383 research outputs found
Suggestive Annotation: A Deep Active Learning Framework for Biomedical Image Segmentation
Image segmentation is a fundamental problem in biomedical image analysis.
Recent advances in deep learning have achieved promising results on many
biomedical image segmentation benchmarks. However, due to large variations in
biomedical images (different modalities, image settings, objects, noise, etc),
to utilize deep learning on a new application, it usually needs a new set of
training data. This can incur a great deal of annotation effort and cost,
because only biomedical experts can annotate effectively, and often there are
too many instances in images (e.g., cells) to annotate. In this paper, we aim
to address the following question: With limited effort (e.g., time) for
annotation, what instances should be annotated in order to attain the best
performance? We present a deep active learning framework that combines fully
convolutional network (FCN) and active learning to significantly reduce
annotation effort by making judicious suggestions on the most effective
annotation areas. We utilize uncertainty and similarity information provided by
FCN and formulate a generalized version of the maximum set cover problem to
determine the most representative and uncertain areas for annotation. Extensive
experiments using the 2015 MICCAI Gland Challenge dataset and a lymph node
ultrasound image segmentation dataset show that, using annotation suggestions
by our method, state-of-the-art segmentation performance can be achieved by
using only 50% of training data.Comment: Accepted at MICCAI 201
Semi-Supervised Deep Learning for Fully Convolutional Networks
Deep learning usually requires large amounts of labeled training data, but
annotating data is costly and tedious. The framework of semi-supervised
learning provides the means to use both labeled data and arbitrary amounts of
unlabeled data for training. Recently, semi-supervised deep learning has been
intensively studied for standard CNN architectures. However, Fully
Convolutional Networks (FCNs) set the state-of-the-art for many image
segmentation tasks. To the best of our knowledge, there is no existing
semi-supervised learning method for such FCNs yet. We lift the concept of
auxiliary manifold embedding for semi-supervised learning to FCNs with the help
of Random Feature Embedding. In our experiments on the challenging task of MS
Lesion Segmentation, we leverage the proposed framework for the purpose of
domain adaptation and report substantial improvements over the baseline model.Comment: 9 pages, 6 figure
Intelligent Data Networking for the Earth System Science Community
Earth system science (ESS) research is generally very data intense. To enable detailed discovery and transparent access of the data stored in heterogeneous and organisationally separated data centres common data and metadata community interfaces are needed. This paper describes the development of a coherent data discovery and data access infrastructure for the ESS community in Germany. To comprehensively and consistently describe the characteristics of geographic data, required for their discovery (discovery metadata) and for their usage (use metadata) the ISO standard 19115 is adopted. Webservice technology is used to hide the details of heterogeneous data access mechanisms and preprocessing implementations. The commitment to international standards and the modular character of the approach facilitates the expandability of the infrastructure as well as the interoperability with international partners and other communities
Efficient Active Learning for Image Classification and Segmentation using a Sample Selection and Conditional Generative Adversarial Network
Training robust deep learning (DL) systems for medical image classification
or segmentation is challenging due to limited images covering different disease
types and severity. We propose an active learning (AL) framework to select most
informative samples and add to the training data. We use conditional generative
adversarial networks (cGANs) to generate realistic chest xray images with
different disease characteristics by conditioning its generation on a real
image sample. Informative samples to add to the training set are identified
using a Bayesian neural network. Experiments show our proposed AL framework is
able to achieve state of the art performance by using about 35% of the full
dataset, thus saving significant time and effort over conventional methods
A deep level set method for image segmentation
This paper proposes a novel image segmentation approachthat integrates fully
convolutional networks (FCNs) with a level setmodel. Compared with a FCN, the
integrated method can incorporatesmoothing and prior information to achieve an
accurate segmentation.Furthermore, different than using the level set model as
a post-processingtool, we integrate it into the training phase to fine-tune the
FCN. Thisallows the use of unlabeled data during training in a
semi-supervisedsetting. Using two types of medical imaging data (liver CT and
left ven-tricle MRI data), we show that the integrated method achieves
goodperformance even when little training data is available, outperformingthe
FCN or the level set model alone
Unsupervised Holistic Image Generation from Key Local Patches
We introduce a new problem of generating an image based on a small number of
key local patches without any geometric prior. In this work, key local patches
are defined as informative regions of the target object or scene. This is a
challenging problem since it requires generating realistic images and
predicting locations of parts at the same time. We construct adversarial
networks to tackle this problem. A generator network generates a fake image as
well as a mask based on the encoder-decoder framework. On the other hand, a
discriminator network aims to detect fake images. The network is trained with
three losses to consider spatial, appearance, and adversarial information. The
spatial loss determines whether the locations of predicted parts are correct.
Input patches are restored in the output image without much modification due to
the appearance loss. The adversarial loss ensures output images are realistic.
The proposed network is trained without supervisory signals since no labels of
key parts are required. Experimental results on six datasets demonstrate that
the proposed algorithm performs favorably on challenging objects and scenes.Comment: 16 page
Volumetric Attention for 3D Medical Image Segmentation and Detection
A volumetric attention(VA) module for 3D medical image segmentation and
detection is proposed. VA attention is inspired by recent advances in video
processing, enables 2.5D networks to leverage context information along the z
direction, and allows the use of pretrained 2D detection models when training
data is limited, as is often the case for medical applications. Its integration
in the Mask R-CNN is shown to enable state-of-the-art performance on the Liver
Tumor Segmentation (LiTS) Challenge, outperforming the previous challenge
winner by 3.9 points and achieving top performance on the LiTS leader board at
the time of paper submission. Detection experiments on the DeepLesion dataset
also show that the addition of VA to existing object detectors enables a 69.1
sensitivity at 0.5 false positive per image, outperforming the best published
results by 6.6 points.Comment: Accepted by MICCAI 201
Tversky loss function for image segmentation using 3D fully convolutional deep networks
Fully convolutional deep neural networks carry out excellent potential for
fast and accurate image segmentation. One of the main challenges in training
these networks is data imbalance, which is particularly problematic in medical
imaging applications such as lesion segmentation where the number of lesion
voxels is often much lower than the number of non-lesion voxels. Training with
unbalanced data can lead to predictions that are severely biased towards high
precision but low recall (sensitivity), which is undesired especially in
medical applications where false negatives are much less tolerable than false
positives. Several methods have been proposed to deal with this problem
including balanced sampling, two step training, sample re-weighting, and
similarity loss functions. In this paper, we propose a generalized loss
function based on the Tversky index to address the issue of data imbalance and
achieve much better trade-off between precision and recall in training 3D fully
convolutional deep neural networks. Experimental results in multiple sclerosis
lesion segmentation on magnetic resonance images show improved F2 score, Dice
coefficient, and the area under the precision-recall curve in test data. Based
on these results we suggest Tversky loss function as a generalized framework to
effectively train deep neural networks
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