Predicting Infarct Core From Computed Tomography Perfusion in Acute Ischemia With Machine Learning: Lessons From the ISLES Challenge.

BACKGROUND AND PURPOSE The ISLES challenge (Ischemic Stroke Lesion Segmentation) enables globally diverse teams to compete to develop advanced tools for stroke lesion analysis with machine learning. Detection of irreversibly damaged tissue on computed tomography perfusion (CTP) is often necessary to determine eligibility for late-time-window thrombectomy. Therefore, the aim of ISLES-2018 was to segment infarcted tissue on CTP based on diffusion-weighted imaging as a reference standard. METHODS The data, from 4 centers, consisted of 103 cases of acute anterior circulation large artery occlusion stroke who underwent diffusion-weighted imaging rapidly after CTP. Diffusion-weighted imaging lesion segmentation was performed manually and acted as a reference standard. The data were separated into 63 cases for training and 40 for testing, upon which quality metrics (dice score coefficient, Hausdorff distance, absolute lesion volume difference, etc) were computed to rank methods based on their overall performance. RESULTS Twenty-four different teams participated in the challenge. Median time to CTP was 185 minutes (interquartile range, 180-238), the time between CTP and magnetic resonance imaging was 36 minutes (interquartile range, 25-79), and the median infarct lesion size was 15.2 mL (interquartile range, 5.7-45). The best performance for Dice score coefficient and absolute volume difference were 0.51 and 10.1 mL, respectively, from different teams. Based on the ranking criteria, the top team's algorithm demonstrated for average Dice score coefficient and average absolute volume difference 0.51 and 10.2 mL, respectively, outperforming the conventional threshold-based method (dice score coefficient, 0.3; volume difference, 15.3). Diverse algorithms were used, almost all based on deep learning, with top-ranked approaches making use of the raw perfusion data as well as methods to synthetically generate complementary information to boost prediction performance. CONCLUSIONS Machine learning methods may predict infarcted tissue from CTP with improved accuracy compared with threshold-based methods used in clinical routine. This dataset will remain public and can be used to test improvement in algorithms over time

SoftSeg: Advantages of soft versus binary training for image segmentation

Most image segmentation algorithms are trained on binary masks formulated as a classification task per pixel. However, in applications such as medical imaging, this "black-and-white" approach is too constraining because the contrast between two tissues is often ill-defined, i.e., the voxels located on objects' edges contain a mixture of tissues. Consequently, assigning a single "hard" label can result in a detrimental approximation. Instead, a soft prediction containing non-binary values would overcome that limitation. We introduce SoftSeg, a deep learning training approach that takes advantage of soft ground truth labels, and is not bound to binary predictions. SoftSeg aims at solving a regression instead of a classification problem. This is achieved by using (i) no binarization after preprocessing and data augmentation, (ii) a normalized ReLU final activation layer (instead of sigmoid), and (iii) a regression loss function (instead of the traditional Dice loss). We assess the impact of these three features on three open-source MRI segmentation datasets from the spinal cord gray matter, the multiple sclerosis brain lesion, and the multimodal brain tumor segmentation challenges. Across multiple cross-validation iterations, SoftSeg outperformed the conventional approach, leading to an increase in Dice score of 2.0% on the gray matter dataset (p=0.001), 3.3% for the MS lesions, and 6.5% for the brain tumors. SoftSeg produces consistent soft predictions at tissues' interfaces and shows an increased sensitivity for small objects. The richness of soft labels could represent the inter-expert variability, the partial volume effect, and complement the model uncertainty estimation. The developed training pipeline can easily be incorporated into most of the existing deep learning architectures. It is already implemented in the freely-available deep learning toolbox ivadomed (https://ivadomed.org)

Optimization with soft Dice can lead to a volumetric bias

status: Published onlin

Efficient evolutionary-based neural architecture search in few GPU hours for image classification and medical image segmentation

