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Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS

Genomics, Proteomics & Bioinformatics 2022年第5期20卷 959-973页

作者： Juexiao Zhou Bin Zhang Haoyang Li Longxi Zhou Zhongxiao Li Yongkang Long Wenkai Han Mengran Wang Huanhuan Cui Jingjing Li Wei Chen Xin Gao Computer Science Program ComputerElectrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and TechnologyThuwal 23955-6900Saudi Arabia Computational Bioscience Research Center King Abdullah University of Science and TechnologyThuwal 23955-6900Saudi Arabia Department of Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Shenzhen Key Laboratory of Gene Regulation and Systems Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Academy for Advanced Interdisciplinary Studies Southern University of Science and TechnologyShenzhen 518055China

The accurate annotation of transcription start sites(TSSs)and their usage are critical for the mechanistic understanding of gene regulation in different biological *** fulfill this,specific high-throughput experimental technologies have been developed to capture TSSs in a genome-wide manner,and various computational tools have also been developed for in silico prediction of TSSs solely based on genomic *** of these computational tools cast the problem as a binary classification task on a balanced dataset,thus resulting in drastic false positive predictions when applied on the genome ***,we present Dee Re CT-TSS,a deep learningbased method that is capable of identifying TSSs across the whole genome based on both DNA sequence and conventional RNA sequencing *** show that by effectively incorporating these two sources of information,Dee Re CT-TSS significantly outperforms other solely sequence-based methods on the precise annotation of TSSs used in different cell ***,we develop a meta-learning-based extension for simultaneous TSS annotations on 10 cell types,which enables the identification of cell type-specific ***,we demonstrate the high precision of DeeReCT-TSS on two independent datasets by correlating our predicted TSSs with experimentally defined TSS chromatin *** source code for Dee Re CT-TSS is available at https://github.-com/Joshua Chou2018/Dee Re CT-TSS_release and https://***/biocode/tools/BT007316.

关键词： Transcription start site Machine learning Deep learning Meta-learning RNA sequencing

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Fine-Tuned MobileNetV2 and VGG16 Algorithm for Fish Image Classification 4

Fine-Tuned MobileNetV2 and VGG16 Algorithm for Fish Image Cl...

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4th International Conference on Informatics, Multimedia, Cyber and Information System, ICIMCIS 2022

作者： Fitrianah, Devi Suryaningrum, Kristien Margi Sagala, Noviyanti Tri Maretta Ayumi, Vina Lim, Siew Mooi School of Computer Science Bina Nusantara University Computer Science Department Jakarta Indonesia School of Computer Science Bina Nusantara University Mathematics Statistics Department Jakarta Indonesia Universitas Mercu Buana Informatics Engineering Program Faculty of Computer Science Jakarta Indonesia Tunku Abdul Rahman University College Faculty of Computing and Information Technology Computer Science Department Kuala Lumpur Malaysia

ISBN: (纸本)9781665473279

Study on the identification and classification of fish is challenging and valuable because of its role in advancing the marine and agricultural fields. This research has benefits interms of monitoring fish populations and ecosystems in a particular area. Furthermore, this research helps monitor fish that are considered threatened or endangered so that it makes iteasier to map prohibited areas for fishing. This research aims to know performance of MobileNetV2 and VGG16 with parameter tuning process by identifying the value of batch size, epoch, learning rate, and optimizer for fish image dataset. The proposed research phase consists of five main stages, including experimental setup, dataset construction, dataset preprocessing, dataset training and modelling and evaluation. As the result, VGG16 obtained the highest accuracy value. For VGG16 without fine-tuning, the testing accuracy is 98.07%. For VGG16 with fine-tuning, the testing accuracy is 96.56%. © 2022 IEEE.

关键词： Fish

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Measurement of Muscle Stimulation and Hot Compression for Rehabilitation 3

Measurement of Muscle Stimulation and Hot Compression for Re...

