A Similarity Searching System for Biological Phenotype Images Using Deep Convolutional Encoder-decoder Architecture

2019 ◽  
Vol 14 (7) ◽  
pp. 628-639 ◽  
Author(s):  
Bizhi Wu ◽  
Hangxiao Zhang ◽  
Limei Lin ◽  
Huiyuan Wang ◽  
Yubang Gao ◽  
...  
Keyword(s):  
Neural Network ◽  
Retrieval System ◽  
Sequence Similarity ◽  
Local Alignment ◽  
Similarity Searching ◽  
Loss Of Function ◽  
Biological Images ◽  
The Neural Network ◽  
Convolutional Autoencoder ◽  
Biological Phenotype

Background: The BLAST (Basic Local Alignment Search Tool) algorithm has been widely used for sequence similarity searching. Analogously, the public phenotype images must be efficiently retrieved using biological images as queries and identify the phenotype with high similarity. Due to the accumulation of genotype-phenotype-mapping data, a system of searching for similar phenotypes is not available due to the bottleneck of image processing. Objective: In this study, we focus on the identification of similar query phenotypic images by searching the biological phenotype database, including information about loss-of-function and gain-of-function. Methods: We propose a deep convolutional autoencoder architecture to segment the biological phenotypic images and develop a phenotype retrieval system to enable a better understanding of genotype–phenotype correlation. Results: This study shows how deep convolutional autoencoder architecture can be trained on images from biological phenotypes to achieve state-of-the-art performance in a phenotypic images retrieval system. Conclusion: Taken together, the phenotype analysis system can provide further information on the correlation between genotype and phenotype. Additionally, it is obvious that the neural network model of image segmentation and the phenotype retrieval system is equally suitable for any species, which has enough phenotype images to train the neural network.

The Adaptable Document Retrieval System Using The Neural Network

1989 ◽  
Vol 25 (Supplement) ◽  
pp. 306-307
Author(s):  
H. Mori ◽  
S. Ko ◽  
Y. Hayashi ◽  
Y. Kinoe
Keyword(s):  
Neural Network ◽  
Retrieval System ◽  
Document Retrieval ◽  
The Neural Network

scholarly journals DeepRibo: precise gene annotation of prokaryotes using deep learning and ribosome profiling data

2018 ◽  
Author(s):  
Jim Clauwaerts ◽  
Gerben Menschaert ◽  
Willem Waegeman
Keyword(s):  
Neural Network ◽  
Gene Annotation ◽  
Sequence Similarity ◽  
Ribosome Profiling ◽  
Single Model ◽  
Alignment Algorithms ◽  
The Neural Network ◽  
Genomic Landscape ◽  
Precise Tool ◽  
Multiple Species

AbstractAnnotation of gene expression in prokaryotes often finds itself corrected due to small variations of the annotated gene regions observed between different (sub-species. It has become apparent that traditional sequence alignment algorithms, used for the curation of genomes, are not able to map the full complexity of the genomic landscape. We present DeepRibo, a novel neural network applying ribosome profiling data that shows to be a precise tool for the delineation and annotation of expressed genes in prokaryotes. The neural network combines recurrent memory cells and convolutional layers, adapting the information gained from both the high-throughput ribosome profiling data and Shine-Dalgarno region into one model. DeepRibo is designed as a single model trained on a variety of ribosome profiling experiments, and is therefore evaluated on independent datasets. Through extensive validation of the model, including the use of multiple species sequence similarity and mass spectrometry, the effectiveness of the model is highlighted.

Neural Network for Automatic Analysis of Motility Data

1994 ◽  
Vol 33 (01) ◽  
pp. 157-160 ◽  
Author(s):  
S. Kruse-Andersen ◽  
J. Kolberg ◽  
E. Jakobsen
Keyword(s):  
Neural Network ◽  
Muscular Activity ◽  
Recording System ◽  
Automatic Analysis ◽  
Biologically Relevant ◽  
System A ◽  
The Neural Network ◽  
Valuable Method ◽  
Motor Abnormalities ◽  
Trained Network

Abstract:Continuous recording of intraluminal pressures for extended periods of time is currently regarded as a valuable method for detection of esophageal motor abnormalities. A subsequent automatic analysis of the resulting motility data relies on strict mathematical criteria for recognition of pressure events. Due to great variation in events, this method often fails to detect biologically relevant pressure variations. We have tried to develop a new concept for recognition of pressure events based on a neural network. Pressures were recorded for over 23 hours in 29 normal volunteers by means of a portable data recording system. A number of pressure events and non-events were selected from 9 recordings and used for training the network. The performance of the trained network was then verified on recordings from the remaining 20 volunteers. The accuracy and sensitivity of the two systems were comparable. However, the neural network recognized pressure peaks clearly generated by muscular activity that had escaped detection by the conventional program. In conclusion, we believe that neu-rocomputing has potential advantages for automatic analysis of gastrointestinal motility data.

