150 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-training with dual uncertainty for semi-supervised medical image segmentation
In the field of semi-supervised medical image segmentation, the shortage of
labeled data is the fundamental problem. How to effectively learn image
features from unlabeled images to improve segmentation accuracy is the main
research direction in this field. Traditional self-training methods can
partially solve the problem of insufficient labeled data by generating pseudo
labels for iterative training. However, noise generated due to the model's
uncertainty during training directly affects the segmentation results.
Therefore, we added sample-level and pixel-level uncertainty to stabilize the
training process based on the self-training framework. Specifically, we saved
several moments of the model during pre-training, and used the difference
between their predictions on unlabeled samples as the sample-level uncertainty
estimate for that sample. Then, we gradually add unlabeled samples from easy to
hard during training. At the same time, we added a decoder with different
upsampling methods to the segmentation network and used the difference between
the outputs of the two decoders as pixel-level uncertainty. In short, we
selectively retrained unlabeled samples and assigned pixel-level uncertainty to
pseudo labels to optimize the self-training process. We compared the
segmentation results of our model with five semi-supervised approaches on the
public 2017 ACDC dataset and 2018 Prostate dataset. Our proposed method
achieves better segmentation performance on both datasets under the same
settings, demonstrating its effectiveness, robustness, and potential
transferability to other medical image segmentation tasks. Keywords: Medical
image segmentation, semi-supervised learning, self-training, uncertainty
estimatio
GLSFormer: Gated - Long, Short Sequence Transformer for Step Recognition in Surgical Videos
Automated surgical step recognition is an important task that can
significantly improve patient safety and decision-making during surgeries.
Existing state-of-the-art methods for surgical step recognition either rely on
separate, multi-stage modeling of spatial and temporal information or operate
on short-range temporal resolution when learned jointly. However, the benefits
of joint modeling of spatio-temporal features and long-range information are
not taken in account. In this paper, we propose a vision transformer-based
approach to jointly learn spatio-temporal features directly from sequence of
frame-level patches. Our method incorporates a gated-temporal attention
mechanism that intelligently combines short-term and long-term spatio-temporal
feature representations. We extensively evaluate our approach on two cataract
surgery video datasets, namely Cataract-101 and D99, and demonstrate superior
performance compared to various state-of-the-art methods. These results
validate the suitability of our proposed approach for automated surgical step
recognition. Our code is released at:
https://github.com/nisargshah1999/GLSFormerComment: Accepted to MICCAI 2023 (Early Accept
Knowledge-driven deep learning for fast MR imaging: undersampled MR image reconstruction from supervised to un-supervised learning
Deep learning (DL) has emerged as a leading approach in accelerating MR
imaging. It employs deep neural networks to extract knowledge from available
datasets and then applies the trained networks to reconstruct accurate images
from limited measurements. Unlike natural image restoration problems, MR
imaging involves physics-based imaging processes, unique data properties, and
diverse imaging tasks. This domain knowledge needs to be integrated with
data-driven approaches. Our review will introduce the significant challenges
faced by such knowledge-driven DL approaches in the context of fast MR imaging
along with several notable solutions, which include learning neural networks
and addressing different imaging application scenarios. The traits and trends
of these techniques have also been given which have shifted from supervised
learning to semi-supervised learning, and finally, to unsupervised learning
methods. In addition, MR vendors' choices of DL reconstruction have been
provided along with some discussions on open questions and future directions,
which are critical for the reliable imaging systems.Comment: 46 pages, 5figures, 1 tabl
A Chebyshev Confidence Guided Source-Free Domain Adaptation Framework for Medical Image Segmentation
Source-free domain adaptation (SFDA) aims to adapt models trained on a
labeled source domain to an unlabeled target domain without the access to
source data. In medical imaging scenarios, the practical significance of SFDA
methods has been emphasized due to privacy concerns. Recent State-of-the-art
SFDA methods primarily rely on self-training based on pseudo-labels (PLs).
