arXiv subjects

Mohammad Zalbagi Darestani

Publications and source records attributed to Mohammad Zalbagi Darestani.

4 recordsLinked to original sources

arXiv2022

MONAI: An open-source framework for deep learning in healthcare

Artificial Intelligence (AI) is having a tremendous impact across most areas of science. Applications of AI in healthcare have the potential to improve our ability to detect, diagnose, prognose, and intervene on human disease. For AI models to be used clinically, they need to be made safe, reproducible and robust, and the underlying software framework must be aware of the particularities (e.g. geometry, physiology, physics) of medical data being processed. This work introduces MONAI, a freely available, community-supported, and consortium-led PyTorch-based framework for deep learning in healthcare. MONAI extends PyTorch to support medical data, with a particular focus on imaging, and provide purpose-specific AI model architectures, transformations and utilities that streamline the development and deployment of medical AI models. MONAI follows best practices for software-development, providing an easy-to-use, robust, well-documented, and well-tested software framework. MONAI preserves the simple, additive, and compositional approach of its underlying PyTorch libraries. MONAI is being used by and receiving contributions from research, clinical and industrial teams from around the world, who are pursuing applications spanning nearly every aspect of healthcare.

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arXiv2022

Test-Time Training Can Close the Natural Distribution Shift Performance Gap in Deep Learning Based Compressed Sensing

Deep learning based image reconstruction methods outperform traditional methods. However, neural networks suffer from a performance drop when applied to images from a different distribution than the training images. For example, a model trained for reconstructing knees in accelerated magnetic resonance imaging (MRI) does not reconstruct brains well, even though the same network trained on brains reconstructs brains perfectly well. Thus there is a distribution shift performance gap for a given neural network, defined as the difference in performance when training on a distribution $P$ and training on another distribution $Q$, and evaluating both models on $Q$. In this work, we propose a domain adaptation method for deep learning based compressive sensing that relies on self-supervision during training paired with test-time training at inference. We show that for four natural distribution shifts, this method essentially closes the distribution shift performance gap for state-of-the-art architectures for accelerated MRI.

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arXiv2021

Measuring Robustness in Deep Learning Based Compressive Sensing

Deep neural networks give state-of-the-art accuracy for reconstructing images from few and noisy measurements, a problem arising for example in accelerated magnetic resonance imaging (MRI). However, recent works have raised concerns that deep-learning-based image reconstruction methods are sensitive to perturbations and are less robust than traditional methods: Neural networks (i) may be sensitive to small, yet adversarially-selected perturbations, (ii) may perform poorly under distribution shifts, and (iii) may fail to recover small but important features in an image. In order to understand the sensitivity to such perturbations, in this work, we measure the robustness of different approaches for image reconstruction including trained and un-trained neural networks as well as traditional sparsity-based methods. We find, contrary to prior works, that both trained and un-trained methods are vulnerable to adversarial perturbations. Moreover, both trained and un-trained methods tuned for a particular dataset suffer very similarly from distribution shifts. Finally, we demonstrate that an image reconstruction method that achieves higher reconstruction quality, also performs better in terms of accurately recovering fine details. Our results indicate that the state-of-the-art deep-learning-based image reconstruction methods provide improved performance than traditional methods without compromising robustness.

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arXiv2021

Accelerated MRI with Un-trained Neural Networks

Convolutional Neural Networks (CNNs) are highly effective for image reconstruction problems. Typically, CNNs are trained on large amounts of training images. Recently, however, un-trained CNNs such as the Deep Image Prior and Deep Decoder have achieved excellent performance for image reconstruction problems such as denoising and inpainting, \emph{without using any training data}. Motivated by this development, we address the reconstruction problem arising in accelerated MRI with un-trained neural networks. We propose a highly optimized un-trained recovery approach based on a variation of the Deep Decoder and show that it significantly outperforms other un-trained methods, in particular sparsity-based classical compressed sensing methods and naive applications of un-trained neural networks. We also compare performance (both in terms of reconstruction accuracy and computational cost) in an ideal setup for trained methods, specifically on the fastMRI dataset, where the training and test data come from the same distribution. We find that our un-trained algorithm achieves similar performance to a baseline trained neural network, but a state-of-the-art trained network outperforms the un-trained one. Finally, we perform a comparison on a non-ideal setup where the train and test distributions are slightly different, and find that our un-trained method achieves similar performance to a state-of-the-art accelerated MRI reconstruction method.

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