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Optimizing genetic prediction: Define-by-run DL approach in DNA sequencing
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Abstract: The utility of DNA sequencing in diagnosing and prognosis of diseases is vital for assessing the risk of genetic disorders, particularly for asymptomatic individuals with a genetic predisposition. Such diagnostic approaches are integral in guiding health and lifestyle decisions and preparing families with the necessary foreknowledge to anticipate potential genetic abnormalities. The present study explores implementing a define-by-run deep learning (DL) model optimized using the Tree-structured Parzen estimator algorithm to enhance the precision of genetic diagnostic tools. Unlike conventional models, the define-by-run model bolsters accuracy through dynamic adaptation to data during the learning process and iterative optimization of critical hyperparameters, such as layer count, neuron count per layer, learning rate, and batch size. Utilizing a diverse dataset comprising DNA sequences fromtwo distinct groups: patients diagnosed with breast cancer and a control group of healthy individuals. The model showcased remarkable performance, with accuracy, precision, recall, F1-score, and area under the curve metrics reaching 0.871, 0.872, 0.871, 0.872, and 0.95, respectively, outperforming previous models. These findings underscore the significant potential of DL techniques in amplifying the accuracy of disease diagnosis and prognosis through DNA sequencing, indicating substantial advancements in personalized medicine and genetic counseling. Collectively, the findings of this investigation suggest that DL presents transformative potential in the landscape of genetic disorder diagnosis and management.

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Publication Date
Wed Jan 01 2014
Journal Name
Scienceasia
A combined compact genetic algorithm and local search method for optimizing the ARMA(1,1) model of a likelihood estimator
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In this paper, a compact genetic algorithm (CGA) is enhanced by integrating its selection strategy with a steepest descent algorithm (SDA) as a local search method to give I-CGA-SDA. This system is an attempt to avoid the large CPU time and computational complexity of the standard genetic algorithm. Here, CGA dramatically reduces the number of bits required to store the population and has a faster convergence. Consequently, this integrated system is used to optimize the maximum likelihood function lnL(φ1, θ1) of the mixed model. Simulation results based on MSE were compared with those obtained from the SDA and showed that the hybrid genetic algorithm (HGA) and I-CGA-SDA can give a good estimator of (φ1, θ1) for the ARMA(1,1) model. Anot

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Publication Date
Thu Sep 08 2022
Journal Name
Al-khwarizmi Engineering Journal
Performance Prediction in EDM Process for Al 6061 Alloy Using Response Surface Methodology and Genetic Algorithm
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The Electric Discharge (EDM) method is a novel thermoelectric manufacturing technique in which materials are removed by a controlled spark erosion process between two electrodes immersed in a dielectric medium. Because of the difficulties of EDM, determining the optimum cutting parameters to improve cutting performance is extremely tough. As a result, optimizing operating parameters is a critical processing step, particularly for non-traditional machining process like EDM. Adequate selection of processing parameters for the EDM process does not provide ideal conditions, due to the unpredictable processing time required for a given function. Models of Multiple Regression and Genetic Algorithm are considered as effective methods for determ

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Publication Date
Sun Jun 30 2024
Journal Name
Iraqi Journal Of Science
Some Games Via (D, DL) Compact Topological Groups
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    The aim of our work is to develop a new type of games which are related to (D, WD, LD) compactness of topological groups. We used an infinite game that corresponds to our work. Also, we used an alternating game in which the response of the second player depends on the choice of the first one. Many results of winning and losing strategies have been studied, consistent with the nature of the topological groups. As well as, we presented some topological groups, which fail to have winning strategies and we give some illustrated examples. Finally, the effect of functions on the aforementioned compactness strategies was studied.  

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Publication Date
Mon Feb 27 2023
Journal Name
Applied Sciences
Comparison of ML/DL Approaches for Detecting DDoS Attacks in SDN
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Software-defined networking (SDN) presents novel security and privacy risks, including distributed denial-of-service (DDoS) attacks. In response to these threats, machine learning (ML) and deep learning (DL) have emerged as effective approaches for quickly identifying and mitigating anomalies. To this end, this research employs various classification methods, including support vector machines (SVMs), K-nearest neighbors (KNNs), decision trees (DTs), multiple layer perceptron (MLP), and convolutional neural networks (CNNs), and compares their performance. CNN exhibits the highest train accuracy at 97.808%, yet the lowest prediction accuracy at 90.08%. In contrast, SVM demonstrates the highest prediction accuracy of 95.5%. As such, an

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Publication Date
Tue Dec 19 2017
Journal Name
Al-khwarizmi Engineering Journal
Prediction of Reaction Kinetic of Al- Doura Heavy Naphtha Reforming Process Using Genetic Algorithm
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In this study, genetic algorithm was used to predict the reaction kinetics of Iraqi heavy naphtha catalytic reforming process located in Al-Doura refinery in Baghdad.  One-dimensional steady state model was derived to describe commercial catalytic reforming unit consisting of four catalytic reforming reactors in series process.

