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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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Line Patterns Segmentation in Blurred Images Using Contrast Enhancement and Local Entropy Thresholding

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Journal of computer and Communications 2024年第2期12卷 116-141页

作者： Marios Vlachos Evangelos Dermatas Institute of Communication and Computer Systems Athens Greece Department of Computer Engineering and Informatics University of Patras Patras Greece

Finger vein extraction and recognition hold significance in various applications due to the unique and reliable nature of finger vein patterns. While recently finger vein recognition has gained popularity, there are still challenges associated with extracting and processing finger vein patterns related to image quality, positioning and alignment, skin conditions, security concerns and processing techniques applied. In this paper, a method for robust segmentation of line patterns in strongly blurred images is presented and evaluated in vessel network extraction from infrared images of human fingers. In a four-step process: local normalization of brightness, image enhancement, segmentation and cleaning were involved. A novel image enhancement method was used to re-establish the line patterns from the brightness sum of the independent close-form solutions of the adopted optimization criterion derived in small windows. In the proposed method, the computational resources were reduced significantly compared to the solution derived when the whole image was processed. In the enhanced image, where the concave structures have been sufficiently emphasized, accurate detection of line patterns was obtained by local entropy thresholding. Typical segmentation errors appearing in the binary image were removed using morphological dilation with a line structuring element and morphological filtering with a majority filter to eliminate isolated blobs. The proposed method performs accurate detection of the vessel network in human finger infrared images, as the experimental results show, applied both in real and artificial images and can readily be applied in many image enhancement and segmentation applications.

关键词： Finger Vein Vessel Enhancement Vessel Network Extraction Non-Uniform Images Binarization Morphological Post-Processing

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Depth and Pitch Control of Autonomous Underwater Glider Using Model Predictive Control with ARX Model

Depth and Pitch Control of Autonomous Underwater Glider Usin...

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2023 International Conference on Electrical engineering and informatics, ICEEI 2023

作者： Jeremy, Jason Hidayat, Egi Muhammad Idris Siregar, Simon Trilaksono, Bambang Riyanto Habibullah, Natsir School of Electrical Engineering and Informatics Bandung Institute of Technology Bandung Indonesia Telkom University Faculty of Applied Science Department Computer Engineering Bandung Indonesia

ISBN: (纸本)9798350381290

Autonomous Underwater Gliders (AUGs) are extensively developed vehicles capable of prolonged exploration and observation in complex marine environments. Control of the AUG is challenging due to its slow response system and its constraints. In this research, a linear model representation of AutoRegressive eXogenous input (ARX) will be constructed using input and output data from the AUG system, built Model Predictive Control (MPC), analyzed the performance, comparing with traditional Proportional-Integral-Derivative (PID). The objective is to enhance setpoint tracking accuracy and minimize energy to extend exploration time while faced with constraints. Simulation results reveal MPC exhibits potential setpoint tracking, low overshoot as low as 0.6% up to 0.3m/s maximum depth rate, has relatively low input changes indicating good efficiency compared to PID. MPC approach effectively addresses slow response systems, managing momentum, and handling actuator constraints commonly encountered in AUG. © 2023 IEEE.

关键词： Model predictive control

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Energy Theft Detection in Smart Grids:Taxonomy,Comparative Analysis,Challenges,and Future Research Directions

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IEEE/CAA Journal of Automatica Sinica 2022年第4期9卷 578-600页

作者： Mohsin Ahmed Abid Khan Mansoor Ahmed Mouzna Tahir Gwanggil Jeon Giancarlo Fortino Francesco Piccialli the Department of Computer Science COMSATS University Islamabad the Department of Computer Science School of ComputingEngineering and Digital TechnologiesTeesside University the Innovative Value Institute Maynooth University the Department of Computer Science Bahria University the School of Electronic Engineering Xidian University the Department of Embedded Systems Engineering Incheon National University IEEE the Department of Informatics ModelingElectronics and SystemsUniversity of Calabria the Department of Mathematics and Applications“R.Caccioppoli” University of Naples FedericoⅡ

