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Vestibular schwannoma growth prediction from longitudinal MRI by time conditioned neural fields
Apr 04, 2024
Vestibular schwannomas (VS) are benign tumors that are generally managed by active surveillance with MRI examination. To further assist clinical decision-making and avoid overtreatment, an accurate prediction of tumor growth based on longitudinal imaging is highly desirable. In this paper, we introduce DeepGrowth, a deep learning method that incorporates neural fields and recurrent neural networks for prospective tumor growth prediction. In the proposed method, each tumor is represented as a signed distance function (SDF) conditioned on a low-dimensional latent code. Unlike previous studies that perform tumor shape prediction directly in the image space, we predict the latent codes instead and then reconstruct future shapes from it. To deal with irregular time intervals, we introduce a time-conditioned recurrent module based on a ConvLSTM and a novel temporal encoding strategy, which enables the proposed model to output varying tumor shapes over time. The experiments on an in-house longitudinal VS dataset showed that the proposed model significantly improved the performance ($\ge 1.6\%$ Dice score and $\ge0.20$ mm 95\% Hausdorff distance), in particular for top 20\% tumors that grow or shrink the most ($\ge 4.6\%$ Dice score and $\ge 0.73$ mm 95\% Hausdorff distance). Our code is available at ~\burl{https://github.com/cyjdswx/DeepGrowth}
Bayesian Uncertainty Estimation by Hamiltonian Monte Carlo: Applications to Cardiac MRI Segmentation
Mar 04, 2024
Deep learning (DL)-based methods have achieved state-of-the-art performance for a wide range of medical image segmentation tasks. Nevertheless, recent studies show that deep neural networks (DNNs) can be miscalibrated and overconfident, leading to "silent failures" that are risky} for clinical applications. Bayesian statistics provide an intuitive approach to DL failure detection, based on posterior probability estimation. However, Bayesian DL, and in particular the posterior estimation, is intractable for large medical image segmentation DNNs. To tackle this challenge, we propose a Bayesian learning framework by Hamiltonian Monte Carlo (HMC), tempered by cold posterior (CP) to accommodate medical data augmentation, named HMC-CP. For HMC computation, we further propose a cyclical annealing strategy, which captures both local and global geometries of the posterior distribution, enabling highly efficient Bayesian DNN training with the same computational budget requirements as training a single DNN. The resulting Bayesian DNN outputs an ensemble segmentation along with the segmentation uncertainty. We evaluate the proposed HMC-CP extensively on cardiac magnetic resonance image (MRI) segmentation, using in-domain steady-state free precession (SSFP) cine images as well as out-of-domain datasets of quantitative $T_1$ and $T_2$ mapping.
Relaxometry Guided Quantitative Cardiac Magnetic Resonance Image Reconstruction
Mar 01, 2024Deep learning-based methods have achieved prestigious performance for magnetic resonance imaging (MRI) reconstruction, enabling fast imaging for many clinical applications. Previous methods employ convolutional networks to learn the image prior as the regularization term. In quantitative MRI, the physical model of nuclear magnetic resonance relaxometry is known, providing additional prior knowledge for image reconstruction. However, traditional reconstruction networks are limited to learning the spatial domain prior knowledge, ignoring the relaxometry prior. Therefore, we propose a relaxometry-guided quantitative MRI reconstruction framework to learn the spatial prior from data and the relaxometry prior from MRI physics. Additionally, we also evaluated the performance of two popular reconstruction backbones, namely, recurrent variational networks (RVN) and variational networks (VN) with U- Net. Experiments demonstrate that the proposed method achieves highly promising results in quantitative MRI reconstruction.
