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A comprehensive evaluation of large language models in mining gene relations and pathway knowledge

Quantitative Biology 2024年第4期12卷 360-374页

作者： Muhammad Azam Yibo Chen Micheal Olaolu Arowolo Haowang Liu Mihail Popescu Dong Xu Department of Electrical Engineering and Computer Science University of MissouriColumbiaMissouriUSA Bond Life Sciences Center University of MissouriColumbiaMissouriUSA Institute for Data Science and Informatics University of MissouriColumbiaMissouriUSA Department of Biomedical Informatics Biostatistics and Medical EpidemiologyUniversity of MissouriColumbiaMissouriUSA

Understanding complex biological pathways,including gene–gene interactions and gene regulatory networks,is critical for exploring disease mechanisms and drug *** literature curation of biological pathways cannot keep up with the exponential growth of new discoveries in the ***-scale language models(LLMs)trained on extensive text corpora contain rich biological information,and they can be mined as a biological knowledge *** study assesses 21 LLMs,including both application programming interface(API)-based models and open-source models in their capacities of retrieving biological *** evaluation focuses on predicting gene regulatory relations(activation,inhibition,and phosphorylation)and the Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway *** indicated a significant disparity in model ***-based models GPT-4 and Claude-Pro showed superior performance,with an F1 score of 0.4448 and 0.4386 for the gene regulatory relation prediction,and a Jaccard similarity index of 0.2778 and 0.2657 for the KEGG pathway prediction,***-source models lagged behind their API-based counterparts,whereas Falcon-180b and llama2-7b had the highest F1 scores of 0.2787 and 0.1923 in gene regulatory relations,*** KEGG pathway recognition had a Jaccard similarity index of 0.2237 for Falcon-180b and 0.2207 for *** study suggests that LLMs are informative in gene network analysis and pathway mapping,but their effectiveness varies,necessitating careful model *** work also provides a case study and insight into using LLMs das knowledge *** code is publicly available at the website of GitHub(Muh-aza).

关键词： biomedical text mining gene-gene interaction KEGG pathway large language model

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Comparison of SVM and Random Forest for Multimodal Hand Gesture Recognition

Comparison of SVM and Random Forest for Multimodal Hand Gest...

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2025 IEEE SoutheastCon, SoutheastCon 2025

作者： Rahman, Farin Samuel, Joshua McFarlane, Nicole University of Tennessee Min H. Kao Department of Electrical Engineering and Computer Science KnoxvilleTN United States Golisano College of Computing and Information Sciences Rochester Institute of Technology RochesterNY United States

ISBN: (纸本)9798331504847

Machine learning has been implemented to detect and identify sign language hand gestures (letters and numbers) using the Photoplethysmography (PPG) and impedance. The sensor data was collected from commercially available wristbands and evaluation boards. Two supervised machine learning algorithms: Random Forest and Support Vector Machine were used for categorizing the data points. The accuracy for each of the algorithms for the letters and numbers was within the range of either 70-75% or 20-28% for the PPG data. The accuracy was between 33-40% and 55-66% using Random Forest. The accuracy was between 61-76% to 80-90% for when using Support Vector Machine for impedance data. Between the two algorithms, the Random forest approach has better consistency of 70-75% with PPG data whereas the Support Vector Machine approach is more consistent for impedance data with 61-76% accuracy to detect the hand gestures. © 2025 IEEE.

关键词： Random forests

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Generative AI in Agri: Sustainability in Smart Precision Farming Yield Prediction Mapping System Based on GIS Using Deep Learning and GPS 4

Generative AI in Agri: Sustainability in Smart Precision Far...

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4th International Conference on Evolutionary computing and Mobile Sustainable Networks, ICECMSN 2024

作者： Senthil, G.A. Suganthi, S.U. Prinslin, L. Selvi, R. Prabha, R. Department of Information Technology Agni College of Technology Chennai India Department of Artificial Intelligence and Data Science Sri Sai Ram Institute of Technology Chennai India Department of Computer Science and Engineering Agni College of Technology Chennai India Assistant Professor Department of Computing Technologies SRM Institute of Science and Technology kattankulathur Chennai India Department of Electronics and Communication Engineering Sri Sai Ram Institute of Technology Chennai India

