Longitudinal MRIs are often used to capture the gradual deterioration of brain structure and function caused by aging or neurological diseases. Analyzing this data via machine learning generally requires a large number of ground-truth labels, which are often missing or expensive to obtain. Reducing the need for labels, we propose a self-supervised strategy for representation learning named Longitudinal Neighborhood Embedding (LNE). Motivated by concepts in contrastive learning, LNE explicitly models the similarity between trajectory vectors across different subjects. We do so by building a graph in each training iteration defining neighborhoods in the latent space so that the progression direction of a subject follows the direction of its neighbors. This results in a smooth trajectory field that captures the global morphological change of the brain while maintaining the local continuity. We apply LNE to longitudinal T1w MRIs of two neuroimaging studies: a dataset composed of 274 healthy subjects, and Alzheimer's Disease Neuroimaging Initiative (ADNI, N=632). The visualization of the smooth trajectory vector field and superior performance on downstream tasks demonstrate the strength of the proposed method over existing self-supervised methods in extracting information associated with normal aging and in revealing the impact of neurodegenerative disorders. The code is available at \url{https://github.com/ouyangjiahong/longitudinal-neighbourhood-embedding.git}.
Multi-modal MR images are widely used in neuroimaging applications to provide complementary information about the brain structures. Recent works have suggested that multi-modal deep learning analysis can benefit from explicitly disentangling anatomical (shape) and modality (appearance) representations from the images. In this work, we challenge existing strategies by showing that they do not naturally lead to representation disentanglement both in theory and in practice. To address this issue, we propose a margin loss that regularizes the similarity relationships of the representations across subjects and modalities. To enable a robust training, we further introduce a modified conditional convolution to design a single model for encoding images of all modalities. Lastly, we propose a fusion function to combine the disentangled anatomical representations as a set of modality-invariant features for downstream tasks. We evaluate the proposed method on three multi-modal neuroimaging datasets. Experiments show that our proposed method can achieve superior disentangled representations compared to existing disentanglement strategies. Results also indicate that the fused anatomical representation has great potential in the downstream task of zero-dose PET reconstruction and brain tumor segmentation.
Interpretability is a critical factor in applying complex deep learning models to advance the understanding of brain disorders in neuroimaging studies. To interpret the decision process of a trained classifier, existing techniques typically rely on saliency maps to quantify the voxel-wise or feature-level importance for classification through partial derivatives. Despite providing some level of localization, these maps are not human-understandable from the neuroscience perspective as they do not inform the specific meaning of the alteration linked to the brain disorder. Inspired by the image-to-image translation scheme, we propose to train simulator networks that can warp a given image to inject or remove patterns of the disease. These networks are trained such that the classifier produces consistently increased or decreased prediction logits for the simulated images. Moreover, we propose to couple all the simulators into a unified model based on conditional convolution. We applied our approach to interpreting classifiers trained on a synthetic dataset and two neuroimaging datasets to visualize the effect of the Alzheimer's disease and alcohol use disorder. Compared to the saliency maps generated by baseline approaches, our simulations and visualizations based on the Jacobian determinants of the warping field reveal meaningful and understandable patterns related to the diseases.
Medical image segmentation is an essential prerequisite for developing healthcare systems, especially for disease diagnosis and treatment planning. On various medical image segmentation tasks, the u-shaped architecture, also known as U-Net, has become the de-facto standard and achieved tremendous success. However, due to the intrinsic locality of convolution operations, U-Net generally demonstrates limitations in explicitly modeling long-range dependency. Transformers, designed for sequence-to-sequence prediction, have emerged as alternative architectures with innate global self-attention mechanisms, but can result in limited localization abilities due to insufficient low-level details. In this paper, we propose TransUNet, which merits both Transformers and U-Net, as a strong alternative for medical image segmentation. On one hand, the Transformer encodes tokenized image patches from a convolution neural network (CNN) feature map as the input sequence for extracting global contexts. On the other hand, the decoder upsamples the encoded features which are then combined with the high-resolution CNN feature maps to enable precise localization. We argue that Transformers can serve as strong encoders for medical image segmentation tasks, with the combination of U-Net to enhance finer details by recovering localized spatial information. TransUNet achieves superior performances to various competing methods on different medical applications including multi-organ segmentation and cardiac segmentation. Code and models are available at https://github.com/Beckschen/TransUNet.
