Predicting brain age with deep learning from raw imaging data results in a reliable and heritable biomarker

Machine learning analysis of neuroimaging data can accurately predict chronological age in healthy people. Deviations from healthy brain ageing have been associated with cognitive impairment and disease. Here we sought to further establish the credentials of ‘brain-predicted age’ as a biomarker of individual differences in the brain ageing process, using a predictive modelling approach based on deep learning, and specifically convolutional neural networks (CNN), and applied to both pre-processed and raw T1-weighted MRI data. Firstly, we aimed to demonstrate the accuracy of CNN brain-predicted age using a large dataset of healthy adults (N = 2001). Next, we sought to establish the heritability of brain-predicted age using a sample of monozygotic and dizygotic female twins (N = 62). Thirdly, we examined the test-retest and multi-centre reliability of brain-predicted age using two samples (within-scanner N = 20; between-scanner N = 11). CNN brain-predicted ages were generated and compared to a Gaussian Process Regression (GPR) approach, on all datasets. Input data were grey matter (GM) or white matter (WM) volumetric maps generated by Statistical Parametric Mapping (SPM) or raw data. CNN accurately predicted chronological age using GM (correlation between brain-predicted age and chronological age r = 0.96, mean absolute error [MAE] = 4.16 years) and raw (r = 0.94, MAE = 4.65 years) data. This was comparable to GPR brain-predicted age using GM data (r = 0.95, MAE = 4.66 years). Brain-predicted age was a heritable phenotype for all models and input data (h2 ≥ 0.5). Brain-predicted age showed high test-retest reliability (intraclass correlation coefficient [ICC] = 0.90–0.99). Multi-centre reliability was more variable within high ICCs for GM (0.83–0.96) and poor-moderate levels for WM and raw data (0.51–0.77). Brain-predicted age represents an accurate, highly reliable and genetically-influenced phenotype, that has potential to be used as a biomarker of brain ageing. Moreover, age predictions can be accurately generated on raw T1-MRI data, substantially reducing computation time for novel data, bringing the process closer to giving real-time information on brain health in clinical settings

Predicting brain age with deep learning from raw imaging data results in a reliable and heritable biomarker.

Machine learning analysis of neuroimaging data can accurately predict chronological age in healthy people. Deviations from healthy brain ageing have been associated with cognitive impairment and disease. Here we sought to further establish the credentials of 'brain-predicted age' as a biomarker of individual differences in the brain ageing process, using a predictive modelling approach based on deep learning, and specifically convolutional neural networks (CNN), and applied to both pre-processed and raw T1-weighted MRI data. Firstly, we aimed to demonstrate the accuracy of CNN brain-predicted age using a large dataset of healthy adults (N = 2001). Next, we sought to establish the heritability of brain-predicted age using a sample of monozygotic and dizygotic female twins (N = 62). Thirdly, we examined the test-retest and multi-centre reliability of brain-predicted age using two samples (within-scanner N = 20; between-scanner N = 11). CNN brain-predicted ages were generated and compared to a Gaussian Process Regression (GPR) approach, on all datasets. Input data were grey matter (GM) or white matter (WM) volumetric maps generated by Statistical Parametric Mapping (SPM) or raw data. CNN accurately predicted chronological age using GM (correlation between brain-predicted age and chronological age r = 0.96, mean absolute error [MAE] = 4.16 years) and raw (r = 0.94, MAE = 4.65 years) data. This was comparable to GPR brain-predicted age using GM data (r = 0.95, MAE = 4.66 years). Brain-predicted age was a heritable phenotype for all models and input data (h(2) ≥ 0.5). Brain-predicted age showed high test-retest reliability (intraclass correlation coefficient [ICC] = 0.90-0.99). Multi-centre reliability was more variable within high ICCs for GM (0.83-0.96) and poor-moderate levels for WM and raw data (0.51-0.77). Brain-predicted age represents an accurate, highly reliable and genetically-influenced phenotype, that has potential to be used as a biomarker of brain ageing. Moreover, age predictions can be accurately generated on raw T1-MRI data, substantially reducing computation time for novel data, bringing the process closer to giving real-time information on brain health in clinical settings

Recurrent Neural Networks for Aortic Image Sequence Segmentation with Sparse Annotations

