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All Journal Perfecting a Video Game with Game Metrics Bulletin of Electrical Engineering and Informatics Indonesian Journal of Electrical Engineering and Computer Science
Afnizanfaizal Abdullah
Universiti Teknologi Malaysia
Computer Science & IT Electrical & Electronics Engineering

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Prediction of Bioprocess Production Using Deep Neural Network Method Amirah Baharin; Afnizanfaizal Abdullah; Siti Noorain Mohmad Yousoff
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 15, No 2: June 2017
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v15i2.6124

Abstract

Deep learning enhanced the state-of-the-art methods in genomics allows it to be used in analysing the biological data with high prediction. The training process of neural network with several hidden layers which has been facilitated by deep learning has been subjected into increased interest in achieving remarkable results in various fields. Thus, the extraction of bioprocess production can be implemented by pathway prediction in genomic metabolic network in eschericia coli. As metabolic engineering involves the manipulation of genes which have the potential to increase the yield of metabolite production. A mathematical model of this network is the foundation for the development of computational procedure that directs genetic manipulations that would eventually lead to optimized bioprocess production. Due to the ability of deep learning to be well suited in terms of genomics, modelling for biological network can be implemented. Each layer reveal the insight of biological network which enable pathway analysis to be implemented in order to extract the target bioprocess production. In this study, deep neural network has been to identify any set of gene deletion models that offers optimal results in xylitol production and its growth yield. 
Co-clustering algorithm for the identification of cancer subtypes from gene expression data Logenthiran Machap; Afnizanfaizal Abdullah; Zuraini Ali Shah
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 17, No 4: August 2019
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v17i4.12773

Abstract

Cancer has been classified as a heterogeneous genetic disease comprising various different subtypes based on gene expression data. Early stages of diagnosis and prognosis for cancer type have become an essential requirement in cancer informatics research because it is helpful for the clinical treatment of patients. Besides this, gene network interaction which is the significant in order to understand the cellular and progressive mechanisms of cancer has been barely considered in current research. Hence, applications of machine learning methods become an important area for researchers to explore in order to categorize cancer genes into high and low risk groups or subtypes. Presently co-clustering is an extensively used data mining technique for analyzing gene expression data. This paper presents an improved network assisted co-clustering for the identification of cancer subtypes (iNCIS) where it combines gene network information with gene expression data to obtain co-clusters. The effectiveness of iNCIS was evaluated on large-scale Breast Cancer (BRCA) and Glioblastoma Multiforme (GBM). This weighted co-clustering approach in iNCIS delivers a distinctive result to integrate gene network into the clustering procedure.
Recognition of brain cancer and cerebrospinal fluid due to the usage of different MRI image by utilizing support vector machine Soobia Saeed; Afnizanfaizal Abdullah
Bulletin of Electrical Engineering and Informatics Vol 9, No 2: April 2020
Publisher : Institute of Advanced Engineering and Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (707.223 KB) | DOI: 10.11591/eei.v9i2.1869

Abstract

Medicinal images assume an important part in the diagnosis of tumors as well as Cerebrospinal fluid (CSF) leak. Similarly, MRI could be the cutting-edge regenerative imaging technology that allows for a sectional angle perspective of the body that gives specialists convenience and will inspect the person-concerned. In this paper, the author has attempted the strategy to classify MRI images at the beginning of production to have a tumor or recognition. The study aims to address the aforementioned problems associated with brain cancer with a CSF leak. This research, the author focuses on brain tumor and applies the statistical model for the testing and also discusses the images of a brain tumor. They can judge the tumor region by conducting a comparative image analysis and applying Histogram function afterwards to construct a classifier that could be prepared to predict tumor and non-tumor MRI examinees based on the support vector machine. Our system is capable of detecting the right region that a pathologist also highlights. In the future, this should be more driven with the objective that tumors can be arranged and describe the solution in the medical terms and implementation with gives some predictions about the future generated by modified technology. 
Deep learning in non coding variant (a brief overview) Lee Kuan Xin; Afnizanfaizal Abdullah
Indonesian Journal of Electrical Engineering and Computer Science Vol 18, No 3: June 2020
Publisher : Institute of Advanced Engineering and Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11591/ijeecs.v18.i3.pp1432-1438

Abstract

The 21st centuries were deemed to be the era of big data. Data driven research had become a necessity. This hold true not only in the business world, yet also in the field of biomedical world. From a few years of biological data extraction and derivation. With the advancement of Next Generation Sequencing, genomics data had grown to become an ambiguous giant which could not keep up with the pace of its advancement in it analysis counter parts. This results in a large amount of unanalysed genomic data. These genomic data consist not only plain information, researcher had discovered the potential of most gene called the non-coding variant and still failing in identifying their function. With the growth in volume of data, there is also a growth of hardware or technologies. With current technologies, we were able to implement a more complex and sophisticated algorithm in analysis these genomics data. The domain of deep learning had become a major interest of researcher as it was proven to have achieve a significant success in deriving insight from various field. This paper aims to review the current trend of non-coding variant analysis using deep learning approach.
Functional analysis of cancer gene subtype from co-clustering and classification Logenthiran Machap; Afnizanfaizal Abdullah
Indonesian Journal of Electrical Engineering and Computer Science Vol 18, No 1: April 2020
Publisher : Institute of Advanced Engineering and Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11591/ijeecs.v18.i1.pp343-350

Abstract

Cancer is a heterogeneity genetic disease with huge phenotypic alterations among dissimilar cancers types or even between same cancer types. Recent expansions of genome-wide profiling technologies offer a chance to explore molecular changes variations throughout advancement of cancer. Therefore, various statistical and machine learning algorithms have been designed and developed for the handling and interpretation of high-throughput microarray molecular data. Discovery of molecular subtypes studies have permitted the cancer to be allocated into similar groups that are deliberated to port similar molecular and clinical characteristics. Thus, the main objective of this research is to discover cancer gene subtypes and classify genes to obtain higher accuracy. In particular improved co-clustering algorithm used to discover cancer subtypes. And then supervised infinite feature selection gene selection method was combined with multi class SVM for classification of selected genes and further biological analysis. The analysis on breast cancer and glioblastoma multiforme evidences that top genes involved in cancer and the pathways present in both cancer top genes. The functional analysis is useful in medical and pharmaceutical field for cancer diagnosis and prognosis.
Co-Authors Amirah Baharin Lee Kuan Xin Logenthiran Machap Siti Noorain Mohmad Yousoff Soobia Saeed Zuraini Ali Shah