Detection of mitotic cells in breast cancer histopathological images using deep versus handcrafted features

One of the most important processes in the diagnosis of breast cancer, which is the leading mortality rate in women, is the detection of the mitosis stage at the cellular level. In literature, many studies have been proposed on the computer-aided diagnosis (CAD) system for detecting mitotic cells in breast cancer histopathological images. In this study, comparative evaluation of conventional and deep learning based feature extraction methods for automatic detection of mitosis in histopathological images are focused. While various handcrafted features are extracted with textural/spatial, statistical and shape-based methods in conventional approach, the convolutional neural network structure proposed on the deep learning approach aims to create an architecture that extracts the features of small cellular structures such as mitotic cells. Mitosis detection/counting is an important process that helps us assess how aggressive or malignant the cancer’s spread is. In the proposed study, approximately 180,000 non-mitotic and 748 mitotic cells are extracted for the evaluations. It is obvious that the classification stage cannot be performed properly due to the imbalanced numbers of mitotic and non-mitotic cells extracted from histopathological images. Hence, the random under-sampling boosting (RUSBoost) method is exploited to overcome this problem. The proposed framework is tested on mitosis detection in breast cancer histopathological images dataset provided from the International Conference on Pattern Recognition (ICPR) 2014 contest. In the results obtained with the deep learning approach, 79.42% recall, 96.78% precision and 86.97% F-measure values are achieved more successfully than handcrafted methods. A client/server-based framework has also been developed as a secondary decision support system for use by pathologists in hospitals. Thus, it is aimed that pathologists will be able to detect mitotic cells in various histopathological images more easily through necessary interfaces.

     

Automatic Detection of COVID-19 Infection Using Chest X-Ray Images Through Transfer Learning

The new coronavirus (COVID-19), declared by the World Health Organization as a pandemic, has infected more than 1 million people and killed more than 50 thousand. An infection caused by COVID-19 can develop into pneumonia, which can be detected by a chest X-ray exam and should be treated appropriately. In this work, we propose an automatic detection method for COVID-19 infection based on chest X-ray images. The datasets constructed for this study are composed of 194 X-ray images of patients diagnosed with coronavirus and 194 X-ray images of healthy patients. Since few images of patients with COVID-19 are publicly available, we apply the concept of transfer learning for this task. We use different architectures of convolutional neural networks (CNNs) trained on ImageNet, and adapt them to behave as feature extractors for the X-ray images. Then, the CNNs are combined with consolidated machine learning methods, such as k-Nearest Neighbor, Bayes, Random Forest, multilayer perceptron (MLP), and support vector machine (SVM). The results show that, for one of the datasets, the extractor-classifier pair with the best performance is the MobileNet architecture with the SVM classifier using a linear kernel, which achieves an accuracy and an F1-score of 98.5%. For the other dataset, the best pair is DenseNet201 with MLP, achieving an accuracy and an F1-score of 95.6%. Thus, the proposed approach demonstrates efficiency in detecting COVID-19 in X-ray images.      

Overexpression and elevated plasma level of tumor-associated antigen 90K/Mac-2 binding protein in colorectal carcinoma

The cancer cell secretome may contain potentially useful biomarkers. Previously, we have analyzed the colorectal carcinoma (CRC) cell secretome. In this study, tumor‐associated antigen 90K (TAA90K)/Mac‐2 binding protein (Mac‐2BP), one of the CRC cell secreted proteins, was chosen for evaluation as a potential CRC biomarker because its mRNA level was also found to be significantly elevated in CRC tissues and in a more metastatic CRC cell line from the analysis of two public domain array‐based datasets. Immunohistochemical analysis of 241 CRC specimens showed that TAA90K/Mac‐2BP was positively detected in 52.7% of the tumors, but weakly or not detected in over 95% of the adjacent nontumor epithelial cells. The plasma TAA90K/Mac‐2BP levels were significantly higher in CRC patients (N = 280) versus healthy controls (N = 147) (7.77 ± 3.49 vs. 5.72 ± 2.67 μg/mL, p<0.001). Moreover, combination of TAA90K/Mac‐2BP and carcinoembryonic antigen (CEA) could outperform CEA alone in discriminating CRC patients from healthy persons in this case‐control study. Our results collectively indicate that analysis of cancer cell secretome is a feasible strategy for identifying cancer biomarker candidates, and the TAA90K/Mac‐2BP may be a potential CRC biomarker.     

