Abstract

Abstract
iReceptor Plus will enable researchers around the world to share and analyse huge immunological distributed datasets, from multiple countries, containing sequencing data pertaining to both healthy and sick individuals. Most of the Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) data is currently stored and curated by individual labs, using a variety of tools and technologies.

Abstract
Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as they record past and ongoing adaptive immune responses. The capacity of machine learning (ML) to identify complex discriminative sequence patterns renders it an ideal approach for AIRR-based diagnostic and therapeutic discovery. So far, widespread adoption of AIRR ML has been inhibited by a lack of reproducibility, transparency and interoperability. immuneML (immuneml.uio.no) addresses these concerns by implementing each step of the AIRR ML process in an extensible, open-source software ecosystem that is based on fully specified and shareable workflows. To facilitate widespread user adoption, immuneML is available as a command-line tool and through an intuitive Galaxy web interface, and extensive documentation of workflows is provided. We demonstrate the broad applicability of immuneML by (1) reproducing a large-scale study on immune state prediction, (2) developing, integrating and applying a novel deep learning method for antigen specificity prediction and (3) showcasing streamlined interpretability-focused benchmarking of AIRR ML.

Abstract
Lung segmentation represents a fundamental step in the development of computer-aided decision systems for the investigation of interstitial lung diseases. In a holistic lung analysis, eliminating background areas from Computed Tomography (CT) images is essential to avoid the inclusion of noise information and spend unnecessary computational resources on non-relevant data. However, the major challenge in this segmentation task relies on the ability of the models to deal with imaging manifestations associated with severe disease. Based on U-net, a general biomedical image segmentation architecture, we proposed a light-weight and faster architecture. In this 2D approach, experiments were conducted with a combination of two publicly available databases to improve the heterogeneity of the training data. Results showed that, when compared to the original U-net, the proposed architecture maintained performance levels, achieving 0.894 +/- 0.060, 4.493 +/- 0.633 and 4.457 +/- 0.628 for DSC, HD and HD-95 metrics, respectively, when using all patients from the ILD database for testing only, while allowing a more efficient computational usage. Quantitative and qualitative evaluations on the ability to cope with high-density lung patterns associated with severe disease were conducted, supporting the idea that more representative and diverse data is necessary to build robust and reliable segmentation tools.

Abstract
Automatic medical image segmentation via convolutional neural networks (CNNs) has shown promising results. However, they may not always be robust enough for clinical use. Sub-optimal segmentation would require clinician's to manually delineate the target object, causing frustration. To address this problem, a novel interactive CNN-based segmentation framework is proposed in this work. The aim is to represent the CNN segmentation contour as B-splines by utilising B-spline explicit active surfaces (BEAS). The interactive element of the framework allows the user to precisely edit the contour in real-time, and by utilising BEAS it ensures the final contour is smooth and anatomically plausible. This framework was applied to the task of 2D segmentation of the levator hiatus from 2D ultrasound (US) images, and compared to the current clinical tools used in pelvic floor disorder clinic (4DView, GE Healthcare; Zipf, Austria). Experimental results show that: 1) the proposed framework is more robust than current state-of-the-art CNNs; 2) the perceived workload calculated via the NASA-TLX index was reduced more than half for the proposed approach in comparison to current clinical tools; and 3) the proposed tool requires at least 13 s less user time than the clinical tools, which was significant (p = 0.001).

Abstract
This paper presents a summary of the Masked Face Recognition Competitions (MFR) held within the 2021 International Joint Conference on Biometrics (IJCB 2021). The competition attracted a total of 10 participating teams with valid submissions. The affiliations of these teams are diverse and associated with academia and industry in nine different countries. These teams successfully submitted 18 valid solutions. The competition is designed to motivate solutions aiming at enhancing the face recognition accuracy of masked faces. Moreover, the competition considered the deployability of the proposed solutions by taking the compactness of the face recognition models into account. A private dataset representing a collaborative, multi-session, real masked, capture scenario is used to evaluate the submitted solutions. In comparison to one of the top-performing academic face recognition solutions, 10 out of the 18 submitted solutions did score higher masked face verification accuracy.