Classification of malignant and benign tissue with logistic regression

The Depth Estimation and Visualization of Dermatological Lesions: Development and Usability Study

BACKGROUND

Thus far, considerable research has been focused on classifying a lesion as benign or malignant. However, there is a requirement for quick depth estimation of a lesion for the accurate clinical staging of the lesion. The lesion could be malignant and quickly grow beneath the skin. While biopsy slides provide clear information on lesion depth, it is an emerging domain to find quick and noninvasive methods to estimate depth, particularly based on 2D images.

OBJECTIVE

This study proposes a novel methodology for the depth estimation and visualization of skin lesions. Current diagnostic methods are approximate in determining how much a lesion may have proliferated within the skin. Using color gradients and depth maps, this method will give us a definite estimate and visualization procedure for lesions and other skin issues. We aim to generate 3D holograms of the lesion depth such that dermatologists can better diagnose melanoma.

METHODS

We started by performing classification using a convolutional neural network (CNN), followed by using explainable artificial intelligence to localize the image features responsible for the CNN output. We used the gradient class activation map approach to perform localization of the lesion from the rest of the image. We applied computer graphics for depth estimation and developing the 3D structure of the lesion. We used the depth from defocus method for depth estimation from single images and Gabor filters for volumetric representation of the depth map. Our novel method, called red spot analysis, measures the degree of infection based on how a conical hologram is constructed. We collaborated with a dermatologist to analyze the 3D hologram output and received feedback on how this method can be introduced to clinical implementation.

RESULTS

The neural model plus the explainable artificial intelligence algorithm achieved an accuracy of 86% in classifying the lesions correctly as benign or malignant. For the entire pipeline, we mapped the benign and malignant cases to their conical representations. We received exceedingly positive feedback while pitching this idea at the King Edward Memorial Institute in India. Dermatologists considered this a potentially useful tool in the depth estimation of lesions. We received a number of ideas for evaluating the technique before it can be introduced to the clinical scene.

CONCLUSIONS

When we map the CNN outputs (benign or malignant) to the corresponding hologram, we observe that a malignant lesion has a higher concentration of red spots (infection) in the upper and deeper portions of the skin, and that the malignant cases have deeper conical sections when compared with the benign cases. This proves that the qualitative results map with the initial classification performed by the neural model. The positive feedback provided by the dermatologist suggests that the qualitative conclusion of the method is sufficient.

Biomarkers and computational models for predicting efficacy to tumor ICI immunotherapy

Numerous studies have shown that immune checkpoint inhibitor (ICI) immunotherapy has great potential as a cancer treatment, leading to significant clinical improvements in numerous cases. However, it benefits a minority of patients, underscoring the importance of discovering reliable biomarkers that can be used to screen for potential beneficiaries and ultimately reduce the risk of overtreatment. Our comprehensive review focuses on the latest advancements in predictive biomarkers for ICI therapy, particularly emphasizing those that enhance the efficacy of programmed cell death protein 1 (PD-1)/programmed cell death-ligand 1 (PD-L1) inhibitors and cytotoxic T-lymphocyte antigen-4 (CTLA-4) inhibitors immunotherapies. We explore biomarkers derived from various sources, including tumor cells, the tumor immune microenvironment (TIME), body fluids, gut microbes, and metabolites. Among them, tumor cells-derived biomarkers include tumor mutational burden (TMB) biomarker, tumor neoantigen burden (TNB) biomarker, microsatellite instability (MSI) biomarker, PD-L1 expression biomarker, mutated gene biomarkers in pathways, and epigenetic biomarkers. TIME-derived biomarkers include immune landscape of TIME biomarkers, inhibitory checkpoints biomarkers, and immune repertoire biomarkers. We also discuss various techniques used to detect and assess these biomarkers, detailing their respective datasets, strengths, weaknesses, and evaluative metrics. Furthermore, we present a comprehensive review of computer models for predicting the response to ICI therapy. The computer models include knowledge-based mechanistic models and data-based machine learning (ML) models. Among the knowledge-based mechanistic models are pharmacokinetic/pharmacodynamic (PK/PD) models, partial differential equation (PDE) models, signal networks-based models, quantitative systems pharmacology (QSP) models, and agent-based models (ABMs). ML models include linear regression models, logistic regression models, support vector machine (SVM)/random forest/extra trees/k-nearest neighbors (KNN) models, artificial neural network (ANN) and deep learning models. Additionally, there are hybrid models of systems biology and ML. We summarized the details of these models, outlining the datasets they utilize, their evaluation methods/metrics, and their respective strengths and limitations. By summarizing the major advances in the research on predictive biomarkers and computer models for the therapeutic effect and clinical utility of tumor ICI, we aim to assist researchers in choosing appropriate biomarkers or computer models for research exploration and help clinicians conduct precision medicine by selecting the best biomarkers.