Contrast-Agnostic Groupwise Registration by Robust PCA for Quantitative Cardiac MRI
Nov 03, 2023
Quantitative cardiac magnetic resonance imaging (MRI) is an increasingly important diagnostic tool for cardiovascular diseases. Yet, co-registration of all baseline images within the quantitative MRI sequence is essential for the accuracy and precision of quantitative maps. However, co-registering all baseline images from a quantitative cardiac MRI sequence remains a nontrivial task because of the simultaneous changes in intensity and contrast, in combination with cardiac and respiratory motion. To address the challenge, we propose a novel motion correction framework based on robust principle component analysis (rPCA) that decomposes quantitative cardiac MRI into low-rank and sparse components, and we integrate the groupwise CNN-based registration backbone within the rPCA framework. The low-rank component of rPCA corresponds to the quantitative mapping (i.e. limited degree of freedom in variation), while the sparse component corresponds to the residual motion, making it easier to formulate and solve the groupwise registration problem. We evaluated our proposed method on cardiac T1 mapping by the modified Look-Locker inversion recovery (MOLLI) sequence, both before and after the Gadolinium contrast agent administration. Our experiments showed that our method effectively improved registration performance over baseline methods without introducing rPCA, and reduced quantitative mapping error in both in-domain (pre-contrast MOLLI) and out-of-domain (post-contrast MOLLI) inference. The proposed rPCA framework is generic and can be integrated with other registration backbones.
CoNeS: Conditional neural fields with shift modulation for multi-sequence MRI translation
Sep 06, 2023
Multi-sequence magnetic resonance imaging (MRI) has found wide applications in both modern clinical studies and deep learning research. However, in clinical practice, it frequently occurs that one or more of the MRI sequences are missing due to different image acquisition protocols or contrast agent contraindications of patients, limiting the utilization of deep learning models trained on multi-sequence data. One promising approach is to leverage generative models to synthesize the missing sequences, which can serve as a surrogate acquisition. State-of-the-art methods tackling this problem are based on convolutional neural networks (CNN) which usually suffer from spectral biases, resulting in poor reconstruction of high-frequency fine details. In this paper, we propose Conditional Neural fields with Shift modulation (CoNeS), a model that takes voxel coordinates as input and learns a representation of the target images for multi-sequence MRI translation. The proposed model uses a multi-layer perceptron (MLP) instead of a CNN as the decoder for pixel-to-pixel mapping. Hence, each target image is represented as a neural field that is conditioned on the source image via shift modulation with a learned latent code. Experiments on BraTS 2018 and an in-house clinical dataset of vestibular schwannoma patients showed that the proposed method outperformed state-of-the-art methods for multi-sequence MRI translation both visually and quantitatively. Moreover, we conducted spectral analysis, showing that CoNeS was able to overcome the spectral bias issue common in conventional CNN models. To further evaluate the usage of synthesized images in clinical downstream tasks, we tested a segmentation network using the synthesized images at inference.
DualHGNN: A Dual Hypergraph Neural Network for Semi-Supervised Node Classification based on Multi-View Learning and Density Awareness
Jun 07, 2023
Graph-based semi-supervised node classification has been shown to become a state-of-the-art approach in many applications with high research value and significance. Most existing methods are only based on the original intrinsic or artificially established graph structure which may not accurately reflect the "true" correlation among data and are not optimal for semi-supervised node classification in the downstream graph neural networks. Besides, while existing graph-based methods mostly utilize the explicit graph structure, some implicit information, for example, the density information, can also provide latent information that can be further exploited. To address these limitations, this paper proposes the Dual Hypergraph Neural Network (DualHGNN), a new dual connection model integrating both hypergraph structure learning and hypergraph representation learning simultaneously in a unified architecture. The DualHGNN first leverages a multi-view hypergraph learning network to explore the optimal hypergraph structure from multiple views, constrained by a consistency loss proposed to improve its generalization. Then, DualHGNN employs a density-aware hypergraph attention network to explore the high-order semantic correlation among data points based on the density-aware attention mechanism. Extensive experiments are conducted in various benchmark datasets, and the results demonstrate the effectiveness of the proposed approach.
