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arXiv 2025年

作者： Park, Junseok Maury, Eduardo A. Oh, Changhoon Shin, Donghoon Denisko, Danielle Lee, Eunjung Alice Division of Genetics and Genomics Boston Children’s Hospital 3 Blackfan Circle BostonMA United States Department of Pediatrics Harvard Medical School 25 Shattuck St BostonMA United States Bioinformatics Integrative Genomics Program Harvard/MIT MD-PHD Program Harvard Medical School BostonMA United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard CambridgeMA United States Graduate School of Information Yonsei University 50 Yonsei-ro Seodaemun-gu Seoul Korea Republic of Department of Human Centered Design and Engineering University of Washington SeattleWA United States Department of Biomedical Informatics Harvard Medical School BostonMA United States

Advances in genome sequencing technologies generate massive amounts of sequence data that are increasingly analyzed and shared through public repositories. On-demand infrastructure services on cloud computing platforms enable the processing of such large-scale genomic sequence data in distributed processing environments with a significant reduction in analysis time. However, parallel processing on cloud computing platforms presents many challenges to researchers, even skillful bioinformaticians. In particular, it is difficult to design a computing architecture optimized to reduce the cost of computing and disk storage as genomic data analysis pipelines often employ many heterogeneous tools with different resource requirements. To address these issues, we developed GenomeFlow, a tool for automated development of computing architecture and resource optimization on Google Cloud Platform, which allows users to process a large number of samples at minimal cost. We outline multiple use cases of GenomeFlow demonstrating its utility to significantly reduce computing time and cost associated with analyzing genomic and transcriptomic data from hundreds to tens of thousands of samples from several consortia. Here, we describe a step-by-step protocol on how to use GenomeFlow for a common genomic data processing task. We introduce this example protocol geared toward a bioinformatician with little experience in cloud computing. © 2025, CC BY.

关键词： Cloud platforms

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Role of simulation models in understanding the generation of behavior in C. elegans

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Current Opinion in Systems Biology 2019年 13卷 93-101页

作者： Izquierdo, Eduardo J. Cognitive Science Program School of Informatics Computing and Engineering Indiana University United States

There has been a proliferation of studies using simulation models to achieve a system-level understanding of behavior in Caenorhabditis elegans. Here I discuss the different aims of these modeling approaches and review examples of each in the context of locomotion and spatial navigation in the worm. I argue that as the focus shifts from understanding sensorimotor transformations to understanding neuromechanical instantiations for how behaviors are generated, simulation models will become a more integral part of the experiment–theory cycle. I discuss the insights that simulation modeling provides that complement information obtained from experimental discovery methods. © 2018 Elsevier Ltd

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VidyaMedic: Smart Alert System For Continous Vital Sign Monitoring

VidyaMedic: Smart Alert System For Continous Vital Sign Moni...

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2023 International Conference on Electrical engineering and informatics, ICEEI 2023

作者： Ikawati, Vidya Prihatmanto, Ary Setijadi School of Electrical Engineering and Informatics Bandung Institute of Technology Doctoral Program of Electrical Engineering and Informatics Bandung Indonesia School of Electrical Engineering and Informatics Bandung Institute of Technology Bandung Indonesia

ISBN: (纸本)9798350381290

The proposed smart system namely VidyaMedic utilizes continuous heart rate monitoring through sensors, with data transmission to the cloud via an IoT platform. Testing was conducted on a 40-year-old male participant who wore the Polar H10 heart rate monitor for 24 days. The heart rate profile captures the circadian rhythm, the natural internal biological clock governing cardiovascular and behavioral processes over a 24-hour cycle, influencing morning, daytime, and nighttime activities. Health conditions can be assessed using an algorithm which calculates the running sum of standard deviation for heart rate data over this period. Initially, standard deviation is computed for each data point, quantifying data dispersion from the mean. Subsequently, the running sum of standard deviation enables the detection of significant changes over time, abrupt fluctuations indicate outliers or extreme values, potentially impacting overall standard deviation and signaling significant data changes. Deviations from the expected or previous standard deviation values, marked by a regression coefficient less than or greater than 1, may suggest cardiac abnormalities or heart rhythm disturbances. © 2023 IEEE.