Supervised segmentation for guiding peripheral revascularization with forward-viewing, robotically steered ultrasound guidewire

BACKGROUND

Approximately 500 000 patients present with critical limb ischemia (CLI) each year in the U.S., requiring revascularization to avoid amputation. While peripheral arteries can be revascularized via minimally invasive procedures, 25% of cases with chronic total occlusions are unsuccessful due to inability to route the guidewire beyond the proximal occlusion. Improvements to guidewire navigation would lead to limb salvage in a greater number of patients.

PURPOSE

Integrating ultrasound imaging into the guidewire could enable direct visualization of routes for guidewire advancement. In order to navigate a robotically-steerable guidewire with integrated imaging beyond a chronic occlusion proximal to the symptomatic lesion for revascularization, acquired ultrasound images must be segmented to visualize the path for guidewire advancement.

METHODS

The first approach for automated segmentation of viable paths through occlusions in peripheral arteries is demonstrated in simulations and experimentally-acquired data with a forward-viewing, robotically-steered guidewire imaging system. B-mode ultrasound images formed via synthetic aperture focusing (SAF) were segmented using a supervised approach (U-net architecture). A total of 2500 simulated images were used to train the classifier to distinguish the vessel wall and occlusion from viable paths for guidewire advancement. First, the size of the synthetic aperture resulting in the highest classification performance was determined in simulations (90 test images) and compared with traditional classifiers (global thresholding, local adaptive thresholding, and hierarchical classification). Next, classification performance as a function of the diameter of the remaining lumen (0.5 to 1.5 mm) in the partially-occluded artery was tested using both simulated (60 test images at each of 7 diameters) and experimental data sets. Experimental test data sets were acquired in four 3D-printed phantoms from human anatomy and six ex vivo porcine arteries. Accuracy of classifying the path through the artery was evaluated using microcomputed tomography of phantoms and ex vivo arteries as a ground truth for comparison.

RESULTS

An aperture size of 3.8 mm resulted in the best-performing classification based on sensitivity and Jaccard index, with a significant increase in Jaccard index (p < 0.05) as aperture diameter increased. In comparing the performance of the supervised classifier and traditional classification strategies with simulated test data, sensitivity and F1 score for U-net were 0.95 ± 0.02 and 0.96 ± 0.01, respectively, compared to 0.83 ± 0.03 and 0.41 ± 0.13 for the best-performing conventional approach, hierarchical classification. In simulated test images, sensitivity (p < 0.05) and Jaccard index both increased with increasing artery diameter (p < 0.05). Classification of images acquired in artery phantoms with remaining lumen diameters ≥ 0.75 mm resulted in accuracies > 90%, while mean accuracy decreased to 82% when artery diameter decreased to 0.5 mm. For testing in ex vivo arteries, average binary accuracy, F1 score, Jaccard index, and sensitivity each exceeded 0.9.

CONCLUSIONS

Segmentation of ultrasound images of partially-occluded peripheral arteries acquired with a forward-viewing, robotically-steered guidewire system was demonstrated for the first-time using representation learning. This could represent a fast, accurate approach for guiding peripheral revascularization.

Accuracy Enhancement for Breast Cancer Detection using Classification and Feature Selection

Chronic disease like kidney failure, heart disease, cancer etc. is the major cause of deaths now days worldwide. Especially for the females the most dangerous type of disease from which the women of every age group are suffering especially the middle age group women’s is the breast cancer. To detect this type of disease at an early stage is a challenging task. In order to predict the breast cancer at an early stage classification algorithm of high accuracy and less error rate are desirable. In this research work we have used 4 classification algorithms K-NN, J48, Logistic regression and Bayes Net for building the predictive model, also the wrapper method of feature selection is used to enhance the accuracy rate and reduce the error rate of the used classifiers. To carry out this research we have used Wisconsin Diagnostic Breast Cancer dataset which contains 569 instances along with 32 attributes and a class attribute which will predict the type of cancer i.e. Benign or Malignant.

