Metaheuristic integrated machine learning classification of colon cancer using STFT LASSO and EHO feature extraction from microarray gene expressions

Deep learning based on lung cancer classification has been used increasingly for the early diagnosis for several reasons such as lack of robust deep learning-based system, complexity of nodule structure, lack of proper lung segmentation technique, high false positive result, lack of best feature extraction and less amount of medical imaging data for training deep learning model, it has been difficult to get high classification performance. The aim of this paper getting high lung cancer classification performance. We introduce the Data, Classification technique and View (DCV) as main components of the system that concern for the better lung cancer classification results, along with them different intermediate components such as Lung nodule segmentation, Feature extraction, Feature reduction are also defined. These components are key for providing better classification performance result which helps radiologist for early diagnosis of lung cancer. We have proposed uses image data having different dimensionality as input to the deep learning based classifier which provides lung cancer classification to be viewed by radiologists for the early diagnosis of lung cancer.We evaluated the proposed DCV system by classifying 30 state-of-art research papers in the field of deep learning based lung cancer classification system. Through this paper, readers will get the result of deep learning based lung cancer classification system. Also, readers will understand the classification groups, validation criteria, future gaps of the 30 literature.

Machine learning (ML) models are cost-effective tools that can establish a prognosis by considering clinical, genomic, and histological data from breast cancer patients. In this study, we evaluate the performance of 12 ML models in predicting the overall survival of breast cancer patients from “The Cancer Genome Atlas-Breast Cancer” database at 60 months of follow-up. The models evaluated were Logistic Regression (LR), Ridge Classifier (RC), Least Absolute Shrinkage and Selection Operator (LASSO), K-Nearest Neighbors (KNN), Naive Bayes (NB), Linear Discriminant Analysis (LDA), Decision Tree (DT), Multilayer Perceptron (MP), Stochastic Gradient Descent (SGD), Support Vector Machine (SVM), Random Forest (RF), and XGBoost (XGB). The most accurate models were NB (86.76%) and SGD (85.29%). The models with the highest sensitivity were SGD (93.75%), MP (91.67%), and NB (89.89%), while the models with the highest specificity were KNN (95.0%), DT (90.0%), and LASSO (85.0%). The models with the highest area under the ROC curve were LDA (90.83%), LASSO (90.1%), and LR (89.79%). The most relevant variables were “Previous Diagnosis of Cancer,” “Presence of Tumor,” “Ancillary Therapy,” and “Histology.” Our findings demonstrate that AI tools for predicting patient outcomes are a viable option when expensive prognostic genomic tools are not available. According to our results, NB and LASSO show promising performance in predicting the prognosis of breast cancer patients. Further studies with data from developing countries are needed to improve the performance of these tools.

In recent years, work has been carried out on clustering gene expression microarray data. Some approaches are developed from an algorithmic viewpoint whereas others are developed via the application of mixture models. In this article, a family of eight mixture models which utilizes the factor analysis covariance structure is extended to 12 models and applied to gene expression microarray data. This modelling approach builds on previous work by introducing a modified factor analysis covariance structure, leading to a family of 12 mixture models, including parsimonious models. This family of models allows for the modelling of the correlation between gene expression levels even when the number of samples is small. Parameter estimation is carried out using a variant of the expectation-maximization algorithm and model selection is achieved using the Bayesian information criterion. This expanded family of Gaussian mixture models, known as the expanded parsimonious Gaussian mixture model (EPGMM) family, is then applied to two well-known gene expression data sets. The performance of the EPGMM family of models is quantified using the adjusted Rand index. This family of models gives very good performance, relative to existing popular clustering techniques, when applied to real gene expression microarray data. The reduced, preprocessed data that were analysed are available at www.paulmcnicholas.info

