Methodology for Good Machine Learning with Multi-Omics Data.

In 2020, Novartis Pharmaceuticals Corporation and the U.S. Food and Drug Administration (FDA) started a 4-year scientific collaboration to approach complex new data modalities and advanced analytics. The scientific question was to find novel radio-genomics-based prognostic and predictive factors for HR+/HER- metastatic breast cancer under a Research Collaboration Agreement. This collaboration has been providing valuable insights to help successfully implement future scientific projects, particularly using artificial intelligence and machine learning. This tutorial aims to provide tangible guidelines for a multi-omics project that includes multidisciplinary expert teams, spanning across different institutions. We cover key ideas, such as "maintaining effective communication" and "following good data science practices," followed by the four steps of exploratory projects, namely (1) plan, (2) design, (3) develop, and (4) disseminate. We break each step into smaller concepts with strategies for implementation and provide illustrations from our collaboration to further give the readers actionable guidance.

To predict the left ventricular endocardial scar tissue pattern using Radon descriptor-based machine learning.

OBJECTIVE: Scar tissue is an identified cause for the development of malignant ventricular arrhythmias in patients of myocardial infarction, which ultimately leads to cardiac death, a fatal outcome. We aim to evaluate the left ventricular endocardial Scar tissue pattern using Radon descriptor-based machine learning. We performed automated Left ventricle (LV) segmentation to find the LV endocardial wall, performed morphological operations, and marked the region of the scar tissue on the endocardial wall of LV. Motivated by a Radon descriptor-based machine learning approach; the patches of 17 patients from Computer tomography (CT) images of the heart were used and categorized into "endocardial Scar tissue" and "normal tissue" groups. The ten feature vectors are extracted from patches using Radon descriptors and fed into a traditional machine learning model. RESULTS: The decision tree has shown the best performance with 98.07% accuracy. This study is the first attempt to provide a Radon transform-based machine learning method to distinguish patterns between "endocardial Scar tissue" and "normal tissue" groups. Our proposed research method could be potentially used in advanced interventions.

Legal and Ethical Consideration in Artificial Intelligence in Healthcare: Who Takes Responsibility?

The legal and ethical issues that confront society due to Artificial Intelligence (AI) include privacy and surveillance, bias or discrimination, and potentially the philosophical challenge is the role of human judgment. Concerns about newer digital technologies becoming a new source of inaccuracy and data breaches have arisen as a result of its use. Mistakes in the procedure or protocol in the field of healthcare can have devastating consequences for the patient who is the victim of the error. Because patients come into contact with physicians at moments in their lives when they are most vulnerable, it is crucial to remember this. Currently, there are no well-defined regulations in place to address the legal and ethical issues that may arise due to the use of artificial intelligence in healthcare settings. This review attempts to address these pertinent issues highlighting the need for algorithmic transparency, privacy, and protection of all the beneficiaries involved and cybersecurity of associated vulnerabilities.

A Feature Extraction Using Probabilistic Neural Network and BTFSC-Net Model with Deep Learning for Brain Tumor Classification.

BACKGROUND AND OBJECTIVES: Brain Tumor Fusion-based Segments and Classification-Non-enhancing tumor (BTFSC-Net) is a hybrid system for classifying brain tumors that combine medical image fusion, segmentation, feature extraction, and classification procedures. MATERIALS AND METHODS: to reduce noise from medical images, the hybrid probabilistic wiener filter (HPWF) is first applied as a preprocessing step. Then, to combine robust edge analysis (REA) properties in magnetic resonance imaging (MRI) and computed tomography (CT) medical images, a fusion network based on deep learning convolutional neural networks (DLCNN) is developed. Here, the brain images' slopes and borders are detected using REA. To separate the sick region from the color image, adaptive fuzzy c-means integrated k-means (HFCMIK) clustering is then implemented. To extract hybrid features from the fused image, low-level features based on the redundant discrete wavelet transform (RDWT), empirical color features, and texture characteristics based on the gray-level cooccurrence matrix (GLCM) are also used. Finally, to distinguish between benign and malignant tumors, a deep learning probabilistic neural network (DLPNN) is deployed. RESULTS: according to the findings, the suggested BTFSC-Net model performed better than more traditional preprocessing, fusion, segmentation, and classification techniques. Additionally, 99.21% segmentation accuracy and 99.46% classification accuracy were reached using the proposed BTFSC-Net model. CONCLUSIONS: earlier approaches have not performed as well as our presented method for image fusion, segmentation, feature extraction, classification operations, and brain tumor classification. These results illustrate that the designed approach performed more effectively in terms of enhanced quantitative evaluation with better accuracy as well as visual performance.

