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Search Results (2,680)

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14 pages, 1612 KiB  
Article
Multi-Label Conditioned Diffusion for Cardiac MR Image Augmentation and Segmentation
by Jianyang Li, Xin Ma and Yonghong Shi
Bioengineering 2025, 12(8), 812; https://doi.org/10.3390/bioengineering12080812 - 28 Jul 2025
Abstract
Accurate segmentation of cardiac MR images using deep neural networks is crucial for cardiac disease diagnosis and treatment planning, as it provides quantitative insights into heart anatomy and function. However, achieving high segmentation accuracy relies heavily on extensive, precisely annotated datasets, which are [...] Read more.
Accurate segmentation of cardiac MR images using deep neural networks is crucial for cardiac disease diagnosis and treatment planning, as it provides quantitative insights into heart anatomy and function. However, achieving high segmentation accuracy relies heavily on extensive, precisely annotated datasets, which are costly and time-consuming to obtain. This study addresses this challenge by proposing a novel data augmentation framework based on a condition-guided diffusion generative model, controlled by multiple cardiac labels. The framework aims to expand annotated cardiac MR datasets and significantly improve the performance of downstream cardiac segmentation tasks. The proposed generative data augmentation framework operates in two stages. First, a Label Diffusion Module is trained to unconditionally generate realistic multi-category spatial masks (encompassing regions such as the left ventricle, interventricular septum, and right ventricle) conforming to anatomical prior probabilities derived from noise. Second, cardiac MR images are generated conditioned on these semantic masks, ensuring a precise one-to-one mapping between synthetic labels and images through the integration of a spatially-adaptive normalization (SPADE) module for structural constraint during conditional model training. The effectiveness of this augmentation strategy is demonstrated using the U-Net model for segmentation on the enhanced 2D cardiac image dataset derived from the M&M Challenge. Results indicate that the proposed method effectively increases dataset sample numbers and significantly improves cardiac segmentation accuracy, achieving a 5% to 10% higher Dice Similarity Coefficient (DSC) compared to traditional data augmentation methods. Experiments further reveal a strong correlation between image generation quality and augmentation effectiveness. This framework offers a robust solution for data scarcity in cardiac image analysis, directly benefiting clinical applications. Full article
20 pages, 9953 KiB  
Article
Dual-Branch Occlusion-Aware Semantic Part-Features Extraction Network for Occluded Person Re-Identification
by Bo Sun, Yulong Zhang, Jianan Wang and Chunmao Jiang
Mathematics 2025, 13(15), 2432; https://doi.org/10.3390/math13152432 - 28 Jul 2025
Abstract
Occlusion remains a major challenge in person re-identification, as it often leads to incomplete or misleading visual cues. To address this issue, we propose a dual-branch occlusion-aware network (DOAN), which explicitly and implicitly enhances the model’s capability to perceive and handle occlusions. The [...] Read more.
Occlusion remains a major challenge in person re-identification, as it often leads to incomplete or misleading visual cues. To address this issue, we propose a dual-branch occlusion-aware network (DOAN), which explicitly and implicitly enhances the model’s capability to perceive and handle occlusions. The proposed DOAN framework comprises two synergistic branches. In the first branch, we introduce an Occlusion-Aware Semantic Attention (OASA) module to extract semantic part features, incorporating a parallel channel and spatial attention (PCSA) block to precisely distinguish between pedestrian body regions and occlusion noise. We also generate occlusion-aware parsing labels by combining external human parsing annotations with occluder masks, providing structural supervision to guide the model in focusing on visible regions. In the second branch, we develop an occlusion-aware recovery (OAR) module that reconstructs occluded pedestrians to their original, unoccluded form, enabling the model to recover missing semantic information and enhance occlusion robustness. Extensive experiments on occluded, partial, and holistic benchmark datasets demonstrate that DOAN consistently outperforms existing state-of-the-art methods. Full article
42 pages, 1131 KiB  
Article
A Hybrid Human-AI Model for Enhanced Automated Vulnerability Scoring in Modern Vehicle Sensor Systems
by Mohamed Sayed Farghaly, Heba Kamal Aslan and Islam Tharwat Abdel Halim
Future Internet 2025, 17(8), 339; https://doi.org/10.3390/fi17080339 - 28 Jul 2025
Abstract
Modern vehicles are rapidly transforming into interconnected cyber–physical systems that rely on advanced sensor technologies and pervasive connectivity to support autonomous functionality. Yet, despite this evolution, standardized methods for quantifying cybersecurity vulnerabilities across critical automotive components remain scarce. This paper introduces a novel [...] Read more.
