Attention-based multiple instance learning (AMIL) algorithms have proven to be successful in utilizing gigapixel whole-slide images (WSIs) for a variety of different computational pathology tasks such as outcome prediction and cancer subtyping problems. We extended an AMIL approach to the task of survival prediction by utilizing the classical Cox partial likelihood as a loss function, converting the AMIL model into a nonlinear proportional hazards model. We applied the model to tissue microarray (TMA) slides of 330 lung cancer patients. The results show that AMIL approaches can handle very small amounts of tissue from a TMA and reach similar C-index performance compared to established survival prediction methods trained with highly discriminative clinical factors such as age, cancer grade, and cancer stage

Nucleolar organizer regions (NORs) are parts of the DNA that are involved in RNA transcription. Due to the silver affinity of associated proteins, argyrophilic NORs (AgNORs) can be visualized using silver-based staining. The average number of AgNORs per nucleus has been shown to be a prognostic factor for predicting the outcome of many tumors. Since manual detection of AgNORs is laborious, automation is of high interest. We present a deep learning-based pipeline for automatically determining the AgNOR-score from histopathological sections. An additional annotation experiment was conducted with six pathologists to provide an independent performance evaluation of our approach. Across all raters and images, we found a mean squared error of 0.054 between the AgNOR- scores of the experts and those of the model, indicating that our approach offers performance comparable to humans.

Mitotic activity is key for the assessment of malignancy in many tumors. Moreover, it has been demonstrated that the proportion of abnormal mitosis to normal mitosis is of prognostic significance. Atypical mitotic figures (MF) can be identified morphologically as having segregation abnormalities of the chromatids. In this work, we perform, for the first time, automatic subtyping of mitotic figures into normal and atypical categories according to characteristic morphological appearances of the different phases of mitosis. Using the publicly available MIDOG21 and TUPAC16 breast cancer mitosis datasets, two experts blindly subtyped mitotic figures into five morphological categories. Further, we set up a state-of-the-art object detection pipeline extending the anchor-free FCOS approach with a gated hierarchical subclassification branch. Our labeling experiment indicated that subtyping of mitotic figures is a challenging task and prone to inter-rater disagreement, which we found in 24.89% of MF. Using the more diverse MIDOG21 dataset for training and TUPAC16 for testing, we reached a mean overall average precision score of 0.552, a ROC AUC score of 0.833 for atypical/normal MF and a mean class-averaged ROC-AUC score of 0.977 for discriminating the different phases of cells undergoing mitosis.

Computer-aided systems in histopathology are often challenged by various sources of domain shift that impact the performance of these algorithms considerably. We investigated the potential of using self-supervised pre-training to overcome scanner-induced domain shifts for the downstream task of tumor segmentation. For this, we present the Barlow Triplets to learn scanner-invariant representations from a multi-scanner dataset with local image correspondences. We show that self-supervised pre-training successfully aligned different scanner representations, which, interestingly only results in a limited benefit for our downstream task. We thereby provide insights into the influence of scanner characteristics for downstream applications and contribute to a better understanding of why established self-supervised methods have not yet shown the same success on histopathology data as they have for natural images.

由于形态的相似性，皮肤肿瘤的组织学切片分化为个体亚型可能具有挑战性。最近，基于深度学习的方法证明了它们在这方面支持病理学家的潜力。但是，这些监督算法中的许多都需要大量的注释数据才能进行稳健开发。我们提供了一个公开可用的数据集，该数据集是七个不同的犬皮肤肿瘤的350张全滑图像，其中有13种组织学类别的12,424个多边形注释，包括7种皮肤肿瘤亚型。在评估者间实验中，我们显示了提供的标签的高稠度，尤其是对于肿瘤注释。我们通过训练深层神经网络来进一步验证数据集，以完成组织分割和肿瘤亚型分类的任务。我们的肿瘤尤其是0.7047的类平均Jaccard系数为0.7047，尤其是0.9044。对于分类，我们达到了0.9857的幻灯片级准确性。由于犬皮肤肿瘤对人肿瘤具有各种组织学同源性，因此该数据集的附加值不限于兽医病理学，而是扩展到更一般的应用领域。

