arXiv subjects

Dominik Müller

Publications and source records attributed to Dominik Müller.

23 records · Page 2Linked to original sources

arXiv2020

Automated Chest CT Image Segmentation of COVID-19 Lung Infection based on 3D U-Net

The coronavirus disease 2019 (COVID-19) affects billions of lives around the world and has a significant impact on public healthcare. Due to rising skepticism towards the sensitivity of RT-PCR as screening method, medical imaging like computed tomography offers great potential as alternative. For this reason, automated image segmentation is highly desired as clinical decision support for quantitative assessment and disease monitoring. However, publicly available COVID-19 imaging data is limited which leads to overfitting of traditional approaches. To address this problem, we propose an innovative automated segmentation pipeline for COVID-19 infected regions, which is able to handle small datasets by utilization as variant databases. Our method focuses on on-the-fly generation of unique and random image patches for training by performing several preprocessing methods and exploiting extensive data augmentation. For further reduction of the overfitting risk, we implemented a standard 3D U-Net architecture instead of new or computational complex neural network architectures. Through a 5-fold cross-validation on 20 CT scans of COVID-19 patients, we were able to develop a highly accurate as well as robust segmentation model for lungs and COVID-19 infected regions without overfitting on the limited data. Our method achieved Dice similarity coefficients of 0.956 for lungs and 0.761 for infection. We demonstrated that the proposed method outperforms related approaches, advances the state-of-the-art for COVID-19 segmentation and improves medical image analysis with limited data. The code and model are available under the following link: https://github.com/frankkramer-lab/covid19.MIScnn

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arXiv2019

MIScnn: A Framework for Medical Image Segmentation with Convolutional Neural Networks and Deep Learning

The increased availability and usage of modern medical imaging induced a strong need for automatic medical image segmentation. Still, current image segmentation platforms do not provide the required functionalities for plain setup of medical image segmentation pipelines. Already implemented pipelines are commonly standalone software, optimized on a specific public data set. Therefore, this paper introduces the open-source Python library MIScnn. The aim of MIScnn is to provide an intuitive API allowing fast building of medical image segmentation pipelines including data I/O, preprocessing, data augmentation, patch-wise analysis, metrics, a library with state-of-the-art deep learning models and model utilization like training, prediction, as well as fully automatic evaluation (e.g. cross-validation). Similarly, high configurability and multiple open interfaces allow full pipeline customization. Running a cross-validation with MIScnn on the Kidney Tumor Segmentation Challenge 2019 data set (multi-class semantic segmentation with 300 CT scans) resulted into a powerful predictor based on the standard 3D U-Net model. With this experiment, we could show that the MIScnn framework enables researchers to rapidly set up a complete medical image segmentation pipeline by using just a few lines of code. The source code for MIScnn is available in the Git repository: https://github.com/frankkramer-lab/MIScnn.

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arXiv2017

Dependence Modeling in Ultra High Dimensions with Vine Copulas and the Graphical Lasso

To model high dimensional data, Gaussian methods are widely used since they remain tractable and yield parsimonious models by imposing strong assumptions on the data. Vine copulas are more flexible by combining arbitrary marginal distributions and (conditional) bivariate copulas. Yet, this adaptability is accompanied by sharply increasing computational effort as the dimension increases. The approach proposed in this paper overcomes this burden and makes the first step into ultra high dimensional non-Gaussian dependence modeling by using a divide-and-conquer approach. First, we apply Gaussian methods to split datasets into feasibly small subsets and second, apply parsimonious and flexible vine copulas thereon. Finally, we reconcile them into one joint model. We provide numerical results demonstrating the feasibility of our approach in moderate dimensions and showcase its ability to estimate ultra high dimensional non-Gaussian dependence models in thousands of dimensions.

stat.ML↗

arXiv2017

Selection of Sparse Vine Copulas in High Dimensions with the Lasso

We propose a novel structure selection method for high dimensional (d > 100) sparse vine copulas. Current sequential greedy approaches for structure selection require calculating spanning trees in hundreds of dimensions and fitting the pair copulas and their parameters iteratively throughout the structure selection process. Our method uses a connection between the vine and structural equation models (SEMs). The later can be estimated very fast using the Lasso, also in very high dimensions, to obtain sparse models. Thus, we obtain a structure estimate independently of the chosen pair copulas and parameters. Additionally, we define the novel concept of regularization paths for R-vine matrices. It relates sparsity of the vine copula model in terms of independence copulas to a penalization coefficient in the structural equation models. We illustrate our approach and provide many numerical examples. These include simulations and data applications in high dimensions, showing the superiority of our approach to other existing methods.

stat.ME↗

arXiv2016

Representing sparse Gaussian DAGs as sparse R-vines allowing for non-Gaussian dependence

Modeling dependence in high dimensional systems has become an increasingly important topic. Most approaches rely on the assumption of a multivariate Gaussian distribution such as statistical models on directed acyclic graphs (DAGs). They are based on modeling conditional independencies and are scalable to high dimensions. In contrast, vine copula models accommodate more elaborate features like tail dependence and asymmetry, as well as independent modeling of the marginals. This flexibility comes however at the cost of exponentially increasing complexity for model selection and estimation. We show a novel connection between DAGs with limited number of parents and truncated vine copulas under sufficient conditions. This motivates a more general procedure exploiting the fast model selection and estimation of sparse DAGs while allowing for non-Gaussian dependence using vine copulas. We demonstrate in a simulation study and using a high dimensional data application that our approach outperforms standard methods for vine structure estimation.

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