Deep learning has shown excellent performance in analysing medical images. However, datasets are difficult to obtain due privacy issues, standardization problems, and lack of annotations. We address these problems by producing realistic synthetic images using a combination of 3D technologies and generative adversarial networks. We propose CUT-seg, a joint training where a segmentation model and a generative model are jointly trained to produce realistic images while learning to segment polyps. We take advantage of recent one-sided translation models because they use significantly less memory, allowing us to add a segmentation model in the training loop. CUT-seg performs better, is computationally less expensive, and requires less real images than other memory-intensive image translation approaches that require two stage training. Promising results are achieved on five real polyp segmentation datasets using only one real image and zero real annotations. As a part of this study we release Synth-Colon, an entirely synthetic dataset that includes 20000 realistic colon images and additional details about depth and 3D geometry: //enric1994.github.io/synth-colon
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The attention towards food products characteristics, such as nutritional properties and traceability, has risen substantially in the recent years. Consequently, we are witnessing an increased demand for the development of modern tools to monitor, analyse and assess food quality and authenticity. Within this framework, an essential set of data collection techniques is provided by vibrational spectroscopy. In fact, methods such as Fourier near infrared and mid infrared spectroscopy have been often exploited to analyze different foodstuffs. Nonetheless, existing statistical methods often struggle to deal with the challenges presented by spectral data, such as their high dimensionality, paired with strong relationships among the wavelengths. Therefore, the definition of proper statistical procedures accounting for the peculiarities of spectroscopy data is paramount. In this work, motivated by two dairy science applications, we propose an adaptive functional regression framework for spectroscopy data. The method stems from the trend filtering literature, allowing the definition of a highly flexible and adaptive estimator able to handle different degrees of smoothness. We provide a fast optimization procedure that is suitable for both Gaussian and non Gaussian scalar responses, and allows for the inclusion of scalar covariates. Moreover, we develop inferential procedures for both the functional and the scalar component thus enhancing not only the interpretability of the results, but also their usability in real world scenarios. The method is applied to two sets of MIR spectroscopy data, providing excellent results when predicting milk chemical composition and cows' dietary treatments. Moreover, the developed inferential routine provides relevant insights, potentially paving the way for a richer interpretation and a better understanding of the impact of specific wavelengths on milk features.
While several previous studies have devised methods for segmentation of polyps, most of these methods are not rigorously assessed on multi-center datasets. Variability due to appearance of polyps from one center to another, difference in endoscopic instrument grades, and acquisition quality result in methods with good performance on in-distribution test data, and poor performance on out-of-distribution or underrepresented samples. Unfair models have serious implications and pose a critical challenge to clinical applications. We adapt an implicit bias mitigation method which leverages Bayesian epistemic uncertainties during training to encourage the model to focus on underrepresented sample regions. We demonstrate the potential of this approach to improve generalisability without sacrificing state-of-the-art performance on a challenging multi-center polyp segmentation dataset (PolypGen) with different centers and image modalities.
Reliable uncertainty quantification (UQ) in machine learning (ML) regression tasks is becoming the focus of many studies in materials and chemical science. It is now well understood that average calibration is insufficient, and most studies implement additional methods testing the conditional calibration with respect to uncertainty, i.e. consistency. Consistency is assessed mostly by so-called reliability diagrams. There exists however another way beyond average calibration, which is conditional calibration with respect to input features, i.e. adaptivity. In practice, adaptivity is the main concern of the final users of a ML-UQ method, seeking for the reliability of predictions and uncertainties for any point in features space. This article aims to show that consistency and adaptivity are complementary validation targets, and that a good consistency does not imply a good adaptivity. Adapted validation methods are proposed and illustrated on a representative example.
We analyse a numerical scheme for a system arising from a novel description of the standard elastic--perfectly plastic response. The elastic--perfectly plastic response is described via rate-type equations that do not make use of the standard elastic-plastic decomposition, and the model does not require the use of variational inequalities. Furthermore, the model naturally includes the evolution equation for temperature. We present a low order discretisation based on the finite element method. Under certain restrictions on the mesh we subsequently prove the existence of discrete solutions, and we discuss the stability properties of the numerical scheme. The analysis is supplemented with computational examples.
This work is motivated by the study of local protein structure, which is defined by two variable dihedral angles that take values from probability distributions on the flat torus. Our goal is to provide the space $\mathcal{P}(\mathbb{R}^2/\mathbb{Z}^2)$ with a metric that quantifies local structural modifications due to changes in the protein sequence, and to define associated two-sample goodness-of-fit testing approaches. Due to its adaptability to the space geometry, we focus on the Wasserstein distance as a metric between distributions. We extend existing results of the theory of Optimal Transport to the $d$-dimensional flat torus $\mathbb{T}^d=\mathbb{R}^d/\mathbb{Z}^d$, in particular a Central Limit Theorem. Moreover, we propose different approaches for two-sample goodness-of-fit testing for the one and two-dimensional case, based on the Wasserstein distance. We prove their validity and consistency. We provide an implementation of these tests in \textsf{R}. Their performance is assessed by numerical experiments on synthetic data and illustrated by an application to protein structure data.