Agriculture faces many challenges of precision farming, such as the need for sustainable practices, improving yields, ensuring high yields. In resolution to these challenges, the present research provides an AI-based system that enables the use of deep learning, Global Positioning System (GPS), and Geographic Information System (GIS) technologies to create a highly intelligent smart agricultural precision farming system. Its goal is to monitoring crop health and reduce disease risk, which will lead to improved resource utilization and environmentally sustainability techniques. The proposed framework addresses the urgent need for consistency in agricultural practices, especially as global agriculture deals with pressures from climate change, resource shortages, and increasing demand for food. Traditional agricultural methods for predicting and optimizing crop yields due to increasing factors affecting crop performance Not enough generative AI, especially the use of deep learning models, supports agricultural research in many cases, allowing patterns to be identified and future results to be predicted accurately. The integration of GPS and GIS allows for more accurate mapping, real-time analysis, and effective decision-making. Weather forecasting variability, resource constraints, and demand for more food are isolated from environmental influences using deep learning models, especially Artificial Neural Networks (ANN). By using large data sets, including historical crop yield performance, soil properties, and weather conditions, the system provides highly accurate crop forecasts. Generative Adversarial Networks (GANs) and You Only Look Once (YOLO) hybrid model is playing a key role in generating crop yield and growth potential under different conditions, adjusting model accuracy over time, and this combination of ANN, GANs and YOLO optimization algorithms ensures that the system continuously enhances its predictive accuracy and overall effectiveness. The proposed gene

关键词： Generative adversarial networks

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A Secured and Optimized Broadcast Authentication Scheme for the Internet of Medical Things 4

A Secured and Optimized Broadcast Authentication Scheme for ...

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4th IEEE International Conference on electrical, computer, and Energy Technologies, ICECET 2024

作者： Riaz, Syed Waleed Khan, Fazlullah Ullah, Insaf Alshawi, Bandar Alturki, Ryan Wedyan, Mohammad Abdul Wali Khan University Mardan Computer Science Department KPK Pakistan School of Computer Science University of Nottingham Ningbo China Faculty of Science and Engineering Zhejiang Ningbo315104 China Institute for Analytics and Data Science University of Essex ColchesterCO4 3SQ United Kingdom College of Computing Umm Al-Qura University Department of Computer and Network Engineering Makkah Saudi Arabia College of Computing Umm Al-Qura University Department of Software Engineering Makkah Saudi Arabia Faculty of Information Technology and Computer Sciences Department of Computer Sciences Irbid21163 Jordan

ISBN: (纸本)9798350395914

This Internet of Medical Things (IoMT), facilitates the medical stop regarding real-time monitoring of patients, medical emergency management, remote surgery, patient information management, medical equipment, drug monitoring, etc. However, IoMT devices communicate with each other in an open environment that makes them vulnerable to a wide range of malicious threats from malicious entities. To protect the devices and their associated data, we designed a broadcast authentication scheme for IoMT devices using identity-based public key cryptography that exploits the lightweight features of the Hyper-Elliptic Curve (HEC). We then performed the security analysis based on the Random Oracle Model (ROM), in which we have proved that the proposed scheme is unforgeable under the hardiness of the hyperelliptic curve discrete logarithm problem. The proposed scheme is analyzed in terms of computational and communication overhead and the experimental results justify the superiority of the proposed work in comparison to the existing schemes. © 2024 IEEE.

关键词： Authentication

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Optimizing Supply Chain Efficiency: Integrating Deep Learning and Blockchain Technologies 1

Optimizing Supply Chain Efficiency: Integrating Deep Learnin...

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1st International Conference on Intelligent Technologies for Sustainable Electric and Communications Systems, iTech SECOM 2023

作者： Shanmugapriyaa, K.R. Swetha, S. Janani, N. Bavithra, K. Padmavathi, K. Coimbatore Institute of Technology Department of Artificial Intelligence and Data Science Tamilnadu India Kathir College of Engineering Department of Computer Engineering Tamilnadu India Psg Institute of Technology and Applied Research Department of Electrical and Electronics Engineering Tamilnadu India Hindusthan Polytechnic College Department of Computer Engineering Tamilnadu India

ISBN: (纸本)9798350371185

The research introduces an innovative supply chain management system tailored for agriculture, aiming to enhance operational efficiency and transparency through cutting-edge technologies such as deep learning and blockchain. The system comprises four modules, each leveraging machine learning algorithms to optimize various agricultural processes. The first module utilizes LSTM models to predict crop yields and diseases, empowering farmers with valuable insights into crop health and potential yields. The second module focuses on inventory management optimization using DQN algorithms, enabling farmers to efficiently utilize resources and minimize waste. The third module employs GNN technology to optimize routes for accessing industry-specific points of interest, simplifying farmers' access to relevant information and resources. Lastly, the fourth module addresses significant challenges in agriculture, including crop demand, rotation planning, market trends, pricing strategies, and market identification, employing a DBN model. This study showcases the transformative power of machine learning algorithms in revolutionizing productivity and profitability within the agriculture sector, offering actionable insights and optimization tools to farmers. © 2023 IEEE.

