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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... 

    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.... 

    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  

    r-Strong edge colorings of graphs

    , Article Discrete Mathematics ; Volume 306, Issue 23 SPEC. ISS , 2006 , Pages 3005-3010 ; 0012365X (ISSN) Akbari, S ; Bidkhori, H ; Nosrati, N ; Sharif University of Technology
    Elsevier  2006
    Abstract
    Let G be a graph and for any natural number r, χs ′ (G, r) denotes the minimum number of colors required for a proper edge coloring of G in which no two vertices with distance at most r are incident to edges colored with the same set of colors. In [Z. Zhang, L. Liu, J. Wang, Adjacent strong edge coloring of graphs, Appl. Math. Lett. 15 (2002) 623-626] it has been proved that for any tree T with at least three vertices, χs ′ (T, 1) ≤ Δ (T) + 1. Here we generalize this result and show that χs ′ (T, 2) ≤ Δ (T) + 1. Moreover, we show that if for any two vertices u and v with maximum degree d (u, v) ≥ 3, then χs ′ (T, 2) = Δ (T). Also for any tree T with Δ (T) ≥ 3 we prove that χs ′ (T, 3) ≤ 2 Δ... 

    Analyzing Harmonic wave Propagation in Two Layered Elastic Anisotropic Prestressed Plate

    , M.Sc. Thesis Sharif University of Technology Nosrati, Mohammad Amin (Author) ; Fallah Rajabzadeh, Famida (Supervisor)
    Abstract
    Obtaining the mechanical properties of body tissues in a non-destructive manner is clinically important and has wide applications in the diagnosis and prevention of diseases. one of non-destructive methods is elastography, which requires proper modeling of the tissue and then analysis of the wave propagation in it and obtaining the propagation relations and the dispersion curves. Study of the literature revealed that many simplifications have been used in most modelings of arteries and so far the anisotropy of the artery and its layers with the effects of surrounding tissues and blood have not been studied Therefore, the aim of this study is to model the artery as a two-layer orthotropic... 

    Biprosimgcn: prediction of drugs-proteins interactions using graph convolutional neural network and proteins similarity

    , Article Proceedings of the 2023 IEEE Asia-Pacific Conference on Computer Science and Data Engineering, CSDE 2023 ; 2023 ; 979-835034107-2 (ISBN) Ghahramani, S. A. G ; Hosseinioun, M ; Nosrati, A ; Kavousi, K ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2023
    Abstract
    The drug discovery process faces challenges due to its length, cost, and experimental failures. Researchers are addressing these issues through 'drug repurposing,' seeking new applications for existing pharmaceuticals. To predict drug-target interactions, computational methods, like drug-target interaction prediction, utilize bipartite graphs and link prediction. In this paper, we propose BiProSimGCN, a framework based on convolutional graph neural networks, to predict drug-protein interactions. BiProSimGCN integrates data from the bipartite drug-protein network and the protein similarity network, aiming to reveal latent factors of drugs and proteins. The performance of BiProSimGCN is... 

    Process optimization and modeling of anaerobic digestion of cow manure for enhanced biogas yield in a mixed plug-flow reactor using response surface methodology

    , Article Biosciences Biotechnology Research Asia ; Volume 12, Issue 3 , 2015 , Pages 2333-2344 ; 09731245 (ISSN) Rasouli, M ; Ajabshirchi, Y ; Mousavi, S. M ; Nosrati, M ; Yaghmaei, S ; Sharif University of Technology
    Oriental Scientific Publishing Company  2015
    Abstract
    Pilot scale experiments were performed on the digestion of dairy cow manure in a semi-continuous process using a mixed plug flow reactor (MPFR) to determine the effects of organic loading rate (OLR), temperature and mixing levels on production biogas and methane yield. Response surface methodology (RSM) was applied for the design and analysis of experiments with the optimization of OLR, temperature and mixing level during the biogas production process. Experiments were designed as per the central composite design technique. Four cubic mathematical models were derived for prediction of the responses. The optimization study has been carried out to identify the highest yields achievable when... 

    Combustion Instability in a Silo Type Gas Turbine Combustor

    , M.Sc. Thesis Sharif University of Technology Nosrati Shoar, Somayeh (Author) ; Farshchi, Mohammad (Supervisor) ; Hejranfar, Kazem (Supervisor)
    Abstract
    Nowadays, one of the most important desires of the human being is to reduce his living environmental pollution. Using the diluted combustion systems in new gas turbines in order to produce the minimum amount of has been done to satisfy this desire. It should be noted that reducing this amount and using the lower flame temperature will result in some consequences. The most important problem occurred in industrial and aerial gas turbines are the instability of the combustion due to dilution of the fuel to air mixture which it results in heat release fluctuations. If the heat release fluctuations and acoustic pressure are in the same phases, the amplitude of the fluctuations will increase which... 

