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.
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.
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.
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.
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.
Unsupervised feature selection is critical for improving clustering performance in high-dimensional data, where irrelevant features can obscure meaningful structure. In this work, we introduce the Minkowski weighted $k$-means++, a novel initialisation strategy for the Minkowski Weighted $k$-means. Our initialisation selects centroids probabilistically using feature relevance estimates derived from the data itself. Building on this, we propose two new feature selection algorithms, FS-MWK++, which aggregates feature weights across a range of Minkowski exponents to identify stable and informative features, and SFS-MWK++, a scalable variant based on subsampling. We support our approach with a theoretical guarantee under mild assumptions and extensive experiments showing that our methods consistently outperform existing alternatives. Our software can be found at https://github.com/xzhang4-ops1/FSMWK.
Graph-based learning provides a powerful framework for modeling complex relational structures; however, its application within the domain of wireless security remains significantly underexplored. In this work, we introduce the first application of graph-based learning for jamming source localization, addressing the imminent threat of jamming attacks in wireless networks. Unlike geometric optimization techniques that struggle under environmental uncertainties and dense interference, we reformulate the localization as an inductive graph regression task. Our approach integrates structured node representations that encode local and global signal aggregation, ensuring spatial coherence and adaptive signal fusion. To enhance robustness, we incorporate an attention-based \ac{GNN} that adaptively refines neighborhood influence and introduces a confidence-guided estimation mechanism that dynamically balances learned predictions with domain-informed priors. We evaluate our approach under complex \ac{RF} environments with various sampling densities, network topologies, jammer characteristics, and signal propagation conditions, conducting comprehensive ablation studies on graph construction, feature selection, and pooling strategies. Results demonstrate that our novel graph-based learning framework significantly outperforms established localization baselines, particularly in challenging scenarios with sparse and obfuscated signal information. Our code is available at https://github.com/tiiuae/gnn-jamming-source-localization.
Gene selection in high-dimensional genomic data is essential for understanding disease mechanisms and improving therapeutic outcomes. Traditional feature selection methods effectively identify predictive genes but often ignore complex biological pathways and regulatory networks, leading to unstable and biologically irrelevant signatures. Prior approaches, such as Lasso-based methods and statistical filtering, either focus solely on individual gene-outcome associations or fail to capture pathway-level interactions, presenting a key challenge: how to integrate biological pathway knowledge while maintaining statistical rigor in gene selection? To address this gap, we propose a novel two-stage framework that integrates statistical selection with biological pathway knowledge using multi-agent reinforcement learning (MARL). First, we introduce a pathway-guided pre-filtering strategy that leverages multiple statistical methods alongside KEGG pathway information for initial dimensionality reduction. Next, for refined selection, we model genes as collaborative agents in a MARL framework, where each agent optimizes both predictive power and biological relevance. Our framework incorporates pathway knowledge through Graph Neural Network-based state representations, a reward mechanism combining prediction performance with gene centrality and pathway coverage, and collaborative learning strategies using shared memory and a centralized critic component. Extensive experiments on multiple gene expression datasets demonstrate that our approach significantly improves both prediction accuracy and biological interpretability compared to traditional methods.
Infrared small target detection (ISTD) is vital for long-range surveillance in military, maritime, and early warning applications. ISTD is challenged by targets occupying less than 0.15% of the image and low distinguishability from complex backgrounds. Existing deep learning methods often suffer from information loss during downsampling and inefficient global context modeling. This paper presents SAMamba, a novel framework integrating SAM2's hierarchical feature learning with Mamba's selective sequence modeling. Key innovations include: (1) A Feature Selection Adapter (FS-Adapter) for efficient natural-to-infrared domain adaptation via dual-stage selection (token-level with a learnable task embedding and channel-wise adaptive transformations); (2) A Cross-Channel State-Space Interaction (CSI) module for efficient global context modeling with linear complexity using selective state space modeling; and (3) A Detail-Preserving Contextual Fusion (DPCF) module that adaptively combines multi-scale features with a gating mechanism to balance high-resolution and low-resolution feature contributions. SAMamba addresses core ISTD challenges by bridging the domain gap, maintaining fine-grained details, and efficiently modeling long-range dependencies. Experiments on NUAA-SIRST, IRSTD-1k, and NUDT-SIRST datasets show SAMamba significantly outperforms state-of-the-art methods, especially in challenging scenarios with heterogeneous backgrounds and varying target scales. Code: https://github.com/zhengshuchen/SAMamba.
