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farahnak-ghazani--fatemeh
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Multi-label classification with feature-aware implicit encoding and generalized cross-entropy loss
, Article 24th Iranian Conference on Electrical Engineering, 10 May 2016 through 12 May 2016 ; 2016 , Pages 1574-1579 ; 9781467387897 (ISBN) ; Soleymani Baghshah, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2016
Abstract
In multi-label classification problems, each instance can simultaneously have multiple labels. Since the whole number of available labels in real-world applications tends to be (very) large, multi-label classification becomes an important challenge and recently label space dimension reduction (LSDR) methods have received attention. These methods first encode the output space to a low-dimensional latent space. Afterwards, they predict the latent space from the feature space and reconstruct the original output space using a suitable decoding method. The encoding method can be implicit which learns a code matrix in the latent space by solving an optimization problem or explicit which learns a...
Multi-label Classification by Considering Label Dependencies
, M.Sc. Thesis Sharif University of Technology ; Soleymani, Mahdieh (Supervisor)
Abstract
In multi-label classification problems each instance can simultaneously have multiple labels. In these problems, in addition to the complexities of the input feature space we encounter the complexities of output label space. In the multi-label classification problems, there are dependencies between different labels that need to be considered. Since the dimensionality of the label space in real-world applications can be (very) high, most methods which explicitly model these dependencies are ineffective in practice and recently those methods that transform the label space into a latent space have received attention. A class of these methods which uses output space dimension reduction, first...
On molecular flow velocity meters
, Article IEEE Transactions on Molecular, Biological, and Multi-Scale Communications ; Volume 7, Issue 4 , 2021 , Pages 224-238 ; 23327804 (ISSN) ; Mirmohseni, M ; Nasiri Kenari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2021
Abstract
Flow velocity is an important characteristic of the fluidic mediums. In this article, we introduce a molecular based flow velocity meter consisting of a molecule releasing node and a receiver that counts these molecules. We consider both flow velocity detection and estimation problems, which are employed in different applications. For the flow velocity detection, we obtain the maximum a posteriori (MAP) decision rule. To analyze the performance of the proposed flow velocity detector, we obtain the error probability, its Gaussian approximation and Chernoff information (CI) upper bound, and investigate the optimum and sub-optimum sampling times accordingly. We show that, for binary hypothesis,...
Interference alignment using reaction in molecular interference channels
, Article IEEE Transactions on Nanobioscience ; 2022 , Pages 1-1 ; 15361241 (ISSN) ; Mirmohseni, M ; Nasiri-Kenari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2022
Abstract
Co-channel interference (CCI) is a performance limiting factor in molecular communication (MC) systems with shared medium. Interference alignment (IA) is a promising scheme to mitigate CCI in traditional communication systems. Due to the signal-dependent noise in MC systems, the traditional IA schemes are less useful in MC systems. In this paper, we propose a novel IA scheme in molecular interference channels (IFCs), based on the choice of releasing/sampling times. To cancel the aligned interference signals and reduce the signal dependent noise, we use molecular reaction in the proposed IA scheme. We obtain the feasible region for the releasing/sampling times in the proposed scheme. Further,...
Interference alignment using reaction in molecular interference channels
, Article IEEE Transactions on Nanobioscience ; Volume 22, Issue 2 , 2023 , Pages 259-267 ; 15361241 (ISSN) ; Mirmohseni, M ; Nasiri Kenari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2023
Abstract
Co-channel interference (CCI) is a performance limiting factor in molecular communication (MC) systems with shared medium. Interference alignment (IA) is a promising scheme to mitigate CCI in traditional communication systems. Due to the signal-dependent noise in MC systems, the traditional IA schemes are less useful in MC systems. In this paper, we propose a novel IA scheme in molecular interference channels (IFCs), based on the choice of releasing/sampling times. To cancel the aligned interference signals and reduce the signal dependent noise, we use molecular reaction in the proposed IA scheme. We obtain the feasible region for the releasing/sampling times in the proposed scheme. Further,...
