Histopathology image classification: highlighting the gap between manual analysis and AI automation.

BackgroundHistopathology image analysis is a gold standard for cancer recognition and diagnosis. Automatic analysis of histopathology images can help pathologists diagnose tumor and cancer subtypes, alleviating the workload of pathologists. There are two basic types of tasks in digital histopathology image analysis: image classification and image segmentation. Typical problems with histopathology images that hamper automatic analysis include complex clinical representations, limited quantities of training images in a dataset, and the extremely large size of singular images (usually up to gigapixels). The property of extremely large size for a single image also makes a histopathology image dataset be considered large-scale, even if the number of images in the dataset is limited.ResultsIn this paper, we propose leveraging deep convolutional neural network (CNN) activation features to perform classification, segmentation and visualization in large-scale tissue histopathology images. Our framework transfers features extracted from CNNs trained by a large natural image database, ImageNet, to histopathology images. We also explore the characteristics of CNN features by visualizing the response of individual neuron components in the last hidden layer. Some of these characteristics reveal biological insights that have been verified by pathologists. According to our experiments, the framework proposed has shown state-of-the-art performance on a brain tumor dataset from the MICCAI 2014 Brain Tumor Digital Pathology Challenge and a colon cancer histopathology image dataset.ConclusionsThe framework proposed is a simple, efficient and effective system for histopathology image automatic analysis. We successfully transfer ImageNet knowledge as deep convolutional activation features to the classification and segmentation of histopathology images with little training data. CNN features are significantly more powerful than expert-designed features.

A deep learning fusion network trained with clinical and high-frequency ultrasound images in the multi-classification of skin diseases in comparison with dermatologists: a prospective and multicenter study

The softmax and binary classifier are commonly preferred for image classification applications. However, as softmax is specifically designed for categorical classification, it assumes each image has just one class label. This limits its applicability for problems where the number of labels does not equal one, most notably zero- and multi-label problems. In these challenging settings, binary classifiers are, in theory, better suited. However, as they ignore the correlation between classes, they are not as accurate and scalable in practice. In this paper, we start from the observation that the only difference between binary and softmax classifiers is their normalization function. Specifically, while the binary classifier self-normalizes its score, the softmax classifier combines the scores from all classes before normalisation. On the basis of this observation we introduce a normalization function that is learnable, constant, and shared between classes and data points. By doing so, we arrive at a new type of binary classifier that we coin quasibinary classifier. We show in a variety of image classification settings, and on several datasets, that quasibinary classifiers are considerably better in classification settings where regular binary and softmax classifiers suffer, including zero-label and multi-label classification. What is more, we show that quasibinary classifiers yield well-calibrated probabilities allowing for direct and reliable comparisons, not only between classes but also between data points.

Digital systems are changing to security systems in contemporary days. It is time for the digital system to have sufficient security to defend against threats and attacks. The intrusion detection system can identify an anomaly from an external or internal source in the network system. Many kinds of threats are present, that is, active and passive. These dangers could lead to anomalies in the system by which data can be attacked and taken by attackers from the beginning to the destination. Machine learning nowadays is a developing topic; its applications are wide. We can forecast the future through machine learning and classify the right class. In this paper, we employed the new binary and multiclass classification model of Convolutional Neural Networks (CNNs) to identify the anomaly of the network system. In this respect, we used the NSLKDD dataset. Our model uses a Convolutional Neural Network (CNN) to conduct binary and multiclass classification. In both datasets, we build a DL-based DoS detection model. We focus on the DoS category in the most extensively used IDS dataset, KDD. As the name implies, CNN is the most extensively used the DL model for image recognition. Adding a pooling layer to the convolution layer minimizes the size of the feature data extracted from the image while maintaining I/O and spatial information. The CNN model has shown the promising results of multiclass and binary classification in terms of validation loss of 0.0012 at 11th epochs and validation accuracy of 98% and 99%, respectively.

