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    Analyzing Microarray Data Via Learning DNA Cross Hybridization

    , M.Sc. Thesis Sharif University of Technology Hassani Bidgoli, Mansoor (Author) ; Motahari, Abolfazl (Supervisor) ; Rabiee, Hamid Reza (Co-Advisor)
    Abstract
    Gene expression microarrays include thousands of probes spotted on their surface to measure the expression level of a set of genes. Identifying the amount of a transcript level by hybridization, each probe is complementary to a fragment of a specific gene transcripts. Although probes are designed to avoid crosshybridization to non-specific transcripts, occurrences of cross-hybridizations is inevitable due to massive probes that are spotted on microarrays. The main question is whether these non-specific cross-hybridization have significant effect on the downstream analysis of gene expression microarray datasets. This thesis aims at answering to this question by considering datasets from... 

    Distributed Processing of Next Generation Sequencing Data Set

    , M.Sc. Thesis Sharif University of Technology Hadadian Nejad Yousefi, Mostafa (Author) ; Goudarzi, Maziar (Supervisor) ; Motahari, Abolfazl (Supervisor)
    Abstract
    DNA analysis plays a significant role in fields such as pharmacy, agriculture, genealogy, and forensics. Next generation sequencing datasets cover a gene several times due to a large number of readings. Therefore, the initial data volume is several times the amount of memory required to store the DNA strand. First, the DNA sequence of a sample should be made using the primary data, and then the difference should be found by comparing the sample DNA sequence with the reference DNA sequence. By finding these differences, one can extract the characteristics of the tested species. The extracted properties are precious for genetics researchers. For example, they can produce drugs that are... 

    Fundamental Limits of Population Stratification From an Information Theoretic View

    , M.Sc. Thesis Sharif University of Technology Tahmasebi, Behrooz (Author) ; Maddah-Ali, Mohammad Ali (Supervisor) ; Motahari, Abolfazl (Co-Supervisor)
    Abstract
    This thesis consists of two parts. For the first, we study the identifiability of finite mixtures of finite product measures. This class of mixture models has a large number of applications in real-world data modeling. An important example is the population genetic application of them in modeling of mixed population datasets. The identifiability means that the mapping between the class parameters and the mixture distributions is one to one. In this manuscript, we define some separability metrics inspired by methods used in clustering mixture models and study the fundamental trade off between identifiability and the number of separable variables of the mixture model. For the second part of... 

    Privacy in DNA Sequencing

    , M.Sc. Thesis Sharif University of Technology Gholami, Ali (Author) ; Maddah-ali, Mohammad Ali (Supervisor) ; Motahari, Abolfazl (Co-Supervisor)
    Abstract
    DNA sequence is the lifetime private information of each individual: it can reveal personal traits, health status, and medical risk of that individual, it can be abused by entities such as insurance companies, it can be used for identity theft, etc. Unfortunately, due to cost, regulations, or some restrictions, we may not be able to complete DNA sequencing in-house and have to outsource it to some unreliable companies in some foreign countries.This would compromise the DNA privacy from the beginning. This would raise the question that how we can guarantee the DNA privacy in the process of sequencing.Here we propose a solution for private DNA sequencing by exploiting the fact that the process... 

    Partial Coded Data Placement in Cache Memories in Information Centric Networks

    , Ph.D. Dissertation Sharif University of Technology Salehi, Mohammad Javad (Author) ; Hossein Khalaj, Babak (Supervisor) ; Motahari, Abolfazl (Supervisor)
    Abstract
    In this research, we have studied the effect of coding techniques, as well as partial data placement in cache memories throughout the network. Cache memories play an important role in information centric networks. As content delivery account for the major part of data transfers in current IP-based data networks, these network structures have gained much attention recently and hence optimizing cache performance in their structure is of great importance.Throughout this research, we first analyze the effect of simultaneous data delivery from multiple cache memories on the network performance. We consider two basic models for the network graph; and show there exists a fundamental trade-off among... 