评估有丝分裂计数具有已知的高度内和帧间间变异性。已证明计算机辅助系统可降低这种可变性并减少标记时间。然而，这些系统通常高度依赖于其培训领域，并表现出对看不见的域的适用性差。在组织病理学中，这些域移位可以由各种来源产生，包括用于数字化组织学样本的不同滑动扫描系统。有丝分裂域泛化挑战的挑战集中在这种特定领域转变对有丝分裂形象检测的任务。这项工作提出了一种主要的有丝分裂形象检测算法作为挑战的基线，基于域对抗训练。在挑战的测试集上，该算法将F $ _1 $得分为0.7183。相应的网络权重和用于实现网络的代码是公开可用的。

Partial differential equations (PDEs) are important tools to model physical systems, and including them into machine learning models is an important way of incorporating physical knowledge. Given any system of linear PDEs with constant coefficients, we propose a family of Gaussian process (GP) priors, which we call EPGP, such that all realizations are exact solutions of this system. We apply the Ehrenpreis-Palamodov fundamental principle, which works like a non-linear Fourier transform, to construct GP kernels mirroring standard spectral methods for GPs. Our approach can infer probable solutions of linear PDE systems from any data such as noisy measurements, or initial and boundary conditions. Constructing EPGP-priors is algorithmic, generally applicable, and comes with a sparse version (S-EPGP) that learns the relevant spectral frequencies and works better for big data sets. We demonstrate our approach on three families of systems of PDE, the heat equation, wave equation, and Maxwell's equations, where we improve upon the state of the art in computation time and precision, in some experiments by several orders of magnitude.

Unbiased learning to rank (ULTR) studies the problem of mitigating various biases from implicit user feedback data such as clicks, and has been receiving considerable attention recently. A popular ULTR approach for real-world applications uses a two-tower architecture, where click modeling is factorized into a relevance tower with regular input features, and a bias tower with bias-relevant inputs such as the position of a document. A successful factorization will allow the relevance tower to be exempt from biases. In this work, we identify a critical issue that existing ULTR methods ignored - the bias tower can be confounded with the relevance tower via the underlying true relevance. In particular, the positions were determined by the logging policy, i.e., the previous production model, which would possess relevance information. We give both theoretical analysis and empirical results to show the negative effects on relevance tower due to such a correlation. We then propose three methods to mitigate the negative confounding effects by better disentangling relevance and bias. Empirical results on both controlled public datasets and a large-scale industry dataset show the effectiveness of the proposed approaches.

G-Enum histograms are a new fast and fully automated method for irregular histogram construction. By framing histogram construction as a density estimation problem and its automation as a model selection task, these histograms leverage the Minimum Description Length principle (MDL) to derive two different model selection criteria. Several proven theoretical results about these criteria give insights about their asymptotic behavior and are used to speed up their optimisation. These insights, combined to a greedy search heuristic, are used to construct histograms in linearithmic time rather than the polynomial time incurred by previous works. The capabilities of the proposed MDL density estimation method are illustrated with reference to other fully automated methods in the literature, both on synthetic and large real-world data sets.

Neural Radiance Fields (NeRFs) are emerging as a ubiquitous scene representation that allows for novel view synthesis. Increasingly, NeRFs will be shareable with other people. Before sharing a NeRF, though, it might be desirable to remove personal information or unsightly objects. Such removal is not easily achieved with the current NeRF editing frameworks. We propose a framework to remove objects from a NeRF representation created from an RGB-D sequence. Our NeRF inpainting method leverages recent work in 2D image inpainting and is guided by a user-provided mask. Our algorithm is underpinned by a confidence based view selection procedure. It chooses which of the individual 2D inpainted images to use in the creation of the NeRF, so that the resulting inpainted NeRF is 3D consistent. We show that our method for NeRF editing is effective for synthesizing plausible inpaintings in a multi-view coherent manner. We validate our approach using a new and still-challenging dataset for the task of NeRF inpainting.