Identification of high-risk genes and classification of acute myocardial infarction patients utilizing deep learning in a restricted cohort.

The increasing prevalence of malware presents a critical challenge to cybersecurity, emphasizing the need for robust detection methods. This study uses a binary tabular classification dataset to evaluate the impact of feature selection, feature scaling, and machine learning (ML) models on malware detection. The methodology involves experimenting with three feature scaling techniques (no scaling, normalization, and min-max scaling), three feature selection methods (no selection, Linear Discriminant Analysis (LDA), and Principal Component Analysis (PCA)), and twelve ML models, including traditional algorithms and ensemble methods. A publicly available dataset with 11,598 samples and 139 features is utilized, and model performance is assessed using metrics such as accuracy, precision, recall, F1-score, and AUC-ROC. Results reveal that the Light Gradient Boosting Machine (LGBM) achieves the highest accuracy of 97.16% when PCA and either min-max scaling or normalization are applied. Additionally, ensemble models consistently outperform traditional ML models, demonstrating their effectiveness in enhancing malware detection. These findings offer valuable insights into optimizing preprocessing and model selection strategies for developing reliable and efficient malware detection systems.

COVID-19 is highly infectious and causes acute respiratory disease. Machine learning (ML) and deep learning (DL) models are vital in detecting disease from computerized chest tomography (CT) scans. The DL models outperformed the ML models. For COVID-19 detection from CT scan images, DL models are used as end-to-end models. Thus, the performance of the model is evaluated for the quality of the extracted feature and classification accuracy. There are four contributions included in this work. First, this research is motivated by studying the quality of the extracted feature from the DL by feeding these extracted to an ML model. In other words, we proposed comparing the end-to-end DL model performance against the approach of using DL for feature extraction and ML for the classification of COVID-19 CT scan images. Second, we proposed studying the effect of fusing extracted features from image descriptors, e.g., Scale-Invariant Feature Transform (SIFT), with extracted features from DL models. Third, we proposed a new Convolutional Neural Network (CNN) to be trained from scratch and then compared to the deep transfer learning on the same classification problem. Finally, we studied the performance gap between classic ML models against ensemble learning models. The proposed framework is evaluated using a CT dataset, where the obtained results are evaluated using five different metrics The obtained results revealed that using the proposed CNN model is better than using the well-known DL model for the purpose of feature extraction. Moreover, using a DL model for feature extraction and an ML model for the classification task achieved better results in comparison to using an end-to-end DL model for detecting COVID-19 CT scan images. Of note, the accuracy rate of the former method improved by using ensemble learning models instead of the classic ML models. The proposed method achieved the best accuracy rate of 99.39%.

Objective: To investigate the feasibility of a machine learning (ML) model based on radiomic features to identify active giant cell arteritis (GCA) in the aorta and differentiate it from atherosclerosis in follow-up [18F]FDG-PET/CT images for therapy monitoring. Methods: To train the ML model, 64 [18F]FDG-PET scans of 34 patients with proven GCA and 34 control subjects with type 2 diabetes mellitus were retrospectively included. The aorta was delineated into the ascending, arch, descending, and abdominal aorta. From each segment, 95 features were extracted. All segments were randomly split into a training/validation (n = 192; 80%) and test set (n = 46; 20%). In total, 441 ML models were trained, using combinations of seven feature selection methods, seven classifiers, and nine different numbers of features. The performance was assessed by area under the curve (AUC). The best performing ML model was compared to the clinical report of nuclear medicine physicians in 19 follow-up scans (7 active GCA, 12 inactive GCA). For explainability, an occlusion map was created to illustrate the important regions of the aorta for the decision of the ML model. Results: The ten-feature model with ANOVA as the feature selector and random forest classifier demonstrated the highest performance (AUC = 0.92 ± 0.01). Compared with the clinical report, this model showed a higher PPV (0.83 vs. 0.80), NPV (0.85 vs. 0.79), and accuracy (0.84 vs. 0.79) in the detection of active GCA in follow-up scans. Conclusions: The current radiomics ML model was able to identify active GCA and differentiate GCA from atherosclerosis in follow-up [18F]FDG-PET/CT scans. This demonstrates the potential of the ML model as a monitoring tool in challenging [18F]FDG-PET scans of GCA patients.