    Distributed Structure Learning of Gaussian Graphical Models

    , M.Sc. Thesis Sharif University of Technology Mirzaeifard, Reza (Author) ; Manzuri Shalmani, Mohammad-Taghi (Supervisor) ; Motahari, Abolfazl (Co-Supervisor)
    Abstract
    Nowadays, the explosion of the volume data provides more accuracy in machine learning models. But, Working with a vast amount of data is not easy, especially in a situation that data are distributed over the systems. In such systems, designing distributed learning algorithms that in communication efficient setting demand reliable and more accurate results, are so important. We studied sparse structure learning of Gaussian graphical model in a situation that our data are distributed over the system and each machine has a dimension of data. Each local machine should send its data to a central machine and the central machine is responsible for learning the structure. For reliable learning under... 

    Simulation and Study of Iso-Dose Curve for Asymmetrical Balloon in Balloon-Brachytherapy with Cs-131

    , M.Sc. Thesis Sharif University of Technology Mohebbi Kojidi, Mohammad Hossein (Author) ; Hosseini, Abolfazl (Supervisor) ; Shirmardi, Pejman (Supervisor)
    Abstract
    Incidence of brain metastases (BM) from any tumor varies according to the method of data collection and date reported, ranging from 8 to 14 per 100,000 people per year. According to current population, about 6400 to 11000 BM Patients per year is expected. Without treatment, prognosis is dismal with survival of only 1–2 months. However, survival can be extended to 3–6 months with whole-brain radiotherapy (WBRT) and to 11 months with either surgery followed by adjuvant WBRT or surgery plus adjuvant stereotactic radiosurgery (SRS). Intravascular brachytherapy (generally iodine-125 (125I)) into the surgical cavity is another treatment strategy. 125I has been shown to confer local control... 

    Modelling Cell`s State in Different Cell Types

    , M.Sc. Thesis Sharif University of Technology Saberi, Amir Hossein (Author) ; Hossein Khalaj, Babak (Supervisor) ; Motahari, Abolfazl (Co-Supervisor)
    Abstract
    Existence of heterogeneity in vital tissues of complex multicellular organisms like mammals, and fatal tissues like cancer on one hand, and limited access to biological properties of their components on the other hand, turn the study of these tissue traits to one of the most interesting fields in bioinformatics. One of the hottest subjects in this field is the recognition of functional components of these tissues by using bulk data extracted from the whole tissue.Almost every method that aims to achieve such a purpose, particularly using gene expression data, assumes that all of the cell types which constitute the studied tissue have a deterministic expression profile.In this thesis we... 

    Flow-driven Design and Evaluation of GTP Protocol on Mobile Networks Transport Layer

    , M.Sc. Thesis Sharif University of Technology Mahdavi Far, Hossein (Author) ; Motahari, Abolfazl (Supervisor) ; Hossein Khalaj, Babak (Co-Supervisor)
    Abstract
    The significant increase in the penetration of mobile phones and the significant growth of traffic generated in these networks has posed many challenges in the field of cost management, and the expansion of the existing network for mobile operators and has encouraged operators to change the current network architecture. On the other hand, the standard of the next mobile communication, i.e. the fifth generation, has a completely different architecture from the current architecture. Many of the logical and physical entities of the current network have undergone fundamental changes in the new network, and at first glance it does not seem that there is a direct transition from the previous... 

    Over-parameterized Neural Networks: Convergence Analysis and Generalization Bounds

    , M.Sc. Thesis Sharif University of Technology Tinati, Mohammad (Author) ; Maddah Ali, Mohammad Ali (Supervisor) ; Motahari, Abolfazl (Supervisor)
    Abstract
    Despite its extraordinary empirical achievements, the theoretical foundation of modern Machine Learning, and in particular deep neural networks (DNN), is still a mystery. In this thesis, we have studied the effect of optimization algorithms on the generalization properties for shallow neural networks. Particularly, we have focused on the implicit biases these optimization procedures, specifically dropout, deal with. As an example for this implicit bias, classical results had shown that for linear regression, in the interpolation regime, gradient descent, among all the possible solutions, converges to the minimum L2-norm interpolation. Due to the complex nature of the neural networks... 

