The increase in high-dimensional multiomics data demands advanced integration models to capture the complexity of human diseases. Graph-based deep learning integration models, despite their promise, struggle with small patient cohorts and high-dimensional features, often applying independent feature selection without modeling relationships among omics. Furthermore, conventional graph-based omics models focus on homogeneous graphs, lacking multiple types of nodes and edges to capture diverse structures. We introduce a Heterogeneous Graph ATtention network for omics integration (HeteroGATomics) to improve cancer diagnosis. HeteroGATomics performs multimodal feature selection through a multi-agent system, creating dedicated networks of feature and patient similarity for each omics modality. These networks are then combined into one heterogeneous graph for learning holistic omics-specific representations and integrating predictions across modalities. Experiments on three cancer multiomics datasets show that HeteroGATomics outperforms baseline methods across most evaluation metrics in cancer diagnosis. External validation on an independent breast cancer cohort further demonstrates its generalizability, where HeteroGATomics outperforms graph-based multiomics integration methods across evaluation metrics. Moreover, HeteroGATomics enhances interpretability by identifying important biomarkers contributing to the diagnosis outcomes.
We propose an automatic approach for manifold nonlinear autoregressive with exogenous inputs (mNARX) modeling that leverages the feature-based structure of functional-NARX (F-NARX) modeling. This novel approach, termed mNARX+, preserves the key strength of the mNARX framework, which is its expressivity allowing it to model complex dynamical systems, while simultaneously addressing a key limitation: the heavy reliance on domain expertise to identify relevant auxiliary quantities and their causal ordering. Our method employs a data-driven, recursive algorithm that automates the construction of the mNARX model sequence. It operates by sequentially selecting temporal features based on their correlation with the model prediction residuals, thereby automatically identifying the most critical auxiliary quantities and the order in which they should be modeled. This procedure significantly reduces the need for prior system knowledge. We demonstrate the effectiveness of the mNARX+ algorithm on two case studies: a Bouc-Wen oscillator with strong hysteresis and a complex aero-servo-elastic wind turbine simulator. The results show that the algorithm provides a systematic, data-driven method for creating accurate and stable surrogate models for complex dynamical systems.
Poultry farming is a vital component of the global food supply chain, yet it remains highly vulnerable to infectious diseases such as coccidiosis, salmonellosis, and Newcastle disease. This study proposes a lightweight machine learning-based approach to detect these diseases by analyzing poultry fecal images. We utilize multi-color space feature extraction (RGB, HSV, LAB) and explore a wide range of color, texture, and shape-based descriptors, including color histograms, local binary patterns (LBP), wavelet transforms, and edge detectors. Through a systematic ablation study and dimensionality reduction using PCA and XGBoost feature selection, we identify a compact global feature set that balances accuracy and computational efficiency. An artificial neural network (ANN) classifier trained on these features achieved 95.85% accuracy while requiring no GPU and only 638 seconds of execution time in Google Colab. Compared to deep learning models such as Xception and MobileNetV3, our proposed model offers comparable accuracy with drastically lower resource usage. This work demonstrates a cost-effective, interpretable, and scalable alternative to deep learning for real-time poultry disease detection in low-resource agricultural settings.
Tensor Network (TN) Kernel Machines speed up model learning by representing parameters as low-rank TNs, reducing computation and memory use. However, most TN-based Kernel methods are deterministic and ignore parameter uncertainty. Further, they require manual tuning of model complexity hyperparameters like tensor rank and feature dimensions, often through trial-and-error or computationally costly methods like cross-validation. We propose Bayesian Tensor Network Kernel Machines, a fully probabilistic framework that uses sparsity-inducing hierarchical priors on TN factors to automatically infer model complexity. This enables automatic inference of tensor rank and feature dimensions, while also identifying the most relevant features for prediction, thereby enhancing model interpretability. All the model parameters and hyperparameters are treated as latent variables with corresponding priors. Given the Bayesian approach and latent variable dependencies, we apply a mean-field variational inference to approximate their posteriors. We show that applying a mean-field approximation to TN factors yields a Bayesian ALS algorithm with the same computational complexity as its deterministic counterpart, enabling uncertainty quantification at no extra computational cost. Experiments on synthetic and real-world datasets demonstrate the superior performance of our model in prediction accuracy, uncertainty quantification, interpretability, and scalability.
