SearcharxivSearch

arXiv subjects

Khalid Raza

Publications and source records attributed to Khalid Raza.

17 recordsLinked to original sources

Medical Image Generation using Generative Adversarial Networks

Generative adversarial networks (GANs) are unsupervised Deep Learning approach in the computer vision community which has gained significant attention from the last few years in identifying the internal structure of multimodal medical imaging data. The adversarial network simultaneously generates realistic medical images and corresponding annotations, which proven to be useful in many cases such as image augmentation, image registration, medical image generation, image reconstruction, and image-to-image translation. These properties bring the attention of the researcher in the field of medical image analysis and we are witness of rapid adaption in many novel and traditional applications. This chapter provides state-of-the-art progress in GANs-based clinical application in medical image generation, and cross-modality synthesis. The various framework of GANs which gained popularity in the interpretation of medical images, such as Deep Convolutional GAN (DCGAN), Laplacian GAN (LAPGAN), pix2pix, CycleGAN, and unsupervised image-to-image translation model (UNIT), continue to improve their performance by incorporating additional hybrid architecture, has been discussed. Further, some of the recent applications of these frameworks for image reconstruction, and synthesis, and future research directions in the area have been covered.

eess.IV

A Tour of Unsupervised Deep Learning for Medical Image Analysis

Interpretation of medical images for diagnosis and treatment of complex disease from high-dimensional and heterogeneous data remains a key challenge in transforming healthcare. In the last few years, both supervised and unsupervised deep learning achieved promising results in the area of medical imaging and image analysis. Unlike supervised learning which is biased towards how it is being supervised and manual efforts to create class label for the algorithm, unsupervised learning derive insights directly from the data itself, group the data and help to make data driven decisions without any external bias. This review systematically presents various unsupervised models applied to medical image analysis, including autoencoders and its several variants, Restricted Boltzmann machines, Deep belief networks, Deep Boltzmann machine and Generative adversarial network. Future research opportunities and challenges of unsupervised techniques for medical image analysis have also been discussed.

eess.IV

Optimizing Deep Neural Network Architecture: A Tabu Search Based Approach

The performance of Feedforward neural network (FNN) fully de-pends upon the selection of architecture and training algorithm. FNN architecture can be tweaked using several parameters, such as the number of hidden layers, number of hidden neurons at each hidden layer and number of connections between layers. There may be exponential combinations for these architectural attributes which may be unmanageable manually, so it requires an algorithm which can automatically design an optimal architecture with high generalization ability. Numerous optimization algorithms have been utilized for FNN architecture determination. This paper proposes a new methodology which can work on the estimation of hidden layers and their respective neurons for FNN. This work combines the advantages of Tabu search (TS) and Gradient descent with momentum backpropagation (GDM) training algorithm to demonstrate how Tabu search can automatically select the best architecture from the populated architectures based on minimum testing error criteria. The proposed approach has been tested on four classification benchmark dataset of different size.

cs.LG

Fuzzy logic based approaches for gene regulatory network inference

The rapid advancement in high-throughput techniques has fueled the generation of large volume of biological data rapidly with low cost. Some of these techniques are microarray and next generation sequencing which provides genome level insight of living cells. As a result, the size of most of the biological databases, such as NCBI-GEO, NCBI-SRA, is exponentially growing. These biological data are analyzed using computational techniques for knowledge discovery - which is one of the objectives of bioinformatics research. Gene regulatory network (GRN) is a gene-gene interaction network which plays pivotal role in understanding gene regulation process and disease studies. From the last couple of decades, the researchers are interested in developing computational algorithms for GRN inference (GRNI) using high-throughput experimental data. Several computational approaches have been applied for inferring GRN from gene expression data including statistical techniques (correlation coefficient), information theory (mutual information), regression based approaches, probabilistic approaches (Bayesian networks, naive byes), artificial neural networks, and fuzzy logic. The fuzzy logic, along with its hybridization with other intelligent approach, is well studied in GRNI due to its several advantages. In this paper, we present a consolidated review on fuzzy logic and its hybrid approaches for GRNI developed during last two decades.

cs.CE

Comprehensive overview and assessment of miRNA target prediction tools in human and drosophila melanogaster

MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression at the post-transcriptional level through complementary base pairing with the target mRNA, leading to mRNA degradation and blocking translation process. Any dysfunctions of these small regulatory molecules have been linked with the development and progression of several diseases. Therefore, it is necessary to reliably predict potential miRNA targets. A large number of computational prediction tools have been developed which provide a faster way to find putative miRNA targets, but at the same time their results are often inconsistent. Hence, finding a reliable, functional miRNA target is still a challenging task. Also, each tool is equipped with different algorithms, and it is difficult for the biologists to know which tool is the best choice for their study. This paper briefly describes fundamental of miRNA target prediction algorithms, discuss frequently used prediction tools, and further, the performance of frequently used prediction tools have been assessed using experimentally validated high confident mature miRNAs and their targets for two organisms Human and Drosophila Melanogaster. Both Drosophila Melanogaster and Human supported miRNA target prediction tools have been evaluated separately to find out best performing tool for each of these two organisms. In the human dataset, TargetScan showed the best results amongst the other predictors followed by the miRmap and microT, whereas in the D. Melanogaster dataset, MicroT tool showed the best performance followed by the TargetScan in the comparison of other tools.