    Palm Vein Pattern Recognition using Deep Convolutional Neural Network (DCNN) with Gabor Filter

    , M.Sc. Thesis Sharif University of Technology Nazari Tavakoli, Amir Ali (Author) ; Motahari, Abolfazl (Supervisor) ; Peyvandi, Hossein (Supervisor)
    Abstract
    Frequently using Personal Identification Information has escalated the security concerns of bank accounts, emails, daily transactions, and other activities. Therefore, user access to such apps must be controlled. Traditional personal verification methods offer limited security because they might need to be remembered or stolen. Therefore, Biometric authentication, which identifies persons by their unique biological information, is gaining popularity. However, palm vein identification is highly secure because the vein patterns are not duplicated in other people, even in monozygotic twins. Moreover, it has a liveness detection and is convenient since the vein pattern cannot be faked,... 

    Experimental and numerical investigations of radial flow compressor component losses

    , Article Journal of Mechanical Science and Technology ; Vol. 28, issue. 6 , 2014 , p. 2189-2196 Mojaddam, M ; Hajilouy-Benisi, A ; Abolfazl Moussavi-Torshizi, S ; Movahhedy, M.R ; Durali, M ; Sharif University of Technology
    2014
    Abstract
    This research numerically and experimentally investigates a small turbocharger radial flow compressor with a vane-less diffuser and volute. The geometry of the compressor is obtained via component scanning, through which a 3D model is prepared. The flow inside this model is numerically analyzed by using a Navier-Stokes solver with a shear-stress transport turbulence model. The characteristic curves of the compressor and the contributions of its components to total pressure drop are acquired by measuring the static and total pressures at different cross sections of the compressor. Numerical results are verified with the experimental test results. The model results exhibit good agreement with... 

    Detecting Large-scale Evolutionary Events and Multiple Alignment of Whole Genomes

    , M.Sc. Thesis Sharif University of Technology Afshinfard, Amir Hossein (Author) ; Motahari, Abolfazl (Supervisor) ; Rabiee, Hamid Reza (Co-Advisor)
    Abstract
    Recent advances in genome sequencing technologies have provided a wide variety of completely sequenced genomes. This opened up the opportunity to study genomic sequences, using pairwise or multiple alignment of the whole-genomes. The aim is to explore the similarities and differences between genomes for further comparative studies. This task is challenging because genomes of different species have undergone not only small mutations but also many large-scale evolutionary events such as insertion, deletion and inversion.There has been a lot of research on developing whole-genome alignment algorithms. Having an optimal trade-off between sensitivity, accuracy and computational expense are very... 

    Preparation and Modification of Lithium-ion Battery Membrane/Separator

    , M.Sc. Thesis Sharif University of Technology Javadi, Omid (Author) ; Soltanieh, Mohammad (Supervisor) ; Mousavi, Abbas (Supervisor) ; Fathollahi, Abolfazl (Co-Supervisor)
    Abstract
    Electrolyte separator is the major component of lithium-ion batteries which the battery safety directly depends on it. In this work, a membrane separator based on the polyvinylidene fluoride (PVdF) was prepared via non-solvent induced phase separation (NIPS) method with water and ethanol as non-solvent and a mixture of dimethylformamide (DMF) and acetone as solvents. The effect of various acetone/DMF ratios and type of non-solvent on the structural, mechanical and electrochemical properties of separator was studied. The separator was characterized by FE-SEM, tensile strength, electrochemical AC-impedance spectroscopy, thermal stability and linear sweep voltammetry (LSV). Additionally, the... 

    Distributed Machine Learning with Communication Constraints

    , Ph.D. Dissertation Sharif University of Technology Tavassolipour, Mostafa (Author) ; Manzuri Shalmani, Mohammad Taghi (Supervisor) ; Motahari, Abolfazl (Supervisor)
    Abstract
    It is of fundamental importance to find algorithms obtaining optimal performance for learning of statistical models in distributed and communication limited systems. In this thesis, we aim at characterizing the best learning strategies over distributed datasets such that the communications between storing machines are minimized. We have addressed two problems in distributed setting: learning of Gaussian processes, and structure learning of Gaussian Graphical Models (GGM). The performance of the proposed methods are analyzed theoritically and verified experimentally. The experimental results show that with spending few bits the proposed distributed methods have close performance to the... 