Cardiac diseases are among the leading causes of morbidity and mortality worldwide, which requires accurate and timely diagnostic strategies. In this study, we introduce an innovative approach that combines deep learning image registration with physics-informed regularization to predict the biomechanical properties of moving cardiac tissues and extract features for disease classification. We utilize the energy strain formulation of Neo-Hookean material to model cardiac tissue deformations, optimizing the deformation field while ensuring its physical and biomechanical coherence. This explainable approach not only improves image registration accuracy, but also provides insights into the underlying biomechanical processes of the cardiac tissues. Evaluation on the Automated Cardiac Diagnosis Challenge (ACDC) dataset achieved Dice scores of 0.945 for the left ventricular cavity, 0.908 for the right ventricular cavity, and 0.905 for the myocardium. Subsequently, we estimate the local strains within the moving heart and extract a detailed set of features used for cardiovascular disease classification. We evaluated five classification algorithms, Logistic Regression, Multi-Layer Perceptron, Support Vector Classifier, Random Forest, and Nearest Neighbour, and identified the most relevant features using a feature selection algorithm. The best performing classifier obtained a classification accuracy of 98% in the training set and 100% in the test set of the ACDC dataset. By integrating explainable artificial intelligence, this method empowers clinicians with a transparent understanding of the model's predictions based on cardiac mechanics, while also significantly improving the accuracy and reliability of cardiac disease diagnosis, paving the way for more personalized and effective patient care.
The advent of single-cell multi-omics technologies has enabled the simultaneous profiling of diverse omics layers within individual cells. Integrating such multimodal data provides unprecedented insights into cellular identity, regulatory processes, and disease mechanisms. However, it remains challenging, as current methods often rely on selecting highly variable genes or peaks during preprocessing, which may inadvertently discard crucial biological information. Here, we present scMamba, a foundation model designed to integrate single-cell multi-omics data without the need for prior feature selection while preserving genomic positional information. scMamba introduces a patch-based cell tokenization strategy that treats genomics regions as words (tokens) and cells as sentences. Building upon the concept of state space duality, scMamba distills rich biological insights from high-dimensional, sparse single-cell multi-omics data. Additionally, our novel contrastive learning approach, enhanced with cosine similarity regularization, enables superior alignment across omics layers compared to traditional methods. Systematic benchmarking across multiple datasets demonstrates that scMamba significantly outperforms state-of-the-art methods in preserving biological variation, aligning omics layers, and enhancing key downstream tasks such as clustering, cell type annotation, and trajectory inference. Our findings position scMamba as a powerful tool for large-scale single-cell multi-omics integration, capable of handling large-scale atlases and advancing biological discovery.
Wind energy significantly contributes to the global shift towards renewable energy, yet operational challenges, such as Leading-Edge Erosion on wind turbine blades, notably reduce energy output. This study introduces an advanced, scalable machine learning framework for condition monitoring of wind turbines, specifically targeting improved detection of anomalies using Supervisory Control and Data Acquisition data. The framework effectively isolates normal turbine behavior through rigorous preprocessing, incorporating domain-specific rules and anomaly detection filters, including Gaussian Mixture Models and a predictive power score. The data cleaning and feature selection process enables identification of deviations indicative of performance degradation, facilitating estimates of annual energy production losses. The data preprocessing methods resulted in significant data reduction, retaining on average 31% of the original SCADA data per wind farm. Notably, 24 out of 35 turbines exhibited clear performance declines. At the same time, seven improved, and four showed no significant changes when employing the power curve feature set, which consisted of wind speed and ambient temperature. Models such as Random Forest, XGBoost, and KNN consistently captured subtle but persistent declines in turbine performance. The developed framework provides a novel approach to existing condition monitoring methodologies by isolating normal operational data and estimating annual energy loss, which can be a key part in reducing maintenance expenditures and mitigating economic impacts from turbine downtime.
