arXiv subjects

Roohallah Alizadehsani

Publications and source records attributed to Roohallah Alizadehsani.

At least 19 recordsLinked to original sources

arXiv2026

Radiomics and artificial Intelligence for thyroid cancer diagnosis: Concepts, challenges, and solutions

Thyroid cancer is an increasing global health concern that requires advanced diagnostic methods. The application of AI and radiomics to thyroid cancer diagnosis is examined in this review. A review of multiple databases was conducted in compliance with PRISMA guidelines until October 2024. A combination of keywords led to the discovery of an English academic publication on thyroid cancer and related subjects. 368 papers were returned from the original search after 112 duplicates were removed. Relevant studies were selected according to predetermined criteria after 176 articles were eliminated based on an examination of their abstract and title. After the comprehensive analysis, an additional six studies were excluded. Among the 42 included studies, radiomics analysis, which incorporates ultrasound (US) images, demonstrated its effectiveness in diagnosing thyroid cancer. Various results were noted, some of the studies presenting new strategies that outperformed the status quo. The literature has emphasized various challenges faced by AI models, including interpretability issues, dataset constraints, and operator dependence. The synthesized findings of the 42 included studies mentioned the need for standardization efforts and prospective multicenter studies to address these concerns. Furthermore, approaches to overcome these obstacles were identified, such as advances in explainable AI technology and personalized medicine techniques. The review focuses on how AI and radiomics could transform the diagnosis and treatment of thyroid cancer. Despite challenges, future research on multidisciplinary cooperation, clinical applicability validation, and algorithm improvement holds the potential to improve patient outcomes and diagnostic precision in the treatment of thyroid cancer.

q-bio.QM↗

arXiv2026

Revolutionizing Genomics with Reinforcement Learning Techniques

In recent years, Reinforcement Learning (RL) has emerged as a powerful tool for solving a wide range of problems, including decision-making and genomics. The exponential growth of raw genomic data over the past two decades has exceeded the capacity of manual analysis, leading to a growing interest in automatic data analysis and processing. RL algorithms are capable of learning from experience with minimal human supervision, making them well-suited for genomic data analysis and interpretation. One of the key benefits of using RL is the reduced cost associated with collecting labeled training data, which is required for supervised learning. While there have been numerous studies examining the applications of Machine Learning (ML) in genomics, this survey focuses exclusively on the use of RL in various genomics research fields, including gene regulatory networks (GRNs), genome assembly, and sequence alignment. We present a comprehensive technical overview of existing studies on the application of RL in genomics, highlighting the strengths and limitations of these approaches. We then discuss potential research directions that are worthy of future exploration, including the development of more sophisticated reward functions as RL heavily depends on the accuracy of the reward function, the integration of RL with other machine learning techniques, and the application of RL to new and emerging areas in genomics research. Finally, we present our findings and conclude by summarizing the current state of the field and the future outlook for RL in genomics.

q-bio.GN↗

arXiv2026

Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability

Immune checkpoint inhibitors (ICIs) have transformed cancer therapy; yet substantial proportion of patients exhibit intrinsic or acquired resistance, making accurate pre-treatment response prediction a critical unmet need. Transcriptomics-based biomarkers derived from bulk and single-cell RNA sequencing (scRNA-seq) offer a promising avenue for capturing tumour-immune interactions, yet the cross-cohort generalisability of existing prediction models remains unclear.We systematically benchmark nine state-of-the-art transcriptomic ICI response predictors, five bulk RNA-seq-based models (COMPASS, IRNet, NetBio, IKCScore, and TNBC-ICI) and four scRNA-seq-based models (PRECISE, DeepGeneX, Tres and scCURE), using publicly available independent datasets unseen during model development. Overall, predictive performance was modest: bulk RNA-seq models performed at or near chance level across most cohorts, while scRNA-seq models showed only marginal improvements. Pathway-level analyses revealed sparse and inconsistent biomarker signals across models. Although scRNA-seq-based predictors converged on immune-related programs such as allograft rejection, bulk RNA-seq-based models exhibited little reproducible overlap. PRECISE and NetBio identified the most coherent immune-related themes, whereas IRNet predominantly captured metabolic pathways weakly aligned with ICI biology. Together, these findings demonstrate the limited cross-cohort robustness and biological consistency of current transcriptomic ICI prediction models, underscoring the need for improved domain adaptation, standardised preprocessing, and biologically grounded model design.