关键词： Blockchain

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Harris Hawks Optimizer with Graph Convolutional Network Based Weed Detection in Precision Agriculture

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computer Systems science & engineering 2023年第8期46卷 1533-1547页

作者： Saud Yonbawi Sultan Alahmari T.Satyanarayana Murthy Padmakar Maddala E.Laxmi Lydia Seifedine Kadry Jungeun Kim Department of Software Engineering College of Computer Science and EngineeringUniversity of JeddahJeddahSaudi Arabia King Abdul Aziz City for Science and Technology RiyadhKingdom of Saudi Arabia Chaitanya Bharathi Institute of Technology HyderabadTelanganaIndia Department of Civil Engineering Vignan’s Institute of Information and Technology(A)DuvvadaVisakhapatnamAP530049India Department of Computer Science and Engineering Vignan’s Institute of Information TechnologyVisakhapatnam530049India Department of Applied Data Science Noroff University CollegeKristiansandNorway Artificial Intelligence Research Center(AIRC) College of Engineering and Information TechnologyAjman UniversityAjmanUnited Arab Emirates Department of Electrical and Computer Engineering Lebanese American UniversityByblosLebanon Department of Software Kongju National UniversityCheonan31080Korea

Precision agriculture includes the optimum and adequate use of resources depending on several variables that govern crop *** agriculture offers a novel solution utilizing a systematic technique for current agricultural problems like balancing production and environmental *** control has become one of the significant problems in the agricultural *** traditional weed control,the entire field is treated uniformly by spraying the soil,a single herbicide dose,weed,and crops in the same *** more precise farming,robots could accomplish targeted weed treatment if they could specifically find the location of the dispensable plant and identify the weed *** may lessen by large margin utilization of agrochemicals on agricultural fields and favour sustainable *** study presents a Harris Hawks Optimizer with Graph Convolutional Network based Weed Detection(HHOGCN-WD)technique for Precision *** HHOGCN-WD technique mainly focuses on identifying and classifying weeds for precision *** image pre-processing,the HHOGCN-WD model utilizes a bilateral normal filter(BNF)for noise *** addition,coupled convolutional neural network(CCNet)model is utilized to derive a set of feature *** detect and classify weed,the GCN model is utilized with the HHO algorithm as a hyperparameter optimizer to improve the detection *** experimental results of the HHOGCN-WD technique are investigated under the benchmark *** results indicate the promising performance of the presented HHOGCN-WD model over other recent approaches,with increased accuracy of 99.13%.

关键词： Weed detection precision agriculture graph convolutional network harris hawks optimizer hyperparameter tuning

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Analyzing the function of smart security in the context of the internet of things 3

Analyzing the function of smart security in the context of t...

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3rd International Conference on Advance computing and Innovative Technologies in engineering, ICACITE 2023

作者： Naidu, K. Venkatagurunatham Pillai, Anchu Krishnan Rajaprabha, C.E. Sharma R, Rajesh Ul Islam, Atowar Khasimbee, Shaik Dr M.G.R Educational and Research Institute Dept. of Computer Science and Engineering Chennai India Xavier Institute of Engineering Applied Science and Humanities Maharashtra Mumbai India Hindusthan Institute of Technology Department of Computer Science and Engineering Coimbatore India Adama Science and Technology University School of Electrical Engineering and Computing Department of Computer Science and Engineering Nazareth1888 Ethiopia University of Science and Technology Meghalaya Department of Computer Science and Electronics Meghalaya Baridua793101 India Aditya College of Engineering Department of Computer Science and Engineering Andhra Pradesh Surampalem533437 India

ISBN: (纸本)9798350399264

Technology is getting better day by day and human beings are using the latest technology possible for their needs and safety. Many devices have been invented that use the internet and with this human safety issues are also taken care of up to a great extent. GPS tracking devices, SHE (Society Harnessing Equipment), AESHS (Advanced Electronic System for Human Safety), ILA Systems are one of the most useful applications and devices that are used for human safety. Human safety and especially the safety of girls have become an emerging and sensitive issue in the present world scenario. This article deals with the role of the Internet of Things in advancing smart security. The issues are taken care of with the help of these upgraded devices that are easily accessible from a remote location with an internet connection. © 2023 IEEE.

