Download or read book Machine Learning and Mathematical Models for Single Cell Data Analysis written by Le Ou-Yang and published by Frontiers Media SA. This book was released on 2022-11-29 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Graph Representation Learning written by William L. William L. Hamilton and published by Springer Nature. This book was released on 2022-06-01 with total page 141 pages. Available in PDF, EPUB and Kindle. Book excerpt: Graph-structured data is ubiquitous throughout the natural and social sciences, from telecommunication networks to quantum chemistry. Building relational inductive biases into deep learning architectures is crucial for creating systems that can learn, reason, and generalize from this kind of data. Recent years have seen a surge in research on graph representation learning, including techniques for deep graph embeddings, generalizations of convolutional neural networks to graph-structured data, and neural message-passing approaches inspired by belief propagation. These advances in graph representation learning have led to new state-of-the-art results in numerous domains, including chemical synthesis, 3D vision, recommender systems, question answering, and social network analysis. This book provides a synthesis and overview of graph representation learning. It begins with a discussion of the goals of graph representation learning as well as key methodological foundations in graph theory and network analysis. Following this, the book introduces and reviews methods for learning node embeddings, including random-walk-based methods and applications to knowledge graphs. It then provides a technical synthesis and introduction to the highly successful graph neural network (GNN) formalism, which has become a dominant and fast-growing paradigm for deep learning with graph data. The book concludes with a synthesis of recent advancements in deep generative models for graphs—a nascent but quickly growing subset of graph representation learning.

Download or read book Machine Learning Approaches to Multi modal Data Integration and Translation in Single cell Biology written by Karren Yang and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Building a complete picture of cell state requires measuring different properties of the cells, such as their gene expression, morphology, etc., and understanding 1) how these properties relate to each other, 2) how they change over time, 3) how they are affected by different perturbations. It is often difficult to collect this information through experimentation alone. High-throughput single-cell assays such as single-cell RNA-sequencing are destructive to cells, making it difficult to make other observations of the same cells at other time points or using different measurement tools. In this thesis, I develop new machine learning methodology to integrate and translate between single-cell data. In the first half, I develop methods based on generative modeling, representation learning and optimal transport to learn mappings between cells collected at different time points. In the second half, I develop methods based on generative modeling and representation learning to map between different data modalities, including both observational measurements and interventions. Overall, this body of work progresses towards the larger goal of complete cell models that predict cell state under different measurements, time points, and perturbations.

Download or read book Towards a Theory of Development written by Alessandro Minelli and published by Oxford University Press. This book was released on 2014 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the foundations of ontogeny by asking how the development of living things should be understood. It explores key concepts of developmental biology, asks whether general principles of development can be discovered, and what the role of models and theories is in developmental biology.

Download or read book A mathematical modeling framework to simulate and analyze cell type transitions written by Daniella Schittler and published by Logos Verlag Berlin GmbH. This book was released on 2015-03-20 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt: The quantitative understanding of changes in cell types, referred to as cell type transitions, is fundamental to advance fields such as stem cell research, immunology, and cancer therapies. This thesis provides a mathematical modeling framework to simulate and analyze cell type transitions. The novel methodological approaches and models presented here address diverse levels which are essential in this context: Gene regulatory network models represent the cell type-determining gene expression dynamics. Here, a novel construction method for gene regulatory network models is introduced, which allows to transfer results from generic low-dimensional to realistic high-dimensional gene regulatory network models. For populations of cells, a generalized model class is proposed that accounts for multiple cell types, division numbers, and the full label distribution. Analysis and solution methods are presented for this new model class, which cover common cell population experiments and allow to exploit the full information from data. The modeling and analysis methods presented here connect formerly isolated approaches, and thereby contribute to a holistic framework for the quantitative understanding of cell type transitions.

