Learning Architecture Research Articles

A Comprehensive Survey on Brain Tumor Detection and Classification Techniques Using Machine Learning and Deep Learning Models

Abstract: Brain tumor detection and classification have become critical areas of research due to the complexities and challenges involved in accurate diagnosis. With the advancement of machine learning and deep learning techniques, numerous intelligent systems have been proposed to automate and enhance the process of detecting and classifying brain tumors. This survey paper reviews recent approaches and techniques used for brain tumor detection, focusing primarily on deep learning architectures like Convolutional Neural Networks (CNNs) and pre-trained models such as VGG, ResNet, and EfficientNet. In particular, methods using MRI images to classify tumors into categories such as glioma, meningioma, pituitary tumors, and healthy tissue are explored. A detailed analysis of various models, their architectures, training strategies, and evaluation metrics is provided. Moreover, the paper identifies the key challenges faced in the field, including imbalanced datasets, generalization issues, and computational efficiency. By comparing different approaches, we aim to highlight the strengths and limitations of each method and provide insights into how future research can address these challenges. The paper concludes with a discussion on promising future directions in the application of intelligent techniques for brain tumor detection, including the integration of multimodal data and the development of more interpretable models. This survey serves as a comprehensive resource for researchers interested in understanding the current landscape of brain tumor detection using advanced deep learning techniques.

A comprehensive comparison of deep learning-based compound-target interaction prediction models to unveil guiding design principles

The evaluation of compound-target interactions (CTIs) is at the heart of drug discovery efforts. Given the substantial time and monetary costs of classical experimental screening, significant efforts have been dedicated to develop deep learning-based models that can accurately predict CTIs. A comprehensive comparison of these models on a large, curated CTI dataset is, however, still lacking. Here, we perform an in-depth comparison of 12 state-of-the-art deep learning architectures that use different protein and compound representations. The models were selected for their reported performance and architectures. To reliably compare model performance, we curated over 300 thousand binding and non-binding CTIs and established several gold-standard datasets of varying size and information. Based on our findings, DeepConv-DTI consistently outperforms other models in CTI prediction performance across the majority of datasets. It achieves an MCC of 0.6 or higher for most of the datasets and is one of the fastest models in training and inference. These results indicate that utilizing convolutional-based windows as in DeepConv-DTI to traverse trainable embeddings is a highly effective approach for capturing informative protein features. We also observed that physicochemical embeddings of targets increased model performance. We therefore modified DeepConv-DTI to include normalized physicochemical properties, which resulted in the overall best performing model Phys-DeepConv-DTI. This work highlights how the systematic evaluation of input features of compounds and targets, as well as their corresponding neural network architectures, can serve as a roadmap for the future development of improved CTI models.Scientific contributionThis work features comprehensive CTI datasets to allow for the objective comparison and benchmarking of CTI prediction algorithms. Based on this dataset, we gained insights into which embeddings of compounds and targets and which deep learning-based algorithms perform best, providing a blueprint for the future development of CTI algorithms. Using the insights gained from this screen, we provide a novel CTI algorithm with state-of-the-art performance.

Federated Deep Learning Model for False Data Injection Attack Detection in Cyber Physical Power Systems

Cyber-physical power systems (CPPS) integrate information and communication technology into conventional electric power systems to facilitate bidirectional communication of information and electric power between users and power grids. Despite its benefits, the open communication environment of CPPS is vulnerable to various security attacks. This paper proposes a federated deep learning-based architecture to detect false data injection attacks (FDIAs) in CPPS. The proposed work offers a strong, decentralized alternative with the ability to boost detection accuracy while maintaining data privacy, presenting a significant opportunity for real-world applications in the smart grid. This framework combines state-of-the-art machine learning and deep learning models, which are used in both centralized and federated learning configurations, to boost the detection of false data injection attacks in cyber-physical power systems. In particular, the research uses a multi-stage detection framework that combines several models, including classic machine learning classifiers like Random Forest and ExtraTrees Classifiers, and deep learning architectures such as Long Short-Term Memory (LSTM) and Gated Recurrent Unit (GRU). The results demonstrate that Bidirectional GRU and LSTM models with attention layers in a federated learning setup achieve superior performance, with accuracy approaching 99.8%. This approach enhances both detection accuracy and data privacy, offering a robust solution for FDIA detection in real-world smart grid applications.