    Dose Reduction Via Development of a Novel Image Reconstruction Method for Few-View Computed Tomography

    , Ph.D. Dissertation Sharif University of Technology Khodajou Chokami, Hamid Reza (Author) ; Hosseini, Abolfazl (Supervisor) ; Ay, Mohammad Reza (Supervisor)
    Abstract
    Sparse-view computed tomography (CT) is recently proposed as a promising method to speed up data acquisition and alleviate the issue of CT high-dose delivery to patients. However, traditional reconstruction algorithms are time-consuming and suffer from image degradation when faced with sparse-view data. To address this problem, we propose two new frameworks based on deep learning (DL) that can quickly produce high-quality CT images from sparsely sampled projections and is able for clinical use. Our first DL-based proposed model is based on the convolution, and residual neural networks in a parallel manner, named the parallel residual neural network (PARS-Net). Besides, our proposed PARS-Net... 

    Stabilizing Control Systems over Communication Channels

    , Ph.D. Dissertation Sharif University of Technology Sanjaroonpouri, Vahideh (Author) ; Hossein Khalaj, Babak (Supervisor) ; Farhadi, Alireza (Supervisor) ; Motahari, Abolfazl (Supervisor)
    Abstract
    In this thesis, we study the observability and stability problems of networked control systems (the control systems which communicate through communication channels) to answer two important questions about different system models. The first is that what is the constraints implied by the stability or observability of systems? (necessary condition on the observability and stability). The second is that under which constraints can we present a design for system to guarantee the observability or stability of systems? (sufficient condition on the observability and stability). Clearly, an efficient design is the one that presents a tight sufficient condition.One of system models addressed in this... 

    Structure Learning From Distributed Noisy Data

    , M.Sc. Thesis Sharif University of Technology Karamzadeh Motlagh, Armin (Author) ; Motahari, Abolfazl (Supervisor) ; Manzuri Shalmani, Mohammad Taghi (Co-Supervisor)
    Abstract
    Probabilistic graphical models have great applications in studying and analyzing realworld data. For instance, these models have been used in reconstructing gene regularity networks. Specifically, learning the edges’ structure of graphical models is of great importance.Knowledge about the underlying structure of a graphical model brings about a valuable framework for the decomposition of the model’s distribution and reveals important information such as dependency among dimensions of samples, etc. Most existing methods for structure learning obtain the underlying structure of the model in a centralized fashion and without considering noise in data. In many applications, data exist in a... 

    Transient Diffusion of Drugs into the Intervertebral Disc using Finite Element Method

    , M.Sc. Thesis Sharif University of Technology Motaghinasab, Samira (Author) ; Parnianpour, Mohammad (Supervisor) ; Hoviattalab, Maryam (Supervisor) ; Shirazi Adl, Abolfazl (Co-Advisor)
    Abstract
    In this study, transient diffusion of drug into the intervertebral disc is considered. The amount of Diffused drug from the blood into the intervertebral disc of dog is measured and concentration of drug is calculated for each region of the intervertebral disc including nucleus pulpous, inner annulus fibroses and outer annulus fibroses. Using finite element method, it is shown that the amount of drug diffusion into the intervertebral disc is affected by some parameters such as the type of drug, dose if drug and endplate calcification. This research is done in two parts: In first part, diffusion of drug (sulphate) into the dog intervertebral disc is investigated to compare the obtained... 

    Simulation and Evaluation of Dosimetric Parameters of 125I Thermobrachytherapy Source with Ferromagnetic Core

    , M.Sc. Thesis Sharif University of Technology Soleymanpoor, Mohammad (Author) ; Hosseini, Abolfazl (Supervisor) ; Sheibani, Shahab (Supervisor) ; Poorbaygi, Hossein (Co-Supervisor) ; Mohagheghpour, Elham (Co-Supervisor)
    Abstract
    In the method treatment of thermobrachytherapy, the method of this project, simultaneously use of two processes of thermotherapy and brachytherapy is considered, which can be a more effective treatment for the destruction of tumor tissue. In thermotherapy, the temperature of the tissue is artificially raised to a temperature that leads to cell dysfunction resulting in cell death. In brachytherapy, the destruction of defective tissue is done by placing a source in the tissue. In the present project, we supposed to consider both mechanisms simultaneously for treatment at the same time. In this project, radioactive material 125I is used as a source of radiation emission for brachytherapy. In...