关键词： Heart

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Fish Freshness Identification Using Machine Learning: Performance Comparison of k-NN and Naïve Bayes Classifier

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Journal of Computing Science and engineering 2022年第3期16卷 153-164页

作者： Yudhana, Anton Umar, Rusydi Saputra, Sabarudin Department of Electrical Engineering Universitas Ahmad Dahlan Yogyakarta Indonesia Master Program of Informatics Universitas Ahmad Dahlan Yogyakarta Indonesia

Fish is one of the food sources that should be examined for freshness before being consumed. The consumption of rotten fish can cause various diseases. The rotten fish have changed color on the gills, skin, flesh, and eyes and have a pungent odour. Fish freshness can be assessed using a variety of conventional methods, but these methods have limitations, such as requiring relatively expensive equipment, trained personnel and being destructive. The machine learning method is used because it is non-destructive, reduces costs, and is easy to use. This study aims to identify the freshness of fish using k-nearest neighbor (k-NN) and Naïve Bayes (NB) classification methods based on the fish-eye image. The features used in the classification process are RGB and GLCM. The research stages consist of the fish collection process, image acquisition and class division, preprocessing and ROI detection, feature extraction and dataset split, and the classification process. Based on these results, it can be stated that the k-NN method has better performance than NB with average accuracy, precision, recall, specificity, and AUC of 0.97, 0.97, 0.97, 0.97, and 0.97. © 2022. The Korean Institute of Information Scientists and Engineers

关键词： Fish

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The implementation of k-means clustering method in classifying undergraduate thesis titles 12

The implementation of k-means clustering method in classifyi...

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12th International Conference on Telecommunication Systems, Services, and Applications, TSSA 2018

作者： Zahrotun, Lisna Putri, Nila Hutami Nur Khusna, Arfiani Informatics Engineering Study Program Ahmad Dahlan University Yogyakarta Indonesia

ISBN: (纸本)9781538669402

One of graduation requirements at university is completing undergraduate thesis. At Industrial engineering Universitas Ahmad Dahlan, undergraduate thesis titles are documented by thesis coordinator. The problem is that students are less knowledgeable on thesis topics, so they do not really know the previous students' thesis topics. Based on the problem, this research aims at developing a program to classify thesis title so the knowledge on the trend of thesis title topic can be got The method used in this research was K-Means clustering, while range measurement method used was cosine similarity. The testing used Silhouette Coefficient method. The phases from text mining were tokenizing, filtering, stemming, similarity, classifying, testing. The result of this research is a program that can process the title data into trend group pattern of thesis title *** 138 data obtained, there are three clusters arranged based on the field on Industrial engineering study program. Silhouette Coefficient testing shows score of 0.5674 that shows the clustering result is classified low. It occurs since the textual data of the thesis title is too widely distributed, so the title has relatively low similarity score © 2018 IEEE.

关键词： K-means clustering

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Decision support system of fruit cultivation using technique for other reference method by similarity to ideal solution (TOPSIS) 2

Decision support system of fruit cultivation using technique...

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2nd International Conference on Technology, Innovation, Society and Science-to-Business, ICTIS 2018

作者： Yulianti, Eva Nanda, Rahmat Rizki Institut Teknologi Padang Informatics Engineering Study Program Padang Indonesia

Fruit cultivation is very promising for farmers. But there are problems faced by farmers, namely the lack of understanding of farmers with natural conditions that can affect crop yields. So with the selection of plants that are not appropriate, it does not get satisfactory results. Various types of fruit crops can be cultivated by farmers, such as oranges, guava, rambutan, watermelon, avocado, and so on. But it should be noted, that in the cultivation is expected to be cultivated plants in accordance with natural circumstances. This Designing created application to help determine the cultivation of fruit crops. In determining the cultivation of fruit crops in accordance with the criteria using the Technique Method for Others Reference by Similarity to Ideal Solution (TOPSIS) as a tool to facilitate decision-making process with several criteria of comparison, namely: temperature, sunlight, rainfall and humidity, height, harvest, selling power, susceptibility to disease, and care levels. This application is made based on the web by using PHP as a programming language and MySQL as the data storage. The use of decision support system application of the cultivation of these fruit crops can provide an output or alternative in accordance with the natural state of the area. And helps in making decisions to determine which fruits are suitable for cultivating for users based on selected criteria. © The Authors, published by EDP Sciences, 2018.

关键词： Fruits

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QoS analysis on OSPFv3 and RIPng Using GRE Tunneling on IPv6 Integrated Ipv4 Network 2

QoS analysis on OSPFv3 and RIPng Using GRE Tunneling on IPv6...

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2nd International Conference on Technology, Innovation, Society and Science-to-Business, ICTIS 2018

作者： Warman, Indra Franozal, Alex Institut Teknologi Padang Informatics Engineering Study Program Padang Indonesia

