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LDA Topic Modeling for Bioinformatics Terms in arXiv Documents

Procedia computer science 2024年 245卷 229-238页

作者： Andrea Stevens Karnyoto Matthew Martianus Henry Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

A wide variety of disciplines contribute to bioinformatics research, including computer science, biology, chemistry, mathematics, and physics. This study determines the number of research articles published on arXiv classified as bioinformatics topics and the most frequently used bioinformatics terms using topic modeling, Latent Dirichlet Allocation (LDA). An algorithm based on LDA is used to discover topics hidden within large collections of documents through the use of statistical analysis. Our research examined 226453 articles on arXiv between January 2023 and January 2024. As a result, there are more than 10521 articles categorized into bioinformatics topics. Most commonly, 6352 documents are in the "Mathematical Physics" category. The second most popular category is "computer science," with 2950 documents. Accordingly, the terms 'RNA,' 'sequence,' 'tree,' and 'homology' are the three most commonly used terms in bioinformatics. The study of RNA plays a vital role in molecular biology; thus, the study of RNA is prevalent in bioinformatics. Sequential data refer to the order in which nucleotides or amino acids can be found in a DNA molecule or a protein.

关键词： arXiv bioinformatics Latent Dirichlet Allocation

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A systematic literature review of machine learning application in COVID-19 medical image classification 7

A systematic literature review of machine learning applicati...

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7th International Conference on computer science and Computational Intelligence, CSCI 2022

作者： Daniel Cenggoro, Tjeng Wawan Pardamean, Bens Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 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. © 2022 Elsevier B.V.. All rights reserved.

关键词： COVID-19

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Exploring EfficientNet Variants for Image Encoding in Auxiliary Signal Guided Knowledge Encoder-Decoder Framework

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Procedia computer science 2024年 245卷 391-398页

作者： Matthew Martianus Henry Nur Adhianti Heryanto Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

The growing number of medical images has led to radiologist burnout, which seriously impacts the radiologist's performance. To address the previously mentioned issue, an Auxiliary Signal Guided Knowledge (ASGK) multimodal encoder-decoder framework was designed to automatically generate the medical report based on the proposed medical graph and natural language decoder. It utilizes DenseNet-121 as the image encoder. With DenseNet-121 lack of computational and memory efficiency, this study aims to explore the potential of EfficientNetB0 to EfficientNetB4 as an ASGK image encoder substitute. The framework is trained with IU X-Ray dataset for 30 epochs, with Adam optimizer, a learning rate of 0.01 with 0.8 decay rate, binary cross entropy loss for the medical tags, and cross-entropy loss for the generated medical captions. During the framework training process with each image encoder, the parameter that achieves the highest CIDEr score on the validation set is considered the best image encoder parameter and will be used on the test set. On the test set, EfficientNetB3 as an ASGK image encoder has been shown to increase the CIDEr score to 0.35, a significant increase from the 0.28 CIDEr score obtained by the ASGK using DenseNet-121. This score is only a 1% decrease from the best validation score. It suggests that not only EfficientNetB3 increases the framework's performance, it is also less prone to overfitting. This study has demonstrated that EfficientNetB3 is a potential image encoder substitute for DenseNet-121 in the ASGK framework.

关键词： Automated medical report generation DenseNet-121 EfficientNet Encoder-decoder framework

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Time-series Analysis of Correlation between Climatic Parameters and Dengue Fever in Indonesia 4

Time-series Analysis of Correlation between Climatic Paramet...

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

作者： Nirwantono, Rudi Trinugroho, Joko Pebrianto Sudigyo, Digdo Hidayat, Alam Ahmad Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Master of Computer Science Program Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665473279

Dengue fever is mainly caused by female mosquitoes from the genus Aedes. It predominantly occurs in equatorial to sub-tropical regions. The weather factors play a significant role in the mosquito life cycle, so a study on the impact of climate parameters on dengue incidence is required. This study aimed to understand the statistical association between the annual fluctuation of dengue cases with climate factors in Indonesia. Climatic data, annual rainfall, and annual mean ambient temperature of Indonesia were obtained from *** from 2010 to 2020, while the data on the annual incidence of dengue fever in Indonesia were collected from the Indonesian Health Profile by the Ministry of Health of Indonesia from 2010 to 2020. The association between climatic factors with dengue cases was calculated with Spearman statistical test after the data was indicated as not normally distributed. In addition, we performed Poisson regression analysis to examine how the changes in climatic parameters affect the dengue cases. The rain precipitation was insignificantly correlated with the dengue incidence in Indonesia during the study time. In contrast, the ambient temperature statistically showed a strong association with the dengue cases. The association between climatic factors and the number of dengue cases suggests that the model would likely be prospectively applied to the dengue early warning system as a nationwide intervention to reduce the epidemic impact in Indonesia. © 2022 IEEE.