关键词： Internet of things

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Contract-Inspired Contest Theory for Controllable Image Generation in Mobile Edge Metaverse

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IEEE Transactions on Mobile computing 2025年

作者： Liu, Guangyuan Du, Hongyang Wang, Jiacheng Niyato, Dusit Kim, Dong In Nanyang Technological University College of Computing and Data Science Energy Research Institute @ NTU Interdisciplinary Graduate Program Singapore University of Hong Kong Department of Electrical and Electronic Engineering Hong Kong Hong Kong Nanyang Technological University College of Computing and Data Science Singapore Sungkyunkwan University Department of Electrical and Computer Engineering Korea Republic of

The rapid advancement of immersive technologies has propelled the development of the Metaverse, where the convergence of virtual and physical realities necessitates the generation of high-quality, photorealistic images to enhance user experience. However, generating these images, especially through Generative Diffusion Models (GDMs), in mobile edge computing environments presents significant challenges due to the limited computing resources of edge devices and the dynamic nature of wireless networks. This paper proposes a novel framework that integrates contract-inspired contest theory, Deep Reinforcement Learning (DRL), and GDMs to optimize image generation in these resource-constrained environments. The framework addresses the critical challenges of resource allocation and semantic data transmission quality by incentivizing edge devices to efficiently transmit high-quality semantic data, which is essential for creating realistic and immersive images. The use of contest and contract theory ensures that edge devices are motivated to allocate resources effectively, while DRL dynamically adjusts to network conditions, optimizing the overall image generation process. Experimental results demonstrate that the proposed approach not only improves the quality of generated images but also achieves superior convergence speed and stability compared to traditional methods. This makes the framework particularly effective for optimizing complex resource allocation tasks in mobile edge Metaverse applications, offering enhanced performance and efficiency in creating immersive virtual environments. © 2002-2012 IEEE.

关键词： Resource allocation

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Building Consensus in Group Decision-Making with Intuitionistic Reciprocal Preference Relations: An Analysis of Various Protocols of Information Granularity Distribution

Building Consensus in Group Decision-Making with Intuitionis...

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2024 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2024

作者： Gonzalez-Quesada, Juan Carlos Cabrerizo, Francisco Javier Herrera-Viedma, Enrique Pedrycz, Witold Andalusian Research Institute in Data Science and Computational Intelligence DaSCI University of Granada Department of Computer Science and Artificial Intelligence Granada18071 Spain University of Alberta Department of Electrical & Computer Engineering EdmontonABT6R 2V4 Canada

ISBN: (纸本)9781665410205

On the one hand, to model experts' preferences in group decision-making, intuitionistic reciprocal preference relations have widely been used because they allow for accommodating hesitation degrees, which are inherent to all decision-making processes. On the other hand, an optimization of information granularity distribution has recently been applied to establish consensus during group decision-making processes. Concretely, a symmetric and uniform distribution of information granularity has been considered for intuitionistic reciprocal preference relations. However, there exist other protocols of information granularity distribution that could be used. Therefore, we aim to analyze all the information granularity distribution protocols and determine their effectiveness in building consensus through intuitionistic reciprocal preference relations. The performance of the different protocols is discussed by conducting some numerical experiments that help provide insights into the effectiveness of the protocols to build consensus. © 2024 IEEE.

关键词： Information granules

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Improving Transitive Embeddings in Neural Reasoning Tasks via Knowledge-Based Policy Networks 2

Improving Transitive Embeddings in Neural Reasoning Tasks vi...

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Joint 2nd Semantic Reasoning Evaluation Challenge and 3rd SeMantic Answer Type, Relation and Entity Prediction Tasks Challenge, SemREC-SMART 2022

作者： Mehryar, Shervin Celebi, Remzi Department of Electrical & Computer Engineering University of Toronto Canada Institute of Data Science Maastricht University Maastricht Netherlands

This paper proposes an approach to embed ontologies in order to deal with reasoning based on transitive relations, using the datasets provided for the SemRec Challenge at ISWC 2022. Knowledge Graph Embedding (KGE) methods provide a low-dimensional representation of the entities and relationships extracted from the knowledge graph and have been successfully used for a variety of applications such as question answering, reasoning, inference, and link prediction. However, most KGE methods cannot handle the underlying constraints and characteristics of ontologies, preventing them from performing important reasoning tasks such as subsumption and instance checking. We propose to extend translation-based embedding methods to include subsumption and instance checking reasoning by leveraging transitive relations. Experimental results show that our approach can achieve Hits@10 as high as %73 using samples generated by a policy network. © 2022 CEUR-WS. All rights reserved.

关键词： Ontology

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