最近关于Covid-19的研究表明，CT成像提供了评估疾病进展和协助诊断的有用信息，以及帮助理解疾病。有越来越多的研究，建议使用深度学习来使用胸部CT扫描提供快速准确地定量Covid-19。兴趣的主要任务是胸部CT扫描的肺和肺病变的自动分割，确认或疑似Covid-19患者。在这项研究中，我们使用多中心数据集比较12个深度学习算法，包括开源和内部开发的算法。结果表明，合并不同的方法可以提高肺部分割，二元病变分割和多种子病变分割的总体测试集性能，从而分别为0.982,0.724和0.469的平均骰子分别。将得到的二元病变分段为91.3ml的平均绝对体积误差。通常，区分不同病变类型的任务更加困难，分别具有152mL的平均绝对体积差，分别为整合和磨碎玻璃不透明度为0.369和0.523的平均骰子分数。所有方法都以平均体积误差进行二元病变分割，该分段优于人类评估者的视觉评估，表明这些方法足以用于临床实践中使用的大规模评估。

The future of population-based breast cancer screening is likely personalized strategies based on clinically relevant risk models. Mammography-based risk models should remain robust to domain shifts caused by different populations and mammographic devices. Modern risk models do not ensure adaptation across vendor-domains and are often conflated to unintentionally rely on both precursors of cancer and systemic/global mammographic information associated with short- and long-term risk, respectively, which might limit performance. We developed a robust, cross-vendor model for long-term risk assessment. An augmentation-based domain adaption technique, based on flavorization of mammographic views, ensured generalization to an unseen vendor-domain. We trained on samples without diagnosed/potential malignant findings to learn systemic/global breast tissue features, called mammographic texture, indicative of future breast cancer. However, training so may cause erratic convergence. By excluding noise-inducing samples and designing a case-control dataset, a robust ensemble texture model was trained. This model was validated in two independent datasets. In 66,607 Danish women with flavorized Siemens views, the AUC was 0.71 and 0.65 for prediction of interval cancers within two years (ICs) and from two years after screening (LTCs), respectively. In a combination with established risk factors, the model's AUC increased to 0.68 for LTCs. In 25,706 Dutch women with Hologic-processed views, the AUCs were not different from the AUCs in Danish women with flavorized views. The results suggested that the model robustly estimated long-term risk while adapting to an unseen processed vendor-domain. The model identified 8.1% of Danish women accounting for 20.9% of ICs and 14.2% of LTCs.

We present a machine-learning framework to accurately characterize morphologies of Active Galactic Nucleus (AGN) host galaxies within $z<1$. We first use PSFGAN to decouple host galaxy light from the central point source, then we invoke the Galaxy Morphology Network (GaMorNet) to estimate whether the host galaxy is disk-dominated, bulge-dominated, or indeterminate. Using optical images from five bands of the HSC Wide Survey, we build models independently in three redshift bins: low $(0<z<0.25)$, medium $(0.25<z<0.5)$, and high $(0.5<z<1.0)$. By first training on a large number of simulated galaxies, then fine-tuning using far fewer classified real galaxies, our framework predicts the actual morphology for $\sim$ $60\%-70\%$ host galaxies from test sets, with a classification precision of $\sim$ $80\%-95\%$, depending on redshift bin. Specifically, our models achieve disk precision of $96\%/82\%/79\%$ and bulge precision of $90\%/90\%/80\%$ (for the 3 redshift bins), at thresholds corresponding to indeterminate fractions of $30\%/43\%/42\%$. The classification precision of our models has a noticeable dependency on host galaxy radius and magnitude. No strong dependency is observed on contrast ratio. Comparing classifications of real AGNs, our models agree well with traditional 2D fitting with GALFIT. The PSFGAN+GaMorNet framework does not depend on the choice of fitting functions or galaxy-related input parameters, runs orders of magnitude faster than GALFIT, and is easily generalizable via transfer learning, making it an ideal tool for studying AGN host galaxy morphology in forthcoming large imaging survey.

Modelling the temperature of Electric Vehicle (EV) batteries is a fundamental task of EV manufacturing. Extreme temperatures in the battery packs can affect their longevity and power output. Although theoretical models exist for describing heat transfer in battery packs, they are computationally expensive to simulate. Furthermore, it is difficult to acquire data measurements from within the battery cell. In this work, we propose a data-driven surrogate model (LiFe-net) that uses readily accessible driving diagnostics for battery temperature estimation to overcome these limitations. This model incorporates Neural Operators with a traditional numerical integration scheme to estimate the temperature evolution. Moreover, we propose two further variations of the baseline model: LiFe-net trained with a regulariser and LiFe-net trained with time stability loss. We compared these models in terms of generalization error on test data. The results showed that LiFe-net trained with time stability loss outperforms the other two models and can estimate the temperature evolution on unseen data with a relative error of 2.77 % on average.

