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    Prediction of DNA/RNA Sequence Binding Site to Protein with the Ability to Implement on GPU

    , M.Sc. Thesis Sharif University of Technology Fatemeh Tabatabaei (Author) ; Koohi, Sommaye (Supervisor)
    Abstract
    Based on the importance of DNA/RNA binding proteins in different cellular processes, finding binding sites of them play crucial role in many applications, like designing drug/vaccine, designing protein, and cancer control. Many studies target this issue and try to improve the prediction accuracy with three strategies: complex neural-network structures, various types of inputs, and ML methods to extract input features. But due to the growing volume of sequences, these methods face serious processing challenges. So, this paper presents KDeep, based on CNN-LSTM and the primary form of DNA/RNA sequences as input. As the key feature improving the prediction accuracy, we propose a new encoding... 

    All-optical wavelength-routed architecture for a power-efficient network on chip

    , Article IEEE Transactions on Computers ; Vol. 63, issue. 3 , 2014 , p. 777-792 Koohi, S ; Hessabi, S ; Sharif University of Technology
    2014
    Abstract
    In this paper, we propose a new architecture for nanophotonic Networks on Chip (NoC), named 2D-HERT, which consists of optical data and control planes. The proposed data plane is built upon a new topology and all-optical switches that passively route optical data streams based on their wavelengths. Utilizing wavelength routing method, the proposed deterministic routing algorithm, and Wavelength Division Multiplexing (WDM) technique, the proposed data plane eliminates the need for optical resource reservation at the intermediate nodes. For resolving end-point contention, we propose an all-optical request-grant arbitration architecture which reduces optical losses compared to the alternative... 

    Hierarchical opto-electrical on-chip network for future multiprocessor architectures

    , Article Journal of Systems Architecture ; Volume 57, Issue 1 , 2011 , Pages 4-23 ; 13837621 (ISSN) Koohi, S ; Hessabi, S ; Sharif University of Technology
    2011
    Abstract
    Importance of power dissipation in NoCs, along with power reduction capability of on-chip optical interconnects, offers optical network-on-chip as a new technology solution for on-chip interconnects. In this paper, we extract analytical models for data transmission delay, power consumption, and energy dissipation of optical and traditional NoCs. Utilizing extracted models, we compare optical NoC with electrical one and calculate lower bound limit on the optical link length below which optical on-chip network loses its efficiency. Based on this constraint, we propose a novel hierarchical on-chip network architecture, named as H2NoC, which benefits from optical transmissions in large scale... 

    Scalable architecture for a contention-free optical network on-chip

    , Article Journal of Parallel and Distributed Computing ; Volume 72, Issue 11 , 2012 , Pages 1493-1506 ; 07437315 (ISSN) Koohi, S ; Hessabi, S ; Sharif University of Technology
    2012
    Abstract
    This paper proposes CoNoC (Contention-free optical NoC) as a new architecture for on-chip routing of optical packets. CoNoC is built upon all-optical switches (AOSs) which passively route optical data streams based on their wavelengths. The key idea of the proposed architecture is the utilization of per-receiver wavelength in the data network to prevent optical contention at the intermediate nodes. Routing optical packets according to their wavelength eliminates the need for resource reservation at the intermediate nodes and the corresponding latency, power, and area overheads. Since passive architecture of the AOS confines the optical contention to the end-points, we propose an electrical... 

    Power efficient nanophotonic on-chip network for future large scale multiprocessor architectures

    , Article Proceedings of the 2011 IEEE/ACM International Symposium on Nanoscale Architectures, NANOARCH 2011, 8 June 2011 through 9 June 2011, San Diego, CA ; 2011 , Pages 114-121 ; 9781457709944 (ISBN) Koohi, S ; Hessabi, S ; Sharif University of Technology
    2011
    Abstract
    This paper proposes new architectures for data and control planes in a nanophotonic networks-on-chip (NoC) with the key advantages of scalability to large scale networks, constant node degree, and simplicity. Moreover, we propose a minimal deterministic routing algorithm for the data network which leads to small and simple photonic switches. Built upon the proposed novel topology, we present a scalable all-optical NoC, referred to as 2D-HERT, which offers passive routing of optical data streams based on their wavelengths. Utilizing wavelength routing method, Wavelength Division Multiplexing (WDM) technique, and a new all-optical control architecture, our proposed optical NoC eliminates the... 