Malware detection using machine learning requires feature extraction from binary files, as models cannot process raw binaries directly. A common approach involves using LIEF for raw feature extraction and the EMBER vectorizer to generate 2381-dimensional feature vectors. However, the high dimensionality of these features introduces significant computational challenges. This study addresses these challenges by applying two dimensionality reduction techniques: XGBoost-based feature selection and Principal Component Analysis (PCA). We evaluate three reduced feature dimensions (128, 256, and 384), which correspond to approximately 5.4%, 10.8%, and 16.1% of the original 2381 features, across four models-XGBoost, LightGBM, Extra Trees, and Random Forest-using a unified training, validation, and testing split formed from the EMBER-2018, ERMDS, and BODMAS datasets. This approach ensures generalization and avoids dataset bias. Experimental results show that LightGBM trained on the 384-dimensional feature set after XGBoost feature selection achieves the highest accuracy of 97.52% on the unified dataset, providing an optimal balance between computational efficiency and detection performance. The best model, trained in 61 minutes using 30 GB of RAM and 19.5 GB of disk space, generalizes effectively to completely unseen datasets, maintaining 95.31% accuracy on TRITIUM and 93.98% accuracy on INFERNO. These findings present a scalable, compute-efficient approach for malware detection without compromising accuracy.
This paper investigates the application of natural language processing (NLP)-based n-gram analysis and machine learning techniques to enhance malware classification. We explore how NLP can be used to extract and analyze textual features from malware samples through n-grams, contiguous string or API call sequences. This approach effectively captures distinctive linguistic patterns among malware and benign families, enabling finer-grained classification. We delve into n-gram size selection, feature representation, and classification algorithms. While evaluating our proposed method on real-world malware samples, we observe significantly improved accuracy compared to the traditional methods. By implementing our n-gram approach, we achieved an accuracy of 99.02% across various machine learning algorithms by using hybrid feature selection technique to address high dimensionality. Hybrid feature selection technique reduces the feature set to only 1.6% of the original features.
While modern segmentation models often prioritize performance over practicality, we advocate a design philosophy prioritizing simplicity and efficiency, and attempted high performance segmentation model design. This paper presents SimpleUNet, a scalable ultra-lightweight medical image segmentation model with three key innovations: (1) A partial feature selection mechanism in skip connections for redundancy reduction while enhancing segmentation performance; (2) A fixed-width architecture that prevents exponential parameter growth across network stages; (3) An adaptive feature fusion module achieving enhanced representation with minimal computational overhead. With a record-breaking 16 KB parameter configuration, SimpleUNet outperforms LBUNet and other lightweight benchmarks across multiple public datasets. The 0.67 MB variant achieves superior efficiency (8.60 GFLOPs) and accuracy, attaining a mean DSC/IoU of 85.76%/75.60% on multi-center breast lesion datasets, surpassing both U-Net and TransUNet. Evaluations on skin lesion datasets (ISIC 2017/2018: mDice 84.86%/88.77%) and endoscopic polyp segmentation (KVASIR-SEG: 86.46%/76.48% mDice/mIoU) confirm consistent dominance over state-of-the-art models. This work demonstrates that extreme model compression need not compromise performance, providing new insights for efficient and accurate medical image segmentation. Codes can be found at https://github.com/Frankyu5666666/SimpleUNet.
Trajectory analysis is not only about obtaining movement data, but it is also of paramount importance in understanding the pattern in which an object moves through space and time, as well as in predicting its next move. Due to the significant interest in the area, data collection has improved substantially, resulting in a large number of features becoming available for training and predicting models. However, this introduces a high-dimensionality-induced feature explosion problem, which reduces the efficiency and interpretability of the data, thereby reducing the accuracy of machine learning models. To overcome this issue, feature selection has become one of the most prevalent tools. Thus, the objective of this paper was to introduce a taxonomy-based feature selection method that categorizes features based on their internal structure. This approach classifies the data into geometric and kinematic features, further categorizing them into curvature, indentation, speed, and acceleration. The comparative analysis indicated that a taxonomy-based approach consistently achieved comparable or superior predictive performance. Furthermore, due to the taxonomic grouping, which reduces combinatorial space, the time taken to select features was drastically reduced. The taxonomy was also used to gain insights into what feature sets each dataset was more sensitive to. Overall, this study provides robust evidence that a taxonomy-based feature selection method can add a layer of interpretability, reduce dimensionality and computational complexity, and contribute to high-level decision-making. It serves as a step toward providing a methodological framework for researchers and practitioners dealing with trajectory datasets and contributing to the broader field of explainable artificial intelligence.
