4,044 research outputs found

    Non-parametric Density Modeling and Outlier Detection in Medical Imaging Datasets

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    International audienceThe statistical analysis of medical images is challenging because of the high dimensionality and low signal-to-noise ratio of the data. Simple parametric statistical models, such as Gaussian distributions, are well-suited to high-dimensional settings. In practice, on medical data made of heterogeneous subjects, the Gaussian hypothesis seldom holds. In addition, alternative parametric models of the data tend to break down due to the presence of outliers that are usually removed manually from studies. Here we focus on interactive detection of these outlying observations, to guide the practitioner through the data inclusion process. Our contribution is to use Local Component Analysis as a non-parametric density estimator for this purpose. Experiments on real and simulated data show that our procedure separates well deviant observations from the relevant and representative ones. We show that it outperforms state-of-the-art approaches, in particular those involving a Gaussian assumption

    TabADM: Unsupervised Tabular Anomaly Detection with Diffusion Models

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    Tables are an abundant form of data with use cases across all scientific fields. Real-world datasets often contain anomalous samples that can negatively affect downstream analysis. In this work, we only assume access to contaminated data and present a diffusion-based probabilistic model effective for unsupervised anomaly detection. Our model is trained to learn the density of normal samples by utilizing a unique rejection scheme to attenuate the influence of anomalies on the density estimation. At inference, we identify anomalies as samples in low-density regions. We use real data to demonstrate that our method improves detection capabilities over baselines. Furthermore, our method is relatively stable to the dimension of the data and does not require extensive hyperparameter tuning

    Inferring Biological Structures from Super-Resolution Single Molecule Images Using Generative Models

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    Localization-based super resolution imaging is presently limited by sampling requirements for dynamic measurements of biological structures. Generating an image requires serial acquisition of individual molecular positions at sufficient density to define a biological structure, increasing the acquisition time. Efficient analysis of biological structures from sparse localization data could substantially improve the dynamic imaging capabilities of these methods. Using a feature extraction technique called the Hough Transform simple biological structures are identified from both simulated and real localization data. We demonstrate that these generative models can efficiently infer biological structures in the data from far fewer localizations than are required for complete spatial sampling. Analysis at partial data densities revealed efficient recovery of clathrin vesicle size distributions and microtubule orientation angles with as little as 10% of the localization data. This approach significantly increases the temporal resolution for dynamic imaging and provides quantitatively useful biological information

    Exploring variability in medical imaging

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    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

    Fast and Sequence-Adaptive Whole-Brain Segmentation Using Parametric Bayesian Modeling

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    AbstractQuantitative analysis of magnetic resonance imaging (MRI) scans of the brain requires accurate automated segmentation of anatomical structures. A desirable feature for such segmentation methods is to be robust against changes in acquisition platform and imaging protocol. In this paper we validate the performance of a segmentation algorithm designed to meet these requirements, building upon generative parametric models previously used in tissue classification. The method is tested on four different datasets acquired with different scanners, field strengths and pulse sequences, demonstrating comparable accuracy to state-of-the-art methods on T1-weighted scans while being one to two orders of magnitude faster. The proposed algorithm is also shown to be robust against small training datasets, and readily handles images with different MRI contrast as well as multi-contrast data
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