Segmentation of image sequences is an important task in medical image analysis, which enables clinicians to assess the anatomy and function of moving organs. However, direct application of a segmentation algorithm to each time frame of a sequence may ignore the temporal continuity inherent in the sequence. In this work, we propose an image sequence segmentation algorithm by combining a fully convolutional network with a recurrent neural network, which incorporates both spatial and temporal information into the segmentation task. A key challenge in training this network is that the available manual annotations are temporally sparse, which forbids end-to-end training. We address this challenge by performing non-rigid label propagation on the annotations and introducing an exponentially weighted loss function for training. Experiments on aortic MR image sequences demonstrate that the proposed method significantly improves both accuracy and temporal smoothness of segmentation, compared to a baseline method that utilises spatial information only. It achieves an average Dice metric of 0.960 for the ascending aorta and 0.953 for the descending aorta

Fast-SCNN: Fast semantic segmentation network

© 2019. The copyright of this document resides with its authors. The encoder-decoder framework is state-of-the-art for offline semantic image segmentation. Since the rise in autonomous systems, real-time computation is increasingly desirable. In this paper, we introduce fast segmentation convolutional neural network (Fast-SCNN), an above real-time semantic segmentation model on high resolution image data (1024×2048px) suited to efficient computation on embedded devices with low memory and power. We introduce a 'learning to downsample' module which computes low-level features for multiple resolution branches simultaneously. Our network combines spatial detail at high resolution with deep features extracted at lower resolution, yielding an accuracy of 68.0% mean intersection over union at 123.5 frames per second on full scale images of Cityscapes. We also show that large scale pre-training is unnecessary. We thoroughly validate our experiments with ImageNet pre-training and the coarse labeled data of Cityscapes. Finally, we show even faster computation with competitive results on subsampled inputs, without any network modifications

Embodied Visual Navigation with Automatic Curriculum Learning in Real Environments

We present NavACL, a method of automatic curriculum learning tailored to the navigation task. NavACL is simple to train and efficiently selects relevant tasks using geometric features. In our experiments, deep reinforcement learning agents trained using NavACL significantly outperform state-of-The-Art agents trained with uniform sampling-the current standard. Furthermore, our agents can navigate through unknown cluttered indoor environments to semantically-specified targets using only RGB images. Obstacle-Avoiding policies and frozen feature networks support transfer to unseen real-world environments, without any modification or retraining requirements. We evaluate our policies in simulation, and in the real world on a ground robot and a quadrotor drone. Videos of real-world results are available in the supplementary material

Calculation of Anatomical and Functional Metrics Using Deep Learning in Cardiac MRI: Comparison Between Direct and Segmentation-Based Estimation

In this paper we propose a collection of left ventricle (LV) quantification methods using different versions of a common neural network architecture. In particular, we compare the accuracy obtained with direct calculation (regression) of the desired metrics, a segmentation network and a novel combined approach. We also introduce temporal dynamics through the use of a Long Short-Term Memory (LSTM) network. We train and evaluate our methods on MICCAI 2018 Left Ventricle Full Quantification Challenge dataset. We perform 5-fold cross-validation on the training dataset and compare our results with the state-of-the-art methods evaluated on the same dataset. In our experiments, segmentation-based methods outperform all the other variants as well as current state of the art. The introduction of LSTM does produces only minor improvements in accuracy. The novel segmentation/estimation network improves the results on estimation-only but does not reach the accuracy of segmentation-based metric calculation

SMOD - Data Augmentation Based on Statistical Models of Deformation to Enhance Segmentation in 2D Cine Cardiac MRI

Deep learning has revolutionized medical image analysis in recent years. Nevertheless, technical, ethical and financial constraints along with confidentiality issues still limit data availability, and therefore the performance of these approaches. To overcome such limitations, data augmentation has proven crucial. Here we propose SMOD, a novel augmentation methodology based on Statistical Models of Deformations, to segment 2D cine scans in cardiac MRI. In brief, the shape variability of the training set space is modelled so new images with the appearance of the original ones but unseen shapes within the space of plausible realistic shapes are generated. SMOD is compared to standard augmentation providing quantitative improvement, especially when the training data available is very limited or the structures to segment are complex and highly variable. We finally propose a state-of-art, deep learning 2D cardiac MRI segmenter for normal and hypertrophic cardiomyopathy hearts with an epicardium and endocardium mean Dice score of 0.968 in short and long axis