128 research outputs found
Deep learning for unsupervised domain adaptation in medical imaging: Recent advancements and future perspectives
Deep learning has demonstrated remarkable performance across various tasks in
medical imaging. However, these approaches primarily focus on supervised
learning, assuming that the training and testing data are drawn from the same
distribution. Unfortunately, this assumption may not always hold true in
practice. To address these issues, unsupervised domain adaptation (UDA)
techniques have been developed to transfer knowledge from a labeled domain to a
related but unlabeled domain. In recent years, significant advancements have
been made in UDA, resulting in a wide range of methodologies, including feature
alignment, image translation, self-supervision, and disentangled representation
methods, among others. In this paper, we provide a comprehensive literature
review of recent deep UDA approaches in medical imaging from a technical
perspective. Specifically, we categorize current UDA research in medical
imaging into six groups and further divide them into finer subcategories based
on the different tasks they perform. We also discuss the respective datasets
used in the studies to assess the divergence between the different domains.
Finally, we discuss emerging areas and provide insights and discussions on
future research directions to conclude this survey.Comment: Under Revie
Data efficient deep learning for medical image analysis: A survey
The rapid evolution of deep learning has significantly advanced the field of
medical image analysis. However, despite these achievements, the further
enhancement of deep learning models for medical image analysis faces a
significant challenge due to the scarcity of large, well-annotated datasets. To
address this issue, recent years have witnessed a growing emphasis on the
development of data-efficient deep learning methods. This paper conducts a
thorough review of data-efficient deep learning methods for medical image
analysis. To this end, we categorize these methods based on the level of
supervision they rely on, encompassing categories such as no supervision,
inexact supervision, incomplete supervision, inaccurate supervision, and only
limited supervision. We further divide these categories into finer
subcategories. For example, we categorize inexact supervision into multiple
instance learning and learning with weak annotations. Similarly, we categorize
incomplete supervision into semi-supervised learning, active learning, and
domain-adaptive learning and so on. Furthermore, we systematically summarize
commonly used datasets for data efficient deep learning in medical image
analysis and investigate future research directions to conclude this survey.Comment: Under Revie
Self-Path: self-supervision for classification of pathology images with limited annotations
While high-resolution pathology images lend themselves well to ‘data hungry’ deep learning algorithms, obtaining exhaustive annotations on these images for learning is a major challenge. In this paper, we propose a self-supervised convolutional neural network (CNN) frame-work to leverage unlabeled data for learning generalizable and domain invariant representations in pathology images. Our proposed framework, termed as Self-Path, employs multi-task learning where the main task is tissue classification and pretext tasks are a variety of self-supervised tasks with labels inherent to the input images.We introduce novel pathology-specific self-supervision tasks that leverage contextual, multi-resolution and semantic features in pathology images for semi-supervised learning and domain adaptation. We investigate the effectiveness of Self-Path on 3 different pathology datasets. Our results show that Self-Path with the pathology-specific pretext tasks achieves state-of-the-art performance for semi-supervised learning when small amounts of labeled data are available. Further, we show that Self-Path improves domain adaptation for histopathology image classification when there is no labeled data available for the target domain. This approach can potentially be employed for other applications in computational pathology, where annotation budget is often limited or large amount of unlabeled image data is available
Learning with Limited Annotations: A Survey on Deep Semi-Supervised Learning for Medical Image Segmentation
Medical image segmentation is a fundamental and critical step in many
image-guided clinical approaches. Recent success of deep learning-based
segmentation methods usually relies on a large amount of labeled data, which is
particularly difficult and costly to obtain especially in the medical imaging
domain where only experts can provide reliable and accurate annotations.
Semi-supervised learning has emerged as an appealing strategy and been widely
applied to medical image segmentation tasks to train deep models with limited
annotations. In this paper, we present a comprehensive review of recently
proposed semi-supervised learning methods for medical image segmentation and
summarized both the technical novelties and empirical results. Furthermore, we
analyze and discuss the limitations and several unsolved problems of existing
approaches. We hope this review could inspire the research community to explore
solutions for this challenge and further promote the developments in medical
image segmentation field
A deep learning approach for complex microstructure inference
Automated, reliable, and objective microstructure inference from micrographs is essential for a comprehensive understanding of process-microstructure-property relations and tailored materials development. However, such inference, with the increasing complexity of microstructures, requires advanced segmentation methodologies. While deep learning offers new opportunities, an intuition about the required data quality/quantity and a methodological guideline for microstructure quantification is still missing. This, along with deep learning’s seemingly intransparent decision-making process, hampers its breakthrough in this field. We apply a multidisciplinary deep learning approach, devoting equal attention to specimen preparation and imaging, and train distinct U-Net architectures with 30–50 micrographs of different imaging modalities and electron backscatter diffraction-informed annotations. On the challenging task of lath-bainite segmentation in complex-phase steel, we achieve accuracies of 90% rivaling expert segmentations. Further, we discuss the impact of image context, pre-training with domain-extrinsic data, and data augmentation. Network visualization techniques demonstrate plausible model decisions based on grain boundary morphology
Deep Networks for Image-based Cell Counting
Cell counting from 2D images and 3D volumes is critical to a wide range of research in biology, medicine, and bioinformatics, among other fields. Current approaches to cell counting have two major limitations: 1) lack of a universal model to handle different cell types, especially in 3D, and 2) reliance on costly labeled data. This dissertation addresses these two issues. First, we present a unified framework for various cell types in both 2D and 3D by leveraging recent advances in deep learning. Specifically, we develop SAU-Net by expanding the segmentation network U-Net with a self-attention module and an extension of Batch Normalization (BN) to simplify the training process for small datasets. In addition, the proposed BN extension is empirically validated on multiple image classification benchmarks, highlighting its versatile nature. SAU-Net uses dot annotations with inverse distance kernel instead of full (whole-cell) annotations as in conventional methods, dramatically reducing the labeling time while maintaining performance. Second, we take advantage of unlabeled data by self-supervised learning with a novel focal consistency loss, designed for our pixel-wise task. This learning paradigm allows a further significant reduction of reliance on labeled data with state-of-the-art results. These two contributions complement each other. Finally, we introduce a labeling tool for dot annotations to expedite the labeling process and a 3D cell counting benchmark with dot annotations to spur further research in this direction.Doctor of Philosoph
Deep Learning in Breast Cancer Imaging: A Decade of Progress and Future Directions
Breast cancer has reached the highest incidence rate worldwide among all
malignancies since 2020. Breast imaging plays a significant role in early
diagnosis and intervention to improve the outcome of breast cancer patients. In
the past decade, deep learning has shown remarkable progress in breast cancer
imaging analysis, holding great promise in interpreting the rich information
and complex context of breast imaging modalities. Considering the rapid
improvement in the deep learning technology and the increasing severity of
breast cancer, it is critical to summarize past progress and identify future
challenges to be addressed. In this paper, we provide an extensive survey of
deep learning-based breast cancer imaging research, covering studies on
mammogram, ultrasound, magnetic resonance imaging, and digital pathology images
over the past decade. The major deep learning methods, publicly available
datasets, and applications on imaging-based screening, diagnosis, treatment
response prediction, and prognosis are described in detail. Drawn from the
findings of this survey, we present a comprehensive discussion of the
challenges and potential avenues for future research in deep learning-based
breast cancer imaging.Comment: Survey, 41 page
- …