Medulloblastoma (MB) is a dangerous malignant pediatric brain tumor that could lead to death. It is considered the most common pediatric cancerous brain tumor. Precise and timely diagnosis of pediatric MB and its four subtypes (defined by the World Health Organization (WHO)) is essential to decide the appropriate follow-up plan and suitable treatments to prevent its progression and reduce mortality rates. Histopathology is the gold standard modality for the diagnosis of MB and its subtypes, but manual diagnosis via a pathologist is very complicated, needs excessive time, and is subjective to the pathologists’ expertise and skills, which may lead to variability in the diagnosis or misdiagnosis. The main purpose of the paper is to propose a time-efficient and reliable computer-aided diagnosis (CADx), namely MB-AI-His, for the automatic diagnosis of pediatric MB and its subtypes from histopathological images. The main challenge in this work is the lack of datasets available for the diagnosis of pediatric MB and its four subtypes and the limited related work. Related studies are based on either textural analysis or deep learning (DL) feature extraction methods. These studies used individual features to perform the classification task. However, MB-AI-His combines the benefits of DL techniques and textural analysis feature extraction methods through a cascaded manner. First, it uses three DL convolutional neural networks (CNNs), including DenseNet-201, MobileNet, and ResNet-50 CNNs to extract spatial DL features. Next, it extracts time-frequency features from the spatial DL features based on the discrete wavelet transform (DWT), which is a textural analysis method. Finally, MB-AI-His fuses the three spatial-time-frequency features generated from the three CNNs and DWT using the discrete cosine transform (DCT) and principal component analysis (PCA) to produce a time-efficient CADx system. MB-AI-His merges the privileges of different CNN architectures. MB-AI-His has a binary classification level for classifying among normal and abnormal MB images, and a multi-classification level to classify among the four subtypes of MB. The results of MB-AI-His show that it is accurate and reliable for both the binary and multi-class classification levels. It is also a time-efficient system as both the PCA and DCT methods have efficiently reduced the training execution time. The performance of MB-AI-His is compared with related CADx systems, and the comparison verified the powerfulness of MB-AI-His and its outperforming results. Therefore, it can support pathologists in the accurate and reliable diagnosis of MB and its subtypes from histopathological images. It can also reduce the time and cost of the diagnosis procedure which will correspondingly lead to lower death rates.

Automated classification of histopathological images is an important research problem in medical imaging. Digital histopathology exhibits two principally distinct characteristics: 1) invariably histopathological images are multi-channel (color) with key geometric information spread across the color channels instead of being captured by luminance alone, and 2) the richness of geometric structures in such tissue imagery makes feature extraction for classification very demanding. Inspired by recent work in the use of sparsity for single channel image classification, we propose a new simultaneous Sparsity model for multi-channel Histopathological Image Representation and Classification (SHIRC). Essentially, we represent a multi-channel histopathological image as a sparse linear combination of training examples under suitable channel-wise constraints and classification is performed by solving a newly formulated simultaneous sparsity-based optimization problem. Experiments on two challenging real-world image databases: 1) provided by pathologists of the Animal Diagnostics Lab (ADL) at Pennsylvania State University, and 2) histopathological images corresponding to intraductal breast lesions [1], reveal the merits of the proposed SHIRC model over state of the art alternatives.

Deep manifold feature fusion for classification of breast histopathology images

Convolutional Neural Networks (CNNs) demonstrate state-of-the-art performance in large-scale multi-class image classification tasks. CNNs consist of convolution layers that progressively construct features and a classification layer. Typically, a softmax function is used in the classification layer to learn joint probabilities for the classes, which are subsequently used for class prediction. We refer to such an approach as the joint approach to multi-class classification. There exists another approach in the literature which determines the multi-class prediction outcome through a sequence of binary decisions, and is christened the class binarization approach. A popular type of class binarization is error-correcting output codes. In this paper, we propose to incorporate error-correcting output codes into convolutional neural networks by inserting a latent binarization layer in a CNN classification layer. This approach encapsulates both encoding and decoding steps of error-correcting output codes into a single CNN architecture that is capable of discovering an optimal coding matrix during training. The latent binarization layer is motivated by the family of latent-trait and latent-class models used in behavioral research. We call the proposed convolutional neural networks with Latent Binarization as LB-CNNs, and develop algorithms combining expectation maximization algorithms and back-propagation to train LB-CNNs. The proposed models and algorithms are applied to several image recognition tasks, producing excellent results. Furthermore, our model enhances the interpretability of the decision process of standard convolutional neural networks.

