Deep Convolutional Neural Network for HEp-2 Fluorescence Intensity Classification

Virtual World as an Interactive Safety Training Platform

Virtual training platform allows interactive and engaging learning through practice without exposing trainees to hazards. In the recent pandemic (COVID-19) situation, online training is gaining importance as it allows learning with social distancing. This research study develops two online training modes—slide-based and virtual world—and assesses them on factors such as knowledge retention, engagement, and attention. Fire safety and emergency evacuation procedures were selected for online training development, focusing on a university community. A Lean Startup methodology was employed to develop training content for virtual and slide-based safety training (SBST). A virtual university building was developed with 15 learning objectives on fire safety. An empirical evaluation of the training modes was conducted with 143 participants. The results validated that a Virtual Safety World (VSW) can provide the same knowledge as SBST but can do so in a more engaging manner. Retention of concepts after a month was higher in VSW participants. The participants’ attention levels, measured by employing qEEG, showed that participants exhibited better-sustained attention while in VSW than in SBST mode. In addition, initial studies of the virtual training platform, designed to be adaptive to the user, are performed using deep learning and qEEG.

Intelligent Scheduling with Reinforcement Learning

In this paper, we present and discuss an innovative approach to solve Job Shop scheduling problems based on machine learning techniques. Traditionally, when choosing how to solve Job Shop scheduling problems, there are two main options: either use an efficient heuristic that provides a solution quickly, or use classic optimization approaches (e.g., metaheuristics) that take more time but will output better solutions, closer to their optimal value. In this work, we aim to create a novel architecture that incorporates reinforcement learning into scheduling systems in order to improve their overall performance and overcome the limitations that current approaches present. It is also intended to investigate the development of a learning environment for reinforcement learning agents to be able to solve the Job Shop scheduling problem. The reported experimental results and the conducted statistical analysis conclude about the benefits of using an intelligent agent created with reinforcement learning techniques. The main contribution of this work is proving that reinforcement learning has the potential to become the standard method whenever a solution is necessary quickly, since it solves any problem in very few seconds with high quality, approximate to the optimal methods.

Machine Learning and Feature Selection Methods for EGFR Mutation Status Prediction in Lung Cancer

The evolution of personalized medicine has changed the therapeutic strategy from classical chemotherapy and radiotherapy to a genetic modification targeted therapy, and although biopsy is the traditional method to genetically characterize lung cancer tumor, it is an invasive and painful procedure for the patient. Nodule image features extracted from computed tomography (CT) scans have been used to create machine learning models that predict gene mutation status in a noninvasive, fast, and easy-to-use manner. However, recent studies have shown that radiomic features extracted from an extended region of interest (ROI) beyond the tumor, might be more relevant to predict the mutation status in lung cancer, and consequently may be used to significantly decrease the mortality rate of patients battling this condition. In this work, we investigated the relation between image phenotypes and the mutation status of Epidermal Growth Factor Receptor (EGFR), the most frequently mutated gene in lung cancer with several approved targeted-therapies, using radiomic features extracted from the lung containing the nodule. A variety of linear, nonlinear, and ensemble predictive classification models, along with several feature selection methods, were used to classify the binary outcome of wild-type or mutant EGFR mutation status. The results show that a comprehensive approach using a ROI that included the lung with nodule can capture relevant information and successfully predict the EGFR mutation status with increased performance compared to local nodule analyses. Linear Support Vector Machine, Elastic Net, and Logistic Regression, combined with the Principal Component Analysis feature selection method implemented with 70% of variance in the feature set, were the best-performing classifiers, reaching Area Under the Curve (AUC) values ranging from 0.725 to 0.737. This approach that exploits a holistic analysis indicates that information from more extensive regions of the lung containing the nodule allows a more complete lung cancer characterization and should be considered in future radiogenomic studies.