Multiple-Access Schemes in Molecular Communication Networks and Performance Analysis
, M.Sc. Thesis Sharif University of Technology ; Nasiri Kenari, Masoumeh (Supervisor)
Abstract
Molecular communication (MC), which has stimulated a great deal of interest in recent years, is a new paradigm for communication among nanoscale biological machines. In MC, molecules are carriers of information and information is encoded into concentration, type or releasing time of molecules. One of the issues in MC is to consider a network consisting of multiple nano-sensors or living cells, which intend to communicate with each other.In this thesis, we first consider multiple-access networks in MC. In multiple-access networks, multiple sender nano-machines intend to communicate with a receiver nano-machine through a common medium. We consider the receiver with ligandreceptors and...
Physical layer network coding in molecular two-way relay networks
, Article IWCIT 2016 - Iran Workshop on Communication and Information Theory, 3 May 2016 through 4 May 2016 ; 2016 ; 9781509019229 (ISBN) ; Aminian, G ; Mirmohseni, M ; Gohari, A ; Nasiri Kenari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2016
Abstract
In traditional wireless networks, physical layer network coding (PNC) exploits the inverse additivity property of broadcast signals in the medium, an idea which is not directly applicable to molecular networks. In this paper, to make the natural XOR operation possible at the physical layer, we exploit the reaction of different molecule types and we propose a PNC scheme in diffusion-based molecular relay networks. For comparison, we consider the straightforward network coding (SNC) scheme in molecular networks. Assuming the ligand-receptor binding process at the receivers, we investigate the error performance of both schemes. It is observed that in addition to the simplicity of the proposed...
On Medium chemical reaction in diffusion-based molecular communication: A two-way relaying example
, Article IEEE Transactions on Communications ; Volume 67, Issue 2 , 2019 , Pages 1117-1132 ; 00906778 (ISSN) ; Aminian, G ; Mirmohseni, M ; Gohari, A ; Nasiri Kenari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2019
Abstract
Chemical reactions are a prominent feature of molecular communication systems, with no direct parallels in wireless communications. While chemical reactions may be used inside the transmitter nodes, receiver nodes, or the communication medium, we focus on its utility in the medium in this paper. Such chemical reactions can be used to perform computation over the medium as molecules diffuse and react with each other (physical-layer computation). We propose the use of chemical reactions for the following purposes: 1) to reduce signal-dependent observation noise of receivers by reducing the signal density; 2) to realize molecular physical-layer network coding (PNC) by performing the natural XOR...
On medium chemical reaction in diffusion-based molecular communication: a two-way relaying example
, Article IEEE Transactions on Communications ; 2018 ; 00906778 (ISSN) ; Aminian, G ; Mirmohseni, M ; Gohari, A ; Nasiri Kenari, M ; Sharif University of Technology
2018
Abstract
Chemical reactions are a prominent feature of molecular communication (MC) systems, with no direct parallels in wireless communications. While chemical reactions may be used inside the transmitter nodes, receiver nodes or the communication medium, we focus on its utility in the medium in this paper. Such chemical reactions can be used to perform computation over the medium as molecules diffuse and react with each other (physical-layer computation). We propose the use of chemical reactions for the following purposes: (i) to reduce signal-dependent observation noise of receivers by reducing the signal density, (ii) to realize molecular physical-layer network coding (molecular PNC) by...
Medium-Based Communication and Modulation in Molecular Communication Networks
, Ph.D. Dissertation Sharif University of Technology ; Nasiri Kenari, Masoumeh (Supervisor) ; Aminzadeh Gohari, Amin (Co-Supervisor)
Abstract
Molecular communication (MC), which utilizes molecules as its carriers of information, is one of the oldest mechanisms among micro-organisms on earth. In recent years, using MC for communication among nanomachines has attracted enormous interest because of its simplicity and bio-compatibility. Diffusion-based MC mechanism is one of the most important communication mechanisms, which has wide applications because of no needs for energy and prior infrastructure. The important challenges in MC systems include node complexity, inter-symbol interference (ISI), and co-channel interference (CCI). Due to the small sizes of the nodes in MC, complexity is a serious issue. Because nanomachines are...