    Hierarchical on-chip routing of optical packets in large scale MPSoCs

    , Article Proceedings of the 18th Euromicro Conference on Parallel, Distributed and Network-Based Processing, PDP 2010, 17 February 2010 through 19 February 2010, Pisa ; 2010 , Pages 515-524 ; 9780769539393 (ISBN) Koohi, S ; Hessabi, S ; Sharif University of Technology
    2010
    Abstract
    In this paper, we extract analytical models for data transmission delay, power consumption, and energy dissipation of optical and traditional NoCs. Utilizing extracted models, we compare optical NoC with electrical one for varying values of link length and degree of multiplexing and calculate lower bound limit on the optical link length below which optical on-chip network loses its efficiency. Based on this constraint, we propose a novel hierarchical on-chip network architecture, named as H2NoC, which benefits from optical transmissions in large scale SoCs and overcomes the scalability problem resulted from lower bound limit on the optical link length. Performing a series of simulation-based... 

    All-Optical Scalable Multi-stage Interconnection Network for Data Centers

    , M.Sc. Thesis Sharif University of Technology Movahederad, Mahdieh (Author) ; Koohi, Somayeh (Supervisor)
    Abstract
    According to the increasing amount of data exchanged among data centers, the need for speeding up and bandwidth and reduced power consumption has been increased. The information show that about 77% of the data is moved into the data centers. On the other hand, 10% of data center’s power consumption is used to data transmission. Improving the interconnection network of data centers can play an important role in reducing power consumption and speeding up. In recent years, optical interconnects have gained attention as a promising solution. Nevertheless, offering an all-optical and efficient architecture is an important issue. In this study, we intend to provide a multi-stage, all-optical... 

    Adopting Dynamic Topology for Energy Management in Optical Interconnection Networks in Data Centers

    , M.Sc. Thesis Sharif University of Technology Rezaei, Negar (Author) ; Koohi, Somayeh (Supervisor)
    Abstract
    Today with the deployment of cloud computing and web applications; We need to have powerful datacenters with provisioning high bandwidth. Current data centers with electronic network interconnects, using excessive power to provisioning requisite bandwidth. Nevertheless, interconnecting networks in data centers isn’t in maximum efficiency and many components of them aren't used efficiently. So it is necessary to use an optical network with dynamic provisioning variable bandwidth and energy management. In this approach, our proposed architecture is designing topology with adopting dynamically for energy management in optical interconnect networks in data centers. To achieve this we can study... 

    DNA Classification Using Optical Processing based on Alignment-free Methods

    , M.Sc. Thesis Sharif University of Technology Kalhor, Reza (Author) ; Koohi, Somayyeh (Supervisor)
    Abstract
    In this research, an optical processing method for DNA classification is presented in order to overcome the problems in the previous methods. With improving in the operational capacity of the sequencing process, which has increased the number of genomes, comparing sequences with a complete database of genomes is a serious challenge to computational methods. Most current classification programs suffer from either slow classification speeds, large memory requirements, or both. To achieve high speed and accuracy at the same time, we suggest using optical processing methods. The performance of electronic processing-based computing, especially in the case of large data processing, is usually... 

    Energy Aware Routing Algorithm with SDN in Data Center Networks

    , M.Sc. Thesis Sharif University of Technology Hadi, Azhar (Author) ; Koohi, Somayyeh (Supervisor)
    Abstract
    It is well known that data centres consume high amounts of energy, which has become a major concern in the field of cloud computing. Therefore, energy consumption could be reduced by using intelligent mechanisms work to adapt the set of network components to the total traffic volume. SDN is an efficient way to do so because it has many benefits over traditional approaches, such as centralised management, low capex, flexibility, scalability and virtualisation of network functions. In our work will we use the heuristic energy-aware routing (HEAR) model, which is composed of the proposed heuristic algorithm and the energy-aware routing algorithm. This work identifies the unused links and... 

