scholarly journals Learning transferable deep convolutional neural networks for the classification of bacterial virulence factors

2020 ◽  
Vol 36 (12) ◽  
pp. 3693-3702 ◽  
Author(s):  
Dandan Zheng ◽  
Guansong Pang ◽  
Bo Liu ◽  
Lihong Chen ◽  
Jian Yang
Keyword(s):  
Virulence Factors ◽  
State Of The Art ◽  
Binary Classification ◽  
Network Models ◽  
Bacterial Virulence ◽  
Supplementary Information ◽  
Deep Convolutional Neural Networks ◽  
Neural Network Models ◽  
Auxiliary Data

Abstract Motivation Identification of virulence factors (VFs) is critical to the elucidation of bacterial pathogenesis and prevention of related infectious diseases. Current computational methods for VF prediction focus on binary classification or involve only several class(es) of VFs with sufficient samples. However, thousands of VF classes are present in real-world scenarios, and many of them only have a very limited number of samples available. Results We first construct a large VF dataset, covering 3446 VF classes with 160 495 sequences, and then propose deep convolutional neural network models for VF classification. We show that (i) for common VF classes with sufficient samples, our models can achieve state-of-the-art performance with an overall accuracy of 0.9831 and an F1-score of 0.9803; (ii) for uncommon VF classes with limited samples, our models can learn transferable features from auxiliary data and achieve good performance with accuracy ranging from 0.9277 to 0.9512 and F1-score ranging from 0.9168 to 0.9446 when combined with different predefined features, outperforming traditional classifiers by 1–13% in accuracy and by 1–16% in F1-score. Availability and implementation All of our datasets are made publicly available at http://www.mgc.ac.cn/VFNet/, and the source code of our models is publicly available at https://github.com/zhengdd0422/VFNet. Supplementary information Supplementary data are available at Bioinformatics online.

Explainable Deep Learning Reproduces a ‘Professional Eye’ on the Diagnosis of Internal Disorders in Persimmon Fruit

2020 ◽  
Vol 61 (11) ◽  
pp. 1967-1973
Author(s):  
Takashi Akagi ◽  
Masanori Onishi ◽  
Kanae Masuda ◽  
Ryohei Kuroki ◽  
Kohei Baba ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Binary Classification ◽  
Network Models ◽  
Plant Biology ◽  
Neural Network Models ◽  
Persimmon Fruit

Abstract Recent rapid progress in deep neural network techniques has allowed recognition and classification of various objects, often exceeding the performance of the human eye. In plant biology and crop sciences, some deep neural network frameworks have been applied mainly for effective and rapid phenotyping. In this study, beyond simple optimizations of phenotyping, we propose an application of deep neural networks to make an image-based internal disorder diagnosis that is hard even for experts, and to visualize the reasons behind each diagnosis to provide biological interpretations. Here, we exemplified classification of calyx-end cracking in persimmon fruit by using five convolutional neural network models with various layer structures and examined potential analytical options involved in the diagnostic qualities. With 3,173 visible RGB images from the fruit apex side, the neural networks successfully made the binary classification of each degree of disorder, with up to 90% accuracy. Furthermore, feature visualizations, such as Grad-CAM and LRP, visualize the regions of the image that contribute to the diagnosis. They suggest that specific patterns of color unevenness, such as in the fruit peripheral area, can be indexes of calyx-end cracking. These results not only provided novel insights into indexes of fruit internal disorders but also proposed the potential applicability of deep neural networks in plant biology.

scholarly journals Dynamic Learning Rate in Deep CNN Model for Metastasis Detection and Classification of Histopathology Images

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Anil Johny ◽  
K. N. Madhusoodanan
Keyword(s):  
Region Of Interest ◽  
Network Models ◽  
Learning Rate ◽  
Dynamic Learning ◽  
Deep Convolutional Neural Networks ◽  
Neural Network Models ◽  
Improve Model ◽  
Histopathology Images ◽  
Artificial Neural Network Models

Diagnosis of different breast cancer stages using histopathology whole slide images (WSI) is the gold standard in determining the grade of tissue metastasis. Computer-aided diagnosis (CAD) assists medical experts as a second opinion tool in early detection to prevent further proliferation. The field of pathology has advanced so rapidly that it is possible to obtain high-quality images from glass slides. Patches from the region of interest in histopathology images are extracted and trained using artificial neural network models. The trained model primarily analyzes and predicts the histology images for the benign or malignant class to which it belongs. Classification of medical images focuses on the training of models with layers of abstraction to distinguish between these two classes with less false-positive rates. The learning rate is the crucial hyperparameter used during the training of deep convolutional neural networks (DCNN) to improve model accuracy. This work emphasizes the relevance of the dynamic learning rate than the fixed learning rate during the training of networks. The dynamic learning rate varies with preset conditions between the lower and upper boundaries and repeats at different iterations. The performance of the model thus improves and attains comparatively high accuracy with fewer iterations.

scholarly journals Improving Land Cover Classification Using Genetic Programming for Feature Construction

2021 ◽  
Vol 13 (9) ◽  
pp. 1623
Author(s):  
João E. Batista ◽  
Ana I. R. Cabral ◽  
Maria J. P. Vasconcelos ◽  
Leonardo Vanneschi ◽  
Sara Silva
Keyword(s):  
Land Cover ◽  
Genetic Programming ◽  
Satellite Images ◽  
State Of The Art ◽  
Binary Classification ◽  
Feature Construction ◽  
Classification Problems ◽  
Construction Methods ◽  
Box Models

Genetic programming (GP) is a powerful machine learning (ML) algorithm that can produce readable white-box models. Although successfully used for solving an array of problems in different scientific areas, GP is still not well known in the field of remote sensing. The M3GP algorithm, a variant of the standard GP algorithm, performs feature construction by evolving hyperfeatures from the original ones. In this work, we use the M3GP algorithm on several sets of satellite images over different countries to create hyperfeatures from satellite bands to improve the classification of land cover types. We add the evolved hyperfeatures to the reference datasets and observe a significant improvement of the performance of three state-of-the-art ML algorithms (decision trees, random forests, and XGBoost) on multiclass classifications and no significant effect on the binary classifications. We show that adding the M3GP hyperfeatures to the reference datasets brings better results than adding the well-known spectral indices NDVI, NDWI, and NBR. We also compare the performance of the M3GP hyperfeatures in the binary classification problems with those created by other feature construction methods such as FFX and EFS.

scholarly journals Classification of Germination Images of Pear Pollen Using Random Forest and Convolution Neural Network Models

IEEE Access ◽  
2021 ◽  
Vol 9 ◽  
pp. 45993-45999
Author(s):  
Ung Yang ◽  
Seungwon Oh ◽  
Seung Gon Wi ◽  
Bok-Rye Lee ◽  
Sang-Hyun Lee ◽  
...  
Keyword(s):  
Neural Network ◽  
Random Forest ◽  
Network Models ◽  
Convolution Neural Network ◽  
Neural Network Models

Detection and Classification of Brain Tumors from MRI Images Using a Deep Convolutional Neural Network Approach

2022 ◽  
Vol 10 (1) ◽  
pp. 0-0
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Brain Tumor ◽  
Convolutional Neural Network ◽  
Binary Classification ◽  
Deep Convolutional Neural Network ◽  
Neural Network Models ◽  
Neural Network Approach ◽  
Cancer Disease

Brain tumor is a severe cancer disease caused by uncontrollable and abnormal partitioning of cells. Timely disease detection and treatment plans lead to the increased life expectancy of patients. Automated detection and classification of brain tumor are a more challenging process which is based on the clinician’s knowledge and experience. For this fact, one of the most practical and important techniques is to use deep learning. Recent progress in the fields of deep learning has helped the clinician’s in medical imaging for medical diagnosis of brain tumor. In this paper, we present a comparison of Deep Convolutional Neural Network models for automatically binary classification query MRI images dataset with the goal of taking precision tools to health professionals based on fined recent versions of DenseNet, Xception, NASNet-A, and VGGNet. The experiments were conducted using an MRI open dataset of 3,762 images. Other performance measures used in the study are the area under precision, recall, and specificity.

scholarly journals Constructive Learning of Deep Neural Networks for Bigdata Analysis