Bacterial receiver prototype for molecular communication using rhamnose operon in a microfluidic environment
, Article IEEE Transactions on Nanobioscience ; Volume 20, Issue 4 , 2021 , Pages 426-435 ; 15361241 (ISSN) ; Mashhadian, A ; Farahnak Ghazani, M ; Arjmandi, H. R ; Alsadat Rad, M ; Shamloo, A ; Vosoughi, M ; Nasiri Kenari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2021
Abstract
Bacterial populations are promising candidates for the development of the receiver and transmitter nanomachines for molecular communication (MC). A bacterial receiver is required to uptake the information molecules and produce the detectable molecules following a regulation mechanism. We have constructed a novel bacterial MC receiver using an inducible bacterial L-rhamnose-regulating operon. The proposed bacterial receiver produces green fluorescent protein (GFP) in response to the L-rhamnose information molecules following a quite fast regulation mechanism. To fabricate the receiver, the bacterial population has been transformed using a plasmid harboring L-rhamnose operon genes and gene...
An experimental platform for macro-scale fluidic medium molecular communication
, Article IEEE Transactions on Molecular, Biological, and Multi-Scale Communications ; 2020 ; Nasiri Kenari, M ; Rouzegar, S. V ; Azizi, A ; Hosseinian, A ; Farahnak Ghazani, M ; Bagheri, N ; Mirmohseni, M ; Arjmandi, H ; Mosayebi, R ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2020
Abstract
The macro-scale molecular communication (MC) recently received considerable attention because of its potential applications. Since most of the experimental research in MC focuses on the micro-scale cases, it is necessary to study and implement experiments to investigate the concept’s feasibility as well as to validate the models and parameters. In this paper, a macro-scale flow-based MC platform with fluidic medium is developed, in a semi-cylindrical channel with laminar flow condition. The transmission medium we consider is water in the plexi pipe, a transmitter releases Hydrochloric acid molecules into this pipe and a chemical sensor is used as the receiver. We propose an LTI model for the...
ChemInform abstract: microwave-assisted rapid ketalization/acetalization of aromatic aldehydes and ketones in aqueous media [electronic resource]
, Article Journal of Chemical Research ; September 1999, Volume -, Number 9; Page(s) 562 to 563 ; Mirjalili, Bibi Fatemeh ; Sharif University of Technology
Abstract
Aromatic aldehydes and ketones are readily acetalized or ketalized under microwave irradiation in the presence of water as a solvent
Synthesis and characterization of poly(methacrylates) containing spiroacetal and norbornene moieties in side chain [electronic resource]
, Article Journal of Applied Polymer Science ; Volume 77, Issue 1, pages 30–38, 5 July 2000 ; Mirjalili, Bibi Fatemeh ; Sharif University of Technology
Abstract
A four-step synthetic strategy was applied to achieve novel methacrylic monomers. 5-Norbornene-2,2-dimethanol was prepared from a Diels–Alder reaction of cyclopentadiene and acrolein, followed by the treatment of the adduct with an HCHO/KOH/MeOH solution. The resulting 1,3-diol (1) was then acetalized with different aromatic aldehydes having OH groups on the ring to produce four spiroacetal derivatives. The reaction of methacryloyl chloride with the phenolic derivatives led to four new methacrylic monomers that were identified spectrochemically (mass, FTIR, 1H-NMR, and 13C-NMR spectroscopy). Free radical solution polymerization was used to prepare novel spiroacetal–norbornene containing...
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...
