Multiobjective deep clustering and its applications in single-cell RNA-seq data

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Single-cell RNA sequencing is a transformative technology that enables us to study the heterogeneity of the tissue at the cellular level. Clustering is used as the key computational approach to group cells under the transcriptome profiles from single-cell RNA-seq data. However, accurate identification of distinct cell types is facing the challenge of high dimensionality, and it could cause uninformative clusters when clustering is directly applied on the original transcriptome. To address such challenge, an evolutionary multiobjective deep clustering (EMDC) algorithm is proposed to identify single-cell RNA-seq data in this study. First, EMDC removes redundant and irrelevant genes by applying the differential gene expression analysis to identify differentially expressed genes across biological conditions. After that, a deep autoencoder is proposed to project the high-dimensional data into different low-dimensional nonlinear embedding subspaces under different bottleneck layers. Then, the basic clustering algorithm is applied in those nonlinear embedding subspaces to generate some basic clustering results to produce the cluster ensemble. To lessen the unnecessary cost produced by those clusterings in the ensemble, the multiobjective evolutionary optimization is designed to prune the basic clustering results in the ensemble, unleashing its cell type discovery performance under three objective functions. Multiple experiments have been conducted on 30 synthetic single-cell RNA-seq datasets and six real single-cell RNA-seq datasets, which reveal that EMDC outperforms eight other clustering methods and three multiobjective optimization algorithms in cell type identification. In addition, we have conducted extensive comparisons to effectively demonstrate the impact of each component in our proposed EMDC

A Survey on Soft Subspace Clustering

Subspace clustering (SC) is a promising clustering technology to identify clusters based on their associations with subspaces in high dimensional spaces. SC can be classified into hard subspace clustering (HSC) and soft subspace clustering (SSC). While HSC algorithms have been extensively studied and well accepted by the scientific community, SSC algorithms are relatively new but gaining more attention in recent years due to better adaptability. In the paper, a comprehensive survey on existing SSC algorithms and the recent development are presented. The SSC algorithms are classified systematically into three main categories, namely, conventional SSC (CSSC), independent SSC (ISSC) and extended SSC (XSSC). The characteristics of these algorithms are highlighted and the potential future development of SSC is also discussed.Comment: This paper has been published in Information Sciences Journal in 201

Data procesing methodologies in the area of e-Health for categorizing therapeutic responses in patients with migraine

Tesis de la Universidad Complutense de Madrid, Facultad de Informática, leída el 19/11/2020La presente tesis doctoral estudia algunas metodologías de procesamiento de datos en el área de e-Health para clasificar las respuestas terapéuticas en pacientes con migraña. En un escenario real de e-Health, este trabajo se centra en la predicción de la respuesta al tratamiento de la migraña mediante el uso de registros médicos retrospectivos recopilados del hospital Clínico Universitario en Valladolid y del Hospital Universitario de La Princesa, en Madrid. el objetivo de este trabajo de investigación es plantear y responder las siguientes preguntas: ¿es posible predecir la respuesta a cada etapa del tratamiento para la migraña con BoNT-A? ¿existe un modelo predictivo para el tratamiento con BoNT-A en la migraña? ¿cómo responden estos modelos bajo registros incompletos? ¿es posible conocer aquellos factores médicos que hacen posible una alta respuesta al tratamiento con BoNT-A? ¿Los factores médicos utilizados para predecir la respuesta del tratamiento son coherentes con el conocimiento de los expertos médicos? Para responder a estas preguntas, este trabajo ha explorado e implementado diferentes enfoques para el entrenamiento de los modelos predictivos...This Ph.D. Thesis studies some data processing methodologies in the area of e-Health for categorizing therapeutic responses in patients with migraine. In a real e-Health scenario, this work focuses on the prediction of the response to the treatment of migraine through the use of retrospective medical records collected from Hospital Clínico Universitario in Valladolid and Hospital Universitario de La Princesa, in Madrid. The goal of this research work is to pose and answer the following questions: is it possible to predict the response to every stage of the BoNT-A treatment for migraine? Does a pre-treatment prediction model for the BoNT-A treatment in migraine exist? how do these models respond under missing values? Is it possible to reveal those medical factors that make it possible a high response to the BoNT-A treatment? Are the medical factors used to predict the response of the treatment coherent with the knowledge of medical experts? To answer these questions, this work has explored and implemented different approaches for the training of the predictive models...Fac. de InformáticaTRUEunpu