Detection of Mesangial hypercellularity of MEST-C score in immunoglobulin A-nephropathy using deep convolutional neural network

Immunoglobulin A (IgA)-nephropathy (IgAN) is one of the major reasons for renal failure. It provides vital clues to estimate the stage and the proliferation rate of end-stage kidney disease. IgA stage can be estimated with the help of MEST-C score. The manual estimation of MEST-C score from whole slide kidney images is a very tedious and difficult task. This study uses some Convolutional neural networks (CNNs) related models to detect mesangial hypercellularity (M score) in MEST-C. CNN learns the features directly from image data without the requirement of analytical data. CNN is trained efficiently when image data size is large enough for a particular class. In the case of smaller data size, transfer learning can be used efficiently in which CNN is pre-trained on some general images and then on subject images. Since the data set size is small, time spent in collecting large data set is saved. The training time of transfer learning is also reduced because the model is already pre-trained. This research work aims at the detection of mesangial hypercellularity from biopsy images with small data size by utilizing the transfer learning. The dataset used in this research work consists of 138 individual glomerulus (× 20 magnification digital biopsy) images of IgA patients received from All India Institute of Medical Science, Delhi. Here, machine learning (k-nearest neighbour (KNN) and support vector machine (SVM)) classifiers are compared to transfer learning CNN methods. The deep extracted image features are used by machine learning classifiers. The different evaluation parameters have been used for comparing the predictions of basic classifiers to the deep learning model. The research work concludes that the transfer learning deep CNN method can improve the detection of mesangial hypercellularity as compare to KNN, SVM methods when using the small data set. This model could help the pathologists to understand the stages of kidney failure.

     

CVSkSA: cross-architecture vulnerability search in firmware based on kNN-SVM and attributed control flow graph

To prevent the same known vulnerabilities from affecting different firmware, searching known vulnerabilities in binary firmware across different architectures is crucial. Because the accuracy of existing cross-architecture vulnerability search methods is not high, we propose a staged approach based on support vector machine (SVM) and attributed control flow graph (ACFG) at the function level to improve the accuracy using prior knowledge. Furthermore, for efficiency, we utilize the k-nearest neighbor (kNN) algorithm to prune and SVM to refine in the function prefilter stage. Although the accuracy of the proposed method using kNN-SVM approach is slightly lower than the accuracy of the method using only SVM, its efficiency is significantly enhanced. We have implemented our approach CVSkSA to search several vulnerabilities in real-world firmware images. The experimental results show that the accuracy of the proposed method using kNN-SVM approach is close to the accuracy of the method using only SVM in most cases, while the former is approximately four times faster than the latter.

     

Deformable and residual convolutional network for image super-resolution

Recent research on image super-resolution (SR) has greatly progressed with the development of convolutional neural networks (CNNs). However, the fixed geometric structures of standard convolution filters largely limit the learning capacity of CNNs for image SR. To effectively address this problem, we propose a deformable and residual convolutional network (DefRCN) for image SR. Specifically, a deformable residual convolution block (DRCB) is developed to augment spatial sampling locations and enhance the transformation modelling capability of CNNs. In addition, we optimize the residual convolution block to reduce the model redundancy and alleviate the vanishing-gradient in backpropagation. In addition, the proposed upsample block allows the network to directly process low-resolution images, which reduces the computational resource cost. Extensive experiments on benchmark datasets verify that the proposed method achieves a high quantitative and qualitative performance.

     

An application of the 2-nitrobenzenesulfenyl method to proteomic profiling of human colorectal carcinoma: A novel approach for biomarker discovery

In the development of novel biomarkers, the proteomic approach is advantageous because using it the cancer-associated proteins can be directly identified. We previously developed a 2-nitrobenzenesulfenyl (NBS) method to improve quantitative proteome analysis. Here, we applied this method to proteomic profiling of colorectal carcinoma (CRC) to identify novel proteins with altered expression in CRC. Each pair of tumor and normal tissue specimens from 12 CRC patients was analyzed, and approximately 5000 NBS-labeled paired peaks were quantified. Peaks with altered signal intensities (>1.5-fold) and occurring frequently in the samples (>70%) were selected, and 128 proteins were identified by MS/MS analyses as differentially expressed proteins in CRC tissues. Many proteins were newly revealed to be CRC related; 30 were reported in earlier studies of CRC. Six proteins that were up-regulated in CRC (ZYX, RAN, RCN1, AHCY, LGALS1, and VIM) were further characterized and validated by Western blot and immunohistochemistry. All six were found to be CRC-localized, either in cancer cells or in stroma cells near the cancer cells. These results indicate that the proteins identified in this study are novel candidates for CRC markers, and that the NBS method is useful in proteome mining to discover novel biomarkers.     