Artificial Intelligence and Its Impact on Urological Diseases and Management: A Comprehensive Review of the Literature.

Recent advances in artificial intelligence (AI) have certainly had a significant impact on the healthcare industry. In urology, AI has been widely adopted to deal with numerous disorders, irrespective of their severity, extending from conditions such as benign prostate hyperplasia to critical illnesses such as urothelial and prostate cancer. In this article, we aim to discuss how algorithms and techniques of artificial intelligence are equipped in the field of urology to detect, treat, and estimate the outcomes of urological diseases. Furthermore, we explain the advantages that come from using AI over any existing traditional methods.

Convolutional Neural Network ensembles for accurate lung nodule malignancy prediction 2 years in the future.

Convolutional Neural Networks (CNNs) have been utilized for to distinguish between benign lung nodules and those that will become malignant. The objective of this study was to use an ensemble of CNNs to predict which baseline nodules would be diagnosed as lung cancer in a second follow up screening after more than one year. Low-dose helical computed tomography images and data were utilized from the National Lung Screening Trial (NLST). The malignant nodules and nodule positive controls were divided into training and test cohorts. T0 nodules were used to predict lung cancer incidence at T1 or T2. To increase the sample size, image augmentation was performed using rotations, flipping, and elastic deformation. Three CNN architectures were designed for malignancy prediction, and each architecture was trained using seven different seeds to create the initial weights. This enabled variability in the CNN models which were combined to generate a robust, more accurate ensemble model. Augmenting images using only rotation and flipping and training with images from T0 yielded the best accuracy to predict lung cancer incidence at T2 from a separate test cohort (Accuracy = 90.29%; AUC = 0.96) based on an ensemble 21 models. Images augmented by rotation and flipping enabled effective learning by increasing the relatively small sample size. Ensemble learning with deep neural networks is a compelling approach that accurately predicted lung cancer incidence at the second screening after the baseline screen mostly 2 years later.

Lung Nodule Sizes Are Encoded When Scaling CT Image for CNN's.

Noninvasive diagnosis of lung cancer in early stages is one task where radiomics helps. Clinical practice shows that the size of a nodule has high predictive power for malignancy. In the literature, convolutional neural networks (CNNs) have become widely used in medical image analysis. We study the ability of a CNN to capture nodule size in computed tomography images after images are resized for CNN input. For our experiments, we used the National Lung Screening Trial data set. Nodules were labeled into 2 categories (small/large) based on the original size of a nodule. After all extracted patches were re-sampled into 100-by-100-pixel images, a CNN was able to successfully classify test nodules into small- and large-size groups with high accuracy. To show the generality of our discovery, we repeated size classification experiments using Common Objects in Context (COCO) data set. From the data set, we selected 3 categories of images, namely, bears, cats, and dogs. For all 3 categories a 5- × 2-fold cross-validation was performed to put them into small and large classes. The average area under receiver operating curve is 0.954, 0.952, and 0.979 for the bear, cat, and dog categories, respectively. Thus, camera image rescaling also enables a CNN to discover the size of an object. The source code for experiments with the COCO data set is publicly available in Github (https://github.com/VisionAI-USF/COCO_Size_Decoding/).

Deep Feature Stability Analysis Using CT Images of a Physical Phantom Across Scanner Manufacturers, Cartridges, Pixel Sizes, and Slice Thickness.

Image acquisition parameters for computed tomography scans such as slice thickness and field of view may vary depending on tumor size and site. Recent studies have shown that some radiomics features were dependent on voxel size (= pixel size × slice thickness), and with proper normalization, this voxel size dependency could be reduced. Deep features from a convolutional neural network (CNN) have shown great promise in characterizing cancers. However, how do these deep features vary with changes in imaging acquisition parameters? To analyze the variability of deep features, a physical radiomics phantom with 10 different material cartridges was scanned on 8 different scanners. We assessed scans from 3 different cartridges (rubber, dense cork, and normal cork). Deep features from the penultimate layer of the CNN before (pre-rectified linear unit) and after (post-rectified linear unit) applying the rectified linear unit activation function were extracted from a pre-trained CNN using transfer learning. We studied both the interscanner and intrascanner dependency of deep features and also the deep features' dependency over the 3 cartridges. We found some deep features were dependent on pixel size and that, with appropriate normalization, this dependency could be reduced. False discovery rate was applied for multiple comparisons, to mitigate potentially optimistic results. We also used stable deep features for prognostic analysis on 1 non-small cell lung cancer data set.

