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  1. Book ; Online: Deep Metric Learning with Soft Orthogonal Proxies

    Saberi-Movahed, Farshad / Ebrahimpour, Mohammad K. / Saberi-Movahed, Farid / Moshavash, Monireh / Rahmatian, Dorsa / Mohazzebi, Mahvash / Shariatzadeh, Mahdi / Eftekhari, Mahdi

    2023  

    Abstract: Deep Metric Learning (DML) models rely on strong representations and similarity-based measures with specific loss functions. Proxy-based losses have shown great performance compared to pair-based losses in terms of convergence speed. However, proxies ... ...

    Abstract Deep Metric Learning (DML) models rely on strong representations and similarity-based measures with specific loss functions. Proxy-based losses have shown great performance compared to pair-based losses in terms of convergence speed. However, proxies that are assigned to different classes may end up being closely located in the embedding space and hence having a hard time to distinguish between positive and negative items. Alternatively, they may become highly correlated and hence provide redundant information with the model. To address these issues, we propose a novel approach that introduces Soft Orthogonality (SO) constraint on proxies. The constraint ensures the proxies to be as orthogonal as possible and hence control their positions in the embedding space. Our approach leverages Data-Efficient Image Transformer (DeiT) as an encoder to extract contextual features from images along with a DML objective. The objective is made of the Proxy Anchor loss along with the SO regularization. We evaluate our method on four public benchmarks for category-level image retrieval and demonstrate its effectiveness with comprehensive experimental results and ablation studies. Our evaluations demonstrate the superiority of our proposed approach over state-of-the-art methods by a significant margin.
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Subject code 006
    Publishing date 2023-06-22
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: High dimensionality reduction by matrix factorization for systems pharmacology.

    Mehrpooya, Adel / Saberi-Movahed, Farid / Azizizadeh, Najmeh / Rezaei-Ravari, Mohammad / Saberi-Movahed, Farshad / Eftekhari, Mahdi / Tavassoly, Iman

    Briefings in bioinformatics

    2021  Volume 23, Issue 1

    Abstract: The extraction of predictive features from the complex high-dimensional multi-omic data is necessary for decoding and overcoming the therapeutic responses in systems pharmacology. Developing computational methods to reduce high-dimensional space of ... ...

    Abstract The extraction of predictive features from the complex high-dimensional multi-omic data is necessary for decoding and overcoming the therapeutic responses in systems pharmacology. Developing computational methods to reduce high-dimensional space of features in in vitro, in vivo and clinical data is essential to discover the evolution and mechanisms of the drug responses and drug resistance. In this paper, we have utilized the matrix factorization (MF) as a modality for high dimensionality reduction in systems pharmacology. In this respect, we have proposed three novel feature selection methods using the mathematical conception of a basis for features. We have applied these techniques as well as three other MF methods to analyze eight different gene expression datasets to investigate and compare their performance for feature selection. Our results show that these methods are capable of reducing the feature spaces and find predictive features in terms of phenotype determination. The three proposed techniques outperform the other methods used and can extract a 2-gene signature predictive of a tyrosine kinase inhibitor treatment response in the Cancer Cell Line Encyclopedia.
    MeSH term(s) Algorithms ; Humans ; Neoplasms/drug therapy ; Neoplasms/genetics ; Network Pharmacology
    Language English
    Publishing date 2021-12-10
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbab410
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Decoding Clinical Biomarker Space of COVID-19: Exploring Matrix Factorization-based Feature Selection Methods.

    Saberi-Movahed, Farshad / Mohammadifard, Mahyar / Mehrpooya, Adel / Rezaei-Ravari, Mohammad / Berahmand, Kamal / Rostami, Mehrdad / Karami, Saeed / Najafzadeh, Mohammad / Hajinezhad, Davood / Jamshidi, Mina / Abedi, Farshid / Mohammadifard, Mahtab / Farbod, Elnaz / Safavi, Farinaz / Dorvash, Mohammadreza / Vahedi, Shahrzad / Eftekhari, Mahdi / Saberi-Movahed, Farid / Tavassoly, Iman

    medRxiv : the preprint server for health sciences

    2021  

    Abstract: One of the most critical challenges in managing complex diseases like COVID-19 is to establish an intelligent triage system that can optimize the clinical decision-making at the time of a global pandemic. The clinical presentation and patients’ ... ...

    Abstract One of the most critical challenges in managing complex diseases like COVID-19 is to establish an intelligent triage system that can optimize the clinical decision-making at the time of a global pandemic. The clinical presentation and patients’ characteristics are usually utilized to identify those patients who need more critical care. However, the clinical evidence shows an unmet need to determine more accurate and optimal clinical biomarkers to triage patients under a condition like the COVID-19 crisis. Here we have presented a machine learning approach to find a group of clinical indicators from the blood tests of a set of COVID-19 patients that are predictive of poor prognosis and morbidity. Our approach consists of two interconnected schemes: Feature Selection and Prognosis Classification. The former is based on different Matrix Factorization (MF)-based methods, and the latter is performed using Random Forest algorithm. Our model reveals that Arterial Blood Gas (ABG) O
    Language English
    Publishing date 2021-07-09
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.07.07.21259699
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Decoding clinical biomarker space of COVID-19: Exploring matrix factorization-based feature selection methods.