Modern vehicles are rapidly transforming into interconnected cyber–physical systems that rely on advanced sensor technologies and pervasive connectivity to support autonomous functionality. Yet, despite this evolution, standardized methods for quantifying cybersecurity vulnerabilities across critical automotive components remain scarce. This paper introduces a novel hybrid model that integrates expert-driven insights with generative AI tools to adapt and extend the Common Vulnerability Scoring System (CVSS) specifically for autonomous vehicle sensor systems. Following a three-phase methodology, the study conducted a systematic review of 16 peer-reviewed sources (2018–2024), applied CVSS version 4.0 scoring to 15 representative attack types, and evaluated four free source generative AI models—ChatGPT, DeepSeek, Gemini, and Copilot—on a dataset of 117 annotated automotive-related vulnerabilities. Expert validation from 10 domain professionals reveals that Light Detection and Ranging (LiDAR) sensors are the most vulnerable (9 distinct attack types), followed by Radio Detection And Ranging (radar) (8) and ultrasonic (6). Network-based attacks dominate (104 of 117 cases), with 92.3% of the dataset exhibiting low attack complexity and 82.9% requiring no user interaction. The most severe attack vectors, as scored by experts using CVSS, include eavesdropping (7.19), Sybil attacks (6.76), and replay attacks (6.35). Evaluation of large language models (LLMs) showed that DeepSeek achieved an F1 score of 99.07% on network-based attacks, while all models struggled with minority classes such as high complexity (e.g., ChatGPT F1 = 0%, Gemini F1 = 15.38%). The findings highlight the potential of integrating expert insight with AI efficiency to deliver more scalable and accurate vulnerability assessments for modern vehicular systems.This study offers actionable insights for vehicle manufacturers and cybersecurity practitioners, aiming to inform strategic efforts to fortify sensor integrity, optimize network resilience, and ultimately enhance the cybersecurity posture of next-generation autonomous vehicles. Full article
28 pages, 5373 KiB  
Article
Transfer Learning Based on Multi-Branch Architecture Feature Extractor for Airborne LiDAR Point Cloud Semantic Segmentation with Few Samples
by Jialin Yuan, Hongchao Ma, Liang Zhang, Jiwei Deng, Wenjun Luo, Ke Liu and Zhan Cai
Remote Sens. 2025, 17(15), 2618; https://doi.org/10.3390/rs17152618 - 28 Jul 2025
Abstract
The existing deep learning-based Airborne Laser Scanning (ALS) point cloud semantic segmentation methods require a large amount of labeled data for training, which is not always feasible in practice. Insufficient training data may lead to over-fitting. To address this issue, we propose a [...] Read more.