BLINKRESNET: COST-EFFECTIVE EYELID LOCALIZATION FOR USE IN A BLINK REFLEXOMETER

Four keypoints corresponding to upper and lower eyelid positions may be localized in the scan videos of a blink reflexometer, an edge device. Images from prior reflexometer scans are tagged in order to train a residual neural network, dubbed BlinkResNet. In order to provide adequate demographic coverage, comprehensive data collection procedures are implemented. The architecture is thoroughly parameterized, allowing for a multidimensional space of compatible architectures to be swept through using a random search. Experimental results on a dataset of annotated reflexometer frames demonstrate significant improvement over a previous algorithm for eyelid localization. A random search identified variants of BlinkResNet best-suited for reflexometer frame annotation, with BlinkResNet-Default achieving a [Formula: see text] score of 0.966 on the validation dataset. Requirements for deployment on an edge device are met: training ease, generalizable inference performance, and low computational cost. A sweep may be conducted on any combination of hyperparameters and datasets, making it an adaptable tool for the continual development of customized machine learning architectures. The analysis of sweep results provides valuable insights into optimal model organization for specific tasks. Thus, methodical data annotation and sweeps over a parameterized machine learning routine are investigated as measures to achieve rapid, accurate inference results.

Deep learning analysis of histopathological images predicts immunotherapy prognosis and reveals tumour microenvironment features in non-small cell lung cancer.

Non-small cell lung cancer (NSCLC) is one of the leading causes of cancer mortality worldwide. Immune checkpoint inhibitors (ICIs) have emerged as a crucial treatment option for patients with advanced NSCLC. However, only a subset of patients experience clinical benefit from ICIs. Therefore, identifying biomarkers that can predict response to ICIs is imperative for optimising patient selection. Hematoxylin and eosin (H&E) images of NSCLC patients were obtained from the local cohort (n = 106) and The Cancer Genome Atlas (TCGA) (n = 899). We developed an ICI-related pathological prognostic signature (ir-PPS) based on H&E stained histopathology images to predict prognosis in NSCLC patients treated with ICIs using deep learning. To accomplish this, we employed a modified ResNet model (ResNet18-PG), a widely-used deep learning architecture well-known for its effectiveness in handling complex image recognition tasks. Our modifications include a progressive growing strategy to improve the stability of model training and the use of the AdamW optimiser, which enhances the optimisation process by adjusting the learning rate based on training dynamics. The deep learning model, ResNet18-PG, achieved an area under the receiver operating characteristic curve (AUC) of 0.918 and a recall of 0.995 on the local cohort. The ir-PPS effectively risk-stratified NSCLC patients. Patients in the low-risk group (n = 40) had significantly improved progression-free survival (PFS) after ICI treatment compared to those in the high-risk group (n = 66, log-rank P = 0.004, hazard ratio (HR) = 3.65, 95%CI: 1.75-7.60). The ir-PPS demonstrated good discriminatory power for predicting 6-month PFS (AUC = 0.750), 12-month PFS (AUC = 0.677), and 18-month PFS (AUC = 0.662). The low-risk group exhibited increased expression of immune checkpoint molecules, cytotoxicity-related genes, an elevated abundance of tumour-infiltrating lymphocytes, and enhanced activity in immune stimulatory pathways. The ir-PPS signature derived from H&E images using deep learning could predict ICIs prognosis in NSCLC patients. The ir-PPS provides a novel imaging biomarker that may help select optimal candidates for ICIs therapy in NSCLC.

