Unsupervised Detection of Lesions in Brain MRI using constrained adversarial auto-encoders

Lesion detection in brain Magnetic Resonance Images (MRI) remains a challenging task. State-of-the-art approaches are mostly based on supervised learning making use of large annotated datasets. Human beings, on the other hand, even non-experts, can detect most abnormal lesions after seeing a handful of healthy brain images. Replicating this capability of using prior information on the appearance of healthy brain structure to detect lesions can help computers achieve human level abnormality detection, specifically reducing the need for numerous labeled examples and bettering generalization of previously unseen lesions. To this end, we study detection of lesion regions in an unsupervised manner by learning data distribution of brain MRI of healthy subjects using auto-encoder based methods. We hypothesize that one of the main limitations of the current models is the lack of consistency in latent representation. We propose a simple yet effective constraint that helps mapping of an image bearing lesion close to its corresponding healthy image in the latent space. We use the Human Connectome Project dataset to learn distribution of healthy-appearing brain MRI and report improved detection, in terms of AUC, of the lesions in the BRATS challenge dataset.Comment: 9 pages, 5 figures, accepted at MIDL 201

Investigating the impact of supervoxel segmentation for unsupervised abnormal brain asymmetry detection

Several brain disorders are associated with abnormal brain asymmetries (asymmetric anomalies). Several computer-based methods aim to detect such anomalies automatically. Recent advances in this area use automatic unsupervised techniques that extract pairs of symmetric supervoxels in the hemispheres, model normal brain asymmetries for each pair from healthy subjects, and treat outliers as anomalies. Yet, there is no deep understanding of the impact of the supervoxel segmentation quality for abnormal asymmetry detection, especially for small anomalies, nor of the added value of using a specialized model for each supervoxel pair instead of a single global appearance model. We aim to answer these questions by a detailed evaluation of different scenarios for supervoxel segmentation and classification for detecting abnormal brain asymmetries. Experimental results on 3D MR-T1 brain images of stroke patients confirm the importance of high-quality supervoxels fit anomalies and the use of a specific classifier for each supervoxel. Next, we present a refinement of the detection method that reduces the number of false-positive supervoxels, thereby making the detection method easier to use for visual inspection and analysis of the found anomalies.</p

Exploring variability in medical imaging

Although recent successes of deep learning and novel machine learning techniques improved the perfor- mance of classification and (anomaly) detection in computer vision problems, the application of these methods in medical imaging pipeline remains a very challenging task. One of the main reasons for this is the amount of variability that is encountered and encapsulated in human anatomy and subsequently reflected in medical images. This fundamental factor impacts most stages in modern medical imaging processing pipelines. Variability of human anatomy makes it virtually impossible to build large datasets for each disease with labels and annotation for fully supervised machine learning. An efficient way to cope with this is to try and learn only from normal samples. Such data is much easier to collect. A case study of such an automatic anomaly detection system based on normative learning is presented in this work. We present a framework for detecting fetal cardiac anomalies during ultrasound screening using generative models, which are trained only utilising normal/healthy subjects. However, despite the significant improvement in automatic abnormality detection systems, clinical routine continues to rely exclusively on the contribution of overburdened medical experts to diagnosis and localise abnormalities. Integrating human expert knowledge into the medical imaging processing pipeline entails uncertainty which is mainly correlated with inter-observer variability. From the per- spective of building an automated medical imaging system, it is still an open issue, to what extent this kind of variability and the resulting uncertainty are introduced during the training of a model and how it affects the final performance of the task. Consequently, it is very important to explore the effect of inter-observer variability both, on the reliable estimation of model’s uncertainty, as well as on the model’s performance in a specific machine learning task. A thorough investigation of this issue is presented in this work by leveraging automated estimates for machine learning model uncertainty, inter-observer variability and segmentation task performance in lung CT scan images. Finally, a presentation of an overview of the existing anomaly detection methods in medical imaging was attempted. This state-of-the-art survey includes both conventional pattern recognition methods and deep learning based methods. It is one of the first literature surveys attempted in the specific research area.Open Acces

Combining Attention-based Multiple Instance Learning and Gaussian Processes for CT Hemorrhage Detection