Equilibrium and non-equilibrium gas–liquid two phase flow in long and short pipelines following a rupture
, Article AIChE Journal ; Volume 63, Issue 7 , 2017 , Pages 3214-3223 ; 00011541 (ISSN) ; Shafiei Ghazani, A ; Sharif University of Technology
John Wiley and Sons Inc
2017
Abstract
The two-phase flow following the blowdown of pipeline carrying flashing liquid is numerically investigated by using thermodynamic equilibrium and non-equilibrium models. Model equations are solved numerically by the finite volume method. The values of fluxes at cell boundaries are obtained by AUSM+-up. To obtain proper values for the coefficients of dissipation, both single phase liquid and two phase shock tube problems are investigated. The transient release from the pressurized pipeline is studied for two cases of long and short pipes. Comparison of the predictions against experimental data reveals non-equilibrium model performs a little better than equilibrium model in the prediction of...
A non-equilibrium relaxation model for fast depressurization of pipelines
, Article Annals of Nuclear Energy ; Volume 111 , 2018 , Pages 1-11 ; 03064549 (ISSN) ; Shafiei Ghazani, A ; Sharif University of Technology
Elsevier Ltd
2018
Abstract
In this paper, transient depressurization of high pressure pipelines containing initially subcooled liquid is simulated numerically by using thermodynamic non-equilibrium and choking condition model. The numerical method relies on finite volume. The convective terms of cell boundaries are discretized by Advection Upstream Splitting Method (AUSM+ - up) with a proposal of partially implicit approach for source terms. Different void fraction correlations are applied to simulate two phase shock tubes as well as the depressurization process. By comparison between the present results and previous experimental data, the best void fraction correlation is introduced. The results indicate that the...
Simulation of compressible and incompressible flows through planar and axisymmetric abrupt expansions
, Article Journal of Fluids Engineering, Transactions of the ASME ; Volume 141, Issue 11 , 2019 ; 00982202 (ISSN) ; Shafiei Ghazani, A ; Sharif University of Technology
American Society of Mechanical Engineers (ASME)
2019
Abstract
In this paper, compressible and incompressible flows through planar and axisymmetric sudden expansion channels are investigated numerically. Both laminar and turbulent flows are taken into consideration. Proper preconditioning in conjunction with a second-order accurate advection upstream splitting method (AUSM+-up) is employed. General equations for the loss coefficient and pressure ratio as a function of expansion ratio, Reynolds number, and the inlet Mach number are obtained. It is found that the reattachment length increases by increasing the Reynolds number. Changing the flow regime to turbulent results in a decreased reattachment length. Reattachment length increases slightly with a...
A pressure-based algorithm for internal compressible turbulent flows through a geometrical singularity
, Article Numerical Heat Transfer, Part B: Fundamentals ; Volume 75, Issue 2 , 2019 , Pages 127-143 ; 10407790 (ISSN) ; Shafiei Ghazani, A ; Sharif University of Technology
Taylor and Francis Ltd
2019
Abstract
Compressible turbulent flow through the abrupt enlargement in pipes is studied numerically by means of Advection Upstream Splitting Method (AUSM+-up). In low Mach numbers, a pressure correction equation of elliptic type is derived. This equation is compatible with the nature of governing equations and retrieves hyperbolic characteristic at higher Mach numbers. It is shown that the proposed numerical algorithm is computationally more efficient than the preconditioned density-based methods. The flow parameters such as reattachment length, pressure loss coefficient and wall shear stress are predicted. It is found that the loss coefficient of the compressible flow rises drastically with...
Physical Modeling to Iimpact of Burial Depth of Pipe in Soil Slopes Under Dynamic Loading
, M.Sc. Thesis Sharif University of Technology ; Jafarzadeh, Fardin (Supervisor)
Abstract
Buried pipelines as vital arteries,which will play a major role in human life should be designed and implemented in such a way that withstand the least possible harm with regard economic issues.In this study we tried to use a physical model, the impact of pipeline buried in soil slope under dynamic load are examined.To achive this goal we use a rigid metal bax with dimensions of 301.5*101.5*155 cubic meters for modeling. Pipes used in these experiments has a diameter of 1.6 cm which are connected by a fulcrum to the wall box. In order to measure strain generated in the pipe we use a series of strain gauges that were installed using the pipe at some points. Physical models made on Sharif...