关键词： Data mining

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Multilabel Machine Learning System for Predicting Gender and Age Group from Human Gait 2

Multilabel Machine Learning System for Predicting Gender and...

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2nd IEEE International Conference on Interdisciplinary Approaches in Technology and Management for Social Innovation, IATMSI 2024

作者： Qomariyah, Nunung Nurul Nurul Fajar, Ahmad Yono, Vincent Kazakov, Dimitar Bina Nusantara University School of Computing and Creative Arts Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Information System Management Information Systems Management Department Jakarta11480 Indonesia University of York Computer Science Department YO10 5GH United Kingdom

ISBN: (纸本)9798350360523

This paper explores the development of a multilabel machine learning system for predicting both gender and age from human gait patterns. Gait analysis, a non-intrusive method of identifying subtle nuances in human movement, has proven to be a rich source of information related to demographic characteristics. The research extends beyond traditional single-label classification approaches, adopting a multilabel framework to simultaneously predict gender and age *** study evaluates various multilabel machine learning algorithms, with the Random k-labeLsets (RAKEL) algorithm demonstrating superior performance in predicting gender and age labels from human gait datasets. The accuracy of the algorithm can reach up to 87%. We also compared the multilabel approach with several multiclass algorithms such as Decision Tree, Random Forest, Gradient Boosting, K-Neighbors and XGBoost. However, when we also considering the training time, Classifier Chain algorithm showed the best trade off with the accuracy of 86% and the training time is twice faster than the RAKEL algorithm. © 2024 IEEE.

关键词： Gait analysis

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Systematic Literature Review on Machine Learning Predictive Models for Indoor Climate in Smart Solar Dryer Dome 4

Systematic Literature Review on Machine Learning Predictive ...

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

作者： Setiawan, Karli Eka Elwirehardja, Gregorius Natanael Pardamean, Bens Bina Nusantara University BINUS Graduate Program Master of Computer Science Program Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia

ISBN: (纸本)9781665453950

Precise predictions of indoor climate conditions are required in the implementation of Smart Solar Dryer Dome (SDD). Trend development of prediction models is discussed in this review from 15 selected research papers (2018-2022) on indoor climate prediction which was obtained from research paper databases The output shows that the most used model for predicting indoor climate is Artificial Neural Network (ANN), especially Recurrent Neural Network (RNN) such as LSTM and GRU. However, there are some potential methods such as Transformer, Combined Support Vector Machines (SVM)-Deep Learning, and sequence-to-sequence which could outperform other commonly used models. Based on findings various opportunities exist to improve the precision of indoor climate prediction, which can bring power consumption efficiency and others benefit to Smart SDD users. Such studies may further be explored to produce more accurate machine learning models. © 2022 IEEE.

关键词： Domes

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Determining Variables Associated with Annual Oil Palm Yield: An Explainable Gradient Boosting Approach 8

Determining Variables Associated with Annual Oil Palm Yield:...

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8th International Conference on computer science and Computational Intelligence, ICCSCI 2023

作者： Elwirehardja, Gregorius Natanael Suparyanto, Teddy Miftakhurrokhmat Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Faculty of Agricultural Technology Institute of Agriculture STIPER Yogyakarta55282 Indonesia Faculty of Industrial Technology Universitas Islam Indonesia Yogyakarta55584 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

With the growing demands for Precision Agriculture (PA) in Indonesia, researchers have evaluated the utilization of Machine Learning for predicting oil palm yields and determining variables affecting them. Previous studies showed that meteorological variables, including rainfalls and wind speed, are associated with oil palm yields. In this research, the Extreme Gradient Boosting (XGBoost) model and the Shapley Additive exPlanations (SHAP) were deployed for analyzing the importance of 15 agrometeorological variables in predicting oil palm yield. The best model attained 1.911 RMSE and 0.855 RRʹ. By analyzing the weights and gains of the XGBoost model along with the SHAP values, it was found that the yield in the previous year, the age and number of plants, the area of peat lands, and meteorological parameters such as rainfall rates and the number of rainy days in the previous three years were considered important. The previous year's yield in particular possesses the greatest weight and gain values according to the model, and the highest SHAP value among all input variables. However, the meteorological data used in this research are only limited to rainfall rates and the number of rainy days. In the future, more diverse variables can be analyzed. © 2023 The Authors. Published by Elsevier B.V.