Hybrid models for lung nodule malignancy prediction utilizing convolutional neural network ensembles and clinical data.

Purpose: Due to the high incidence and mortality rates of lung cancer worldwide, early detection of a precancerous lesion is essential. Low-dose computed tomography is a commonly used technique for screening, diagnosis, and prognosis of non-small-cell lung cancer. Recently, convolutional neural networks (CNN) had shown great potential in lung nodule classification. Clinical information (family history, gender, and smoking history) together with nodule size provide information about lung cancer risk. Large nodules have greater risk than small nodules. Approach: A subset of cases from the National Lung Screening Trial was chosen as a dataset in our study. We divided the nodules into large and small nodules based on different clinical guideline thresholds and then analyzed the groups individually. Similarly, we also analyzed clinical features by dividing them into groups. CNNs were designed and trained over each of these groups individually. To our knowledge, this is the first study to incorporate nodule size and clinical features for classification using CNN. We further made a hybrid model using an ensemble with the CNN models of clinical and size information to enhance malignancy prediction. Results: From our study, we obtained 0.9 AUC and 83.12% accuracy, which was a significant improvement over our previous best results. Conclusions: In conclusion, we found that dividing the nodules by size and clinical information for building predictive models resulted in improved malignancy predictions. Our analysis also showed that appropriately integrating clinical information and size groups could further improve risk prediction.

Arrhythmia-related Hospitalization and Comorbid Cannabis Use Disorder: Trend Analysis in US Hospitals (2010-2014).

Objective To study the trends of arrhythmia hospitalizations with cannabis use disorders (CUDs) in terms of demographic characteristics and inpatient outcomes. Methods We used the nationwide inpatient sample (NIS) data during the post-legalization period (2010-2014) and included 570,556 arrhythmia inpatients (age, 15-54 years), and 14,426 inpatients had comorbid CUD (2.53%). We used the linear-by-linear association test and independent-sample T-test for assessing the change in hospital outcomes in inpatients with CUD. Results Arrhythmia hospitalizations with CUD increased by 31% (2010-2014). This increasing trend was seen in adults (45-54 years, P < 0.001) and was predominant in males (77.6%). Hypertension (40.6%), hyperlipidemia (17.6%), and obesity (15%) were prevalent medical comorbidities with variable trends over the five years. Among substance use disorders, tobacco (50.9%), and alcohol (31.4%) were major comorbidities with a variable trend (P = 0.003 for each). There was a 71.4% increase in the inpatient mortality rate between 2010 (0.7%) and 2014 (1.2%). The mean length of stay was three days, and the total hospitalization charges have been increasing (P < 0.001), averaging $35,812 per hospital admission. Conclusion Chronic cannabis use or abuse worsens hospitalization outcomes in arrhythmic patients, and more clinical studies are needed to study the causal association between these conditions due to the rising mortality risk.

Explaining Deep Features Using Radiologist-Defined Semantic Features and Traditional Quantitative Features.

Quantitative features are generated from a tumor phenotype by various data characterization, feature-extraction approaches and have been used successfully as a biomarker. These features give us information about a nodule, for example, nodule size, pixel intensity, histogram-based information, and texture information from wavelets or a convolution kernel. Semantic features, on the other hand, can be generated by an experienced radiologist and consist of the common characteristics of a tumor, for example, location of a tumor, fissure, or pleural wall attachment, presence of fibrosis or emphysema, concave cut on nodule surface. These features have been derived for lung nodules by our group. Semantic features have also shown promise in predicting malignancy. Deep features from images are generally extracted from the last layers before the classification layer of a convolutional neural network (CNN). By training with the use of different types of images, the CNN learns to recognize various patterns and textures. But when we extract deep features, there is no specific naming approach for them, other than denoting them by the feature column number (position of a neuron in a hidden layer). In this study, we tried to relate and explain deep features with respect to traditional quantitative features and semantic features. We discovered that 26 deep features from the Vgg-S neural network and 12 deep features from our trained CNN could be explained by semantic or traditional quantitative features. From this, we concluded that those deep features can have a recognizable definition via semantic or quantitative features.

