Sharif Digital Repository

Ising model is a Markov Random Field (MRF) with binary random variables which has a vast literature in both theoretical and practical sides. In this thesis, we investigate two important statistical problems on this model. Learning the structure of MRFs has a long history and had a significant progress in the recent years. The goal of this problem is to find the independence graph of MRF using the samples generated from it. Specifically, we focus on the structure learning of ising models. Important algorithms for finding the structures had been reviewed. Additionally, we introduced information-theoretical and computational limitations of this problem. The second problem is community detection... 

To study the structure of materials, among materials containing hydrogen, an instrument called the "small-angle neutron scattering instrument" is used. Having a monochromatic neutron beam is the most basic component of this instrument. This beam is often produced using a device called the "neutron velocity selector". The neutron velocity selector is a rotating mechanical piece that allows for passage of neutrons at a certain speed, according to its rotational speed. In fact, this device produces a monochromatic neutron beam with continuous flux. Until now, it has been designed and manufactured in a variety of models, which are generally divided into two groups of multi-disc and multi-blade... 

Characterizing cellular states in response to various disease conditions is an important issue which is addressed by different methods such as Large-scale gene expression profiling. One of the most important challenges in front of bioinformaticians is the loss of data because expression profiling is still very expensive. It is understood that profiling a group of selected genes could be enough for understanding all of the gene expression profile.In this research, we propose a fast method for estimation of the missing values inlow-rank matrices. We consider the highly correlated expression profiles as a low-rank matrix. Then, we used this new method in a proposed algorithm which will select... 

Positron emission tomography (PET) imaging is a cross-sectional imaging method in nuclear medicine. In recent years, there have been increasing interest in this method.PET imaging is very sensitive and the presence of noise in the results decreases the the image quality and precision of detection. Thus it is critical to to investigate noise in PET systems with noisy images, since it could decrease the system’s ability to detect tumors. The common method to decrease noise in nuclear medicine images is the Fourier transform (FT). The method has many applications in image processing and analysis. However, in the FT method, information regarding time and position are lost in the frequency... 

In recent decades, genetics has become one of the key pillars in medical and scientific research, and haplotype analysis plays a crucial role in understanding the genetic structure of populations. Haplotypes are specific combinations of alleles at different loci in the genome that are inherited together and provide valuable information about genetic history and intra-population diversity. One of the challenges in this field is the mismatch between the existing reference panels and the genetic characteristics of the Iranian population, as many of these panels have been developed based on data from non-Iranian populations. This mismatch can lead to incorrect results in genetic analyses. In... 

Water resources planning and management projects are done in order to accomplish several goals. Moreover, social, environmental, political etc impacts of such projects increase the complexity of the problem of choosing the best alternative among others. The project of diversion of water form Zab Watershed into Lake Urmia Watershed is one of these projects which regarding water demands and problems in Lake Urmia Watershed and also Zab Watershed water resources that exceed its water demands has been considered. Therefore, after conducting research studies, five locations have been determined as potential places to build a dam on the Zab River and transferring its water to Lake Urmia Watershed.... 

Histopathology images exhibit significant variations across different datasets, which can pose challenges for machine learning models. When a model is trained on a certain domain, its performance may severely deteriorate when applied to unseen domains, magnifying the necessity of out-of-distribution generalization. To address this problem, we present a novel framework that harnesses the strengths of self-supervised training to extract domain-invariant features, and combine it with domain transfer techniques. Our approach is built on the premise that pre-trained vision transformers, highly effective in natural image analysis, can be adapted for histopathology image analysis in a... 

The problem of separation of audio sources is one of the oldest issues raised in the field of audio processing, which has been studied for more than half a century. The main focus of recent research in this field has been on improving the sound quality resulting from the separation of sound sources with the help of deep neural networks. This is despite the fact that in most applications of audio source separation, such as the application of meeting transcription, we do not need the separated audio of people. Rather, we need a pipeline of converting overlapping speech to text, which, by receiving the audio in which several people have spoken, outputs the text spoken by the people present in... 

There are six core concepts in the organization theories that theorists rely on. These six concepts are: environment , social structure, technology, culture, physical structure, power and control. the insights of theorists about each of these concepts lead to different theory in case, they argue. The enactment environment theory by carl weik, is one way of conceptualizing the organizational environment within the interpretive paradigm and offer an approach about the organization and its environment. The logic of the enactment environment theory based on the belief that organizational realities parallel to people interact and negotiate and make sense of their experiences are socially... 

Study of hydraulic characteristics of two-phase flow is one of the important issues in hydraulic engineering. Two-phase flows usually accur in hydraulic structures such as pressurized flow tunnels, culverts, sewer pipes, junctions, and similar conduits. Under certain conditions, air may also be introduced into pressurized intake systems, which may form large bubbles in portions of the pipe. The bubbles may, in turn, cause an unstable slug flow, or other flow patterns. Slug flow is one of the most probable patterns in these flows. Prediction of pressure in this situation is a complex subject which despite its great importance is rarely discussed. In this study, the results of a laboratory... 

