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"Mallik, Saurav"
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Drug discovery and telemedicine : through artificial intelligence, computer vision, and IoT
Emerges in response to the critical need for an interdisciplinary resource that encapsulates the burgeoning role of artificial intelligence (AI) in reshaping drug discovery and telemedicine. As these sectors witness transformative changes driven by AI technologies, there's a pressing demand for a comprehensive guide that navigates through these advancements, offering insights, methodologies, and practical applications to professionals at the forefront of healthcare and pharmaceutical research. At its core, the book delves into the intricate ways in which AI and machine learning algorithms are being harnessed to streamline the drug development process, from initial discovery through to clinical trials, and how these technologies are concurrently revolutionizing the delivery of healthcare services via telemedicine.
BOOK
Detecting methylation signatures in neurodegenerative disease by density-based clustering of applications with reducing noise
There have been numerous genetic and epigenetic datasets generated for the study of complex disease including neurodegenerative disease. However, analysis of such data often suffers from detecting the outliers of the samples, which subsequently affects the extraction of the true biological signals involved in the disease. To address this critical issue, we developed a novel framework for identifying methylation signatures using consecutive adaptation of a well-known outlier detection algorithm, density based clustering of applications with reducing noise (DBSCAN) followed by hierarchical clustering. We applied the framework to two representative neurodegenerative diseases, Alzheimer’s disease (AD) and Down syndrome (DS), using DNA methylation datasets from public sources (Gene Expression Omnibus, GEO accession ID: GSE74486). We first applied DBSCAN algorithm to eliminate outliers, and then used Limma statistical method to determine differentially methylated genes. Next, hierarchical clustering technique was applied to detect gene modules. Our analysis identified a methylation signature comprising 21 genes for AD and a methylation signature comprising 89 genes for DS, respectively. Our evaluation indicated that these two signatures could lead to high classification accuracy values (92% and 70%) for these two diseases. In summary, this framework will be useful to better detect outlier-free genetic and epigenetic signatures in various complex diseases and their developmental stages.
Journal Article
Machine learning-based optimal crop selection system in smart agriculture
The cultivation of most crops depends upon the regional weather conditions. So, the analysis of the agro-climatic conditions of a zone contributes significantly to deciding the right crop for the right land in the right season to obtain a better yield. Machine learning algorithms facilitate this process to a great extent for better results. In this paper, the authors proposed an ML-based crop selection model based on the weather conditions and soil parameters, collectively. Weather analysis is done using LSTM RNN and the process of crop selection is completed using Random Forest Classifier. This model gives better results for weather prediction in comparison to ANN. With LSTM RNN, the RMSE observed in Min. Temp. prediction is 5.023%, Max. Temp. Prediction is 7.28%, and Rainfall Prediction is 8.24%. In the second phase, the Random Forest Classifier showed 97.235% accuracy for crop selection, 96.437% accuracy in predicting resource dependency, and 97.647 accuracies in giving the appropriate sowing time for the crop. The model construction time taken with a random forest classifier using mentioned data size is 5.34 s. The authors also suggested the future research direction to further improve this work.
Journal Article
Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer
Background
As many complex omics data have been generated during the last two decades, dimensionality reduction problem has been a challenging issue in better mining such data. The omics data typically consists of many features. Accordingly, many feature selection algorithms have been developed. The performance of those feature selection methods often varies by specific data, making the discovery and interpretation of results challenging.
Methods and results
In this study, we performed a comprehensive comparative study of five widely used supervised feature selection methods (mRMR, INMIFS, DFS, SVM-RFE-CBR and VWMRmR) for multi-omics datasets. Specifically, we used five representative datasets: gene expression (Exp), exon expression (ExpExon), DNA methylation (hMethyl27), copy number variation (Gistic2), and pathway activity dataset (Paradigm IPLs) from a multi-omics study of acute myeloid leukemia (LAML) from The Cancer Genome Atlas (TCGA). The different feature subsets selected by the aforesaid five different feature selection algorithms are assessed using three evaluation criteria: (1) classification accuracy (Acc), (2) representation entropy (RE) and (3) redundancy rate (RR). Four different classifiers, viz., C4.5, NaiveBayes, KNN, and AdaBoost, were used to measure the classification accuary (Acc) for each selected feature subset. The VWMRmR algorithm obtains the best Acc for three datasets (ExpExon, hMethyl27 and Paradigm IPLs). The VWMRmR algorithm offers the best RR (obtained using normalized mutual information) for three datasets (Exp, Gistic2 and Paradigm IPLs), while it gives the best RR (obtained using Pearson correlation coefficient) for two datasets (Gistic2 and Paradigm IPLs). It also obtains the best RE for three datasets (Exp, Gistic2 and Paradigm IPLs). Overall, the VWMRmR algorithm yields best performance for all three evaluation criteria for majority of the datasets. In addition, we identified signature genes using supervised learning collected from the overlapped top feature set among five feature selection methods. We obtained a 7-gene signature (
ZMIZ1, ENG, FGFR1, PAWR, KRT17, MPO
and
LAT2
) for EXP, a 9-gene signature for ExpExon, a 7-gene signature for hMethyl27, one single-gene signature (
PIK
3
CG
) for Gistic2 and a 3-gene signature for Paradigm IPLs.
