| Literature DB >> 31355445 |
Esther Abels1, Liron Pantanowitz2, Famke Aeffner3, Mark D Zarella4, Jeroen van der Laak5,6, Marilyn M Bui7, Venkata Np Vemuri8, Anil V Parwani9, Jeff Gibbs10, Emmanuel Agosto-Arroyo7, Andrew H Beck11, Cleopatra Kozlowski12.
Abstract
In this white paper, experts from the Digital Pathology Association (DPA) define terminology and concepts in the emerging field of computational pathology, with a focus on its application to histology images analyzed together with their associated patient data to extract information. This review offers a historical perspective and describes the potential clinical benefits from research and applications in this field, as well as significant obstacles to adoption. Best practices for implementing computational pathology workflows are presented. These include infrastructure considerations, acquisition of training data, quality assessments, as well as regulatory, ethical, and cyber-security concerns. Recommendations are provided for regulators, vendors, and computational pathology practitioners in order to facilitate progress in the field.Entities:
Keywords: artificial intelligence; computational pathology; convolutional neural networks; deep learning; digital pathology; image analysis; machine learning
Mesh:
Year: 2019 PMID: 31355445 PMCID: PMC6852275 DOI: 10.1002/path.5331
Source DB: PubMed Journal: J Pathol ISSN: 0022-3417 Impact factor: 7.996
Definitions of CPATH terms
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| Indication of the position and/or outline of structures or objects within digital images, usually produced by humans using a computer mouse or drawing tablet. Annotations may have associated labels and possible other meta‐data. Annotations can be manually generated or can be established by algorithm tools |
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| A branch of computer science dealing with the simulation of intelligent behavior in computers |
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| A neural network can be perceived as a black box that lacks a clear depiction of the image features used for a decision. However, methods can be employed to transform it into a glass box in an effort to understand the relationship between the input parameters and the output of the network |
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| The practice of using a network of remote servers hosted on the internet to store, manage, and process data, rather than a local server or a personal computer |
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| A branch of pathology that involves computational analysis of a broad array of methods to analyze patient specimens for the study of disease. In this paper, we focus on the extraction of information from digitized pathology images in combination with their associated meta‐data, typically using AI methods such as deep learning |
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| A type of deep neural network particularly designed for images. It uses a kernel or filter to convolve an image, which results in features useful for differentiating images |
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| Method commonly used in deep learning to increase the training data using operations such as rotating, cropping, zooming, and image histogram‐based modifications. This provides a number of advantages such as promoting positional and rotational invariance, robustness to staining variability, and improves the generalizability of the classifier |
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| The subset of machine learning composed of algorithms that permit software to train itself to perform tasks by exposing multilayered artificial neural networks to vast amounts of data. Data are fed into the input layers and are sequentially processed in a hierarchical manner with increasing complexity at each layer, modeled loosely after the hierarchical organization in the brain. Optimization functions are iteratively trained to shape the processing functions of the layers and the connections between them |
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| A blanket term that encompasses tools and systems to digitize pathology slides and associated meta‐data, their storage, review, analysis, and enabling infrastructure |
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| The practical standard that is used to capture the ‘ground truth’. The gold standard may not always be perfectly correct, but in general is viewed as the best approximation |
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| A category, quantity, or label assigned to a dataset that provides guidance to an algorithm during training. Depending on the task, the ground truth can be a patient‐ or slide‐level characterization or can be applied to objects or regions within the image. The ground truth is an abstract concept of the ‘truth’ |
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| A method to extract typically quantifiable information from images. In this paper, we only discuss image analysis as applied to images of histology slides, but the term itself is broader, and applies to the extraction of information from any image, biomedical or not |
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| A branch of AI in which computer software learns to perform a task by being exposed to representative data |
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| In the context of digital pathology, the term meta‐data describes descriptive data associated with the individual, sample, or slide. They may include image acquisition information, patient demographic data, pathologist annotation or classification, or outcome data from treatment. Typically, meta‐data are entries that allow searches in databases, for example. Highly complex, large, multiple‐time‐point associated data, such as longitudinal image data (such as radiology) or genomic data, are not usually called ‘meta‐data’ |
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| Supervised learning is used to train a model to predict an outcome or to classify a dataset based on a label associated with a data point (i.e. ground truth). An example of supervised machine learning includes the design of classifiers to distinguish benign from malignant regions based on manual annotations |
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| Unsupervised learning seeks to identify natural divisions in a dataset without the need for a ground truth, often using methods such as cluster analysis or pattern matching. Examples of unsupervised machine learning include the identification of images with similar attributes or the clustering of tumors into subtypes |
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| Digital representation of an entire histopathological glass slide, digitized at microscope resolution. These whole slide scans are typically produced using slide scanners. Slide scan viewing software enables inspection of the image in a way that mimics the use of a traditional microscope; the image can be viewed at different magnifications |