q-bio.GN

Recent advancement in Next Generation Sequencing techniques and its computational analysis

Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. This novel approach is a newbie and has critical advantages over the traditional Capillary Electrophoresis (CE) based Sanger Sequencing. The advancement of NGS has led to numerous important discoveries, which could have been costlier and time taking in case of traditional CE based Sanger sequencing. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which need to be analysed to conclude valuable information. Specific data analysis algorithms are written for specific task to be performed. The algorithms in group, act as a tool in analysing the NGS data. Analysis of NGS data unravels important clues in quest for the treatment of various life-threatening diseases; improved crop varieties and other related scientific problems related to human welfare. In this review, an effort was made to address basic background of NGS technologies, possible applications, computational approaches and tools involved in NGS data analysis, future opportunities and challenges in the area.

q-bio.GN

Recurrent Neural Network Based Hybrid Model of Gene Regulatory Network

Systems biology is an emerging interdisciplinary area of research that focuses on study of complex interactions in a biological system, such as gene regulatory networks. The discovery of gene regulatory networks leads to a wide range of applications, such as pathways related to a disease that can unveil in what way the disease acts and provide novel tentative drug targets. In addition, the development of biological models from discovered networks or pathways can help to predict the responses to disease and can be much useful for the novel drug development and treatments. The inference of regulatory networks from biological data is still in its infancy stage. This paper proposes a recurrent neural network (RNN) based gene regulatory network (GRN) model hybridized with generalized extended Kalman filter for weight update in backpropagation through time training algorithm. The RNN is a complex neural network that gives a better settlement between the biological closeness and mathematical flexibility to model GRN. The RNN is able to capture complex, non-linear and dynamic relationship among variables. Gene expression data are inherently noisy and Kalman filter performs well for estimation even in noisy data. Hence, non-linear version of Kalman filter, i.e., generalized extended Kalman filter has been applied for weight update during network training. The developed model has been applied on DNA SOS repair network, IRMA network, and two synthetic networks from DREAM Challenge. We compared our results with other state-of-the-art techniques that show superiority of our model. Further, 5% Gaussian noise has been added in the dataset and result of the proposed model shows negligible effect of noise on the results.

cs.NE

Analysis of Microarray Data using Artificial Intelligence Based Techniques

Microarray is one of the essential technologies used by the biologist to measure genome-wide expression levels of genes in a particular organism under some particular conditions or stimuli. As microarrays technologies have become more prevalent, the challenges of analyzing these data for getting better insight about biological processes have essentially increased. Due to availability of artificial intelligence based sophisticated computational techniques, such as artificial neural networks, fuzzy logic, genetic algorithms, and many other nature-inspired algorithms, it is possible to analyse microarray gene expression data in more better way. Here, we reviewed artificial intelligence based techniques for the analysis of microarray gene expression data. Further, challenges in the field and future work direction have also been suggested.

cs.AI

Formal Concept Analysis for Knowledge Discovery from Biological Data

Due to rapid advancement in high-throughput techniques, such as microarrays and next generation sequencing technologies, biological data are increasing exponentially. The current challenge in computational biology and bioinformatics research is how to analyze these huge raw biological data to extract biologically meaningful knowledge. This review paper presents the applications of formal concept analysis for the analysis and knowledge discovery from biological data, including gene expression discretization, gene co-expression mining, gene expression clustering, finding genes in gene regulatory networks, enzyme/protein classifications, binding site classifications, and so on. It also presents a list of FCA-based software tools applied in biological domain and covers the challenges faced so far.

cs.AI

Ant Colony Optimization for Inferring Key Gene Interactions

Inferring gene interaction network from gene expression data is an important task in systems biology research. The gene interaction network, especially key interactions, plays an important role in identifying biomarkers for disease that further helps in drug design. Ant colony optimization is an optimization algorithm based on natural evolution and has been used in many optimization problems. In this paper, we applied ant colony optimization algorithm for inferring the key gene interactions from gene expression data. The algorithm has been tested on two different kinds of benchmark datasets and observed that it successfully identify some key gene interactions.

cs.NE

A Comprehensive Evaluation of Machine Learning Techniques for Cancer Class Prediction Based on Microarray Data