Application of Supervised Machine Learning to Recognize Competent Level and Mixed Antinuclear Antibody Patterns Based on ICAP International Consensus

Background: Antinuclear antibody pattern recognition is vital for autoimmune disease diagnosis but labor-intensive for manual interpretation. To develop an automated pattern recognition system, we established machine learning models based on the International Consensus on Antinuclear Antibody Patterns (ICAP) at a competent level, mixed patterns recognition, and evaluated their consistency with human reading. Methods: 51,694 human epithelial cells (HEp-2) cell images with patterns assigned by experienced medical technologists collected in a medical center were used to train six machine learning algorithms and were compared by their performance. Next, we choose the best performing model to test the consistency with five experienced readers and two beginners. Results: The mean F1 score in each classification of the best performing model was 0.86 evaluated by Testing Data 1. For the inter-observer agreement test on Testing Data 2, the average agreement was 0.849 (κ) among five experienced readers, 0.844 between the best performing model and experienced readers, 0.528 between experienced readers and beginners. The results indicate that the proposed model outperformed beginners and achieved an excellent agreement with experienced readers. Conclusions: This study demonstrated that the developed model could reach an excellent agreement with experienced human readers using machine learning methods.

A Classification Method for the Cellular Images Based on Active Learning and Cross-Modal Transfer Learning

In computer-aided diagnosis (CAD) systems, the automatic classification of the different types of the human epithelial type 2 (HEp-2) cells represents one of the critical steps in the diagnosis procedure of autoimmune diseases. Most of the methods prefer to tackle this task using the supervised learning paradigm. However, the necessity of having thousands of manually annotated examples constitutes a serious concern for the state-of-the-art HEp-2 cells classification methods. We present in this work a method that uses active learning in order to minimize the necessity of annotating the majority of the examples in the dataset. For this purpose, we use cross-modal transfer learning coupled with parallel deep residual networks. First, the parallel networks, which take simultaneously different wavelet coefficients as inputs, are trained in a fully supervised way by using a very small and already annotated dataset. Then, the trained networks are utilized on the targeted dataset, which is quite larger compared to the first one, using active learning techniques in order to only select the images that really need to be annotated among all the examples. The obtained results show that active learning, when mixed with an efficient transfer learning technique, can allow one to achieve a quite pleasant discrimination performance with only a few annotated examples in hands. This will help in building CAD systems by simplifying the burdensome task of labeling images while maintaining a similar performance with the state-of-the-art methods.

Adaptive Aggregated Attention Network for Pulmonary Nodule Classification

Lung cancer has one of the highest cancer mortality rates in the world and threatens people’s health. Timely and accurate diagnosis can greatly reduce the number of deaths. Therefore, an accurate diagnosis system is extremely important. The existing methods have achieved significant performances on lung cancer diagnosis, but they are insufficient in fine-grained representations. In this paper, we propose a novel attentive method to differentiate malignant and benign pulmonary nodules. Firstly, the residual attention network (RAN) and squeeze-and-excitation network (SEN) were utilized to extract spatial and contextual features. Secondly, a novel multi-scale attention network (MSAN) was proposed to capture multi-scale attention features automatically, and the MSAN integrated the advantages of the spatial attention mechanism and contextual attention mechanism, which are very important for capturing the salient features of nodules. Finally, the gradient boosting machine (GBM) algorithm was used to differentiate malignant and benign nodules. We conducted a series of experiments on the Lung Image Database Consortium image collection (LIDC-IDRI) database, achieving an accuracy of 91.9%, a sensitivity of 91.3%, a false positive rate of 8.0%, and an F1-score of 91.0%. The experimental results demonstrate that our proposed method outperforms the state-of-the-art methods with respect to accuracy, false positive rate, and F1-Score.

Performance of Fine-Tuning Convolutional Neural Networks for HEp-2 Image Classification

The search for anti-nucleus antibodies (ANA) represents a fundamental step in the diagnosis of autoimmune diseases. The test considered the gold standard for ANA research is indirect immunofluorescence (IIF). The best substrate for ANA detection is provided by Human Epithelial type 2 (HEp-2) cells. The first phase of HEp-2 type image analysis involves the classification of fluorescence intensity in the positive/negative classes. However, the analysis of IIF images is difficult to perform and particularly dependent on the experience of the immunologist. For this reason, the interest of the scientific community in finding relevant technological solutions to the problem has been high. Deep learning, and in particular the Convolutional Neural Networks (CNNs), have demonstrated their effectiveness in the classification of biomedical images. In this work the efficacy of the CNN fine-tuning method applied to the problem of classification of fluorescence intensity in HEp-2 images was investigated. For this purpose, four of the best known pre-trained networks were analyzed (AlexNet, SqueezeNet, ResNet18, GoogLeNet). The classifying power of CNN was investigated with different training modalities; three levels of freezing weights and scratch. Performance analysis was conducted, in terms of area under the ROC (Receiver Operating Characteristic) curve (AUC) and accuracy, using a public database. The best result achieved an AUC equal to 98.6% and an accuracy of 93.9%, demonstrating an excellent ability to discriminate between the positive/negative fluorescence classes. For an effective performance comparison, the fine-tuning mode was compared to those in which CNNs are used as feature extractors, and the best configuration found was compared with other state-of-the-art works.

