The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

由多种因素引起的组织学图像的染色变化不仅是病理学家的视觉诊断，而且是细胞分割算法的挑战。为了消除颜色变化，已经提出了许多染色归一化方法。但是，大多数是为苏木精和曙红染色图像而设计的，并且在免疫组织化学染色图像上表现不佳。当前的细胞分割方法系统地将染色归一化作为预处理步骤，但是尚未定量研究颜色变化带来的影响。在本文中，我们制作了五组具有不同颜色的Neun染色图像。我们应用了一种深度学习的图像录制方法来在组织学图像组之间执行色彩转移。最后，我们改变了分割集的颜色，并量化了颜色变化对细胞分割的影响。结果证明了在后续分析之前必须进行颜色归一化的必要性。

在嘈杂和致密的荧光显微镜数据中跟踪胚胎的所有核是一项具有挑战性的任务。我们建立在最新的核跟踪方法的基础上，该方法结合了弱监督的学习，从一小部分核中心点注释与整数线性程序（ILP）结合了最佳的细胞谱系提取。我们的工作专门解决了秀丽隐杆线虫胚胎记录的以下具有挑战性的特性：（1）与其他生物的基准记录相比，许多细胞分裂以及（2）很容易被误认为是细胞核的极性体。为了应付（1），我们设计并纳入了学习的细胞分裂检测器。为了应付（2），我们采用了学到的极性身体探测器。我们进一步提出了通过结构化的SVM调整自动化的ILP权重，从而减轻了对各自的网格搜索进行乏味的手动设置的需求。我们的方法的表现优于Fluo-N3DH-CE胚胎数据集上细胞跟踪挑战的先前领导者。我们报告了另外两个秀丽隐杆线虫数据集的进一步广泛的定量评估。我们将公开这些数据集作为未来方法开发的扩展基准。我们的结果表明，我们的方法产生了可观的改进，尤其是在分区事件检测的正确性以及完全正确的轨道段的数量和长度方面。代码：https：//github.com/funkelab/linajea

数据增强是自然语言处理（NLP）模型的鲁棒性评估的重要组成部分，以及增强他们培训的数据的多样性。在本文中，我们呈现NL-Cogmenter，这是一种新的参与式Python的自然语言增强框架，它支持创建两个转换（对数据的修改）和过滤器（根据特定功能的数据拆分）。我们描述了框架和初始的117个变换和23个过滤器，用于各种自然语言任务。我们通过使用其几个转换来分析流行自然语言模型的鲁棒性来证明NL-Upmenter的功效。基础架构，Datacards和稳健性分析结果在NL-Augmenter存储库上公开可用（\ url {https://github.com/gem-benchmark/nl-augmenter}）。

对脑组织学数据分析的重大挑战是精确地识别解剖区域，以便进行准确的局部量化并评估治疗溶液。通常，这项任务是手动执行的，因此变得繁琐和主观。另一种选择是使用自动或半自动方法，其中使用数字atlase共同注册的分段。但是，最具可用的地图集是3D，而数字化的组织学数据是2D。需要从地图集执行此类2D-3D分段的方法。本文采用线性注册提出了一种在ATLA的3D体积内自动和准确地分割单个2D冠状切片的策略。我们使用全脑规模的探索方法验证了其鲁棒性和性能。

细胞个体化对数字病理图像分析具有重要作用。深度学习被认为是用于实例分割任务的有效工具，包括细胞个性化。然而，深度学习模型的精度依赖于大规模的无偏见数据集和手动像素级注释，这是劳动密集型的。此外，大多数深度学习的应用已经开发用于加工肿瘤数据。为了克服这些挑战，i）我们建立了一个管道，以合成具有所提供的点注释的像素级标签;ii）我们测试了一项集体深度学习算法，以对神经数据进行细胞个体化。结果表明，所提出的方法成功地分离了物体级和像素水平的神经元细胞，平均检测精度为0.93。

Modeling lies at the core of both the financial and the insurance industry for a wide variety of tasks. The rise and development of machine learning and deep learning models have created many opportunities to improve our modeling toolbox. Breakthroughs in these fields often come with the requirement of large amounts of data. Such large datasets are often not publicly available in finance and insurance, mainly due to privacy and ethics concerns. This lack of data is currently one of the main hurdles in developing better models. One possible option to alleviating this issue is generative modeling. Generative models are capable of simulating fake but realistic-looking data, also referred to as synthetic data, that can be shared more freely. Generative Adversarial Networks (GANs) is such a model that increases our capacity to fit very high-dimensional distributions of data. While research on GANs is an active topic in fields like computer vision, they have found limited adoption within the human sciences, like economics and insurance. Reason for this is that in these fields, most questions are inherently about identification of causal effects, while to this day neural networks, which are at the center of the GAN framework, focus mostly on high-dimensional correlations. In this paper we study the causal preservation capabilities of GANs and whether the produced synthetic data can reliably be used to answer causal questions. This is done by performing causal analyses on the synthetic data, produced by a GAN, with increasingly more lenient assumptions. We consider the cross-sectional case, the time series case and the case with a complete structural model. It is shown that in the simple cross-sectional scenario where correlation equals causation the GAN preserves causality, but that challenges arise for more advanced analyses.

Deep learning models are known to put the privacy of their training data at risk, which poses challenges for their safe and ethical release to the public. Differentially private stochastic gradient descent is the de facto standard for training neural networks without leaking sensitive information about the training data. However, applying it to models for graph-structured data poses a novel challenge: unlike with i.i.d. data, sensitive information about a node in a graph cannot only leak through its gradients, but also through the gradients of all nodes within a larger neighborhood. In practice, this limits privacy-preserving deep learning on graphs to very shallow graph neural networks. We propose to solve this issue by training graph neural networks on disjoint subgraphs of a given training graph. We develop three random-walk-based methods for generating such disjoint subgraphs and perform a careful analysis of the data-generating distributions to provide strong privacy guarantees. Through extensive experiments, we show that our method greatly outperforms the state-of-the-art baseline on three large graphs, and matches or outperforms it on four smaller ones.

Data-driven models such as neural networks are being applied more and more to safety-critical applications, such as the modeling and control of cyber-physical systems. Despite the flexibility of the approach, there are still concerns about the safety of these models in this context, as well as the need for large amounts of potentially expensive data. In particular, when long-term predictions are needed or frequent measurements are not available, the open-loop stability of the model becomes important. However, it is difficult to make such guarantees for complex black-box models such as neural networks, and prior work has shown that model stability is indeed an issue. In this work, we consider an aluminum extraction process where measurements of the internal state of the reactor are time-consuming and expensive. We model the process using neural networks and investigate the role of including skip connections in the network architecture as well as using l1 regularization to induce sparse connection weights. We demonstrate that these measures can greatly improve both the accuracy and the stability of the models for datasets of varying sizes.

Machine learning models are typically evaluated by computing similarity with reference annotations and trained by maximizing similarity with such. Especially in the bio-medical domain, annotations are subjective and suffer from low inter- and intra-rater reliability. Since annotations only reflect the annotation entity's interpretation of the real world, this can lead to sub-optimal predictions even though the model achieves high similarity scores. Here, the theoretical concept of Peak Ground Truth (PGT) is introduced. PGT marks the point beyond which an increase in similarity with the reference annotation stops translating to better Real World Model Performance (RWMP). Additionally, a quantitative technique to approximate PGT by computing inter- and intra-rater reliability is proposed. Finally, three categories of PGT-aware strategies to evaluate and improve model performance are reviewed.