Abstract
Training machine learning models for artificial intelligence (AI) applications in pathology often requires extensive annotation by human experts, but there is little guidance on the subject. In this work, we aimed to describe our experience and provide a simple, useful, and practical guide addressing annotation strategies for AI development in computational pathology. Annotation methodology will vary significantly depending on the specific study's objectives, but common difficulties will be present across different settings. We summarize key aspects and issue guiding principles regarding team interaction, ground-truth quality assessment, different annotation types, and available software and hardware options and address common difficulties while annotating. This guide was specifically designed for pathology annotation, intending to help pathologists, other researchers, and AI developers with this process.(c) 2022 THE AUTHORS. Published by Elsevier Inc. on behalf of the United States & Canadian Academy of Pathology. This is an open access article under the CC BY-NC-ND license (http://creativecommons. org/licenses/by-nc-nd/4.0/).

Abstract
The original version of this Article contained an error in the Acknowledgements section. “This work was partially funded by the Project TAMI—Transparent Artificial Medical Intelligence (NORTE- 01-0247-FEDER-045905) financed by ERDF—European Regional Fund through the North Portugal Regional Operational Program—NORTE 2020 and by the Portuguese Foundation for Science and Technology—FCT under the CMU—Portugal International Partnership, and also by the Portuguese Foundation for Science and Technology—FCT within PhD grants SFRH/BD/139468/2018 and 2020.06434.BD. The authors thank the Swiss National Science Foundation grant number 198388, as well as the Lindenhof foundation for their grant support.” now reads: “This work was supported by National Funds through the Portuguese Funding Agency, FCT–Foundation for Science and Technology Portugal, under Project LA/P/0063/2020, and also by the Portuguese Foundation for Science and Technology - FCT within PhD grants SFRH/BD/139468/2018 and 2020.06434.BD. The authors thank the Swiss National Science Foundation grant number 198388, as well as the Lindenhof foundation for their grant support.” The original Article has been corrected. © The Author(s) 2023.

Abstract
Breast cancer conservative treatment (BCCT) is a form of treatment commonly used for patients with early breast cancer. This procedure consists of removing the cancer and a small margin of surrounding tissue, while leaving the healthy tissue intact. In recent years, this procedure has become increasingly common due to identical survival rates and better cosmetic outcomes than other alternatives. Although significant research has been conducted on BCCT, there is no gold-standard for evaluating the aesthetic results of the treatment. Recent works have proposed the automatic classification of cosmetic results based on breast features extracted from digital photographs. The computation of most of these features requires the representation of the breast contour, which becomes key to the aesthetic evaluation of BCCT. State-of-the-art methods use conventional image processing tools that automatically detect breast contours based on the shortest path applied to the Sobel filter result in a 2D digital photograph of the patient. However, because the Sobel filter is a general edge detector, it treats edges indistinguishably, i.e., it detects too many edges that are not relevant to breast contour detection and too few weak breast contours. In this paper, we propose an improvement to this method that replaces the Sobel filter with a novel neural network solution to improve breast contour detection based on the shortest path. The proposed solution learns effective representations for the edges between the breasts and the torso wall. We obtain state of the art results on a dataset that was used for developing previous models. Furthermore, we tested these models on a new dataset that contains more variable photographs and show that this new approach shows better generalization capabilities as the previously developed deep models do not perform so well when faced with a different dataset for testing. The main contribution of this paper is to further improve the capabilities of models that perform the objective classification of BCCT aesthetic results automatically by improving upon the current standard technique for detecting breast contours in digital photographs. To that end, the models introduced are simple to train and test on new datasets which makes this approach easily reproducible.

Abstract
Cervical cancer is the fourth most common female cancer worldwide and the fourth leading cause of cancer-related death in women. Nonetheless, it is also among the most successfully preventable and treatable types of cancer, provided it is early identified and properly managed. As such, the detection of pre-cancerous lesions is crucial. These lesions are detected in the squamous epithelium of the uterine cervix and are graded as low- or high-grade intraepithelial squamous lesions, known as LSIL and HSIL, respectively. Due to their complex nature, this classification can become very subjective. Therefore, the development of machine learning models, particularly directly on whole-slide images (WSI), can assist pathologists in this task. In this work, we propose a weakly-supervised methodology for grading cervical dysplasia, using different levels of training supervision, in an effort to gather a bigger dataset without the need of having all samples fully annotated. The framework comprises an epithelium segmentation step followed by a dysplasia classifier (non-neoplastic, LSIL, HSIL), making the slide assessment completely automatic, without the need for manual identification of epithelial areas. The proposed classification approach achieved a balanced accuracy of 71.07% and sensitivity of 72.18%, at the slide-level testing on 600 independent samples, which are publicly available upon reasonable request.

Abstract
Coupled multi-scale finite element analyses have gained traction over the last years due to the increasing available computational resources. Nevertheless, in the pursuit of accurate results within a reasonable time frame, replacing these high-fidelity micromechanical simulations with reduced-order data-driven models has been explored recently by the modelling community. In this work, two classes of machine learning models are trained for a porous hyperelastic microstructure to predict (i) whether the microscopic equilibrium problem is likely to fail and (ii) the stress-strain response. The former may be used to identify critical macroscopic points where one may fall back to the high-fidelity analysis and possibly apply convergence bowl-widening techniques. For the latter, both a linear regression with polynomial features and artificial Neural Networks have been used, and the required stress-strain derivatives for solving the equilibrium problem have been derived analytically. A weight regularisation is introduced to stabilise the tangent operator and several strategies are discussed for imposing null stresses in undeformed configurations for both regression models. The regression techniques, here analysed exclusively in the context of porous hyperelastic materials, evidence very promising prospects to accelerate multi-scale analyses of solids under large deformation.

Abstract
The development of accurate methods for OCT image analysis is highly dependent on the availability of large annotated datasets. As such datasets are usually expensive and hard to obtain, novel approaches based on deep generative models have been proposed for data augmentation. In this work, a flow-based network (SRFlow) and a generative adversarial network (ESRGAN) are used for synthesizing high-resolution OCT B-scans from low-resolution versions of real OCT images. The quality of the images generated by the two models is assessed using two standard fidelity-oriented metrics and a learned perceptual quality metric. The performance of two classification models trained on real and synthetic images is also evaluated. The obtained results show that the images generated by SRFlow preserve higher fidelity to the ground truth, while the outputs of ESRGAN present, on average, better perceptual quality. Independently of the architecture of the network chosen to classify the OCT B-scans, the model's performance always improves when images generated by SRFlow are included in the training set.