Breast cancer is widely prevalent in women. To diagnose it, pathologists evaluate breast histopathology images under a microscope in various magnifications. However, the number of pathologists per population is low in many countries, and a mistake is probable. Nowadays, deep learning has become a popular artificial intelligence research trends. Even though deep neural networks have obtained promising results in image processing, the need for extensive training data avoids its use in medical image processing. After the evaluation of various state-of-the-art deep learning methods and algorithms in medical data processing, this study proposes an effective deep transfer learning-based model, relying on pre-trained DCNN using an extensive data of ImageNet dataset which improves state-of the-art systems in both binary and multi-class classification. The weights of the pre-trained DesneNet121 on the Imagenet are transferred as initial weights first, and then the model is fine-tuned with a deep classifier along with data augmentation to distinguish various malignant and benign samples in the two categories of binary and multi-class classification. In the multi-class classification, the proposed model obtained up to 97% image-level accuracy. In binary classification, the model obtained up to 100% image-level accuracy. The achieved-results are outperforming previous studies accuracies in multiple performance metrics in breast cancer CAD systems. Moreover, the proposed method is both flexible and scalable, meaning it can be easily expanded to cover the detection of other types of diseases in the future and be integrated with more CNNs to increase its generalization capabilities.

Alzheimer's Disease (AD), the most common type of dementia, is characterized by memory issues that worsen with time. When evaluating single modalities, there are specific efficient learning techniques that produce a poor identification rate. The clinical significance of Mild Cognitive Impairment (MCI) has clinical importance, which is crucial for identifying and categorizing AD patients. This study includes the utilization of 3D T1 weighted /Magnetic Resonance Imaging (3D T1WI MRI) images where the structural changes in the brain are identified for predicting early AD. The classification accuracy for AD, MCI, and Normal Control (NC) has also increased due to cognitive evaluations when comparing three one vs one classifications, i.e. AD vs. NC, MCI vs. NC, AD vs. MCI, and multi-class classification. The proposed approach’s novelty is a binary and multi-class classification of structural MRI images using a Siamese 3D Convolutional Neural Network (Siamese 3D-CNN). The Stochastic Gradient Descent (SGD) has been employed to modify the proposed network's weights, and 5-Fold Cross-Validation (CV) has been used for each binary classification task. Our study used the neuropsychological data of 417 people from the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset to validate the suggested methodology. Experimental results demonstrate that accuracy, sensitivity, and specificity for three binary classifications produce the maximum percentage, in contrast to other relevant approaches found in the literature. In addition, the multi-class classification accuracy of 99.8% was attained.

Pathology diagnosis of colorectal cancer is time-consuming and requires a high level of expertise. However, it is an essential step towards establishing the adequate treatment. The need to analyse a large number of these histopathological images calls for automatic tools capable of aiding pathologists in this arduous task. Deep learning techniques, together with the wealth of data available nowadays, provide a promising candidate for such job. Adopting state-of-the-art artificial intelligence algorithms, we developed a model to accurately detect colorectal cancer in digitalised histopathological whole-slide images. Our end-to-end approach uses the principles of multiple-instance learning combined with deep convolutional neural networks in order to fully leverage the information contained within each image and make robust predictions at the patient's level. The model also allows to highlight the areas in the slide most likely to harbour tumour tissue. Given the finite computational resources available, working at maximum resolution can be detrimental. Therefore, we explored the impact of lowering the working image resolution. The algorithms were trained and validated on a subset of more than 1300 patients of the Molecular Epidemiology of Colorectal Cancer study with histopathology images available. These images gave rise to [Formula: see text] tiles of [Formula: see text] pixels each. Once we identified the best-performing model we put it to the test on images from The Cancer Genome Atlas. We obtained the best outcomes working at 4 μm/pix, achieving the following metrics on the test dataset: F1-Score of 0.96, a Matthews correlation coefficient of 0.92 and an area under the receiver operating characteristic curve of 0.99. These results are exceptional and prove that computational costs can be reduced while keeping the performance up to standard.