BackgroundIn recent years, multi-omics models based on a variety of biomarkers have been continuously developed and increasingly applied in the field of oncology, especially in the early diagnosis of lung cancer. This study aimed to integrate computed tomography (CT) radiomics with seven lung cancer-associated autoantibodies (AABs) to develop multi-omics predictive models for pulmonary nodule (PN) characterization.MethodsThis retrospective study enrolled 179 patients with PNs measuring from 5 to 30 mm in diameter who underwent thoracic surgery at Zhongda Hospital, Southeast University between January 2020 and December 2024. The patients were pathologically categorized into lung cancer (n=87) and non-lung cancer (n=92) groups, and then randomly allocated into training and test sets at a ratio of 7 to 3. Least absolute shrinkage and selection operator (LASSO) regression was used for feature screening to construct a clinical model based on five clinical characteristics. A radiomics prediction model was constructed based on the radiomics features identified after delineating the regions of interest and extracting the radiomics features; the rad-score for each patient was calculated to develop a multi-analytic comprehensive model by combining different markers. The diagnostic performances of the models were compared using the area under the curve (AUC), accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value.ResultsThe multi-omics model demonstrated superior diagnostic accuracy with an AUC of 0.902 [95% confidence interval (CI): 0.817–0.986], accuracy of 82.4%, sensitivity of 88.5%, and specificity of 80.0%, outperforming the clinical (AUC =0.848; 95% CI: 0.777–0.919) and radiomics (AUC =0.854; 95% CI: 0.786–0.922) models. Notably, the radiomics model exhibited high sensitivity (96.6%) but poor specificity (63.6%), while the multi-omics model resolved this trade-off via the synergistic integration of clinical-radiomic-biomarker features, achieving significant improvements in the PPV (81.5% vs. 72.7%) compared to the clinical model.ConclusionsIntegrating CT radiomics with seven lung cancer-AABs established a robust multi-omics framework for PN diagnosis. Compared to the standalone clinical or radiomics models, this comprehensive model demonstrated superior diagnostic performance.

As an emerging technology, radiomics is being widely used in the diagnosis of early lung cancer due to its excellent diagnostic performance. However, there is a lack of studies that apply radiomics to the diagnosis of malignancy of lung adenocarcinoma. Thus, we used computed tomography (CT)-based radiomics to construct a model for the diagnosis of high-risk lung adenocarcinoma. Data of 170 patients who underwent surgical treatment at the First Affiliated Hospital of Soochow University and had a maximum nodule diameter ≤2 cm on preoperative CT images between January 2020 and December 2021 were retrospectively analyzed. All enrolled patients were randomly divided into experimental and validation groups according to the ratio of 7:3. The diagnosis of lung adenocarcinoma was based on postoperative pathological results. The region of interest was delineated on preoperative CT images, and the radiomics features were extracted. The least absolute shrinkage and selection operator (LASSO) was used to screen the radiomics features thus obtaining the radiomics score (Radscore), which was the basis of the radiomics model. Based on the multivariate regression analysis, independent predictors were screened from the clinical baseline data and imaging features thus constructing clinical model. Multivariate logistic regression was used to combine independent predictors and the Radscore to form a comprehensive nomogram. The diagnostic performance of constructed models was evaluated based on receiver operating characteristic (ROC) curves and decision curve analysis (DCA). The sensitivity and specificity of the clinical model based on consolidation-to-tumor ratio (CTR), lobulated signs and vascular anomaly signs was 70.0% and 76.7% in the validation group. The radiomics model [area under the curve (AUC) 0.926; 95% confidence interval (CI): 0.857-0.995] and the comprehensive model (AUC 0.922; 95% CI: 0.851-0.992) performed better than clinical model (AUC 0.839; 95% CI: 0.720-0.958) in the validation group. The sensitivity and specificity of the comprehensive model was 85.0% and 80.0% in the validation group. DCA of radiomics model and comprehensive model suggested they have better net survival benefit than clinical model. Compared with clinical model, radiomics model and comprehensive model had better diagnostic performance in distinguishing malignant degree of lung adenocarcinoma.

Multi-center study on the application potential of Siaα-2,6Gal in early and differential diagnosis of lung cancer.

Differentiation Between Fibro-Adipose Vascular Anomaly and Intramuscular Venous Malformation Using Grey-Scale Ultrasound-Based Radiomics and Machine Learning.

Cancer tumor classification based on morphological characteristics alone has been shown to have serious limitations. Breast, lung, colorectal, thyroid, and ovarian are the most commonly diagnosed cancers among women. Precise classification of cancers into their types is considered a vital problem for cancer diagnosis and therapy. In this paper, we proposed a stacking ensemble deep learning model based on one-dimensional convolutional neural network (1D-CNN) to perform a multi-class classification on the five common cancers among women based on RNASeq data. The RNASeq gene expression data was downloaded from Pan-Cancer Atlas using GDCquery function of the TCGAbiolinks package in the R software. We used least absolute shrinkage and selection operator (LASSO) as feature selection method. We compared the results of the new proposed model with and without LASSO with the results of the single 1D-CNN and machine learning methods which include support vector machines with radial basis function, linear, and polynomial kernels; artificial neural networks; k-nearest neighbors; bagging trees. The results show that the proposed model with and without LASSO has a better performance compared to other classifiers. Also, the results show that the machine learning methods (SVM-R, SVM-L, SVM-P, ANN, KNN, and bagging trees) with under-sampling have better performance than with over-sampling techniques. This is supported by the statistical significance test of accuracy where the p-values for differences between the SVM-R and SVM-P, SVM-R and ANN, SVM-R and KNN are found to be p = 0.003, p = < 0.001, and p = < 0.001, respectively. Also, SVM-L had a significant difference compared to ANN p = 0.009. Moreover, SVM-P and ANN, SVM-P and KNN are found to be significantly different with p-values p = < 0.001 and p = < 0.001, respectively. In addition, ANN and bagging trees, ANN and KNN were found to be significantly different with p-values p = < 0.001 and p = 0.004, respectively. Thus, the proposed model can help in the early detection and diagnosis of cancer in women, and hence aid in designing early treatment strategies to improve survival.