The experimental information (Reformate composition and output temperature) for each four reactors collected at different operating conditions was used to predict the parameters of the proposed kinetic model. The kinetic model involving 24 components, 1 to 11 carbon atoms for paraffins and 6 to 11 carbon atom for naphthenes and aromatics with 71 reactions. The pre-exponential Arrhenius constants and a

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Publication Date
Sat Apr 01 2017
Journal Name
Iosr Journal Of Computer Engineering (iosr-jce)
A New Approach to DNA, RNA, and Protein Motifs Templates Visualization and Analysis via Compilation Technique
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Motifs template is the input for many bioinformatics systems such codons finding, transcription, transaction, sequential pattern miner, and bioinformatics databases analysis. The size of motifs arranged from one base up to several Mega bases, therefore, the typing errors increase according to the size of motifs. In addition, when the structures motifs are submitted to bioinformatics systems, the specifications of motifs components are required, i.e. the simple motifs, gaps, and the lower bound and upper bound of each gap. The motifs can be of DNA, RNA, or Protein. In this research, a motif parser and visualization module is designed depending on a proposed a context free grammar, CFG, and colors human recognition system. GFC describes the m

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Publication Date
Sun Dec 09 2018
Journal Name
Baghdad Science Journal
Application of Randomly Amplified Polymorphic DNA (RAPD) Technique to Estimate Genetic Distance among Some Methicillin Resistant Staphylococcus aureus Isolated from Different Iraqi Hospitals
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Methicillin resistant Staphylococcus aureus (MRSA) is one of the principal nosocomial causative agents. This bacterium has the capability to resist wide range of antibiotics and it is responsible for many diseases like skin, nose and wounds infection. In this study, randomly amplified polymorphic DNA (RAPD)-PCR was applied with ten random primers to examine the molecular diversity among methicillin resistant Staphylococcus aureus (MRSA) isolates in the hospitals and to investigate the genetic distance between them. 90 Isolates were collected from clinical specimens from Iraqi hospitals for a total of 90 isolates. Only 10 strains (11.11%) were found to be MRSA. From these 10 primers, only 9 gave clear amplification products. 91 fragment l

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Publication Date
Sun Jan 01 2017
Journal Name
The Iraqi Journal Of Agricultural Science 48 (5), 1197-1205‏
Sex identification of date palm by using dna molecular markers
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Publication Date
Mon Apr 10 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Role of Extracted Genomic DNA on Biofilm Formation by Pseudomonas aeruginosa and Klebsiella pneumoniae in vitro
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   Bacteria form complex and highly elaborate surface adherent communities known as biofilms.Biofilm have been shown to be associated with several human diseases ,and to colonize a wide variety of medical devices . The current study focuses on contribution of extracted genomic   DNA in  biofilm formation by   P. aeruginosa and  K. pneumoniae isolates   .The percentages of Pseudomonas aeruginosa recovery from drinking water  in this study were  10%(20 positive P. aeruginosa  samples ) and K. pneumonia.,  7%(14 positive K. pneumonia samples).The results showed that all P.aeruginosa and K. pneumoniae isolates (100%) were slime producer but in different degrees by forming  of black

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Publication Date
Wed May 17 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Image Compression Using Proposed Enhanced Run Length Encoding Algorithm
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In this paper, we will present proposed enhance process of image compression by using RLE algorithm. This proposed yield to decrease the size of compressing image, but the original method used primarily for compressing a binary images [1].Which will yield increasing the size of an original image mostly when used for color images. The test of an enhanced algorithm is performed on sample consists of ten BMP 24-bit true color images, building an application by using visual basic 6.0 to show the size after and before compression process and computing the compression ratio for RLE and for the enhanced RLE algorithm

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