Electricity theft is one of the major issues in developing countries which is affecting their economy *** with the introduction of emerging technologies,this issue became more *** many new energy theft detection(ETD)techniques have been proposed by utilising different data mining(DM)techniques,state&network(S&N)based techniques,and game theory(GT)***,a detailed survey is presented where many state-of-the-art ETD techniques are studied and analysed for their strengths and *** levels of taxonomy are presented to classify state-of-the-art ETD *** types and ways of energy theft and their consequences are studied and summarised and different parameters to benchmark the performance of proposed techniques are extracted from *** challenges of different ETD techniques and their mitigation are suggested for future *** is observed that the literature on ETD lacks knowledge management techniques that can be more effective,not only for ETD but also for theft *** can help in the prevention of energy theft,in the future,as well as for ETD.

关键词： Challenges comparative analysis energy theft detection future research directions smart grid taxonomy

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Classification of Tuna Meat Grade Quality Based on Color Space Using Wavelet and k-Nearest Neighbor Algorithm

Classification of Tuna Meat Grade Quality Based on Color Spa...

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2023 International Conference on Smart-Green Technology in Electrical and Information Systems, ICSGTEIS 2023

作者： Gede Sujana Eka Putra, I. Ketut Gede Darma Putra, I. Sudarma, Made Sudana, Anak Agung Kompiang Oka Institute of Business and Technology Indonesia Department of Computer Informatics Denpasar Indonesia Udayana University Department of Information Technology Denpasar Indonesia Udayana University Department of Electrical and Computer Engineering Denpasar Indonesia

ISBN: (纸本)9798350382822

Tuna products are one of Indonesia's leading export commodity products. Accuracy in determining the quality grade of tuna is necessary to ensure food safety and product quality. Several cases of rejection of Indonesian fishery products by the United States and cases of food poisoning show a lack of food safety management in Indonesia. Determination of fish quality grade was done manually by identifying the eyes condition, gills, and meat color, taking a sample of tuna meat using a spike, which is the manual grading process causing human error. Previous studies had been carried out to identify the freshness and quality of fish using odor profiles, and color profiles from color sensors, measuring fish freshness and quality based on fish eye images. According to Robert DiGregorio, five parameters determine the grade quality of tuna, namely freshness, fish size and shape, meat color, texture, and fat content. Fish grades are grouped into grade 1, grade 2+, grade 2, and grade 3. This study aims to determine the grade quality of tuna meat based on color space through image preprocessing, dataset training, and classification. Image preprocessing consists of image cropping, converting images from RGB to HSV, and feature extraction using a wavelet. The training phase uses the k-NN algorithm using k=4 based on the number of classes. The result shows the correlation coefficient between grades of feature extraction using wavelet Symlet better than Haar. Classification of 65 images test dataset using Symlet wavelet and k-NN has a better accuracy of 81.8% compared to the Haar wavelet k-NN with an accuracy of 80.3%. © 2023 IEEE.

关键词： Feature extraction

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Conflict Between Artificial Intelligence and Traditional Designers: How Artificial Intelligence Transforms the Design Process 3rd

Conflict Between Artificial Intelligence and Traditional Des...

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3rd International Conference on Emerging Trends in Expert Applications and Security, ICE-TEAS 2024

作者： Gupta, Keshav Dev Pandey, Rishi Pathak, Devendra Nath Ranjan, Rakesh Gupta, Vijay Department of Computer Science Engineering Poornima College of Engineering Rajsthan Jaipur India Department of Animation & Multimedia Birla Institute of Technology Ranchi Mesra India Department of Computer Science & Engineering Poornima College of Engineering ISI-6 RIICO Institutional Area Sitapura Rajasthan Jaipur India Department of Computer Science & Engineering Babu Banarasi Das University Lucknow India Department of Computer Science International School of Informatics and Management Sector 12 Mahaveer Marg Jaipur Mansarovar India

