2,587 research outputs found
MILD-Net: Minimal Information Loss Dilated Network for Gland Instance Segmentation in Colon Histology Images
The analysis of glandular morphology within colon histopathology images is an
important step in determining the grade of colon cancer. Despite the importance
of this task, manual segmentation is laborious, time-consuming and can suffer
from subjectivity among pathologists. The rise of computational pathology has
led to the development of automated methods for gland segmentation that aim to
overcome the challenges of manual segmentation. However, this task is
non-trivial due to the large variability in glandular appearance and the
difficulty in differentiating between certain glandular and non-glandular
histological structures. Furthermore, a measure of uncertainty is essential for
diagnostic decision making. To address these challenges, we propose a fully
convolutional neural network that counters the loss of information caused by
max-pooling by re-introducing the original image at multiple points within the
network. We also use atrous spatial pyramid pooling with varying dilation rates
for preserving the resolution and multi-level aggregation. To incorporate
uncertainty, we introduce random transformations during test time for an
enhanced segmentation result that simultaneously generates an uncertainty map,
highlighting areas of ambiguity. We show that this map can be used to define a
metric for disregarding predictions with high uncertainty. The proposed network
achieves state-of-the-art performance on the GlaS challenge dataset and on a
second independent colorectal adenocarcinoma dataset. In addition, we perform
gland instance segmentation on whole-slide images from two further datasets to
highlight the generalisability of our method. As an extension, we introduce
MILD-Net+ for simultaneous gland and lumen segmentation, to increase the
diagnostic power of the network.Comment: Initial version published at Medical Imaging with Deep Learning
(MIDL) 201
An end-to-end convolutional selective autoencoder approach to Soybean Cyst Nematode eggs detection
This paper proposes a novel selective autoencoder approach within the
framework of deep convolutional networks. The crux of the idea is to train a
deep convolutional autoencoder to suppress undesired parts of an image frame
while allowing the desired parts resulting in efficient object detection. The
efficacy of the framework is demonstrated on a critical plant science problem.
In the United States, approximately $1 billion is lost per annum due to a
nematode infection on soybean plants. Currently, plant-pathologists rely on
labor-intensive and time-consuming identification of Soybean Cyst Nematode
(SCN) eggs in soil samples via manual microscopy. The proposed framework
attempts to significantly expedite the process by using a series of manually
labeled microscopic images for training followed by automated high-throughput
egg detection. The problem is particularly difficult due to the presence of a
large population of non-egg particles (disturbances) in the image frames that
are very similar to SCN eggs in shape, pose and illumination. Therefore, the
selective autoencoder is trained to learn unique features related to the
invariant shapes and sizes of the SCN eggs without handcrafting. After that, a
composite non-maximum suppression and differencing is applied at the
post-processing stage.Comment: A 10 pages, 8 figures International Conference on Machine
Leaning(ICML) Submissio
Reducing model bias in a deep learning classifier using domain adversarial neural networks in the MINERvA experiment
We present a simulation-based study using deep convolutional neural networks
(DCNNs) to identify neutrino interaction vertices in the MINERvA passive
targets region, and illustrate the application of domain adversarial neural
networks (DANNs) in this context. DANNs are designed to be trained in one
domain (simulated data) but tested in a second domain (physics data) and
utilize unlabeled data from the second domain so that during training only
features which are unable to discriminate between the domains are promoted.
MINERvA is a neutrino-nucleus scattering experiment using the NuMI beamline at
Fermilab. -dependent cross sections are an important part of the physics
program, and these measurements require vertex finding in complicated events.
To illustrate the impact of the DANN we used a modified set of simulation in
place of physics data during the training of the DANN and then used the label
of the modified simulation during the evaluation of the DANN. We find that deep
learning based methods offer significant advantages over our prior track-based
reconstruction for the task of vertex finding, and that DANNs are able to
improve the performance of deep networks by leveraging available unlabeled data
and by mitigating network performance degradation rooted in biases in the
physics models used for training.Comment: 41 page
Direction-aware Spatial Context Features for Shadow Detection
Shadow detection is a fundamental and challenging task, since it requires an
understanding of global image semantics and there are various backgrounds
around shadows. This paper presents a novel network for shadow detection by
analyzing image context in a direction-aware manner. To achieve this, we first
formulate the direction-aware attention mechanism in a spatial recurrent neural
network (RNN) by introducing attention weights when aggregating spatial context
features in the RNN. By learning these weights through training, we can recover
direction-aware spatial context (DSC) for detecting shadows. This design is
developed into the DSC module and embedded in a CNN to learn DSC features at
different levels. Moreover, a weighted cross entropy loss is designed to make
the training more effective. We employ two common shadow detection benchmark
datasets and perform various experiments to evaluate our network. Experimental
results show that our network outperforms state-of-the-art methods and achieves
97% accuracy and 38% reduction on balance error rate.Comment: Accepted for oral presentation in CVPR 2018. The journal version of
this paper is arXiv:1805.0463
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