This work has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska Curie grant agreement No 860627 (CLARIFY Project) and also from the Spanish Ministry of Science and Innovation under project PID2019-105142RB-C22.Intracranial hemorrhage (ICH) is a life-threatening emer- gency with high rates of mortality and morbidity. Rapid and accurate de- tection of ICH is crucial for patients to get a timely treatment. In order to achieve the automatic diagnosis of ICH, most deep learning models rely on huge amounts of slice labels for training. Unfortunately, the manual annotation of CT slices by radiologists is time-consuming and costly. To diagnose ICH, in this work, we propose to use an attention-based multiple instance learning (Att-MIL) approach implemented through the combi- nation of an attention-based convolutional neural network (Att-CNN) and a variational Gaussian process for multiple instance learning (VGP- MIL). Only labels at scan-level are necessary for training. Our method (a) trains the model using scan labels and assigns each slice with an at- tention weight, which can be used to provide slice-level predictions, and (b) uses the VGPMIL model based on low-dimensional features extracted by the Att-CNN to obtain improved predictions both at slice and scan levels. To analyze the performance of the proposed approach, our model has been trained on 1150 scans from an RSNA dataset and evaluated on 490 scans from an external CQ500 dataset. Our method outperforms other methods using the same scan-level training and is able to achieve comparable or even better results than other methods relying on slice- level annotations.European Commission 860627Spanish Government PID2019-105142RB-C2

Unsupervised brain anomaly detection in MR images

Brain disorders are characterized by morphological deformations in shape and size of (sub)cortical structures in one or both hemispheres. These deformations cause deviations from the normal pattern of brain asymmetries, resulting in asymmetric lesions that directly affect the patient’s condition. Unsupervised methods aim to learn a model from unlabeled healthy images, so that an unseen image that breaks priors of this model, i.e., an outlier, is considered an anomaly. Consequently, they are generic in detecting any lesions, e.g., coming from multiple diseases, as long as these notably differ from healthy training images. This thesis addresses the development of solutions to leverage unsupervised machine learning for the detection/analysis of abnormal brain asymmetries related to anomalies in magnetic resonance (MR) images. First, we propose an automatic probabilistic-atlas-based approach for anomalous brain image segmentation. Second, we explore an automatic method for the detection of abnormal hippocampi from abnormal asymmetries based on deep generative networks and a one-class classifier. Third, we present a more generic framework to detect abnormal asymmetries in the entire brain hemispheres. Our approach extracts pairs of symmetric regions — called supervoxels — in both hemispheres of a test image under study. One-class classifiers then analyze the asymmetries present in each pair. Experimental results on 3D MR-T1 images from healthy subjects and patients with a variety of lesions show the effectiveness and robustness of the proposed unsupervised approaches for brain anomaly detection

Application of deep learning methods in materials microscopy for the quality assessment of lithium-ion batteries and sintered NdFeB magnets

Die Qualitätskontrolle konzentriert sich auf die Erkennung von Produktfehlern und die Überwachung von Aktivitäten, um zu überprüfen, ob die Produkte den gewünschten Qualitätsstandard erfüllen. Viele Ansätze für die Qualitätskontrolle verwenden spezialisierte Bildverarbeitungssoftware, die auf manuell entwickelten Merkmalen basiert, die von Fachleuten entwickelt wurden, um Objekte zu erkennen und Bilder zu analysieren. Diese Modelle sind jedoch mühsam, kostspielig in der Entwicklung und schwer zu pflegen, während die erstellte Lösung oft spröde ist und für leicht unterschiedliche Anwendungsfälle erhebliche Anpassungen erfordert. Aus diesen Gründen wird die Qualitätskontrolle in der Industrie immer noch häufig manuell durchgeführt, was zeitaufwändig und fehleranfällig ist. Daher schlagen wir einen allgemeineren datengesteuerten Ansatz vor, der auf den jüngsten Fortschritten in der Computer-Vision-Technologie basiert und Faltungsneuronale Netze verwendet, um repräsentative Merkmale direkt aus den Daten zu lernen. Während herkömmliche Methoden handgefertigte Merkmale verwenden, um einzelne Objekte zu erkennen, lernen Deep-Learning-Ansätze verallgemeinerbare Merkmale direkt aus den Trainingsproben, um verschiedene Objekte zu erkennen. In dieser Dissertation werden Modelle und Techniken für die automatisierte Erkennung von Defekten in lichtmikroskopischen Bildern von materialografisch präparierten Schnitten entwickelt. Wir entwickeln Modelle zur Defekterkennung, die sich grob in überwachte und unüberwachte Deep-Learning-Techniken einteilen lassen. Insbesondere werden verschiedene überwachte Deep-Learning-Modelle zur Erkennung von Defekten in der Mikrostruktur von Lithium-Ionen-Batterien entwickelt, von binären Klassifizierungsmodellen, die auf einem Sliding-Window-Ansatz mit begrenzten Trainingsdaten basieren, bis hin zu komplexen Defekterkennungs- und Lokalisierungsmodellen, die auf ein- und zweistufigen Detektoren basieren. Unser endgültiges Modell kann mehrere Klassen von Defekten in großen Mikroskopiebildern mit hoher Genauigkeit und nahezu in Echtzeit erkennen und lokalisieren. Das erfolgreiche Trainieren von überwachten Deep-Learning-Modellen erfordert jedoch in der Regel eine ausreichend große Menge an markierten Trainingsbeispielen, die oft nicht ohne weiteres verfügbar sind und deren Beschaffung sehr kostspielig sein kann. Daher schlagen wir zwei Ansätze vor, die auf unbeaufsichtigtem Deep Learning zur Erkennung von Anomalien in der Mikrostruktur von gesinterten NdFeB-Magneten basieren, ohne dass markierte Trainingsdaten benötigt werden. Die Modelle sind in der Lage, Defekte zu erkennen, indem sie aus den Trainingsdaten indikative Merkmale von nur "normalen" Mikrostrukturmustern lernen. Wir zeigen experimentelle Ergebnisse der vorgeschlagenen Fehlererkennungssysteme, indem wir eine Qualitätsbewertung an kommerziellen Proben von Lithium-Ionen-Batterien und gesinterten NdFeB-Magneten durchführen