LON-GNN: Spectral GNNs with Learnable Orthonormal Basis
Mar 30, 2023
In recent years, a plethora of spectral graph neural networks (GNN) methods have utilized polynomial basis with learnable coefficients to achieve top-tier performances on many node-level tasks. Although various kinds of polynomial bases have been explored, each such method adopts a fixed polynomial basis which might not be the optimal choice for the given graph. Besides, we identify the so-called over-passing issue of these methods and show that it is somewhat rooted in their less-principled regularization strategy and unnormalized basis. In this paper, we make the first attempts to address these two issues. Leveraging Jacobi polynomials, we design a novel spectral GNN, LON-GNN, with Learnable OrthoNormal bases and prove that regularizing coefficients becomes equivalent to regularizing the norm of learned filter function now. We conduct extensive experiments on diverse graph datasets to evaluate the fitting and generalization capability of LON-GNN, where the results imply its superiority.
Local implicit neural representations for multi-sequence MRI translation
Feb 02, 2023
In radiological practice, multi-sequence MRI is routinely acquired to characterize anatomy and tissue. However, due to the heterogeneity of imaging protocols and contra-indications to contrast agents, some MRI sequences, e.g. contrast-enhanced T1-weighted image (T1ce), may not be acquired. This creates difficulties for large-scale clinical studies for which heterogeneous datasets are aggregated. Modern deep learning techniques have demonstrated the capability of synthesizing missing sequences from existing sequences, through learning from an extensive multi-sequence MRI dataset. In this paper, we propose a novel MR image translation solution based on local implicit neural representations. We split the available MRI sequences into local patches and assign to each patch a local multi-layer perceptron (MLP) that represents a patch in the T1ce. The parameters of these local MLPs are generated by a hypernetwork based on image features. Experimental results and ablation studies on the BraTS challenge dataset showed that the local MLPs are critical for recovering fine image and tumor details, as they allow for local specialization that is highly important for accurate image translation. Compared to a classical pix2pix model, the proposed method demonstrated visual improvement and significantly improved quantitative scores (MSE 0.86 x 10^-3 vs. 1.02 x 10^-3 and SSIM 94.9 vs 94.3)
Efficient Bayesian Uncertainty Estimation for nnU-Net
Dec 12, 2022The self-configuring nnU-Net has achieved leading performance in a large range of medical image segmentation challenges. It is widely considered as the model of choice and a strong baseline for medical image segmentation. However, despite its extraordinary performance, nnU-Net does not supply a measure of uncertainty to indicate its possible failure. This can be problematic for large-scale image segmentation applications, where data are heterogeneous and nnU-Net may fail without notice. In this work, we introduce a novel method to estimate nnU-Net uncertainty for medical image segmentation. We propose a highly effective scheme for posterior sampling of weight space for Bayesian uncertainty estimation. Different from previous baseline methods such as Monte Carlo Dropout and mean-field Bayesian Neural Networks, our proposed method does not require a variational architecture and keeps the original nnU-Net architecture intact, thereby preserving its excellent performance and ease of use. Additionally, we boost the segmentation performance over the original nnU-Net via marginalizing multi-modal posterior models. We applied our method on the public ACDC and M&M datasets of cardiac MRI and demonstrated improved uncertainty estimation over a range of baseline methods. The proposed method further strengthens nnU-Net for medical image segmentation in terms of both segmentation accuracy and quality control.
Density-Aware Hyper-Graph Neural Networks for Graph-based Semi-supervised Node Classification
Jan 27, 2022
Graph-based semi-supervised learning, which can exploit the connectivity relationship between labeled and unlabeled data, has been shown to outperform the state-of-the-art in many artificial intelligence applications. One of the most challenging problems for graph-based semi-supervised node classification is how to use the implicit information among various data to improve the performance of classifying. Traditional studies on graph-based semi-supervised learning have focused on the pairwise connections among data. However, the data correlation in real applications could be beyond pairwise and more complicated. The density information has been demonstrated to be an important clue, but it is rarely explored in depth among existing graph-based semi-supervised node classification methods. To develop a flexible and effective model for graph-based semi-supervised node classification, we propose a novel Density-Aware Hyper-Graph Neural Networks (DA-HGNN). In our proposed approach, hyper-graph is provided to explore the high-order semantic correlation among data, and a density-aware hyper-graph attention network is presented to explore the high-order connection relationship. Extensive experiments are conducted in various benchmark datasets, and the results demonstrate the effectiveness of the proposed approach.