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ATP_mCNN: Predicting ATP binding sites through pretrained language models and multi-window neural networks

computers in Biology and Medicine 2025年 185卷 109541-109541页

作者： Le, Van-The Malik, Muhammad-Shahid Lin, Yi-Jing Liu, Yu-Chen Chang, Yan-Yun Ou, Yu-Yen Department of Computer Science and Engineering Yuan Ze University Chung-Li32003 Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Chung-Li32003 Taiwan Department of Computer Sciences Karakoram International University Gilgit-Baltistan 15100 Pakistan

Adenosine triphosphate plays a vital role in providing energy and enabling key cellular processes through interactions with binding proteins. The increasing amount of protein sequence data necessitates computational methods for identifying binding sites. However, experimental identification of adenosine triphosphate-binding residues remains challenging. To address the challenge, we developed a multi-window convolutional neural network architecture taking pre-trained protein language model embeddings as input features. In particular, multiple parallel convolutional layers scan for motifs localized to different window sizes. Max pooling extracts salient features concatenated across windows into a final multi-scale representation for residue-level classification. On benchmark datasets, our model achieves an area under the ROC curve of 0.95, significantly improving on prior sequence-based models and outperforming convolutional neural network baselines. This demonstrates the utility of pre-trained language models and multi-window convolutional neural networks for advanced sequence-based prediction of adenosine triphosphate-binding residues. Our approach provides a promising new direction for elucidating binding mechanisms and interactions from primary structure. © 2024 Elsevier Ltd

关键词： Convolutional neural networks

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Dynamic programming Algorithm using Furniture Industry 0/1 Knapsack Problem 5

Dynamic Programming Algorithm using Furniture Industry 0/1 K...

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5th International Conference on Cybernetics and Intelligent Systems, ICORIS 2023

作者： Anditta, Mietha Amartya, Natashya Warnars, Laurens Spits Warnars, Harco Leslie Hendric Spits Ramadhan, Arief Siswanto, Teddy Mantoro, Teddy Noordin, Nurulhuda Bina Nusantara University School of Computer Science Computer Science Departement Jakarta11530 Indonesia Bina Nusantara University School of Information Systems Information Systems Departement Jakarta11530 Indonesia Bina Nusantara University Binus Graduate Program - Computer Science Computer Science Departement Jakarta11530 Indonesia Telkom University Pjj Informatika Bandung40257 Indonesia Trisakti University Information Systems Department Jakarta11440 Indonesia Sampoerna University Faculty of Engineering and Technology Jakarta12760 Indonesia Universiti Teknologi Mara School of Computing Sciences College of Computing Informatics and Mathematics Selangor Malaysia

ISBN: (纸本)9798350369489

Dynamic programming is a fundamental algorithm that can be found in our daily lives easily. One of the dynamic programming algorithm implementations consists of solving the 0/1 knapsack problem. A 0/1 knapsack problem can be seen from industrial production cost. It is prevalent that a production cost has to be as efficient as possible, but the expectation is to get the proceeds of the products higher. Thus, the dynamic programming algorithm can be implemented to solve the diverse knapsack problem, one of which is the 0/1 knapsack problem, which would be the main focus of this paper. The implementation was implemented using C language. This paper was created as an early implementation algorithm using a Dynamic program algorithm applied to an Automatic Identification System (AIS) dataset. © 2023 IEEE.

关键词： Dynamic programming

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The Recommendation System for Increasing the Independence of Micro, Small and Medium Enterprises (MSMEs) Using the Normalized Rating Frequency (NRF) Method 4

The Recommendation System for Increasing the Independence of...

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4th International Conference on Information and Communications Technology, ICOIACT 2021

作者： Lestari, Sri Yulmaini Aswin Kurniawan, Rio Sulyono Pratama, Yan Aditiya Faculty of Computer Science Informatics Engineering Study Program Bandar Lampung Indonesia Faculty of Business Economics Management Study Program Bandar Lampung Indonesia

ISBN: (纸本)9781665433945

Micro, Small, and Medium Enterprises (MSMEs) have an important role in improving the economy of small communities and the stability of the Indonesian economy. However, they still face various problems such as capital, raw materials, distribution, licensing, and others. This study developed a special treatment recommendation system to increase the independence of MSMEs by adopting a ranking-based method to produce recommendations related to problem-solving steps from MSMEs. The ranking method used Normalized Rating Frequency (NRF). This method performed an aggregation process of the ratings given by MSMEs in looking at the priority level of problem-solving based on previous experience. The result of the experiment showed that an average NDCG value was 0.7916. This explained that the quality of the ranking was good so that it was feasible to be recommended in solving problems in the form of special treatment to acquire to the independence of MSMEs. © 2021 IEEE

关键词： Recommender systems

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White Bread Mold Detection using K-Means Clustering Based on Grey Level Co-Occurrence Matrix and Region of Interest

White Bread Mold Detection using K-Means Clustering Based on...