Orientador: Lucas Ferrari de OliveiraTese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Exatas, Programa de Pós-Graduação em Informática. Defesa : Curitiba, 20/09/2021Inclui referências: p. 132-139Área de concentração: Ciência da ComputaçãoResumo: O uso de aprendizagem profunda (AP) está crescendo rapidamente, já que o poder computacional atual fornece otimização e inferência rápidas. Além disso, vários métodos exclusivos de AP estão evoluindo, permitindo resultados superiores em visão computacional, reconhecimento de voz e análise de texto. Os métodos AP extraem característica automaticamente para melhor representação de um problema específico, removendo o árduo trabalho do desenvolvimento de descritores de características dos métodos convencionais. Mesmo que esse processo sejaautomatizado, a criação inteligente de redes neurais é necessária para o aprendizado adequado da representação, o que requer conhecimento em AP. O campo de busca de arquiteturas neurais (BAN) foca no desenvolvimento de abordagens inteligentes que projetam redes robustas automaticamente para reduzir o conhecimento exigido para o desenvolvimento de redes eficientes. BAN pode fornecer maneiras de descobrir diferentes representações de rede, melhorando o estado da arte em diferentes aplicações. Embora BAN seja relativamente nova, várias abordagens foram desenvolvidas para descobrir modelos robustos. Métodos eficientes baseados em evolução são amplamente populares em BAN, mas seu alto consumo de placa gráfica (de alguns dias a meses)desencoraja o uso prático. No presente trabalho, propomos duas abordagens BAN baseadas na evolução eficiente com baixo custo de processamento, exigindo apenas algumas horas de processamento na placa gráfica (menos de doze em uma RTX 2080Ti) para descobrir modelos competitivos. Nossas abordagens extraem conceitos da programação de expressão gênica para representar e gerar redes baseadas em células robustas combinadas com rápido treinamento de candidatos, compartilhamento de peso e combinações dinâmicas. Além disso, os métodos propostos são empregados em um espaço de busca mais amplo, com mais células representando uma rede única. Nossa hipótese central é que BAN baseado na evolução pode ser usado em uma busca com baixo custo (combinada com uma estratégia robusta e busca eficiente) em diversas tarefas de visão computacional sem perder competitividade. Nossos métodos são avaliados em diferentes problemas para validar nossa hipótese: classificação de imagens e segmentação semântica de imagens médicas. Para tanto, as bases de dados CIFAR são estudadas para atarefa de classificação e o desafio CHAOS para a tarefa de segmentação. As menores taxas de erro encontradas nas bases CIFAR-10 e CIFAR-100 foram 2,17% ± 0,10 e 15,47% ± 0,51,respectivamente. Quanto às tarefas do desafio CHAOS, os valores de Dice ficaram entre 90% e96%. Os resultados obtidos com nossas propostas em ambas as tarefas mostraram a descoberta de redes robustas para ambas as tarefas com baixo custo na fase de busca, sendo competitivas em relação ao estado da arte em ambos os desafios.Abstract: Deep learning (DL) usage is growing fast since current computational power provides fast optimization and inference. Furthermore, several unique DL methods are evolving, enabling superior computer vision, speech recognition, and text analysis results. DL methods automatically extract features to represent a specific problem better, removing the hardworking of feature engineering from conventional methods. Even if this process is automated, intelligent network design is necessary for proper representation learning, which requires expertise in DL. The neural architecture search (NAS) field focuses on developing intelligent approaches that automatically design robust networks to reduce the expertise required for developing efficient networks. NAS may provide ways to discover different network representations, improving the state-of-the-art indifferent applications. Although NAS is relatively new, several approaches were developed for discovering robust models. Efficient evolutionary-based methods are widely popular in NAS, buttheir high GPU consumption (from a few days to months) discourages practical use. In the presentwork, we propose two efficient evolutionary-based NAS approaches with low-GPU cost, requiring only a few GPU hours (less than twelve in an RTX 2080Ti) to discover competitive models. Our approaches extract concepts from gene expression programming to represent and generate robust cell-based networks combined with fast candidate training, weight sharing, and dynamic combinations. Furthermore, the proposed methods are employed in a broader search space, withmore cells representing a unique network. Our central hypothesis is that evolutionary-based NAScan be used in a low-cost GPU search (combined with a robust strategy and efficient search) indiverse computer vision tasks without losing competitiveness. Our methods are evaluated indifferent problems to validate our hypothesis: image classification and medical image semantic segmentation. For this purpose, the CIFAR datasets are studied for the classification task andthe CHAOS challenge for the segmentation task. The lowest error rates found in CIFAR-10 andCIFAR-100 datasets were 2.17% ± 0.10 and 15.47% ± 0.51, respectively. As for the CHAOS challenge tasks, the dice scores were between 90% and 96%. The obtained results from our proposal in both tasks shown the discovery of robust networks for both tasks with little GPU costin the search phase, being competitive to state-of-the-art approaches in both challenges