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WalkIm: Compact image-based encoding for high-performance classification of biological sequences using simple tuning-free CNNs
, Article PLoS ONE ; Volume 17, Issue 4 April , 2022 ; 19326203 (ISSN) ; Mohammadi, A ; Koohi, S ; Sharif University of Technology
Public Library of Science
2022
Abstract
The classification of biological sequences is an open issue for a variety of data sets, such as viral and metagenomics sequences. Therefore, many studies utilize neural network tools, as the well-known methods in this field, and focus on designing customized network structures. However, a few works focus on more effective factors, such as input encoding method or implementation technology, to address accuracy and efficiency issues in this area. Therefore, in this work, we propose an image-based encoding method, called as WalkIm, whose adoption, even in a simple neural network, provides competitive accuracy and superior efficiency, compared to the existing classification methods (e.g. VGDC,...
An accurate alignment-free protein sequence comparator based on physicochemical properties of amino acids
, Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) ; Abdosalehi, A. S ; Pouyamehr, F ; Koohi, S ; Sharif University of Technology
Nature Research
2022
Abstract
Bio-sequence comparators are one of the most basic and significant methods for assessing biological data, and so, due to the importance of proteins, protein sequence comparators are particularly crucial. On the other hand, the complexity of the problem, the growing number of extracted protein sequences, and the growth of studies and data analysis applications addressing protein sequences have necessitated the development of a rapid and accurate approach to account for the complexities in this field. As a result, we propose a protein sequence comparison approach, called PCV, which improves comparison accuracy by producing vectors that encode sequence data as well as physicochemical properties...
Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture
, Article PloS one ; Volume 16, Issue 1 , 2021 , Pages e0245095- ; 19326203 (ISSN) ; Hashemi Dijujin, N ; Koohi, S ; Sharif University of Technology
NLM (Medline)
2021
Abstract
In this study, optical technology is considered as SA issues' solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,...
Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture
, Article PLoS ONE ; Volume 16, Issue 1 January 2021 , 2021 ; 19326203 (ISSN) ; Dijujin, N. H ; Koohi, S ; Sharif University of Technology
Public Library of Science
2021
Abstract
In this study, optical technology is considered as SA issues’ solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,...
Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture
, Article PloS one ; Volume 16, Issue 1 , 2021 , Pages e0245095- ; 19326203 (ISSN) ; Hashemi Dijujin, N ; Koohi, S ; Sharif University of Technology
NLM (Medline)
2021
Abstract
In this study, optical technology is considered as SA issues' solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,...
Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture
, Article PLoS ONE ; Volume 16, Issue 1 , 2021 ; 19326203 (ISSN) ; Dijujin, N. H ; Koohi, S ; Sharif University of Technology
Public Library of Science
2021
Abstract
In this study, optical technology is considered as SA issues’ solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,...
Design and optimization of Gregorian-based reflector systems for thz imaging system optics
, Article 4th West Asian Symposium on Optical and Millimeter-Wave Wireless Communications, WASOWC 2022, 12 May 2022 through 13 May 2022 ; 2022 ; 9781665409131 (ISBN) ; Ahmadi Boroujeni, M ; Babanejad, S ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2022
Abstract
The application of reflector antenna configurations in designing the optical section of terahertz imaging systems has attracted great attention in recent years. The advantages of reflective optics in comparison with refractive optics is one of the main reasons for this trend. Specular reflection in a broad spectral range, no or little reflection and transmission loss, no chromatic aberration, and high reliability in high power applications configuration are just some of these advantages. In this paper, the optical performance of a modified off-axis aberrations-free Gregorian-based reflector antenna system is studied as an optical section of a terahertz imaging system. By applying a precise...
All-Optical Scalable Multi-stage Interconnection Network for Data Centers
, M.Sc. Thesis Sharif University of Technology ; 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 ; 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 ; 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 ; 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...
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 ; 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...
MHC-Peptide Binding Prediction Using a Deep Learning Method with Efficient GPU Implementation Approach
, M.Sc. Thesis Sharif University of Technology ; 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...
Prediction of DNA/RNA Sequence Binding Site to Protein with the Ability to Implement on GPU
, M.Sc. Thesis Sharif University of Technology ; 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...
Motif Finding Application Using Edit Distance Approuch
, M.Sc. Thesis Sharif University of Technology ; 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...
Free space Optical Spiking Neural Network
, M.Sc. Thesis Sharif University of Technology ; 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...
High-level modeling approach for analyzing the effects of traffic models on power and throughput in mesh-based NoCs
, Article Proceedings of the IEEE International Frequency Control Symposium and Exposition, 4 January 2008 through 8 January 2008, Hyderabad ; 2008 , Pages 415-420 ; 0769530834 (ISBN); 9780769530833 (ISBN) ; Mirza Aghatabar, M ; Hessabi, S ; Pedram, M ; VLSI Society of India ; Sharif University of Technology
2008
Abstract
Traffic models exert different message flows in a network and have a considerable effect on power consumption through different applications. So a good power analysis should consider traffic models. In this paper we present power and throughput models in terms of traffic rate parameters for the most popular traffic models, i.e. Uniform, Local, HotSpot and First Matrix Transpose (FMT) as a permutational traffic model. We also select Mesh topology as the most prominent NoC topology and validate the presented models by comparing our results against simulation results from Synopsys Power Compiler and Modelsim From the comparison, we show that our modeling approach leads to average error of 2%...
Enabling Optical Interconnection Networks in Data Centers for Data Multicasting
, M.Sc. Thesis Sharif University of Technology ; 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...
Fault Rate Modeling in Terms of Power Consumption and Thermal Variation in Optical Networks-on-Chip
, M.Sc. Thesis Sharif University of Technology ; 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...
Protein Interaction Prediction Through Efficient FPGA and GPU Implementation
, M.Sc. Thesis Sharif University of Technology ; Koohi, Somayyeh (Supervisor)
Abstract
Alignment of genetic sequences is a fundamental part of genetic and bio-science. Alignment of DNA and protein sequences has an effective role in accelerating and simplifying problems in Bioinformatics like predicting protein interactions. Smith-Waterman algorithm is a precise algorithm for performing local alignment, suffering from computation complexity. There are some implementations on CPU, GPU, and FPGA platforms in order to reduce the run time of this algorithm. FPGA implementation is considered because of low power consumption and high degree of parallelism. With using pipeline and hardware redundancy techniques, various architectures have been proposed and implemented. In the best...