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tefagh--mojtaba
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Context-Specific Reconstruction and Gap-Filling of Metabolic Networks by Sparse Reconciliation of Data Inconsistencies
, M.Sc. Thesis Sharif University of Technology ; Tefagh, Mojtaba (Supervisor)
Abstract
With the increasingly collected biological data, appropriate usage of this data is of great importance for understanding and predicting biological systems and has been the aim of experiments and data collections. A famous category of biological data is known as “omics” which refers to transcriptomics, proteomics, metabolomics, and fluxomics, from different cells or tissues in various media and conditions. This set of data is regularly used for tasks such as studying cells and organisms, understanding cell states, cancer prediction, etc. and is of great importance in Systems Biology.In this thesis, we concentrate on studying cells or organisms using such data, where during that process, we...
Multi-agent based Blockchain Simulation Framework
, M.Sc. Thesis Sharif University of Technology ; Tefagh, Mojtaba (Supervisor)
Abstract
A multi-agent system is a system consisting of several intelligent agents. In fact, a multi-agent system is a system that includes a large number of agents that communicate with each other through message transmission in a network structure. Multi-agent systems can solve problems that are difficult or impossible for a single agent or an integrated system to solve. Blockchain is an example of these multi-agent systems that has many use cases in different fields for example cryptocurrencies . A blockchain is a growing ledger consisting of records called blocks. In this thesis, we want to provide tools for the simulation of this multi-agent system so that we can model the issues surrounding...
A Library For Developing Optimization Algorithms In Metabolic Network Analysis
, M.Sc. Thesis Sharif University of Technology ; Tefagh, Mojtaba (Supervisor)
Abstract
In systems biology, one of the most important biological systems that is analyzed and investigated is the metabolic network. A metabolic network is a complete set of metabolic and physical processes that determine the physiological and biochemical characteristics of a cell. These networks encompass metabolic chemical reactions, metabolic pathways, and regulatory interactions that govern these reactions. Therefore, metabolic networks at the genome scale are immensely large, making even efficient algorithms time-consuming for their analysis. To address this issue, reducing metabolic networks is crucial, as it significantly decreases the execution time of algorithms and enhances computational...
Analysis and Investigation of Miner Extractable Value in Constant Product Market Makers with Random Ordering
, M.Sc. Thesis Sharif University of Technology ; Maddah Ali, Mohammad Ali (Supervisor) ; Tefagh, Mojtaba (Supervisor)
Abstract
Blockchain technology presents a decentralized management structure designed to cater to various needs, such as decentralization and the elimination of single points of failure. With the evolution of blockchain technology, smart contracts have emerged as a remarkable platform for facilitating financial activities in a decentralized manner. Among the different types of smart contracts, decentralized exchanges stand out by their absence of a central authority overseeing user transactions. This lack of a central oversight exposes users of such exchanges to potential attacks from malicious entities. A key challenge faced by these exchanges is the concept of Miner Extractable Value. Miner...