q-bio.GN↗

arXiv2026

A Q-learning-based QoS-aware multipath routing protocol in IoMT-based wireless body area network

The Internet of Medical Things (IoMT) enables intelligent healthcare services but faces challenges such as dynamic topology, energy constraints, and diverse QoS requirements. This paper proposes QQMR, a Q-learning-based QoS-aware multipath routing method for WBANs. QQMR classifies data into three priority levels and employs adaptive multi-level queuing and fuzzy C-means clustering to optimize routing decisions. It maintains separate learning policies for each data type and selects primary and backup paths accordingly. Experimental results demonstrate improved packet delivery ratio and significant reductions in delay, routing overhead, and energy consumption compared to existing methods.

cs.NI↗

arXiv2026

The Role of Natural Language Understanding in Multimodal Video-Based Dengue Diagnosis

Detecting infection-related behavioral changes in mosquitoes from video data is challenging because mosquitoes are small, move rapidly and irregularly, and are affected by environmental factors such as background, lighting, and shadows, which can make reliable feature extraction difficult. In this study, a YOLO- and Contrastive Language-Image Pre-training (CLIP)-based vision-language framework is proposed to classify mosquito flight frames of uninfected and Dengue virus serotype 2 (DENV2)-infected mosquitoes. First, YOLO is used to isolate mosquito regions from the background. Then, visual features extracted from video frames are aligned with biologically meaningful textual prompts in a shared embedding space. The multimodal model was fine-tuned using supervised bidirectional contrastive learning and evaluated through frame-level image-text similarity-based classification. The results show that the proposed method achieved 98.54% accuracy and 99.91% sensitivity at the frame level. After temporal aggregation of frame-level information, the model achieved complete video-level performance. The ablation results showed that fine-tuning and CLIP-based representations were essential for this domain, while the textual branch provided semantic image-text alignment rather than an accuracy advantage over the vision-only model. These findings suggest that vision-language models can provide a useful framework for analyzing infection-related biological behaviors from video data.

cs.AI↗

arXiv2026

A Hybrid Framework of Vision Transformer and Gated Recurrent Unit for Detection of Mosquito Diseases

Identifying dengue virus-infected mosquitoes from control mosquitoes is a major challenge in analyzing mosquito locomotion behavior due to the small size and complexity of the video background. Conventional AI methods are often unable to extract accurate features from video frames and produce erroneous features. In this study, a three-step framework is introduced: first, mosquitoes are identified and the background is removed using the YOLO 11M model, then visual features are extracted using the Vision Transformer (ViT), and finally the videos are classified with a convolutional GRU (ConvGRU) classifier. A comparative analysis of different models, including Recurrent Neural Network (RNN), Long Short-Term Memory (LSTM), Gated Recurrent Unit (GRU), and their convolutional versions showed that the ConvGRU model achieved the best performance; it achieved 88.88% accuracy, 84.45% precision, 82.82% recall, and 82.81% F1 score. These results demonstrate that combining convolutional models with sequence-based networks, especially in the ConvGRU model, allows the simultaneous extraction of precise spatial features and long-term temporal dependencies from mosquito movements. Finally, the proposed framework provides a reliable solution for analyzing mosquito behavior in complex environments.

cs.CV↗

arXiv2026

Towards Self-Evolving Agents: A Human-Inspired Adaptive Exploration-Exploitation Framework for Genetic Network Programming