Small data, big challenges: Machine- and deep-learning strategies for data-limited drug discovery.

The accurate estimation of aboveground biomass (AGB) in rubber plantations is essential for predicting rubber production and assessing carbon storage. Multispectral sensors mounted on unmanned aerial vehicles (UAVs) can obtain high spatiotemporal resolution imagery of rubber plantations, offering significant advantages in capturing fine structural details and heterogeneity. However, most previous studies primarily focused on developing biomass estimation models for rubber using machine learning (ML) algorithms in conjunction with feature selection methods based on UAV-acquired multispectral imagery. The reliance on feature selection methods limits the model’s generalizability, robustness, and predictive accuracy. In contrast, deep learning (DL) exhibits considerable promise in extracting features from high-resolution UAV-based multispectral imagery without the need for manual selection. Nonetheless, it remains unclear whether DL can surpass traditional ML methods in improving the AGB estimation accuracy in rubber plantations. To address this, our study evaluated the performance of three ML algorithms (random forest regression, RFR; XGBoost regression, XGBR; categorical boosting regression, CatBoost) combined with feature selection techniques and a deep convolutional neural network (DCNN) using multispectral imagery obtained from UAV for the AGB estimation of rubber plantations. The results indicate that the RFR combined with a principal component analysis (PCA) for feature selection yielded the best performance (R2 = 0.81, RMSE = 11.63 t/ha, MAE = 9.27 t/ha) between the three ML algorithms. Meanwhile, the DCNN model derived from the G, R, and NIR spectral bands achieved the highest estimation accuracy (R2 = 0.89, RMSE = 6.44 t/ha, MAE = 5.72 t/ha), where it outperformed the other ML methods. Our study highlights the great potential of combining UAV-based multispectral imagery with DL techniques to improve AGB estimation in rubber plantations, offering a new perspective for estimating the physiological and biochemical growth parameters of forests.

Contemporary deep learning approaches exhibit state-of-the-art performance in various areas. In healthcare, the application of deep learning remains limited since deep learning methods are often considered as non-interpretable black-box models. However, the Machine Learning (ML) community made recent elaborations to develop the methods of eXplainable Artificial Intelligence (XAI). The explanation methods explain single decisions of an ML model when a single data point is fed into the model’s input. In a clinical setup, a data point can represent a single patient. Data point-specific explanations could possibly assist the need in personalized precision medicine decisions via explaining patient-specific predictions. Convolutional Neural Networks (CNNs) as deep learning methods have been already applied to classify transformed into images gene expression profiles of patients. Gene expression data can be structured by a prior knowledge molecular network (encoded as a graph) representing connections between genes. Each vertex of a molecular network is assigned a gene expression value as an attribute. The set of the attributes creates a graph signal representing a patient. Emerging field of geometric deep learning deals with methods applicable to graph structured data and extends CNNs as Graph Convolutional Neural Networks (GCNNs) classifying graph signals. Layer-wise Relevance Propagation (LRP) is a method to explain decisions of CNNs classifying image data. I extended the LRP method to make it available for GCNNs. Graph Layer-wise Relevance Propagation (GLRP) is presented as a new method to explain single decisions made by a GCNN model. In this thesis, I present a novel methodology generating patient-specific molecular subnetworks as explanations for classification decisions of an ML approach utilizing prior knowledge of molecular networks. GCNN serves as a ML approach, and its decisions are explained by developed GLRP. A sanity check of the developed GLRP method was demonstrated on a hand-written digits dataset. The biological validation was performed by applying the developed methodology to gene expression data from Human Umbilical Vein Endothelial Cells (HUVEC) treated or not treated with tumor necrosis factor alpha. To show the utility of introduced methodology in the scopes of precision medicine, it was applied to a large breast cancer dataset. The generated patient-specific subnetworks largely agree with clinical knowledge and could assist precision medicine approaches by identifying common as well as novel, and potentially druggable, drivers of tumor progression. Apart from generating patient-specific subnetworks, the developed methodology can be used as a general feature selection approach. The outcome of a feature selection approach is a subset of important for classification genes corresponding to a whole dataset. It is essential to sustain stability of selected feature subsets across different datasets with the same clinical endpoint since the selected genes are possible candidates for prognostic biomarkers. I analysed the stability of feature selection performed by GCNN+LRP. I have implemented a graph convolutional layer of GCNN as a Keras layer so that the SHapley Additive exPlanations (SHAP) method could be also applied to a Keras version of a GCNN model. The stability of feature selection performed by GCNN+LRP was compared to the stability of GCNN+SHAP and other ML-based feature selection approaches. The GCNN+LRP approach shows the highest stability. GCNN+LRP subnetworks were compared to GCNN+SHAP subnetworks in terms of connectivity and permutation feature importance. While GCNN+SHAP subnetworks demonstrate higher permutation importance than GCNN+LRP subnetworks, a GCNN+LRP subnetwork of an individual patient is on average substantially more connected and, therefore more interpretable in the context of prior knowledge than a GCNN+SHAP subnetwork which consists mainly of single vertices.

