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      Artificial intelligence and computational pathology

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          Abstract

          Data processing and learning has become a spearhead for the advancement of medicine, with pathology and laboratory medicine has no exception. The incorporation of scientific research through clinical informatics, including genomics, proteomics, bioinformatics, and biostatistics, into clinical practice unlocks innovative approaches for patient care. Computational pathology is burgeoning subspecialty in pathology that promises a better-integrated solution to whole-slide images, multi-omics data, and clinical informatics. However, computational pathology faces several challenges, including the ability to integrate raw data from different sources, limitation of hardware processing capacity, and a lack of specific training programs, as well as issues on ethics and larger societal acceptable practices that are still solidifying. The establishment of the entire industry of computational pathology requires far-reaching changes of the three essential elements connecting patients and doctors: the local laboratory, the scan center, and the central cloud hub/portal for data processing and retrieval. Computational pathology, unlocked through information integration and advanced digital communication networks, has the potential to improve clinical workflow efficiency, diagnostic quality, and ultimately create personalized diagnosis and treatment plans for patients. This review describes clinical perspectives and discusses the statistical methods, clinical applications, potential obstacles, and future directions of computational pathology.

          Abstract

          Data processing and learning has become a spearhead for the advancement of medicine. Computational pathology is burgeoning subspecialty that promises a better-integrated solution to whole-slide images, multi-omics data and clinical informatics as innovative approach for patient care. This review describes clinical perspectives and discusses the statistical methods, clinical applications, potential obstacles, and future directions of computational pathology.

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          Most cited references60

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          Clinical-grade computational pathology using weakly supervised deep learning on whole slide images

          The development of decision support systems for pathology and their deployment in clinical practice have been hindered by the need for large manually annotated datasets. To overcome this problem, we present a multiple instance learning-based deep learning system that uses only the reported diagnoses as labels for training, thereby avoiding expensive and time-consuming pixel-wise manual annotations. We evaluated this framework at scale on a dataset of 44,732 whole slide images from 15,187 patients without any form of data curation. Tests on prostate cancer, basal cell carcinoma and breast cancer metastases to axillary lymph nodes resulted in areas under the curve above 0.98 for all cancer types. Its clinical application would allow pathologists to exclude 65–75% of slides while retaining 100% sensitivity. Our results show that this system has the ability to train accurate classification models at unprecedented scale, laying the foundation for the deployment of computational decision support systems in clinical practice.
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            Artificial intelligence in digital pathology — new tools for diagnosis and precision oncology

            In the past decade, advances in precision oncology have resulted in an increased demand for predictive assays that enable the selection and stratification of patients for treatment. The enormous divergence of signalling and transcriptional networks mediating the crosstalk between cancer, stromal and immune cells complicates the development of functionally relevant biomarkers based on a single gene or protein. However, the result of these complex processes can be uniquely captured in the morphometric features of stained tissue specimens. The possibility of digitizing whole-slide images of tissue has led to the advent of artificial intelligence (AI) and machine learning tools in digital pathology, which enable mining of subvisual morphometric phenotypes and might, ultimately, improve patient management. In this Perspective, we critically evaluate various Al-based computational approaches for digital pathology, focusing on deep neural networks and ‘hand-crafted’ feature-based methodologies. We aim to provide a broad framework for incorporating AI and machine learning tools into clinical oncology, with an emphasis on biomarker development. We discuss some of the challenges relating to the use of AI, including the need for well-curated validation datasets, regulatory approval and fair reimbursement strategies. Finally, we present potential future opportunities for precision oncology.
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              Is Open Access

              Opportunities and obstacles for deep learning in biology and medicine

              Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems—patient classification, fundamental biological processes and treatment of patients—and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.
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                Author and article information

                Contributors
                dyzhang01@gmail.com
                Journal
                Lab Invest
                Lab Invest
                Laboratory Investigation; a Journal of Technical Methods and Pathology
                Nature Publishing Group US (New York )
                0023-6837
                1530-0307
                16 January 2021
                : 1-11
                Affiliations
                [1 ]GRID grid.59734.3c, ISNI 0000 0001 0670 2351, St. Luke’s Roosevelt Hospital Center, Icahn School of Medicine at Mount Sinai, ; New York, NY 10025 USA
                [2 ]GRID grid.274295.f, ISNI 0000 0004 0420 1184, Pathology and Laboratory Services, VA Medical Center, ; New York, NY 10010 USA
                Author information
                http://orcid.org/0000-0002-3402-8664
                Article
                514
                10.1038/s41374-020-00514-0
                7811340
                33454724
                98087e6a-7d27-4fb7-9f5d-dfe6cd4a3794
                © The Author(s), under exclusive licence to United States and Canadian Academy of Pathology 2021

                This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

                History
                : 8 June 2020
                : 8 November 2020
                : 10 November 2020
                Categories
                Review Article

                Pathology
                preventive medicine,bioinformatics
                Pathology
                preventive medicine, bioinformatics

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