Download or read book Mathematical Models for Biological Networks and Machine Learning with Applications written by Yushan Qiu and published by . This book was released on 2017-01-26 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation, "Mathematical Models for Biological Networks and Machine Learning With Applications" by Yushan, Qiu, 邱育珊, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Systems biology studies complex systems which involve a large number of interacting entities such that their dynamics follow systematical regulations for transition. To develop computational models becomes an urgent need for studying and manipulating biologically relevant systems. The properties and behaviors of complex biological systems can be analyzed and studied by using computational biological network models. In this thesis, construction and computation methods are proposed for studying biological networks. Modeling Genetic Regulatory Networks (GRNs) is an important topic in genomic research. A number of promising formalisms have been developed in capturing the behavior of gene regulations in biological systems. Boolean Network (BN) has received sustainable attentions. Furthermore, it is possible to control one or more genes in a network so as to avoid the network entering into undesired states. Many works have been done on the control policy for a single randomly generated BN, little light has been shed on the analysis of attractor control problem for multiple BNs. An efficient algorithm was developed to study the attractor control problem for multiple BNs. However, one should note that a BN is a deterministic model, a stochastic model is more preferable in practice. Probabilistic Boolean Network (PBN), was proposed to better describe the behavior of genetic process. A PBN can be considered as a Markov chain process and the construction of a PBN is an inverse problem which is computationally challenging. Given a positive stationary distribution, the problem of constructing a sparse PBN was discussed. For the related inverse problems, an efficient algorithm was developed based on entropy approach to estimate the model parameters. The metabolite biomarker discovery problem is a hot topic in bioinformatics. Biomarker identification plays a vital role in the study of biochemical reactions and signalling networks. The lack of essential metabolites may result in triggering human diseases. An effective computational approach is proposed to identify metabolic biomarkers by integrating available biomedical data and disease-specific gene expression data. Pancreatic cancer prediction problem is another hot topic. Pancreatic cancer is known to be difficult to diagnose in the early stage, and early research mainly focused on predicting the survival rate of pancreatic cancer patients. The correct prediction of various disease states can greatly benefit patients and also assist in design of effective and personalized therapeutics. The issue of how to integrating the available laboratory data with classification techniques is an important and challenging issue. An effective approach was suggested to construct a feature space which serves as a significant predictor for classification. Furthermore, a novel method for identifying the outliers was proposed for improving the classification performance. Using our preoperative clinical laboratory data and histologically confirmed pancreatic cancer samples, computational experiments are conducted successfully with the use of Support Vector Machine (SVM) to predict the status of patients. Subjects: Biomathematics Biology - Mathematical models

Download or read book Machine Learning and Knowledge Discovery in Databases written by Ulf Brefeld and published by Springer Nature. This book was released on 2020-04-30 with total page 819 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three volume proceedings LNAI 11906 – 11908 constitutes the refereed proceedings of the European Conference on Machine Learning and Knowledge Discovery in Databases, ECML PKDD 2019, held in Würzburg, Germany, in September 2019. The total of 130 regular papers presented in these volumes was carefully reviewed and selected from 733 submissions; there are 10 papers in the demo track. The contributions were organized in topical sections named as follows: Part I: pattern mining; clustering, anomaly and outlier detection, and autoencoders; dimensionality reduction and feature selection; social networks and graphs; decision trees, interpretability, and causality; strings and streams; privacy and security; optimization. Part II: supervised learning; multi-label learning; large-scale learning; deep learning; probabilistic models; natural language processing. Part III: reinforcement learning and bandits; ranking; applied data science: computer vision and explanation; applied data science: healthcare; applied data science: e-commerce, finance, and advertising; applied data science: rich data; applied data science: applications; demo track.

Download or read book Computational Biology for Stem Cell Research written by Pawan Raghav and published by Elsevier. This book was released on 2024-01-12 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Biology for Stem Cell Research is an invaluable guide for researchers as they explore HSCs and MSCs in computational biology. With the growing advancement of technology in the field of biomedical sciences, computational approaches have reduced the financial and experimental burden of the experimental process. In the shortest span, it has established itself as an integral component of any biological research activity. HSC informatics (in silico) techniques such as machine learning, genome network analysis, data mining, complex genome structures, docking, system biology, mathematical modeling, programming (R, Python, Perl, etc.) help to analyze, visualize, network constructions, and protein-ligand or protein-protein interactions. This book is aimed at beginners with an exact correlation between the biomedical sciences and in silico computational methods for HSCs transplantation and translational research and provides insights into methods targeting HSCs properties like proliferation, self-renewal, differentiation, and apoptosis. Modeling Stem Cell Behavior: Explore stem cell behavior through animal models, bridging laboratory studies to real-world clinical allogeneic HSC transplantation (HSCT) scenarios. Bioinformatics-Driven Translational Research: Navigate a path from bench to bedside with cutting-edge bioinformatics approaches, translating computational insights into tangible advancements in stem cell research and medical applications. Interdisciplinary Resource: Discover a single comprehensive resource catering to biomedical sciences, life sciences, and chemistry fields, offering essential insights into computational tools vital for modern research.

