April 2025
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2 Reads
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April 2025
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2 Reads
April 2025
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5 Reads
April 2025
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24 Reads
Chemometrics and Intelligent Laboratory Systems
April 2025
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7 Reads
Computational Toxicology
March 2025
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12 Reads
Food Bioscience
March 2025
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7 Reads
Toxicology
March 2025
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16 Reads
Measurement
February 2025
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46 Reads
Briefings in Bioinformatics
Anomalous DNA methylation has wide-ranging implications, spanning from neurological disorders to cancer and cardiovascular complications. Current methods for single-cell DNA methylation analysis face limitations in coverage, leading to information loss and hampering our understanding of disease associations. The primary goal of this study is the imputation of CpG site methylation states in a given cell by leveraging the CpG states of other cells of the same type. To address this, we introduce CpGFuse, a novel methodology that combines information from diverse genomic features. Leveraging two benchmark datasets, we employed a careful preprocessing approach and conducted a comprehensive ablation study to assess the individual and collective contributions of DNA sequence, intercellular, and intracellular features. Our proposed model, CpGFuse, employs a convolutional neural network with an attention mechanism, surpassing existing models across HCCs and HepG2 datasets. The results highlight the effectiveness of our approach in enhancing accuracy and providing a robust tool for CpG site prediction in genomics. CpGFuse’s success underscores the importance of integrating multiple genomic features for accurate identification of methylation states of CpG site.
February 2025
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18 Reads
Two‐dimensional (2D) lead halide perovskites (LHPs) have captured a range of interest for the advancement of state‐of‐the‐art optoelectronic devices, highly efficient solar cells, next‐generation energy harvesting technologies owing to their hydrophobic nature, layered configuration, and remarkable chemical/environmental stabilities. These 2D LHPs have been categorized into the Dion‐Jacobson (DJ) and Ruddlesden‐Popper (RP) systems based on their layered configuration respectively. To efficiently classify the RP and DJ phases synthetically and reduce reliance on trial/error method, machine learning (ML) techniques needs to develop. Herein, this work effectively identifies RP and DJ phases of 2D LHPs by implementing various ML models. ML models were trained on 264 experimental data set using 10‐fold stratified cross‐validation, hyperparameter optimization with Optuna, and Shapley Additive Explanations (SHAP) were employed. The stacking classifier efficiently classified RP and DJ phases, demonstrating a minimal variation between the sensitivity and specificity and achieved a high Balance Accuracy (BA) of (0.83) on independent test data set. Our best model tested on 17 hybrid 2D LHPs and three experimental synthesized 2D LHPs aligns well experimental outcomes, a significant advance in cutting edge ML models. Thus, this proposed study has unlocked a new route toward the rational classification of RP and DJ phases of 2D LHPs.
January 2025
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72 Reads
IEEE Open Journal of Vehicular Technology
Highway accidents pose serious challenges and safety risks, often resulting in severe injuries and fatalities due to delayed detection and response. Traditional accident management methods heavily rely on manual reporting, which can be sometime inefficient and error-prone resulting in valuable life loss. This paper proposes a novel framework that integrates autonomous aerial systems (drones) with advanced deep learning models to enhance real-time accident detection and response capabilities. The system not only dispatch the drones but also provide live accident footage, accident identification and aids in coordinating emergency response. In this study we implemented our system in Gazebo simulation environment, where an autonomous drone navigates to specified location based on the navigation commands generated by Large Language Model (LLM) by processing the emergency call/transcript. Additionally, we created a dedicated accident dataset to train YOLOv11 m model for precise accident detection. At accident location the drone provides live video feeds and our YOLO model detects the incident, these high-resolution captured images after detection are analyzed by Moondream2, a Vision language model (VLM), for generating detailed textual descriptions of the scene, which are further refined by GPT 4-Turbo, large language model (LLM) for producing concise incident reports and actionable suggestions. This end-to-end system combines autonomous navigation, incident detection and incident response, thus showcasing its potential by providing scalable and efficient solutions for incident response management. The initial implementation demonstrates promising results and accuracy, validated through Gazebo simulation. Future work will focus on implementing this framework to the hardware implementation for real-world deployment in highway incident system.