Every year, the availability of public IPv4 addresses is running low. However, the IETF (Internet engineering Task Force) has set a new addressing standard called IPv6 (Internet Protocol version 6). IPv6 implementations can not be immediately performed on all end-to-end lines, a transition phase is required, one of which is the GRE tunneling method. IPv6 has some differences with IPv4, then in line with the presence of IPv6 will required the protocol that compatible with IPv6, among which is the routing protocol. Some dynamic routing protocols are created to support and can run on IPv6 such as RIPng and OSPFv3. Aim of this study is examines OSPFv3 routing protocols and RIPng routing protocols in terms of Quality of Service (QoS). The test is done by using seven routers with three scenarios in each routing protocol, ie scenario with best path active condition, when the network changes in other words best path down, and the scenario with best path condition has changed and the network has returned to normal. Testing is done by testing QoS parameters (delay, packet loss, and throughput) when the client computer downloads files with *** extension from the server. Downloaded files have different sizes, from 100 Mega Byte to 1 Giga Byte. From the results obtained that OSPFv3 provides better QoS (delay, packet loss, and throughput) than RIPng on integrated IPv6 network using GRE tunnel and can be a reference when going to transition from IPv4 to IPv6 using GRE Tunnel. © The Authors, published by EDP Sciences, 2018.

关键词： Routing protocols

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Detection of CT - Scan Lungs COVID-19 Image Using Convolutional Neural Network and CLAHE 3

Detection of CT - Scan Lungs COVID-19 Image Using Convolutio...

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3rd International Conference on Information and Communications Technology, ICOIACT 2020

作者： James, Ronaldus Morgan Sunyoto, Andi Universitas Amikom Yogyakarta Master Program of Informatics Engineering Yogyakarta Indonesia

ISBN: (纸本)9781728173566

Detecting COVID-19 is a significant task for medical professionals today because of its rapid spread. To overcome this problem, medical professionals have used various techniques and methods todetect to inhibit the proliferation of COVID-19. CT (Computed Tomography) Scan is currently the best method for detecting COVID-19. This diagnostic method is very accurate because it can see organs in three dimensions. However, this method requires a radiologist to detect the disease and requiresa long time, which means it will cut valuable time for medical practitioners if a patient is sick. Therefore it is necessary to implement a system to detect the coronavirus automatically as an alternative quickly. This study intends to help medical practitioners to detect computed tomography (CT)Scans of lungs infected with COVID-19. The methods to be used are Limited Adaptive histogram equalization (CLAHE) contrast to improve the quality of CT (Computed Tomography) Scan images of COVID-19 lungs and Convolutional Neural Network (CNN) for the image classification process. The dataset usedis 698 RGB images. This study uses three convolutional layers, 3 Max-Pooling layers, and two fully connected layers, resulting in 83.28% accuracy. © 2020 IEEE.

关键词： Coronavirus

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Digital image analysis of beef color using euclidean distance method 3

Digital image analysis of beef color using euclidean distanc...

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3rd International Conference on informatics and Computing, ICIC 2018

作者： Handayani, Hanny Hikmayanti Wahiddin, Deden Informatics Engineering Program Buana Perjuangan Karawang University Karawang Indonesia

ISBN: (纸本)9781538669204

Beef color is an important indicator in determining the quality of beef. Unfortunately, currently there is no quantitative and standardized method for classifying and analyzing the color of beef. In the SNI 3932: 2008 Document any procedures undertaken for the assessment of the quality of beef are done organoleptically (Organoleptic test or sensory test is a way of testing by using the human senses as the primary means of measuring the reception power of the product) using the sense of sight of physical appearance of muscle and fat. The physical appearance value of meat and fat is then determined by using standard quality assistive devices. This method is highly subjective and unstable, as well as the speed of slow classification process with low accuracy. In this research, the image color classification system of beef is done by extracting RGB image feature of beef image by using Color feature extraction method to RGB (Red, Green, Blue). The method used to classify the color of the beef image is the Euclidean Distance method. Results obtained from the Color Classification System of Beef Image using Euclidean Distance Method in this study has an accuracy of 60%. © 2018 IEEE.

关键词： Beef

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Automated Test on Multiple Platform Framework Development 7

Automated Test on Multiple Platform Framework Development

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7th International Conference on Sustainable Information engineering and Technology, SIET 2022

作者： Ubaidilah, Muhammad Fadhli Permatasari, Desy Intan Hardiansyah, Fadilah Fahrul Informatics Engineering Study Program Politeknik Elektronika Negeri Surabaya Indonesia

ISBN: (纸本)9781450397117

Software testing is a phase in software development to ensure software quality. As more and more software is developed for web and mobile platforms, Software Quality Assurance (SQA) Engineer is responsible to test software on both platforms to ensure functionality on each platform. While automated test can be implemented to reduce the workload of SQA Engineer, it has its setbacks as automated test needs a huge effort to maintain it and available tools to develop automated test currently only support one platform. In this research, an automated test framework is proposed and developed that can test both web and mobile platforms. Compared to an automated test project that uses separate tools, a project that uses the proposed framework has 2.57% higher maintainability index. A user test to 3 SQA Engineers has also been conducted and the proposed framework has generally been given high maintainability rating. © 2022 ACM.

关键词： Software testing

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