Steerable convolutional neural networks (CNNs) provide a general framework for building neural networks equivariant to translations and other transformations belonging to an origin-preserving group $G$, such as reflections and rotations. They rely on standard convolutions with $G$-steerable kernels obtained by analytically solving the group-specific equivariance constraint imposed onto the kernel space. As the solution is tailored to a particular group $G$, the implementation of a kernel basis does not generalize to other symmetry transformations, which complicates the development of group equivariant models. We propose using implicit neural representation via multi-layer perceptrons (MLPs) to parameterize $G$-steerable kernels. The resulting framework offers a simple and flexible way to implement Steerable CNNs and generalizes to any group $G$ for which a $G$-equivariant MLP can be built. We apply our method to point cloud (ModelNet-40) and molecular data (QM9) and demonstrate a significant improvement in performance compared to standard Steerable CNNs.

While the interaction of ultra-intense ultra-short laser pulses with near- and overcritical plasmas cannot be directly observed, experimentally accessible quantities (observables) often only indirectly give information about the underlying plasma dynamics. Furthermore, the information provided by observables is incomplete, making the inverse problem highly ambiguous. Therefore, in order to infer plasma dynamics as well as experimental parameter, the full distribution over parameters given an observation needs to considered, requiring that models are flexible and account for the information lost in the forward process. Invertible Neural Networks (INNs) have been designed to efficiently model both the forward and inverse process, providing the full conditional posterior given a specific measurement. In this work, we benchmark INNs and standard statistical methods on synthetic electron spectra. First, we provide experimental results with respect to the acceptance rate, where our results show increases in acceptance rates up to a factor of 10. Additionally, we show that this increased acceptance rate also results in an increased speed-up for INNs to the same extent. Lastly, we propose a composite algorithm that utilizes INNs and promises low runtimes while preserving high accuracy.

The need for data privacy and security -- enforced through increasingly strict data protection regulations -- renders the use of healthcare data for machine learning difficult. In particular, the transfer of data between different hospitals is often not permissible and thus cross-site pooling of data not an option. The Personal Health Train (PHT) paradigm proposed within the GO-FAIR initiative implements an 'algorithm to the data' paradigm that ensures that distributed data can be accessed for analysis without transferring any sensitive data. We present PHT-meDIC, a productively deployed open-source implementation of the PHT concept. Containerization allows us to easily deploy even complex data analysis pipelines (e.g, genomics, image analysis) across multiple sites in a secure and scalable manner. We discuss the underlying technological concepts, security models, and governance processes. The implementation has been successfully applied to distributed analyses of large-scale data, including applications of deep neural networks to medical image data.

Motivation: The size of available omics datasets is steadily increasing with technological advancement in recent years. While this increase in sample size can be used to improve the performance of relevant prediction tasks in healthcare, models that are optimized for large datasets usually operate as black boxes. In high stakes scenarios, like healthcare, using a black-box model poses safety and security issues. Without an explanation about molecular factors and phenotypes that affected the prediction, healthcare providers are left with no choice but to blindly trust the models. We propose a new type of artificial neural networks, named Convolutional Omics Kernel Networks (COmic). By combining convolutional kernel networks with pathway-induced kernels, our method enables robust and interpretable end-to-end learning on omics datasets ranging in size from a few hundred to several hundreds of thousands of samples. Furthermore, COmic can be easily adapted to utilize multi-omics data. Results: We evaluate the performance capabilities of COmic on six different breast cancer cohorts. Additionally, we train COmic models on multi-omics data using the METABRIC cohort. Our models perform either better or similar to competitors on both tasks. We show how the use of pathway-induced Laplacian kernels opens the black-box nature of neural networks and results in intrinsically interpretable models that eliminate the need for \textit{post-hoc} explanation models.

Image segmentation is a largely researched field where neural networks find vast applications in many facets of technology. Some of the most popular approaches to train segmentation networks employ loss functions optimizing pixel-overlap, an objective that is insufficient for many segmentation tasks. In recent years, their limitations fueled a growing interest in topology-aware methods, which aim to recover the correct topology of the segmented structures. However, so far, none of the existing approaches achieve a spatially correct matching between the topological features of ground truth and prediction. In this work, we propose the first topologically and feature-wise accurate metric and loss function for supervised image segmentation, which we term Betti matching. We show how induced matchings guarantee the spatially correct matching between barcodes in a segmentation setting. Furthermore, we propose an efficient algorithm to compute the Betti matching of images. We show that the Betti matching error is an interpretable metric to evaluate the topological correctness of segmentations, which is more sensitive than the well-established Betti number error. Moreover, the differentiability of the Betti matching loss enables its use as a loss function. It improves the topological performance of segmentation networks across six diverse datasets while preserving the volumetric performance. Our code is available in https://github.com/nstucki/Betti-matching.

Human skeleton point clouds are commonly used to automatically classify and predict the behaviour of others. In this paper, we use a contrastive self-supervised learning method, SimCLR, to learn representations that capture the semantics of skeleton point clouds. This work focuses on systematically evaluating the effects that different algorithmic decisions (including augmentations, dataset partitioning and backbone architecture) have on the learned skeleton representations. To pre-train the representations, we normalise six existing datasets to obtain more than 40 million skeleton frames. We evaluate the quality of the learned representations with three downstream tasks: skeleton reconstruction, motion prediction, and activity classification. Our results demonstrate the importance of 1) combining spatial and temporal augmentations, 2) including additional datasets for encoder training, and 3) and using a graph neural network as an encoder.