Microbiome Learning Repo (ML Repo): A public repository of microbiome regression and classification tasks.
Ontology highlight
ABSTRACT:
SUBMITTER: Vangay P
PROVIDER: S-EPMC6493971 | biostudies-literature | 2019 May
REPOSITORIES: biostudies-literature
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Project description:Deep learning has become a leading subset of machine learning and has been successfully employed in diverse areas, ranging from natural language processing to medical image analysis. In medical imaging, researchers have progressively turned towards multi-center neuroimaging studies to address complex questions in neuroscience, leveraging larger sample sizes and aiming to enhance the accuracy of deep learning models. However, variations in image pixel/voxel characteristics can arise between centers due to factors including differences in magnetic resonance imaging scanners. Such variations create challenges, particularly inconsistent performance in machine learning-based approaches, often referred to as domain shift, where the trained models fail to achieve satisfactory or improved results when confronted with dissimilar test data. This study analyzes the performance of multiple disease classification tasks using multi-center MRI data obtained from three widely used scanner manufacturers (GE, Philips, and Siemens) across several deep learning-based networks. Furthermore, we investigate the efficacy of mitigating scanner vendor effects using ComBat-based harmonization techniques when applied to multi-center datasets of 3D structural MR images. Our experimental results reveal a substantial decline in classification performance when models trained on one type of scanner manufacturer are tested with data from different manufacturers. Moreover, despite applying ComBat-based harmonization, the harmonized images do not demonstrate any noticeable performance enhancement for disease classification tasks.
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Project description:Minimally perturbed adversarial examples were shown to drastically reduce the performance of one-stage classifiers while being imperceptible. This paper investigates the susceptibility of hierarchical classifiers, which use fine and coarse level output categories, to adversarial attacks. We formulate a program that encodes minimax constraints to induce misclassification of the coarse class of a hierarchical classifier (e.g., changing the prediction of a ‘monkey’ to a ‘vehicle’ instead of some ‘animal’). Subsequently, we develop solutions based on convex relaxations of said program. An algorithm is obtained using the alternating direction method of multipliers with competitive performance in comparison with state-of-the-art solvers. We show the ability of our approach to fool the coarse classification through a set of measures such as the relative loss in coarse classification accuracy and imperceptibility factors. In comparison with perturbations generated for one-stage classifiers, we show that fooling a classifier about the ‘big picture’ requires higher perturbation levels which results in lower imperceptibility. We also examine the impact of different label groupings on the performance of the proposed attacks. Supplementary Information The online version contains supplementary material available at 10.1007/s00034-022-02226-w.
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Project description:Jointly identifying brain diseases and predicting clinical scores have attracted increasing attention in the domain of computer-aided diagnosis using magnetic resonance imaging (MRI) data, since these two tasks are highly correlated. Although several joint learning models have been developed, most existing methods focus on using human-engineered features extracted from MRI data. Due to the possible heterogeneous property between human-engineered features and subsequent classification/regression models, those methods may lead to sub-optimal learning performance. In this paper, we propose a deep multi-task multi-channel learning (DM2L) framework for simultaneous classification and regression for brain disease diagnosis, using MRI data and personal information (i.e., age, gender, and education level) of subjects. Specifically, we first identify discriminative anatomical landmarks from MR images in a data-driven manner, and then extract multiple image patches around these detected landmarks. A deep multi-task multi-channel convolutional neural network is then developed for joint disease classification and clinical score regression. We train our model on a large multi-center cohort (i.e., ADNI-1) and test it on an independent cohort (i.e., ADNI-2). Experimental results demonstrate that DM2L is superior to the state-of-the-art approaches in brain diasease diagnosis.
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