A Review of Convolutional Neural Network Applied to Fruit Image Processing

Agriculture has always been an important economic and social sector for humans. Fruit production is especially essential, with a great demand from all households. Therefore, the use of innovative technologies is of vital importance for the agri-food sector. Currently artificial intelligence is one very important technological tool widely used in modern society. Particularly, Deep Learning (DL) has several applications due to its ability to learn robust representations from images. Convolutional Neural Networks (CNN) is the main DL architecture for image classification. Based on the great attention that CNNs have had in the last years, we present a review of the use of CNN applied to different automatic processing tasks of fruit images: classification, quality control, and detection. We observe that in the last two years (2019–2020), the use of CNN for fruit recognition has greatly increased obtaining excellent results, either by using new models or with pre-trained networks for transfer learning. It is worth noting that different types of images are used in datasets according to the task performed. Besides, this article presents the fundamentals, tools, and two examples of the use of CNNs for fruit sorting and quality control.

Gradient-Guided Convolutional Neural Network for MRI Image Super-Resolution

Super-resolution (SR) technology is essential for improving image quality in magnetic resonance imaging (MRI). The main challenge of MRI SR is to reconstruct high-frequency (HR) details from a low-resolution (LR) image. To address this challenge, we develop a gradient-guided convolutional neural network for improving the reconstruction accuracy of high-frequency image details from the LR image. A gradient prior is fully explored to supply the information of high-frequency details during the super-resolution process, thereby leading to a more accurate reconstructed image. Experimental results of image super-resolution on public MRI databases demonstrate that the gradient-guided convolutional neural network achieves better performance over the published state-of-art approaches.

Deep CNN for IIF Images Classification in Autoimmune Diagnostics

The diagnosis and monitoring of autoimmune diseases are very important problem in medicine. The most used test for this purpose is the antinuclear antibody (ANA) test. An indirect immunofluorescence (IIF) test performed by Human Epithelial type 2 (HEp-2) cells as substrate antigen is the most common methods to determine ANA. In this paper we present an automatic HEp-2 specimen system based on a convolutional neural network method able to classify IIF images. The system consists of a module for features extraction based on a pre-trained AlexNet network and a classification phase for the cell-pattern association using six support vector machines and a k-nearest neighbors classifier. The classification at the image-level was obtained by analyzing the pattern prevalence at cell-level. The layers of the pre-trained network and various system parameters were evaluated in order to optimize the process. This system has been developed and tested on the HEp-2 images indirect immunofluorescence images analysis (I3A) public database. To test the generalisation performance of the method, the leave-one-specimen-out procedure was used in this work. The performance analysis showed an accuracy of 96.4% and a mean class accuracy equal to 93.8%. The results have been evaluated comparing them with some of the most representative works using the same database.

Classification of Pulmonary CT Images by Using Hybrid 3D-Deep Convolutional Neural Network Architecture

Lung cancer is the most common cause of cancer-related deaths worldwide. Hence, the survival rate of patients can be increased by early diagnosis. Recently, machine learning methods on Computed Tomography (CT) images have been used in the diagnosis of lung cancer to accelerate the diagnosis process and assist physicians. However, in conventional machine learning techniques, using handcrafted feature extraction methods on CT images are complicated processes. Hence, deep learning as an effective area of machine learning methods by using automatic feature extraction methods could minimize the process of feature extraction. In this study, two Convolutional Neural Network (CNN)-based models were proposed as deep learning methods to diagnose lung cancer on lung CT images. To investigate the performance of the two proposed models (Straight 3D-CNN with conventional softmax and hybrid 3D-CNN with Radial Basis Function (RBF)-based SVM), the altered models of two-well known CNN architectures (3D-AlexNet and 3D-GoogleNet) were considered. Experimental results showed that the performance of the two proposed models surpassed 3D-AlexNet and 3D-GoogleNet. Furthermore, the proposed hybrid 3D-CNN with SVM achieved more satisfying results (91.81%, 88.53% and 91.91% for accuracy rate, sensitivity and precision respectively) compared to straight 3D-CNN with softmax in the diagnosis of lung cancer.