Nowadays, many progresses in biology and medicine such as diagnosis of diseases and drug discoveries depend heavily on analyzing biological datasets collected from advanced machines. DNA Microarrays are amongst such machines applicable in measuring the expressions levels of thousand of genes and genotyping of a set of single nucleotide polymorphic sites to name a few. Compared to the more advanced Next Generation Sequencing (NGS) technology, the microarray platform produces lower quality of datasets. However, there has been tones of efforts to produce, process, and curate datasets from microarrays based on well designed protocols for sample preparation, hybridization, image processing, and... 

The present M.Sc. thesis consists of two sections including the static calculation and neutron noise calculation in rectangular and hexagonal geometries. The multi-group, two dimensional neutron diffusion equations and corresponding adjoint equations are solved in the static calculation. The spatial discretization of equations is based on Average Current Nodal Expansion Method (ACNEM). Size of nodes is the same size of the fuel assemblies in modeling both of rectangular and hexagonal geometries. The results are benchmarked against the valid results for BIBLIS-2D and IAEA-2D benchmark problems. In the second section, neutron noise calculations are performed for two types of noise sources,... 

One of the ways to enhance the safety and economic performance of nuclear power plants, is to choose an appropriate policy for arrange the reactor fuel assembly in the beginning of each cycle. There are variety of ways to optimize the layout of the fuel in the reactor core, but to achieve more than one goal, choosing multi-objective method can be used.One of the intelligent optimization methods is the genetic algorithms that emulate nature of biological processes and can be used to optimize two or more of the target.The goals of this research is to increase the neutron multiplication factor is to make maximum use of the fuel in the reactor and maintain the radial power peaking factor for... 

Genome sequencing is one of the fundamental problems in today’s Biology. It has applications in significant problems such as finding association between an individual’s genome sequence and his phenotypes, discovering new genes, and finding evolutionary relations between organisms. Following the rapid advances in sequencing technologies and generation of a huge amount of short reads, efficient computational tools are needed for processing sequencing data. Shortness of reads is a factor that makes the task of reconstructing repetitive genomic regions complicated. In fact, the main challenge in both sequencing and resequencing problems is reconstruction of repeat regions. Common resequencing... 

Datasets extracted from gene expression microarrays contain information about the phenotypic behavior of organisms. Turning this information into knowledge, i.e. finding associative genes with a given phenotype, is a daunting task. This is due to the high dimensionality of the data as the number of features on a gene expression microarray is usually very large. Moreover, a phenotype may change the expression pattern of a set of genes rather than changing each gene’s expression independently. To tackle the second problem, integrating other sources of information such as Protein-Protein Interaction (PPI) networks is required. In this thesis, the PPI network extracted from the String database... 

Dnase I Hypersensitive Sites (DHSs) are known as comprehensive markers of DNA regulatory elements. The main function of regulatory elements is repressing or enhancing transcription of genes. Hence, the recruitment of the data is prevalent in many studies of genome. One of the applications of this data is to utilize it to predict active regulatory regions (Transcription Factor Binding Sites).There are different means to do this, divided in three major groups: first, the methods only use the number of DNase-seq reads that surround a candidate binding site. While robust, these methods do not reflect the shape of the signal. A second strategy uses a variety of approaches to model and identify... 

Conventional MRI has been used to diagnose different types of brain injuries. However these methods have generally failed to diagnose mild types of injury. We are working on the specification of mild traumatic brain injury, using diffusion MRI data, based on a multi compartment simulation of white matter tissue. This effort is essential for better understanding of underlying tissue micro-structure changes in patients with trauma. Some studies have been used in similar data fitting approaches in order to estimate axon diameter distribution. Specifically, a comparative study between different Compartment Models has shown that “ActiveAx” model has the best agreement with underlying tissue... 

Isoforms are mRNAs that are produced from a same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of multiexon genes in humans have undergone Alternative Splicing. Although there are few changes in mRNA sequence, They may have a systematic effect on cell function and regulation. It is widely reported that isoforms of a gene have distinct or even contrasting functions. Most studies have shown that alternative splicing plays a significant role in human health and disease. Despite the wide range of gene function studies, there is little information about isoforms’ functionalities. Recently, some computational methods based on Multiple Instance... 

Nowadays, in the world and our country, Iran, sediment transport and the phenomenon of sedimentation are of great importance. The entry of water flow with suspended sediments into the dam reservoir by floods with different return periods during the initial period of dam construction causes a considerable part of the helpful volume of the reservoir to be filled with sediments. As a result, the discharge of these sediments and the methods that exist in this field should be studied so that a large volume of reservoir water is not wasted during the discharge of these sediments. In this research, the opening time and extent of the bottom outlets of Qeshlaq Dam when the flood enters the reservoir... 

Dams are constructed for various purposes, including flood control, drinking water supply, agriculture irrigation, electricity generation, etc. The dam converts the river's natural and dynamic flow into a stagnant artificial lake where humans control the outflow of water, reducing the velocity of water movement and increasing residence time, followed by the entry and accumulation of nutrients in the reservoir, resulting in phenomena such as thermal stratification and eutrophication. Due to the changing climatic conditions of Iran and sudden droughts and wet periods, the need to monitor the water level of dam reservoirs and their water quality to keep them in the best operational condition...