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

作者： Qori Alfatah Putra Christy Atika Sari Eko Hari Rachmawanto Nur Ryan Dwi Cahyo Edy Mulyanto Mohamed Ayad Alkhafaji Study Program in Informatics Engineering University of Dian Nuswantoro Semarang Indonesia Department of Informatics Engineering University of Dian Nuswantoro Semarang Indonesia Department of Computer Science National University of Science and Technology DhiQar Iraq

This research paper presents a bread mold identification system that utilizes digital image processing techniques, specifically K-means clustering and thresholding, to accurately detect and classify mold-infected areas on bread. The system aims to provide valuable information regarding the safety of consuming mold-contaminated bread, enabling consumers to make informed decisions and reduce the risk of health issues associated with consuming mold-infested bread. the K-means clustering algorithm for mold classification, considering factors such as the number of iterations and the distance metric within the feature space to determine its accuracy. The GLCM feature extraction technique is employed to extract texture information from bread images, encompassing features such as standard deviation (110.62), contrast (1.46), energy, and homogeneity (0.96 and 0.77, respectively). Experimental results demonstrate that the Euclidean Distance yielded the highest result of 72.73, the Cosine Distance obtained the highest result of 8.25, and the City Block Distance obtained the highest result of 92.11. These findings showcase the effectiveness of the system in accurately detecting and classifying mold-infected areas on bread, thereby aiding in ensuring food safety and reducing health risks for consumers.

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Mapping and Visualization of Artificial Intelligence for Digital Economy Research: A Bibliometric Approach 4

Mapping and Visualization of Artificial Intelligence for Dig...

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4th IEEE International Conference of computer science and Information Technology, ICOSNIKOM 2022

作者： Maulana, Fairuz Iqbal Purnomo, Agung Pramono, Andi Arifin, Mohammad Nazir School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Binus Business School Undergraduate Program Bina Nusantara University Entrepreneurship Department Jakarta11480 Indonesia School of Design Bina Nusantara University Interior Design Department Jakarta11480 Indonesia Informatics Engineering Study Program University of Madura Pamekasan Indonesia

ISBN: (纸本)9798350399073

Artificial Intelligence (AI) seems to be a disruptive technology that defines and reshapes the economy, more efficient industrial processes, new business models, and the service sector, becoming the development of different practices than before. The literature shows that it will be included in all fields and people's lives, as is the case in the digital economy. Artificial Intelligence for Digital Economy has not been studied significantly. This study uses bibliometric analysis to graphically map scientific publications and research trends in the Artificial Intelligence for Digital Economy sector around the world in the last ten years. The Scopus database was used to collect metadata information for this study, and VOSViewer was used to demonstrate bibliometric network mapping. We use an article selection procedure starting with the searched keywords and year constraints and then exporting the database to a RIS file format. Over the last ten years, we retrieved 540 scientific publications published between 2012 and 2021 from the Scopus database. From the data obtained, researchers at the Russian Federation have the most published papers indexed by Scopus among the most productive countries (N=131), the most productive authors are Petrenko, S.A. (N=4), and the most subject area is computer science (N=246). We also use VOSViewer to map the Network Theme. This study recommends incorporating research subjects Artificial Intelligence for Digital Economy: Thing, Education, Platform, Global Economy, abbreviated as TEPGE research theme. © 2022 IEEE.

