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    Drug-Target Interaction Prediction with Deep Learning and Recommender Systems

    , M.Sc. Thesis Sharif University of Technology Nosrati, Amir Hossein (Author) ; Ghafourian Ghahramani, Amir Ali (Supervisor) ; Kavousi, Kaveh (Supervisor)
    Abstract
    A drug can be defined as a substance made to prevent disease, cure a specific symptom, relieve pain, and reduce anomalies in the body. The process of drug designing is so laborious, complex, costly, and time-consuming that chance of failure during the lab experiment stages is high. These challenges have persuaded researchers to find new usage for existing drugs, referred to as drug repurposing, with the main advantage of reducing cost, risk, and time. To this aim, computational methods have been applied to discover hidden pharmaceutical capabilities of drugs in terms of predicting whether a particular drug can interact with a particular protein.Graph Neural Networks (GNNs) have recently... 

    Graph homomorphisms through random walks [electronic resource]

    , Article Journal of Graph Theory ; 2003, Volume 44, Issue 1, pages 15–38 Daneshgar, A. (Amir) ; Hajiabolhassan, Hossein ; Sharif University of Technology
    Abstract
    In this paper we introduce some general necessary conditions for the existence of graph homomorphisms, which hold in both directed and undirected cases. Our method is a combination of Diaconis and Saloff–Coste comparison technique for Markov chains and a generalization of Haemers interlacing theorem. As some applications, we obtain a necessary condition for the spanning subgraph problem, which also provides a generalization of a theorem of Mohar (1992) as a necessary condition for Hamiltonicity. In particular, in the case that the range is a Cayley graph or an edge-transitive graph, we obtain theorems with a corollary about the existence of homomorphisms to cycles. This, specially, provides... 

    Unique list-colourability and the fixing chromatic number of graphs [electronic resource]

    , Article Discrete Applied Mathematics ; Volume 152, Issues 1–3, 1 November 2005, Pages 123–138 Daneshgar, A. (Amir) ; Hajiabolhassan, Hossein ; Sharif University of Technology
    Abstract
    In this paper we introduce a chromatic parameter, called the fixing chromatic number, which is related to unique colourability of graphs, in the sense that it measures how one can embed the given graph G in G∪Kt by adding edges between G and Kt to make the whole graph uniquely t-colourable. We study some basic properties of this parameter as well as its relationships to some other well-known chromatic numbers as the acyclic chromatic number. We compute the fixing chromatic number of some graph products by applying a modified version of the exponential graph construction  

    Circular colouring and algebraic no-homomorphism theorems

    , Article European Journal of Combinatorics ; Volume 28, Issue 6, August 2007, Pages 1843–1853 Daneshgar, A. (Amir) ; Hajiabolhassan, Hossein ; Sharif University of Technology
    Abstract
    In this paper, we apply some new algebraic no-homomorphism theorems in conjunction with some new chromatic parameters to estimate the circular chromatic number of graphs. To show the applicability of the general results, as a couple of examples, we generalize a well known inequality for the fractional chromatic number of graphs and we also show that the circular chromatic number of the graph obtained from the Petersen graph by excluding one vertex is equal to 3. Also, we focus on the Johnson–Holroyd–Stahl conjecture about the circular chromatic number of Kneser graphs and we propose an approach to this conjecture. In this regard, we introduce a new related conjecture on Kneser graphs and we... 

