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Reuben Dorent, Aaron Kujawa, Marina Ivory, Spyridon Bakas, Nikola Rieke, Samuel Joutard, et al. (2023). CrossMoDA 2021 challenge: Benchmark of Cross-Modality Domain Adaptation techniques for Vestibular Schwannoma and Cochlea Segmentation. MIA - Medical Image Analysis, 83, 102628.
Abstract: Domain Adaptation (DA) has recently raised strong interests in the medical imaging community. While a large variety of DA techniques has been proposed for image segmentation, most of these techniques have been validated either on private datasets or on small publicly available datasets. Moreover, these datasets mostly addressed single-class problems. To tackle these limitations, the Cross-Modality Domain Adaptation (crossMoDA) challenge was organised in conjunction with the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). CrossMoDA is the first large and multi-class benchmark for unsupervised cross-modality DA. The challenge's goal is to segment two key brain structures involved in the follow-up and treatment planning of vestibular schwannoma (VS): the VS and the cochleas. Currently, the diagnosis and surveillance in patients with VS are performed using contrast-enhanced T1 (ceT1) MRI. However, there is growing interest in using non-contrast sequences such as high-resolution T2 (hrT2) MRI. Therefore, we created an unsupervised cross-modality segmentation benchmark. The training set provides annotated ceT1 (N=105) and unpaired non-annotated hrT2 (N=105). The aim was to automatically perform unilateral VS and bilateral cochlea segmentation on hrT2 as provided in the testing set (N=137). A total of 16 teams submitted their algorithm for the evaluation phase. The level of performance reached by the top-performing teams is strikingly high (best median Dice – VS:88.4%; Cochleas:85.7%) and close to full supervision (median Dice – VS:92.5%; Cochleas:87.7%). All top-performing methods made use of an image-to-image translation approach to transform the source-domain images into pseudo-target-domain images. A segmentation network was then trained using these generated images and the manual annotations provided for the source image.
Keywords: Domain Adaptation; Segmen tation; Vestibular Schwnannoma
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Penny Tarling, Mauricio Cantor, Albert Clapes, & Sergio Escalera. (2022). Deep learning with self-supervision and uncertainty regularization to count fish in underwater images. Plos - PloS One, 17(5), e0267759.
Abstract: Effective conservation actions require effective population monitoring. However, accurately counting animals in the wild to inform conservation decision-making is difficult. Monitoring populations through image sampling has made data collection cheaper, wide-reaching and less intrusive but created a need to process and analyse this data efficiently. Counting animals from such data is challenging, particularly when densely packed in noisy images. Attempting this manually is slow and expensive, while traditional computer vision methods are limited in their generalisability. Deep learning is the state-of-the-art method for many computer vision tasks, but it has yet to be properly explored to count animals. To this end, we employ deep learning, with a density-based regression approach, to count fish in low-resolution sonar images. We introduce a large dataset of sonar videos, deployed to record wild Lebranche mullet schools (Mugil liza), with a subset of 500 labelled images. We utilise abundant unlabelled data in a self-supervised task to improve the supervised counting task. For the first time in this context, by introducing uncertainty quantification, we improve model training and provide an accompanying measure of prediction uncertainty for more informed biological decision-making. Finally, we demonstrate the generalisability of our proposed counting framework through testing it on a recent benchmark dataset of high-resolution annotated underwater images from varying habitats (DeepFish). From experiments on both contrasting datasets, we demonstrate our network outperforms the few other deep learning models implemented for solving this task. By providing an open-source framework along with training data, our study puts forth an efficient deep learning template for crowd counting aquatic animals thereby contributing effective methods to assess natural populations from the ever-increasing visual data.
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Victor M. Campello, Carlos Martin-Isla, Cristian Izquierdo, Andrea Guala, Jose F. Rodriguez Palomares, David Vilades, et al. (2022). Minimising multi-centre radiomics variability through image normalisation: a pilot study. ScR - Scientific Reports, 12(1), 12532.
