6 research outputs found
Automatically Designing CNN Architectures for Medical Image Segmentation
Deep neural network architectures have traditionally been designed and
explored with human expertise in a long-lasting trial-and-error process. This
process requires huge amount of time, expertise, and resources. To address this
tedious problem, we propose a novel algorithm to optimally find hyperparameters
of a deep network architecture automatically. We specifically focus on
designing neural architectures for medical image segmentation task. Our
proposed method is based on a policy gradient reinforcement learning for which
the reward function is assigned a segmentation evaluation utility (i.e., dice
index). We show the efficacy of the proposed method with its low computational
cost in comparison with the state-of-the-art medical image segmentation
networks. We also present a new architecture design, a densely connected
encoder-decoder CNN, as a strong baseline architecture to apply the proposed
hyperparameter search algorithm. We apply the proposed algorithm to each layer
of the baseline architectures. As an application, we train the proposed system
on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC)
MICCAI 2017. Starting from a baseline segmentation architecture, the resulting
network architecture obtains the state-of-the-art results in accuracy without
performing any trial-and-error based architecture design approaches or close
supervision of the hyperparameters changes.Comment: Accepted to Machine Learning in Medical Imaging (MLMI 2018
Dilated Convolutions in Neural Networks for Left Atrial Segmentation in 3D Gadolinium Enhanced-MRI
Segmentation of the left atrial chamber and assessing its morphology, are essential for improving our understanding of atrial fibrillation, the most common type of cardiac arrhythmia. Automation of this process in 3D gadolinium enhanced-MRI (GE-MRI) data is desirable, as manual delineation is time-consuming, challenging and observer-dependent. Recently, deep convolutional neural networks (CNNs) have gained tremendous traction and achieved state-of-the-art results in medical image segmentation. However, it is difficult to incorporate local and global information without using contracting (pooling) layers, which in turn reduces segmentation accuracy for smaller structures. In this paper, we propose a 3D CNN for volumetric segmentation of the left atrial chamber in LGE-MRI. Our network is based on the well known U-Net architecture. We employ a 3D fully convolutional network, with dilated convolutions in the lowest level of the network, and residual connections between encoder blocks to incorporate local and global knowledge. The results show that including global context through the use of dilated convolutions, helps in domain adaptation, and the overall segmentation accuracy is improved in comparison to a 3D U-Net
The International Workshop on Osteoarthritis Imaging Knee MRI Segmentation Challenge: A Multi-Institute Evaluation and Analysis Framework on a Standardized Dataset
Purpose: To organize a knee MRI segmentation challenge for characterizing the
semantic and clinical efficacy of automatic segmentation methods relevant for
monitoring osteoarthritis progression.
Methods: A dataset partition consisting of 3D knee MRI from 88 subjects at
two timepoints with ground-truth articular (femoral, tibial, patellar)
cartilage and meniscus segmentations was standardized. Challenge submissions
and a majority-vote ensemble were evaluated using Dice score, average symmetric
surface distance, volumetric overlap error, and coefficient of variation on a
hold-out test set. Similarities in network segmentations were evaluated using
pairwise Dice correlations. Articular cartilage thickness was computed per-scan
and longitudinally. Correlation between thickness error and segmentation
metrics was measured using Pearson's coefficient. Two empirical upper bounds
for ensemble performance were computed using combinations of model outputs that
consolidated true positives and true negatives.
Results: Six teams (T1-T6) submitted entries for the challenge. No
significant differences were observed across all segmentation metrics for all
tissues (p=1.0) among the four top-performing networks (T2, T3, T4, T6). Dice
correlations between network pairs were high (>0.85). Per-scan thickness errors
were negligible among T1-T4 (p=0.99) and longitudinal changes showed minimal
bias (<0.03mm). Low correlations (<0.41) were observed between segmentation
metrics and thickness error. The majority-vote ensemble was comparable to top
performing networks (p=1.0). Empirical upper bound performances were similar
for both combinations (p=1.0).
Conclusion: Diverse networks learned to segment the knee similarly where high
segmentation accuracy did not correlate to cartilage thickness accuracy. Voting
ensembles did not outperform individual networks but may help regularize
individual models.Comment: Submitted to Radiology: Artificial Intelligence; Fixed typo