The existing deep learning-based Airborne Laser Scanning (ALS) point cloud semantic segmentation methods require a large amount of labeled data for training, which is not always feasible in practice. Insufficient training data may lead to over-fitting. To address this issue, we propose a novel Multi-branch Feature Extractor (MFE) and a three-stage transfer learning strategy that conducts pre-training on multi-source ALS data and transfers the model to another dataset with few samples, thereby improving the model’s generalization ability and reducing the need for manual annotation. The proposed MFE is based on a novel multi-branch architecture integrating Neighborhood Embedding Block (NEB) and Point Transformer Block (PTB); it aims to extract heterogeneous features (e.g., geometric features, reflectance features, and internal structural features) by leveraging the parameters contained in ALS point clouds. To address model transfer, a three-stage strategy was developed: (1) A pre-training subtask was employed to pre-train the proposed MFE if the source domain consisted of multi-source ALS data, overcoming parameter differences. (2) A domain adaptation subtask was employed to align cross-domain feature distributions between source and target domains. (3) An incremental learning subtask was proposed for continuous learning of novel categories in the target domain, avoiding catastrophic forgetting. Experiments conducted on the source domain consisted of DALES and Dublin datasets and the target domain consists of ISPRS benchmark dataset. The experimental results show that the proposed method achieved the highest OA of 85.5% and an average F1 score of 74.0% using only 10% training samples, which means the proposed framework can reduce manual annotation by 90% while keeping competitive classification accuracy. Full article
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18 pages, 7213 KiB  
Article
DFCNet: Dual-Stage Frequency-Domain Calibration Network for Low-Light Image Enhancement
by Hui Zhou, Jun Li, Yaming Mao, Lu Liu and Yiyang Lu
J. Imaging 2025, 11(8), 253; https://doi.org/10.3390/jimaging11080253 - 28 Jul 2025
Abstract
Imaging technologies are widely used in surveillance, medical diagnostics, and other critical applications. However, under low-light conditions, captured images often suffer from insufficient brightness, blurred details, and excessive noise, degrading quality and hindering downstream tasks. Conventional low-light image enhancement (LLIE) methods not only [...] Read more.
Imaging technologies are widely used in surveillance, medical diagnostics, and other critical applications. However, under low-light conditions, captured images often suffer from insufficient brightness, blurred details, and excessive noise, degrading quality and hindering downstream tasks. Conventional low-light image enhancement (LLIE) methods not only require annotated data but also often involve heavy models with high computational costs, making them unsuitable for real-time processing. To tackle these challenges, a lightweight and unsupervised LLIE method utilizing a dual-stage frequency-domain calibration network (DFCNet) is proposed. In the first stage, the input image undergoes the preliminary feature modulation (PFM) module to guide the illumination estimation (IE) module in generating a more accurate illumination map. The final enhanced image is obtained by dividing the input by the estimated illumination map. The second stage is used only during training. It applies a frequency-domain residual calibration (FRC) module to the first-stage output, generating a calibration term that is added to the original input to darken dark regions and brighten bright areas. This updated input is then fed back to the PFM and IE modules for parameter optimization. Extensive experiments on benchmark datasets demonstrate that DFCNet achieves superior performance across multiple image quality metrics while delivering visually clearer and more natural results. Full article
(This article belongs to the Section Image and Video Processing)
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30 pages, 92065 KiB  
Article
A Picking Point Localization Method for Table Grapes Based on PGSS-YOLOv11s and Morphological Strategies
by Jin Lu, Zhongji Cao, Jin Wang, Zhao Wang, Jia Zhao and Minjie Zhang
Agriculture 2025, 15(15), 1622; https://doi.org/10.3390/agriculture15151622 - 26 Jul 2025
Viewed by 75
Abstract
During the automated picking of table grapes, the automatic recognition and segmentation of grape pedicels, along with the positioning of picking points, are vital components for all the following operations of the harvesting robot. In the actual scene of a grape plantation, however, [...] Read more.