Representation of Deep Features using Radiologist defined Semantic Features.

Semantic features are common radiological traits used to characterize a lesion by a trained radiologist. These features have been recently formulated, quantified on a point scale in the context of lung nodules by our group. Certain radiological semantic traits have been shown to extremely predictive of malignancy [26]. Semantic traits observed by a radiologist at examination describe the nodules and the morphology of the lung nodule shape, size, border, attachment to vessel or pleural wall, location and texture etc. Deep features are numeric descriptors often obtained from a convolutional neural network (CNN) which are widely used for classification and recognition. Deep features may contain information about texture and shape, primarily. Lately, with the advancement of deep learning, convolutional neural networks (CNN) are also being used to analyze lung nodules. In this study, we relate deep features to semantic features by looking for similarity in ability to classify. Deep features were obtained using a transfer learning approach from both an ImageNet pre-trained CNN and our trained CNN architecture. We found that some of the semantic features can be represented by one or more deep features. In this process, we can infer that some deep feature(s) have similar discriminatory ability as semantic features.

Predicting Nodule Malignancy using a CNN Ensemble Approach.

Lung cancer is the leading cause of cancer-related deaths globally, which makes early detection and diagnosis a high priority. Computed tomography (CT) is the method of choice for early detection and diagnosis of lung cancer. Radiomics features extracted from CT-detected lung nodules provide a good platform for early detection, diagnosis, and prognosis. In particular when using low dose CT for lung cancer screening, effective use of radiomics can yield a precise non-invasive approach to nodule tracking. Lately, with the advancement of deep learning, convolutional neural networks (CNN) are also being used to analyze lung nodules. In this study, our own trained CNNs, a pre-trained CNN and radiomics features were used for predictive analysis. Using subsets of participants from the National Lung Screening Trial, we investigated if the prediction of nodule malignancy could be further enhanced by an ensemble of classifiers using different feature sets and learning approaches. We extracted probability predictions from our different models on an unseen test set and combined them to generate better predictions. Ensembles were able to yield increased accuracy and area under the receiver operating characteristic curve (AUC). The best-known AUC of 0.96 and accuracy of 89.45% were obtained, which are significant improvements over the previous best AUC of 0.87 and accuracy of 76.79%.

Predicting malignant nodules by fusing deep features with classical radiomics features.

Lung cancer has a high incidence and mortality rate. Early detection and diagnosis of lung cancers is best achieved with low-dose computed tomography (CT). Classical radiomics features extracted from lung CT images have been shown as able to predict cancer incidence and prognosis. With the advancement of deep learning and convolutional neural networks (CNNs), deep features can be identified to analyze lung CTs for prognosis prediction and diagnosis. Due to a limited number of available images in the medical field, the transfer learning concept can be helpful. Using subsets of participants from the National Lung Screening Trial (NLST), we utilized a transfer learning approach to differentiate lung cancer nodules versus positive controls. We experimented with three different pretrained CNNs for extracting deep features and used five different classifiers. Experiments were also conducted with deep features from different color channels of a pretrained CNN. Selected deep features were combined with radiomics features. A CNN was designed and trained. Combinations of features from pretrained, CNNs trained on NLST data, and classical radiomics were used to build classifiers. The best accuracy (76.79%) was obtained using feature combinations. An area under the receiver operating characteristic curve of 0.87 was obtained using a CNN trained on an augmented NLST data cohort.

Primary central nervous system teratoma with sarcomatous transformation in a young girl: Report of a rare case.

A 13-year-old girl presented with chief complaints of severe headache and vomiting followed by hemiparesis. Radiological examination suggested a space occupying lesion in the right parietal lobe. Craniotomy and debulking of the tumor mass were done. Histopathological and subsequent immunohistochemical examination showed a tumor composed of fascicle of atypical spindle cells which revealed reactivity to vimentin with interspersed areas of well-differentiated cartilage tissue. Hence, the diagnosis of teratoma with sarcomatous transformation was given. Detailed discussion including review of literature has been made regarding different aspect of the tumor.

Deep Feature Transfer Learning in Combination with Traditional Features Predicts Survival Among Patients with Lung Adenocarcinoma.

