In recent years, many papers have reported state-of-the-art performance on Alzheimer's Disease classification with MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset using convolutional neural networks. However, we discover that when we split that data into training and testing sets at the subject level, we are not able to obtain similar performance, bringing the validity of many of the previous studies into question. Furthermore, we point out that previous works use different subsets of the ADNI data, making comparison across similar works tricky. In this study, we present the results of three splitting methods, discuss the motivations behind their validity, and report our results using all of the available subjects.
@cite_16 pretrained a sparse autoencoder on randomly generated @math patches and used the weights as part of a 3D CNN to perform classification on the ADNI dataset, splitting randomly by MRI. @cite_9 employed a similar approach of using sparse autoencoder to pretrain on scans, but instead of randomly selecting patches from the training dataset, they used scans from the CADDementia dataset @cite_13 , and performed ten-fold cross-validation on the ADNI dataset.
@cite_9 @cite_16 @cite_13
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We present an adversarial domain adaptation based deep learning approach for automatic tumor segmentation from T2-weighted MRI. Our approach is composed of two steps: (i) a tumor-aware unsupervised cross-domain adaptation (CT to MRI), followed by (ii) semi-supervised tumor segmentation using Unet trained with synthesized and limited number of original MRIs. We introduced a novel target specific loss, called tumor-aware loss, for unsupervised cross-domain adaptation that helps to preserve tumors on synthesized MRIs produced from CT images. In comparison, state-of-the art adversarial networks trained without our tumor-aware loss produced MRIs with ill-preserved or missing tumors. All networks were trained using labeled CT images from 377 patients with non-small cell lung cancer obtained from the Cancer Imaging Archive and unlabeled T2w MRIs from a completely unrelated cohort of 6 patients with pre-treatment and 36 on-treatment scans. Next, we combined 6 labeled pre-treatment MRI scans with the synthesized MRIs to boost tumor segmentation accuracy through semi-supervised learning. Semi-supervised training of cycle-GAN produced a segmentation accuracy of 0.66 computed using Dice Score Coefficient (DSC). Our method trained with only synthesized MRIs produced an accuracy of 0.74 while the same method trained in semi-supervised setting produced the best accuracy of 0.80 on test. Our results show that tumor-aware adversarial domain adaptation helps to achieve reasonably accurate cancer segmentation from limited MRI data by leveraging large CT datasets. A significant proportion of patients scanned in a clinical setting have follow-up scans. We show in this work that such longitudinal scans alone can be used as a form of “free” self-supervision for training a deep network. We demonstrate this self-supervised learning for the case of T2-weighted sagittal lumbar Magnetic Resonance Images (MRIs). A Siamese convolutional neural network (CNN) is trained using two losses: (i) a contrastive loss on whether the scan is of the same person (i.e. longitudinal) or not, together with (ii) a classification loss on predicting the level of vertebral bodies. The performance of this pre-trained network is then assessed on a grading classification task. We experiment on a dataset of 1016 subjects, 423 possessing follow-up scans, with the end goal of learning the disc degeneration radiological gradings attached to the intervertebral discs. We show that the performance of the pre-trained CNN on the supervised classification task is (i) superior to that of a network trained from scratch; and (ii) requires far fewer annotated training samples to reach an equivalent performance to that of the network trained from scratch. A deep neural network (DNN)-based new pan-sharpening method for the remote sensing image fusion problem is proposed in this letter. Research on representation learning suggests that the DNN can effectively model complex relationships between variables via the composition of several levels of nonlinearity. Inspired by this observation, a modified sparse denoising autoencoder (MSDA) algorithm is proposed to train the relationship between high-resolution (HR) and low-resolution (LR) image patches, which can be represented by the DNN. The HR LR image patches only sample from the HR LR panchromatic (PAN) images at hand, respectively, without requiring other training images. By connecting a series of MSDAs, we obtain a stacked MSDA (S-MSDA), which can effectively pretrain the DNN. Moreover, in order to better train the DNN, the entire DNN is again trained by a back-propagation algorithm after pretraining. Finally, assuming that the relationship between HR LR multispectral (MS) image patches is the same as that between HR LR PAN image patches, the HR MS image will be reconstructed from the observed LR MS image using the trained DNN. Comparative experimental results with several quality assessment indexes show that the proposed method outperforms other pan-sharpening methods in terms of visual perception and numerical measures. The work explores the use of denoising autoencoders (DAEs) for brain lesion detection, segmentation, and false-positive reduction. Stacked denoising autoencoders (SDAEs) were pretrained using a large number of unlabeled patient volumes and fine-tuned with patches drawn from a limited number of patients (n=20, 40, 65). The results show negligible loss in performance even when SDAE was fine-tuned using 20 labeled patients. Low grade glioma (LGG) segmentation was achieved using a transfer learning approach in which a network pretrained with high grade glioma data was fine-tuned using LGG image patches. The networks were also shown to generalize well and provide good segmentation on unseen BraTS 2013 and BraTS 2015 test data. The manuscript also includes the use of a single layer DAE, referred to as novelty detector (ND). ND was trained to accurately reconstruct nonlesion patches. The reconstruction error maps of test data were used to localize lesions. The error maps were shown to assign unique error distributions to various constituents of the glioma, enabling localization. The ND learns the nonlesion brain accurately as it was also shown to provide good segmentation performance on ischemic brain lesions in images from a different database.