Ultrasound image analysis technology under deep belief networks in evaluation on the effects of diagnosis and chemotherapy of cervical cancer

The purpose of this study was to explore the value of extraction of tumor features in contrast-enhanced ultrasonography (CEUS) images based on the deep belief networks (DBN) for the diagnosis of cervical cancer patients and realize the intelligent evaluation on effects of diagnosis and chemotherapy of the cervical cancer. An automatic extraction algorithm with the time-intensity curve (TIC) was proposed based on Sparse nonnegative matrix factorization (SNMF) in this study, and was applied to the framework of automatic analysis of cervical cancer tumors based on the deep belief networks, to assist doctors in the analysis of cervical cancer tumors. The framework was applied to the real clinical diagnostic data, and the feasibility of the method was verified by comparing the accuracy, sensitivity, and specificity. Later, the parameters of patients’ time to peak (TP), peak intensity (PI), mean transit time (MTT), and area under the curve (AUC) were obtained by drawing TICs, and the changes of p53 protein and ki-67 protein obtained by pathological section staining were analyzed to evaluate the therapeutic effect in the patients. It was found that the proposed model of tumor feature extraction based on the DBN had the higher accuracy (86.36%), sensitivity (83.33%), and specificity (87.50%). The related parameters of TIC curve obtained based on SNMF showed that there was a significant difference in p53 content between tissues with different degrees of disease (p?<?0.05), the PI of poorly differentiated tissues was significantly higher than that of those with high to medium differentiation (p?<?0.05). In addition, PI and AUC of patients after chemotherapy were significantly lower than that before chemotherapy (p?<?0.05), while MTT was significantly higher than that before chemotherapy (p?<?0.05). Therefore, the proposed TIC feature extraction of CEUS images based on SNMF and the automatic tumor classification based on deep learning can be used in the diagnosis and efficacy evaluation of cervical cancer patients.

     

Matrix-product neural network based on sequence block matrix product

Convolution neural networks (CNNs) based on the discrete convolutional operation have achieved great success in image processing, voice and audio processing, natural language processing and other fields. However, it is still an open problem how to develop new models instead of CNNs. Using the idea of the sequence block matrix product, we propose a novel operation and its corresponding neural network, namely two-dimensional discrete matrix-product operation (TDDMPO) and matrix-product neural network (MPNN). We present the definition of the TDDMPO, a series of its properties and matrix-product theorem in detail, and then construct its corresponding MPNN. Experimental results on Fashion-MNIST, SVHN, FLOWER17 and FLOWER102 datasets show that MPNNs obtain 1.65–13.04% relative performance improvement in comparison with the corresponding CNNs, and the amount of calculation of matrix-product layers of MPNNs obtains 41× to 57× reduction in comparison with the corresponding convolutional layers of CNNs. Hence, it is a potential model that may open some new directions for deep neural networks, particularly alternatives to CNNs.

     

A Performance Evaluation of Classic Convolutional Neural Networks for 2D and 3D Palmprint and Palm Vein Recognition

Palmprint recognition and palm vein recognition are two emerging biometrics technologies. In the past two decades, many traditional methods have been proposed for palmprint recognition and palm vein recognition, and have achieved impressive results. However, the research on deep learning-based palmprint recognition and palm vein recognition is still very preliminary. In this paper, in order to investigate the problem of deep learning based 2D and 3D palmprint recognition and palm vein recognition in-depth, we conduct performance evaluation of seventeen representative and classic convolutional neural networks (CNNs) on one 3D palmprint database, five 2D palmprint databases and two palm vein databases. A lot of experiments have been carried out in the conditions of different network structures, different learning rates, and different numbers of network layers. We have also conducted experiments on both separate data mode and mixed data mode. Experimental results show that these classic CNNs can achieve promising recognition results, and the recognition performance of recently proposed CNNs is better. Particularly, among classic CNNs, one of the recently proposed classic CNNs, i.e., EfficientNet achieves the best recognition accuracy. However, the recognition performance of classic CNNs is still slightly worse than that of some traditional recognition methods.

