scholarly journals Single-Cell Phenotype Classification Using Deep Convolutional Neural Networks

2016 ◽  
Vol 21 (9) ◽  
pp. 998-1003 ◽  
Author(s):  
Oliver Dürr ◽  
Beate Sick
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Single Cell ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Misclassification Rate ◽  
Support Vector ◽  
Learning Methods ◽  
Phenotype Classification

Deep learning methods are currently outperforming traditional state-of-the-art computer vision algorithms in diverse applications and recently even surpassed human performance in object recognition. Here we demonstrate the potential of deep learning methods to high-content screening–based phenotype classification. We trained a deep learning classifier in the form of convolutional neural networks with approximately 40,000 publicly available single-cell images from samples treated with compounds from four classes known to lead to different phenotypes. The input data consisted of multichannel images. The construction of appropriate feature definitions was part of the training and carried out by the convolutional network, without the need for expert knowledge or handcrafted features. We compare our results against the recent state-of-the-art pipeline in which predefined features are extracted from each cell using specialized software and then fed into various machine learning algorithms (support vector machine, Fisher linear discriminant, random forest) for classification. The performance of all classification approaches is evaluated on an untouched test image set with known phenotype classes. Compared to the best reference machine learning algorithm, the misclassification rate is reduced from 8.9% to 6.6%.

scholarly journals Evaluation of Different Machine Learning Methods and Deep-Learning Convolutional Neural Networks for Landslide Detection

2019 ◽  
Vol 11 (2) ◽  
pp. 196 ◽  
Author(s):  
Omid Ghorbanzadeh ◽  
Thomas Blaschke ◽  
Khalil Gholamnia ◽  
Sansar Meena ◽  
Dirk Tiede ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Expert Knowledge ◽  
Accuracy Assessment ◽  
Window Size ◽  
Optical Data ◽  
Support Vector ◽  
Learning Methods ◽  
Machine Learning Methods

There is a growing demand for detailed and accurate landslide maps and inventories around the globe, but particularly in hazard-prone regions such as the Himalayas. Most standard mapping methods require expert knowledge, supervision and fieldwork. In this study, we use optical data from the Rapid Eye satellite and topographic factors to analyze the potential of machine learning methods, i.e., artificial neural network (ANN), support vector machines (SVM) and random forest (RF), and different deep-learning convolution neural networks (CNNs) for landslide detection. We use two training zones and one test zone to independently evaluate the performance of different methods in the highly landslide-prone Rasuwa district in Nepal. Twenty different maps are created using ANN, SVM and RF and different CNN instantiations and are compared against the results of extensive fieldwork through a mean intersection-over-union (mIOU) and other common metrics. This accuracy assessment yields the best result of 78.26% mIOU for a small window size CNN, which uses spectral information only. The additional information from a 5 m digital elevation model helps to discriminate between human settlements and landslides but does not improve the overall classification accuracy. CNNs do not automatically outperform ANN, SVM and RF, although this is sometimes claimed. Rather, the performance of CNNs strongly depends on their design, i.e., layer depth, input window sizes and training strategies. Here, we conclude that the CNN method is still in its infancy as most researchers will either use predefined parameters in solutions like Google TensorFlow or will apply different settings in a trial-and-error manner. Nevertheless, deep-learning can improve landslide mapping in the future if the effects of the different designs are better understood, enough training samples exist, and the effects of augmentation strategies to artificially increase the number of existing samples are better understood.

Convolutional Neural Networks for Water Body Extraction from Landsat Imagery

2017 ◽  
Vol 16 (01) ◽  
pp. 1750001 ◽  
Author(s):  
Long Yu ◽  
Zhiyin Wang ◽  
Shengwei Tian ◽  
Feiyue Ye ◽  
Jianli Ding ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Water Body ◽  
Spatial Information ◽  
Landsat Imagery ◽  
Classification Performance ◽  
Support Vector ◽  
Learning Methods ◽  
Wide Range

Traditional machine learning methods for water body extraction need complex spectral analysis and feature selection which rely on wealth of prior knowledge. They are time-consuming and hard to satisfy our request for accuracy, automation level and a wide range of application. We present a novel deep learning framework for water body extraction from Landsat imagery considering both its spectral and spatial information. The framework is a hybrid of convolutional neural networks (CNN) and logistic regression (LR) classifier. CNN, one of the deep learning methods, has acquired great achievements on various visual-related tasks. CNN can hierarchically extract deep features from raw images directly, and distill the spectral–spatial regularities of input data, thus improving the classification performance. Experimental results based on three Landsat imagery datasets show that our proposed model achieves better performance than support vector machine (SVM) and artificial neural network (ANN).