Machine learning for base transceiver stations power failure prediction: A multivariate approach

The widespread deployment of cellular networks has improved communication access, driving economic growth and enhancing social connections across diverse regions. Base Transceiver Stations (BTSs), are foundational to mobile networks but are vulnerable to power failures, disrupting service delivery and causing user inconvenience. This paper proposes a machine-learning-based framework for preemptive BTS power failure prediction using multivariate time-series data from power and environmental monitoring systems. We employ a combination of deep learning architectures, including Convolutional Neural Networks (CNNs), Long Short-Term Memory (LSTM) networks, and hybrid CNN-LSTM models, to achieve accurate and timely predictions of BTS power failures. CNNs were selected for extracting dependencies among features of a multivariate time-series data, while LSTMs effectively capture temporal dependencies, making them suitable for predicting power failures.The proposed models exhibit noteworthy predictive performance, with the LSTM network emerging as the most accurate model (MSE: 0.001, MAPE: 2.528), followed by the hybrid CNN-LSTM (MSE: 0.001, MAPE: 2.843) and the CNN (MSE: 0.223, MAPE: 2.843). This work demonstrates deep learning’s effectiveness in preemptive BTS failure prediction, enabling proactive maintenance and improved network resilience.

U-Net and Its Variants Based Automatic Tracking of Radial Artery in Ultrasonic Short-Axis Views: A Pilot Study

Background/Objectives: Radial artery tracking (RAT) in the short-axis view is a pivotal step for ultrasound-guided radial artery catheterization (RAC), which is widely employed in various clinical settings. To eliminate disparities and lay the foundations for automated procedures, a pilot study was conducted to explore the feasibility of U-Net and its variants in automatic RAT. Methods: Approved by the institutional ethics committee, patients as potential RAC candidates were enrolled, and the radial arteries were continuously scanned by B-mode ultrasonography. All acquired videos were processed into standardized images, and randomly divided into training, validation, and test sets in an 8:1:1 ratio. Deep learning models, including U-Net and its variants, such as Attention U-Net, UNet++, Res-UNet, TransUNet, and UNeXt, were utilized for automatic RAT. The performance of the deep learning architectures was assessed using loss functions, dice similarity coefficient (DSC), and Jaccard similarity coefficient (JSC). Performance differences were analyzed using the Kruskal–Wallis test. Results: The independent datasets comprised 7233 images extracted from 178 videos of 135 patients (53.3% women; mean age: 41.6 years). Consistent convergence of loss functions between the training and validation sets was achieved for all models except Attention U-Net. Res-UNet emerged as the optimal architecture in terms of DSC and JSC (93.14% and 87.93%), indicating a significant improvement compared to U-Net (91.79% vs. 86.19%, p < 0.05) and Attention U-Net (91.20% vs. 85.02%, p < 0.05). Conclusions: This pilot study validates the feasibility of U-Net and its variants in automatic RAT, highlighting the predominant performance of Res-UNet among the evaluated architectures.

Deep Learning Approaches for Wildfire Severity Prediction: A Comparative Study of Image Segmentation Networks and Visual Transformers on the EO4WildFires Dataset

