机器学习（ML）为生物处理工程的发展做出了重大贡献，但其应用仍然有限，阻碍了生物过程自动化的巨大潜力。用于模型构建自动化的ML可以看作是引入另一种抽象水平的一种方式，将专家的人类集中在生物过程开发的最认知任务中。首先，概率编程用于预测模型的自动构建。其次，机器学习会通过计划实验来测试假设并进行调查以收集信息性数据来自动评估替代决策，以收集基于模型预测不确定性的模型选择的信息数据。这篇评论提供了有关生物处理开发中基于ML的自动化的全面概述。一方面，生物技术和生物工程社区应意识到现有ML解决方案在生物技术和生物制药中的应用的限制。另一方面，必须确定缺失的链接，以使ML和人工智能（AI）解决方案轻松实施在有价值的生物社区解决方案中。我们总结了几个重要的生物处理系统的ML实施，并提出了两个至关重要的挑战，这些挑战仍然是生物技术自动化的瓶颈，并减少了生物技术开发的不确定性。没有一个合适的程序；但是，这项综述应有助于确定结合生物技术和ML领域的潜在自动化。

Objective: Convolutional neural networks (CNNs) have demonstrated promise in automated cardiac magnetic resonance image segmentation. However, when using CNNs in a large real-world dataset, it is important to quantify segmentation uncertainty and identify segmentations which could be problematic. In this work, we performed a systematic study of Bayesian and non-Bayesian methods for estimating uncertainty in segmentation neural networks. Methods: We evaluated Bayes by Backprop, Monte Carlo Dropout, Deep Ensembles, and Stochastic Segmentation Networks in terms of segmentation accuracy, probability calibration, uncertainty on out-of-distribution images, and segmentation quality control. Results: We observed that Deep Ensembles outperformed the other methods except for images with heavy noise and blurring distortions. We showed that Bayes by Backprop is more robust to noise distortions while Stochastic Segmentation Networks are more resistant to blurring distortions. For segmentation quality control, we showed that segmentation uncertainty is correlated with segmentation accuracy for all the methods. With the incorporation of uncertainty estimates, we were able to reduce the percentage of poor segmentation to 5% by flagging 31--48% of the most uncertain segmentations for manual review, substantially lower than random review without using neural network uncertainty (reviewing 75--78% of all images). Conclusion: This work provides a comprehensive evaluation of uncertainty estimation methods and showed that Deep Ensembles outperformed other methods in most cases. Significance: Neural network uncertainty measures can help identify potentially inaccurate segmentations and alert users for manual review.

Diversity Searcher is a tool originally developed to help analyse diversity in news media texts. It relies on a form of automated content analysis and thus rests on prior assumptions and depends on certain design choices related to diversity and fairness. One such design choice is the external knowledge source(s) used. In this article, we discuss implications that these sources can have on the results of content analysis. We compare two data sources that Diversity Searcher has worked with - DBpedia and Wikidata - with respect to their ontological coverage and diversity, and describe implications for the resulting analyses of text corpora. We describe a case study of the relative over- or under-representation of Belgian political parties between 1990 and 2020 in the English-language DBpedia, the Dutch-language DBpedia, and Wikidata, and highlight the many decisions needed with regard to the design of this data analysis and the assumptions behind it, as well as implications from the results. In particular, we came across a staggering over-representation of the political right in the English-language DBpedia.

Artificial intelligence(AI) systems based on deep neural networks (DNNs) and machine learning (ML) algorithms are increasingly used to solve critical problems in bioinformatics, biomedical informatics, and precision medicine. However, complex DNN or ML models that are unavoidably opaque and perceived as black-box methods, may not be able to explain why and how they make certain decisions. Such black-box models are difficult to comprehend not only for targeted users and decision-makers but also for AI developers. Besides, in sensitive areas like healthcare, explainability and accountability are not only desirable properties of AI but also legal requirements -- especially when AI may have significant impacts on human lives. Explainable artificial intelligence (XAI) is an emerging field that aims to mitigate the opaqueness of black-box models and make it possible to interpret how AI systems make their decisions with transparency. An interpretable ML model can explain how it makes predictions and which factors affect the model's outcomes. The majority of state-of-the-art interpretable ML methods have been developed in a domain-agnostic way and originate from computer vision, automated reasoning, or even statistics. Many of these methods cannot be directly applied to bioinformatics problems, without prior customization, extension, and domain adoption. In this paper, we discuss the importance of explainability with a focus on bioinformatics. We analyse and comprehensively overview of model-specific and model-agnostic interpretable ML methods and tools. Via several case studies covering bioimaging, cancer genomics, and biomedical text mining, we show how bioinformatics research could benefit from XAI methods and how they could help improve decision fairness.