Recent advancements in agentic AI have increasingly moved toward graph-based methods, driven by the demand for explainable, human-centered, and non-linear reasoning workflows. A prominent example is Genetic Network Programming (GNP), a self-evolving algorithm that utilizes directed graphs to evolve interpretable decision structures for agents. As in most evolutionary algorithms, effectively balancing exploration and exploitation is a key aspect of GNP. However, this trade-off has received limited attention in the GNP literature. To address this gap, we draw inspiration from human developmental patterns, where children prioritize broad experimentation and action over deliberation, with this tendency reversing with age. By mapping transitions between GNP's judgment nodes to deliberation and processing nodes to action, we propose Human-Inspired GNP (HGNP), a novel adaptive framework that dynamically regulates the exploration-exploitation balance throughout the evolutionary process. The method consists of novel adaptive crossover and mutation operators, and a cycle elimination mechanism. HGNP not only improves the evolutionary process but also provides a framework for adjusting the exploration-exploitation balance based on the characteristics of the target environment and its search space. This approach is more effective than tuning via crossover and mutation probabilities in standard GNP. The modifications are general and can be applied to almost all GNP variants. When integrated with standard GNP and two recently introduced GNP variants and evaluated on the Tileworld benchmark, HGNP demonstrated significant performance improvement in agents' strategy. The combination of HGNP with Situation-based GNP (HGNP-SBGNP) achieved the best overall results.

cs.NE↗

arXiv2026

NeuroStrata: An Electroencephalographic Connectivity-Aware Deep Representation Learning Framework for Dynamic Brain Network Analysis of Mental Stress

This study introduces NeuroStrata, a connectivity-aware deep representation learning framework for EEG-based mental stress analysis using Time-Varying Partial Directed Coherence (TV-PDC). Unlike conventional EEG classification approaches based on static features, NeuroStrata models the temporal evolution of frequency-specific directed connectivity across distributed brain regions. EEG signals from the 32-channel SAM 40 dataset recorded during mental arithmetic tasks were used to generate TV-PDC connectivity maps. These maps were processed using pretrained Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) to extract deep connectivity embeddings, which were subsequently classified using lightweight machine learning models. Experimental results demonstrate that beta-band connectivity provides the highest discriminative capability, achieving a peak accuracy of 97.3% using the LAION-CLIP-ViT-L14 backbone with a Support Vector Machine classifier, while alpha-band connectivity exhibits consistently stable performance across model configurations. Connectivity analysis revealed prominent frontal-driven alpha influences and centrally integrated beta connectivity patterns associated with stress-related neural dynamics. Temporal evaluation further indicated that classification performance stabilizes in mid-to-late temporal windows, suggesting progressive consolidation of stress-related connectivity signatures. The proposed framework integrates time-varying effective connectivity modelling with deep representation learning to provide an interpretable and automated approach for EEG-based mental stress analysis.

q-bio.NC↗

arXiv2026

Artificial intelligence applications in Parkinson's disease via retinal imaging

Parkinson's disease (PD) is projected to increase substantially due to population aging, making early diagnosis increasingly important, as timely detection may delay progression and reduce long-term complications. Retinal microvasculature has emerged as a promising anatomical biomarker of neurodegeneration, and when combined with artificial intelligence AI, retinal imaging may provide an advanced, noninvasive, and cost-effective screening strategy for PD. This study evaluated the evidence from the past 35 years regarding the capability of AI to detect early PD-related changes in retinal vascular structure. Five electronic databases including PubMed, Web of Science, Scopus, ScienceDirect, and ProQuest were systematically searched from January 1990 to January 2025. In addition, Annals of Neurology and Frontiers in Neuroscience were hand-searched, and the reference lists of included studies were screened for additional eligible publications. Nineteen studies met the inclusion criteria. Three principal diagnostic AI tasks were identified, including disease classification, retinal vessel segmentation, and PD risk stratification. The best-performing models were ShAMBi-LSTM on the Drishti dataset with 97.2 percent accuracy, 99.5 percent precision, 96.9 percent sensitivity, and an F1 score of 0.981 for classification, nnU-Net with 99.7 percent accuracy, 98.7 percent precision, 98.9 percent sensitivity, 99.8 percent specificity, and a Dice score of 98.9 percent for segmentation, and AlexNet for risk prediction with area under the curve values of 0.77, 0.68, and 0.73 across datasets. Overall, application of AI algorithms to retinal vasculature for detecting early signs of PD and predicting disease severity suggests that integration of AI with retinal biomarkers holds substantial potential for earlier and more accurate detection compared with traditional clinical evaluation alone.

q-bio.TO↗

arXiv2026

UCTECG-Net: Uncertainty-aware Convolution Transformer ECG Network for Arrhythmia Detection