2020 ◽  
Vol 9 (12) ◽  
pp. 311-322
Author(s):  
Soha Abd Mohamed El-Moamen ◽  
Marghany Hassan Mohamed ◽  
Mohammed F. Farghally
Keyword(s):  
Neural Network ◽  
Lung Cancer ◽  
Binary Classification ◽  
Network Models ◽  
Classification Model ◽  
Neural Network Models ◽  
Constructive Learning ◽  
The Neural Network ◽  
Rapid Pace ◽  
Better Than

The need for tracking and evaluation of patients in real-time has contributed to an increase in knowing people’s actions to enhance care facilities. Deep learning is good at both a rapid pace in collecting frameworks of big data healthcare and good predictions for detection the lung cancer early. In this paper, we proposed a constructive deep neural network with Apache Spark to classify images and levels of lung cancer. We developed a binary classification model using threshold technique classifying nodules to benign or malignant. At the proposed framework, the neural network models training, defined using the Keras API, is performed using BigDL in a distributed Spark clusters. The proposed algorithm has metrics AUC-0.9810, a misclassifying rate from which it has been shown that our suggested classifiers perform better than other classifiers.

scholarly journals Definition Extraction from Generic and Mathematical Domains with Deep Ensemble Learning

Mathematics ◽  
2021 ◽  
Vol 9 (19) ◽  
pp. 2502
Author(s):  
Natalia Vanetik ◽  
Marina Litvak
Keyword(s):  
Semantic Information ◽  
State Of The Art ◽  
Binary Classification ◽  
Ensemble Model ◽  
Classification Models ◽  
New Materials ◽  
Educational Materials ◽  
Efficient Learning ◽  
Mathematical Definitions

Definitions are extremely important for efficient learning of new materials. In particular, mathematical definitions are necessary for understanding mathematics-related areas. Automated extraction of definitions could be very useful for automated indexing educational materials, building taxonomies of relevant concepts, and more. For definitions that are contained within a single sentence, this problem can be viewed as a binary classification of sentences into definitions and non-definitions. In this paper, we focus on automatic detection of one-sentence definitions in mathematical and general texts. We experiment with different classification models arranged in an ensemble and applied to a sentence representation containing syntactic and semantic information, to classify sentences. Our ensemble model is applied to the data adjusted with oversampling. Our experiments demonstrate the superiority of our approach over state-of-the-art methods in both general and mathematical domains.

CONVOLUTIONAL NEURAL NETWORKS AS AN AID TO BIOSTRATIGRAPHY AND MICROPALEONTOLOGY: A TEST ON LATE PALEOZOIC MICROFOSSILS

Palaios ◽  
2020 ◽  
Vol 35 (9) ◽  
pp. 391-402 ◽  
Author(s):  
RAFAEL PIRES DE LIMA ◽  
KATIE F. WELCH ◽  
JAMES E. BARRICK ◽  
KURT J. MARFURT ◽  
ROGER BURKHALTER ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cross Validation ◽  
Network Models ◽  
Late Paleozoic ◽  
Neural Network Models ◽  
Thin Sections ◽  
Machine Learning Approach ◽  
Taxonomic Groups ◽  
And Training

ABSTRACT Accurate taxonomic classification of microfossils in thin-sections is an important biostratigraphic procedure. As paleontological expertise is typically restricted to specific taxonomic groups and experts are not present in all institutions, geoscience researchers often suffer from lack of quick access to critical taxonomic knowledge for biostratigraphic analyses. Moreover, diminishing emphasis on education and training in systematics poses a major challenge for the future of biostratigraphy, and on associated endeavors reliant on systematics. Here we present a machine learning approach to classify and organize fusulinids—microscopic index fossils for the late Paleozoic. The technique we employ has the potential to use such important taxonomic knowledge in models that can be applied to recognize and categorize fossil specimens. Our results demonstrate that, given adequate images and training, convolutional neural network models can correctly identify fusulinids with high levels of accuracy. Continued efforts in digitization of biological and paleontological collections at numerous museums and adoption of machine learning by paleontologists can enable the development of highly accurate and easy-to-use classification tools and, thus, facilitate biostratigraphic analyses by non-experts as well as allow for cross-validation of disparate collections around the world. Automation of classification work would also enable expert paleontologists and others to focus efforts on exploration of more complex interpretations and concepts.

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