Clostridioides difficile infection (CDI) is an enteric bacterial disease that is increasing in incidence worldwide. Symptoms of CDI range from mild diarrhea to severe life-threatening inflammation of the colon. While antibiotics are standard-of-care treatments for CDI, they are also the biggest risk factor for development of CDI and recurrence. Therefore, novel therapies that successfully treat CDI and protect against recurrence are an unmet clinical need. Screening for novel drug leads is often tested by manual image analysis. The process is slow, tedious and is subject to human error and bias. So far, little work has focused on computer-aided screening for drug leads based on fluorescence images. Here, we propose a novel method to identify characteristic morphological changes in human fibroblast cells exposed to C. difficile toxins based on computer vision algorithms supported by deep learning methods. Classical image processing algorithms for the pre-processing stage are used together with an adjusted pre-trained deep convolutional neural network responsible for cell classification. In this study, we take advantage of transfer learning methodology by examining pre-trained VGG-19, ResNet50, Xception, and DenseNet121 convolutional neural network (CNN) models with adjusted, densely connected classifiers. We compare the obtained results with those of other machine learning algorithms and also visualize and interpret them. The proposed models have been evaluated on a dataset containing 369 images with 6112 cases. DenseNet121 achieved the highest results with a 93.5% accuracy, 92% sensitivity, and 95% specificity, respectively.
One of the biggest challenge in the field of deep learning is the parameter selection and optimization process. In recent years different algorithms have been proposed including bio-inspired solutions to solve this problem, however, there are many challenges including local minima, saddle points, and vanishing gradients. In this paper, we introduce the Whale Optimisation Algorithm (WOA) based on the swarm foraging behavior of humpback whales to optimise neural network hyperparameters. We wish to stress that to the best of our knowledge this is the first attempt that uses Whale Optimisation Algorithm for the optimisation task of hyperparameters. After a detailed description of the WOA algorithm we formulate and explain the application in deep learning, present the implementation, and compare the proposed algorithm with other well-known algorithms including widely used Grid and Random Search methods. Additionally, we have implemented a third dimension feature analysis to the original WOA algorithm to utilize 3D search space (3D-WOA). Simulations show that the proposed algorithm can be successfully used for hyperparameters optimization, achieving accuracy of 89.85% and 80.60% for Fashion MNIST and Reuters datasets, respectively.
Deep learning methods, used in machine vision challenges, often face the problem of the amount and quality of data. To address this issue, we investigate the transfer learning method. In this study, we briefly describe the idea and introduce two main strategies of transfer learning. We also present the widely-used neural network models, that in recent years performed best in ImageNet classification challenges. Furthermore, we shortly describe three different experiments from computer vision field, that confirm the developed algorithms ability to classify images with overall accuracy 87.2-95%. Achieved numbers are state-of-the-art results in melanoma thickness prediction, anomaly detection and Clostridium di cile cytotoxicity classification problems.
Over the past few decades, different clinical diagnostic algorithms have been proposed to diagnose malignant melanoma in its early stages. Furthermore, the detection of skin moles driven by current deep learning based approaches yields impressive results in the classification of malignant melanoma. However, in all these approaches, the researchers do not take into account the origin of the skin lesion. It has been observed that the specific criteria for in situ and early invasive melanoma highly depend on the anatomic site of the body. To address this problem, we propose a deep learning architecture based framework to classify skin lesions into the three most important anatomic sites, including the face, trunk and extremities, and acral lesions. In this study, we take advantage of pretrained networks, including VGG19, ResNet50, Xception, DenseNet121, and EfficientNetB0, to calculate the features with an adjusted and densely connected classifier. Furthermore, we perform in depth analysis on database, architecture, and result regarding the effectiveness of the proposed framework. Experiments confirm the ability of the developed algorithms to classify skin lesions into the most important anatomical sites with 91.45% overall accuracy for the EfficientNetB0 architecture, which is a state-of-the-art result in this domain.
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