The shortage of annotated medical images is one of the biggest challenges in the field of medical image computing. Without a sufficient number of training samples, deep learning based models are very likely to suffer from over-fitting problem. The common solution is image manipulation such as image rotation, cropping, or resizing. Those methods can help relieve the over-fitting problem as more training samples are introduced. However, they do not really introduce new images with additional information and may lead to data leakage as the test set may contain similar samples which appear in the training set. To address this challenge, we propose to generate diverse images with generative adversarial network. In this paper, we develop a novel generative method named generative adversarial U-Net , which utilizes both generative adversarial network and U-Net. Different from existing approaches, our newly designed model is domain-free and generalizable to various medical images. Extensive experiments are conducted over eight diverse datasets including computed tomography (CT) scan, pathology, X-ray, etc. The visualization and quantitative results demonstrate the efficacy and good generalization of the proposed method on generating a wide array of high-quality medical images.
While state-of-the-art 3D Convolutional Neural Networks (CNN) achieve very good results on action recognition datasets, they are computationally very expensive and require many GFLOPs. While the GFLOPs of a 3D CNN can be decreased by reducing the temporal feature resolution within the network, there is no setting that is optimal for all input clips. In this work, we, therefore, introduce a differentiable Similarity Guided Sampling (SGS) module, which can be plugged into any existing 3D CNN architecture. SGS empowers 3D CNNs by learning the similarity of temporal features and grouping similar features together. As a result, the temporal feature resolution is not anymore static but it varies for each input video clip. By integrating SGS as an additional layer within current 3D CNNs, we can convert them into much more efficient 3D CNNs with adaptive temporal feature resolutions (ATFR). Our evaluations show that the proposed module improves the state-of-the-art by reducing the computational cost (GFLOPs)by half while preserving or even improving the accuracy. We evaluate our module by adding it to multiple state-of-the-art 3D CNNs on various datasets such as Kinetics-600, Kinetics-400, mini-Kinetics, Something-Something V2, UCF101, and HMDB51
Parkinson's disease (PD) is a progressive neurological disorder primarily affecting motor function resulting in tremor at rest, rigidity, bradykinesia, and postural instability. The physical severity of PD impairments can be quantified through the Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS), a widely used clinical rating scale. Accurate and quantitative assessment of disease progression is critical to developing a treatment that slows or stops further advancement of the disease. Prior work has mainly focused on dopamine transport neuroimaging for diagnosis or costly and intrusive wearables evaluating motor impairments. For the first time, we propose a computer vision-based model that observes non-intrusive video recordings of individuals, extracts their 3D body skeletons, tracks them through time, and classifies the movements according to the MDS-UPDRS gait scores. Experimental results show that our proposed method performs significantly better than chance and competing methods with an F1-score of 0.83 and a balanced accuracy of 81%. This is the first benchmark for classifying PD patients based on MDS-UPDRS gait severity and could be an objective biomarker for disease severity. Our work demonstrates how computer-assisted technologies can be used to non-intrusively monitor patients and their motor impairments. The code is available at https://github.com/mlu355/PD-Motor-Severity-Estimation.
Smooth and seamless robot navigation while interacting with humans depends on predicting human movements. Forecasting such human dynamics often involves modeling human trajectories (global motion) or detailed body joint movements (local motion). Prior work typically tackled local and global human movements separately. In this paper, we propose a novel framework to tackle both tasks of human motion (or trajectory) and body skeleton pose forecasting in a unified end-to-end pipeline. To deal with this real-world problem, we consider incorporating both scene and social contexts, as critical clues for this prediction task, into our proposed framework. To this end, we first couple these two tasks by i) encoding their history using a shared Gated Recurrent Unit (GRU) encoder and ii) applying a metric as loss, which measures the source of errors in each task jointly as a single distance. Then, we incorporate the scene context by encoding a spatio-temporal representation of the video data. We also include social clues by generating a joint feature representation from motion and pose of all individuals from the scene using a social pooling layer. Finally, we use a GRU based decoder to forecast both motion and skeleton pose. We demonstrate that our proposed framework achieves a superior performance compared to several baselines on two social datasets.
Longitudinal neuroimaging or biomedical studies often acquire multiple observations from each individual over time, which entails repeated measures with highly interdependent variables. In this paper, we discuss the implication of repeated measures design on unsupervised learning by showing its tight conceptual connection to self-supervised learning and factor disentanglement. Leveraging the ability for `self-comparison' through repeated measures, we explicitly separate the definition of the factor space and the representation space enabling an exact disentanglement of time-related factors from the representations of the images. By formulating deterministic multivariate mapping functions between the two spaces, our model, named Longitudinal Self-Supervised Learning (LSSL), uses a standard autoencoding structure with a cosine loss to estimate the direction linked to the disentangled factor. We apply LSSL to two longitudinal neuroimaging studies to show its unique advantage in extracting the `brain-age' information from the data and in revealing informative characteristics associated with neurodegenerative and neuropsychological disorders. For a downstream task of supervised diagnosis classification, the representations learned by LSSL permit faster convergence and higher (or similar) prediction accuracy compared to several other representation learning techniques.