Download or read book Machine Learning Methods for Multi Omics Data Integration written by Abedalrhman Alkhateeb and published by Springer Nature. This book was released on 2023-12-15 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: The advancement of biomedical engineering has enabled the generation of multi-omics data by developing high-throughput technologies, such as next-generation sequencing, mass spectrometry, and microarrays. Large-scale data sets for multiple omics platforms, including genomics, transcriptomics, proteomics, and metabolomics, have become more accessible and cost-effective over time. Integrating multi-omics data has become increasingly important in many research fields, such as bioinformatics, genomics, and systems biology. This integration allows researchers to understand complex interactions between biological molecules and pathways. It enables us to comprehensively understand complex biological systems, leading to new insights into disease mechanisms, drug discovery, and personalized medicine. Still, integrating various heterogeneous data types into a single learning model also comes with challenges. In this regard, learning algorithms have been vital in analyzing and integrating these large-scale heterogeneous data sets into one learning model. This book overviews the latest multi-omics technologies, machine learning techniques for data integration, and multi-omics databases for validation. It covers different types of learning for supervised and unsupervised learning techniques, including standard classifiers, deep learning, tensor factorization, ensemble learning, and clustering, among others. The book categorizes different levels of integrations, ranging from early, middle, or late-stage among multi-view models. The underlying models target different objectives, such as knowledge discovery, pattern recognition, disease-related biomarkers, and validation tools for multi-omics data. Finally, the book emphasizes practical applications and case studies, making it an essential resource for researchers and practitioners looking to apply machine learning to their multi-omics data sets. The book covers data preprocessing, feature selection, and model evaluation, providing readers with a practical guide to implementing machine learning techniques on various multi-omics data sets.

Download or read book Computational Reconstruction of Missing Data in Biological Research written by Feng Bao and published by Springer Nature. This book was released on 2021-08-06 with total page 105 pages. Available in PDF, EPUB and Kindle. Book excerpt: The emerging biotechnologies have significantly advanced the study of biological mechanisms. However, biological data usually contain a great amount of missing information, e.g. missing features, missing labels or missing samples, which greatly limits the extensive usage of the data. In this book, we introduce different types of biological data missing scenarios and propose machine learning models to improve the data analysis, including deep recurrent neural network recovery for feature missings, robust information theoretic learning for label missings and structure-aware rebalancing for minor sample missings. Models in the book cover the fields of imbalance learning, deep learning, recurrent neural network and statistical inference, providing a wide range of references of the integration between artificial intelligence and biology. With simulated and biological datasets, we apply approaches to a variety of biological tasks, including single-cell characterization, genome-wide association studies, medical image segmentations, and quantify the performances in a number of successful metrics. The outline of this book is as follows. In Chapter 2, we introduce the statistical recovery of missing data features; in Chapter 3, we introduce the statistical recovery of missing labels; in Chapter 4, we introduce the statistical recovery of missing data sample information; finally, in Chapter 5, we summarize the full text and outlook future directions. This book can be used as references for researchers in computational biology, bioinformatics and biostatistics. Readers are expected to have basic knowledge of statistics and machine learning.

Download or read book Towards Precision Medicine for Immune Mediated Disorders Advances in Using Big Data and Artificial Intelligence to Understand Heterogeneity in Inflammatory Responses written by Xu-jie Zhou and published by Frontiers Media SA. This book was released on 2022-08-16 with total page 227 pages. Available in PDF, EPUB and Kindle. Book excerpt: Topic Editor Dr. MacLeod is employed by Janssen. All other Topic Editors declare no competing interests with regards to the Research Topic subject.