During the automated picking of table grapes, the automatic recognition and segmentation of grape pedicels, along with the positioning of picking points, are vital components for all the following operations of the harvesting robot. In the actual scene of a grape plantation, however, it is extremely difficult to accurately and efficiently identify and segment grape pedicels and then reliably locate the picking points. This is attributable to the low distinguishability between grape pedicels and the surrounding environment such as branches, as well as the impacts of other conditions like weather, lighting, and occlusion, which are coupled with the requirements for model deployment on edge devices with limited computing resources. To address these issues, this study proposes a novel picking point localization method for table grapes based on an instance segmentation network called Progressive Global-Local Structure-Sensitive Segmentation (PGSS-YOLOv11s) and a simple combination strategy of morphological operators. More specifically, the network PGSS-YOLOv11s is composed of an original backbone of the YOLOv11s-seg, a spatial feature aggregation module (SFAM), an adaptive feature fusion module (AFFM), and a detail-enhanced convolutional shared detection head (DE-SCSH). And the PGSS-YOLOv11s have been trained with a new grape segmentation dataset called Grape-⊥, which includes 4455 grape pixel-level instances with the annotation of ⊥-shaped regions. After the PGSS-YOLOv11s segments the ⊥-shaped regions of grapes, some morphological operations such as erosion, dilation, and skeletonization are combined to effectively extract grape pedicels and locate picking points. Finally, several experiments have been conducted to confirm the validity, effectiveness, and superiority of the proposed method. Compared with the other state-of-the-art models, the main metrics F1 score and mask mAP@0.5 of the PGSS-YOLOv11s reached 94.6% and 95.2% on the Grape-⊥ dataset, as well as 85.4% and 90.0% on the Winegrape dataset. Multi-scenario tests indicated that the success rate of positioning the picking points reached up to 89.44%. In orchards, real-time tests on the edge device demonstrated the practical performance of our method. Nevertheless, for grapes with short pedicels or occluded pedicels, the designed morphological algorithm exhibited the loss of picking point calculations. In future work, we will enrich the grape dataset by collecting images under different lighting conditions, from various shooting angles, and including more grape varieties to improve the method’s generalization performance. Full article
(This article belongs to the Section Artificial Intelligence and Digital Agriculture)
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24 pages, 1990 KiB  
Article
Evaluating Skin Tone Fairness in Convolutional Neural Networks for the Classification of Diabetic Foot Ulcers
by Sara Seabra Reis, Luis Pinto-Coelho, Maria Carolina Sousa, Mariana Neto, Marta Silva and Miguela Sequeira
Appl. Sci. 2025, 15(15), 8321; https://doi.org/10.3390/app15158321 - 26 Jul 2025
Viewed by 72
Abstract
The present paper investigates the application of convolutional neural networks (CNNs) for the classification of diabetic foot ulcers, using VGG16, VGG19 and MobileNetV2 architectures. The primary objective is to develop and compare deep learning models capable of accurately identifying ulcerated regions in clinical [...] Read more.
The present paper investigates the application of convolutional neural networks (CNNs) for the classification of diabetic foot ulcers, using VGG16, VGG19 and MobileNetV2 architectures. The primary objective is to develop and compare deep learning models capable of accurately identifying ulcerated regions in clinical images of diabetic feet, thereby aiding in the prevention and effective treatment of foot ulcers. A comprehensive study was conducted using an annotated dataset of medical images, evaluating the performance of the models in terms of accuracy, precision, recall and F1-score. VGG19 achieved the highest accuracy at 97%, demonstrating superior ability to focus activations on relevant lesion areas in complex images. MobileNetV2, while slightly less accurate, excelled in computational efficiency, making it a suitable choice for mobile devices and environments with hardware constraints. The study also highlights the limitations of each architecture, such as increased risk of overfitting in deeper models and the lower capability of MobileNetV2 to capture fine clinical details. These findings suggest that CNNs hold significant potential in computer-aided clinical diagnosis, particularly in the early and precise detection of diabetic foot ulcers, where timely intervention is crucial to prevent amputations. Full article
(This article belongs to the Special Issue Advances and Applications of Machine Learning for Bioinformatics)
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21 pages, 977 KiB  
Article
Fall Detection Using Federated Lightweight CNN Models: A Comparison of Decentralized vs. Centralized Learning
by Qasim Mahdi Haref, Jun Long and Zhan Yang
Appl. Sci. 2025, 15(15), 8315; https://doi.org/10.3390/app15158315 - 25 Jul 2025
Viewed by 130
Abstract
Fall detection is a critical task in healthcare monitoring systems, especially for elderly populations, for whom timely intervention can significantly reduce morbidity and mortality. This study proposes a privacy-preserving and scalable fall-detection framework that integrates federated learning (FL) with transfer learning (TL) to [...] Read more.