Towards an Information Theoretic Framework for Evolutionary Learning

The vital essence of evolutionary learning consists of information flows between the environment and the entities differentially surviving and reproducing therein. Gain or loss of information in individuals and populations due to evolutionary steps should be considered in evolutionary algorithm theory and practice. Information theory has rarely been applied to evolutionary computation - a lacuna that this dissertation addresses, with an emphasis on objectively and explicitly evaluating the ensemble models implicit in evolutionary learning. Information theoretic functionals can provide objective, justifiable, general, computable, commensurate measures of fitness and diversity. We identify information transmission channels implicit in evolutionary learning. We define information distance metrics and indices for ensembles. We extend Price\u27s Theorem to non-random mating, give it an effective fitness interpretation and decompose it to show the key factors influencing heritability and evolvability. We argue that heritability and evolvability of our information theoretic indicators are high. We illustrate use of our indices for reproductive and survival selection. We develop algorithms to estimate information theoretic quantities on mixed continuous and discrete data via the empirical copula and information dimension. We extend statistical resampling. We present experimental and real world application results: chaotic time series prediction; parity; complex continuous functions; industrial process control; and small sample social science data. We formalize conjectures regarding evolutionary learning and information geometry

Collected Papers (on Neutrosophic Theory and Applications), Volume VIII

This eighth volume of Collected Papers includes 75 papers comprising 973 pages on (theoretic and applied) neutrosophics, written between 2010-2022 by the author alone or in collaboration with the following 102 co-authors (alphabetically ordered) from 24 countries: Mohamed Abdel-Basset, Abduallah Gamal, Firoz Ahmad, Ahmad Yusuf Adhami, Ahmed B. Al-Nafee, Ali Hassan, Mumtaz Ali, Akbar Rezaei, Assia Bakali, Ayoub Bahnasse, Azeddine Elhassouny, Durga Banerjee, Romualdas Bausys, Mircea Boșcoianu, Traian Alexandru Buda, Bui Cong Cuong, Emilia Calefariu, Ahmet Çevik, Chang Su Kim, Victor Christianto, Dae Wan Kim, Daud Ahmad, Arindam Dey, Partha Pratim Dey, Mamouni Dhar, H. A. Elagamy, Ahmed K. Essa, Sudipta Gayen, Bibhas C. Giri, Daniela Gîfu, Noel Batista Hernández, Hojjatollah Farahani, Huda E. Khalid, Irfan Deli, Saeid Jafari, Tèmítópé Gbóláhàn Jaíyéolá, Sripati Jha, Sudan Jha, Ilanthenral Kandasamy, W.B. Vasantha Kandasamy, Darjan Karabašević, M. Karthika, Kawther F. Alhasan, Giruta Kazakeviciute-Januskeviciene, Qaisar Khan, Kishore Kumar P K, Prem Kumar Singh, Ranjan Kumar, Maikel Leyva-Vázquez, Mahmoud Ismail, Tahir Mahmood, Hafsa Masood Malik, Mohammad Abobala, Mai Mohamed, Gunasekaran Manogaran, Seema Mehra, Kalyan Mondal, Mohamed Talea, Mullai Murugappan, Muhammad Akram, Muhammad Aslam Malik, Muhammad Khalid Mahmood, Nivetha Martin, Durga Nagarajan, Nguyen Van Dinh, Nguyen Xuan Thao, Lewis Nkenyereya, Jagan M. Obbineni, M. Parimala, S. K. Patro, Peide Liu, Pham Hong Phong, Surapati Pramanik, Gyanendra Prasad Joshi, Quek Shio Gai, R. Radha, A.A. Salama, S. Satham Hussain, Mehmet Șahin, Said Broumi, Ganeshsree Selvachandran, Selvaraj Ganesan, Shahbaz Ali, Shouzhen Zeng, Manjeet Singh, A. Stanis Arul Mary, Dragiša Stanujkić, Yusuf Șubaș, Rui-Pu Tan, Mirela Teodorescu, Selçuk Topal, Zenonas Turskis, Vakkas Uluçay, Norberto Valcárcel Izquierdo, V. Venkateswara Rao, Volkan Duran, Ying Li, Young Bae Jun, Wadei F. Al-Omeri, Jian-qiang Wang, Lihshing Leigh Wang, Edmundas Kazimieras Zavadskas