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4th International Conference on Cybernetics and Intelligent System, ICORIS 2022

作者： Azizatikarna, Kians Parung, Deby Erina Amirullah, Dian Hidayat, Alam Ahmad Cenggoro, Tjeng Wawan Budiarto, Arif Simon Pardamean, Bens Genetics Indonesia Jakarta12940 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Bina Nusantara University BINUS Graduate Program - Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665453950

As the cost of genetic testing becomes more affordable each year, direct-to-customer (DTC) genetic testing services witness rapid market growth. This has encouraged the development of an easy-to-use website application to optimize potential customers to obtain informed choice regarding the offered DTC genetic testing as well as purchasing information. We present a wireframing process as a part of the agile software development process to build a web portal prototype for an Indonesia-based genetic testing service called DNAku. The approach in building the prototype used in this case is a part of the Agile Software Development Method. In brief, the wireframing stage resulted in this work consists of three main important outcomes. The first one is the use case diagram as a blueprint of this web-based system. A site map is then proposed as an extended version of the use case diagram which visualizes the whole pages with the links. Finally, based on this site map a series of page mock-ups are designed using Hyper Text Marking Language (HTML) and Cascading Style Sheets (CSS). The result of the prototype can be used as the basis for the next development stage, which is the coding stage based on the collected feedback from users. Considering the continuous application development via the wireframing method by taking into account the cycle of feedbacks from involved parties, this approach can strengthen the infrastructure to sustain DTC genetic business model, which has a niche market in Indonesia. © 2022 IEEE.

关键词： Sales

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A Novel Machine Learning Classifier Based on Genetic Algorithms and data Importance Reformatting

arXiv

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arXiv 2024年

作者： Alkhayyat, A.K. Hewahi, N.M. Big Data Science and Analytics Program College of Science University of Bahrain Bahrain Department of Computer Science College of Information Technology University of Bahrain Bahrain

In this paper, a novel classification algorithm that is based on data Importance (DI) reformatting and Genetic Algorithms (GA) named GADIC is proposed to overcome the issues related to the nature of data which may hinder the performance of the Machine Learning (ML) classifiers. GADIC comprises three phases which are data reformatting phase which depends on DI concept, training phase where GA is applied on the reformatted training dataset, and testing phase where the instances of the reformatted testing dataset are being averaged based on similar instances in the training dataset. GADIC is an approach that utilizes the exiting ML classifiers with involvement of data reformatting, using GA to tune the inputs, and averaging the similar instances to the unknown instance. The averaging of the instances becomes the unknown instance to be classified in the stage of testing. GADIC has been tested on five existing ML classifiers which are Support Vector Machine (SVM), K-Nearest Neighbour (KNN), Logistic Regression (LR), Decision Tree (DT), and Naïve Bayes (NB). All were evaluated using seven open-source UCI ML repository and Kaggle datasets which are Cleveland heart disease, Indian liver patient, Pima Indian diabetes, employee future prediction, telecom churn prediction, bank customer churn, and tech students. In terms of accuracy, the results showed that, with the exception of approximately 1% decrease in the accuracy of NB classifier in Cleveland heart disease dataset, GADIC significantly enhanced the performance of most ML classifiers using various datasets. In addition, KNN with GADIC showed the greatest performance gain when compared with other ML classifiers with GADIC followed by SVM while LR had the lowest improvement. The lowest average improvement that GADIC could achieve is 5.96%, whereas the maximum average improvement reached 16.79%. © 2024, CC BY.

关键词： Adversarial machine learning

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Bioinformatics exploration into potential mechanisms of Calamus draco for colorectal cancer treatment

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Procedia computer science 2024年 245卷 127-136页

作者： Christian Kenneth Rudi Nirwantono Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Biotechnology Department Faculty of Engineering Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program – Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

As one of the cancer types with the highest incidence rates, colorectal cancer (CRC) would benefit from treatments with fewer side effects and reduced treatment-resistant potential. One of the options is to harness the anti-CRC potential of natural products. Previous studies have shown that Calamus draco exudate, dragon's blood, has anticancer activity in liver cancer and acute myeloid leukemia, but its bioactivity has not been studied in CRC. Here we conduct a bioinformatics study based on network pharmacology to explore the anti-CRC potential and mechanism of C. draco -derived compounds. The bioinformatics pipeline is composed of compound and target collection, biological network evaluation, and enrichment analysis. We found that there are 43 bioactive compounds from C. draco targeting 91 CRC-related targets, of which most compounds target MEN1, PTGS2, and IDH1. Further analyses show that the targets of C. draco are involved in the cellular response to hypoxia. By inhibiting those targets, C. draco bioactive compounds can potentially hinder angiogenesis and increase treatment response efficacy.

关键词： bioinformatics network pharmacology Calamus draco colorectal cancer drug discovery

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A systematic literature review of machine learning application in COVID-19 medical image classification

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Procedia computer science 2023年 216卷 749-756页

作者： Tjeng Wawan Cenggoro Bens Pardamean Computer Science Department School of Computer Science Bina Nusantara University Jakarta 11480 Indonesia. Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia. Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta 11480 Indonesia.

Detecting COVID-19 as early as possible and quickly is one way to stop the spread of COVID-19. Machine learning development can help to diagnose COVID-19 more quickly and accurately. This report aims to find out how far research has progressed and what lessons can be learned for future research in this sector. By filtering titles, abstracts, and content in the Google Scholar database, this literature review was able to find 19 related papers to answer two research questions, i.e. what medical images are commonly used for COVID-19 classification and what are the methods for COVID-19 classification. According to the findings, chest X-ray were the most commonly used data to categorize COVID-19 and transfer learning techniques were the method used in this study. Researchers also concluded that lung segmentation and use of multimodal data could improve performance.