Fall detection is a critical task in healthcare monitoring systems, especially for elderly populations, for whom timely intervention can significantly reduce morbidity and mortality. This study proposes a privacy-preserving and scalable fall-detection framework that integrates federated learning (FL) with transfer learning (TL) to train deep learning models across decentralized data sources without compromising user privacy. The pipeline begins with data acquisition, in which annotated video-based fall-detection datasets formatted in YOLO are used to extract image crops of human subjects. These images are then preprocessed, resized, normalized, and relabeled into binary classes (fall vs. non-fall). A stratified 80/10/10 split ensures balanced training, validation, and testing. To simulate real-world federated environments, the training data is partitioned across multiple clients, each performing local training using pretrained CNN models including MobileNetV2, VGG16, EfficientNetB0, and ResNet50. Two FL topologies are implemented: a centralized server-coordinated scheme and a ring-based decentralized topology. During each round, only model weights are shared, and federated averaging (FedAvg) is applied for global aggregation. The models were trained using three random seeds to ensure result robustness and stability across varying data partitions. Among all configurations, decentralized MobileNetV2 achieved the best results, with a mean test accuracy of 0.9927, F1-score of 0.9917, and average training time of 111.17 s per round. These findings highlight the model’s strong generalization, low computational burden, and suitability for edge deployment. Future work will extend evaluation to external datasets and address issues such as client drift and adversarial robustness in federated environments. Full article
(This article belongs to the Section Computing and Artificial Intelligence)
20 pages, 547 KiB  
Article
Empirical Assessment of Sequence-Based Predictions of Intrinsically Disordered Regions Involved in Phase Separation
by Xuantai Wu, Kui Wang, Gang Hu and Lukasz Kurgan
Biomolecules 2025, 15(8), 1079; https://doi.org/10.3390/biom15081079 - 25 Jul 2025
Viewed by 222
Abstract
Phase separation processes facilitate the formation of membrane-less organelles and involve interactions within structured domains and intrinsically disordered regions (IDRs) in protein sequences. The literature suggests that the involvement of proteins in phase separation can be predicted from their sequences, leading to the [...] Read more.
Phase separation processes facilitate the formation of membrane-less organelles and involve interactions within structured domains and intrinsically disordered regions (IDRs) in protein sequences. The literature suggests that the involvement of proteins in phase separation can be predicted from their sequences, leading to the development of over 30 computational predictors. We focused on intrinsic disorder due to its fundamental role in related diseases, and because recent analysis has shown that phase separation can be accurately predicted for structured proteins. We evaluated eight representative amino acid-level predictors of phase separation, capable of identifying phase-separating IDRs, using a well-annotated, low-similarity test dataset under two complementary evaluation scenarios. Several methods generate accurate predictions in the easier scenario that includes both structured and disordered sequences. However, we demonstrate that modern disorder predictors perform equally well in this scenario by effectively differentiating phase-separating IDRs from structured regions. In the second, more challenging scenario—considering only predictions in disordered regions—disorder predictors underperform, and most phase separation predictors produce only modestly accurate results. Moreover, some predictors are broadly biased to classify disordered residues as phase-separating, which results in low predictive performance in this scenario. Finally, we recommend PSPHunter as the most accurate tool for identifying phase-separating IDRs in both scenarios. Full article
(This article belongs to the Collection Feature Papers in Bioinformatics and Systems Biology Section)
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24 pages, 12286 KiB  
Article
A UAV-Based Multi-Scenario RGB-Thermal Dataset and Fusion Model for Enhanced Forest Fire Detection
by Yalin Zhang, Xue Rui and Weiguo Song
Remote Sens. 2025, 17(15), 2593; https://doi.org/10.3390/rs17152593 - 25 Jul 2025
Viewed by 179
Abstract
UAVs are essential for forest fire detection due to vast forest areas and inaccessibility of high-risk zones, enabling rapid long-range inspection and detailed close-range surveillance. However, aerial photography faces challenges like multi-scale target recognition and complex scenario adaptation (e.g., deformation, occlusion, lighting variations). [...] Read more.