Speculative decoding (SD) has emerged as a powerful method for accelerating autoregressive generation in large language models (LLMs), yet its integration into vision-language models (VLMs) remains underexplored. We introduce DREAM, a novel speculative decoding framework tailored for VLMs that combines three key innovations: (1) a cross-attention-based mechanism to inject intermediate features from the target model into the draft model for improved alignment, (2) adaptive intermediate feature selection based on attention entropy to guide efficient draft model training, and (3) visual token compression to reduce draft model latency. DREAM enables efficient, accurate, and parallel multimodal decoding with significant throughput improvement. Experiments across a diverse set of recent popular VLMs, including LLaVA, Pixtral, SmolVLM and Gemma3, demonstrate up to 3.6x speedup over conventional decoding and significantly outperform prior SD baselines in both inference throughput and speculative draft acceptance length across a broad range of multimodal benchmarks. The code is publicly available at: https://github.com/SAI-Lab-NYU/DREAM.git
Ransomware remains a critical threat to cybersecurity, yet publicly available datasets for training machine learning-based ransomware detection models are scarce and often have limited sample size, diversity, and reproducibility. In this paper, we introduce MLRan, a behavioural ransomware dataset, comprising over 4,800 samples across 64 ransomware families and a balanced set of goodware samples. The samples span from 2006 to 2024 and encompass the four major types of ransomware: locker, crypto, ransomware-as-a-service, and modern variants. We also propose guidelines (GUIDE-MLRan), inspired by previous work, for constructing high-quality behavioural ransomware datasets, which informed the curation of our dataset. We evaluated the ransomware detection performance of several machine learning (ML) models using MLRan. For this purpose, we performed feature selection by conducting mutual information filtering to reduce the initial 6.4 million features to 24,162, followed by recursive feature elimination, yielding 483 highly informative features. The ML models achieved an accuracy, precision and recall of up to 98.7%, 98.9%, 98.5%, respectively. Using SHAP and LIME, we identified critical indicators of malicious behaviour, including registry tampering, strings, and API misuse. The dataset and source code for feature extraction, selection, ML training, and evaluation are available publicly to support replicability and encourage future research, which can be found at https://github.com/faithfulco/mlran.
Respiratory viral infections pose a global health burden, yet the cellular immune responses driving protection or pathology remain unclear. Natural infection cohorts often lack pre-exposure baseline data and structured temporal sampling. In contrast, inoculation and vaccination trials generate insightful longitudinal transcriptomic data. However, the scattering of these datasets across platforms, along with inconsistent metadata and preprocessing procedure, hinders AI-driven discovery. To address these challenges, we developed the Human Respiratory Viral Immunization LongitudinAl Gene Expression (HR-VILAGE-3K3M) repository: an AI-ready, rigorously curated dataset that integrates 14,136 RNA-seq profiles from 3,178 subjects across 66 studies encompassing over 2.56 million cells. Spanning vaccination, inoculation, and mixed exposures, the dataset includes microarray, bulk RNA-seq, and single-cell RNA-seq from whole blood, PBMCs, and nasal swabs, sourced from GEO, ImmPort, and ArrayExpress. We harmonized subject-level metadata, standardized outcome measures, applied unified preprocessing pipelines with rigorous quality control, and aligned all data to official gene symbols. To demonstrate the utility of HR-VILAGE-3K3M, we performed predictive modeling of vaccine responders and evaluated batch-effect correction methods. Beyond these initial demonstrations, it supports diverse systems immunology applications and benchmarking of feature selection and transfer learning algorithms. Its scale and heterogeneity also make it ideal for pretraining foundation models of the human immune response and for advancing multimodal learning frameworks. As the largest longitudinal transcriptomic resource for human respiratory viral immunization, it provides an accessible platform for reproducible AI-driven research, accelerating systems immunology and vaccine development against emerging viral threats.