    Effect of low-level laser irradiation on the function of glycated catalase

    , Article Journal of Lasers in Medical Sciences ; Volume 9, Issue 3 , 2018 , Pages 212-218 ; 20089783 (ISSN) Mirmiranpour, H ; Shams Nosrati, F ; Sobhani, O ; Nazifi Takantape, S ; Amjadi, A ; Sharif University of Technology
    Laser Application in Medical Sciences Research Center  2018
    Abstract
    Introduction: The aim of this work is to evaluate the effect of low-level laser irradiation (LLLI), by lasers with different wavelengths, on glycated catalase enzyme in vitro experimentally. Methods: This is done by measuring the activity and structure properties of glycated catalase enzyme. The structure properties were evaluated with circular dichroism (CD) and fluoroscopy methods. Three continuous wave (CW) lasers in the visible spectrum (λ = 450, 530, 638 nm) and a 100-ns pulsed laser in the infrared spectrum (λ = 905 nm) were chosen for comparison. For the infrared laser, same effects have been investigated for different energy doses. The effect of photon energy (hλ) at different... 

    Incorporating fault-proneness estimations into coverage-based test case prioritization methods

    , Article Information and Software Technology ; Volume 121 , May , 2020 Mahdieh, M ; Mirian Hosseinabadi, S. H ; Etemadi, K ; Nosrati, A ; Jalali, S ; Sharif University of Technology
    Elsevier B. V  2020
    Abstract
    Context: During the development process of a software program, regression testing is used to ensure that the correct behavior of the software is retained after updates to the source code. This regression testing becomes costly over time as the number of test cases increases and it makes sense to prioritize test cases in order to execute fault-detecting test cases as soon as possible. There are many coverage-based test case prioritization (TCP) methods that only use the code coverage data to prioritize test cases. By incorporating the fault-proneness estimations of code units into the coverage-based TCP methods, we can improve such techniques. Objective: In this paper, we aim to propose an... 

    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... 

    A quantization noise robust object's shape prediction algorithm

    , Article 13th European Signal Processing Conference, EUSIPCO 2005, Antalya, 4 September 2005 through 8 September 2005 ; 2005 , Pages 1770-1773 ; 1604238216 (ISBN); 9781604238211 (ISBN) Khansari, M ; Rabiee, H. R ; Asadi, M ; Nosrati, M ; Amiri, M ; Ghanbari, M ; Sharif University of Technology
    2005
    Abstract
    This paper introduces a quantization noise robust algorithm for object's shape prediction in a video sequence. The algorithm is based on pixel representation in the undecimated wavelet domain for tracking of the user-defined shapes contaminated by the compression noise of video sequences. In the proposed algorithm, the amplitude of coefficients in the best basis tree expansion of the undecimated wavelet packet transform is used as feature vectors (FVs). FVs robustness against quantization noise has been achieved through inherent denoising and edge component separation in the best basis selection algorithm. The algorithm uses these FVs to track the pixels of small square blocks located at the... 

    Prioritizing adoption barriers of platforms based on blockchain technology from balanced scorecard perspectives in healthcare industry: a structural approach

    , Article International Journal of Production Research ; 2022 ; 00207543 (ISSN) Govindan, K ; Nasr, A. K ; Saeed Heidary, M ; Nosrati-Abargooee, S ; Mina, H ; Sharif University of Technology
    Taylor and Francis Ltd  2022
    Abstract
    Since the advent of blockchain technology (BT), extensive research has explored using this technology in non-financial cases. The healthcare industry is one of the non-financial sectors that BT has significantly impacted. In this paper, for the first time, barriers to implement BT-based platforms from a balanced scorecard perspective in the healthcare sector are introduced, and these barriers are prioritized using a structural approach based on the weighted influence non-linear gauge system. Unlike other structural models such as decision-making trial and evaluation laboratory (DEMATEL), in this approach, both strength and influence intensity of components are considered in the ranking... 