Download or read book Data Science and Machine Learning written by Dirk P. Kroese and published by CRC Press. This book was released on 2019-11-20 with total page 538 pages. Available in PDF, EPUB and Kindle. Book excerpt: Focuses on mathematical understanding Presentation is self-contained, accessible, and comprehensive Full color throughout Extensive list of exercises and worked-out examples Many concrete algorithms with actual code

Download or read book Principles of Tissue Engineering written by Robert Lanza and published by Academic Press. This book was released on 2020-03-26 with total page 1679 pages. Available in PDF, EPUB and Kindle. Book excerpt: Now in its fifth edition, Principles of Tissue Engineering has been the definite resource in the field of tissue engineering for more than a decade. The fifth edition provides an update on this rapidly progressing field, combining the prerequisites for a general understanding of tissue growth and development, the tools and theoretical information needed to design tissues and organs, as well as a presentation by the world’s experts of what is currently known about each specific organ system. As in previous editions, this book creates a comprehensive work that strikes a balance among the diversity of subjects that are related to tissue engineering, including biology, chemistry, material science, and engineering, among others, while also emphasizing those research areas that are likely to be of clinical value in the future. This edition includes greatly expanded focus on stem cells, including induced pluripotent stem (iPS) cells, stem cell niches, and blood components from stem cells. This research has already produced applications in disease modeling, toxicity testing, drug development, and clinical therapies. This up-to-date coverage of stem cell biology and the application of tissue-engineering techniques for food production – is complemented by a series of new and updated chapters on recent clinical experience in applying tissue engineering, as well as a new section on the emerging technologies in the field. Organized into twenty-three parts, covering the basics of tissue growth and development, approaches to tissue and organ design, and a summary of current knowledge by organ system Introduces a new section and chapters on emerging technologies in the field Full-color presentation throughout

Download or read book Systems Biology and Single cell Analysis of Cancer Metabolism and its Role in Cancer Emergent Properties written by Dongya Jia and published by Frontiers Media SA. This book was released on 2023-06-21 with total page 153 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Systems Biology of Cell Signaling written by Zhike Zi and published by Frontiers Media SA. This book was released on 2022-02-17 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: Topic Editor Prof. Xing is in collaboration with ATCC (https://www.atcc.org/) on testing some of their cell lines in research. All other Topic Editors declare no competing interests with regards to the Research Topic subject.

Download or read book Computational Intelligence in Oncology written by Khalid Raza and published by Springer Nature. This book was released on 2022-03-01 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book encapsulates recent applications of CI methods in the field of computational oncology, especially cancer diagnosis, prognosis, and its optimized therapeutics. The cancer has been known as a heterogeneous disease categorized in several different subtypes. According to WHO’s recent report, cancer is a leading cause of death worldwide, accounting for over 10 million deaths in the year 2020. Therefore, its early diagnosis, prognosis, and classification to a subtype have become necessary as it facilitates the subsequent clinical management and therapeutics plan. Computational intelligence (CI) methods, including artificial neural networks (ANNs), fuzzy logic, evolutionary computations, various machine learning and deep learning, and nature-inspired algorithms, have been widely utilized in various aspects of oncology research, viz. diagnosis, prognosis, therapeutics, and optimized clinical management. Appreciable progress has been made toward the understanding the hallmarks of cancer development, progression, and its effective therapeutics. However, notwithstanding the extrinsic and intrinsic factors which lead to drastic increment in incidence cases, the detection, diagnosis, prognosis, and therapeutics remain an apex challenge for the medical fraternity. With the advent in CI-based approaches, including nature-inspired techniques, and availability of clinical data from various high-throughput experiments, medical consultants, researchers, and oncologists have seen a hope to devise and employ CI in various aspects of oncology. The main aim of the book is to occupy state-of-the-art applications of CI methods which have been derived from core computer sciences to back medical oncology. This edited book covers artificial neural networks, fuzzy logic and fuzzy inference systems, evolutionary algorithms, various nature-inspired algorithms, and hybrid intelligent systems which are widely appreciated for the diagnosis, prognosis, and optimization of therapeutics of various cancers. Besides, this book also covers multi-omics exploration, gene expression analysis, gene signature identification of cancers, genomic characterization of tumors, anti-cancer drug design and discovery, drug response prediction by means of CI, and applications of IoT, IoMT, and blockchain technology in cancer research.

Download or read book Characterizing the Multi faceted Dynamics of Tumor Cell Plasticity written by Satyendra Chandra Tripathi and published by Frontiers Media SA. This book was released on 2021-03-01 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt: