Deep Learning Methods For Fibrotic Tissue Microenvironment Analysis

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Deep Learning Methods For Fibrotic Tissue Microenvironment Analysis

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Author : Bin Li
language : en
Publisher:
Release Date : 2023

Deep Learning Methods For Fibrotic Tissue Microenvironment Analysis written by Bin Li and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023 with categories.

Whole slide imaging and multimodal optical microscopy methods developed in the last several decades are currently transforming the conventional practices of histopathology. These imaging methods including associated computational tools are introducing quantitative and comprehensive views of tissue microenvironment to pathologists and researchers for a better understanding of disease development and biological processes. Many of these computational analysis pipelines are powered by machine learning and artificial intelligence (AI), where models are trained on example data and perform predictions on new samples. The performance of computational workflows is further increased attributed to the recent advances of deep learning and the ability to train large deep neural networks (DNNs) on graphics processing units (GPUs).Meanwhile, the development of modern quantitative optical microscopy has greatly increased the contrasts available for characterizing tissue microenvironment for histopathological assessment. The rapid progress of digital histopathology also gave rise to many challenges and opportunities that appeal to more robust and efficient computational workflows, such as whole slide screening, tumor detection, and survival analysis. On the other hand, the clinical use of multimodal microscopy in histopathology still remains limited due to the high cost and complexity of these optical imaging modalities. In this thesis, we present the designs of deep learning-based methods targeting two topics in digital histopathology, namely histological image classification and image generation in tissue microscopy. The first topic involves building classification workflows following the idea of weakly supervised learning, where models are trained with slide-level labels or coarsely annotated region-level labels. The workflows can be further improved regarding computation efficiency and image feature quality, utilizing compression domain processing and graph neural networks, respectively. The second topic focuses on pixel-wise prediction problems where synthetic images are generated by DNNs. We developed such a model capable of synthesizing SHG images from standard clinical modality such that collagen topography can be directly visualized without operating costly and complex SHG imaging instruments. A similar idea can be applied to improve the resolution of WSIs collected using low-cost devices with less expensive optics and lower storage costs. We also show that deep generative models can be used to generate synthetic image data for training a collagen fiber centerline extraction network. The network produces high-quality fiber centerline extraction results for analyzing collagen fiber alignment, length, and density that are previously shown to correlate with disease diagnosis and prognosis. Lastly, we present an open-source automatic multimodal whole slide histopathology imaging system empowered by an open hardware controlling platform and run-time image processing functionality, where deep learning-based selective acquisition and image restoration can be integrated into the acquisition workflow.

Unveiling The Tumor Microenvironment By Machine Learning To Develop New Immunotherapeutic Strategies Volume I B

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Author : Nan Zhang
language : en
Publisher: Frontiers Media SA
Release Date : 2023-10-24

Unveiling The Tumor Microenvironment By Machine Learning To Develop New Immunotherapeutic Strategies Volume I B written by Nan Zhang and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-10-24 with Medical categories.

The tumor microenvironment (TME) plays a critical role in tumor proliferation, progression, and therapeutic responses. TME is a complex network of cancer cells, stromal cells, and, most importantly, infiltrating immune cells. Cancer cells regulate numerous biological functions through direct or indirect interaction with TME components. Emerging evidence suggests that TME crucially influences the response to both chemotherapy and immunotherapy. As scientific research has entered the big data era with the fast development of high-throughput sequencing technologies, machine learning has been gradually widely applied to extract important knowledge from big data bioinformatics. Thus, characterizing the TME landscape in cancer and identifying different immune-related TME phenotypes using machine learning-based bioinformatics analyses, in vitro experiments, and in vivo experiments are of great interest and significance.

Artificial Intelligence In Predicting Determining And Controlling Cell Phenotype Or Tissue Function In Inflammatory Diseases

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Author : Melanie L. Hart
language : en
Publisher: Frontiers Media SA
Release Date : 2024-05-10

Artificial Intelligence In Predicting Determining And Controlling Cell Phenotype Or Tissue Function In Inflammatory Diseases written by Melanie L. Hart and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-05-10 with Medical categories.

The last decade has seen rapid development in the use of computational techniques at bulk tissue and single-cell level. However, our knowledge remains limited in this regard, and further progress is needed, especially in inflammatory and degenerative diseases. Controlling, modeling, or predicting cellular phenotype in this context using artificial intelligence (AI) will greatly improve the available in vitro, in situ, in vivo, and in silico methods, but also aid in the understanding of disease pathology and therapeutic efficiency. These methods not only have ramifications for our pathophysiological understanding of tissue function but are also important for advancing AI methods in cell culture, tissue explants, or in vivo for immunologically relevant characteristics of single cells, cell populations, and tissues to predict cell or tissue function.

Innovative In Vitro Models For Pulmonary Physiology And Drug Delivery In Health And Disease

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Author : Josue Sznitman
language : en
Publisher: Frontiers Media SA
Release Date : 2021-12-28

Innovative In Vitro Models For Pulmonary Physiology And Drug Delivery In Health And Disease written by Josue Sznitman and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-12-28 with Medical categories.

Advanced Interpretable Machine Learning Methods For Clinical Ngs Big Data Of Complex Hereditary Diseases Volume Ii

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Author : Yudong Cai
language : en
Publisher: Frontiers Media SA
Release Date : 2023-02-13

Advanced Interpretable Machine Learning Methods For Clinical Ngs Big Data Of Complex Hereditary Diseases Volume Ii written by Yudong Cai and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-02-13 with Science categories.

Fibrosis And Inflammation In Tissue Pathophysiology

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Author : Elvira Forte
language : en
Publisher: Frontiers Media SA
Release Date : 2022-02-23

Fibrosis And Inflammation In Tissue Pathophysiology written by Elvira Forte and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-02-23 with Science categories.

Macsween S Pathology Of The Liver E Book

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Author : Alastair D. Burt
language : en
Publisher: Elsevier Health Sciences
Release Date : 2022-11-14

Macsween S Pathology Of The Liver E Book written by Alastair D. Burt and has been published by Elsevier Health Sciences this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-11-14 with Medical categories.

Written and edited by an international team of renowned authorities, MacSween's Pathology of the Liver, 8th Edition, remains the field’s definitive reference on liver pathology. This must-have text is ideal for surgical pathologists in practice and in training who examine liver specimens on a day-to-day basis. It provides invaluable assistance in recognizing the huge variety of appearances of the liver that result from infections, tumors, and tumor-like lesions, as well as organ damage caused by drugs and toxins. With expert, comprehensive coverage of all malignant and benign hepatobiliary disorders, MacSween’s is a convenient, one-stop resource for use in the reporting room as well as in personal study. Shares the knowledge and experience of a “who’s who list of experts in the field of hepatobiliary pathology, led by editors Alastair D. Burt, Linda D. Ferrell, and Stefan G. Hübscher. Features more than 1,000 high-quality, full color illustrations, providing a complete visual guide to each tumor or tumor-like lesion. Discusses advances in molecular diagnostic testing, its capabilities, and its limitations, including targeted/personalized medicine. Incorporates the latest TNM staging and WHO classification systems, as well as new diagnostic biomarkers and their utility in differential diagnosis, newly described variants, and new histologic entities. Includes relevant data from ancillary techniques (immunohistochemistry, cytogenetics, and molecular genetics), giving you the necessary tools required to master the latest breakthroughs in diagnostic technology. Provides you with all of the necessary diagnostic tools to make a complete and accurate pathologic report, including clinicopathologic background throughout. Directs you to the most recent and authoritative sources for further reading with a comprehensive reference list that highlights key articles and up-to-date citations.

Biocomputing 2024 Proceedings Of The Pacific Symposium

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Author : Russ B Altman
language : en
Publisher: World Scientific
Release Date : 2023-12-18

Biocomputing 2024 Proceedings Of The Pacific Symposium written by Russ B Altman and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-12-18 with Science categories.

The Pacific Symposium on Biocomputing (PSB) 2024 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2024 will be held on January 3 - 7, 2024 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2024 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's 'hot topics.' In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.

Intravoxel Incoherent Motion Ivim Mri

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Author : Denis Le Bihan
language : en
Publisher: CRC Press
Release Date : 2018-11-05

Intravoxel Incoherent Motion Ivim Mri written by Denis Le Bihan and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-11-05 with Medical categories.

First book ever on the topic Discusses current concepts and methodological issues for the successful implementation of IVIM MRI to investigate tissue perfusion non-invasively Covers a wide range of clinical applications Contributions by leading experts in the field from USA, Europe, and Asia and written with a good balance of methodological and clinical chapters Includes an extensive bibliography for further reading

Machine Learning Based Methods For Rna Data Analysis

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Author : Lihong Peng
language : en
Publisher: Frontiers Media SA
Release Date : 2022-06-16

Machine Learning Based Methods For Rna Data Analysis written by Lihong Peng and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-06-16 with Science categories.