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3rd International Conference on Electrical, Communication and computer engineering, ICECCE 2021

作者： Chirakanphaisarn, Neramitr Thongkanluang, Thadsanee Thammasat University Faculty of Engineering Department of Electrical and Computer Engineering Thailand Suratthani Rajabhat University Program in Materials Technology Manufacturing Faculty of Science and Technology Thailand

ISBN: (纸本)9781665438971

This research is to study the electric muscle stimulation system and hot compress. As well as focusing on building tools for applications in rehabilitation medicine and physical therapy. The neuromuscular system is an important mechanism in human life. In the event that the muscles are stressed or contracted while the subject is recovering, the need for recovery and stimulation tools is an important part of the physical therapy. We designed electrical circuits for automatic control and used an ARDUINO microcontroller to connect analog and digital ports to transmit and receive clinical parameters. The number of voluntary subjects was 20. Each subject remembered to perform 5 stimulation sessions for 10 minutes. Total period that the researcher collects data is approximately 3 months. The trials were based on ethical studies in humans, where trials and researches showed that subjects were 980% satisfied with very few side effects, and subjects had improved muscle development. © 2021 IEEE.

关键词： Muscle

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Email Spam Detection Using Logistic Regression and Explainable AI

Email Spam Detection Using Logistic Regression and Explainab...

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International Conference on Electrical, computer and Communication engineering (ECCE)

作者： Sumit Kanti Sarker Ratul Bhattacharjee Md Abu Sufian Md Solaiman Ahamed Md Abu Talha Faiza Tasnim K.M. Nazmul Islam Sharia Tasnim Adrita Department of Computer Science & Engineering (CSE) Faculty of Science & Technology (FST) American International University Bangladesh Dhaka Bangladesh Bachelor of Science in Information Technology (BSIT) Cybersecurity Program Concentrations Washington University of Science and Technology (WUST) VA USA Department of Electrical and Electronics Engineering (EEE) Faculty of Engineering (FE) American International University Bangladesh Dhaka Bangladesh Department of Computer Science and Engineering (CSE) Faculty of Science & Engineering Northern University Bangladesh-(NUB) Dhaka Bangladesh

ISBN: (数字)9798350357509

ISBN: (纸本)9798350357516

Email spam detection is crucial for ensuring a positive user experience and maintaining communication security. This study presents a novel spam detection approach leveraging Logistic Regression, optimized through hyperparameter tuning and enhanced with Explainable Artificial Intelligence. The proposed method is evaluated on a large-scale dataset of emails collected from a real-world spam detection system. Term Frequency-Inverse Document Frequency is utilized for feature extraction, converting email text into numerical representations. XAI introduces interpretability by highlighting critical features such as "pill," "PHP," and "Businessweek," which indicate spam classification patterns. Metrics such as precision, recall, and the confusion matrix are employed to assess the model’s performance, ensuring a balanced evaluation. Hyperparameter optimization using Grid Search CV achieves an optimal regularization parameter (C = 100) and maximum iterations (maxiter=100), resulting in an impressive F1 score of 98.76%, accuracy of 98.82%, precision of 98.62%, and recall of 98.90%.

关键词： Logistic regression Explainable AI Filtering Unsolicited e-mail Computational modeling Predictive models Transformers Frequency conversion Feature extraction Tuning

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Mammogram Breast Cancer Classification Based on Deep-Convolutional Neural Network

Mammogram Breast Cancer Classification Based on Deep-Convolu...

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International Seminar on Application for technology of Information and Communication (ISemantic)

作者： Avissa Aurellia Amadea Christy Atika Sari Eko Hari Rachmawanto Wellia Shinta Sari Mohammed S. Noori Mohamed Ayad Alkhafaji Study Program in Informatics Engineering University of Dian Nuswantoro Semarang Indonesia Study Program in Information Systems University of Dian Nuswantoro Semarang Indonesia Department of Computer Engineering Technology Northern Technical University Mosul Iraq Department of Computer Science National University of Science and Technology DhiQar Iraq

Based on WHO’s data, breast cancer is one of the most deadly diseases that has claimed many victims, especially women. This disease begins with the presence of an undetected and eventually turns into malignant (cancer). This happens due to ignorance of the importance of having a medical check-up even though in good health. Doctors and researchers can prevent the development of tumor cells through treatment that begins with radiological examinations to identify the possibility of a person being affected by this disease. One of the most frequently used techniques is Mammography. This technique can detect the presence of tumor cells using advanced technology and several methods in displaying the patient’s diagnostic results on low-dose X-rays in the form of mammogram images. The technology is inseparable from the methods used to identify the presence of tumor cells. In this study, we have proposed the CNN method based on the deep-CNN model to identify mammogram images in the detection of breast cancer cells with average evaluation results in terms of accuracy, precision, recall, specificity, and f-measure on mammogram image datasets of 99.52%, 99.72%, 99.31%, 99.72%, and 99.5%. These results showed that this method has a good performance in breast cancer detection.