ISBN: (纸本)9789819739905

The development of technology, especially the use of resources provided by artificial intelligence (AI), has advanced in areas where business is gaining importance and is an important fear of economic growth. The use of technical skills in the creation of products and services is not unique to design. In today's world, artificial intelligence (AI) has become an industry in many countries, and design is no exception. However, the lines of work performed by humans and machines are changing rapidly, and as a result, the global market is also changing a lot. This is the result of very rapidly developing technology. This raises the question of how this progress has and will continue to influence the future work of designers. What skills do designers need to enter or stay in this industry? The purpose of this article is to provide a summary of research findings on the impact of intelligence on the performance of designers, as well as an analysis that includes an evaluation of the potential and benefits of intelligent design solutions. Case studies and other scientific studies are used to analyze the applications and benefits of AI-based solutions. Studies can be theoretical or empirical. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2024.

关键词： International trade

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Optimizing Magnetic Induction Sensors for Non-Obtrusive Vital Signs Monitoring: Impact of Current Control on Operational Quality 46

Optimizing Magnetic Induction Sensors for Non-Obtrusive Vita...

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46th Annual International Conference of the IEEE engineering in Medicine and Biology Society, EMBC 2024

作者： Momeni, Mahdi Radomski, Adrian Guler, Ulkuhan Teichmann, Daniel University of Southern Denmark Sdu Health Informatics and Technology The Maersk Mc-Kinney Moller Institute Denmark Worcester Polytechnic Institute Department of Electrical and Computer Engineering WorcesterMA United States

ISBN: (纸本)9798350371499

This paper investigates the advancement of magnetic induction-based heart and respiration rate sensing by actively controlling the coil current. This is realized through the implementation of a current-starved inverter mechanism. Experiments show a notable level of accuracy of the proposed circuit in measuring heart and respiration activity when compared to a reference sensor. The direct manipulation of current levels was found to have a direct impact on the signal strength. Incrementing the overall current within the proposed circuit from 60 mA to 100 mA resulted in an augmentation of the output amplitude of the heart rate signal from 8.5 mV to 27 mV, accompanied by a marginal enhancement in beat-to-beat interval accuracy. Moreover, the proposed sensor demonstrates noteworthy precision in monitoring the respiratory rate when compared with the reference sensor under different current values, exhibiting the same trend in signal strength. This finding offers valuable insight for the development of future power-optimized magnetic induction sensors with enhanced robustness. © 2024 IEEE.

关键词： Contact sensors

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Open-Source Online Mission-Planning in Emergent Environments with PDDL for Multi-robot Applications 13th

Open-Source Online Mission-Planning in Emergent Environments...

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13th Mining Humanistic Data Workshop, MHDW 2024, 9th Workshop on 5G-Putting Intelligence to the Network Edge, 5G-PINE 2024 and 1st Workshop on AI in Applications for Achieving the Green Deal Targets, AI4GD 2024 held as parallel events of the IFIP WG 12.5 International Workshops on Artificial Intelligence Applications and Innovations, AIAI 2024

作者： Michailidis, Iakovos T. Michailidis, Panagiotis Kosmatopoulos, Elias Bassiliades, Nick Information Technologies Institute Thessaloniki Greece Department of Electrical and Computer Engineering Democritus University of Thrace Xanthi Greece School of Informatics Aristotle University of Thessaloniki Thessaloniki Greece

ISBN: (纸本)9783031632266

The current study focuses on the development of an open-source framework which is outsourcing the lack of expressivity of the standardized Planning Domain Definition Language – PDDL, leveraging the capacity and flexibility of the hosting environment in Python 3.8. The implementation was based on the definition and logic of a PDDL domain modeling an object stacking/collecting problem, in specified order and locations, by a fleet of autonomous synergetic vehicles by a centralized management agent. A PDDL-parser was utilized to instantiate the solver. Random changes were imposed in the fully-observable environment during mission execution. The proposed framework considered dynamic replanning of the currently valid mission, every time the state space – and consequently the corresponding state graph representation – is stochastically changed. Appropriate test scenarios were defined, to validate the capacity of the implemented framework and establish that it could serve as an interoperable and extensible foundation for other add-ons and graph-searching tools. The evidence from the simulation results indicates the speed and flexibility of the implemented environment for emulating the dynamic replanning problems in highly emergent scenario cases where the state space changes stochastically. © IFIP International Federation for Information Processing 2024.

