机器学习方法可以检测变量之间的复杂关系，但通常不利用域知识。这是一个限制，因为在许多科学学科（例如系统生物学）中，域知识以图形或网络的形式获得，并且其使用可以改善模型性能。我们需要在许多研究领域中使用广泛且适用的基于网络的算法。在这项工作中，我们使用具有固有的可解释性的新型贪婪决策森林来证明基于多模式节点特征的子网检测。后者将是保留专家并获得对这种算法的信任的关键因素。为了展示一个具体的应用示例，我们专注于生物信息学，系统生物学，尤其是生物医学，但是提出的方法也适用于许多其他领域。系统生物学是统计数据驱动的机器学习能够分析大量多模式生物医学数据的一个很好的例子。这对于达到精密医学的未来目标很重要，在该目标中，患者的复杂性是在系统层面上建模的，以最佳量身定制医疗决策，健康实践和疗法。我们提出的方法可以帮助揭示从多词数据数据的引起疾病的网络模块，以更好地了解诸如癌症之类的复杂疾病。

The release of ChatGPT, a language model capable of generating text that appears human-like and authentic, has gained significant attention beyond the research community. We expect that the convincing performance of ChatGPT incentivizes users to apply it to a variety of downstream tasks, including prompting the model to simplify their own medical reports. To investigate this phenomenon, we conducted an exploratory case study. In a questionnaire, we asked 15 radiologists to assess the quality of radiology reports simplified by ChatGPT. Most radiologists agreed that the simplified reports were factually correct, complete, and not potentially harmful to the patient. Nevertheless, instances of incorrect statements, missed key medical findings, and potentially harmful passages were reported. While further studies are needed, the initial insights of this study indicate a great potential in using large language models like ChatGPT to improve patient-centered care in radiology and other medical domains.

Deep learning-based 3D human pose estimation performs best when trained on large amounts of labeled data, making combined learning from many datasets an important research direction. One obstacle to this endeavor are the different skeleton formats provided by different datasets, i.e., they do not label the same set of anatomical landmarks. There is little prior research on how to best supervise one model with such discrepant labels. We show that simply using separate output heads for different skeletons results in inconsistent depth estimates and insufficient information sharing across skeletons. As a remedy, we propose a novel affine-combining autoencoder (ACAE) method to perform dimensionality reduction on the number of landmarks. The discovered latent 3D points capture the redundancy among skeletons, enabling enhanced information sharing when used for consistency regularization. Our approach scales to an extreme multi-dataset regime, where we use 28 3D human pose datasets to supervise one model, which outperforms prior work on a range of benchmarks, including the challenging 3D Poses in the Wild (3DPW) dataset. Our code and models are available for research purposes.

We propose an end-to-end inverse rendering pipeline called SupeRVol that allows us to recover 3D shape and material parameters from a set of color images in a super-resolution manner. To this end, we represent both the bidirectional reflectance distribution function (BRDF) and the signed distance function (SDF) by multi-layer perceptrons. In order to obtain both the surface shape and its reflectance properties, we revert to a differentiable volume renderer with a physically based illumination model that allows us to decouple reflectance and lighting. This physical model takes into account the effect of the camera's point spread function thereby enabling a reconstruction of shape and material in a super-resolution quality. Experimental validation confirms that SupeRVol achieves state of the art performance in terms of inverse rendering quality. It generates reconstructions that are sharper than the individual input images, making this method ideally suited for 3D modeling from low-resolution imagery.

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.

Yggdrasil Decision Forests is a library for the training, serving and interpretation of decision forest models, targeted both at research and production work, implemented in C++, and available in C++, command line interface, Python (under the name TensorFlow Decision Forests), JavaScript, and Go. The library has been developed organically since 2018 following a set of four design principles applicable to machine learning libraries and frameworks: simplicity of use, safety of use, modularity and high-level abstraction, and integration with other machine learning libraries. In this paper, we describe those principles in detail and present how they have been used to guide the design of the library. We then showcase the use of our library on a set of classical machine learning problems. Finally, we report a benchmark comparing our library to related solutions.

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.

Segmenting humans in 3D indoor scenes has become increasingly important with the rise of human-centered robotics and AR/VR applications. In this direction, we explore the tasks of 3D human semantic-, instance- and multi-human body-part segmentation. Few works have attempted to directly segment humans in point clouds (or depth maps), which is largely due to the lack of training data on humans interacting with 3D scenes. We address this challenge and propose a framework for synthesizing virtual humans in realistic 3D scenes. Synthetic point cloud data is attractive since the domain gap between real and synthetic depth is small compared to images. Our analysis of different training schemes using a combination of synthetic and realistic data shows that synthetic data for pre-training improves performance in a wide variety of segmentation tasks and models. We further propose the first end-to-end model for 3D multi-human body-part segmentation, called Human3D, that performs all the above segmentation tasks in a unified manner. Remarkably, Human3D even outperforms previous task-specific state-of-the-art methods. Finally, we manually annotate humans in test scenes from EgoBody to compare the proposed training schemes and segmentation models.

Traditionally, monocular 3D human pose estimation employs a machine learning model to predict the most likely 3D pose for a given input image. However, a single image can be highly ambiguous and induces multiple plausible solutions for the 2D-3D lifting step which results in overly confident 3D pose predictors. To this end, we propose \emph{DiffPose}, a conditional diffusion model, that predicts multiple hypotheses for a given input image. In comparison to similar approaches, our diffusion model is straightforward and avoids intensive hyperparameter tuning, complex network structures, mode collapse, and unstable training. Moreover, we tackle a problem of the common two-step approach that first estimates a distribution of 2D joint locations via joint-wise heatmaps and consecutively approximates them based on first- or second-moment statistics. Since such a simplification of the heatmaps removes valid information about possibly correct, though labeled unlikely, joint locations, we propose to represent the heatmaps as a set of 2D joint candidate samples. To extract information about the original distribution from these samples we introduce our \emph{embedding transformer} that conditions the diffusion model. Experimentally, we show that DiffPose slightly improves upon the state of the art for multi-hypothesis pose estimation for simple poses and outperforms it by a large margin for highly ambiguous poses.

Network intrusion detection systems (NIDS) to detect malicious attacks continues to meet challenges. NIDS are vulnerable to auto-generated port scan infiltration attempts and NIDS are often developed offline, resulting in a time lag to prevent the spread of infiltration to other parts of a network. To address these challenges, we use hypergraphs to capture evolving patterns of port scan attacks via the set of internet protocol addresses and destination ports, thereby deriving a set of hypergraph-based metrics to train a robust and resilient ensemble machine learning (ML) NIDS that effectively monitors and detects port scanning activities and adversarial intrusions while evolving intelligently in real-time. Through the combination of (1) intrusion examples, (2) NIDS update rules, (3) attack threshold choices to trigger NIDS retraining requests, and (4) production environment with no prior knowledge of the nature of network traffic 40 scenarios were auto-generated to evaluate the ML ensemble NIDS comprising three tree-based models. Results show that under the model settings of an Update-ALL-NIDS rule (namely, retrain and update all the three models upon the same NIDS retraining request) the proposed ML ensemble NIDS produced the best results with nearly 100% detection performance throughout the simulation, exhibiting robustness in the complex dynamics of the simulated cyber-security scenario.