Explainable Biomarkers for Automated Glomerular and Patient-Level Disease Classification

Pathologists use multiple microscopy modalities to assess renal biopsy specimens. Besides usual diagnostic features, some changes are too subtle to be properly defined. Computational approaches have the potential to systematically quantitate subvisual clues, provide pathogenetic insight, and link to clinical outcomes. To this end, a proof-of-principle study is presented demonstrating that explainable biomarkers through machine learning can distinguish between glomerular disorders at the light-microscopy level. The proposed system used image analysis techniques and extracted 233 explainable biomarkers related to color, morphology, and microstructural texture. Traditional machine learning was then used to classify minimal change disease (MCD), membranous nephropathy (MN), and thin basement membrane nephropathy (TBMN) diseases on a glomerular and patient-level basis. The final model combined the Gini feature importance set and linear discriminant analysis classifier. Six morphologic (nuclei-to-glomerular tuft area, nuclei-to-glomerular area, glomerular tuft thickness greater than ten, glomerular tuft thickness greater than three, total glomerular tuft thickness, and glomerular circularity) and four microstructural texture features (luminal contrast using wavelets, nuclei energy using wavelets, nuclei variance using color vector LBP, and glomerular correlation using GLCM) were, together, the best performing biomarkers. Accuracies of 77% and 87% were obtained for glomerular and patient-level classification, respectively. Computational methods, using explainable glomerular biomarkers, have diagnostic value and are compatible with our existing knowledge of disease pathogenesis. Furthermore, this algorithm can be applied to clinical datasets for novel prognostic and mechanistic biomarker discovery.

Prediction of Micronucleus Assay Outcome Using In Vivo Activity Data and Molecular Structure Features

In vivo micronucleus assay is the widely used genotoxic test to determine the extent of chromosomal aberrations caused by the chemicals in human beings, which plays a significant role in the drug discovery paradigm. To reduce the uncertainties of the in vivo experiments and the expenses, we intended to develop novel machine learning-based tools to predict the toxicity of the compounds with high precision. A total of 372 compounds with known toxicity information were retrieved from the PubChem Bioassay database and literature. The fingerprints and descriptors of the compounds were generated using PaDEL and ChemSAR, respectively, for the analysis. The performance of the models was assessed using the three tires of evaluation strategies such as fivefold, tenfold, and validation by external dataset. Further, structural alerts causing genotoxicity of the compounds were identified using SARpy method. Of note, fingerprint-based random forest model built in our analysis is able to demonstrate the highest accuracy of about 0.97 during tenfold cross-validation. In essence, our study highlights that structural alerts such as chlorocyclohexane and trimethylamine are likely to be the leading cause of toxicity in humans. Indeed, we believe that random forest model generated in this study is appropriate for reduction of test animals and should be considered in the future for the good practice of animal welfare.

Disease type detection in lung and colon cancer images using the complement approach of inefficient sets

Lung and colon cancers are deadly diseases that can develop simultaneously in organs and adversely affect human life in some special cases. Although the frequency of simultaneous occurrence of these two types of cancer is unlikely, there is a high probability of metastasis between the two organs if not diagnosed early. Traditionally, specialists have to go through a lengthy and complicated process to examine histopathological images and diagnose cancer cases; yet, it is now possible to achieve this process faster with the available technological possibilities. In this study, artificial intelligence-supported model and optimization methods were used to realize the classification of lung and colon cancers' histopathological images. The used dataset has five classes of histopathological images consisting of two colon cancer classes and three lung cancer classes. In the proposed approach, the image classes were trained from scratch with the DarkNet-19 model, which is one of the deep learning models. In the feature set extracted from the DarkNet-19 model, selection of the inefficient features was performed by using Equilibrium and Manta Ray Foraging optimization algorithms. Then, the set containing the inefficient features was distinguished from the rest of the set features, creating an efficient feature set (complementary rule insets). The efficient features obtained by the two used optimization algorithms were combined and classified with the Support Vector Machine (SVM) method. The overall accuracy rate obtained in the classification process was 99.69%. Based on the outcomes of this study, it has been observed that using the complementary method together with some optimization methods improved the classification performance of the dataset.