Missing data frequently occurs in datasets across various domains, such as medicine, sports, and finance. In many cases, to enable proper and reliable analyses of such data, the missing values are often imputed, and it is necessary that the method used has a low root mean square error (RMSE) between the imputed and the true values. In addition, for some critical applications, it is also often a requirement that the imputation method is scalable and the logic behind the imputation is explainable, which is especially difficult for complex methods that are, for example, based on deep learning. Based on these considerations, we propose a new algorithm named "conditional Distribution-based Imputation of Missing Values with Regularization" (DIMV). DIMV operates by determining the conditional distribution of a feature that has missing entries, using the information from the fully observed features as a basis. As will be illustrated via experiments in the paper, DIMV (i) gives a low RMSE for the imputed values compared to state-of-the-art methods; (ii) fast and scalable; (iii) is explainable as coefficients in a regression model, allowing reliable and trustable analysis, makes it a suitable choice for critical domains where understanding is important such as in medical fields, finance, etc; (iv) can provide an approximated confidence region for the missing values in a given sample; (v) suitable for both small and large scale data; (vi) in many scenarios, does not require a huge number of parameters as deep learning approaches; (vii) handle multicollinearity in imputation effectively; and (viii) is robust to the normally distributed assumption that its theoretical grounds rely on.
The increasing availability of large clinical datasets collected from patients can enable new avenues for computational characterization of complex diseases using different analytic algorithms. One of the promising new methods for extracting knowledge from large clinical datasets involves temporal pattern mining integrated with machine learning workflows. However, mining these temporal patterns is a computational intensive task and has memory repercussions. Current algorithms, such as the temporal sequence pattern mining (tSPM) algorithm, are already providing promising outcomes, but still leave room for optimization. In this paper, we present the tSPM+ algorithm, a high-performance implementation of the tSPM algorithm, which adds a new dimension by adding the duration to the temporal patterns. We show that the tSPM+ algorithm provides a speed up to factor 980 and a up to 48 fold improvement in memory consumption. Moreover, we present a docker container with an R-package, We also provide vignettes for an easy integration into already existing machine learning workflows and use the mined temporal sequences to identify Post COVID-19 patients and their symptoms according to the WHO definition.
Besov priors are nonparametric priors that can model spatially inhomogeneous functions. They are routinely used in inverse problems and imaging, where they exhibit attractive sparsity-promoting and edge-preserving features. A recent line of work has initiated the study of their asymptotic frequentist convergence properties. In the present paper, we consider the theoretical recovery performance of the posterior distributions associated to Besov-Laplace priors in the density estimation model, under the assumption that the observations are generated by a possibly spatially inhomogeneous true density belonging to a Besov space. We improve on existing results and show that carefully tuned Besov-Laplace priors attain optimal posterior contraction rates. Furthermore, we show that hierarchical procedures involving a hyper-prior on the regularity parameter lead to adaptation to any smoothness level.
The inherent nature of patient data poses several challenges. Prevalent cases amass substantial longitudinal data owing to their patient volume and consistent follow-ups, however, longitudinal laboratory data are renowned for their irregularity, temporality, absenteeism, and sparsity; In contrast, recruitment for rare or specific cases is often constrained due to their limited patient size and episodic observations. This study employed self-supervised learning (SSL) to pretrain a generalized laboratory progress (GLP) model that captures the overall progression of six common laboratory markers in prevalent cardiovascular cases, with the intention of transferring this knowledge to aid in the detection of specific cardiovascular event. GLP implemented a two-stage training approach, leveraging the information embedded within interpolated data and amplify the performance of SSL. After GLP pretraining, it is transferred for TVR detection. The proposed two-stage training improved the performance of pure SSL, and the transferability of GLP exhibited distinctiveness. After GLP processing, the classification exhibited a notable enhancement, with averaged accuracy rising from 0.63 to 0.90. All evaluated metrics demonstrated substantial superiority (p < 0.01) compared to prior GLP processing. Our study effectively engages in translational engineering by transferring patient progression of cardiovascular laboratory parameters from one patient group to another, transcending the limitations of data availability. The transferability of disease progression optimized the strategies of examinations and treatments, and improves patient prognosis while using commonly available laboratory parameters. The potential for expanding this approach to encompass other diseases holds great promise.
Breast cancer remains a global challenge, causing over 1 million deaths globally in 2018. To achieve earlier breast cancer detection, screening x-ray mammography is recommended by health organizations worldwide and has been estimated to decrease breast cancer mortality by 20-40%. Nevertheless, significant false positive and false negative rates, as well as high interpretation costs, leave opportunities for improving quality and access. To address these limitations, there has been much recent interest in applying deep learning to mammography; however, obtaining large amounts of annotated data poses a challenge for training deep learning models for this purpose, as does ensuring generalization beyond the populations represented in the training dataset. Here, we present an annotation-efficient deep learning approach that 1) achieves state-of-the-art performance in mammogram classification, 2) successfully extends to digital breast tomosynthesis (DBT; "3D mammography"), 3) detects cancers in clinically-negative prior mammograms of cancer patients, 4) generalizes well to a population with low screening rates, and 5) outperforms five-out-of-five full-time breast imaging specialists by improving absolute sensitivity by an average of 14%. Our results demonstrate promise towards software that can improve the accuracy of and access to screening mammography worldwide.
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