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.

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.

经典的多个实例学习（MIL）方法通常基于实例之间的相同和独立的分布式假设，因此忽略了个人实体以外的潜在丰富的上下文信息。另一方面，已经提出了具有全球自我发场模块的变压器来对所有实例之间的相互依赖性进行建模。但是，在本文中，我们质疑：是否需要使用自我注意力进行全球关系建模，或者我们是否可以适当地将自我注意计算限制为大规模整个幻灯片图像（WSIS）中的本地制度？我们为MIL（LA-MIL）提出了一个通用的基于局部注意力图的变压器，通过在自适应局部任意大小的自适应局部方案中明确化情境化实例，从而引入了归纳偏见。此外，有效适应的损失函数使我们可以学习表达性WSI嵌入的方法，以进行多种生物标志物的联合分析。我们证明，LA-MIL实现了最新的胃肠癌预测，从而超过了重要生物标志物（例如微卫星不稳定性的结直肠癌）的现有模型。我们的发现表明，本地自我注意力足够模型与全球模块相同的依赖性。我们的LA-MIL实施可从https://github.com/agentdr1/la_mil获得。

用于核细胞分割的注释显微镜图像是费力且耗时的。为了利用少数现有的注释，也跨越多种方式，我们提出了一种基于生成的对抗网络（GAN）的新型显微镜式增强技术。与其他风格转移方法不同，它不仅可以处理不同的细胞测定类型和照明条件，还可以与不同的成像方式，例如亮场和荧光显微镜。使用Disentangled表示的内容和风格，我们可以在增强期间改变其风格的同时保留原始图像的结构。我们在2018年数据科学碗数据集上评估我们的数据增强，包括各种细胞测定，照明条件和成像方式。凭借我们的增强，竞争中两个排名排名蒙版R-CNN的核细胞分割算法的分割精度显着增加。因此，我们的增强技术使下游任务更加强大地对测试数据异质性，并有助于抵消类别不平衡而不重新采样少数类。

We test grip strength and shock absorption properties of various granular material in granular jamming robotic components. The granular material comprises a range of natural, manufactured, and 3D printed material encompassing a wide range of shapes, sizes, and Shore hardness. Two main experiments are considered, both representing compelling use cases for granular jamming in soft robotics. The first experiment measures grip strength (retention force measured in Newtons) when we fill a latex balloon with the chosen grain type and use it as a granular jamming gripper to pick up a range of test objects. The second experiment measures shock absorption properties recorded by an Inertial Measurement Unit which is suspended in an envelope of granular material and dropped from a set height. Our results highlight a range of shape, size and softness effects, including that grain deformability is a key determinant of grip strength, and interestingly, that larger grain sizes in 3D printed grains create better shock absorbing materials.

Machine learning models are known to be susceptible to adversarial perturbation. One famous attack is the adversarial patch, a sticker with a particularly crafted pattern that makes the model incorrectly predict the object it is placed on. This attack presents a critical threat to cyber-physical systems that rely on cameras such as autonomous cars. Despite the significance of the problem, conducting research in this setting has been difficult; evaluating attacks and defenses in the real world is exceptionally costly while synthetic data are unrealistic. In this work, we propose the REAP (REalistic Adversarial Patch) benchmark, a digital benchmark that allows the user to evaluate patch attacks on real images, and under real-world conditions. Built on top of the Mapillary Vistas dataset, our benchmark contains over 14,000 traffic signs. Each sign is augmented with a pair of geometric and lighting transformations, which can be used to apply a digitally generated patch realistically onto the sign. Using our benchmark, we perform the first large-scale assessments of adversarial patch attacks under realistic conditions. Our experiments suggest that adversarial patch attacks may present a smaller threat than previously believed and that the success rate of an attack on simpler digital simulations is not predictive of its actual effectiveness in practice. We release our benchmark publicly at https://github.com/wagner-group/reap-benchmark.

Self-supervised image denoising techniques emerged as convenient methods that allow training denoising models without requiring ground-truth noise-free data. Existing methods usually optimize loss metrics that are calculated from multiple noisy realizations of similar images, e.g., from neighboring tomographic slices. However, those approaches fail to utilize the multiple contrasts that are routinely acquired in medical imaging modalities like MRI or dual-energy CT. In this work, we propose the new self-supervised training scheme Noise2Contrast that combines information from multiple measured image contrasts to train a denoising model. We stack denoising with domain-transfer operators to utilize the independent noise realizations of different image contrasts to derive a self-supervised loss. The trained denoising operator achieves convincing quantitative and qualitative results, outperforming state-of-the-art self-supervised methods by 4.7-11.0%/4.8-7.3% (PSNR/SSIM) on brain MRI data and by 43.6-50.5%/57.1-77.1% (PSNR/SSIM) on dual-energy CT X-ray microscopy data with respect to the noisy baseline. Our experiments on different real measured data sets indicate that Noise2Contrast training generalizes to other multi-contrast imaging modalities.

Accurate uncertainty measurement is a key step to building robust and reliable machine learning systems. Conformal prediction is a distribution-free uncertainty quantification algorithm popular for its ease of implementation, statistical coverage guarantees, and versatility for underlying forecasters. However, existing conformal prediction algorithms for time series are limited to single-step prediction without considering the temporal dependency. In this paper we propose a Copula Conformal Prediction algorithm for multivariate, multi-step Time Series forecasting, CopulaCPTS. On several synthetic and real-world multivariate time series datasets, we show that CopulaCPTS produces more calibrated and sharp confidence intervals for multi-step prediction tasks than existing techniques.

Incorporating computed tomography (CT) reconstruction operators into differentiable pipelines has proven beneficial in many applications. Such approaches usually focus on the projection data and keep the acquisition geometry fixed. However, precise knowledge of the acquisition geometry is essential for high quality reconstruction results. In this paper, the differentiable formulation of fan-beam CT reconstruction is extended to the acquisition geometry. This allows to propagate gradient information from a loss function on the reconstructed image into the geometry parameters. As a proof-of-concept experiment, this idea is applied to rigid motion compensation. The cost function is parameterized by a trained neural network which regresses an image quality metric from the motion affected reconstruction alone. Using the proposed method, we are the first to optimize such an autofocus-inspired algorithm based on analytical gradients. The algorithm achieves a reduction in MSE by 35.5 % and an improvement in SSIM by 12.6 % over the motion affected reconstruction. Next to motion compensation, we see further use cases of our differentiable method for scanner calibration or hybrid techniques employing deep models.

For conceptual design, engineers rely on conventional iterative (often manual) techniques. Emerging parametric models facilitate design space exploration based on quantifiable performance metrics, yet remain time-consuming and computationally expensive. Pure optimisation methods, however, ignore qualitative aspects (e.g. aesthetics or construction methods). This paper provides a performance-driven design exploration framework to augment the human designer through a Conditional Variational Autoencoder (CVAE), which serves as forward performance predictor for given design features as well as an inverse design feature predictor conditioned on a set of performance requests. The CVAE is trained on 18'000 synthetically generated instances of a pedestrian bridge in Switzerland. Sensitivity analysis is employed for explainability and informing designers about (i) relations of the model between features and/or performances and (ii) structural improvements under user-defined objectives. A case study proved our framework's potential to serve as a future co-pilot for conceptual design studies of pedestrian bridges and beyond.