    Prioritizing adoption barriers of platforms based on blockchain technology from balanced scorecard perspectives in healthcare industry: a structural approach

    , Article International Journal of Production Research ; Volume 61, Issue 11 , 2023 , Pages 3512-3526 ; 00207543 (ISSN) Govindan, K ; Khalili Nasr, A ; Heidary, M. S ; Nosrati Abarghooee, S ; Mina, H ; Sharif University of Technology
    Taylor and Francis Ltd  2023
    Abstract
    Since the advent of blockchain technology (BT), extensive research has explored using this technology in non-financial cases. The healthcare industry is one of the non-financial sectors that BT has significantly impacted. In this paper, for the first time, barriers to implement BT-based platforms from a balanced scorecard perspective in the healthcare sector are introduced, and these barriers are prioritized using a structural approach based on the weighted influence non-linear gauge system. Unlike other structural models such as decision-making trial and evaluation laboratory (DEMATEL), in this approach, both strength and influence intensity of components are considered in the ranking... 

    Technical English for mechanical engineers

    , Book Alemi, Minoo ; Meghdari,Ali
    Sharif University Press  2014
    Abstract
    Local educational institutions produce in-house English for Specific Purpose (ESP) materials according to the curriculum policies designated and developed by the Ministry of Higher Education In Iran. To this end, this book aims to be used in the Iranian setting at the tertiary level for undergraduate students majoring in Mechanical Engineering. Moreover, the style of English usage in this ESP textbook is American.
    Regarding the content of the textbook, it has both thematic organizations in which the topics are relevant and includes sufficient treatment of the target language areas necessary for the students. The principle organizing approach of this textbook is theme-based. In addition,... 

    Feedback control of the neuro-musculoskeletal system in a forward dynamics simulation of stair locomotion [electronic resource]

    , Article Proc. of IMechE Part H: Journal of Engineering in Medicine ; 2009, Vol. 223, No. 6, pp. 663-675 Journal of NeuroEngineering and Rehabilitation ; Volume 11, Issue 1, 30 April 2014, Article number 78 Selk Ghafari, A. (Ali) ; Meghdari, Ali ; Vossough, Gholam Reza ; Sharif University of Technology
    Abstract
    The aim of this study is to employ feedback control loops to provide a stable forward dynamics simulation of human movement under repeated position constraint conditions in the environment, particularly during stair climbing. A ten-degrees-of-freedom skeletal model containing 18 Hill-type musculotendon actuators per leg was employed to simulate the model in the sagittal plane. The postural tracking and obstacle avoidance were provided by the proportional—integral—derivative controller according to the modulation of the time rate change of the joint kinematics. The stability of the model was maintained by controlling the velocity of the body's centre of mass according to the desired centre of... 

    Design and Construction of a Soft Actuated Exoskeleton for Hand Rehabilitation of Stroke Patients

    , M.Sc. Thesis Sharif University of Technology Razavi Zadehgan, Ali Akbar (Author) ; Ghafari, Ali (Supervisor) ; Meghdari, Ali (Supervisor)
    Abstract
    The main goal of this thesis is the design and development of a rehabilitation device for helping patients “to improve blood circulation” & retain and recover their abilities if possible that were lost during the stroke or a accident like that (my research in karaj/iran shows that it is possible by just movement of the specific body part). The focus is on hand in this thesis because Injuries to the hand are common and can be very debilitating since our hands are our primary means for interacting with our world. For rehabilitation in case of human hand there are several practices that should be done for patients either in home or in a rehabilitation center, time and money that is supposed to... 

    Silica chloride/wet SiO2 as a novel heterogeneous system for the deprotection of acetals under mild conditions [electronic resource]

    , Article Phosphorus, Sulfur, and Silicon and the Related Elements ; Volume 178:2667-2670, Issue 12, 2003 Mirjalili, B. F. (BiBi Fatemeh) ; Pourjavadi, Ali ; Zolfigol, Mohammad Ali ; Bamoniri, Abdolhamid
    Abstract
    A combination of silica chloride and wet SiO2 was used as an effective deacetalizating agent for the conversion of acetals to their corresponding carbonyl derivatives under mild and heterogeneous condition  

    Earthquake Branch

    , M.Sc. Thesis Sharif University of Technology Bagher Shemirani, Ali Reza (Author) ; Bakhshi, Ali (Supervisor)
    Abstract
    In the past few decades, shaking tables are widely used to evaluate system response of structures under seismic excitations. These devices are used without any fundamental research performed on a shaking table system as an entity model. In most of these studies for simplicity, it is assumed that there exist no considerable vibration and displacement around the shaking tables, and no attention is paid to the peripheral substances such as soil settled under the foundation.
    In this thesis, result of ambient vibration test on shaking table system (solid deck, concrete foundation and soil layer) has been presented. Precise sensors known as low frequency and high accuracy accelerometers have...