Adversarial attacks, wherein slight inputs are carefully crafted to mislead intelligent models, have attracted increasing attention. However, a critical gap persists between theoretical advancements and practical application, particularly in structured data like network traffic, where interdependent features complicate effective adversarial manipulations. Moreover, ambiguity in current approaches restricts reproducibility and limits progress in this field. Hence, existing defenses often fail to handle evolving adversarial attacks. This paper proposes a novel approach for black-box adversarial attacks, that addresses these limitations. Unlike prior work, which often assumes system access or relies on repeated probing, our method strictly respect black-box constraints, reducing interaction to avoid detection and better reflect real-world scenarios. We present an adaptive feature selection strategy using change-point detection and causality analysis to identify and target sensitive features to perturbations. This lightweight design ensures low computational cost and high deployability. Our comprehensive experiments show the attack's effectiveness in evading detection with minimal interaction, enhancing its adaptability and applicability in real-world scenarios. By advancing the understanding of adversarial attacks in network traffic, this work lays a foundation for developing robust defenses.
An Advanced Persistent Threat (APT) is a multistage, highly sophisticated, and covert form of cyber threat that gains unauthorized access to networks to either steal valuable data or disrupt the targeted network. These threats often remain undetected for extended periods, emphasizing the critical need for early detection in networks to mitigate potential APT consequences. In this work, we propose a feature selection method for developing a lightweight intrusion detection system capable of effectively identifying APTs at the initial compromise stage. Our approach leverages the XGBoost algorithm and Explainable Artificial Intelligence (XAI), specifically utilizing the SHAP (SHapley Additive exPlanations) method for identifying the most relevant features of the initial compromise stage. The results of our proposed method showed the ability to reduce the selected features of the SCVIC-APT-2021 dataset from 77 to just four while maintaining consistent evaluation metrics for the suggested system. The estimated metrics values are 97% precision, 100% recall, and a 98% F1 score. The proposed method not only aids in preventing successful APT consequences but also enhances understanding of APT behavior at early stages.
Kernel-based hypothesis tests offer a flexible, non-parametric tool to detect high-order interactions in multivariate data, beyond pairwise relationships. Yet the scalability of such tests is limited by the computationally demanding permutation schemes used to generate null approximations. Here we introduce a family of permutation-free high-order tests for joint independence and partial factorisations of $d$ variables. Our tests eliminate the need for permutation-based approximations by leveraging V-statistics and a novel cross-centring technique to yield test statistics with a standard normal limiting distribution under the null. We present implementations of the tests and showcase their efficacy and scalability through synthetic datasets. We also show applications inspired by causal discovery and feature selection, which highlight both the importance of high-order interactions in data and the need for efficient computational methods.
Postoperative stroke remains a critical complication in elderly surgical intensive care unit (SICU) patients, contributing to prolonged hospitalization, elevated healthcare costs, and increased mortality. Accurate early risk stratification is essential to enable timely intervention and improve clinical outcomes. We constructed a combined cohort of 19,085 elderly SICU admissions from the MIMIC-III and MIMIC-IV databases and developed an interpretable machine learning (ML) framework to predict in-hospital stroke using clinical data from the first 24 hours of Intensive Care Unit (ICU) stay. The preprocessing pipeline included removal of high-missingness features, iterative Singular Value Decomposition (SVD) imputation, z-score normalization, one-hot encoding, and class imbalance correction via the Adaptive Synthetic Sampling (ADASYN) algorithm. A two-stage feature selection process-combining Recursive Feature Elimination with Cross-Validation (RFECV) and SHapley Additive exPlanations (SHAP)-reduced the initial 80 variables to 20 clinically informative predictors. Among eight ML models evaluated, CatBoost achieved the best performance with an AUROC of 0.8868 (95% CI: 0.8802--0.8937). SHAP analysis and ablation studies identified prior cerebrovascular disease, serum creatinine, and systolic blood pressure as the most influential risk factors. Our results highlight the potential of interpretable ML approaches to support early detection of postoperative stroke and inform decision-making in perioperative critical care.
The accurate prediction of chromosomal instability from the morphology of circulating tumor cells (CTCs) enables real-time detection of CTCs with high metastatic potential in the context of liquid biopsy diagnostics. However, it presents a significant challenge due to the high dimensionality and complexity of single-cell digital pathology data. Here, we introduce the application of Quantum Cognition Machine Learning (QCML), a quantum-inspired computational framework, to estimate morphology-predicted chromosomal instability in CTCs from patients with metastatic breast cancer. QCML leverages quantum mechanical principles to represent data as state vectors in a Hilbert space, enabling context-aware feature modeling, dimensionality reduction, and enhanced generalization without requiring curated feature selection. QCML outperforms conventional machine learning methods when tested on out of sample verification CTCs, achieving higher accuracy in identifying predicted large-scale state transitions (pLST) status from CTC-derived morphology features. These preliminary findings support the application of QCML as a novel machine learning tool with superior performance in high-dimensional, low-sample-size biomedical contexts. QCML enables the simulation of cognition-like learning for the identification of biologically meaningful prediction of chromosomal instability from CTC morphology, offering a novel tool for CTC classification in liquid biopsy.