... The overall system framework is depicted in Figure D, integrates the simulated environment, image based scene analysis and emergency alert generation to enable realtime traffic incident response. This framework represents a significant advancement by building upon our previous work for developing a practical and efficient solution for highway accident management [65]. The simulation analysis section as illustrated in Figure D comprises of four main subsections: (1) LLM for Command Generation: The GPT 4-Turbo API processes emergency transcripts to generate precise commands for autonomous drone control commands including navigation and location based-specific operations. ...
December 2024
... The obtained binding scores were evaluated to identify the most favorable configurations, and the results were compared with available experimental data to validate the predictions. Additional simulations were considered to confirm the predicted interactions, and the results were interpreted in terms of potential mechanisms of action of Calothrixin A in the insect olfactory system [60][61][62]. ...
November 2024
Food Bioscience
... In addition, in deep convolutional networks, the back layer is mainly responsible for extracting deep abstract features, but to some ex-tent, it is insufficiently combined with the low-level features of the front layer, which leads to insufficient ability to capture certain detailed features [13]. For this reason, the introduction of an attention mechanism [14] is expected to enhance the network's ability to jointly capture global and local information, thus better supporting complex recognition tasks [15]. Furthermore, significant advancements have been made in large-scale character recognition in other countries. ...
November 2024
... On the other hand, with the rapid advancements in artificial intelligence, there is an emergence in its utilization for image segmentation [15], [16], medical image analysis [17], [18], computational bio-informatics [19]- [21], object detection [22] and visual scene understanding using visual language models. Integrating the collaborative perception, YOLO models, Large Language Models (LLMs), and Vision-Language Models (VLMs) offer transformative potential for enhancing road safety [23], [24]. ...
November 2024
IEEE/ACM Transactions on Computational Biology and Bioinformatics
... Additionally, the typical object detection performance in agriculture ranges from 0.7 to 0.9 in F1-score (Rai et al., 2023;Ruigrok et al., 2023;Rehman et al., 2024), which is comparable with the detection performance observed in our experiments. This indicates that the orthomosaic provides an accurate simulation of images taken in a real-world flight. ...
October 2024
Knowledge-Based Systems
... Additionally, the base estimators are paired with a final estimator, also known as Meta learner. As the name suggests final estimator it is responsible for taking the most accurate prediction from the base estimators as input and ultimately producing the final predictions [45][46][47]. While constructing the stacking classifier the mechanism involves the two stages of the training process. ...
October 2024
Archives of Toxicology
... ProtGPT2 [21], a GPT2-based language model, has been trained on protein sequence space to generate novel proteins adhering to natural protein principles. Furthermore, fine-tuning pre-trained language models on specific datasets has been successfully applied in tasks such as enzyme design [22] and post-translational modification prediction [23], making them ideal for conotoxin generation. ...
August 2024
... Host phenotype classification mainly focuses on age prediction [24], cancer prediction [31], and disease condition prediction [27]. For drug response prediction, Maryam et al. utilized graph neural network (GNN) models to screen drugs inf luenced by the gut microbiome, contributing to the optimization of drug dosage and formulation [64]. Jiangsheng Pi et al. developed MDGNN, a deep learning algorithm based on graph convolutional networks (GCNs) to predict microbe-drug associations, successfully identifying two drugs associated with SARS-CoV-2 [61]. ...
July 2024
Computers in Biology and Medicine
... This study used seven different feature descriptors: AAC, PAAC, APAAC, SOCN, DPC, CKSAAGP, and GAAC, alongside five distinct classifiers: RF, XGB, LGBM, ETC, and SVM, for constructing prediction models. Machine learning, deep learning, and graph neural networks are extensively employed in the fields of bioinformatics Mir et al. 2023;Hassan et al. 2024b;Rehman et al. 2024, chemoinformatics Ahmad et al. 2023Mir et al. 2024, and image analysis Noor et al. 2020;Komura and Ishikawa 2018;Eesaar et al. 2023. We used the Optuna framework Akiba et al. 2019 to optimize each baseline model against every descriptor. ...
June 2024
Computational Biology and Chemistry
... Among these, 7 articles [257,6,360,295,357,37,207] focus solely on antimicrobial peptides. Additionally, two review articles [124,300] have been published for cell-penetrating peptides, two for anti-viral peptides [17,188], and three for anti-cancer peptides [271,286,34]. For therapeutic [220], anti-inflammatory [261], and bitter peptides [218], a single review article has been published for each type. ...
June 2024
Journal of Chemical Information and Modeling