A Very Large-Scale Bioactivity Comparison of Deep Learning and Multiple Machine Learning Algorithms for Drug Discovery

2020 ◽  
Author(s):  
Thomas R. Lane ◽  
Daniel H. Foil ◽  
Eni Minerali ◽  
Fabio Urbina ◽  
Kimberley M. Zorn ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Drug Discovery ◽  
Deep Neural Networks ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Learning Methods ◽  
Machine Learning Methods

<p>Machine learning methods are attracting considerable attention from the pharmaceutical industry for use in drug discovery and applications beyond. In recent studies we have applied multiple machine learning algorithms, modeling metrics and in some cases compared molecular descriptors to build models for individual targets or properties on a relatively small scale. Several research groups have used large numbers of datasets from public databases such as ChEMBL in order to evaluate machine learning methods of interest to them. The largest of these types of studies used on the order of 1400 datasets. We have now extracted well over 5000 datasets from CHEMBL for use with the ECFP6 fingerprint and comparison of our proprietary software Assay Central<sup>TM</sup> with random forest, k-Nearest Neighbors, support vector classification, naïve Bayesian, AdaBoosted decision trees, and deep neural networks (3 levels). Model performance <a>was</a> assessed using an array of five-fold cross-validation metrics including area-under-the-curve, F1 score, Cohen’s kappa and Matthews correlation coefficient. <a>Based on ranked normalized scores for the metrics or datasets all methods appeared comparable while the distance from the top indicated Assay Central<sup>TM</sup> and support vector classification were comparable. </a>Unlike prior studies which have placed considerable emphasis on deep neural networks (deep learning), no advantage was seen in this case where minimal tuning was performed of any of the methods. If anything, Assay Central<sup>TM</sup> may have been at a slight advantage as the activity cutoff for each of the over 5000 datasets representing over 570,000 unique compounds was based on Assay Central<sup>TM</sup>performance, but support vector classification seems to be a strong competitor. We also apply Assay Central<sup>TM</sup> to prospective predictions for PXR and hERG to further validate these models. This work currently appears to be the largest comparison of machine learning algorithms to date. Future studies will likely evaluate additional databases, descriptors and algorithms, as well as further refining methods for evaluating and comparing models. </p><p><b> </b></p>

scholarly journals 3D Convolutional Neural Networks Initialized from Pretrained 2D Convolutional Neural Networks for Classification of Industrial Parts

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1078
Author(s):  
Ibon Merino ◽  
Jon Azpiazu ◽  
Anthony Remazeilles ◽  
Basilio Sierra
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Learning Methods ◽  
Depth Cameras ◽  
Convolutional Networks ◽  
Vision Sensors ◽  
Industrial Object

Deep learning methods have been successfully applied to image processing, mainly using 2D vision sensors. Recently, the rise of depth cameras and other similar 3D sensors has opened the field for new perception techniques. Nevertheless, 3D convolutional neural networks perform slightly worse than other 3D deep learning methods, and even worse than their 2D version. In this paper, we propose to improve 3D deep learning results by transferring the pretrained weights learned in 2D networks to their corresponding 3D version. Using an industrial object recognition context, we have analyzed different combinations of 3D convolutional networks (VGG16, ResNet, Inception ResNet, and EfficientNet), comparing the recognition accuracy. The highest accuracy is obtained with EfficientNetB0 using extrusion with an accuracy of 0.9217, which gives comparable results to state-of-the art methods. We also observed that the transfer approach enabled to improve the accuracy of the Inception ResNet 3D version up to 18% with respect to the score of the 3D approach alone.

scholarly journals A Research on Deep Learning Advance for Landslide Classification using Convolutional Neural Networks

2019 ◽  
Vol 8 (6S4) ◽  
pp. 903-906
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Feature Extraction ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Data Set ◽  
Proposed Model

Landslides can easily be tragic to human life and property. Increase in the rate of human settlement in the mountains has resulted in safety concerns. Landslides have caused economic loss between 1-2% of the GDP in many developing countries. In this study, we discuss a deep learning approach to detect landslides. Convolutional Neural Networks are used for feature extraction for our proposed model. As there was no source of an exact and precise data set for feature extraction, therefore, a new data set was built for testing the model. We have tested and compared this work with our proposed model and with other machine-learning algorithms such as Logistic Regression, Random Forest, AdaBoost, K-Nearest Neighbors and Support Vector Machine. Our proposed deep learning model produces a classification accuracy of 96.90% outperforming the classical machine-learning algorithms.