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A Comparison Diagnosis Algorithm for Conditional Fault Local Diagnosis of Multiprocessor Systems 25th

A Comparison Diagnosis Algorithm for Conditional Fault Loca...

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25th International computer Symposium on New Trends in computer Technologies and Applications, ICS 2022

作者： Lv, Yali Lin, Cheng-Kuan Hsu, D. Frank Fan, Jianxi School of Information Technology Henan University of Chinese Medicine Zhengzhou China Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan Undergraduate Degree Program of Systems Engineering and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan Computer Science and Information Engineering Chung Cheng Institute of Technology NDU Taoyuan City Taiwan Department of Computer and Information Science Fordham University New York United States School of Computer Science and Technology Soochow University Suzhou China

ISBN: (纸本)9789811995811

An efficient diagnosis is very important for a multiprocessor system. In this paper, we present a (α, β) -trees combination S(u, X, α, β) and give some conclusions about the local diagnosis. Based on the (α, β) -trees combination, we give a conditional fault local diagnosis algorithm to identify the fault or fault-free status of each processor correctly under the MM ∗ model when the number of faulty nodes does not exceed α+ 2 β- 3 and every node has at least one fault-free neighboring node. According to our results, a connected network with a (α, β) -trees combination S(u, X, α, β) for a node u is conditionally locally (α+ 2 β- 3 ) -diagnosable at node u and the time complexity of our algorithm to diagnose u is O(α2β+ αβ2). As an application, we show that our algorithm can identify all the faulty nodes of n-dimensional star graph Sn if the faulty node number does not exceed 3 n- 8. Compared with existing algorithms, our algorithm allows more faulty node in a multiprocessor system. © 2022, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Computational complexity

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Enhancement of Channel Capacity in 5G Ultra Dense Network-UDN 2

Enhancement of Channel Capacity in 5G Ultra Dense Network-UD...

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2nd International Conference on Edge Computing and Applications, ICECAA 2023

作者： Rastogi, Ritesh Shanthi, T. Kumar Naik, Pramod Sheela, M. Sahaya Mishra, A.K. Nandhini, T.J. Delhi India Paavai Engineering College Department of Ece Chennai India Dayananda Sagar University Departmeny of Computer Science Engineering Bangalore India Vel Tech Rangarajan Dr.Sagunthala R&d Institute of Science and Technology Department of Ece Chennai India Dhofar University Math Unit Foundation Program Salalah Oman Chennai India

ISBN: (纸本)9798350347579

A 5G ultra dense network architecture makes use of a high density of micro cell base stations to provide increased coverage, capacity, and performance for 5G communication systems. This is accomplished by the utilization of a very densely packed network. A 5G ultradense network is another name for this particular category of network. Ultradense networks are built to overcome the limitations of ordinary cellular networks. This is accomplished by increasing the number of base stations that are located inside a given area. This is performed by reducing the coverage area provided by each base station, which ultimately leads to an increase in the capacity of the entire network. The maximum data rate or capacity that may be obtained through a certain wireless channel is referred to as the 'channel capacity' in a 5G ultradense network, when the phrase 'channel capacity' is used. One possibility is that this represents the maximum quantity of data that can be transmitted across the channel. These criteria, which represent the capabilities of the channel, can be used to evaluate the performance of channels and equipment on 5G networks. This article presents for further research a model for improving the channel capacity of the 5G ultradense network. The model can be found at the end of the article. This change will result in an increase in both the usefulness of the channel and the amount of bandwidth that it consumes;both of these aspects will improve. The fact that it uses a very small quantity of energy and power in compared to other methods is the major trait that sets it apart from other methods. This technology is superior to others in terms of both the amount of data it can communicate and the amount of electricity it consumes in the process. © 2023 IEEE.

关键词： Energy efficiency

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Improving Out-of-Distribution Generalization in Graphs via Hierarchical Semantic Environments

Improving Out-of-Distribution Generalization in Graphs via H...

