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Register a new userDeepACC:Automate Chromosome Classification based on Metaphase Images using Deep Learning Framework Fused with Prior Knowledge
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Added by
Li Xiao
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Chromosome classification is an important but difficult and tedious task in karyotyping. Previous methods only classify manually segmented single chromosome, which is far from clinical practice. In this work, we propose a detection based method, DeepACC, to locate and fine classify chromosomes simultaneously based on the whole metaphase image. We firstly introduce the Additive Angular Margin Loss to enhance the discriminative power of model. To alleviate batch effects, we transform decision boundary of each class case-by-case through a siamese network which make full use of prior knowledges that chromosomes usually appear in pairs. Furthermore, we take the clinically seven group criterion as a prior knowledge and design an additional Group Inner-Adjacency Loss to further reduce inter-class similarities. 3390 metaphase images from clinical laboratory are collected and labelled to evaluate the performance. Results show that the new design brings encouraging performance gains comparing to the state-of-the-art baselines.
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Chromosome classification is critical for karyotyping in abnormality diagnosis. To expedite the diagnosis, we present a novel method named Varifocal-Net for simultaneous classification of chromosomes type and polarity using deep convolutional networks. The approach consists of one global-scale network (G-Net) and one local-scale network (L-Net). It follows three stages. The first stage is to learn both global and local features. We extract global features and detect finer local regions via the G-Net. By proposing a varifocal mechanism, we zoom into local parts and extract local features via the L-Net. Residual learning and multi-task learning strategies are utilized to promote high-level feature extraction. The detection of discriminative local parts is fulfilled by a localization subnet of the G-Net, whose training process involves both supervised and weakly-supervised learning. The second stage is to build two multi-layer perceptron classifiers that exploit features of both two scales to boost classification performance. The third stage is to introduce a dispatch strategy of assigning each chromosome to a type within each patient case, by utilizing the domain knowledge of karyotyping. Evaluation results from 1909 karyotyping cases showed that the proposed Varifocal-Net achieved the highest accuracy per patient case (%) 99.2 for both type and polarity tasks. It outperformed state-of-the-art methods, demonstrating the effectiveness of our varifocal mechanism, multi-scale feature ensemble, and dispatch strategy. The proposed method has been applied to assist practical karyotype diagnosis.
The recently proposed Multilinear Compressive Learning (MCL) framework combines Multilinear Compressive Sensing and Machine Learning into an end-to-end system that takes into account the multidimensional structure of the signals when designing the sensing and feature synthesis components. The key idea behind MCL is the assumption of the existence of a tensor subspace which can capture the essential features from the signal for the downstream learning task. Thus, the ability to find such a discriminative tensor subspace and optimize the system to project the signals onto that data manifold plays an important role in Multilinear Compressive Learning. In this paper, we propose a novel solution to address both of the aforementioned requirements, i.e., How to find those tensor subspaces in which the signals of interest are highly separable? and How to optimize the sensing and feature synthesis components to transform the original signals to the data manifold found in the first question? In our proposal, the discovery of a high-quality data manifold is conducted by training a nonlinear compressive learning system on the inference task. Its knowledge of the data manifold of interest is then progressively transferred to the MCL components via multi-stage supervised training with the supervisory information encoding how the compressed measurements, the synthesized features, and the predictions should be like. The proposed knowledge transfer algorithm also comes with a semi-supervised adaption that enables compressive learning models to utilize unlabeled data effectively. Extensive experiments demonstrate that the proposed knowledge transfer method can effectively train MCL models to compressively sense and synthesize better features for the learning tasks with improved performances, especially when the complexity of the learning task increases.
Deep learning has gained great success in various classification tasks. Typically, deep learning models learn underlying features directly from data, and no underlying relationship between classes are included. Similarity between classes can influence the performance of classification. In this article, we propose a method that incorporates class similarity knowledge into convolutional neural networks models using a graph convolution layer. We evaluate our method on two benchmark image datasets: MNIST and CIFAR10, and analyze the results on different data and model sizes. Experimental results show that our model can improve classification accuracy, especially when the amount of available data is small.
Thermal Images profile the passive radiation of objects and capture them in grayscale images. Such images have a very different distribution of data compared to optical colored images. We present here a work that produces a grayscale thermo-optical fused mask given a thermal input. This is a deep learning based pioneering work since to the best of our knowledge, there exists no other work on thermal-optical grayscale fusion. Our method is also unique in the sense that the deep learning method we are proposing here works on the Discrete Wavelet Transform (DWT) domain instead of the gray level domain. As a part of this work, we also present a new and unique database for obtaining the region of interest in thermal images based on an existing thermal visual paired database, containing the Region of Interest on 5 different classes of data. Finally, we are proposing a simple low cost overhead statistical measure for identifying the region of interest in the fused images, which we call as the Region of Fusion (RoF). Experiments on the database show encouraging results in identifying the region of interest in the fused images. We also show that they can be processed better in the mixed form rather than with only thermal images.
Ultrasound image diagnosis of breast tumors has been widely used in recent years. However, there are some problems of it, for instance, poor quality, intense noise and uneven echo distribution, which has created a huge obstacle to diagnosis. To overcome these problems, we propose a novel method, a breast cancer classification with ultrasound images based on SLIC (BCCUI). We first utilize the Region of Interest (ROI) extraction based on Simple Linear Iterative Clustering (SLIC) algorithm and region growing algorithm to extract the ROI at the super-pixel level. Next, the features of ROI are extracted. Furthermore, the Support Vector Machine (SVM) classifier is applied. The calculation states that the accuracy of this segment algorithm is up to 88.00% and the sensitivity of the algorithm is up to 92.05%, which proves that the classifier presents in this paper has certain research meaning and applied worthiness.
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