12074 Background: Skeletal-related events (SREs) are detrimental clinical events in bone metastasis from advanced cancer, defined by pathologic fracture, spinal cord compression, and inevitable surgical or radiational intervention to the bone. Given their negative impact on quality of life and prognosis and interpatient heterogeneity in the SRE risk, accurate identification of patients with high SRE risk is critical. Methods: The patient-level data from three randomized clinical trials that administered zoledronic acid (ZA) to patients with bone-metastatic breast cancer, castration-resistant prostate cancer (CRPC), and other types of cancer were analyzed. (N = 460, 452, and 315, respectively) Machine learning (ML) models to predict SREs within 18 months (breast cancer), 12 months (CRPC), and 9 months (other cancers) were developed based on more than 40 baseline clinical and laboratory data. Seven ML algorithms and five feature selection methods were utilized to develop multiple models. The ML model with the best performance was identified based on the F1 score and the area under the receiver operating characteristic curve (AUC-ROC) for each cancer type and interrogated for important features with Shapley additive explanations. Lastly, the ML models’ ability to stratify patients by the cumulative SRE risk was evaluated by calculating hazard ratio (HR) with Cox-proportional hazards models. Results: Among the multiple ML models developed with different algorithms and feature selection methods, the model developed utilizing the random forests algorithm and the Boruta method for selecting features demonstrated the best performance in all types of cancer (F1 0.70, 0.67, and 0.67, and AUC-ROC 0.72, 0.68, and 0.73 for breast cancer, CRPC, and other cancers, respectively). In the ML model for breast cancer, performance status (PS), history of SRE, serum alkaline phosphatase (ALP), history of anti-neoplastic surgery, radiation therapy, and pathologic fracture were included as important features. Serum ALP, albumin, sodium, Gleason scores, and geographic regions were shown to be relevant in the CRPC model. For other cancers, serum ALP, albumin, total protein, phosphorus, red blood cell count, white blood cell count, visceral metastases, and history of arthritis were incorporated in the ML model. The ML model prediction successfully stratified the patients for cumulative SRE risk in all three cohorts. (HR with 95% confidence interval: 2.43 [1.86 – 3.18], 1.92 [1.51 – 2.45], and 3.06 [2.29 – 4.09] for breast cancer, CRPC, and other types of cancer, respectively). Conclusions: ML models incorporating baseline clinical and laboratory data can identify patients with bone metastasis on ZA harboring a high SRE risk.

Causal machine learning is an approach that combines causal inference and machine learning to understand and utilize causal relationships in data. In current research and applications, traditional machine learning and deep learning models always focus on prediction and pattern recognition. In contrast, causal machine learning goes a step further by revealing causal relationships between different variables. We explore a novel concept called Double Machine Learning that embraces causal machine learning in this research. The core goal is to select independent variables from a gesture identification problem that are causally related to final gesture results. This selection allows us to classify and analyze gestures more efficiently, thereby improving models’ performance and interpretability. Compared to commonly used feature selection methods such as Variance Threshold, Select From Model, Principal Component Analysis, Least Absolute Shrinkage and Selection Operator, Artificial Neural Network, and TabNet, Double Machine Learning methods focus more on causal relationships between variables rather than correlations. Our research shows that variables selected using the Double Machine Learning method perform well under different classification models, with final results significantly better than those of traditional methods. This novel Double Machine Learning-based approach offers researchers a valuable perspective for feature selection and model construction. It enhances the model’s ability to uncover causal relationships within complex data. Variables with causal significance can be more informative than those with only correlative significance, thus improving overall prediction performance and reliability.