Deep learning has improved automated electrocardiogram (ECG) classification, but limited insight into prediction reliability hinders its use in safety-critical settings. This paper proposes UCTECG-Net, an uncertainty-aware hybrid architecture that combines one-dimensional convolutions and Transformer encoders to process raw ECG signals and their spectrograms jointly. Evaluated on the MIT-BIH Arrhythmia and PTB Diagnostic datasets, UCTECG-Net outperforms LSTM, CNN1D, and Transformer baselines in terms of accuracy, precision, recall and F1 score, achieving up to 98.58% accuracy on MIT-BIH and 99.14% on PTB. To assess predictive reliability, we integrate three uncertainty quantification methods (Monte Carlo Dropout, Deep Ensembles, and Ensemble Monte Carlo Dropout) into all models and analyze their behavior using an uncertainty-aware confusion matrix and derived metrics. The results show that UCTECG-Net, particularly with Ensemble or EMCD, provides more reliable and better-aligned uncertainty estimates than competing architectures, offering a stronger basis for risk-aware ECG decision support.

cs.LG↗

arXiv2026

SSI-GAN: Semi-Supervised Swin-Inspired Generative Adversarial Networks for Neuronal Spike Classification

Mosquitos are the main transmissive agents of arboviral diseases. Manual classification of their neuronal spike patterns is very labor-intensive and expensive. Most available deep learning solutions require fully labeled spike datasets and highly preprocessed neuronal signals. This reduces the feasibility of mass adoption in actual field scenarios. To address the scarcity of labeled data problems, we propose a new Generative Adversarial Network (GAN) architecture that we call the Semi-supervised Swin-Inspired GAN (SSI-GAN). The Swin-inspired, shifted-window discriminator, together with a transformer-based generator, is used to classify neuronal spike trains and, consequently, detect viral neurotropism. We use a multi-head self-attention model in a flat, window-based transformer discriminator that learns to capture sparser high-frequency spike features. Using just 1 to 3% labeled data, SSI-GAN was trained with more than 15 million spike samples collected at five-time post-infection and recording classification into Zika-infected, dengue-infected, or uninfected categories. Hyperparameters were optimized using the Bayesian Optuna framework, and performance for robustness was validated under fivefold Monte Carlo cross-validation. SSI-GAN reached 99.93% classification accuracy on the third day post-infection with only 3% labeled data. It maintained high accuracy across all stages of infection with just 1% supervision. This shows a 97-99% reduction in manual labeling effort relative to standard supervised approaches at the same performance level. The shifted-window transformer design proposed here beat all baselines by a wide margin and set new best marks in spike-based neuronal infection classification.

cs.LG↗

arXiv2025

Functional Classification of Spiking Signal Data Using Artificial Intelligence Techniques: A Review

Human brain neuron activities are incredibly significant nowadays. Neuronal behavior is assessed by analyzing signal data such as electroencephalography (EEG), which can offer scientists valuable information about diseases and human-computer interaction. One of the difficulties researchers confront while evaluating these signals is the existence of large volumes of spike data. Spikes are some considerable parts of signal data that can happen as a consequence of vital biomarkers or physical issues such as electrode movements. Hence, distinguishing types of spikes is important. From this spot, the spike classification concept commences. Previously, researchers classified spikes manually. The manual classification was not precise enough as it involves extensive analysis. Consequently, Artificial Intelligence (AI) was introduced into neuroscience to assist clinicians in classifying spikes correctly. This review discusses the importance and use of AI in spike classification, focusing on the recognition of neural activity noises. The task is divided into three main components: preprocessing, classification, and evaluation. Existing methods are introduced and their importance is determined. The review also highlights the need for more efficient algorithms. The primary goal is to provide a perspective on spike classification for future research and provide a comprehensive understanding of the methodologies and issues involved. The review organizes materials in the spike classification field for future studies. In this work, numerous studies were extracted from different databases. The PRISMA-related research guidelines were then used to choose papers. Then, research studies based on spike classification using machine learning and deep learning approaches with effective preprocessing were selected.