This paper explores Uncertainty Quantification (UQ) in SVM predictions, particularly for regression and forecasting tasks. Unlike the Neural Network, the SVM solutions are typically more stable, sparse, optimal and interpretable. However, there are only few literature which addresses the UQ in SVM prediction. At first, we provide a comprehensive summary of existing Prediction Interval (PI) estimation and probabilistic forecasting methods developed in the SVM framework and evaluate them against the key properties expected from an ideal PI model. We find that none of the existing SVM PI models achieves a sparse solution. To introduce sparsity in SVM model, we propose the Sparse Support Vector Quantile Regression (SSVQR) model, which constructs PIs and probabilistic forecasts by solving a pair of linear programs. Further, we develop a feature selection algorithm for PI estimation using SSVQR that effectively eliminates a significant number of features while improving PI quality in case of high-dimensional dataset. Finally we extend the SVM models in Conformal Regression setting for obtaining more stable prediction set with finite test set guarantees. Extensive experiments on artificial, real-world benchmark datasets compare the different characteristics of both existing and proposed SVM-based PI estimation methods and also highlight the advantages of the feature selection in PI estimation. Furthermore, we compare both, the existing and proposed SVM-based PI estimation models, with modern deep learning models for probabilistic forecasting tasks on benchmark datasets. Furthermore, SVM models show comparable or superior performance to modern complex deep learning models for probabilistic forecasting task in our experiments.
Parkinson's disease (PD) poses a growing global health challenge, with Bangladesh experiencing a notable rise in PD-related mortality. Early detection of PD remains particularly challenging in resource-constrained settings, where voice-based analysis has emerged as a promising non-invasive and cost-effective alternative. However, existing studies predominantly focus on English or other major languages; notably, no voice dataset for PD exists for Bengali - posing a significant barrier to culturally inclusive and accessible healthcare solutions. Moreover, most prior studies employed only a narrow set of acoustic features, with limited or no hyperparameter tuning and feature selection strategies, and little attention to model explainability. This restricts the development of a robust and generalizable machine learning model. To address this gap, we present BenSparX, the first Bengali conversational speech dataset for PD detection, along with a robust and explainable machine learning framework tailored for early diagnosis. The proposed framework incorporates diverse acoustic feature categories, systematic feature selection methods, and state-of-the-art machine learning algorithms with extensive hyperparameter optimization. Furthermore, to enhance interpretability and trust in model predictions, the framework incorporates SHAP (SHapley Additive exPlanations) analysis to quantify the contribution of individual acoustic features toward PD detection. Our framework achieves state-of-the-art performance, yielding an accuracy of 95.77%, F1 score of 95.57%, and AUC-ROC of 0.982. We further externally validated our approach by applying the framework to existing PD datasets in other languages, where it consistently outperforms state-of-the-art approaches. To facilitate further research and reproducibility, the dataset has been made publicly available at https://github.com/Riad071/BenSParX.
Pretrained vision-language models (VLMs), e.g., CLIP, demonstrate impressive zero-shot capabilities on downstream tasks. Prior research highlights the crucial role of visual augmentation techniques, like random cropping, in alignment with fine-grained class descriptions generated by large language models (LLMs), significantly enhancing zero-shot performance by incorporating multi-view information. However, the inherent randomness of these augmentations can inevitably introduce background artifacts and cause models to overly focus on local details, compromising global semantic understanding. To address these issues, we propose an \textbf{A}ttention-\textbf{B}ased \textbf{S}election (\textbf{ABS}) method from local details to global context, which applies attention-guided cropping in both raw images and feature space, supplement global semantic information through strategic feature selection. Additionally, we introduce a soft matching technique to effectively filter LLM descriptions for better alignment. \textbf{ABS} achieves state-of-the-art performance on out-of-distribution generalization and zero-shot classification tasks. Notably, \textbf{ABS} is training-free and even rivals few-shot and test-time adaptation methods. Our code is available at \href{https://github.com/BIT-DA/ABS}{\textcolor{darkgreen}{https://github.com/BIT-DA/ABS}}.