Decision Support for Psychiatric Diagnosis Based on a Simple Questionnaire

1997 ◽  
Vol 36 (04/05) ◽  
pp. 349-351
Author(s):  
H. Mizuta ◽  
K. Kawachi ◽  
H. Yoshida ◽  
K. Iida ◽  
Y. Okubo ◽  
...  
Keyword(s):  
Neural Network ◽  
Decision Support ◽  
Psychiatric Diagnosis ◽  
Psychiatric Patients ◽  
Bayesian Classifier ◽  
Neural Network Classifier ◽  
Correct Decision ◽  
Neurotic Disorders ◽  
The Neural Network

Abstract:This paper compares two classifiers: Pseudo Bayesian and Neural Network for assisting in making diagnoses of psychiatric patients based on a simple yes/no questionnaire which is provided at the outpatient’s first visit to the hospital. The classifiers categorize patients into three most commonly seen ICD classes, i.e. schizophrenic, emotional and neurotic disorders. One hundred completed questionnaires were utilized for constructing and evaluating the classifiers. Average correct decision rates were 73.3% for the Pseudo Bayesian Classifier and 77.3% for the Neural Network classifier. These rates were higher than the rate which an experienced psychiatrist achieved based on the same restricted data as the classifiers utilized. These classifiers may be effectively utilized for assisting psychiatrists in making their final diagnoses.

SCORING MODELING BASED ON NEURAL NETWORKS FOR DETERMINING A BANK BORROWER'S RATING

2020 ◽  
Vol 2020 (10) ◽  
pp. 54-62
Author(s):  
Oleksii VASYLIEV ◽  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Network Architecture ◽  
Statistical Data ◽  
Activation Function ◽  
Decision Making Process ◽  
Neural Network Architecture ◽  
Acceptable Accuracy ◽  
The Neural Network ◽  
Sigmoid Activation Function

The problem of applying neural networks to calculate ratings used in banking in the decision-making process on granting or not granting loans to borrowers is considered. The task is to determine the rating function of the borrower based on a set of statistical data on the effectiveness of loans provided by the bank. When constructing a regression model to calculate the rating function, it is necessary to know its general form. If so, the task is to calculate the parameters that are included in the expression for the rating function. In contrast to this approach, in the case of using neural networks, there is no need to specify the general form for the rating function. Instead, certain neural network architecture is chosen and parameters are calculated for it on the basis of statistical data. Importantly, the same neural network architecture can be used to process different sets of statistical data. The disadvantages of using neural networks include the need to calculate a large number of parameters. There is also no universal algorithm that would determine the optimal neural network architecture. As an example of the use of neural networks to determine the borrower's rating, a model system is considered, in which the borrower's rating is determined by a known non-analytical rating function. A neural network with two inner layers, which contain, respectively, three and two neurons and have a sigmoid activation function, is used for modeling. It is shown that the use of the neural network allows restoring the borrower's rating function with quite acceptable accuracy.

Classification and Identification of Power System Disturbances Using Wavalet and Artificial Neural Network Technique

2005 ◽  
Vol 2 (2) ◽  
pp. 25
Author(s):  
Noraliza Hamzah ◽  
Wan Nor Ainin Wan Abdullah ◽  
Pauziah Mohd Arsad
Keyword(s):  
Neural Network ◽  
Power Quality ◽  
Probabilistic Neural Network ◽  
Microsoft Excel ◽  
Waveform Data ◽  
The Neural Network ◽  
Harmonic Voltage ◽  
Power Quality Disturbances ◽  
Electronic Load ◽  
Wavelet Technique

Power Quality disturbances problems have gained widespread interest worldwide due to the proliferation of power electronic load such as adjustable speed drives, computer, industrial drives, communication and medical equipments. This paper presents a technique based on wavelet and probabilistic neural network to detect and classify power quality disturbances, which are harmonic, voltage sag, swell and oscillatory transient. The power quality disturbances are obtained from the waveform data collected from premises, which include the UiTM Sarawak, Faculty of Science Computer in Shah Alam, Jati College, Menara UiTM, PP Seksyen 18 and Putra LRT. Reliable Power Meter is used for data monitoring and the data is further processed using the Microsoft Excel software. From the processed data, power quality disturbances are detected using the wavelet technique. After the disturbances being detected, it is then classified using the Probabilistic Neural Network. Sixty data has been chosen for the training of the Probabilistic Neural Network and ten data has been used for the testing of the neural network. The results are further interfaced using matlab script code.  Results from the research have been very promising which proved that the wavelet technique and Probabilistic Neural Network is capable to be used for power quality disturbances detection and classification.

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