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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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IoT for Water Quality Categorization 5

IoT for Water Quality Categorization

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

作者： Sastrohartono, Hermantoro Krisdiarto, Andreas Wahyu Uktoro, Arief Ika Rahutomo, Reza Suparyanto, Teddy Pardamean, Bens Institute of Agriculture Stiper Faculty of Agricultural Technology Agricultural Engineering Department Yogyakarta Indonesia Bina Nusantara University School of Information Systems Information System Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics & Data Science Research Center Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798350369489

In agricultural water research, the adoption of Internet of Things (IoT) technology has emerged as a pivotal approach for large-scale data collection. Water availability in the context of water quality is very important, both for domestic and industrial purposes. For domestic purposes, drinking water and bathing water are separated. Meanwhile, for the palm oil industry, boiler filler is differentiated from additional process water (dilution water). Water quality parameters can be assessed from turbidity and Total Dissolve Solid (TDS). Measurements using measuring instruments separately and repeatedly require significant energy, time, and costs. This research was conducted with the primary objective of presenting a novel method for categorizing water quality with the approach of IoT sensor technology. The research methodology entailed the utilization of an integrated IoT water sensors system in conjunction with manual water categorization. The methods consist of (1) system design, (2) design and installation of sensor and IoT-based microcontrollers, and (3) accuracy and precision testing compared with laboratory measurements. The precision of the integrated IoT water sensors was assessed through a dedicated sensor precision test, resulting in an accuracy rate of 94.4% for the turbidity sensor and 97.5% for the TDS sensor. Notably, this approach successfully discriminated drinking water with valid categorization, while other water types, including groundwater, water with tea, and water with coffee, yielded null categorization results. © 2023 IEEE.

关键词： Internet of things

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bioinformatics tools and resources for cancer and application

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Chinese Medical Journal 2024年第17期137卷 2052-2064页

作者： Jin Huang Lingzi Mao Qian Lei An-Yuan Guo Department of Thoracic Surgery West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengduSichuan 610041China Hubei Bioinformatics&Molecular Imaging Key Laboratory College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei 430074China

Tumor bioinformatics plays an important role in cancer research and precision *** primary focus of traditional cancer research has been molecular and clinical studies of a number of fundamental pathways and *** recent years,driven by breakthroughs in high-throughput technologies,large-scale cancer omics data have accumulated *** to effectively utilize and share these data is particularly *** address this crucial task,many computational tools and databases have been developed over the past few *** help researchers quickly learn and understand the functions of these tools,in this review,we summarize publicly available bioinformatics tools and resources for pan-cancer multi-omics analysis,regulatory analysis of tumorigenesis,tumor treatment and prognosis,immune infiltration analysis,immune repertoire analysis,cancer driver gene and driver mutation analysis,and cancer single-cell analysis,which may further help researchers find more suitable tools for their research.

关键词： Tumor bioinformatics Cancer research Tools databases

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

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

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International Conference on Cybernetics and Intelligent System (ICORIS)

作者： Nicholas Dominic 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)9798331539603

ISBN: (纸本)9798331539610

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.

关键词： Radio frequency Social networking (online) High dimensional data Linear regression Nearest neighbor methods data science Electronic commerce Intelligent systems Cybernetics Context modeling

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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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Mobile Application Implementation as Agriculture 4.0 Strategy for Sugarcane Yield Prediction 9

Mobile Application Implementation as Agriculture 4.0 Strateg...

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9th International HCI and UX Conference in Indonesia, CHIuXiD 2023

作者： Mawandha, Hangger Gahara Rahutomo, Reza Suparyanto, Teddy Pardamean, Bens Institut Pertanian Stiper Faculty of Agricultural Technology Yogyakarta55282 Indonesia Bina Nusantara University School of Information Systems Information Systems Department Jakarta 11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta 11480 Indonesia Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta 11480 Indonesia

ISBN: (纸本)9798350304084

Information engineering strategies play a significant and transformative role in shaping the landscape of digital agriculture. It drives innovation and efficiency in modern farming practices, with a specific focus on enhancing the value of agricultural commodities, such as sugarcane. The application of mobile technology plays a crucial part in achieving increased sugarcane productivity. Mobile applications, equipped with advanced developer features, offer rapid and user-friendly access to vital information. Traditional methods of estimating sugarcane production relied on manual data recording on paper, followed by data transfer to computer systems, typically managed by sugar factory junior plant officers. This conventional approach presents several inherent weaknesses, including time and effort intensiveness during data recording and entry. Additionally, the potential for errors in calculation and data input is a concern. The storage capacity for paper-based documents is finite, and farmers are often unable to autonomously assess their production potential. The objective of this research is to confront these obstacles by creating a sugarcane production application for Android. This application functions as an information engineering approach focused on forecasting sugarcane yields for plantation owners and their assistants. The development procedure adhered to the systematic waterfall method, following the principles of the Software Development Life Cycle (SDLC) model. data collection was carried out through observations, while interviews with junior plant officers provided valuable insights into sugarcane estimation techniques. Analysis involved the synthesis of observational and interview data to inform the design of the application's interface and algorithmic system. The resulting application significantly simplifies the process of estimating production potential for farmers, enabling them to access sugarcane productivity data during harvest. Consequently, sugar

关键词： Forecasting

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BERT-based Topic Modeling Approach for Malaria Research Publication 4

BERT-based Topic Modeling Approach for Malaria Research Publ...

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

作者： Hidayat, Alam Ahmad Nirwantono, Rudi Budiarto, Arif Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665473279

Malaria is a communicable disease with half of the global population at risk due to its high morbidity and mortality rates. A massive number of studies are dedicated to malaria research, so it plays a key role in formulating the proper prevention strategy and effective malaria treatment. With the overwhelming number of updated publications in the field, an unsupervised text mining approach such as topic modeling may provide an alternative method for the malaria researcher to keep pace with new insights. In this work, we collect metadata of malaria publications from the PubMed database to perform BERT-based topic modeling to find well-defined topics regarding malaria research. The method is largely based on the popular BERTopic pipeline. We compare the performance of three different language models to generate document embeddings from the data. The dimension reduction and the density-based clustering algorithm are used to cluster the embeddings. The topic representation is computed based on the semantic similarity of the class TF-IDF representation. The substance of the resulting topics is then manually annotated based on the top words of each topic. We demonstrate that by merging initial topics into larger topics using hierarchical clustering and manual content-based examination, the evaluated coherence measure can be further improved, thus enhancing the topic's interpretability. Our modeling result is able to extract ten major topics recurring in the malaria research publication published from 2017-2022. The result provides preliminary insight to understand the dynamics and patterns of malaria research over the years © 2022 IEEE.

关键词： Diseases

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