scholarly journals Classification of Skin cancer using deep learning, Convolutional Neural Networks - Opportunities and vulnerabilities- A systematic Review

2020 ◽  
Vol 6 (11) ◽  
pp. 101-108
Author(s):  
Ravi Manne, Snigdha Kantheti and Sneha Kantheti
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Skin Cancer ◽  
Convolutional Neural Networks ◽  
Skin Lesions ◽  
Misclassification Rate ◽  
Research Articles ◽  
Original Research ◽  
Cancer Type

Background: Skin cancer classificationusing convolutional neural networks (CNNs) proved better results in classifying skin lesions compared with dermatologists which is lifesaving in terms of diagnosing. This will help people diagnosetheir cancer on their own by just installing app on mobile devices. It is estimated that 6.3 billion people will use the subscriptions by the end of year 2021[28] for diagnosing their skin cancer. Objective: This study represents review of many research articles on classifying skin lesions using CNNs. With the recent enhancement in machine learning algorithms, misclassification rate of skin lesions has reduced compared to a dermatologist classifying them.In this article we discuss how using CNNs has evolved in successfully classifying skin cancer type, and methods implemented, and the success rate. Even though Deep learning using CNN has advantages compared to a dermatologist, it also has some vulnerabilities, in terms of misclassifying images under some Criteria, and situations. We also discuss about those Vulnerabilities in this review study. Methods: We searched theScienceDirect, PubMed,Elsevier, Web of Science databases and Google Scholar for original research articles that are published. We selected papers that have sufficient data and information regarding their research, and we created a review on their approaches and methods they have used. From the articles we searched online So far no review paper has discussed both opportunities and vulnerabilities that existed in skin cancer classification using deep learning. Conclusions: The improvements in machine learning, Deep learning techniques, can avoid human mistakes that could be possible in misclassifying and diagnosing the disease. We will discuss, how Deep learning using CNN helped us and its vulnerabilities.

A Very Large-Scale Bioactivity Comparison of Deep Learning and Multiple Machine Learning Algorithms for Drug Discovery

2020 ◽  
Author(s):  
Thomas R. Lane ◽  
Daniel H. Foil ◽  
Eni Minerali ◽  
Fabio Urbina ◽  
Kimberley M. Zorn ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Drug Discovery ◽  
Deep Neural Networks ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Learning Methods ◽  
Machine Learning Methods

<p>Machine learning methods are attracting considerable attention from the pharmaceutical industry for use in drug discovery and applications beyond. In recent studies we have applied multiple machine learning algorithms, modeling metrics and in some cases compared molecular descriptors to build models for individual targets or properties on a relatively small scale. Several research groups have used large numbers of datasets from public databases such as ChEMBL in order to evaluate machine learning methods of interest to them. The largest of these types of studies used on the order of 1400 datasets. We have now extracted well over 5000 datasets from CHEMBL for use with the ECFP6 fingerprint and comparison of our proprietary software Assay Central<sup>TM</sup> with random forest, k-Nearest Neighbors, support vector classification, naïve Bayesian, AdaBoosted decision trees, and deep neural networks (3 levels). Model performance <a>was</a> assessed using an array of five-fold cross-validation metrics including area-under-the-curve, F1 score, Cohen’s kappa and Matthews correlation coefficient. <a>Based on ranked normalized scores for the metrics or datasets all methods appeared comparable while the distance from the top indicated Assay Central<sup>TM</sup> and support vector classification were comparable. </a>Unlike prior studies which have placed considerable emphasis on deep neural networks (deep learning), no advantage was seen in this case where minimal tuning was performed of any of the methods. If anything, Assay Central<sup>TM</sup> may have been at a slight advantage as the activity cutoff for each of the over 5000 datasets representing over 570,000 unique compounds was based on Assay Central<sup>TM</sup>performance, but support vector classification seems to be a strong competitor. We also apply Assay Central<sup>TM</sup> to prospective predictions for PXR and hERG to further validate these models. This work currently appears to be the largest comparison of machine learning algorithms to date. Future studies will likely evaluate additional databases, descriptors and algorithms, as well as further refining methods for evaluating and comparing models. </p><p><b> </b></p>

scholarly journals Toward Audio Beehive Monitoring: Deep Learning vs. Standard Machine Learning in Classifying Beehive Audio Samples