Cancer is fundamentally a genetic disease characterized by genetic and epigenetic alterations that disrupt normal gene expression, leading to uncontrolled cell growth and metastasis. High-dimensional microarray datasets pose challenges for classification models due to the "small n, large p" problem, resulting in overfitting. This study makes three different key contributions: 1) we propose a machine learning-based approach integrating the Feature Selection Without Re-placement (FSWOR) technique and a projection method to improve classification accuracy. 2) We apply the Kendall statistical test to identify the most significant genes from the brain cancer mi-croarray dataset (GSE50161), reducing the feature space from 54,675 to 20,890 genes.3) we apply machine learning models using k-fold cross validation techniques in which our model incorpo-rates ensemble classifiers with LDA projection and Na\"ive Bayes, achieving a test score of 96%, outperforming existing methods by 9.09%. The results demonstrate the effectiveness of our ap-proach in high-dimensional gene expression analysis, improving classification accuracy while mitigating overfitting. This study contributes to cancer biomarker discovery, offering a robust computational method for analyzing microarray data.
During the wake of the Covid-19 pandemic, the educational paradigm has experienced a major change from in person learning traditional to online platforms. The change of learning convention has impacted the teacher-student especially in non-verbal communication. The absent of non-verbal communication has led to a reliance on verbal feedback which diminished the efficacy of the educational experience. This paper explores the integration of sentiment analysis into learning management systems (LMS) to bridge the student-teacher's gap by offering an alternative approach to interpreting student feedback beyond its verbal context. The research involves data preparation, feature selection, and the development of a deep neural network model encompassing word embedding, LSTM, and attention mechanisms. This model is compared against a logistic regression baseline to evaluate its efficacy in understanding student feedback. The study aims to bridge the communication gap between instructors and students in online learning environments, offering insights into the emotional context of student feedback and ultimately improving the quality of online education.
We introduce FailureSensorIQ, a novel Multi-Choice Question-Answering (MCQA) benchmarking system designed to assess the ability of Large Language Models (LLMs) to reason and understand complex, domain-specific scenarios in Industry 4.0. Unlike traditional QA benchmarks, our system focuses on multiple aspects of reasoning through failure modes, sensor data, and the relationships between them across various industrial assets. Through this work, we envision a paradigm shift where modeling decisions are not only data-driven using statistical tools like correlation analysis and significance tests, but also domain-driven by specialized LLMs which can reason about the key contributors and useful patterns that can be captured with feature engineering. We evaluate the Industrial knowledge of over a dozen LLMs-including GPT-4, Llama, and Mistral-on FailureSensorIQ from different lens using Perturbation-Uncertainty-Complexity analysis, Expert Evaluation study, Asset-Specific Knowledge Gap analysis, ReAct agent using external knowledge-bases. Even though closed-source models with strong reasoning capabilities approach expert-level performance, the comprehensive benchmark reveals a significant drop in performance that is fragile to perturbations, distractions, and inherent knowledge gaps in the models. We also provide a real-world case study of how LLMs can drive the modeling decisions on 3 different failure prediction datasets related to various assets. We release: (a) expert-curated MCQA for various industrial assets, (b) FailureSensorIQ benchmark and Hugging Face leaderboard based on MCQA built from non-textual data found in ISO documents, and (c) LLMFeatureSelector, an LLM-based feature selection scikit-learn pipeline. The software is available at https://github.com/IBM/FailureSensorIQ.
Feature selection is a critical step in high-dimensional classification tasks, particularly under challenging conditions of double imbalance, namely settings characterized by both class imbalance in the response variable and dimensional asymmetry in the data $(n \gg p)$. In such scenarios, traditional feature selection methods applied to Random Forests (RF) often yield unstable or misleading importance rankings. This paper proposes a novel thresholding scheme for feature selection based on minimal depth, which exploits the tree topology to assess variable relevance. Extensive experiments on simulated and real-world datasets demonstrate that the proposed approach produces more parsimonious and accurate subsets of variables compared to conventional minimal depth-based selection. The method provides a practical and interpretable solution for variable selection in RF under double imbalance conditions.