UAVs are essential for forest fire detection due to vast forest areas and inaccessibility of high-risk zones, enabling rapid long-range inspection and detailed close-range surveillance. However, aerial photography faces challenges like multi-scale target recognition and complex scenario adaptation (e.g., deformation, occlusion, lighting variations). RGB-Thermal fusion methods integrate visible-light texture and thermal infrared temperature features effectively, but current approaches are constrained by limited datasets and insufficient exploitation of cross-modal complementary information, ignoring cross-level feature interaction. A time-synchronized multi-scene, multi-angle aerial RGB-Thermal dataset (RGBT-3M) with “Smoke–Fire–Person” annotations and modal alignment via the M-RIFT method was constructed as a way to address the problem of data scarcity in wildfire scenarios. Finally, we propose a CP-YOLOv11-MF fusion detection model based on the advanced YOLOv11 framework, which can learn heterogeneous features complementary to each modality in a progressive manner. Experimental validation proves the superiority of our method, with a precision of 92.5%, a recall of 93.5%, a mAP50 of 96.3%, and a mAP50-95 of 62.9%. The model’s RGB-Thermal fusion capability enhances early fire detection, offering a benchmark dataset and methodological advancement for intelligent forest conservation, with implications for AI-driven ecological protection. Full article
(This article belongs to the Special Issue Advances in Spectral Imagery and Methods for Fire and Smoke Detection)
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17 pages, 1907 KiB  
Article
A Comparative Analysis and Limited Phylogenetic Implications of Mitogenomes in Infraorder-Level Diptera
by Huan Yuan and Bin Chen
Int. J. Mol. Sci. 2025, 26(15), 7222; https://doi.org/10.3390/ijms26157222 - 25 Jul 2025
Viewed by 105
Abstract
Diptera comprises more than 154,000 described species, representing approximately 10–12% of insects. Members have successfully colonized all continents and a wide range of habitats. However, higher-level phylogenetic relationships within Diptera have remained ambiguous. Mitochondrial genomes (mitogenomes) have been used as valuable molecular markers [...] Read more.
Diptera comprises more than 154,000 described species, representing approximately 10–12% of insects. Members have successfully colonized all continents and a wide range of habitats. However, higher-level phylogenetic relationships within Diptera have remained ambiguous. Mitochondrial genomes (mitogenomes) have been used as valuable molecular markers for resolving phylogenetic issues. To explore the effect of such markers in solving the higher-level phylogenetic relationship of Diptera, we sequenced and annotated the mitogenomes of 25 species, combined with 180 mitogenomes from 33 superfamilies of dipteran insects to conduct a phylogenetic analysis based on the PCGsrRNA and PCGs12rRNA datasets using IQ-TREE under the partition model. The phylogenetic analysis failed to recover the monophyly of the two suborders Nematocera and Brachycera. Two of six infraorders within the Nematocera—Tipulomorpha and Ptychopteromorpha—were monophyletic. The ancestral Deuterophlebiidae were a strongly supported sister group of all remaining Diptera, but Anisopodidae, as the closest relative of Brachycera, received only weak support. Three of four infraorders within Branchycera—Tabanomorpha, Xylophagomorpha, and Stratiomyomorpha—were, respectively, supported as a monophyletic clade, except Muscomorpha due to the strong long-branch attraction between Cecidomyiidae and Nycteribiidae. The inferred infraordinal relationships followed the topology Tabanomorpha + (Xylophagomorpha + (Stratiomyomorpha + Muscomorpha)). However, the proposed topology lacks strong statistical support, suggesting alternative relationships remain plausible. Based on mitogenome data alone, we infer that Diptera originated earlier than the Late Triassic at 223.43 Mya (95% highest posterior density [HPD] 166.60–272.02 Mya) and the earliest brachyeran Diptera originated in the mid-Jurassic (171.61 Mya). Full article
(This article belongs to the Section Molecular Genetics and Genomics)
18 pages, 8446 KiB  
Article
Evaluation of Single-Shot Object Detection Models for Identifying Fanning Behavior in Honeybees at the Hive Entrance
by Tomyslav Sledevič
Agriculture 2025, 15(15), 1609; https://doi.org/10.3390/agriculture15151609 - 25 Jul 2025
Viewed by 151
Abstract
Thermoregulatory fanning behavior in honeybees is a vital indicator of colony health and environmental response. This study presents a novel dataset of 18,000 annotated video frames containing 57,597 instances capturing fanning behavior at the hive entrance across diverse conditions. Three state-of-the-art single-shot object [...] Read more.
