected by edges whose weights can be determined by either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure, and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.

scholarly journals Application of Deep Learning Architectures for Satellite Image Time Series Prediction: A Review

2021 ◽  
Vol 13 (23) ◽  
pp. 4822
Author(s):  
Waytehad Rose Moskolaï ◽  
Wahabou Abdou ◽  
Albert Dipanda ◽  
Kolyang
Keyword(s):  
Machine Learning ◽  
Time Series ◽  
Deep Learning ◽  
Satellite Images ◽  
Spatial Information ◽  
Time Series Prediction ◽  
Satellite Image ◽  
Machine Learning Algorithms ◽  
Temporal Dimension ◽  
Prediction Problems

Satellite image time series (SITS) is a sequence of satellite images that record a given area at several consecutive times. The aim of such sequences is to use not only spatial information but also the temporal dimension of the data, which is used for multiple real-world applications, such as classification, segmentation, anomaly detection, and prediction. Several traditional machine learning algorithms have been developed and successfully applied to time series for predictions. However, these methods have limitations in some situations, thus deep learning (DL) techniques have been introduced to achieve the best performance. Reviews of machine learning and DL methods for time series prediction problems have been conducted in previous studies. However, to the best of our knowledge, none of these surveys have addressed the specific case of works using DL techniques and satellite images as datasets for predictions. Therefore, this paper concentrates on the DL applications for SITS prediction, giving an overview of the main elements used to design and evaluate the predictive models, namely the architectures, data, optimization functions, and evaluation metrics. The reviewed DL-based models are divided into three categories, namely recurrent neural network-based models, hybrid models, and feed-forward-based models (convolutional neural networks and multi-layer perceptron). The main characteristics of satellite images and the major existing applications in the field of SITS prediction are also presented in this article. These applications include weather forecasting, precipitation nowcasting, spatio-temporal analysis, and missing data reconstruction. Finally, current limitations and proposed workable solutions related to the use of DL for SITS prediction are also highlighted.

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