BackgroundGene expression microarray and other multiplex data hold promise for addressing the challenges of cellular complexity, refined diagnoses and the discovery of well-targeted treatments. A new approach to the construction and quantification of transcriptional regulatory networks (TRNs) is presented that integrates gene expression microarray data and cell modeling through information theory. Given a partial TRN and time series data, a probability density is constructed that is a functional of the time course of transcription factor (TF) thermodynamic activities at the site of gene control, and is a function of mRNA degradation and transcription rate coefficients, and equilibrium constants for TF/gene binding.ResultsOur approach yields more physicochemical information that compliments the results of network structure delineation methods, and thereby can serve as an element of a comprehensive TRN discovery/quantification system. The most probable TF time courses and values of the aforementioned parameters are obtained by maximizing the probability obtained through entropy maximization. Observed time delays between mRNA expression and activity are accounted for implicitly since the time course of the activity of a TF is coupled by probability functional maximization, and is not assumed to be proportional to expression level of the mRNA type that translates into the TF. This allows one to investigate post-translational and TF activation mechanisms of gene regulation. Accuracy and robustness of the method are evaluated. A kinetic formulation is used to facilitate the analysis of phenomena with a strongly dynamical character while a physically-motivated regularization of the TF time course is found to overcome difficulties due to omnipresent noise and data sparsity that plague other methods of gene expression data analysis. An application to Escherichia coli is presented.ConclusionMultiplex time series data can be used for the construction of the network of cellular processes and the calibration of the associated physicochemical parameters. We have demonstrated these concepts in the context of gene regulation understood through the analysis of gene expression microarray time series data. Casting the approach in a probabilistic framework has allowed us to address the uncertainties in gene expression microarray data. Our approach was found to be robust to error in the gene expression microarray data and mistakes in a proposed TRN.

This study provides a comparative assessment on the different techniques of classifying human activities performed while wearing inertial and magnetic sensor units on the chest, arms and legs. The gyroscope, accelerometer and the magnetometer in each unit are tri-axial. Naive Bayesian classifier, artificial neural networks (ANNs), dissimilarity-based classifier, three types of decision trees, Gaussian mixture models (GMMs) and support vector machines (SVMs) are considered. A feature set extracted from the raw sensor data using principal component analysis is used for classification. Three different cross-validation techniques are employed to validate the classifiers. A performance comparison of the classifiers is provided in terms of their correct differentiation rates, confusion matrices and computational cost. The highest correct differentiation rates are achieved with ANNs (99.2%), SVMs (99.2%) and a GMM (99.1%). GMMs may be preferable because of their lower computational requirements. Regarding the position of sensor units on the body, those worn on the legs are the most informative. Comparing the different sensor modalities indicates that if only a single sensor type is used, the highest classification rates are achieved with magnetometers, followed by accelerometers and gyroscopes. The study also provides a comparison between two commonly used open source machine learning environments (WEKA and PRTools) in terms of their functionality, manageability, classifier performance and execution times.

