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Implementation of Fine-Tuned BERT for Enzyme Classification Based on Gene Ontology

Implementation of Fine-Tuned BERT for Enzyme Classification ...

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International Conference of Advanced Informatics: Concept, Theory and Application (ICAICTA)

作者： Matthew Martianus Henry Christian Kenneth Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331520311

ISBN: (纸本)9798331520328

Enzymes are biocatalysts with vital roles in biological functions and many industrial applications. Diverse enzymes are classified using Enzyme Commission (EC) nomenclature, making differentiation challenging. On the other hand, another biological information, gene ontology (GO), can describe the biological aspects of enzymes, covering related biological processes (BP), molecular functions (MF), and their locations within cells (CC). This study proposes a novel EC class and subclass classification of enzymes within the ontology subclass based on their GO semantics using a Bidirectional Encoder Representation of Transformer (BERT). The BERT model is first fine-tuned using the preprocessed GO term name and definition, with the enzymes in each ontology class (BP, MF, or CC) are also divided based on how the GO assigned, either through manual annotation (NONIEA) or electronically inferred (IEA). BERT successfully obtained 0.93, 0.60, 0.99, 0.90, 0.40, and 0.35 F1 scores during fine-tuning for BP IEA, BP NONIEA, MF IEA, MF NONIEA, CC IEA, and CC NONIEA, respectively. On the test set, the fine-tuned BERT significantly outperformed GOntoSim, a framework to calculate semantic similarity based on classical information theory, in EC class classification across all metrics with less inference time in all ontology subclass. Expanded further to the EC subclass, BERT can classify the enzyme on the EC subclass level in BP IEA and MF IEA ontology subclass. However, longer epochs are needed in fine-tuning. This result shows that the names and definitions of GO terms are distinguishable features in classifying enzymes as an alternative to the information content approach.

关键词： Measurement Enzymes Semantics Bidirectional control Manuals Ontologies Transformers Encoding Biological information theory Informatics

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Systematic Literature Review on Metaheuristic Algorithms in SNP Analysis for Diseases

Systematic Literature Review on Metaheuristic Algorithms in ...

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International Conference on Cybernetics and Intelligent System (ICORIS)

作者： Jason Sebastian Sulistyawan Kuncahyo Setyo Nugroho Bens Pardamean Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331539603

ISBN: (纸本)9798331539610

Single-nucleotide polymorphism (SNP) analysis has become a pivotal strategy for drug discovery within bioinformatics, especially for incurable diseases like cancer. With the increasing number of researchers starting to embrace metaheuristic methods, a review was done by gathering papers from the Google Scholar database from 2018 to 2023, which resulted in 20 papers after title, abstract, and content filtering. The findings show that the Genetic Algorithm and the Harmony Search Algorithm have become popular approaches in SNP analysis, particularly in studies on breast cancer, age-related macular degeneration, and colorectal cancer. However, the review shows that while researchers have proven most methods effective in finding disease-related SNPs, a more measurable study in SNP analysis is needed, due to the lack of elaboration on measurement metrics in the found studies.

关键词： Macular degeneration Filtering Databases Metaheuristics Time measurement Internet Drug discovery Intelligent systems Genetic algorithms Systematic literature review

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Mitigating Berkson's Paradox with Neural Propensity Score Matching in E-Commerce Deals 6

Mitigating Berkson's Paradox with Neural Propensity Score Ma...

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6th International Conference on Cybernetics and Intelligent System, ICORIS 2024

作者： Dominic, Nicholas Pardamean, Bens Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta Indonesia BINUS Graduate Program - Master of Computer Science Bina Nusantara University Computer Science Department Jakarta Indonesia

ISBN: (纸本)9798331539603

Within observational Data science workloads, Berkson's paradox can lead to false causal inferences. One of the prominent quasi-experimental methods to mitigate this selection bias is Propensity Score Matching (PSM). An approach called Neural PSM (NPSM) was developed to overcome the drawbacks of conventional regression-based PSM, including its limited flexibility to model high-dimensional data and non-linear relationships that could cause imperfect covariate balance. In this study, a three-layer depth of Deep Neural Networks was designed to estimate propensity scores and finally balance both control and treatment groups of the Groupon dataset. An unsupervised k-Nearest Neighbor algorithm then helped the model to efficiently detect and cluster similar matching points. From the five salient features presented, NPSM successfully achieved lower differences in Cohen's d effect size, i.e., 0.313 for coupon duration, 0.017 for promotion length, 0.425 for quantity sold, -0.199 for limited supply, and 0.395 for Facebook likes. While these results mostly outperformed Linear Regression (LR) and Random Forest (RF) models, further evaluation is needed to verify the true effectiveness of NPSM in mitigating Berkson's paradox in broader e-commerce contexts. © 2024 IEEE.

关键词： Marketplaces

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Software Quality Assessment Methods and Standards in Weld Defect Detection for Shipbuilding

Software Quality Assessment Methods and Standards in Weld De...