Kernel machines have sustained continuous progress in the field of quantum chemistry. In particular, they have proven to be successful in the low-data regime of force field reconstruction. This is because many physical invariances and symmetries can be incorporated into the kernel function to compensate for much larger datasets. So far, the scalability of this approach has however been hindered by its cubical runtime in the number of training points. While it is known, that iterative Krylov subspace solvers can overcome these burdens, they crucially rely on effective preconditioners, which are elusive in practice. Practical preconditioners need to be computationally efficient and numerically robust at the same time. Here, we consider the broad class of Nystr\"om-type methods to construct preconditioners based on successively more sophisticated low-rank approximations of the original kernel matrix, each of which provides a different set of computational trade-offs. All considered methods estimate the relevant subspace spanned by the kernel matrix columns using different strategies to identify a representative set of inducing points. Our comprehensive study covers the full spectrum of approaches, starting from naive random sampling to leverage score estimates and incomplete Cholesky factorizations, up to exact SVD decompositions.

We present an automatic method for annotating images of indoor scenes with the CAD models of the objects by relying on RGB-D scans. Through a visual evaluation by 3D experts, we show that our method retrieves annotations that are at least as accurate as manual annotations, and can thus be used as ground truth without the burden of manually annotating 3D data. We do this using an analysis-by-synthesis approach, which compares renderings of the CAD models with the captured scene. We introduce a 'cloning procedure' that identifies objects that have the same geometry, to annotate these objects with the same CAD models. This allows us to obtain complete annotations for the ScanNet dataset and the recent ARKitScenes dataset.

Objective: Imbalances of the electrolyte concentration levels in the body can lead to catastrophic consequences, but accurate and accessible measurements could improve patient outcomes. While blood tests provide accurate measurements, they are invasive and the laboratory analysis can be slow or inaccessible. In contrast, an electrocardiogram (ECG) is a widely adopted tool which is quick and simple to acquire. However, the problem of estimating continuous electrolyte concentrations directly from ECGs is not well-studied. We therefore investigate if regression methods can be used for accurate ECG-based prediction of electrolyte concentrations. Methods: We explore the use of deep neural networks (DNNs) for this task. We analyze the regression performance across four electrolytes, utilizing a novel dataset containing over 290000 ECGs. For improved understanding, we also study the full spectrum from continuous predictions to binary classification of extreme concentration levels. To enhance clinical usefulness, we finally extend to a probabilistic regression approach and evaluate different uncertainty estimates. Results: We find that the performance varies significantly between different electrolytes, which is clinically justified in the interplay of electrolytes and their manifestation in the ECG. We also compare the regression accuracy with that of traditional machine learning models, demonstrating superior performance of DNNs. Conclusion: Discretization can lead to good classification performance, but does not help solve the original problem of predicting continuous concentration levels. While probabilistic regression demonstrates potential practical usefulness, the uncertainty estimates are not particularly well-calibrated. Significance: Our study is a first step towards accurate and reliable ECG-based prediction of electrolyte concentration levels.

Earthquakes, fire, and floods often cause structural collapses of buildings. The inspection of damaged buildings poses a high risk for emergency forces or is even impossible, though. We present three recent selected missions of the Robotics Task Force of the German Rescue Robotics Center, where both ground and aerial robots were used to explore destroyed buildings. We describe and reflect the missions as well as the lessons learned that have resulted from them. In order to make robots from research laboratories fit for real operations, realistic test environments were set up for outdoor and indoor use and tested in regular exercises by researchers and emergency forces. Based on this experience, the robots and their control software were significantly improved. Furthermore, top teams of researchers and first responders were formed, each with realistic assessments of the operational and practical suitability of robotic systems.

Fine-grained semantic segmentation of a person's face and head, including facial parts and head components, has progressed a great deal in recent years. However, it remains a challenging task, whereby considering ambiguous occlusions and large pose variations are particularly difficult. To overcome these difficulties, we propose a novel framework termed Mask-FPAN. It uses a de-occlusion module that learns to parse occluded faces in a semi-supervised way. In particular, face landmark localization, face occlusionstimations, and detected head poses are taken into account. A 3D morphable face model combined with the UV GAN improves the robustness of 2D face parsing. In addition, we introduce two new datasets named FaceOccMask-HQ and CelebAMaskOcc-HQ for face paring work. The proposed Mask-FPAN framework addresses the face parsing problem in the wild and shows significant performance improvements with MIOU from 0.7353 to 0.9013 compared to the state-of-the-art on challenging face datasets.

Deep unfolding networks (DUNs) have proven to be a viable approach to compressive sensing (CS). In this work, we propose a DUN called low-rank CS network (LR-CSNet) for natural image CS. Real-world image patches are often well-represented by low-rank approximations. LR-CSNet exploits this property by adding a low-rank prior to the CS optimization task. We derive a corresponding iterative optimization procedure using variable splitting, which is then translated to a new DUN architecture. The architecture uses low-rank generation modules (LRGMs), which learn low-rank matrix factorizations, as well as gradient descent and proximal mappings (GDPMs), which are proposed to extract high-frequency features to refine image details. In addition, the deep features generated at each reconstruction stage in the DUN are transferred between stages to boost the performance. Our extensive experiments on three widely considered datasets demonstrate the promising performance of LR-CSNet compared to state-of-the-art methods in natural image CS.