关键词： Mapping

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A Low Complexity ML-Based Methods for Malware Classification

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computers, Materials & Continua 2024年第9期80卷 4833-4857页

作者： Mahmoud E.Farfoura Ahmad Alkhatib Deema Mohammed Alsekait Mohammad Alshinwan Sahar A.El-Rahman Didi Rosiyadi Diaa Salama Abd Elminaam Cybersecurity Department Al-Zaytoonah University of JordanAmman11733Jordan Department of Computer Science and Information Technology Applied CollegePrincess Nourah Bint Abdulrahman UniversityP.O.Box 84428Riyadh11671Saudi Arabia Faculty of Information Technology Applied Science Private UniversityAmman11931Jordan Computer Systems Program-Electrical Engineering Department Faculty of Engineering-ShoubraBenha UniversityCairo11629Egypt Research Center for Artificial Intelligence and Cybersecurity Electronics and Informatics OrganizationNational Research and Innovation Agency(BRIN)KST Samaun SamadikunBandung40135Republic of Indonesia Jadara Research Center Jadara UniversityIrbid21110Jordan MEU Research Unit Middle East UniversityAmman11831Jordan

The article describes a new method for malware classification,based on a Machine Learning(ML)model architecture specifically designed for malware detection,enabling real-time and accurate malware *** an innovative feature dimensionality reduction technique called the Interpolation-based Feature Dimensionality Reduction Technique(IFDRT),the authors have significantly reduced the feature space while retaining critical information necessary for malware *** technique optimizes the model’s performance and reduces computational *** proposed method is demonstrated by applying it to the BODMAS malware dataset,which contains 57,293 malware samples and 77,142 benign samples,each with a 2381-feature *** the IFDRT method,the dataset is transformed,reducing the number of features while maintaining essential data for accurate *** evaluation results show outstanding performance,with an F1 score of 0.984 and a high accuracy of 98.5%using only two reduced *** demonstrates the method’s ability to classify malware samples accurately while minimizing processing *** method allows for improving computational efficiency by reducing the feature space,which decreases the memory and time requirements for training and *** new method’s effectiveness is confirmed by the calculations,which indicate significant improvements in malware classification accuracy and *** research results enhance existing malware detection techniques and can be applied in various cybersecurity applications,including real-timemalware detection on resource-constrained *** and scientific contribution lie in the development of the IFDRT method,which provides a robust and efficient solution for feature reduction in ML-based malware classification,paving the way for more effective and scalable cybersecurity measures.

关键词： Malware detection ML-based models dimensionality reduction feature engineering

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Determination of Giving 'Tips' Using Fuzzy Logic to Determine Restaurant Customer Service Satisfaction 3

Determination of Giving 'Tips' Using Fuzzy Logic to Determin...

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3rd International Conference on Computational science and Information Management, ICoCSIM 2019

作者： Priyanto, Dadang Zarlis, Muhammad Anggrawan, Anthony Graduate Program of Computer Science Department of Computer Science Faculty of Computer Science and Information Technology Universitas Sumatera Utara Medan Indonesia Department of Computer Science Faculty of Computer Science and Information Technology Universitas Sumatera Utara Medan Indonesia Informatics Engineering Universitas Bumigora Mataram Indonesia

Fuzzy logic can be used to represent obscurity based on terms such as high, old, hot, cold, and so on. Fuzzy logic can extend the range of truth values to all real numbers in intervals between 0 and 1. Numbers in this interval represent the possibility that the statement given is "true"or "wrong". The use of fuzzy logic can be used in everyday life, such as in the fields of medicine, engineering, agriculture, transportation, environmental science and also in economic and business applications. As in this study, it was used to calculate the ideal amount of 'tips' for restaurant waiters based on the service provided by restaurant waiters. The method used in this study is to use Mamdani fuzzy logic with the process of defuzzyfication using the Centroid of area (COA). The results of this study are that it can be determined the value crisp of giving tips to restaurant waiters is 45 thousand rupiah provided that the service provided for service = 7 (Excellent) and food service = 8 (Delicious).. © Published under licence by IOP Publishing Ltd.

关键词： Fuzzy logic

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Hybrid Encryption Based on Fernet and Rivest Shamir Adleman (RSA)

Hybrid Encryption Based on Fernet and Rivest Shamir Adleman ...

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

作者： Muhammad Dafi Hisbullah Christy Atika Sari Eko Hari Rachmawanto Lekso Budi Handoko Chaerul Umam Folasade Isinkaye Study Program in Informatics Engineering University of Dian Nuswantoro Semarang Indonesia Department of Computer Science Ekiti State University Ekiti Nigeria

RSA is an asymmetric encryption algorithm that uses two different keys, a public key to encrypt the plain text and a private key to decrypt the cipher text. Fernet is a symmetric encryption algorithm that uses a single key to encrypt and decrypt information. This study uses Fernet and RSA which is the combination of symmetric and asymmetric encryption called hybrid encryption. In addition, the cipher text will be hidden inside an image using Stepic. Hybrid Encryption uses asymmetric encryption to encrypt the symmetric encryption secret key, it will secure the symmetric encryption. The result of this study is the lowest error that we got as the MSE is 0.00% and is inversely proportional with the Peak Signal to Noise Ratio (PSNR) and Avalanche (AVA) with 79.00% and 42.34% in order. Inversely proportional to the length of the text that is hidden in the image, the longest text that is hidden, the more changes that we get in the image with the highest Unified Average Changing Intensity (UACI) and Number of Pixels Change Rate (NPCR) with the biggest image size with 46.48% for UACI and 99.86% for the NPCR.