cs.AI↗

arXiv2025

Rewiring Human Brain Networks via Lightweight Dynamic Connectivity Framework: An EEG-Based Stress Validation

In recent years, Electroencephalographic analysis has gained prominence in stress research when combined with AI and Machine Learning models for validation. In this study, a lightweight dynamic brain connectivity framework based on Time Varying Directed Transfer Function is proposed, where TV DTF features were validated through ML based stress classification. TV DTF estimates the directional information flow between brain regions across distinct EEG frequency bands, thereby capturing temporal and causal influences that are often overlooked by static functional connectivity measures. EEG recordings from the 32 channel SAM 40 dataset were employed, focusing on mental arithmetic task trials. The dynamic EEG-based TV-DTF features were validated through ML classifiers such as Support Vector Machine, Random Forest, Gradient Boosting, Adaptive Boosting, and Extreme Gradient Boosting. Experimental results show that alpha-TV-DTF provided the strongest discriminative power, with SVM achieving 89.73% accuracy in 3-class classification and with XGBoost achieving 93.69% accuracy in 2 class classification. Relative to absolute power and phase locking based functional connectivity features, alpha TV DTF and beta TV DTF achieved higher performance across the ML models, highlighting the advantages of dynamic over static measures. Feature importance analysis further highlighted dominant long-range frontal parietal and frontal occipital informational influences, emphasizing the regulatory role of frontal regions under stress. These findings validate the lightweight TV-DTF as a robust framework, revealing spatiotemporal brain dynamics and directional influences across different stress levels.

q-bio.NC↗

arXiv2025

A Lightweight and Robust Framework for Real-Time Colorectal Polyp Detection Using LOF-Based Preprocessing and YOLO-v11n

Objectives: Timely and accurate detection of colorectal polyps plays a crucial role in diagnosing and preventing colorectal cancer, a major cause of mortality worldwide. This study introduces a new, lightweight, and efficient framework for polyp detection that combines the Local Outlier Factor (LOF) algorithm for filtering noisy data with the YOLO-v11n deep learning model. Study design: An experimental study leveraging deep learning and outlier removal techniques across multiple public datasets. Methods: The proposed approach was tested on five diverse and publicly available datasets: CVC-ColonDB, CVC-ClinicDB, Kvasir-SEG, ETIS, and EndoScene. Since these datasets originally lacked bounding box annotations, we converted their segmentation masks into suitable detection labels. To enhance the robustness and generalizability of our model, we apply 5-fold cross-validation and remove anomalous samples using the LOF method configured with 30 neighbors and a contamination ratio of 5%. Cleaned data are then fed into YOLO-v11n, a fast and resource-efficient object detection architecture optimized for real-time applications. We train the model using a combination of modern augmentation strategies to improve detection accuracy under diverse conditions. Results: Our approach significantly improves polyp localization performance, achieving a precision of 95.83%, recall of 91.85%, F1-score of 93.48%, mAP@0.5 of 96.48%, and mAP@0.5:0.95 of 77.75%. Compared to previous YOLO-based methods, our model demonstrates enhanced accuracy and efficiency. Conclusions: These results suggest that the proposed method is well-suited for real-time colonoscopy support in clinical settings. Overall, the study underscores how crucial data preprocessing and model efficiency are when designing effective AI systems for medical imaging.

cs.CV↗

arXiv2025

Exploring the Relationships Between Physiological Signals During Automated Fatigue Detection

Fatigue detection using physiological signals is critical in domains such as transportation, healthcare, and performance monitoring. While most studies focus on single modalities, this work examines statistical relationships between signal pairs to improve classification robustness. Using the DROZY dataset, we extracted features from ECG, EMG, EOG, and EEG across 15 signal combinations and evaluated them with Decision Tree, Random Forest, Logistic Regression, and XGBoost. Results show that XGBoost with the EMG EEG combination achieved the best performance. SHAP analysis highlighted ECG EOG correlation as a key feature, and multi signal models consistently outperformed single signal ones. These findings demonstrate that feature level fusion of physiological signals enhances accuracy, interpretability, and practical applicability of fatigue monitoring systems.