Conclusion
We performed a comprehensive comparison of the performance evaluation of five well-known feature selection methods for mining features from various high-dimensional datasets. We identified signature genes using supervised learning for the specific omic data for the disease. The study will help incorporate higher order dependencies among features.
Journal Article
Chronic kidney disease prediction using boosting techniques based on clinical parameters
Chronic kidney disease (CKD) has become a major global health crisis, causing millions of yearly deaths. Predicting the possibility of a person being affected by the disease will allow timely diagnosis and precautionary measures leading to preventive strategies for health. Machine learning techniques have been popularly applied in various disease diagnoses and predictions. Ensemble learning approaches have become useful for predicting many complex diseases. In this paper, we utilise the boosting method, one of the popular ensemble learnings, to achieve a higher prediction accuracy for CKD. Five boosting algorithms are employed: XGBoost, CatBoost, LightGBM, AdaBoost, and gradient boosting. We experimented with the CKD data set from the UCI machine learning repository. Various preprocessing steps are employed to achieve better prediction performance, along with suitable hyperparameter tuning and feature selection. We assessed the degree of importance of each feature in the dataset leading to CKD. The performance of each model was evaluated with accuracy, precision, recall, F1-score, Area under the curve-receiving operator characteristic (AUC-ROC), and runtime. AdaBoost was found to have the overall best performance among the five algorithms, scoring the highest in almost all the performance measures. It attained 100% and 98.47% accuracy for training and testing sets. This model also exhibited better precision, recall, and AUC-ROC curve performance.
Journal Article
Wrapper-based deep feature optimization for activity recognition in the wearable sensor networks of healthcare systems
The Human Activity Recognition (HAR) problem leverages pattern recognition to classify physical human activities as they are captured by several sensor modalities. Remote monitoring of an individual’s activities has gained importance due to the reduction in travel and physical activities during the pandemic. Research on HAR enables one person to either remotely monitor or recognize another person’s activity via the ubiquitous mobile device or by using sensor-based Internet of Things (IoT). Our proposed work focuses on the accurate classification of daily human activities from both accelerometer and gyroscope sensor data after converting into spectrogram images. The feature extraction process follows by leveraging the pre-trained weights of two popular and efficient transfer learning convolutional neural network models. Finally, a wrapper-based feature selection method has been employed for selecting the optimal feature subset that both reduces the training time and improves the final classification performance. The proposed HAR model has been tested on the three benchmark datasets namely, HARTH, KU-HAR and HuGaDB and has achieved 88.89%, 97.97% and 93.82% respectively on these datasets. It is to be noted that the proposed HAR model achieves an improvement of about 21%, 20% and 6% in the overall classification accuracies while utilizing only 52%, 45% and 60% of the original feature set for HuGaDB, KU-HAR and HARTH datasets respectively. This proves the effectiveness of our proposed wrapper-based feature selection HAR methodology.
Journal Article
VER-Net: a hybrid transfer learning model for lung cancer detection using CT scan images
Background
Lung cancer is the second most common cancer worldwide, with over two million new cases per year. Early identification would allow healthcare practitioners to handle it more effectively. The advancement of computer-aided detection systems significantly impacted clinical analysis and decision-making on human disease. Towards this, machine learning and deep learning techniques are successfully being applied. Due to several advantages, transfer learning has become popular for disease detection based on image data.
Methods
In this work, we build a novel transfer learning model (VER-Net) by stacking three different transfer learning models to detect lung cancer using lung CT scan images. The model is trained to map the CT scan images with four lung cancer classes. Various measures, such as image preprocessing, data augmentation, and hyperparameter tuning, are taken to improve the efficacy of VER-Net. All the models are trained and evaluated using multiclass classifications chest CT images.
