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Deep learning achieves radiologist-level performance of tumor segmentation in breast MRI
Sep 21, 2020
Purpose: The goal of this research was to develop a deep network architecture that achieves fully-automated radiologist-level segmentation of breast tumors in MRI. Materials and Methods: We leveraged 38,229 clinical MRI breast exams collected retrospectively from women aged 12-94 (mean age 54) who presented between 2002 and 2014 at a single clinical site. The training set for the network consisted of 2,555 malignant breasts that were segmented in 2D by experienced radiologists, as well as 60,108 benign breasts that served as negative controls. The test set consisted of 250 exams with tumors segmented independently by four radiologists. We selected among several 3D deep convolutional neural network architectures, input modalities and harmonization methods. The outcome measure was the Dice score for 2D segmentation, and was compared between the network and radiologists using the Wilcoxon signed-rank test and the TOST procedure. Results: The best-performing network on the training set was a volumetric U-Net with contrast enhancement dynamic as input and with intensity normalized for each exam. In the test set the median Dice score of this network was 0.77. The performance of the network was equivalent to that of the radiologists (TOST procedure with radiologist performance of 0.69-0.84 as equivalence bounds: p = 5e-10 and p = 2e-5, respectively; N = 250) and compares favorably with published state of the art (0.6-0.77). Conclusion: When trained on a dataset of over 60 thousand breasts, a volumetric U-Net performs as well as expert radiologists at segmenting malignant breast lesions in MRI.
Tissue segmentation with deep 3D networks and spatial priors
May 24, 2019
Conventional automated segmentation of the human head distinguishes different tissues based on image intensities in an MRI volume and prior tissue probability maps (TPM). This works well for normal head anatomies, but fails in the presence of unexpected lesions. Deep convolutional neural networks leverage instead volumetric spatial patterns and can be trained to segment lesions, but have thus far not integrated prior probabilities. Here we add to a three-dimensional convolutional network spatial priors with a TPM, morphological priors with conditional random fields, and context with a wider field-of-view at lower resolution. The new architecture, which we call MultiPrior, was designed to be a fully-trainable, three-dimensional convolutional network. Thus, the resulting architecture represents a neural network with learnable spatial memories. When trained on a set of stroke patients and healthy subjects, MultiPrior outperforms the state-of-the-art segmentation tools such as DeepMedic and SPM segmentation. The approach is further demonstrated on patients with disorders of consciousness, where we find that cognitive state correlates positively with gray-matter volumes and negatively with the extent of ventricles. We make the code and trained networks freely available to support future clinical research projects.
Multi-set Canonical Correlation Analysis simply explained
Feb 11, 2018There are a multitude of methods to perform multi-set correlated component analysis (MCCA), including some that require iterative solutions. The methods differ on the criterion they optimize and the constraints placed on the solutions. This note focuses perhaps on the simplest version, which can be solved in a single step as the eigenvectors of matrix ${\bf D}^{-1} {\bf R}$. Here ${\bf R}$ is the covariance matrix of the concatenated data, and ${\bf D}$ is its block-diagonal. This note shows that this solution maximizes inter-set correlation (ISC) without further constraints. It also relates the solution to a two step procedure, which first whitens each dataset using PCA, and then performs an additional PCA on the concatenated and whitened data. Both these solutions are known, although a clear derivation and simple implementation are hard to find. This short note aims to remedy this.