Chemical language models (CLMs), inspired by natural language processing (NLP), have recently emerged as powerful tools for various cheminformatics tasks such as molecular property prediction and molecule generation. The simplified molecular input line entry system (SMILES) is commonly employed in CLMs for representing molecular structures. However, despite attempts at standardization through Canonical SMILES, significant representational inconsistencies remain due to variations in canonicalization methods (grammatical inconsistencies) and incomplete stereochemical annotations (stereochemical inconsistencies). This study systematically investigates the prevalence and impact of these inconsistencies. Our literature review reveals that nearly half (45.4%) of the studies employing CLMs omit explicit mention of SMILES canonicalization, potentially impairing reproducibility. Through quantitative analysis of publicly available datasets, we observed substantial variability in SMILES representations, particularly highlighting significant gaps in stereochemical information approximately 50% of enantiomers and 30% of geometric isomers lacked complete annotations. Empirical evaluations using an encoder-decoder CLM demonstrated that representational variations significantly affect latent molecular representations, notably reducing translation accuracy. Interestingly, these variations minimally impacted downstream property prediction tasks, likely due to robust feature selection driven by label information. Furthermore, explicit manipulation of stereochemical annotations confirmed their crucial role in accurate cyclic structure reconstruction.
The fusion technique is the key to the multimodal emotion recognition task. Recently, cross-modal attention-based fusion methods have demonstrated high performance and strong robustness. However, cross-modal attention suffers from redundant features and does not capture complementary features well. We find that it is not necessary to use the entire information of one modality to reinforce the other during cross-modal interaction, and the features that can reinforce a modality may contain only a part of it. To this end, we design an innovative Transformer-based Adaptive Cross-modal Fusion Network (TACFN). Specifically, for the redundant features, we make one modality perform intra-modal feature selection through a self-attention mechanism, so that the selected features can adaptively and efficiently interact with another modality. To better capture the complementary information between the modalities, we obtain the fused weight vector by splicing and use the weight vector to achieve feature reinforcement of the modalities. We apply TCAFN to the RAVDESS and IEMOCAP datasets. For fair comparison, we use the same unimodal representations to validate the effectiveness of the proposed fusion method. The experimental results show that TACFN brings a significant performance improvement compared to other methods and reaches the state-of-the-art. All code and models could be accessed from https://github.com/shuzihuaiyu/TACFN.
Understanding the decision-making process of machine learning models provides valuable insights into the task, the data, and the reasons behind a model's failures. In this work, we propose a method that performs inherently interpretable predictions through the instance-wise sparsification of input images. To align the sparsification with human perception, we learn the masking in the space of semantically meaningful pixel regions rather than on pixel-level. Additionally, we introduce an explicit way to dynamically determine the required level of sparsity for each instance. We show empirically on semi-synthetic and natural image datasets that our inherently interpretable classifier produces more meaningful, human-understandable predictions than state-of-the-art benchmarks.
Object localization in satellite imagery is particularly challenging due to the high variability of objects, low spatial resolution, and interference from noise and dominant features such as clouds and city lights. In this research, we focus on three satellite datasets: upper atmospheric Gravity Waves (GW), mesospheric Bores (Bore), and Ocean Eddies (OE), each presenting its own unique challenges. These challenges include the variability in the scale and appearance of the main object patterns, where the size, shape, and feature extent of objects of interest can differ significantly. To address these challenges, we introduce YOLO-DCAP, a novel enhanced version of YOLOv5 designed to improve object localization in these complex scenarios. YOLO-DCAP incorporates a Multi-scale Dilated Residual Convolution (MDRC) block to capture multi-scale features at scale with varying dilation rates, and an Attention-aided Spatial Pooling (AaSP) module to focus on the global relevant spatial regions, enhancing feature selection. These structural improvements help to better localize objects in satellite imagery. Experimental results demonstrate that YOLO-DCAP significantly outperforms both the YOLO base model and state-of-the-art approaches, achieving an average improvement of 20.95% in mAP50 and 32.23% in IoU over the base model, and 7.35% and 9.84% respectively over state-of-the-art alternatives, consistently across all three satellite datasets. These consistent gains across all three satellite datasets highlight the robustness and generalizability of the proposed approach. Our code is open sourced at https://github.com/AI-4-atmosphere-remote-sensing/satellite-object-localization.