Abstract: Radiomics is an emerging technique for the quantification of imaging data that has recently shown great promise for deeper phenotyping of cardiovascular disease. Thus far, the technique has been mostly applied in single-centre studies. However, one of the main difficulties in multi-centre imaging studies is the inherent variability of image characteristics due to centre differences. In this paper, a comprehensive analysis of radiomics variability under several image- and feature-based normalisation techniques was conducted using a multi-centre cardiovascular magnetic resonance dataset. 218 subjects divided into healthy (n = 112) and hypertrophic cardiomyopathy (n = 106, HCM) groups from five different centres were considered. First and second order texture radiomic features were extracted from three regions of interest, namely the left and right ventricular cavities and the left ventricular myocardium. Two methods were used to assess features’ variability. First, feature distributions were compared across centres to obtain a distribution similarity index. Second, two classification tasks were proposed to assess: (1) the amount of centre-related information encoded in normalised features (centre identification) and (2) the generalisation ability for a classification model when trained on these features (healthy versus HCM classification). The results showed that the feature-based harmonisation technique ComBat is able to remove the variability introduced by centre information from radiomic features, at the expense of slightly degrading classification performance. Piecewise linear histogram matching normalisation gave features with greater generalisation ability for classification ( balanced accuracy in between 0.78 ± 0.08 and 0.79 ± 0.09). Models trained with features from images without normalisation showed the worst performance overall ( balanced accuracy in between 0.45 ± 0.28 and 0.60 ± 0.22). In conclusion, centre-related information removal did not imply good generalisation ability for classification.
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Zhen Xu, Sergio Escalera, Adrien Pavao, Magali Richard, Wei-Wei Tu, Quanming Yao, et al. (2022). Codabench: Flexible, easy-to-use, and reproducible meta-benchmark platform. PATTERNS - Patterns, 3(7), 100543.
Abstract: Obtaining a standardized benchmark of computational methods is a major issue in data-science communities. Dedicated frameworks enabling fair benchmarking in a unified environment are yet to be developed. Here, we introduce Codabench, a meta-benchmark platform that is open sourced and community driven for benchmarking algorithms or software agents versus datasets or tasks. A public instance of Codabench is open to everyone free of charge and allows benchmark organizers to fairly compare submissions under the same setting (software, hardware, data, algorithms), with custom protocols and data formats. Codabench has unique features facilitating easy organization of flexible and reproducible benchmarks, such as the possibility of reusing templates of benchmarks and supplying compute resources on demand. Codabench has been used internally and externally on various applications, receiving more than 130 users and 2,500 submissions. As illustrative use cases, we introduce four diverse benchmarks covering graph machine learning, cancer heterogeneity, clinical diagnosis, and reinforcement learning.
Keywords: Machine learning; data science; benchmark platform; reproducibility; competitions
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Ajian Liu, Chenxu Zhao, Zitong Yu, Jun Wan, Anyang Su, Xing Liu, et al. (2022). Contrastive Context-Aware Learning for 3D High-Fidelity Mask Face Presentation Attack Detection. TIForensicSEC - IEEE Transactions on Information Forensics and Security, 17, 2497–2507.
Abstract: Face presentation attack detection (PAD) is essential to secure face recognition systems primarily from high-fidelity mask attacks. Most existing 3D mask PAD benchmarks suffer from several drawbacks: 1) a limited number of mask identities, types of sensors, and a total number of videos; 2) low-fidelity quality of facial masks. Basic deep models and remote photoplethysmography (rPPG) methods achieved acceptable performance on these benchmarks but still far from the needs of practical scenarios. To bridge the gap to real-world applications, we introduce a large-scale Hi gh- Fi delity Mask dataset, namely HiFiMask . Specifically, a total amount of 54,600 videos are recorded from 75 subjects with 225 realistic masks by 7 new kinds of sensors. Along with the dataset, we propose a novel C ontrastive C ontext-aware L earning (CCL) framework. CCL is a new training methodology for supervised PAD tasks, which is able to learn by leveraging rich contexts accurately (e.g., subjects, mask material and lighting) among pairs of live faces and high-fidelity mask attacks. Extensive experimental evaluations on HiFiMask and three additional 3D mask datasets demonstrate the effectiveness of our method. The codes and dataset will be released soon.
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