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International Conference on Cybernetics and Intelligent System (ICORIS)

作者： Yonky Pernando Ford Lumban Gaol Haryono Soeparno Yulyani Arifin Computer Science Department BINUS Graduate Program Doctor of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331539603

ISBN: (纸本)9798331539610

Shipbuilder safety and performance, structural integrity of welded joints in shipbuilding is of utmost importance. Traditional manual inspection methods to detect any potential defect can be time consuming and susceptible to human errors; alternative inspection systems have proven more cost effective and accurate solutions than manual approaches for defect identification. This paper investigates how advanced software quality assessment standards and machine learning techniques such as Convolutional Neural Networks (CNNs) and You Only Look Once (YOLO) object identification framework can enhance weld defect detection. Research undertaken for this thesis addresses three core questions. 1) Which standards provide effective software quality assessments used for weld defect detection systems?; and 2) In what ways will they impact efficiency and reliability. How will implementation of these standards increase accuracy in manufacturing processes? Integrating high-quality annotated datasets, optimizing joint preparation and parameter settings, and using cloud solutions for computing needs can enable industries to achieve more reliable, efficient, and scalable defect detection. This proactive approach not only enhances immediate product quality, but also contributes to long-term durability and performance, decreasing maintenance costs and increasing overall reliability for steel plates used for marine applications. Furthermore, evidence has revealed that adopting software quality assessment standards in weld defect detection significantly enhances structural integrity as well as operational efficiency of shipbuilding operations.

关键词： YOLO Costs Welding Software quality Manuals Inspection Software reliability Convolutional neural networks Standards Defect detection

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Knowledge Graph-Enhanced Semantic Cache for Low-Latency and Cost-Effective Inference in Large Language Models

Knowledge Graph-Enhanced Semantic Cache for Low-Latency and ...

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International Conference on Information Management and Technology (ICIMTech)

作者： Nicholas Dominic Bens Pardamean Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798350390025

ISBN: (纸本)9798350390032

In organizational knowledge management, Large Language Model (LLM) caches act as a semantic repository gathered from previous LLM responses. Due to intensive calls from multiple users, LLM may suffer from high inference latency. While there are many prior available approaches to solve this problem, most of them are inherently complex. This paper introduced a Knowledge Graph-enhanced Semantic Cache mechanism as an alternative, lightweight technique to boost retrieval for similar prompts. The latest state-of-the-art open-source LLM, named Google's Gemma-2B-it, was used to generate sample prompts and responses as a draft, while a knowledge graph (KG) was built from Wikipedia sentences. To create embeddings of prompts and KG, all-MiniLM-L6-v2 from SentenceTransformer was used. This new cache system resulted in up to 28% improvement over a standard model. In particular, reinforcement with KG cache embeddings yielded more than 85% semantic cache accuracy. To map the next trajectory of this pilot study, an overview of the extended framework for LLM knowledge management was also presented in this paper. The framework includes the new KG- enhanced cache system equipped with scalable security and fallback mechanisms that can promote green technology through substantial improvements in latency, throughput, and overall LLM costs.

关键词： Large language models Semantics Throughput Knowledge management Internet Trajectory Security Online services Low latency communication Standards

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Measurement of Web-Based Merchant Application Portal (MAP) Using Function Point Analysis and Constructive Cost Model II 4

Measurement of Web-Based Merchant Application Portal (MAP) U...

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4th Asia Pacific Conference on Research in Industrial and Systems Engineering: Building Business Resilience to Face the Challenge in Pandemic Era, APCORISE 2021

作者： Santoso, Irvan Warnars, Harco Leslie Hendric Spits Gaol, Ford Lumban Abdurachman, Edi Soewito, Benfano Cyber Security Program Computer Science Department School of Computer Science Computer Science Program Binus Graduate Program Doctor of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Program Binus Graduate Program Doctor of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department Binus Graduate Program Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia

ISBN: (纸本)9781450390385

The development of technology and the internet is one of the critical factors that must be considered by companies especially those engaged in e-commerce. The web-based application is one of the tools used by e-commerce in making it easier for users to conduct transactions and data processing. The application that developed must be calculated carefully so the effectiveness and efficiency can be appropriately maintained. In this research, the calculation of the size of the software, effort, time, staff, and the total cost needed to work on an application was calculated using the Function Point Analysis (FPA) and Constructive Cost Model II (CoCoMo II) methods. The application that has been analyzed and estimated is Merchant Application Portal (MAP) which is an application designed by one of the companies in Indonesia. The estimation results obtained, scilicet the size of software amounted to 10,02972 KLOC, effort amounted to 48.521 Person Month, time development of 13 months, staff needed as many as four staff, and the estimated cost amounted to IDR 13,828,852.79 or $ 971.54. In addition, this calculation can be used by other companies to find out the resources needed in making a software to be more effective and efficient. © 2021 ACM.

关键词： Portals

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Leveraging ChemBERTa Robustness in Drug-Drug Interaction Classification via Molecular Decomposition

Leveraging ChemBERTa Robustness in Drug-Drug Interaction Cla...