     

Recognizing plankton images from the shadow image particle profiling evaluation recorder

We present a system to recognize underwater plankton images from the shadow image particle profiling evaluation recorder (SIPPER). The challenge of the SIPPER image set is that many images do not have clear contours. To address that, shape features that do not heavily depend on contour information were developed. A soft margin support vector machine (SVM) was used as the classifier. We developed a way to assign probability after multiclass SVM classification. Our approach achieved approximately 90% accuracy on a collection of plankton images. On another larger image set containing manually unidentifiable particles, it also provided 75.6% overall accuracy. The proposed approach was statistically significantly more accurate on the two data sets than a C4.5 decision tree and a cascade correlation neural network. The single SVM significantly outperformed ensembles of decision trees created by bagging and random forests on the smaller data set and was slightly better on the other data set. The 15-feature subset produced by our feature selection approach provided slightly better accuracy than using all 29 features. Our probability model gave us a reasonable rejection curve on the larger data set.     

Classification of complex environments using pixel level fusion of satellite data

The present study reports classification and analysis of composite land features using fusion images obtained by fusing two original hyperspectral and multispectral datasets. The high spatial-spectral resolution, multi-instrument and multi-period satellite images were used for fusion. Three pixel level fusion based techniques, Color Normalized Spectral Sharpening (CNSS), Principal Component Spectral Sharpening Transform (PCSST) and Gram-Schmidt Transform (GST), were implemented on the datasets. Performance evaluations of three fusion algorithms were done using classification results. The Support Vector Machine (SVM) and Gaussian Maximum Likelihood Classification (MLC) were used for classification using five types of images, viz. hyperspectral, multispectral and three fused images. Number of classes considered was eight. Sufficient number of ground field data for each class has also been acquired which was needed for supervise based classification. The accuracy was improved from 74.44 to 97.65% when the fused images were considered with SVM classifier. Similarly, the results were improved from 69.25 to 94.61% with original and fused data using MLC classifier. The fusion image technique was found to be superior to the single original image and the SVM is better than the MLC method.

     

1D convolutional neural networks for chart pattern classification in financial time series

This paper proposes a novel deep learning-based approach for financial chart patterns classification. Convolutional neural networks (CNNs) have made notable achievements in image recognition and computer vision applications. These networks are usually based on two-dimensional convolutional neural networks (2D CNNs). In this paper, we describe the design and implementation of one-dimensional convolutional neural networks (1D CNNs) for the classification of chart patterns from financial time series. The proposed 1D CNN model is compared against support vector machine, extreme learning machine, long short-term memory, rule-based and dynamic time warping. Experimental results on synthetic datasets reveal that the accuracy of 1D CNN is highest among all the methods evaluated. Results on real datasets also reveal that chart patterns identified by 1D CNN are also the most recognized instances when they are compared to those classified by other methods.

     

Deep interactive encoding with capsule networks for image classification

With new architectures providing astonishing performance on many vision tasks, the interest in Convolutional Neural Networks (CNNs) has grown exponentially in the recent past. Such architectures, however, are not problem-free. For instance, one of the many issues is that they require a huge amount of labeled data and are not able to encode pose and deformation information. Capsule Networks (CapsNets) have been recently proposed as a solution to the issues related to CNNs. CapsNet achieved interesting results in images recognition by addressing pose and deformation encoding challenges. Despite their success, CapsNets are still an under-investigated architecture with respect to the more classical CNNs. Following the ideas of CapsNet, we propose to introduce Residual Capsule Network (ResNetCaps) and Dense Capsule Network (DenseNetCaps) to tackle the image recognition problem. With these two architectures, we expand the encoding phase of CapsNet by adding residual convolutional and densely connected convolutional blocks. In addition to this, we investigate the application of feature interaction methods between capsules to promote their cooperation while dealing with complex data. Experiments on four benchmark datasets demonstrate that the proposed approach performs better than existing solutions.

     

Transfer learning from synthetic labels for histopathological images classification

This study introduces a new strategy that combines unsupervised learning (clustering) and transfer learning. Clustering methods are employed to generate synthetic labels for the source dataset (ICAR-2018). The generated dataset is then used for transfer learning to other histopathological datasets (KimiaPath960, CRC, Biomaging??2015, Breakhis, and Lymphoma). The comparative study based on two clustering algorithms (K-means and multi-objective clustering stream) demonstrates the efficiency of MOC-Stream. The generated synthetic histopathological dataset by this clustering algorithm outperformed the original labeled dataset and the imageNet models in transfer learning.