关键词： Autonomous agents

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XMeta-OS: A Conceptual Framework for Unified Resource Management in Distributed Edge-Cloud Environments 3rd

XMeta-OS: A Conceptual Framework for Unified Resource Manag...

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3rd International Conference on Advances in Computing Research, ACR 2025

作者： Zacharioudakis, Eleftherios Kakoulli, Elena Evripidou, Salomi Intelligent Systems Laboratory Department of Computer Science Neapolis University Pafos Pafos Cyprus National Technical University of Ukraine Igor Sikorsky Kyiv Polytechnic Institute Kyiv Ukraine Electrical Engineering and Computer Engineering and Informatics Cyprus University of Technology Limassol Cyprus

ISBN: (纸本)9783031876462

This paper introduces XMeta-OS, a meta-operating system specially designed with Linux as its foundation to unify and optimize resource management for the distributed edge-cloud when dynamic use of GPU resources is possible. This approach offer a new GPU abstraction layer and dynamic edge-cloud allocation model that offer enhanced flexibility and resource utilization over existing systems like Kubernetes and OpenStack. By using likely sensitive data, the model applied cloud-pushed deployment model. XMeta-OS manages computer resources in real-time. Therefore, fulfilling high performance various needs. It allocates CPU and GPU in real-time to workloads requiring massive parallel processing, such as machine learning, scientific simulations, real-time data analytics, and transportation tasks. Fabrication in the laboratory of an edge-cloud environment can help to assess the scalability, fault tolerance and efficiency of the system. It showcases the overall architectural design of XMeta-OS. Changes to the kernel and security solutions for safe and effective distribution are suggested. This article presents the design of the XMeta-OS. The future of XMeta-OS entails usage and testing with which we see latency, energy, computation and other such measurements in labs. XMeta-OS is a solution to cost performance, emerging application, large-scale edge-cloud deployments, and distributed GPU-enabled infrastructures. Meta-Operating System in Edge-Cloud Continuum for dynamic resource management of GPU. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2025.

关键词： Cluster computing

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Ultrasound Image Analysis in Breast Cancer: A Comparative Study of Decision Trees and Random Forests 16

Ultrasound Image Analysis in Breast Cancer: A Comparative St...

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16th IEEE International Conference on Computational Intelligence and Communication Networks, CICN 2024

作者： Sivagami, S. Sathya, A. Afsin, S. Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Saveetha University Department of Computer Science and Engineering India Vel Tech Rangarajan Dr. Sagunthala R&d Institute of Science and Technology Department of Computer Science and Engineering Tamilnadu Chennai India Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Saveetha University Department of Bio Informatics Tamil Nadu Chennai India

ISBN: (数字)9798331505264

ISBN: (纸本)9798331505264

Breast cancer remains a leading cause of cancer-related mortality among women globally, underscoring the critical need for early detection and accurate diagnosis. Ultrasound imaging serves as a non-invasive diagnostic tool for identifying breast abnormalities, yet the complexity of these images presents significant interpretation challenges. This study explores the application of Machine Learning (ML) models, specifically Decision Tree (DT) and Random Forest (RF) classifiers, for the classification of breast cancer ultrasound images into benign, malignant, and normal categories. Data augmentation techniques are employed to address class imbalance and enhance model generalization using the Breast Cancer Ultrasonic Image dataset. Among preprocessing steps, pixel values were normalized to provide a consistent input for the models. RF model performed better than DT with an accuracy of 88.75% against an accuracy of 86.25% and those masks for ultrasound images contribute a lot to the overall classification accuracy. In summary, the results of our study can provide support for grand challenges in health and emphasize implications such as the potentiality of ML models to advance breast cancer diagnosis and it implies a necessity for an even further expansion that will allow complete patient outcomes optimization. © 2024 IEEE.

关键词： Radio frequency Accuracy Ultrasonic imaging Training data Predictive models Breast cancer Data models Decision trees Random forests Tumors

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