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Low-Cost Air Box Application for Indoor Environment Classification and LSTM Microclimate Prediction 6

Low-Cost Air Box Application for Indoor Environment Classifi...

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6th International Conference on Control and Robotics, ICCR 2024

作者： Hsun-Jui, Hu Yu-Hsien, Chiu Pei-Ching, Yang Chang Jung Christian University Master Degree Program in Information and Design Tainan Taiwan Kaohsiung Medical University Department of Healthcare Administration and Medical Informatics Kaohsiung Taiwan Artificial Intelligence Research Center Chang Jung Christian University Tainan Taiwan Chang Jung Christian University Department of Computer Science and Information Engineering Tainan Taiwan

ISBN: (纸本)9798331518158

Air pollution is a significant issue because it burdens human health and the environment. Particulate matter with a diameter of 2.5 micrometers or smaller (PM2.5) can penetrate the lungs and enter the bloodstream, seriously affecting the cardiovascular system, causing strokes, and impacting the respiratory system. Modern individuals spend 70% to 90% of their time indoors, making indoor air quality even more important than outdoor air quality. To estimate and predict indoor air quality, this study utilizes low-cost, self-assembled air boxes based on the Internet of Things to collect various air quality data. The collected data is then used in an indoor air quality forecasting system that combines Long Short-Term Memory (LSTM) and K-means clustering methods to compare the overall performance of the algorithms. The experimental results are analyzed and statistically described based on each model method prediction accuracy and clustering results. These methods are integrated to develop an indoor air quality forecasting system to help indoor populations prevent issues in advance or optimize energy usage. © 2024 IEEE.

关键词： Indoor air pollution

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Automatic Identification and Reconstruction 3D Image of the Rhinosinusitis Mucus

Automatic Identification and Reconstruction 3D Image of the ...

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International Conference of Information and Communication Technology (ICoICT)

作者： Ondra Eka Putra Sumijan Muhammad Tajuddin Department of Informatics Technology Faculty of Computer Science Universitas Putra Indonesia YPTK Padang Padang Indonesia Doctoral Program in Information Technology Universitas Putra Indonesia YPTK Padang Padang Indonesia Department of Computer Science Bumigora University Mataram Indonesia

ISBN: (数字)9798350363432

ISBN: (纸本)9798350363449

Rhinosinusitis Mucus is mucus produced by mucus glands found in the nose in the paranasal sinus area which indicates inflammation. Segmentation of rhinosinusitis mucus is very difficult to do because of the many characteristics of different objects in the image of the paranasal Sinus CT-Scan in separating the mucus object with its background before the extraction process. The purpose of this study was to accurately identify and measure the mucus area of rhinosinusitis from CT-scan images of rhinosinusitis patients. The test data used in this study is secondary data from CT-Scan of paranasal sinus sagittal view in radiology RSUP M. Djamil Padang, Padang City, West Sumatra, Indonesia, using the Philips Ingenuity CT CT-Scan model type MRC880 numbered Tube series 163889. The segmentation process is carried out to obtain the optimal multi threshold value from each slice of the test image using the Improved Adaptive Multi Threshold (IAMT) segmentation method which produces a binary image to separate the mucus object with its background before the extraction process. Furthermore, the results of IAMT are applied to the identification and extraction model automatically to obtain the area of the rhinosinusitis mucus object. The extraction results were used for 2D to 3D image reconstruction in calculating the volume of rhinosinusitis mucus objects. The test results showed that the smallest area of rhinosinusitis mucus was 0.516 cm 2 and the largest was 1.807 cm 2 , and the average volume was 0.95 cm 3 with Accuracy is 96,5%. The identified areas and volumes indicate inflammation in the area of the paranasal sinuses and require treatment. Thus, this study can help doctors in making the right decision to take further medical action.

关键词： Image segmentation Visualization Adaptation models Three-dimensional displays Computed tomography Urban areas Nose Radiology Object recognition Image reconstruction

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