Determining environmental chemical carcinogenicity is urgently needed as humans are increasingly exposed to these chemicals. In this study, we developed a hybrid neural network (HNN) method called HNN-Cancer to predict potential carcinogens of real-life chemicals. The HNN-Cancer included a new SMILES feature representation method by modifying our previous 3D array representation of 1D SMILES simulated by the convolutional neural network (CNN). We developed binary classification, multiclass classification, and regression models based on diverse non-congeneric chemicals. Along with the HNN-Cancer model, we developed models based on the random forest (RF), bootstrap aggregating (Bagging), and adaptive boosting (AdaBoost) methods for binary and multiclass classification. We developed regression models using HNN-Cancer, RF, support vector regressor (SVR), gradient boosting (GB), kernel ridge (KR), decision tree with AdaBoost (DT), KNeighbors (KN), and a consensus method. The performance of the models for all classifications was assessed using various statistical metrics. The accuracy of the HNN-Cancer, RF, and Bagging models were 74%, and their AUC was ~0.81 for binary classification models developed with 7994 chemicals. The sensitivity was 79.5% and the specificity was 67.3% for the HNN-Cancer, which outperforms the other methods. In the case of multiclass classification models with 1618 chemicals, we obtained the optimal accuracy of 70% with an AUC 0.7 for HNN-Cancer, RF, Bagging, and AdaBoost, respectively. In the case of regression models, the correlation coefficient (R) was around 0.62 for HNN-Cancer and RF higher than the SVM, GB, KR, DTBoost, and NN machine learning methods. Overall, the HNN-Cancer performed better for the majority of the known carcinogen experimental datasets. Further, the predictive performance of HNN-Cancer on diverse chemicals is comparable to the literature-reported models that included similar and less diverse molecules. Our HNN-Cancer could be used in identifying potentially carcinogenic chemicals for a wide variety of chemical classes.

Oral squamous cell carcinoma (OSCC) is a malignancy that destroys the ability of the tissues surrounding the mouth to develop layers and membranes. Automated early diagnosis of oral histopathological images has allowed for the successful diagnosis of oral cancer, thanks to recent advancements in Deep Learning (DL) for biomedical image classification. By using a convolutional neural network (CNN) model based on deep learning for the initial analysis of oral squamous cell carcinoma (OSCC), this work aims to automate the classification of benign and malignant oral biopsy histopathological images. For this study, the CNN model Inception-Resnet-V2 is selected using the transfer learning approach. To enhance OSCC detection, additional layers are incorporated into this pretrained model. By mining a repository of oral cancer histopathology images, we can gauge how well these tweaked models perform. We examine the modified structure of the pre-trained Inception-Resnet-V2 model and suggest a DL-CNN model that uses it. With an accuracy of 91.78%, it has outperformed in terms of performance metrics.

In this research paper we are introducing a classification approach for determining the texture feature and the subsequent classification of histopathological digital image i.e. applied computer-aided grading of follicular lymphoma (FL) and Neuroblastoma (NB) from whole-slide tissue samples. Basic idea behind this research is to distinguish among nuclei, cytoplasm, extracellular material and red blood cells from H&E stained input image so that doctors (radiologist) can provide better judgment during the prognosis of histopathological image that sometimes wrongly concluded. In this study we proposed a noble algorithm in which we convolve our H&E stained pathological images with 12 different orientation masks, resulting in an output of 12 different representations (corresponding to 12 different orientations) of our H&E stained input image. The information included in the 12 representations coming from the application of Gaussian filter is summarized in twelve images that correspond to each of the orientations used in the filters. We then combine these 12 images into one textured image represented as a 3-dimensional representation of input image. Experimental results on FL & NB demonstrate that the proposed approach outperforms the gray level based texture analysis.

As security threats become more complex, the need for effective intrusion detection systems (IDSs) has grown. Traditional machine learning methods are limited by the need for extensive feature engineering and data preprocessing. To overcome this, we propose two enhanced hybrid deep learning models, an autoencoder–convolutional neural network (Autoencoder–CNN) and a transformer–deep neural network (Transformer–DNN). The Autoencoder reshapes network traffic data, addressing class imbalance, and the CNN performs precise classification. The transformer component extracts contextual features, which the DNN uses for accurate classification. Our approach utilizes an enhanced hybrid adaptive synthetic sampling–synthetic minority oversampling technique (ADASYN-SMOTE) for binary classification and enhanced SMOTE for multi-class classification, along with edited nearest neighbors (ENN) for further class imbalance handling. The models were designed to minimize false positives and negatives, improve real-time detection, and identify zero-day attacks. Evaluations based on the CICIDS2017 dataset showed 99.90% accuracy for Autoencoder–CNN and 99.92% for Transformer–DNN in binary classification, and 99.95% and 99.96% in multi-class classification, respectively. On the NF-BoT-IoT-v2 dataset, the Autoencoder–CNN achieved 99.98% in binary classification and 97.95% in multi-class classification, while the Transformer–DNN reached 99.98% and 97.90%, respectively. These results demonstrate the superior performance of the proposed models compared with traditional methods for handling diverse network attacks.