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Conference on computer Vision and Pattern Recognition (CVPR)

作者： Yinhua Piao Sangseon Lee Yijingxiu Lu Sun Kim Department of Computer Science and Engineering Seoul National University Institute of Computer Technology Seoul National University AIGENDRUG Co. Ltd. Interdisciplinary Program in Artificial Intelligence Seoul National University

ISBN: (数字)9798350353006

ISBN: (纸本)9798350353013

Out-of-distribution (OOD) generalization in the graph domain is challenging due to complex distribution shifts and a lack of environmental contexts. Recent methods attempt to enhance graph OOD generalization by generating flat environments. However, such flat environments come with inherent limitations to capture more complex data distributions. Considering the DrugOOD dataset, which contains diverse training environments (e.g., scaffold, size, etc.), flat contexts cannot sufficiently address its high heterogeneity. Thus, a new challenge is posed to generate more seman-tically enriched environments to enhance graph invariant learning for handling distribution shifts. In this paper, we propose a novel approach to generate hierarchical seman-tic environments for each graph. Firstly, given an input graph, we explicitly extract variant subgraphs from the in-put graph to generate proxy predictions on local environ-ments. Then, stochastic attention mechanisms are employed to re-extract the subgraphs for regenerating global environ-ments in a hierarchical manner. In addition, we introduce a new learning objective that guides our model to learn the diversity of environments within the same hierarchy while maintaining consistency across different hierarchies. This approach enables our model to consider the relationships between environments and facilitates robust graph invariant learning. Extensive experiments on real-world graph data have demonstrated the effectiveness of our framework. Par-ticularly, in the challenging dataset DrugOOD, our method achieves up to 1.29% and 2.83% improvement over the best baselines on IC50 and EC50 prediction tasks, respectively.

关键词： Training computer vision Attention mechanisms Computational modeling Semantics Stochastic processes Pattern recognition

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Features Reduction with PCA Technique for Malware Detection Using Machine Learning

Features Reduction with PCA Technique for Malware Detection ...

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International Conference on Computing, engineering, and Design (ICCED)

作者： Teddy Mantoro Agung Ginanjar Media Anugerah Ayu Umar Aditiawarman Department of Computer Science Faculty of Engineering and Technology Sampoerna University Jakarta Indonesia Postgraduate Program - School of Computer Science Nusa Putra University Sukabumi Indonesia

Malware had been a problem for quite some times since it spreads easily and can cause various problems. Currently, malware is also one of the big threats for internet users. With a huge number of internet users today, techniques that can automatically detect malware before it infects the system is required. This study aims to develop malware detection using machine learning approach with Principal Component Analysis (PCA) as feature reduction. PCA (Principal Component Analysis) is expected to be able to reduce the number of features which then could also reduce the learning time but do not reduce its accuracy significantly. There were four machine learning classifiers used in this study, i.e. K-Nearest Neighbor, Decision Tree, Naïve bayes, and Random Forest. The n-components used in this study were 20 and 34 and the ratio of test and train in the dataset was 35% for test and 65% for training. The results have shown that the best performance come from the detection using random forest with 34 n-component and 100 n-estimator with the average accuracy was 0.991688.

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Enhancing Security Information and Event Management (SIEM) by Incorporating Machine Learning for Cyber Attack Detection

Enhancing Security Information and Event Management (SIEM) b...

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International Conference on Computing, engineering, and Design (ICCED)

作者： Media Anugerah Ayu Dimas Erlangga Teddy Mantoro Dini Handayani Department of Computer Science Faculty of Engineering and Technology Sampoerna University Jakarta Indonesia Postgraduate Program - School of Computer Science Nusa Putra University - Sukabumi Indonesia

Network security is a crucial component of Information technology, yet organizations continue to grapple with meeting established security benchmarks. Given the rise in cyber-attacks and the continuous emergence of new attack types, it’s practically infeasible to persistently update attack patterns or signatures within security parameters. Key tools such as Intrusion Detection Systems (IDS) and Security Information and Event Management (SIEM) are instrumental in monitoring network traffic and identifying potential threats. However, these tools face limitations, such as the high volume of alerts produced by IDS and the use of rule-based method, also the inability of SIEM tools to analyze logs comprehensively to identify inappropriate activities. This research has conducted anomaly detection using machine learning process to classify cyber-attacks network flow collected from IDS that installed incident network infrastructure. The analysis of IDS using machine learning, integrated with SIEM. The algorithm used in this research was Random Forest Classifier using CSE-CID-IDS2018 dataset pre-processed with Principal Component Analysis (PCA). Results of the experiments show that Random Forest Classifier Model, when combined with Principal Component Analysis (PCA), yields the most commendable results when applied to a 70/30 training/testing data ratio with accuracy of 0.99953.

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