Thermoregulatory fanning behavior in honeybees is a vital indicator of colony health and environmental response. This study presents a novel dataset of 18,000 annotated video frames containing 57,597 instances capturing fanning behavior at the hive entrance across diverse conditions. Three state-of-the-art single-shot object detection models (YOLOv8, YOLO11, YOLO12) are evaluated using standard RGB input and two motion-enhanced encodings: Temporally Stacked Grayscale (TSG) and Temporally Encoded Motion (TEM). Results show that models incorporating temporal information via TSG and TEM significantly outperform RGB-only input, achieving up to 85% mAP@50 with real-time inference capability on high-performance GPUs. Deployment tests on the Jetson AGX Orin platform demonstrate feasibility for edge computing, though with accuracy–speed trade-offs in smaller models. This work advances real-time, non-invasive monitoring of hive health, with implications for precision apiculture and automated behavioral analysis. Full article
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20 pages, 5107 KiB  
Article
Enhancing Ferroptosis-Related Protein Prediction Through Multimodal Feature Integration and Pre-Trained Language Model Embeddings
by Jie Zhou and Chunhua Wang
Algorithms 2025, 18(8), 465; https://doi.org/10.3390/a18080465 - 25 Jul 2025
Viewed by 160
Abstract
Ferroptosis, an iron-dependent form of regulated cell death, plays a critical role in various diseases. Accurate identification of ferroptosis-related proteins (FRPs) is essential for understanding their underlying mechanisms and developing targeted therapeutic strategies. Existing computational methods for FRP prediction often exhibit limited accuracy [...] Read more.
Ferroptosis, an iron-dependent form of regulated cell death, plays a critical role in various diseases. Accurate identification of ferroptosis-related proteins (FRPs) is essential for understanding their underlying mechanisms and developing targeted therapeutic strategies. Existing computational methods for FRP prediction often exhibit limited accuracy and suboptimal performance. In this study, we harnessed the power of pre-trained protein language models (PLMs) to develop a novel machine learning framework, termed PLM-FRP, which utilizes deep learning-derived features for FRP identification. By integrating ESM2 embeddings with traditional sequence-based features, PLM-FRP effectively captures complex evolutionary relationships and structural patterns within protein sequences, achieving a remarkable accuracy of 96.09% on the benchmark dataset and significantly outperforming previous state-of-the-art methods. We anticipate that PLM-FRP will serve as a powerful computational tool for FRP annotation and facilitate deeper insights into ferroptosis mechanisms, ultimately advancing the development of ferroptosis-targeted therapeutics. Full article
(This article belongs to the Special Issue Advanced Research on Machine Learning Algorithms in Bioinformatics)
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18 pages, 516 KiB  
Article
A Nested Named Entity Recognition Model Robust in Few-Shot Learning Environments Using Label Description Information
by Hyunsun Hwang, Youngjun Jung, Changki Lee and Wooyoung Go
Appl. Sci. 2025, 15(15), 8255; https://doi.org/10.3390/app15158255 - 24 Jul 2025
Viewed by 142
Abstract
Nested named entity recognition (NER) is a task that identifies hierarchically structured entities, where one entity can contain other entities within its span. This study introduces a nested NER model for few-shot learning environments, addressing the difficulty of building extensive datasets for general [...] Read more.
