Dataset Information

DeepTRIAGE: interpretable and individualised biomarker scores using attention mechanism for the classification of breast cancer sub-types.

ABSTRACT: BACKGROUND:Breast cancer is a collection of multiple tissue pathologies, each with a distinct molecular signature that correlates with patient prognosis and response to therapy. Accurately differentiating between breast cancer sub-types is an important part of clinical decision-making. Although this problem has been addressed using machine learning methods in the past, there remains unexplained heterogeneity within the established sub-types that cannot be resolved by the commonly used classification algorithms. METHODS:In this paper, we propose a novel deep learning architecture, called DeepTRIAGE (Deep learning for the TRactable Individualised Analysis of Gene Expression), which uses an attention mechanism to obtain personalised biomarker scores that describe how important each gene is in predicting the cancer sub-type for each sample. We then perform a principal component analysis of these biomarker scores to visualise the sample heterogeneity, and use a linear model to test whether the major principal axes associate with known clinical phenotypes. RESULTS:Our model not only classifies cancer sub-types with good accuracy, but simultaneously assigns each patient their own set of interpretable and individualised biomarker scores. These personalised scores describe how important each feature is in the classification of any patient, and can be analysed post-hoc to generate new hypotheses about latent heterogeneity. CONCLUSIONS:We apply the DeepTRIAGE framework to classify the gene expression signatures of luminal A and luminal B breast cancer sub-types, and illustrate its use for genes as well as the GO and KEGG gene sets. Using DeepTRIAGE, we calculate personalised biomarker scores that describe the most important features for classifying an individual patient as luminal A or luminal B. In doing so, DeepTRIAGE simultaneously reveals heterogeneity within the luminal A biomarker scores that significantly associate with tumour stage, placing all luminal samples along a continuum of severity.

SUBMITTER: Beykikhoshk A

PROVIDER: S-EPMC7038647 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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DeepTRIAGE: interpretable and individualised biomarker scores using attention mechanism for the classification of breast cancer sub-types.

Beykikhoshk Adham A Quinn Thomas P TP Lee Samuel C SC Tran Truyen T Venkatesh Svetha S

BMC medical genomics 20200224 Suppl 3

<h4>Background</h4>Breast cancer is a collection of multiple tissue pathologies, each with a distinct molecular signature that correlates with patient prognosis and response to therapy. Accurately differentiating between breast cancer sub-types is an important part of clinical decision-making. Although this problem has been addressed using machine learning methods in the past, there remains unexplained heterogeneity within the established sub-types that cannot be resolved by the commonly used cl ...[more]

PMID: 32093737

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Project description:BackgroundOne of the key elements in maintaining the consistent marketing of tomato fruit is tomato quality. Since ripeness is the most important factor for tomato quality in the viewpoint of consumers, determining the stages of tomato ripeness is a fundamental industrial concern with regard to tomato production to obtain a high quality product. Since tomatoes are one of the most important crops in the world, automatic ripeness evaluation of tomatoes is a significant study topic as it may prove beneficial in ensuring an optimal production of high-quality product, increasing profitability. This article explores and categorises the various maturity/ripeness phases to propose an automated multi-class classification approach for tomato ripeness testing and evaluation.MethodsObject detection is the critical component in a wide variety of computer vision problems and applications such as manufacturing, agriculture, medicine, and autonomous driving. Due to the tomato fruits' complex identification background, texture disruption, and partial occlusion, the classic deep learning object detection approach (YOLO) has a poor rate of success in detecting tomato fruits. To figure out these issues, this article proposes an improved YOLOv5 tomato detection algorithm. The proposed algorithm CAM-YOLO uses YOLOv5 for feature extraction, target identification and Convolutional Block Attention Module (CBAM). The CBAM is added to the CAM-YOLO to focus the model on improving accuracy. Finally, non-maximum suppression and distance intersection over union (DIoU) are applied to enhance the identification of overlapping objects in the image.ResultsSeveral images from the dataset were chosen for testing to assess the model's performance, and the detection performance of the CAM-YOLO and standard YOLOv5 models under various conditions was compared. The experimental results affirms that CAM-YOLO algorithm is efficient in detecting the overlapped and small tomatoes with an average precision of 88.1%.

Dataset Information

DeepTRIAGE: interpretable and individualised biomarker scores using attention mechanism for the classification of breast cancer sub-types.

Publications

DeepTRIAGE: interpretable and individualised biomarker scores using attention mechanism for the classification of breast cancer sub-types.

Similar Datasets

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