70 research outputs found
A Survey on Deep Learning in Medical Image Analysis
Deep learning algorithms, in particular convolutional networks, have rapidly
become a methodology of choice for analyzing medical images. This paper reviews
the major deep learning concepts pertinent to medical image analysis and
summarizes over 300 contributions to the field, most of which appeared in the
last year. We survey the use of deep learning for image classification, object
detection, segmentation, registration, and other tasks and provide concise
overviews of studies per application area. Open challenges and directions for
future research are discussed.Comment: Revised survey includes expanded discussion section and reworked
introductory section on common deep architectures. Added missed papers from
before Feb 1st 201
Recurrent Saliency Transformation Network: Incorporating Multi-Stage Visual Cues for Small Organ Segmentation
We aim at segmenting small organs (e.g., the pancreas) from abdominal CT
scans. As the target often occupies a relatively small region in the input
image, deep neural networks can be easily confused by the complex and variable
background. To alleviate this, researchers proposed a coarse-to-fine approach,
which used prediction from the first (coarse) stage to indicate a smaller input
region for the second (fine) stage. Despite its effectiveness, this algorithm
dealt with two stages individually, which lacked optimizing a global energy
function, and limited its ability to incorporate multi-stage visual cues.
Missing contextual information led to unsatisfying convergence in iterations,
and that the fine stage sometimes produced even lower segmentation accuracy
than the coarse stage.
This paper presents a Recurrent Saliency Transformation Network. The key
innovation is a saliency transformation module, which repeatedly converts the
segmentation probability map from the previous iteration as spatial weights and
applies these weights to the current iteration. This brings us two-fold
benefits. In training, it allows joint optimization over the deep networks
dealing with different input scales. In testing, it propagates multi-stage
visual information throughout iterations to improve segmentation accuracy.
Experiments in the NIH pancreas segmentation dataset demonstrate the
state-of-the-art accuracy, which outperforms the previous best by an average of
over 2%. Much higher accuracies are also reported on several small organs in a
larger dataset collected by ourselves. In addition, our approach enjoys better
convergence properties, making it more efficient and reliable in practice.Comment: Accepted to CVPR 2018 (10 pages, 6 figures
Automated skin lesion segmentation using multi-scale feature extraction scheme and dual-attention mechanism
Segmenting skin lesions from dermoscopic images is essential for diagnosing
skin cancer. But the automatic segmentation of these lesions is complicated due
to the poor contrast between the background and the lesion, image artifacts,
and unclear lesion boundaries. In this work, we present a deep learning model
for the segmentation of skin lesions from dermoscopic images. To deal with the
challenges of skin lesion characteristics, we designed a multi-scale feature
extraction module for extracting the discriminative features. Further in this
work, two attention mechanisms are developed to refine the post-upsampled
features and the features extracted by the encoder. This model is evaluated
using the ISIC2018 and ISBI2017 datasets. The proposed model outperformed all
the existing works and the top-ranked models in two competitions
The impact of pre- and post-image processing techniques on deep learning frameworks: A comprehensive review for digital pathology image analysis
Recently, deep learning frameworks have rapidly become the main methodology for analyzing medical images. Due to their powerful learning ability and advantages in dealing with complex patterns, deep learning algorithms are ideal for image analysis challenges, particularly in the field of digital pathology. The variety of image analysis tasks in the context of deep learning includes classification (e.g., healthy vs. cancerous tissue), detection (e.g., lymphocytes and mitosis counting), and segmentation (e.g., nuclei and glands segmentation). The majority of recent machine learning methods in digital pathology have a pre- and/or post-processing stage which is integrated with a deep neural network. These stages, based on traditional image processing methods, are employed to make the subsequent classification, detection, or segmentation problem easier to solve. Several studies have shown how the integration of pre- and post-processing methods within a deep learning pipeline can further increase the model's performance when compared to the network by itself. The aim of this review is to provide an overview on the types of methods that are used within deep learning frameworks either to optimally prepare the input (pre-processing) or to improve the results of the network output (post-processing), focusing on digital pathology image analysis. Many of the techniques presented here, especially the post-processing methods, are not limited to digital pathology but can be extended to almost any image analysis field
The impact of pre- and post-image processing techniques on deep learning frameworks: A comprehensive review for digital pathology image analysis.
Recently, deep learning frameworks have rapidly become the main methodology for analyzing medical images. Due to their powerful learning ability and advantages in dealing with complex patterns, deep learning algorithms are ideal for image analysis challenges, particularly in the field of digital pathology. The variety of image analysis tasks in the context of deep learning includes classification (e.g., healthy vs. cancerous tissue), detection (e.g., lymphocytes and mitosis counting), and segmentation (e.g., nuclei and glands segmentation). The majority of recent machine learning methods in digital pathology have a pre- and/or post-processing stage which is integrated with a deep neural network. These stages, based on traditional image processing methods, are employed to make the subsequent classification, detection, or segmentation problem easier to solve. Several studies have shown how the integration of pre- and post-processing methods within a deep learning pipeline can further increase the model's performance when compared to the network by itself. The aim of this review is to provide an overview on the types of methods that are used within deep learning frameworks either to optimally prepare the input (pre-processing) or to improve the results of the network output (post-processing), focusing on digital pathology image analysis. Many of the techniques presented here, especially the post-processing methods, are not limited to digital pathology but can be extended to almost any image analysis field
Attention-based Neural Cellular Automata
Recent extensions of Cellular Automata (CA) have incorporated key ideas from
modern deep learning, dramatically extending their capabilities and catalyzing
a new family of Neural Cellular Automata (NCA) techniques. Inspired by
Transformer-based architectures, our work presents a new class of
NCAs formed using a spatially
localized\unicode{x2014}yet globally organized\unicode{x2014}self-attention
scheme. We introduce an instance of this class named (ViTCA). We present quantitative and
qualitative results on denoising autoencoding across six benchmark datasets,
comparing ViTCA to a U-Net, a U-Net-based CA baseline (UNetCA), and a Vision
Transformer (ViT). When comparing across architectures configured to similar
parameter complexity, ViTCA architectures yield superior performance across all
benchmarks and for nearly every evaluation metric. We present an ablation study
on various architectural configurations of ViTCA, an analysis of its effect on
cell states, and an investigation on its inductive biases. Finally, we examine
its learned representations via linear probes on its converged cell state
hidden representations, yielding, on average, superior results when compared to
our U-Net, ViT, and UNetCA baselines.Comment: NeurIPS 202
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