This paper investigates the applicability of deep learning models for predicting the severity of forest wildfires, utilizing an innovative benchmark dataset called EO4WildFires. EO4WildFires integrates multispectral imagery from Sentinel-2, SAR data from Sentinel-1, and meteorological data from NASA Power annotated with EFFIS data for forest fire detection and size estimation. These data cover 45 countries with a total of 31,730 wildfire events from 2018 to 2022. All of these various sources of data are archived into data cubes, with the intention of assessing wildfire severity by considering both current and historical forest conditions, utilizing a broad range of data including temperature, precipitation, and soil moisture. The experimental setup has been arranged to test the effectiveness of different deep learning architectures in predicting the size and shape of wildfire-burned areas. This study incorporates both image segmentation networks and visual transformers, employing a consistent experimental design across various models to ensure the comparability of the results. Adjustments were made to the training data, such as the exclusion of empty labels and very small events, to refine the focus on more significant wildfire events and potentially improve prediction accuracy. The models’ performance was evaluated using metrics like F1 score, IoU score, and Average Percentage Difference (aPD). These metrics offer a multi-faceted view of model performance, assessing aspects such as precision, sensitivity, and the accuracy of the burned area estimation. Through extensive testing the final model utilizing LinkNet and ResNet-34 as backbones, we obtained the following metric results on the test set: 0.86 F1 score, 0.75 IoU, and 70% aPD. These results were obtained when all of the available samples were used. When the empty labels were absent during the training and testing, the model increased its performance significantly: 0.87 F1 score, 0.77 IoU, and 44.8% aPD. This indicates that the number of samples, as well as their respectively size (area), tend to have an impact on the model’s robustness. This restriction is well known in the remote sensing domain, as accessible, accurately labeled data may be limited. Visual transformers like TeleViT showed potential but underperformed compared to segmentation networks in terms of F1 and IoU scores.

Backdoor Attacks in Peer-to-Peer Federated Learning

Most machine learning applications rely on centralized learning processes, opening up the risk of exposure of their training datasets. While federated learning (FL) mitigates to some extent these privacy risks, it relies on a trusted aggregation server for training a shared global model. Recently, new distributed learning architectures based on Peer-to-Peer Federated Learning (P2PFL) offer advantages in terms of both privacy and reliability. Still, their resilience to poisoning attacks during training has not been investigated. In this paper, we propose new backdoor attacks for P2PFL that leverage structural graph properties to select the malicious nodes, and achieve high attack success, while remaining stealthy. We evaluate our attacks under various realistic conditions, including multiple graph topologies, limited adversarial visibility of the network, and clients with non-IID data. Finally, we show the limitations of existing defenses adapted from FL and design a new defense that successfully mitigates the backdoor attacks, without an impact on model accuracy.

In-Bed Monitoring: A Systematic Review of the Evaluation of In-Bed Movements Through Bed Sensors

The growing popularity of smart beds and devices for remote healthcare monitoring is based on advances in artificial intelligence (AI) applications. This systematic review aims to evaluate and synthesize the growing literature on the use of machine learning (ML) techniques to characterize patient in-bed movements and bedsore development. This review is conducted according to the principles of PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) and is registered in the International Prospective Register of Systematic Reviews (PROSPERO CRD42022314329). The search was performed through nine scientific databases. The review included 78 articles, including 142 ML models. The applied ML models revealed significant heterogeneity in the various methodologies used to identify and classify patient behaviors and postures. The assortment of ML models encompassed artificial neural networks, deep learning architectures, and multimodal sensor integration approaches. This review shows that the models for analyzing and interpreting in-bed movements perform well in experimental settings. Large-scale real-life studies are lacking in diverse patient populations.

Classification of Faults in Power System Transmission Lines Using Deep Learning Methods with Real, Synthetic, and Public Datasets

Every part of society relies on energy systems due to the growing population and the constant demand for energy. Because of the high energy demands of transportation, industry, and daily life, energy systems are crucial to every part of society. Electrical transmission lines are a crucial component of the electrical power system. Therefore, in order to determine the power system’s protection plan and increase its reliability, it is critical to foresee and classify fault types. With this motivation, the main goal of this paper is to design a deep network model to classify faults in transmission lines based on real, generated, and publicly available datasets. A deep learning architecture that was based on a one-dimensional convolutional neural network (CNN) was utilized in this study. Accuracy, specificity, recall, precision, F1 score, ROC curves, and AUC were employed as performance criteria for the suggested model. Not only synthetic but also real data were used in this study. It has been seen that the created model can be used successfully for both real data and synthetic data. In order to measure the robustness of the network, it was tested with three different datasets consisting of real, generated, and publicly available datasets. In the paper, 1D CNN, one of the machine learning methods, was used on three different power systems, and it was observed that the machine learning method was successful in all three power systems.

Deep attention for enhanced OCT image analysis in clinical retinal diagnosis

AbstractRetinal illnesses such as age-related macular degeneration (AMD) and diabetic maculopathy pose serious risks to vision in the developed world. The diagnosis and assessment of these disorders have undergone revolutionary change with the development of optical coherence tomography (OCT). This study proposes a novel method for improving clinical precision in retinal disease diagnosis by utilizing the strength of Attention-Based DenseNet, a deep learning architecture with attention processes. For model building and evaluation, a dataset of 84495 high-resolution OCT images divided into NORMAL, CNV, DME, and DRUSEN classes was used. Data augmentation techniques were employed to enhance the model's robustness. The Attention-Based DenseNet model achieved a validation accuracy of 0.9167 with a batch size of 32 and 50 training epochs. This discovery presents a promising route for more precise and speedy identification of retinal illnesses, ultimately enhancing patient care and outcomes in clinical settings by integrating cutting-edge technology with powerful neural network architectures.

Cloud Detection Using a UNet3+ Model with a Hybrid Swin Transformer and EfficientNet (UNet3+STE) for Very-High-Resolution Satellite Imagery

It is necessary to extract and recognize the cloud regions presented in imagery to generate satellite imagery as analysis-ready data (ARD). In this manuscript, we proposed a new deep learning model to detect cloud areas in very-high-resolution (VHR) satellite imagery by fusing two deep learning architectures. The proposed UNet3+ model with a hybrid Swin Transformer and EfficientNet (UNet3+STE) was based on the structure of UNet3+, with the encoder sequentially combining EfficientNet based on mobile inverted bottleneck convolution (MBConv) and the Swin Transformer. By sequentially utilizing convolutional neural networks (CNNs) and transformer layers, the proposed algorithm aimed to extract the local and global information of cloud regions effectively. In addition, the decoder used MBConv to restore the spatial information of the feature map extracted by the encoder and adopted the deep supervision strategy of UNet3+ to enhance the model’s performance. The proposed model was trained using the open dataset derived from KOMPSAT-3 and 3A satellite imagery and conducted a comparative evaluation with the state-of-the-art (SOTA) methods on fourteen test datasets at the product level. The experimental results confirmed that the proposed UNet3+STE model outperformed the SOTA methods and demonstrated the most stable precision, recall, and F1 score values with fewer parameters and lower complexity.

Automated lesion detection in cotton leaf visuals using deep learning

Cotton is one of the major cash crop in the agriculture led economies across the world. Cotton leaf diseases affects its yield globally. Determining cotton lesions on leaves is difficult when the area is big and the size of lesions is varied. Automated cotton lesion detection is quite useful; however, it is challenging due to fewer disease class, limited size datasets, class imbalance problems, and need of comprehensive evaluation metrics. We propose a novel deep learning based method that augments the data using generative adversarial networks (GANs) to reduce the class imbalance issue and an ensemble-based method that combines the feature vector obtained from the three deep learning architectures including VGG16, Inception V3, and ResNet50. The proposed method offers a more precise, efficient and scalable method for automated detection of diseases of cotton crops. We have implemented the proposed method on publicly available dataset with seven disease and one health classes and have achieved highest accuracy of 95% and F-1 score of 98%. The proposed method performs better than existing state of the art methods.