A machine-learning-based model for predicting the effective stiffness of precast concrete columns

Prediction of the stage of cancer plays an important role in planning the course of treatment and has been largely reliant on imaging tools which do not capture molecular events that cause cancer progression. Gene-expression data-based analyses are able to identify these events, allowing RNA-sequence and microarray cancer data to be used for cancer analyses. Breast cancer is the most common cancer worldwide, and is classified into four stages - stages 1, 2, 3, and 4 [2]. While machine learning models have previously been explored to perform stage classification with limited success, multi-class stage classification has not had significant progress. There is a need for improved multi-class classification models, such as by investigating deep learning models. Gene-expression-based cancer data is characterised by the small size of available datasets, class imbalance, and high dimensionality. Class balancing methods must be applied to the dataset. Since all the genes are not necessary for stage prediction, retaining only the necessary genes can improve classification accuracy. The breast cancer samples are to be classified into 4 classes of stages 1 to 4. Invasive ductal carcinoma breast cancer samples are obtained from The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) datasets and combined. Two class balancing techniques are explored, synthetic minority oversampling technique (SMOTE) and SMOTE followed by random undersampling. A hybrid feature selection pipeline is proposed, with three pipelines explored involving combinations of filter and embedded feature selection methods: Pipeline 1 - minimum-redundancy maximum-relevancy (mRMR) and correlation feature selection (CFS), Pipeline 2 - mRMR, mutual information (MI) and CFS, and Pipeline 3 - mRMR and support vector machine-recursive feature elimination (SVM-RFE). The classification is done using deep learning models, namely deep neural network, convolutional neural network, recurrent neural network, a modified deep neural network, and an AutoKeras generated model. Classification performance post class-balancing and various feature selection techniques show marked improvement over classification prior to feature selection. The best multiclass classification was found to be by a deep neural network post SMOTE and random undersampling, and feature selection using mRMR and recursive feature elimination, with a Cohen-Kappa score of 0.303 and a classification accuracy of 53.1%. For binary classification into early and late-stage cancer, the best performance is obtained by a modified deep neural network (DNN) post SMOTE and random undersampling, and feature selection using mRMR and recursive feature elimination, with an accuracy of 81.0% and a Cohen-Kappa score (CKS) of 0.280. This pipeline also showed improved multiclass classification performance on neuroblastoma cancer data, with a best area under the receiver operating characteristic (auROC) curve score of 0.872, as compared to 0.71 obtained in previous work, an improvement of 22.81%. The results and analysis reveal that feature selection techniques play a vital role in gene-expression data-based classification, and the proposed hybrid feature selection pipeline improves classification performance. Multi-class classification is possible using deep learning models, though further improvement particularly in late-stage classification is necessary and should be explored further.

Metabolic dysfunction-associated steatotic liver disease (MASLD) can progress to metabolic dysfunction-associated steatohepatitis (MASH) and liver fibrosis, contributing to a heavier global health burden. Non-invasive diagnostic tools developed using machine learning (ML) and deep learning (DL), two representative artificial intelligence algorithms, are increasingly being explored for MASH and its related fibrosis assessment. This study aimed to compare the diagnostic performance of different ML and DL models and identify the top-performing models for diagnosing MASH and associated liver fibrosis. A systematic review and meta-analysis were conducted across PubMed, Web of Science, Embase and Cochrane Library from inception to May 18, 2025. Pooled area under the receiver operator characteristic curve (AUROC) values with 95 % confidence interval (CI) were calculated. Accuracy, specificity, sensitivity, positive predictive values, and negative predictive values were also recorded. Of 4,314 studies initially identified, 106 met the inclusion criteria, with 35 studies (ML: n=28; DL: n=7) providing data for analysis. Logistic Regression and Neural Network are the most commonly algorithms applied in ML and DL, respectively. The pooled AUROCs for diagnosing MASH were 0.833 (95 %CI: 0.806-0.860) for ML models and 0.841 (95 %CI: 0.782-0.900) for DL models. Light Gradient Boosting Machine (LightGBM) and ResNet50 were the best-performing models for diagnosing MASH within ML and DL algorithms, respectively, achieving corresponding AUROCs of 0.920 (95 %CI: 0.916-0.924) and 0.960 (95 %CI: 0.951-0.969). For fibrosis diagnosis, ML models had a pooled AUROC of 0.826 (95 %CI: 0.792-0.860), with Categorical Boosting (CatBoost) achieving the highest AUROC of 0.960 (95 %CI: 0.950-0.970). DL models yielded the pooled AUROC of 0.875 (95 %CI: 0.816-0.934) for fibrosis diagnosis. Both ML and DL models demonstrated strong diagnostic performance for MASH and liver fibrosis, with DL achieving marginally higher AUROCs. AI-driven approaches show promise in MASLD management.

