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Register a new userTowards Lower-Dose PET using Physics-Based Uncertainty-Aware Multimodal Learning with Robustness to Out-of-Distribution Data
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Radiation exposure in positron emission tomography (PET) imaging limits its usage in the studies of radiation-sensitive populations, e.g., pregnant women, children, and adults that require longitudinal imaging. Reducing the PET radiotracer dose or acquisition time reduces photon counts, which can deteriorate image quality. Recent deep-neural-network (DNN) based methods for image-to-image translation enable the mapping of low-quality PET images (acquired using substantially reduced dose), coupled with the associated magnetic resonance imaging (MRI) images, to high-quality PET images. However, such DNN methods focus on applications involving test data that match the statistical characteristics of the training data very closely and give little attention to evaluating the performance of these DNNs on new out-of-distribution (OOD) acquisitions. We propose a novel DNN formulation that models the (i) underlying sinogram-based physics of the PET imaging system and (ii) the uncertainty in the DNN output through the per-voxel heteroscedasticity of the residuals between the predicted and the high-quality reference images. Our sinogram-based uncertainty-aware DNN framework, namely, suDNN, estimates a standard-dose PET image using multimodal input in the form of (i) a low-dose/low-count PET image and (ii) the corresponding multi-contrast MRI images, leading to improved robustness of suDNN to OOD acquisitions. Results on in vivo simultaneous PET-MRI, and various forms of OOD data in PET-MRI, show the benefits of suDNN over the current state of the art, quantitatively and qualitatively.
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Synchrotron-based X-ray computed tomography is widely used for investigating inner structures of specimens at high spatial resolutions. However, potential beam damage to samples often limits the X-ray exposure during tomography experiments. Proposed strategies for eliminating beam damage also decrease reconstruction quality. Here we present a deep learning-based method to enhance low-dose tomography reconstruction via a hybrid-dose acquisition strategy composed of extremely sparse-view normal-dose projections and full-view low-dose projections. Corresponding image pairs are extracted from low-/normal-dose projections to train a deep convolutional neural network, which is then applied to enhance full-view noisy low-dose projections. Evaluation on two experimental datasets under different hybrid-dose acquisition conditions show significantly improved structural details and reduced noise levels compared to uniformly distributed acquisitions with the same number of total dosage. The resulting reconstructions also preserve more structural information than reconstructions processed with traditional analytical and regularization-based iterative reconstruction methods from uniform acquisitions. Our performance comparisons show that our implementation, HDrec, can perform denoising of a real-world experimental data 410x faster than the state-of-the-art Xlearn method while providing better quality. This framework can be applied to other tomographic or scanning based X-ray imaging techniques for enhanced analysis of dose-sensitive samples and has great potential for studying fast dynamic processes.
Positron emission tomography (PET) is widely used in various clinical applications, including cancer diagnosis, heart disease and neuro disorders. The use of radioactive tracer in PET imaging raises concerns due to the risk of radiation exposure. To minimize this potential risk in PET imaging, efforts have been made to reduce the amount of radio-tracer usage. However, lowing dose results in low Signal-to-Noise-Ratio (SNR) and loss of information, both of which will heavily affect clinical diagnosis. Besides, the ill-conditioning of low-dose PET image reconstruction makes it a difficult problem for iterative reconstruction algorithms. Previous methods proposed are typically complicated and slow, yet still cannot yield satisfactory results at significantly low dose. Here, we propose a deep learning method to resolve this issue with an encoder-decoder residual deep network with concatenate skip connections. Experiments shows the proposed method can reconstruct low-dose PET image to a standard-dose quality with only two-hundredth dose. Different cost functions for training model are explored. Multi-slice input strategy is introduced to provide the network with more structural information and make it more robust to noise. Evaluation on ultra-low-dose clinical data shows that the proposed method can achieve better result than the state-of-the-art methods and reconstruct images with comparable quality using only 0.5% of the original regular dose.
Mammography is using low-energy X-rays to screen the human breast and is utilized by radiologists to detect breast cancer. Typically radiologists require a mammogram with impeccable image quality for an accurate diagnosis. In this study, we propose a deep learning method based on Convolutional Neural Networks (CNNs) for mammogram denoising to improve the image quality. We first enhance the noise level and employ Anscombe Transformation (AT) to transform Poisson noise to white Gaussian noise. With this data augmentation, a deep residual network is trained to learn the noise map of the noisy images. We show, that the proposed method can remove not only simulated but also real noise. Furthermore, we also compare our results with state-of-the-art denoising methods, such as BM3D and DNCNN. In an early investigation, we achieved qualitatively better mammogram denoising results.
Although machine learning models typically experience a drop in performance on out-of-distribution data, accuracies on in- versus out-of-distribution data are widely observed to follow a single linear trend when evaluated across a testbed of models. Models that are more accurate on the out-of-distribution data relative to this baseline exhibit effective robustness and are exceedingly rare. Identifying such models, and understanding their properties, is key to improving out-of-distribution performance. We conduct a thorough empirical investigation of effective robustness during fine-tuning and surprisingly find that models pre-trained on larger datasets exhibit effective robustness during training that vanishes at convergence. We study how properties of the data influence effective robustness, and we show that it increases with the larger size, more diversity, and higher example difficulty of the dataset. We also find that models that display effective robustness are able to correctly classify 10% of the examples that no other current testbed model gets correct. Finally, we discuss several strategies for scaling effective robustness to the high-accuracy regime to improve the out-of-distribution accuracy of state-of-the-art models.
The goal of this tutorial is to explain step-by-step how to implement physics-based learning for the rapid prototyping of a computational imaging system. We provide a basic overview of physics-based learning, the construction of a physics-based network, and its reduction to practice. Specifically, we advocate exploiting the auto-differentiation functionality twice, once to build a physics-based network and again to perform physics-based learning. Thus, the user need only implement the forward model process for their system, speeding up prototyping time. We provide an open-source Pytorch implementation of a physics-based network and training procedure for a generic sparse recovery problem
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