XU-NetFullSharp: The Novel Deep Learning Architecture for Chest X-ray Bone Shadow Suppression

Background and objectivesChest X-ray image (CXR) is vital for screening, preventing, and monitoring various lung diseases. In particular, the early detection of lung cancer can significantly improve patients’ chances of survival and quality of life. Unfortunately, approximately 82–95 % of missed pulmonary nodules are estimated to be obscured by rib shadows, making them difficult to recognize. This study addresses this problem by considering the rib shadows in CXRs as noise that can be reduced using deep learning. The result of the proposed model is a CXR with improved clarity for easier and more accurate analysis by radiologists or computer algorithms. MethodsAn automated deep learning-based model for bone shadow suppression from frontal CXRs, called xU-NetFullSharp, was proposed. This network is inspired by the most modern U-NetSharp architecture and was modified using different approaches to preserve as many details as possible and accurately suppress bone shadows. For comparison, recent state-of-the-art models were implemented and trained. JSRT, VinDr-CXR, and Gusarev DES datasets were utilized for the experiments, where the JSRT dataset was extensively augmented. ResultsThe performance of the proposed xU-NetFullSharp was analyzed using statistical measures and compared with that of other architectures. The proposed model significantly outperformed the others, reaching the best values of the most used metrics (0.9846 SSIM; 0.9870 MS-SSIM). It also achieves a correlation of 96.31 % and an intersection of 10.0285 between the predicted and ground truth histograms, together with the smallest value of the Bhattacharyya distance. The obtained results were validated by experts from the University Hospital Olomouc with positive feedback, thus achieving the best objective and subjective results. The proposed method has the potential to be implemented in hospital environments. ConclusionA comprehensive comparison of the proposed architecture with state-of-the-art methods proves its efficiency in suppressing noise in CXRs and its ability to distinguish the signals of important tissues from noise components. This methodology can potentially improve the performance of the existing CXR processing methods. The source code is released in a GitHub repository that can be accessed from the following link: https://github.com/xKev1n/xU-NetFullSharp.

Adaptive MPC path-tracking controller based on reinforcement learning and preview-based PID controller

Path-tracking control is a crucial process for autonomous vehicles, ensuring that the vehicle drives safely along the reference path, and the suitable controller parameters ensure the accuracy and stability of this process. To enhance the adaptability of traditional path-tracking controller parameters, this paper proposes an adaptive model predictive control (MPC) controller based on a preview-based PID controller and deep deterministic policy gradient (DDPG) algorithm to achieve adaptive tuning of the controller parameters. Starting with the design of the dynamics tracking error model of the vehicle and the MPC controller. Based on the actor-critic reinforcement learning architecture, the DDPG agent is designed to tune the prediction horizon and weight matrix of the MPC controller. A preview-based PID controller is proposed to improve the efficiency and stability of reinforcement learning and compensate for the error in vehicle modeling. The improved algorithm performance is verified through the simulation scenarios of high-speed lane changing and accelerated overtaking scenarios constructed by MATLAB/Simulink. The results show that the improved algorithm significantly improves the adaptive ability of the traditional MPC controller to time-varying conditions and achieves higher tracking accuracy and stability.

Advances in Medical Image Segmentation: A Comprehensive Review of Traditional, Deep Learning and Hybrid Approaches.

Medical image segmentation plays a critical role in accurate diagnosis and treatment planning, enabling precise analysis across a wide range of clinical tasks. This review begins by offering a comprehensive overview of traditional segmentation techniques, including thresholding, edge-based methods, region-based approaches, clustering, and graph-based segmentation. While these methods are computationally efficient and interpretable, they often face significant challenges when applied to complex, noisy, or variable medical images. The central focus of this review is the transformative impact of deep learning on medical image segmentation. We delve into prominent deep learning architectures such as Convolutional Neural Networks (CNNs), Fully Convolutional Networks (FCNs), U-Net, Recurrent Neural Networks (RNNs), Adversarial Networks (GANs), and Autoencoders (AEs). Each architecture is analyzed in terms of its structural foundation and specific application to medical image segmentation, illustrating how these models have enhanced segmentation accuracy across various clinical contexts. Finally, the review examines the integration of deep learning with traditional segmentation methods, addressing the limitations of both approaches. These hybrid strategies offer improved segmentation performance, particularly in challenging scenarios involving weak edges, noise, or inconsistent intensities. By synthesizing recent advancements, this review provides a detailed resource for researchers and practitioners, offering valuable insights into the current landscape and future directions of medical image segmentation.