Deep Gaussian processes for multiple instance learning: Application to CT intracranial hemorrhage detection

Background and objective: Intracranial hemorrhage (ICH) is a life-threatening emergency that can lead to brain damage or death, with high rates of mortality and morbidity. The fast and accurate detection of ICH is important for the patient to get an early and efficient treatment. To improve this diagnostic process, the application of Deep Learning (DL) models on head CT scans is an active area of research. Although promising results have been obtained, many of the proposed models require slice-level annotations by radiologists, which are costly and time-consuming. Methods: We formulate the ICH detection as a problem of Multiple Instance Learning (MIL) that allows training with only scan-level annotations. We develop a new probabilistic method based on Deep Gaussian Processes (DGP) that is able to train with this MIL setting and accurately predict ICH at both slice- and scan-level. The proposed DGPMIL model is able to capture complex feature relations by using multiple Gaussian Process (GP) layers, as we show experimentally. Results: To highlight the advantages of DGPMIL in a general MIL setting, we first conduct several controlled experiments on the MNIST dataset. We show that multiple GP layers outperform one-layer GP models, especially for complex feature distributions. For ICH detection experiments, we use two public brain CT datasets (RSNA and CQ500). We first train a Convolutional Neural Network (CNN) with an attention mechanism to extract the image features, which are fed into our DGPMIL model to perform the final predictions. The results show that DGPMIL model outperforms VGPMIL as well as the attention-based CNN for MIL and other state-of-the-art methods for this problem. The best performing DGPMIL model reaches an AUC-ROC of 0.957 (resp. 0.909) and an AUC-PR of 0.961 (resp. 0.889) on the RSNA (resp. CQ500) dataset. Conclusion: The competitive performance at slice- and scan-level shows that DGPMIL model provides an accurate diagnosis on slices without the need for slice-level annotations by radiologists during training. As MIL is a common problem setting, our model can be applied to a broader range of other tasks, especially in medical image classification, where it can help the diagnostic process.Project P20_00286 funded by FEDER/Junta de Andalucía-Consejería de Transformación Económica, Industria, Conocimiento y Universidadesthe European Union’s Horizon 2020 research and innovation programme under the Marie Skodowska Curie grant agreement No 860627 (CLARIFY Project).Funding for open access charge: Universidad de Granada / CBUA

3D Deep Learning on Medical Images: A Review

The rapid advancements in machine learning, graphics processing technologies and availability of medical imaging data has led to a rapid increase in use of deep learning models in the medical domain. This was exacerbated by the rapid advancements in convolutional neural network (CNN) based architectures, which were adopted by the medical imaging community to assist clinicians in disease diagnosis. Since the grand success of AlexNet in 2012, CNNs have been increasingly used in medical image analysis to improve the efficiency of human clinicians. In recent years, three-dimensional (3D) CNNs have been employed for analysis of medical images. In this paper, we trace the history of how the 3D CNN was developed from its machine learning roots, give a brief mathematical description of 3D CNN and the preprocessing steps required for medical images before feeding them to 3D CNNs. We review the significant research in the field of 3D medical imaging analysis using 3D CNNs (and its variants) in different medical areas such as classification, segmentation, detection, and localization. We conclude by discussing the challenges associated with the use of 3D CNNs in the medical imaging domain (and the use of deep learning models, in general) and possible future trends in the field.Comment: 13 pages, 4 figures, 2 table