Lung cancer is the most common cause of cancer-related deaths in the USA. It can be detected and diagnosed using computed tomography images. For an automated classifier, identifying predictive features from medical images is a key concern. Deep feature extraction using pretrained convolutional neural networks (CNNs) has recently been successfully applied in some image domains. Here, we applied a pretrained CNN to extract deep features from 40 computed tomography images, with contrast, of non-small cell adenocarcinoma lung cancer, and combined deep features with traditional image features and trained classifiers to predict short- and long-term survivors. We experimented with several pretrained CNNs and several feature selection strategies. The best previously reported accuracy when using traditional quantitative features was 77.5% (area under the curve [AUC], 0.712), which was achieved by a decision tree classifier. The best reported accuracy from transfer learning and deep features was 77.5% (AUC, 0.713) using a decision tree classifier. When extracted deep neural network features were combined with traditional quantitative features, we obtained an accuracy of 90% (AUC, 0.935) with the 5 best post-rectified linear unit features extracted from a vgg-f pretrained CNN and the 5 best traditional features. The best results were achieved with the symmetric uncertainty feature ranking algorithm followed by a random forests classifier.

Effect of tooth bleaching on orthodontic stainless steel bracket bond strength.

OBJECTIVES: The objective was to assess the shear bond strength (SBS) of composite resins on stainless steel brackets immediately bonded to previously bleached teeth with 35% hydrogen peroxide and to compare the neutralization effect of various antioxidant agents on the bond strength after bleaching. MATERIALS AND METHODS: One hundred sound human maxillary premolars were used for the study. Teeth were divided into 5 groups (n = 20); Group 1 (control), Group 2 (bleach treatment), Group 3 (sodium ascorbate treatment), Group 4 (tocopherol acetate treatment), and Group 5 (retinol acetate treatment). Teeth in Group 3, 4, and 5 were treated as in Group 2, but after that and before bleaching received treatment with sodium ascorbate, tocopherol acetate, and retinol acetate, respectively. Subsequently, teeth were bonded with stainless steel brackets (Ormco) using 3M Transbond XT. After 24 h, each specimen was loaded into a universal testing machine to determine the SBS at debonding. The data were exposed to the analysis of variance, Bonferroni, and Weibull Analysis. RESULT: There significant SBS difference (P = 0.000, F = 32.125) between various groups. Group 1 had the highest SBS (12.182 ± 1.41 MPa) and Group 2 the least SBS (6.182 ± 1.49 MPa). Significant SBS differences observed between Group 1 and 2; Group 2 and 3; Group 2 and 4; and Group 2 and 5 (P = 0.000). There was no significant SBS difference between Group 1 and 3; Group 1 and 4; and Group 3 and 4 (P = 1.000). Bonferroni results also indicated that there was a significant difference between Group 1 and 5 (P = 0.002); Group 3 and 5 (P = 0.144); and between Group 4 and 5 (P = 0.008). Weibull analysis indicated that bond strength for a 90% probability of failure, which was highest for Group 1 (13.99 MPa) and lowest for Group 2 (8.49 MPa). CONCLUSION: The in-vitro study showed that bleaching with 35% hydrogen peroxide reduced the SBS significantly and this could be effectively reversed by the application of 10% sodium ascorbate, 10% tocopherol acetate, or 10% retinol acetate. Thus, treatment of bleached teeth with antioxidants can be a good clinical option for bonding immediately after bleaching.

Appearance can be deceptive: Dentigerous cyst crossing the midline.

Dentigerous cyst is a developmental odontogenic cyst, which develops by accumulation of fluid between reduced enamel epithelium and the tooth crown of an unerupted tooth. Dentigerous cysts are usually solitary, slow growing, asymptomatic lesions that are incidentally found during routine radiographs They most frequently involve the mandibular third molar followed in order of frequency by the maxillary canine, mandibular second pre-molar and maxillary third molar. Occasionally, these cysts become painful when infected causing swelling and erythema. The cyst is usually small, however, when large, results in the expansion and thinning of the cortex leading to pathological fracture. Radiographic features are specific to the lesion characterized by a well-defined radiolucency circumscribed by a sclerotic border, associated with the crown of an impacted or unerupted tooth. Dentigerous cysts are treated most commonly by enucleation, Marsupialization and decompression of cyst by fenestration. The criteria for selecting the treatment modality is based on the age, size, location, stage of root development, position of the involved tooth and relation of the lesion to the adjacent tooth and vital structure. The prognosis is an excellent when the cyst is enucleated and recurrence is rare. In this article, we present a case of a Dentigerous cyst in an 80-year-old man in the anterior aspect of the mandible enveloping an impacted canine and crossing the midline but with no clinical expansion or discomfort.