Prostate cancer is among the most common cancer in males and its heterogeneity is well known. Its early detection helps making therapeutic decision. There is no standard technique or procedure yet which is full-proof in predicting cancer class. The genomic level changes can be detected in gene expression data and those changes may serve as standard model for any random cancer data for class prediction. Various techniques were implied on prostate cancer data set in order to accurately predict cancer class including machine learning techniques. Huge number of attributes and few number of sample in microarray data leads to poor machine learning, therefore the most challenging part is attribute reduction or non significant gene reduction. In this work we have compared several machine learning techniques for their accuracy in predicting the cancer class. Machine learning is effective when number of attributes (genes) are larger than the number of samples which is rarely possible with gene expression data. Attribute reduction or gene filtering is absolutely required in order to make the data more meaningful as most of the genes do not participate in tumor development and are irrelevant for cancer prediction. Here we have applied combination of statistical techniques such as inter-quartile range and t-test, which has been effective in filtering significant genes and minimizing noise from data. Further we have done a comprehensive evaluation of ten state-of-the-art machine learning techniques for their accuracy in class prediction of prostate cancer. Out of these techniques, Bayes Network out performed with an accuracy of 94.11% followed by Navie Bayes with an accuracy of 91.17%. To cross validate our results, we modified our training dataset in six different way and found that average sensitivity, specificity, precision and accuracy of Bayes Network is highest among all other techniques used.

cs.LG

Reconstruction of gene regulatory network of colon cancer using information theoretic approach

Reconstruction of gene regulatory networks or 'reverse-engineering' is a process of identifying gene interaction networks from experimental microarray gene expression profile through computation techniques. In this paper, we tried to reconstruct cancer-specific gene regulatory network using information theoretic approach - mutual information. The considered microarray data consists of large number of genes with 20 samples - 12 samples from colon cancer patient and 8 from normal cell. The data has been preprocessed and normalized. A t-test statistics has been applied to filter differentially expressed genes. The interaction between filtered genes has been computed using mutual information and ten different networks has been constructed with varying number of interactions ranging from 30 to 500. We performed the topological analysis of the reconstructed network, revealing a large number of interactions in colon cancer. Finally, validation of the inferred results has been done with available biological databases and literature.

cs.CE

Reconstruction and Analysis of Cancer-specific Gene Regulatory Networks from Gene Expression Profiles

The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput data generated by microarray experiments fueled researchers to use whole-genome gene expression profiles to understand cancer and to reconstruct key cancer-specific gene regulatory network. Now, the researchers are taking a keen interest in the development of algorithm for the reconstruction of gene regulatory network from whole genome expression profiles. In this study, a cancer-specific gene regulatory network (prostate cancer) has been constructed using a simple and novel statistics based approach. First, significant genes differentially expressing them self in the disease condition has been identified using a two-stage filtering approach t-test and fold-change measure. Next, regulatory relationships between the identified genes has been computed using Pearson correlation coefficient. The obtained results has been validated with the available databases and literature. We obtained a cancer-specific regulatory network of 29 genes with a total of 55 regulatory relations in which some of the genes has been identified as hub genes that can act as drug target for the cancer diagnosis.

eess.SY

A Novel Anticlustering Filtering Algorithm for the Prediction of Genes as a Drug Target

The high-throughput data generated by microarray experiments provides complete set of genes being expressed in a given cell or in an organism under particular conditions. The analysis of these enormous data has opened a new dimension for the researchers. In this paper we describe a novel algorithm to microarray data analysis focusing on the identification of genes that are differentially expressed in particular internal or external conditions and which could be potential drug targets. The algorithm uses the time-series gene expression data as an input and recognizes genes which are expressed differentially. This algorithm implements standard statistics-based gene functional investigations, such as the log transformation, mean, log-sigmoid function, coefficient of variations, etc. It does not use clustering analysis. The proposed algorithm has been implemented in Perl. The time-series gene expression data on yeast Saccharomyces cerevisiae from the Stanford Microarray Database (SMD)consisting of 6154 genes have been taken for the validation of the algorithm. The developed method extracted 48 genes out of total 6154 genes. These genes are mostly responsible for the yeast's resistants at a high temperature.

cs.CE

Evolutionary algorithms in genetic regulatory networks model

Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding their complex relationships. Understanding the interactions between genes gives rise to develop better method for drug discovery and diagnosis of the disease since many diseases are characterized by abnormal behaviour of the genes. In this paper we have reviewed various evolutionary algorithms-based approach for modeling GRNs and discussed various opportunities and challenges.

cs.CE

Application Of Data Mining In Bioinformatics

This article highlights some of the basic concepts of bioinformatics and data mining. The major research areas of bioinformatics are highlighted. The application of data mining in the domain of bioinformatics is explained. It also highlights some of the current challenges and opportunities of data mining in bioinformatics.

cs.CE

A Comprehensive Study of CRM through Data Mining Techniques

In today's competitive scenario in corporate world, "Customer Retention" strategy in Customer Relationship Management (CRM) is an increasingly pressed issue. Data mining techniques play a vital role in better CRM. This paper attempts to bring a new perspective by focusing the issue of data mining applications, opportunities and challenges in CRM. It covers the topic such as customer retention, customer services, risk assessment, fraud detection and some of the data mining tools which are widely used in CRM.

cs.DB