Nested named entity recognition (NER) is a task that identifies hierarchically structured entities, where one entity can contain other entities within its span. This study introduces a nested NER model for few-shot learning environments, addressing the difficulty of building extensive datasets for general named entities. We enhance the Biaffine nested NER model by modifying its output layer to incorporate label semantic information through a novel label description embedding (LDE) approach, improving performance with limited training data. Our method replaces the traditional biaffine classifier with a label attention mechanism that leverages comprehensive natural language descriptions of entity types, encoded using BERT to capture rich semantic relationships between labels and input spans. We conducted comprehensive experiments on four benchmark datasets: GENIA (nested NER), ACE 2004 (nested NER), ACE 2005 (nested NER), and CoNLL 2003 English (flat NER). Performance was evaluated across multiple few-shot scenarios (1-shot, 5-shot, 10-shot, and 20-shot) using F1-measure as the primary metric, with five different random seeds to ensure robust evaluation. We compared our approach against strong baselines including BERT-LSTM-CRF with nested tags, the original Biaffine model, and recent few-shot NER methods (FewNER, FIT, LPNER, SpanNER). Results demonstrate significant improvements across all few-shot scenarios. On GENIA, our LDE model achieves 45.07% F1 in five-shot learning compared to 30.74% for the baseline Biaffine model (46.4% relative improvement). On ACE 2005, we obtain 44.24% vs. 32.38% F1 in five-shot scenarios (36.6% relative improvement). The model shows consistent gains in 10-shot (57.19% vs. 49.50% on ACE 2005) and 20-shot settings (64.50% vs. 58.21% on ACE 2005). Ablation studies confirm that semantic information from label descriptions is the key factor enabling robust few-shot performance. Transfer learning experiments demonstrate the model’s ability to leverage knowledge from related domains. Our findings suggest that incorporating label semantic information can substantially enhance NER models in low-resource settings, opening new possibilities for applying NER in specialized domains or languages with limited annotated data. Full article
(This article belongs to the Special Issue Applications of Natural Language Processing to Data Science)
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31 pages, 855 KiB  
Article
A Comparative Evaluation of Transformer-Based Language Models for Topic-Based Sentiment Analysis
by Spyridon Tzimiris, Stefanos Nikiforos, Maria Nefeli Nikiforos, Despoina Mouratidis and Katia Lida Kermanidis
Electronics 2025, 14(15), 2957; https://doi.org/10.3390/electronics14152957 - 24 Jul 2025
Viewed by 250
Abstract
This research investigates topic-based sentiment classification in Greek educational-related data using transformer-based language models. A comparative evaluation is conducted on GreekBERT, XLM-r-Greek, mBERT, and Palobert using three original sentiment-annotated datasets representing parents of students with functional diversity, school directors, and teachers, each capturing [...] Read more.
This research investigates topic-based sentiment classification in Greek educational-related data using transformer-based language models. A comparative evaluation is conducted on GreekBERT, XLM-r-Greek, mBERT, and Palobert using three original sentiment-annotated datasets representing parents of students with functional diversity, school directors, and teachers, each capturing diverse educational perspectives. The analysis examines both overall sentiment performance and topic-specific evaluations across four thematic classes: (i) Material and Technical Conditions, (ii) Educational Dimension, (iii) Psychological/Emotional Dimension, and (iv) Learning Difficulties and Emergency Remote Teaching. Results indicate that GreekBERT consistently outperforms other models, achieving the highest overall F1 score (0.91), particularly excelling in negative sentiment detection (F1 = 0.95) and showing robust performance for positive sentiment classification. The Psychological/Emotional Dimension emerged as the most reliably classified category, with GreekBERT and mBERT demonstrating notably high accuracy and F1 scores. Conversely, Learning Difficulties and Emergency Remote Teaching presented significant classification challenges, especially for Palobert. This study contributes significantly to the field of sentiment analysis with Greek-language data by introducing original annotated datasets, pioneering the application of topic-based sentiment analysis within the Greek educational context, and offering a comparative evaluation of transformer models. Additionally, it highlights the superior performance of Greek-pretrained models in capturing emotional detail, and provides empirical evidence of the negative emotional responses toward Emergency Remote Teaching. Full article
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