    Density and power graphs in graph homomorphism problem

    , Article Discrete Mathematics ; Volume 308, Issue 17, 6 September 2008, Pages 4027–4030 Daneshgar, A. (Amir) ; Hajiabolhassan, Hossein ; Sharif University of Technology
    Abstract
    We introduce two necessary conditions for the existence of graph homomorphisms based on the concepts of density and power graph. As corollaries, we obtain a lower bound for the fractional chromatic number, and we set forward elementary proofs of the facts that the circular chromatic number of the Petersen graph is equal to three and the fact that the Coxeter graph is a core  

    A Technique for Program Fault Location Using External Information Sources

    , M.Sc. Thesis Sharif University of Technology Nosrati, Ali (Author) ; Mirian Hossein Abadi, Hassan (Supervisor) ; Habibi, Jafar (Co-Advisor)
    Abstract
    In recent years, there have been many studies aimed at finding program defect using information of previous ones. These studies, by using the program text, previous bugs, and information related to version control and project management systems create an defect prediction model to find other defect prone areas in the program. The output of defect prediction methods is part of the program’s text, which is likely to have defects. Considering that the result of this method is just the text of the program and does not provide any extra information for finding defects to the user, these methods have not yet been applied to the software industry. On the other hand, by spreading the use of Q & A... 

    On the isoperimetric spectrum of graphs and its approximations [electronic resource]

    , Article Journal of Combinatorial Theory, Series B ; Volume 100, Issue 4, July 2010, Pages 390–412 Daneshgar, A. (Amir) ; Hajiabolhassan, Hossein ; Javadi, Ramin ; Sharif University of Technology
    Abstract
    In this paper1 we consider higher isoperimetric numbers of a (finite directed) graph. In this regard we focus on the nth mean isoperimetric constant of a directed graph as the minimum of the mean outgoing normalized flows from a given set of n disjoint subsets of the vertex set of the graph. We show that the second mean isoperimetric constant in this general setting, coincides with (the mean version of) the classical Cheeger constant of the graph, while for the rest of the spectrum we show that there is a fundamental difference between the nth isoperimetric constant and the number obtained by taking the minimum over all n-partitions. In this direction, we show that our definition is the... 

    Structural Health Monitoring Using Optimal Finite Element Model Based on Digital Image Correlation

    , M.Sc. Thesis Sharif University of Technology Amir Hossein Amir Ahmadi (Author) ; Khaloo, Alireza (Supervisor)
    Abstract
    The purpose of this research is to monitor the health of structures using the updated finite element model, in which digital images are used to optimize the numerical model. Structural Health Monitoring (SHM) is always an important and significant issue that has attracted the attention of many researchers in recent years. In general, some researches have been conducted in this field using physical sensors that provide discrete data to the system for analysis. Using cameras to monitor the structure makes it possible to extract continuous and integrated data from the structure using digital images, which is a significant advantage compared to physical sensors.In this research, a steel... 

    Semisolid Stir Joining of As-Cast Silicon-Aluminum Bronze

    , M.Sc. Thesis Sharif University of Technology Ferasat, Keyvan (Author) ; Kokabi, Amir Hossein (Supervisor) ; Ashuri, Hossein (Supervisor)
    Abstract
    Aluminum Bronzes have many applications in marine environments. These alloys suffer from both hot cracking and cold cracking. In order to overcome the hot cracking and cold cracking, Semisolid Stir Joining method and a proper thermal cycle was used respectively. Effects of temperature, stirring rate, and tool type were investigated in Semisolid Stir joining method. In this method, butt joint design was used in order to place specimens, and the specimens were heated up to specific temperatures (920, 925, 930°C). A stirrer (Cylindrical and Grooved tool) with three rotational speeds (800, 1200, 1600 RPM) was introduced into the stir weld seam. Welded specimens were cooled to the 900°C... 

    Cosmic voids are emptier in the presence of symmetron's domain walls

    , Article Physical Review D ; Volume 108, Issue 8 , 2023 ; 24700010 (ISSN) Nosrati, B ; Khosravi, N ; Sharif University of Technology
    American Physical Society  2023
    Abstract
    The symmetron field has an environment (density) dependent behavior which is a common feature of the models with the screening mechanism and results in a rich phenomenology. This model can produce domain walls between regions with different densities. We consider this aspect and study the physics of domain walls in between (underdensity) voids and (overdensity) halo structures. The (spherical) domain walls exert a repulsive force on a test mass outside of the wall while a test mass inside of the wall sees no force because of it. This makes the structures outside the voids go further to a larger radius. Effectively, this means the voids are becoming larger in this scenario in comparison to... 