Unfortunately, PLs suffer from accuracy deterioration caused by domain shift,
and thus limit the effectiveness of the adaptation process. To address this
issue, we propose a Chebyshev confidence guided SFDA framework to accurately
assess the reliability of PLs and generate self-improving PLs for
self-training. The Chebyshev confidence is estimated by calculating probability
lower bound of the PL confidence, given the prediction and the corresponding
uncertainty. Leveraging the Chebyshev confidence, we introduce two
confidence-guided denoising methods: direct denoising and prototypical
denoising. Additionally, we propose a novel teacher-student joint training
scheme (TJTS) that incorporates a confidence weighting module to improve PLs
iteratively. The TJTS, in collaboration with the denoising methods, effectively
prevents the propagation of noise and enhances the accuracy of PLs. Extensive
experiments in diverse domain scenarios validate the effectiveness of our
proposed framework and establish its superiority over state-of-the-art SFDA
methods. Our paper contributes to the field of SFDA by providing a novel
approach for precisely estimating the reliability of pseudo-labels and a
framework for obtaining high-quality PLs, resulting in improved adaptation
performance
Dynamic Data Augmentation via MCTS for Prostate MRI Segmentation
Medical image data are often limited due to the expensive acquisition and
annotation process. Hence, training a deep-learning model with only raw data
can easily lead to overfitting. One solution to this problem is to augment the
raw data with various transformations, improving the model's ability to
generalize to new data. However, manually configuring a generic augmentation
combination and parameters for different datasets is non-trivial due to
inconsistent acquisition approaches and data distributions. Therefore,
automatic data augmentation is proposed to learn favorable augmentation
strategies for different datasets while incurring large GPU overhead. To this
end, we present a novel method, called Dynamic Data Augmentation (DDAug), which
is efficient and has negligible computation cost. Our DDAug develops a
hierarchical tree structure to represent various augmentations and utilizes an
efficient Monte-Carlo tree searching algorithm to update, prune, and sample the
tree. As a result, the augmentation pipeline can be optimized for each dataset
automatically. Experiments on multiple Prostate MRI datasets show that our
method outperforms the current state-of-the-art data augmentation strategies
Dual-Decoder Consistency via Pseudo-Labels Guided Data Augmentation for Semi-Supervised Medical Image Segmentation
Medical image segmentation methods often rely on fully supervised approaches
to achieve excellent performance, which is contingent upon having an extensive
set of labeled images for training. However, annotating medical images is both
expensive and time-consuming. Semi-supervised learning offers a solution by
leveraging numerous unlabeled images alongside a limited set of annotated ones.
In this paper, we introduce a semi-supervised medical image segmentation method
based on the mean-teacher model, referred to as Dual-Decoder Consistency via
Pseudo-Labels Guided Data Augmentation (DCPA). This method combines consistency
regularization, pseudo-labels, and data augmentation to enhance the efficacy of
semi-supervised segmentation. Firstly, the proposed model comprises both
student and teacher models with a shared encoder and two distinct decoders
employing different up-sampling strategies. Minimizing the output discrepancy
between decoders enforces the generation of consistent representations, serving
as regularization during student model training. Secondly, we introduce mixup
operations to blend unlabeled data with labeled data, creating mixed data and
thereby achieving data augmentation. Lastly, pseudo-labels are generated by the
teacher model and utilized as labels for mixed data to compute unsupervised
loss. We compare the segmentation results of the DCPA model with six
state-of-the-art semi-supervised methods on three publicly available medical
datasets. Beyond classical 10\% and 20\% semi-supervised settings, we
investigate performance with less supervision (5\% labeled data). Experimental
outcomes demonstrate that our approach consistently outperforms existing
semi-supervised medical image segmentation methods across the three
semi-supervised settings
Probabilistic 3D surface reconstruction from sparse MRI information
Surface reconstruction from magnetic resonance (MR) imaging data is
indispensable in medical image analysis and clinical research. A reliable and
effective reconstruction tool should: be fast in prediction of accurate well
localised and high resolution models, evaluate prediction uncertainty, work
with as little input data as possible. Current deep learning state of the art
(SOTA) 3D reconstruction methods, however, often only produce shapes of limited
variability positioned in a canonical position or lack uncertainty evaluation.
In this paper, we present a novel probabilistic deep learning approach for
concurrent 3D surface reconstruction from sparse 2D MR image data and aleatoric
uncertainty prediction. Our method is capable of reconstructing large surface
meshes from three quasi-orthogonal MR imaging slices from limited training sets
whilst modelling the location of each mesh vertex through a Gaussian
distribution. Prior shape information is encoded using a built-in linear
principal component analysis (PCA) model. Extensive experiments on cardiac MR
data show that our probabilistic approach successfully assesses prediction
uncertainty while at the same time qualitatively and quantitatively outperforms
SOTA methods in shape prediction. Compared to SOTA, we are capable of properly
localising and orientating the prediction via the use of a spatially aware
neural network.Comment: MICCAI 202
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