关键词： COVID-19 classification disease machine learning medical images

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Optimal Deep Canonically Correlated Autoencoder-Enabled Prediction Model for Customer Churn Prediction

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computers, Materials & Continua 2022年第11期73卷 3757-3769页

作者： Olfat M.Mirza GJose Moses R.Rajender E.Laxmi Lydia Seifedine Kadry Cheadchai Me-Ead Orawit Thinnukool Department of Computer Science College of Computers and Information SystemsUmm Al-Qura UniversityMakkahSaudi Arabia Department of Computer Science Engineering Malla Reddy Engineering College500100India Department of Computer Science Engineering Lendi Institute of Engineering&TechnologyDenkada535005India Department of Computer Science and Engineering Vignan’s Institute of Information TechnologyVisakhapatnam530049India Department of Applied Data Science Noroff University CollegeNorway Program in Statistics and Information Management Faculty of ScienceMaejo UniversityChiang Mai50290Thailand Department of Modern Management and Information Technology College of Arts Media and TechnologyChiang Mai UniversityChiang Mai50200Thailand

Presently,customer retention is essential for reducing customer churn in telecommunication *** churn prediction(CCP)is important to predict the possibility of customer retention in the quality of *** risks of customer churn also get essential,the rise of machine learning(ML)models can be employed to investigate the characteristics of customer ***,deep learning(DL)models help in prediction of the customer behavior based characteristic *** the DL models necessitate hyperparameter modelling and effort,the process is difficult for research communities and business *** this view,this study designs an optimal deep canonically correlated autoencoder based prediction(ODCCAEP)model for competitive customer dependent application *** addition,the O-DCCAEP method purposes for determining the churning nature of the *** O-DCCAEP technique encompasses preprocessing,classification,and hyperparameter ***,the DCCAE model is employed to classify the churners or ***,the hyperparameter optimization of the DCCAE technique occurs utilizing the deer hunting optimization algorithm(DHOA).The experimental evaluation of the O-DCCAEP technique is carried out against an own dataset and the outcomes highlighted the betterment of the presented O-DCCAEP approach on existing approaches.

关键词： Churn prediction customer retention deep learning machine learning archimedes optimization algorithm

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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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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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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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A Hybrid CNN-SVM Approach for Malaria in Blood Cell Detection

A Hybrid CNN-SVM Approach for Malaria in Blood Cell Detectio...

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Software Engineering and Information Technology (ICoSEIT), International Conference on

作者： Andrea Stevens Karnyoto Mahmud Isnan 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

There is still a severe malaria problem worldwide, particularly in regions with limited access to diagnostic tools. It is crucial to develop a system for detecting malaria in blood cells. This paper presents a hybrid Convolutional Neural Network (CNN), and as a classifier, we use a Support Vector Machine (SVM) framework for the automated detection of malaria parasites in blood cell images. The proposed system leverages the strengths of CNNs in feature extraction and representation learning from images, combined with the discriminative power of SVMs for classification. Initially, CNN extracts intricate features from blood cell images, capturing essential patterns indicative of malaria infection. Subsequently, the extracted features are used to train an SVM classifier, enabling accurate discrimination between parasitized and uninfected blood cells. Experimental dataset evaluations were obtained from the Lister Hill National Center for Biomedical Communications website of the National Library of Medicine. The proposed model achieves a better f1-score, outperforming individual CNN or SVM models, around 0.015 compared to individual CNN models and 0.27 compared to individual SVM models. This hybrid CNN-SVM methodology offers a promising solution for accurately and efficiently detecting malaria parasites in blood cell images.

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Ensuring Ethical, Transparent, and Auditable Use of Education data and Algorithms on AutoML 23

Ensuring Ethical, Transparent, and Auditable Use of Educatio...

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Proceedings of the 2023 6th International Conference on Machine Learning and Natural Language Processing

作者： Kylie Griep Leah Stone Stephen Edwards Malik Hill Jialin Cui Chengyuan Liu Qinjin Jia Yang Song Department of Computer Science University of North Carolina Wilmington USA Master of Data Science Program University of North Carolina Wilmington USA Department of Computer Science NC State University USA

ISBN: (纸本)9798400709241

Automated machine learning (AutoML) creates additional opportunities for less advanced users to build and test their own data mining models. Even though AutoML creates the models for the user, there is still technical knowledge and tools needed to evaluate those models, and due to the black-box nature of the machine learning models, problems can arise with regard to algorithmic biases and fairness. Such biases can escalate in future applications, necessitating a structured approach for fairness evaluation in AutoML. This involves defining fairness criteria, selecting appropriate metrics, assessing fairness across groups, and addressing biases. In the realm of educational data mining, where AutoML is prevalent, biases related to attributes like gender or race can lead to unethical outcomes. Since fairness metrics vary in definition and strength, and some may even contradict others, making fairness evaluation more complex. In this paper, ten fairness metrics were chosen, explored, and implemented on four AutoML tools, Vertex AI, AutoSklearn, AutoKeras, and PyCaret. We identified two open educational datasets and built both prediction and classification models on those AutoML frameworks. We report our work in evaluating different machine learning models created by AutoML and provide discussions about the challenges in evaluating fairness in those models and our effort to mitigate and resolve the problems of algorithmic bias in educational data mining.

关键词： AutoML Automated machine learning algorithmic bias educational data mining fairness

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