A hierarchical naive Bayesian network classifier embedded GMM for textural image

BackgroundDistal cholangiocarcinoma (dCCA), originating from the common bile duct, is greatly associated with a dismal prognosis. A series of different studies based on cancer classification have been developed, aimed to optimize therapy and predict and improve prognosis. In this study, we explored and compared several novel machine learning models that might lead to an improvement in prediction accuracy and treatment options for patients with dCCA.MethodsIn this study, 169 patients with dCCA were recruited and randomly divided into the training cohort (n = 118) and the validation cohort (n = 51), and their medical records were reviewed, including survival outcomes, laboratory values, treatment strategies, pathological results, and demographic information. Variables identified as independently associated with the primary outcome by least absolute shrinkage and selection operator (LASSO) regression, the random survival forest (RSF) algorithm, and univariate and multivariate Cox regression analyses were introduced to establish the following different machine learning models and canonical regression model: support vector machine (SVM), SurvivalTree, Coxboost, RSF, DeepSurv, and Cox proportional hazards (CoxPH). We measured and compared the performance of models using the receiver operating characteristic (ROC) curve, integrated Brier score (IBS), and concordance index (C-index) following cross-validation. The machine learning model with the best performance was screened out and compared with the TNM Classification using ROC, IBS, and C-index. Finally, patients were stratified based on the model with the best performance to assess whether they benefited from postoperative chemotherapy through the log-rank test.ResultsAmong medical features, five variables, including tumor differentiation, T-stage, lymph node metastasis (LNM), albumin-to-fibrinogen ratio (AFR), and carbohydrate antigen 19-9 (CA19-9), were used to develop machine learning models. In the training cohort and the validation cohort, C-index achieved 0.763 vs. 0.686 (SVM), 0.749 vs. 0.692 (SurvivalTree), 0.747 vs. 0.690 (Coxboost), 0.745 vs. 0.690 (RSF), 0.746 vs. 0.711 (DeepSurv), and 0.724 vs. 0.701 (CoxPH), respectively. The DeepSurv model (0.823 vs. 0.754) had the highest mean area under the ROC curve (AUC) than other models, including SVM (0.819 vs. 0.736), SurvivalTree (0.814 vs. 0.737), Coxboost (0.816 vs. 0.734), RSF (0.813 vs. 0.730), and CoxPH (0.788 vs. 0.753). The IBS of the DeepSurv model (0.132 vs. 0.147) was lower than that of SurvivalTree (0.135 vs. 0.236), Coxboost (0.141 vs. 0.207), RSF (0.140 vs. 0.225), and CoxPH (0.145 vs. 0.196). Results of the calibration chart and decision curve analysis (DCA) also demonstrated that DeepSurv had a satisfactory predictive performance. In addition, the performance of the DeepSurv model was better than that of the TNM Classification in C-index, mean AUC, and IBS (0.746 vs. 0.598, 0.823 vs. 0.613, and 0.132 vs. 0.186, respectively) in the training cohort. Patients were stratified and divided into high- and low-risk groups based on the DeepSurv model. In the training cohort, patients in the high-risk group would not benefit from postoperative chemotherapy (p = 0.519). In the low-risk group, patients receiving postoperative chemotherapy might have a better prognosis (p = 0.035).ConclusionsIn this study, the DeepSurv model was good at predicting prognosis and risk stratification to guide treatment options. AFR level might be a potential prognostic factor for dCCA. For the low-risk group in the DeepSurv model, patients might benefit from postoperative chemotherapy.

Mild cognitive impairment (MCI) is a clinical condition characterized by a decline in cognitive ability and progression of cognitive impairment. It is often considered a transitional stage between normal aging and Alzheimer's disease (AD). This study aimed to compare deep learning (DL) and traditional machine learning (ML) methods in predicting MCI using plasma proteomic biomarkers. A total of 239 adults were selected from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort along with a pool of 146 plasma proteomic biomarkers. We evaluated seven traditional ML models (support vector machines (SVMs), logistic regression (LR), naïve Bayes (NB), random forest (RF), k-nearest neighbor (KNN), gradient boosting machine (GBM), and extreme gradient boosting (XGBoost)) and six variations of a deep neural network (DNN) model-the DL model in the H2O package. Least Absolute Shrinkage and Selection Operator (LASSO) selected 35 proteomic biomarkers from the pool. Based on grid search, the DNN model with an activation function of "Rectifier With Dropout" with 2 layers and 32 of 35 selected proteomic biomarkers revealed the best model with the highest accuracy of 0.995 and an F1 Score of 0.996, while among seven traditional ML methods, XGBoost was the best with an accuracy of 0.986 and an F1 Score of 0.985. Several biomarkers were correlated with the APOE-ε4 genotype, polygenic hazard score (PHS), and three clinical cerebrospinal fluid biomarkers (Aβ42, tTau, and pTau). Bioinformatics analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed several molecular functions and pathways associated with the selected biomarkers, including cytokine-cytokine receptor interaction, cholesterol metabolism, and regulation of lipid localization. The results showed that the DL model may represent a promising tool in the prediction of MCI. These plasma proteomic biomarkers may help with early diagnosis, prognostic risk stratification, and early treatment interventions for individuals at risk for MCI.