    Concept Drift Detection in Spam Filtering

    , M.Sc. Thesis Sharif University of Technology Nosrati, Leili (Author) ; Beigy, Hamid (Supervisor)
    Abstract
    As part of the definition of concept drift as an online learning task, concepts change or drift as time goes by. Consequently, these changes have to be monitored and their implication for learning should be recognized. An example of concept drift detection is needed for spam filtering problem. An effective spam filter must be able to handle various changes, including changes in the user’s criteria for filtering spam, changes in message topics, and changes caused by the people sending spam messages. In this thesis, spam detection system has been considered in which emails are given sequentially and learns them one by one. As we mentioned, the purpose of this thesis is detecting spam emails.... 

    Analysis and Evaluation of Routing Protocols Conformance Test

    , M.Sc. Thesis Sharif University of Technology Tabatabaee, Hosein (Author) ; Jahangir, Amir Hossein (Supervisor)
    Abstract
    Nowadays, one of the problems of network designers and users is the correctness of network equipment functionality. Since routers play an important role in information transfer between various networks and communicate with each other through a routing protocol, any violation of such protocol can result in the network's failure or defective transfer of data. Thus, being assured of the conformance of the implemented protocol in a router with what has been defined in the protocol's standard is of great significance. To this end, before using or exposing a router, network equipment testers should run protocol conformance tests on it and insure its correct functionality. This brings up the... 

    Network Traffic Analyzer

    , M.Sc. Thesis Sharif University of Technology Silavi, Ehsan (Author) ; Jahangir, Amir Hossein (Supervisor)
    Abstract
    In order to increase the network performance, to discover network security threats, to guarantee the quality of services, to simulate networks and develop new network protocols, network designers and operators need software tools to analyze the network traffic. The first step to do this analysis is network monitoring. This can be done by using various software and hardware tools.
    In this research we developed a tool which analyzes the network traffic using appropriate statistical methods. The models which are analyzed in this application are: Poisson, Self-similar and Weibull. This application analyzes the network traffic based on this statistical models and calculates their parameters.... 

    Analysis and Evaluation of Real Timeliness and Safety of VANET

    , M.Sc. Thesis Sharif University of Technology Ahmadvand, Hossein (Author) ; Jahangir, Amir Hossein (Supervisor)
    Abstract
    The increasing number of road accidents and fatalities have yielded the introduction of several solutions by related industries such as automobile manufacture. Proposed solutions can be classified into two categories: passive, such as airbags, and active such as ABS ad ITS-based technologies. Inter vehicles communication let the communication between vehicles(V2V) or between vehicles and road infrastructure (V2I) by relying on DSRC technology and standards. Intelligent Transportation System (ITS) has three main types of applications namely safety, traffic and commercial. Safety applications are the main goal of vehicular communication, and real time guarantee in safety applications is so... 

    An Efficient Approach for Improving the Performance of Real-time Flow Routing in SDN Controllers

    , M.Sc. Thesis Sharif University of Technology Heidari, Hossein (Author) ; Jahangir, Amir Hossein (Supervisor)
    Abstract
    In real-time systems, jobs that miss their deadline are considered worthless or ineffective. Nowadays, real-time applications (such as multimedia) that communicate through software-defined networks (SDN) are widely used and will continue to expand in the future. SDN is an emerging network architecture in which control plane is separated from data plane to manage it directly. In this research, we make changes to the controller and the switch used in such network to deliver real time packets or real-time flows (such as video) on time, as much as possible. As missed deadline packets are worthless and they waste bandwidth, dropping them is a solution. Moreover, the controller can drop flows that... 