2018 ◽  
Vol 8 (9) ◽  
pp. 1573 ◽  
Author(s):  
Vladimir Kulyukin ◽  
Sarbajit Mukherjee ◽  
Prakhar Amlathe
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Convolutional Neural Networks ◽  
Feature Engineering ◽  
Learning Methods ◽  
Machine Learning Methods

Electronic beehive monitoring extracts critical information on colony behavior and phenology without invasive beehive inspections and transportation costs. As an integral component of electronic beehive monitoring, audio beehive monitoring has the potential to automate the identification of various stressors for honeybee colonies from beehive audio samples. In this investigation, we designed several convolutional neural networks and compared their performance with four standard machine learning methods (logistic regression, k-nearest neighbors, support vector machines, and random forests) in classifying audio samples from microphones deployed above landing pads of Langstroth beehives. On a dataset of 10,260 audio samples where the training and testing samples were separated from the validation samples by beehive and location, a shallower raw audio convolutional neural network with a custom layer outperformed three deeper raw audio convolutional neural networks without custom layers and performed on par with the four machine learning methods trained to classify feature vectors extracted from raw audio samples. On a more challenging dataset of 12,914 audio samples where the training and testing samples were separated from the validation samples by beehive, location, time, and bee race, all raw audio convolutional neural networks performed better than the four machine learning methods and a convolutional neural network trained to classify spectrogram images of audio samples. A trained raw audio convolutional neural network was successfully tested in situ on a low voltage Raspberry Pi computer, which indicates that convolutional neural networks can be added to a repertoire of in situ audio classification algorithms for electronic beehive monitoring. The main trade-off between deep learning and standard machine learning is between feature engineering and training time: while the convolutional neural networks required no feature engineering and generalized better on the second, more challenging dataset, they took considerably more time to train than the machine learning methods. To ensure the replicability of our findings and to provide performance benchmarks for interested research and citizen science communities, we have made public our source code and our curated datasets.

scholarly journals Recursive Convolutional Neural Networks for Epigenomics

2020 ◽  
Author(s):  
Aikaterini Symeonidi ◽  
Anguelos Nicolaou ◽  
Frank Johannes ◽  
Vincent Christlein
Keyword(s):  
Gene Expression ◽  
Neural Networks ◽  
Deep Learning ◽  
Functional Genomics ◽  
Convolutional Neural Networks ◽  
Histone Modifications ◽  
State Of The Art ◽  
Learning Methods ◽  
Arbitrary Size

AbstractDeep learning methods have proved to be powerful classification tools in the fields of structural and functional genomics. In this paper, we introduce a Recursive Convolutional Neural Networks (RCNN) for the analysis of epigenomic data. We focus on the task of predicting gene expression from the intensity of histone modifications. The proposed RCNN architecture can be applied to data of an arbitrary size, and has a single meta-parameter that quantifies the models capacity, thus making it flexible for experimenting. The proposed architecture outperforms state-of-the-art systems, while having several orders of magnitude fewer parameters.

scholarly journals Representing Deep Neural Networks Latent Space Geometries with Graphs

Algorithms ◽  
2021 ◽  
Vol 14 (2) ◽  
pp. 39
Author(s):  
Carlos Lassance ◽  
Vincent Gripon ◽  
Antonio Ortega
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Objective Function ◽  
Learning Process ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
The Core ◽  
Learning Tasks ◽  
Latent Space

Deep Learning (DL) has attracted a lot of attention for its ability to reach state-of-the-art performance in many machine learning tasks. The core principle of DL methods consists of training composite architectures in an end-to-end fashion, where inputs are associated with outputs trained to optimize an objective function. Because of their compositional nature, DL architectures naturally exhibit several intermediate representations of the inputs, which belong to so-called latent spaces. When treated individually, these intermediate representations are most of the time unconstrained during the learning process, as it is unclear which properties should be favored. However, when processing a batch of inputs concurrently, the corresponding set of intermediate representations exhibit relations (what we call a geometry) on which desired properties can be sought. In this work, we show that it is possible to introduce constraints on these latent geometries to address various problems. In more detail, we propose to represent geometries by constructing similarity graphs from the intermediate representations obtained when processing a batch of inputs. By constraining these Latent Geometry Graphs (LGGs), we address the three following problems: (i) reproducing the behavior of a teacher architecture is achieved by mimicking its geometry, (ii) designing efficient embeddings for classification is achieved by targeting specific geometries, and (iii) robustness to deviations on inputs is achieved via enforcing smooth variation of geometry between consecutive latent spaces. Using standard vision benchmarks, we demonstrate the ability of the proposed geometry-based methods in solving the considered problems.

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