    Free space Optical Spiking Neural Network

    , M.Sc. Thesis Sharif University of Technology Ahmadi, Reyhane (Author) ; Koohi, Somayyeh (Supervisor)
    Abstract
    Due to the increasing volume of data in various fields, existing electronic processors face a major challenge. While processing power has increased, solving complex problems in a timely manner remains a major challenge for today's processors. Neuromorphic engineering offers a potential solution by looking to processors found in nature, such as the human brain. This field of research involves investigating natural processors and designing new ones based on these models. To address issues related to manufacturing and integrating transistors, increasing processor costs, and the limitations of Moore's law, it is possible to use analog signals, such as sound or light, instead of electrical... 

    MHC-Peptide Binding Prediction Using a Deep Learning Method with Efficient GPU Implementation Approach

    , M.Sc. Thesis Sharif University of Technology Darvishi, Saeed (Author) ; Koohi, Somayyeh (Supervisor)
    Abstract
    The Major Histocompatibility Complex (MHC) binds to the derived peptides from pathogens to present them to killer T cells on the cell surface. Developing computational methods for accurate, fast, and explainable peptide-MHC binding prediction can facilitate immunotherapies and vaccine development. Various deep learning-based methods rely on feature extraction from the peptide and MHC sequences separately and ignore their valuable binding information. This paper develops a capsule neural network-based method to efficiently capture and model the peptide-MHC complex features to predict the peptide- MHC class I binding. Various evaluations over multiple datasets using popular performance metrics... 

    An Optimized Graph-Based Structure for Single-Cell RNA-Seq Cell-Type Classification Based on Nonlinear Dimension Reduction

    , M.Sc. Thesis Sharif University of Technology Laghaee, Pouria (Author) ; Koohi, Somayyeh (Supervisor)
    Abstract
    As sequencing technologies have advanced in the field of single cells, it has become possible to investigate complex and rare cell populations and discover regulatory relationships between genes. The detection of rare cells has been greatly facilitated by this technology. However, due to the large volume of data and the complex and uncertain distribution of data, as well as the high rate of technical zeros, the analysis of single cell data clusters remains a computational and statistical challenge. Dimensionality reduction is a significant component of big data analysis. Machine learning methods provide the possibility of better analysis by reducing the non-linear dimensions of data. A graph... 

    Motif Finding Application Using Edit Distance Approuch

    , M.Sc. Thesis Sharif University of Technology Mohammadi, Farzin (Author) ; Koohi, Somayyeh (Supervisor)
    Abstract
    Motif finding problem in biology is a search for repeated patterns to reveal information about gene expression, one of the most complex subsystems in genomics. ChIP-seq technology abled researchers to investigate location of protein-DNA interactions but analyzing downstream results of such experiments to find actual regulatory signals in genome is challenging. For many years, applications of motif finding had models based on limiting assumption as an exchange for lower computational complexity. Results: AKAGI program is build upon upgraded methods and new general models to investigate statistical and experimental evidences for accurately finding significant patterns among biological... 

    Drug-target Interaction Prediction through Learning Methods for SARS-COV2 Based on Sequence and Structural Data

    , M.Sc. Thesis Sharif University of Technology Gheysari, Maryam (Author) ; Koohi, Somayyeh (Supervisor)
    Abstract
    Predicting the binding affinity of drug molecules and proteins is one of the most important stages of drug discovery, development and screening, for which numerous laboratory, simulation and computational solutions have been provided. Laboratory and simulation methods require molecular structures, are time and financial expense, and computational methods do not provide accurate predictions. Therefore, the use of deep neural networks in extracting features from data with a simpler and more accessible structure of protein sequences and molecules solves these challenges with lower cost and higher accuracy. In this article, the use of a new molecular sequence named selfies, which has solved the... 