    Saberi-Movahed, Farshad / Mohammadifard, Mahyar / Mehrpooya, Adel / Rezaei-Ravari, Mohammad / Berahmand, Kamal / Rostami, Mehrdad / Karami, Saeed / Najafzadeh, Mohammad / Hajinezhad, Davood / Jamshidi, Mina / Abedi, Farshid / Mohammadifard, Mahtab / Farbod, Elnaz / Safavi, Farinaz / Dorvash, Mohammadreza / Mottaghi-Dastjerdi, Negar / Vahedi, Shahrzad / Eftekhari, Mahdi / Saberi-Movahed, Farid /
    Alinejad-Rokny, Hamid / Band, Shahab S / Tavassoly, Iman

    Computers in biology and medicine

    2022  Volume 146, Page(s) 105426

    Abstract: One of the most critical challenges in managing complex diseases like COVID-19 is to establish an intelligent triage system that can optimize the clinical decision-making at the time of a global pandemic. The clinical presentation and patients' ... ...

    Abstract One of the most critical challenges in managing complex diseases like COVID-19 is to establish an intelligent triage system that can optimize the clinical decision-making at the time of a global pandemic. The clinical presentation and patients' characteristics are usually utilized to identify those patients who need more critical care. However, the clinical evidence shows an unmet need to determine more accurate and optimal clinical biomarkers to triage patients under a condition like the COVID-19 crisis. Here we have presented a machine learning approach to find a group of clinical indicators from the blood tests of a set of COVID-19 patients that are predictive of poor prognosis and morbidity. Our approach consists of two interconnected schemes: Feature Selection and Prognosis Classification. The former is based on different Matrix Factorization (MF)-based methods, and the latter is performed using Random Forest algorithm. Our model reveals that Arterial Blood Gas (ABG) O
    MeSH term(s) Biomarkers ; COVID-19 ; Humans ; Machine Learning ; Pandemics ; Triage/methods
    Chemical Substances Biomarkers
    Language English
    Publishing date 2022-04-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2022.105426
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Guanine-Based DNA Biosensor Amplified with Pt/SWCNTs Nanocomposite as Analytical Tool for Nanomolar Determination of Daunorubicin as an Anticancer Drug: A Docking/Experimental Investigation

    Karimi-Maleh, Hassan / Alizadeh, Marzieh / Orooji, Yasin / Karimi, Fatemeh / Baghayeri, Mehdi / Rouhi, Jalal / Tajik, Somayeh / Beitollahi, Hadi / Agarwal, Shilpi / Gupta, Vinod K / Rajendran, Saravanan / Rostamnia, Sadegh / Fu, Li / Saberi-Movahed, Farshad / Malekmohammadi, Samira

    Industrial & engineering chemistry process design and development. 2021 Jan. 08, v. 60, no. 2

    2021  

    Abstract: Daunorubicin is a famous anthracycline anticancer chemotherapy drug with many side effects that is very important to measure in biological samples. A daunorubicin electrochemical biosensor was fabricated in this study using ds-DNA as the biorecognition ... ...

    Abstract Daunorubicin is a famous anthracycline anticancer chemotherapy drug with many side effects that is very important to measure in biological samples. A daunorubicin electrochemical biosensor was fabricated in this study using ds-DNA as the biorecognition element and glassy carbon electrode (GCE) amplified by Pt/SWCNTs as a sensor. The synthetization of Pt/SWCNTs was done by the polyol method, and their characterization was accomplished via XRD, EDS, and TEM methods. The results showed a diameter of about 5.0 nm for the Pt nanoparticle decorated at the surface of SWCNTs. The morphological and conductivity properties of Pt/SWCNTs/GCE were investigated by EIS and AFM methods, and the results confirmed that Pt/SWCNTs/GCE had a high surface area and high conductivity. ds-DNA/Pt/SWCNTs/GCE showed an oxidation signal relative to that of the guanine base at the potential of 847 mV and a positive shift after interaction with the daunorubicin anticancer drug. This point confirms the intercalation reaction between the guanine base in the ds-DNA structure and the drug that could be used as an analytical factor for the determination of daunorubicin. Furthermore, molecular docking study is used to predict the interaction site of daunorubicin with DNA. It is found that daunorubicin interacts with guanine bases of DNA via an intercalative mode. Kinetic investigation showed an association equilibrium constant (Kₐ) of about 5.044 × 10³ M–¹ between ds-DNA and daunorubicin. The differential pulse voltammetric results showed a linear dynamic range of 4.0 nM to 250.0 μM with a detection limit of 1.0 nM for determination of daunorubicin on the surface of ds-DNA/Pt/SWCNTs/GCE. Finally, ds-DNA/Pt/SWCNTs/GCE was successfully used for the determination of daunorubicin in injection samples with a recovery range of 98.27–10313%.
    Keywords DNA ; biosensors ; daunorubicin ; detection limit ; drug therapy ; glassy carbon electrode ; guanine ; nanocomposites ; oxidation ; polyols ; process design ; surface area ; voltammetry
    Language English
    Dates of publication 2021-0108
    Size p. 816-823.
    Publishing place American Chemical Society
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1484436-9
    ISSN 1520-5045 ; 0888-5885
    ISSN (online) 1520-5045
    ISSN 0888-5885
    DOI 10.1021/acs.iecr.0c04698
    Database NAL-Catalogue (AGRICOLA)

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