Background and purpose: Adaptive radiotherapy (ART) can compensate for the dosimetric impacts induced by anatomic and geometric variations in patients with nasopharyngeal carcinoma (NPC); Yet, the need for ART can only be assessed during the radiation treatment and the implementation of ART is resource intensive. Therefore, we aimed to determine tumoral biomarkers using pre-treatment MR images for predicting ART eligibility in NPC patients prior to the start of treatment.Methods: Seventy patients with biopsy-proven NPC (Stage II-IVB) in 2015 were enrolled into this retrospective study. Pre-treatment contrast-enhanced T1-w (CET1-w), T2-w MR images were processed and filtered using Laplacian of Gaussian (LoG) filter before radiomic features extraction. A total of 479 radiomics features, including the first-order (n = 90), shape (n = 14), and texture features (n = 375), were initially extracted from Gross-Tumor-Volume of primary tumor (GTVnp) using CET1-w, T2-w MR images. Patients were randomly divided into a training set (n = 51) and testing set (n = 19). The least absolute shrinkage and selection operator (LASSO) logistic regression model was applied for radiomic model construction in training set to select the most predictive features to predict patients who were replanned and assessed in the testing set. A double cross-validation approach of 100 resampled iterations with 3-fold nested cross-validation was employed in LASSO during model construction. The predictive performance of each model was evaluated using the area under the receiver operator characteristic (ROC) curve (AUC).Results: In the present cohort, 13 of 70 patients (18.6%) underwent ART. Average AUCs in training and testing sets were 0.962 (95%CI: 0.961–0.963) and 0.852 (95%CI: 0.847–0.857) with 8 selected features for CET1-w model; 0.895 (95%CI: 0.893–0.896) and 0.750 (95%CI: 0.745–0.755) with 6 selected features for T2-w model; and 0.984 (95%CI: 0.983–0.984) and 0.930 (95%CI: 0.928–0.933) with 6 selected features for joint T1-T2 model, respectively. In general, the joint T1-T2 model outperformed either CET1-w or T2-w model alone.Conclusions: Our study successfully showed promising capability of MRI-based radiomics features for pre-treatment identification of ART eligibility in NPC patients.

<title>Abstract</title> Objective To construct various radiomics models based on CT venous phase images for the quantitative assessment of gastric cancer (GC) invasion depth into the gastric wall, and to compare the diagnostic performance of different models in distinguishing early (T1-T2 stage) from advanced (T3-T4 stage) GC, aiming to identify the optimal model and evaluate its potential for clinical application. Methods In this retrospective study, 223 pathologically confirmed GC patients (66 early-stage, 157 advanced-stage) treated between January 2022 and May 2025 were enrolled. Patients were allocated into a training set (n = 156) and an independent test set (n = 67) through stratified random sampling at a 7:3 ratio. All patients underwent enhanced CT within one week prior to surgery. Venous phase images were selected, and three-dimensional regions of interest (ROIs) encompassing the tumor were manually delineated using 3D Slicer for radiomics feature extraction. In the training set, feature selection was performed using Least Absolute Shrinkage and Selection Operator (LASSO) regression. Four machine learning models were subsequently constructed: Logistic Regression (LR), Random Forest (RF), XGBoost (XGB), and Support Vector Machine (SVM). Model optimization was conducted via 5-fold cross-validation. Performance was evaluated using receiver operating characteristic (ROC) curves, precision-recall (PR) curves, confusion matrices, and decision curve analysis (DCA). Results A total of 148 radiomics features were extracted, from which 11 key features were selected by LASSO. In the training set under 5-fold cross-validation, the LR, RF, SVM, and XGB models demonstrated strong discriminatory ability, with AUCs of 0.912, 0.910, 0.899, and 0.880, respectively. In the independent test set, the LR model exhibited the best overall performance: AUC 0.912 (95% CI: 0.853–0.948), accuracy 0.791, sensitivity 0.787, specificity 0.800, F1-score 0.841, and average precision (AP) 0.966. DeLong's test revealed statistically significant differences in AUC among models (all P &lt; 0.001), though the difference between LR and RF was minimal (0.0021, 95% CI: − 0.0459–0.0502). All models showed good calibration (Hosmer–Lemeshow test P &gt; 0.05). DCA indicated that the LR model provided higher net clinical benefit within a threshold probability range of 0.3–0.8. Conclusion Among the multiple radiomics models constructed based on CT venous phase images, the LR model demonstrated the best performance in distinguishing early from advanced GC T stages, showing favorable diagnostic efficacy and clinical utility. It can serve as a quantitative auxiliary tool for preoperative staging and treatment decision-making, providing an objective basis for precise GC diagnosis and treatment.