Functionalized Graphene Platforms for Anticancer Drug Delivery

Two-dimensional nanomaterials are emerging as promising candidates for a wide range of biomedical applications including tissue engineering, biosensing, pathogen incapacitation, wound healing, and gene and drug delivery. Graphene, due to its high surface area, photothermal property, high loading capacity, and efficient cellular uptake, is at the forefront of these materials and plays a key role in this multidisciplinary research field. Poor water dispersibility and low functionality of graphene, however, hamper its hybridization into new nanostructures for future nanomedicine. Functionalization of graphene, either by covalent or non-covalent methods, is the most useful strategy to improve its dispersion in water and functionality as well as processability into new materials and devices. In this review, recent advances in functionalization of graphene derivatives by different (macro)molecules for future biomedical applications are reported and explained. In particular, hydrophilic functionalization of graphene and graphene oxide (GO) to improve their water dispersibility and physicochemical properties is discussed. We have focused on the anticancer drug delivery of polyfunctional graphene sheets.

Identification of People with Diabetes Treatment through Lipids Profile Using Machine Learning Algorithms

Diabetes incidence has been a problem, because according with the World Health Organization and the International Diabetes Federation, the number of people with this disease is increasing very fast all over the world. Diabetic treatment is important to prevent the development of several complications, also lipid profile monitoring is important. For that reason the aim of this work is the implementation of machine learning algorithms that are able to classify cases, that corresponds to patients diagnosed with diabetes that have diabetes treatment, and controls that refers to subjects who do not have diabetes treatment but some of them have diabetes, bases on lipids profile levels. Logistic regression, K-nearest neighbor, decision trees and random forest were implemented, all of them were evaluated with accuracy, sensitivity, specificity and AUC-ROC curve metrics. Artificial neural network obtain an acurracy of 0.685 and an AUC value of 0.750, logistic regression achieve an accuracy of 0.729 and an AUC value of 0.795, K-nearest neighbor gets an accuracy of 0.669 and an AUC value of 0.709, on the other hand, decision tree reached an accuracy pg 0.691 and a AUC value of 0.683, finally random forest achieve an accuracy of 0.704 and an AUC curve of 0.776. The performance of all models was statistically significant, but the best performance model for this problem corresponds to logistic regression.

An Efficient Lightweight CNN and Ensemble Machine Learning Classification of Prostate Tissue Using Multilevel Feature Analysis

Prostate carcinoma is caused when cells and glands in the prostate change their shape and size from normal to abnormal. Typically, the pathologist’s goal is to classify the staining slides and differentiate normal from abnormal tissue. In the present study, we used a computational approach to classify images and features of benign and malignant tissues using artificial intelligence (AI) techniques. Here, we introduce two lightweight convolutional neural network (CNN) architectures and an ensemble machine learning (EML) method for image and feature classification, respectively. Moreover, the classification using pre-trained models and handcrafted features was carried out for comparative analysis. The binary classification was performed to classify between the two grade groups (benign vs. malignant) and quantile-quantile plots were used to show their predicted outcomes. Our proposed models for deep learning (DL) and machine learning (ML) classification achieved promising accuracies of 94.0% and 92.0%, respectively, based on non-handcrafted features extracted from CNN layers. Therefore, these models were able to predict nearly perfectly accurately using few trainable parameters or CNN layers, highlighting the importance of DL and ML techniques and suggesting that the computational analysis of microscopic anatomy will be essential to the future practice of pathology.

Detection of Malignant and Benign Breast Cancer Using the ANOVA-BOOTSTRAP-SVM

Purpose

The aim of this research is to propose a modification of the ANOVA-SVM method that can increase accuracy when detecting benign and malignant breast cancer.

Methodology

We proposed a new method ANOVA-BOOTSTRAP-SVM. It involves applying the analysis of variance (ANOVA) to support vector machines (SVM) but we use the bootstrap instead of cross validation as a train/test splitting procedure. We have tuned the kernel and the C parameter and tested our algorithm on a set of breast cancer datasets.

Findings

By using the new method proposed, we succeeded in improving accuracy ranging from 4.5 percentage points to 8 percentage points depending on the dataset.

Research limitations

The algorithm is sensitive to the type of kernel and value of the optimization parameter C.

Practical implications

We believe that the ANOVA-BOOTSTRAP-SVM can be used not only to recognize the type of breast cancer but also for broader research in all types of cancer.

Originality/value

Our findings are important as the algorithm can detect various types of cancer with higher accuracy compared to standard versions of the Support Vector Machines.