BackgroundDifferential expression and feature selection analyses are essential steps for the development of accurate diagnostic/prognostic classifiers of complicated human diseases using transcriptomics data. These steps are particularly challenging due to the curse of dimensionality and the presence of technical and biological noise. A promising strategy for overcoming these challenges is the incorporation of pre-existing transcriptomics data in the identification of differentially expressed (DE) genes. This approach has the potential to improve the quality of selected genes, increase classification performance, and enhance biological interpretability. While a number of methods have been developed that use pre-existing data for differential expression analysis, existing methods do not leverage the identities of experimental conditions to create a robust metric for identifying DE genes.ResultsIn this study, we propose a novel differential expression and feature selection method—GEOlimma—which combines pre-existing microarray data from the Gene Expression Omnibus (GEO) with the widely-applied Limma method for differential expression analysis. We first quantify differential gene expression across 2481 pairwise comparisons from 602 curated GEO Datasets, and we convert differential expression frequencies to DE prior probabilities. Genes with high DE prior probabilities show enrichment in cell growth and death, signal transduction, and cancer-related biological pathways, while genes with low prior probabilities were enriched in sensory system pathways. We then applied GEOlimma to four differential expression comparisons within two human disease datasets and performed differential expression, feature selection, and supervised classification analyses. Our results suggest that use of GEOlimma provides greater experimental power to detect DE genes compared to Limma, due to its increased effective sample size. Furthermore, in a supervised classification analysis using GEOlimma as a feature selection method, we observed similar or better classification performance than Limma given small, noisy subsets of an asthma dataset.ConclusionsOur results demonstrate that GEOlimma is a more effective method for differential gene expression and feature selection analyses compared to the standard Limma method. Due to its focus on gene-level differential expression, GEOlimma also has the potential to be applied to other high-throughput biological datasets.

To enhance the performance of machine learning (ML) models for the post-embolization recanalization of cerebral aneurysms, we evaluated the impact of hemodynamic feature derivation and selection method on six ML algorithms. We utilized computational fluid dynamics (CFD) to simulate hemodynamics in 66 cerebral aneurysms from 65 patients, including 57 stable and nine recanalized aneurysms. We derived a total of 107 features for each aneurysm, encompassing four clinical features, 12 morphological features, and 91 hemodynamic features. To investigate the influence of feature derivation and selection methods on the ML models, we employed two derivation methods, simplified and fully derived, in combination with four selection methods: all features, statistically significant analysis, stepwise multivariate logistic regression analysis (stepwise-LR), and recursive feature elimination (RFE). Model performance was assessed using the area under the receiver operating characteristic curve (AUROC) and precision-recall curve (AUPRC) on both the training and testing datasets. The AUROC values on the testing dataset exhibited a wide-ranging spectrum, spanning from 0.373 to 0.863. Fully derived features and the RFE selection method demonstrated superior performance in intra-model comparisons. The multi-layer perceptron (MLP) model, trained with RFE-selected fully derived features, achieved the best performance on the testing dataset, with an AUROC value of 0.863 (95% CI: 0.684- 1.000). Our study demonstrated the importance of feature derivation and selection in determining the performance of ML models. This enabled the development of accurate decision-making models without the need to invade the patient.