Deep learning architecture for scatter estimation in cone-beam computed tomography head imaging with varying field-of-measurement settings.

X-ray scatter causes considerable degradation in the cone-beam computed tomography (CBCT) image quality. To estimate the scatter, deep learning-based methods have been demonstrated to be effective. Modern CBCT systems can scan a wide range of field-of-measurement (FOM) sizes. Variations in the size of FOM can cause a major shift in the scatter-to-primary ratio in CBCT. However, the scatter estimation performance of deep learning networks has not been extensively evaluated under varying FOMs. Therefore, we train the state-of-the-art scatter estimation neural networks for varying FOMs and develop a method to utilize FOM size information to improve performance. We used FOM size information as additional features by converting it into two channels and then concatenating it to the encoder of the networks. We compared our approach for a U-Net, Spline-Net, and DSE-Net, by training them with and without the FOM information. We utilized a Monte Carlo-simulated dataset to train the networks on 18 FOM sizes and test on 30 unseen FOM sizes. In addition, we evaluated the models on the water phantoms and real clinical CBCT scans. The simulation study demonstrates that our method reduced average mean-absolute-percentage-error for U-Net by 38%, Spline-Net by 40%, and DSE-net by 33% for the scatter estimation in the 2D projection domain. Furthermore, the root-mean-square error on the 3D reconstructed volumes was improved for U-Net by 43%, Spline-Net by 30%, and DSE-Net by 23%. Furthermore, our method improved contrast and image quality on real datasets such as water phantom and clinical data. Providing additional information about FOM size improves the robustness of the neural networks for scatter estimation. Our approach is not limited to utilizing only FOM size information; more variables such as tube voltage, scanning geometry, and patient size can be added to improve the robustness of a single network.

LLM4THP: a computing tool to identify tumor homing peptides by molecular and sequence representation of large language model based on two-layer ensemble model strategy

Tumor homing peptides (THPs) have a distinctive capacity to specifically attach to tumor cells, providing a promising approach for targeted cancer treatment and detection. Although THPs have the potential for significant impact, their detection by conventional methods is both time-consuming and expensive. To tackle this issue, we provide LLM4THP, an innovative computational approach that utilizes large language models (LLMs) to quickly and effectively detect THPs. LLM4THP utilizes two protein LLMs, ESM2 and Prot_T5_XL_UniRef50, to encode peptide sequences. This allows for the capture of complex patterns and relationships within the peptide data. In addition, we utilize inherent sequence characteristics such as Amino Acid Composition (AAC), Pseudo Amino Acid Composition (PAAC), Amphiphilic Pseudo Amino Acid Composition (APAAC), and Composition, Transition, and Distribution (CTD) to improve the representation of peptides. The RDKitDescriptors feature representation approach transforms peptide sequences into molecular objects and computes chemical characteristics, resulting in enhanced THP identification. The LLM4THP ensemble strategy incorporates various features into a two-layer learning architecture. The first layer consists of LightGBM, XGBoost, Random Forest, and Extremely Randomized Trees, which generate a set of meta results. The second layer utilizes Logistic Regression to further refine the identification of sequences as either THP or non-THP. LLM4THP exhibits exceptional performance compared to the most advanced methods, showcasing enhancements in accuracy, Matthew’s correlation coefficient, F1 score, area under the curve, and average precision. The source code and dataset can be accessed at the following URL: https://github.com/abcair/LLM4THP.

Retraction Note: Nanoparticle analysis based on optical ion beam in nuclear imaging by deep learning architectures

Retraction Note: Nanoparticle analysis based on optical ion beam in nuclear imaging by deep learning architectures