    All-optical wavelength-routed NoC based on a novel hierarchical topology

    , Article NOCS 2011: The 5th ACM/IEEE International Symposium on Networks-on-Chip, 1 May 2011 through 4 May 2011 ; May , 2011 , Pages 97-104 ; 9781450307208 (ISBN) Koohi, S ; Abdollahi, M ; Hessabi, S ; Sharif University of Technology
    2011
    Abstract
    This paper proposes a novel topology for optical Network on Chip (NoC) architectures with the key advantages of regularity, vertex symmetry, scalability to large scale networks, constant node degree, and simplicity. Moreover, we propose a minimal deterministic routing algorithm for the proposed topology which leads to small and simple photonic routers. Built upon our novel network topology, we present a scalable all-optical NoC, referred to as 2D-HERT, which offers passive routing of optical data streams based on their wavelengths. Utilizing wavelength routing method along with Wavelength Division Multiplexing technique, our proposed optical NoC eliminates the need for electrical resource... 

    An optical wavelength switching architecture for a high-performance low-power photonic NoC

    , Article Proceedings - 25th IEEE International Conference on Advanced Information Networking and Applications Workshops, WAINA 2011, 22 March 2011 through 25 March 2011 ; March , 2011 , Pages 1-6 ; 9780769543383 (ISBN) Koohi, S ; Shafaei, A ; Hessabi, S ; Sharif University of Technology
    2011
    Abstract
    The paper proposes a scalable wavelength-switched optical NoC, named as SWS-ONoC. The proposed architecture is built upon a novel all-optical router which passively routes optical data streams based on their wavelengths. Utilizing wavelength routing method, SWS-ONoC eliminates electrical transactions for optical resource reservation and hence, reduces latency and area overheads of the electrical units. The proposed architecture benefits from Wavelength Division Multiplexing (WDM) scheme to efficiently route multicast optical packets concurrent with unicast data streams. Performing a series of simulation-based experiments, we study efficiency of the proposed architecture, its power and energy... 

    Scalable architecture for wavelength-switched optical NoC with multicasting capability

    , Article Proceedings - 13th Euromicro Conference on Digital System Design: Architectures, Methods and Tools, DSD 2010, 1 September 2010 through 3 September 2010, Lille ; 2010 , Pages 398-403 ; 9780769541716 (ISBN) Koohi, S ; Shafaei, A ; Hessabi, S ; Sharif University of Technology
    2010
    Abstract
    This paper proposes a novel all-optical router as a building block for a scalable wavelength-switched optical NoC. The proposed optical router, named as AOR, performs passive routing of optical data streams based on their wavelengths. Utilizing wavelength routing method, AOR eliminates the need for electrical resource reservation and the corresponding latency and area overheads. Taking advantage of Wavelength Division Multiplexing (WDM) technique, the proposed architecture is capable of data multicasting, concurrent with unicast data transmission, with high bandwidth and low power dissipation, without imposing noticeable area and latency overheads. Comparing AOR against previously proposed... 

    Fault Rate Modeling in Terms of Power Consumption and Thermal Variation in Optical Networks-on-Chip

    , M.Sc. Thesis Sharif University of Technology Abolhasani Zeraatkar, Alireza (Author) ; Koohi, Somayyeh (Supervisor)
    Abstract
    Global on chip communication becomes a critical power bottleneck in high performance many core architectures. The importance of power dissipation in networks-on-chip along with power reduction capability of on-chip nanophotonic interconnects has made optical network on chip a novel technology. Major advantages like high bandwidth, light speed latency and low power consumption, provide a promising solution for future of communications in many core architectures. However, the basic elements that are embedded in optical networks on chip are extremely temperature sensitive. This would lead to change in the physical characteristics of nanophotonic elements which may cause failure in network on... 

    Enabling Optical Interconnection Networks in Data Centers for Data Multicasting

    , M.Sc. Thesis Sharif University of Technology Nezhadi Khelejani, Ali (Author) ; Koohi, Somayyeh (Supervisor)
    Abstract
    Exponential growth of traffic and bandwidth demands in current data center networks, requires low-latency high-throughput interconnection networks, considering power consumption. Furthermore, increasing multicast intensive applications, alongside conventional unicast applications, arises power efficient communication in today’s data center networks as the main design challenge. Addressing these demands, optical networks suggest several benefits as well as circumventing most disadvantages of electrical networks. In this thesis, we propose an all-optical scalable architecture, for communicating intra-data centers. This architecture utilizes passive optical devices and enables optical circuit...