cs.LG↗

arXiv2025

No-Reference Image Contrast Assessment with Customized EfficientNet-B0

Image contrast was a fundamental factor in visual perception and played a vital role in overall image quality. However, most no reference image quality assessment NR IQA models struggled to accurately evaluate contrast distortions under diverse real world conditions. In this study, we proposed a deep learning based framework for blind contrast quality assessment by customizing and fine-tuning three pre trained architectures, EfficientNet B0, ResNet18, and MobileNetV2, for perceptual Mean Opinion Score, along with an additional model built on a Siamese network, which indicated a limited ability to capture perceptual contrast distortions. Each model is modified with a contrast-aware regression head and trained end to end using targeted data augmentations on two benchmark datasets, CID2013 and CCID2014, containing synthetic and authentic contrast distortions. Performance is evaluated using Pearson Linear Correlation Coefficient and Spearman Rank Order Correlation Coefficient, which assess the alignment between predicted and human rated scores. Among these three models, our customized EfficientNet B0 model achieved state-of-the-art performance with PLCC = 0.9286 and SRCC = 0.9178 on CCID2014 and PLCC = 0.9581 and SRCC = 0.9369 on CID2013, surpassing traditional methods and outperforming other deep baselines. These results highlighted the models robustness and effectiveness in capturing perceptual contrast distortion. Overall, the proposed method demonstrated that contrast aware adaptation of lightweight pre trained networks can yield a high performing, scalable solution for no reference contrast quality assessment suitable for real time and resource constrained applications.

cs.CV↗

arXiv2025

A Quad-Step Approach to Uncertainty-Aware Deep Learning for Skin Cancer Classification

Accurate skin cancer diagnosis is vital for early treatment and improved patient outcomes. Deep learning (DL) models have shown promise in automating skin cancer classification, yet challenges remain due to data scarcity and limited uncertainty awareness. This study presents a comprehensive evaluation of DL-based skin lesion classification with transfer learning and uncertainty quantification (UQ) on the HAM10000 dataset. We benchmark several pre-trained feature extractors -- including CLIP variants, ResNet50, DenseNet121, VGG16, and EfficientNet-V2-Large -- combined with traditional classifiers such as SVM, XGBoost, and logistic regression. Multiple principal component analysis (PCA) settings (64, 128, 256, 512) are explored, with LAION CLIP ViT-H/14 and ViT-L/14 at PCA-256 achieving the strongest baseline results. In the UQ phase, Monte Carlo Dropout (MCD), Ensemble, and Ensemble Monte Carlo Dropout (EMCD) are applied and evaluated using uncertainty-aware metrics (UAcc, USen, USpe, UPre). Ensemble methods with PCA-256 provide the best balance between accuracy and reliability. Further improvements are obtained through feature fusion of top-performing extractors at PCA-256. Finally, we propose a feature-fusion based model trained with a predictive entropy (PE) loss function, which outperforms all prior configurations across both standard and uncertainty-aware evaluations, advancing trustworthy DL-based skin cancer diagnosis.

cs.CV↗

arXiv2025

Enhancing Monte Carlo Dropout Performance for Uncertainty Quantification

Knowing the uncertainty associated with the output of a deep neural network is of paramount importance in making trustworthy decisions, particularly in high-stakes fields like medical diagnosis and autonomous systems. Monte Carlo Dropout (MCD) is a widely used method for uncertainty quantification, as it can be easily integrated into various deep architectures. However, conventional MCD often struggles with providing well-calibrated uncertainty estimates. To address this, we introduce innovative frameworks that enhances MCD by integrating different search solutions namely Grey Wolf Optimizer (GWO), Bayesian Optimization (BO), and Particle Swarm Optimization (PSO) as well as an uncertainty-aware loss function, thereby improving the reliability of uncertainty quantification. We conduct comprehensive experiments using different backbones, namely DenseNet121, ResNet50, and VGG16, on various datasets, including Cats vs. Dogs, Myocarditis, Wisconsin, and a synthetic dataset (Circles). Our proposed algorithm outperforms the MCD baseline by 2-3% on average in terms of both conventional accuracy and uncertainty accuracy while achieving significantly better calibration. These results highlight the potential of our approach to enhance the trustworthiness of deep learning models in safety-critical applications.

cs.CV↗