In recent years, infections and damage caused by malware have increased at exponential rates. At the same time, machine learning (ML) techniques have shown tremendous promise in many domains, often out performing human efforts by learning from large amounts of data. Results in the open literature suggest that ML is able to provide similar results for malware detection, achieving greater than 99% classification accuracy [49]. However, the same detection rates when applied in deployed settings have not been achieved. Malware is distinct from many other domains in which ML has shown success in that (1) it purposefully tries to hide, leading to noisy labels and (2) often its behavior is similar to benign software only differing in intent, among other complicating factors. This report details the reasons for the difficultly of detecting novel malware by ML methods and offers solutions to improve the detection of novel malware. We propose to detect malware by detecting behaviors commonly exhibited by malware such as DLL injection, and process hollowing. This is based on the assumption that there is a set of behaviors that are common to most malware samples and detecting them will generalize to novel malware. Additionally, detected behaviors point analysts toward appropriate handling and mitigation strategies, which is not the case with a binary benign/malicious classification. A behavior labeling method was developed and was used to label an existing malware dataset. Results show that detecting malicious behaviors is much more difficult than simply classifying malware and goodware?achieving 80% accuracy compared to reported 99% accuracy from classifying malware and goodware. This drop is due to several reasons which are detailed in the report. We also propose to evaluate the performance of detecting novel malware by holding out a malware family for testing and training on the other families. Traditional ML evaluation will shuffle the data and then split the data into training and testing. Our method addresses the use-case when novel malware families are encountered and they require more than just a malicious or benign designation. Our results suggest that this type of evaluation is much more difficult than traditional methods and provides more realistic results, albeit, significantly worse. For our behavior detection, accuracy decreases from 80% to 68% across all behaviors when holding out a malware family from training. We show that the degradation in performance is because each malware family has distinct characteristics resulting in high extrapolations by an ML model. Here, an ML model should return an "I do not know" response and request further analysis from an analyst. We run a number of experiments that compare novel malware families to the training data using different feature representations including a genomics-inspired distance measure and features extracted by deep learning. Generally, held-out families are significantly different from the training data, resulting in unpredictable results. This has been observed generally in the ML community [22, 9]. We empirically demonstrate this in the domain of malware detection. In an attempt to improve the detection of malware behaviors, we examine the impact that additional synthetic data has on the performance of an ML model in detecting behaviors in novel malware families. We find that while synthetic data does improve the performance of ML models, often simpler methods perform better than more complicated ones. Two generative modeling techniques were examined to produce synthetic malware samples such that the behaviors present are able to be specified externally. The difficulty is due to finer grained analysis of the executable and modifying the problem from a binary classification problem to a multi-label problem. The addition of synthetic data increases the overall accuracy from 68% to 70%. While far less accurate than measures presented in academic analyses, we believe that this is more representative of real-world performance and allows models to be properly placed within a malware detection system. We suggest that in highly dynamic environments ML pipelines should determine whether an ML model is competent in the area of new data and should involve mechanisms to improve over time with a human in the loop.

Social media platforms provide valuable insights into mental health trends by capturing user-generated discussions on conditions such as depression, anxiety, and suicidal ideation. Machine learning (ML) and deep learning (DL) models have been increasingly applied to classify mental health conditions from textual data, but selecting the most effective model involves trade-offs in accuracy, interpretability, and computational efficiency. This study evaluates multiple ML models, including logistic regression, random forest, and LightGBM, alongside DL architectures such as ALBERT and Gated Recurrent Units (GRUs), for both binary and multi-class classification of mental health conditions. Our findings indicate that ML and DL models achieve comparable classification performance on medium-sized datasets, with ML models offering greater interpretability through variable importance scores, while DL models are more robust to complex linguistic patterns. Additionally, ML models require explicit feature engineering, whereas DL models learn hierarchical representations directly from text. Logistic regression provides the advantage of capturing both positive and negative associations between features and mental health conditions, whereas tree-based models prioritize decision-making power through split-based feature selection. This study offers empirical insights into the advantages and limitations of different modeling approaches and provides recommendations for selecting appropriate methods based on dataset size, interpretability needs, and computational constraints.