Results
The experimental results confirm that VER-Net outperformed the other eight transfer learning models compared with. VER-Net scored 91%, 92%, 91%, and 91.3% when tested for accuracy, precision, recall, and F1-score, respectively. Compared to the state-of-the-art, VER-Net has better accuracy.
Conclusion
VER-Net is not only effectively used for lung cancer detection but may also be useful for other diseases for which CT scan images are available.
Journal Article
A novel and innovative cancer classification framework through a consecutive utilization of hybrid feature selection
Cancer prediction in the early stage is a topic of major interest in medicine since it allows accurate and efficient actions for successful medical treatments of cancer. Mostly cancer datasets contain various gene expression levels as features with less samples, so firstly there is a need to eliminate similar features to permit faster convergence rate of classification algorithms. These features (genes) enable us to identify cancer disease, choose the best prescription to prevent cancer and discover deviations amid different techniques. To resolve this problem, we proposed a hybrid novel technique CSSMO-based gene selection for cancer classification. First, we made alteration of the fitness of spider monkey optimization (SMO) with cuckoo search algorithm (CSA) algorithm viz., CSSMO for feature selection, which helps to combine the benefit of both metaheuristic algorithms to discover a subset of genes which helps to predict a cancer disease in early stage. Further, to enhance the accuracy of the CSSMO algorithm, we choose a cleaning process, minimum redundancy maximum relevance (mRMR) to lessen the gene expression of cancer datasets. Next, these subsets of genes are classified using deep learning (DL) to identify different groups or classes related to a particular cancer disease. Eight different benchmark microarray gene expression datasets of cancer have been utilized to analyze the performance of the proposed approach with different evaluation matrix such as recall, precision, F1-score, and confusion matrix. The proposed gene selection method with DL achieves much better classification accuracy than other existing DL and machine learning classification models with all large gene expression dataset of cancer.
Journal Article
Computational learning of features for automated colonic polyp classification
Shape, texture, and color are critical features for assessing the degree of dysplasia in colonic polyps. A comprehensive analysis of these features is presented in this paper. Shape features are extracted using generic Fourier descriptor. The nonsubsampled contourlet transform is used as texture and color feature descriptor, with different combinations of filters. Analysis of variance (ANOVA) is applied to measure statistical significance of the contribution of different descriptors between two colonic polyps: non-neoplastic and neoplastic. Final descriptors selected after ANOVA are optimized using the fuzzy entropy-based feature ranking algorithm. Finally, classification is performed using Least Square Support Vector Machine and Multi-layer Perceptron with five-fold cross-validation to avoid overfitting. Evaluation of our analytical approach using two datasets suggested that the feature descriptors could efficiently designate a colonic polyp, which subsequently can help the early detection of colorectal carcinoma. Based on the comparison with four deep learning models, we demonstrate that the proposed approach out-performs the existing feature-based methods of colonic polyp identification.
Journal Article
MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors
Recent studies have revealed that feed-forward loops (FFLs) as regulatory motifs have synergistic roles in cellular systems and their disruption may cause diseases including cancer. FFLs may include two regulators such as transcription factors (TFs) and microRNAs (miRNAs). In this study, we extensively investigated TF and miRNA regulation pairs, their FFLs, and TF-miRNA mediated regulatory networks in two major types of testicular germ cell tumors (TGCT): seminoma (SE) and non-seminoma (NSE). Specifically, we identified differentially expressed mRNA genes and miRNAs in 103 tumors using the transcriptomic data from The Cancer Genome Atlas. Next, we determined significantly correlated TF-gene/miRNA and miRNA-gene/TF pairs with regulation direction. Subsequently, we determined 288 and 664 dysregulated TF-miRNA-gene FFLs in SE and NSE, respectively. By constructing dysregulated FFL networks, we found that many hub nodes (12 out of 30 for SE and 8 out of 32 for NSE) in the top ranked FFLs could predict subtype-classification (Random Forest classifier, average accuracy ≥90%). These hub molecules were validated by an independent dataset. Our network analysis pinpointed several SE-specific dysregulated miRNAs (miR-200c-3p, miR-25-3p, and miR-302a-3p) and genes (
EPHA2, JUN, KLF4, PLXDC2, RND3, SPI1
, and
TIMP3
) and NSE-specific dysregulated miRNAs (miR-367-3p, miR-519d-3p, and miR-96-5p) and genes (
NR2F1
and
NR2F2
). This study is the first systematic investigation of TF and miRNA regulation and their co-regulation in two major TGCT subtypes.
Journal Article