    Packet Processing Acceleration for Virtualized Network Functions

    , M.Sc. Thesis Sharif University of Technology Barati Sedeh, Amir Reza (Author) ; Jahangir, Amir Hossein (Supervisor)
    Abstract
    Network Function Virtualization (NFV) is a new paradigm in computer networks for implementing network functions on general-purpose common-of-the-shelf processors. The revolutionized NFV architecture has shown to be a suitable replacement for hardware middleboxes. NFV is in high demand because of its lower costs, increased flexibility, and more scalability. However, the ever-growing volume of network traffic and increased data transfer speed in computer networks have made achieving high performance the major issue in this area. With thousands of processing cores and high memory bandwidth, Graphical Processing Units (GPUs) are potentially an appropriate solution to accelerate network... 

    DWM-CDD: Dynamic weighted majority concept drift detection for spam mail filtering

    , Article World Academy of Science, Engineering and Technology ; Volume 80 , 2011 , Pages 291-294 ; 2010376X (ISSN) Nosrati, L ; Pour, A. N ; Sharif University of Technology
    2011
    Abstract
    Although e-mail is the most efficient and popular communication method, unwanted and mass unsolicited e-mails, also called spam mail, endanger the existence of the mail system. This paper proposes a new algorithm called Dynamic Weighted Majority Concept Drift Detection (DWM-CDD) for content-based filtering. The design purposes of DWM-CDD are first to accurate the performance of the previously proposed algorithms, and second to speed up the time to construct the model. The results show that DWM-CDD can detect both sudden and gradual changes quickly and accurately. Moreover, the time needed for model construction is less than previously proposed algorithms  

    Reconfigurable Architecture For Cryptanalysis Applications

    , M.Sc. Thesis Sharif University of Technology Noshadravan, Mohammad Reza (Author) ; Jahangir, Amir Hossein (Supervisor)
    Abstract
    Nowadays, the significance of securing data and information is undeniable. Cryptography is being used to provide data security. In addition, cryptanalysis is required to evaluate the effectiveness of cryptography methods, and hence, it is an essential concept for securing data. In general, the cryptography functions shall be designed in a way to impose a high load of time-intensive operations to prevent an adversary from accessing the main data from the encrypted data. As a result, cryptography and cryptanalysis algorithms need high performance computations. So far, a number of methods have been proposed to support the required performance. These methods include: distributed computing and... 

    Performance Ehancement of Congestion Control Algorithm Through Traffic Flow Istinction

    , M.Sc. Thesis Sharif University of Technology Peyman, Zakariaei (Author) ; Jahangir, Amir Hossein (Supervisor)
    Abstract
    Congestion is an important issue in the network environment. To keep stable the perfor-mance of the network, congestion control algorithms have been extensively studied. Queue management method employed by the routers is one of the important issues in the congestion control study. Active Queue Management (AQM) has been proposed for early detection of congestion inside the network. AQM mechanisms control the queue length in a router by dropping arriving packets. The Random Early Detection (RED) is the most popular AQM mechanism used in routers on the Intenet to allow network users to simultaneously achieve high throughput and low average delay. The RED algorithm may cause heavy oscillation of... 

    Modeling and Analysis of Real-time Behaviour of Wireless Sensor Networks

    , Ph.D. Dissertation Sharif University of Technology Mizanian, Kambiz (Author) ; Jahangir, Amir Hossein (Supervisor)
    Abstract
    Nowadays, information gathering based on wireless sensor network (WSN) has formed various applications and it also seems to be spreading more in future. Wireless sensor network, is a network composed of multiple nodes, without any infrastructure, each having one or more sensors, wireless communications unit, processing unit, memory, and power supply. Memory capacity, computation power, and power supply are usually considered as valuable resources and limited in nodes. Most of sensor nodes are located in a dense mode and they are susceptible to failure. Therefore network topology may vary dynamically. A sensor network can support real-time communications independent of its type of structure...