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International Seminar on Research of Information Technology and Intelligent Systems (ISRITI)

作者： Christian Kenneth Alyssa Imani Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331519643

ISBN: (纸本)9798331519650

Understanding drug-drug interactions (DDIs) can benefit us by enhancing drug effectiveness and preventing side effects that arise from consuming multiple drugs administered together. However, as the number of novel drugs increases, predicting potential DDIs becomes more challenging. Previous studies have used the molecular language model ChemBERTa to predict potential DDIs, but the predictions were only tested on unseen drugs and not dissimilar drugs, while also performing poorly. In this study, we demonstrate that a simple molecular preprocessing method using BRICS decomposition can enhance ChemBERTa robustness in predicting potential DDIs for unseen-dissimilar drugs. Specifically, we employ fragmentation with a minimum fragment size of 5 (BRICS-5), which balances the number of fragments and decomposition speed. Using this method, we were able to improve ChemBERTa robustness, reflected by an approximate increase of 1.5% in recall and 2.2% in the f1-score compared to non-decomposed molecules. Our findings suggest that this preprocessing method could be useful in the development of future AI-based approaches for solving challenging molecular tasks across different settings and various model architectures.

关键词： Drugs Seminars Accuracy Data preprocessing Predictive models Robustness Data models Intelligent systems Information technology

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Explainable Tree-Based Boosting Algorithms for Smoker Detection Using Bio-Signals

Explainable Tree-Based Boosting Algorithms for Smoker Detect...

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International Seminar on Research of Information Technology and Intelligent Systems (ISRITI)

作者： Jason Sebastian Sulistyawan Kuncahyo Setyo Nugroho Bens Pardamean Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331519643

ISBN: (纸本)9798331519650

Many smoking-related diseases are difficult to treat and often fatal. Rather than treating diseased smokers, preventing the diseased is more achievable, though, many of them deny to being smokers, leading to another problem. Thus, this study aims to detect important aspects that can detect that the person is a smoker or not through their bio-signals through using SHAP, along with a comprehensive analysis of the used methods, gradient-boosting algorithms XGBoost, LightGBM, and CatBoost, known for their efficiency in handling complex datasets and non-linear relationships. The study then found that triglyceride, Gtp, hemoglobins significantly affect the body's responses to smoking, based on the CatBoosts’ results, having an AUC score of up to 0.8612 and an accuracy score of up to 0.7776 with the selected features.

关键词： Seminars Measurement Accuracy Predictive models Feature extraction Boosting Physiology Classification algorithms Reliability Diseases

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Cardiovascular Disease Analysis Using Correlational Analysis and Association Rules Mining for In-depth Analysis to Identify Predominant Variables

Cardiovascular Disease Analysis Using Correlational Analysis...

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2023 International Conference on computer science, Information Technology and Engineering, ICCoSITE 2023

作者： Siswanto, Boby Soeparno, Haryono Sianipar, Nesti F. Budiharto, Widodo Bina Nusantara University BINUS Graduate Program- Computer Science Computer Science Department Jakarta Indonesia Bina Nusantara University Engineering Faculty Food Technology Department Jakarta Indonesia Bina Nusantara University School of Computer Science Computer Science Department Jakarta Indonesia

ISBN: (纸本)9798350320954

Cardiovascular disease is one of the dangerous non-communicable disorders or diseases that has become one of the causes of death worldwide. Various studies have been conducted to prevent cardiovascular disease in the world. This study analyzed cardiovascular disease medical record data from the Kaggle public dataset by implementing correlational analysis combined with association rule mining to identify variables that are the predominant cause of cardiovascular disease. Correlational analysis can analyze the interrelationships between variables in a dataset, but not in depth. Association rule mining can identify the interrelationships of variables in the form of frequent item sets, which can be calculated for their support and confidence values. The result of this study is a combination of correlation analysis with association rule mining that can identify predominant variables to cause cardiovascular disease. Found that the variable gender=woman, height=short ( © 2023 IEEE.

关键词： Association rules

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Multi Fuzzy Criteria based Decision Model for Presidential Election in Indonesia

Multi Fuzzy Criteria based Decision Model for Presidential E...

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International Conference on Informatics and Computing (ICIC)

作者： Ditdit Nugeraha Utama Bagas Rizky Ramadhan Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta Indonesia Research Transfer Technology Office Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331517601

ISBN: (纸本)9798331517618

Inevery nation, the main goal of a presidential election is to choose a good leader. Citizens of a country need to thoroughly observe and assess the presidential presidential candidates before making their selection. A study was conducted to create a simple decision model using multiple fuzzy criteria, taking into account the constrained perspective of Indonesian citizens. In this context, the primary methods employed for respectively designing and developing the model were object-oriented design and fuzzy logic. According to 7 free-selected presidential candidates, the model simulation revealed that candi- date number 2 received the highest decision value, scoring $\mathbf{6 8. 5 4 2}$ points; with a gap value of $\mathbf{0. 4 9}$.

关键词： Fuzzy logic Object oriented modeling Voting Computational modeling Informatics Context modeling

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