     

Brain tumor segmentation and classification in MRI using SVM and its variants: a survey

The process of separation of brain tumor from normal brain tissues is Brain tumor segmentation. Segmentation of tumor from the MR images is a very challenging task as brain tumors are of different shapes and sizes. There are multiple phases to achieve the segmentation and the phases are pre-processing, segmentation, feature extraction, feature reduction, and classification of the tumor into benign and malignant. In this paper, Otsu thresholding is used in segmentation phase, Discrete Wavelet Transform (DWT) in feature extraction phase, Principal Component Analysis (PCA) in feature reduction phase and Support Vector Machine (SVM), Least Squared-Support Vector Machine (LS-SVM), Proximal Support Vector Machine (PSVM) and Twin Support Vector Machine (TWSVM) in the classification phase. We have compared the performances of all these classifiers, where TWSVM outperformed all other classifiers with 100% accuracy.

     

Modulated T-complex protein 1 ζ and peptidyl-prolyl cis-trans isomerase B are two novel indicators for evaluating lymph node metastasis in colorectal cancer: Evidence from proteomics and bioinformatics

Lymph node metastasis (LNM) is an important indicator for systematic therapy, which could increase the survival of colorectal cancer (CRC) patients. However, effective clinical evaluation for LNM is still absent to date. In this study, protein expression profiles of CRC tissues were compared between patients with and without LNM. Based on average expression level, 12 proteins were found to be differentially expressed in the CRC tissues with LNM, whose discrimination reliability was confirmed by PCA. With stepwise linear discriminant analysis, T-complex protein 1 ζ subunit and peptidyl-prolyl cis-trans isomerase B (PPIB) were identified as two main contributors for separating CRC tissues with positive LNM from those negative ones in both original-grouped and cross-validated-grouped cases, which was also supported in subsequent linear support vector machine analysis. In addition, the expression alterations of the two proteins were verified by Western blot and immunohistochemistry. Functional studies also confirmed the role of PPIB in migration and invasion of cancer cells. Taken together, the down-regulated T-complex protein 1 ζ subunit and up-regulated PPIB were identified as two promising indicators for the clinical evaluation of LNM in CRC patients.     

基于支持向量机的磁共振脑组织图像分割

脑组织图像分割在医学图像分析中具有重要的理论和应用价值。由于支持向量机被看作是对传统学习分类器的一个好的替代,特别是在小样本、高维情况下,具有较好的泛化性能,因此可采用支持向量机方法对磁共振脑组织图像进行分割研究。为了验证支持向量机分割磁共振脑组织图像的效果,利用支持向量机进行了脑组织图像分割实验。实验结果表明:核函数及模型参数对支持向量机的分割性能有较大的影响;支持向量机方法适合作为小样本情况下的学习分类器;对目标边界模糊、目标灰度不均匀及目标不连续等情况下的图像(如医学图像)分割,支持向量机方法也是一个好的选择。     

Zernike-CNNs for image preprocessing and classification in printed register detection

In the register detection of printing field, a new approach based on Zernike-CNNs is proposed. The edge feature of image is extracted by Zernike moments (ZMs), and a recursive algorithm of ZMs called Kintner method is derived. An improved convolutional neural networks (CNNs) are investigated to improve the accuracy of classification. Based on the classic convolutional neural network (CNN), the improved CNNs adopt parallel CNN to enhance local features, and adopt auxiliary classification part to modify classification layer weights. A printed image is trained with 7?×?400 samples and tested with 7?×?100 samples, and then the method in this paper is compared with other methods. In image processing, Zernike is compared with Sobel method, Laplacian of Gaussian (LoG) method, Smallest Univalue Segment Assimilating Nucleus (SUSAN) method, Finite Impusle Response (FIR) method, Multi-scale Morphological Gradient (MMG) method. In image classification, improved CNNs are compared with classical CNN. The experimental results show that Zernike-CNNs have the best performance, the mean square error (MSE) of the training samples reaches 0.0143, and the detection accuracy of training samples and test samples reached 91.43% and 94.85% respectively. The experiments reveal that Zernike-CNNs are a feasible approach for register detection.