关键词： Machine Learning Oil Palm Yield SHAP XAI XGBoost

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Automatic question generation for bahasa indonesia examination using copynet

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Procedia computer science 2024年 245卷 953-962页

作者： Matthew Martianus Henry Gregorius Natanael Elwirehardja Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

In educational institutions, an educator is responsible for assessing the student's knowledge grasp through examination. Creating exam questions, even the low-level factoid questions, is time-consuming, especially for inexperienced educators. Therefore, this study aims to create a sequence-to-sequence model using CopyNet by exploiting its copying mechanism advantage to automatically generate Bahasa Indonesia factoid questions to ease the educator's burden. Indonesian records in the TyDi QA dataset are used as the model input. GRU and Bi-GRU are employed as the CopyNet encoder, while LSTM is used as the CopyNet decoder. The model that utilizes GRU as the encoder achieves BLEU1, BLEU2, BLEU3, BLEU4, and ROUGE-L scores of 0.28, 0.19, 0.14, 0.1, and 0.32, respectively. Bi-GRU utilization as the model encoder achieves BLEU1, BLEU2, BLEU3, BLEU4, and ROUGE-L scores of 0.26, 0.17, 0.12, 0.09, and 0.30, respectively. Models using either encoder still achieve low scores. However, compared with the previous work, the result is still on par regarding the BLEU score. Further examination found that the generated questions do not adhere to semantic and syntactical correctness. Adding more records to the dataset and utilizing a more advanced architecture like CopyBERT are encouraged to improve the model performance in future work. Despite the result, this study has shown that CopyNet, primarily designed for text summarization or single-turn dialogue, can be tailored for factoid question generation.

关键词： Automatic question generation Bahasa Indonesia Copying mechanism Natural language generation Sequence-to-sequence

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Utilization of Augmented Reality Technology in the Campus Environment 4th

Utilization of Augmented Reality Technology in the Campus En...

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4th International Conference on Inventive Computation and Information Technologies, ICICIT 2022

作者： Gaol, Ford Lumban Kamil, Mufti Ikhsan Iswardhana, Aria Muhammad Firnandes, Steven Gusda Fahrezi, Fazri Matsuo, Tokuro Hutagalung, Fonny Binus Graduate Program—Doctor of Computer Science Jakarta Indonesia Alam Sutera School of Information System Bina Nusantara University Jakarta Indonesia Advanced Institute of Industrial Technology Tokyo Japan University of Malaya Kuala Lumpur Malaysia

ISBN: (纸本)9789811974014

Technological advancements are accelerating in the modern day;one such advancement is augmented reality (AR) technology. Naturally, these advancements have an effect on various sectors of life, one of which is education. The education industry will be the most impacted if campuses implement and deploy augmented reality technology. One of these is through the use of augmented reality technology as an application-based learning medium for students in order to motivate them to learn and make it easier for them to improve their academic performance on campus. The issue at hand is the absence of utilization of augmentation reality technology as a learning medium on campus, which, of course, does not capitalize on technical advancements to improve student interest in learning. This study employs a research and development model. The method is divided into four phases: (1) planning;(2) data collecting;(3) analysis, discussion, and development;and (4) documentation. The findings of this study reveal that students enthusiastically support the usage of augmented reality technology as a learning medium in order to boost accomplishment and introduce new experiences through its use. However, it is required to have a system capable of serving as a technological medium, so that the construction of a system capable of serving as a medium for augmented reality may be easily accessed by students, who hope that this system would enable them to better their academic performance. © 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Students

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Hybrid approach sentiment analysis using Transformer-LSTM in the Indonesian language

Hybrid approach sentiment analysis using Transformer-LSTM in...

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

作者： Angel Karentia Ferdinand Winaya Derwin Suhartono Computer Science Department BINUS Graduate Program – Master of Bina Nusantara University Jakarta Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331519643

ISBN: (纸本)9798331519650

Sentiment analysis is widely used as a tool to find valuable insight from texts without explicitly expressed. Lots of techniques have already been used to get it but there still have shortcomings in data source or the model strategy itself. Indonesian language approximately has 199 million speakers across the world where 44 million speakers natively. Even with that great number, the resources for the Indonesian language's natural language processing are still limited, and hard to find the perfect way to define sentiment analysis in the Indonesian language. The state-of-the-art sentiment analysis method uses LSTM on a small corpus while the best in town is Transformer where it's easy to transfer learning from the Transformer pre-trained model into specific tasks. From this potential, combining the Transformer pre-trained model with LSTM can be an innovative strategy. This research compared the hybrid model of Transformer-LSTM build using three Indonesian languages’ Transformer-based pre-trained model on sentiment analysis task which can surpass the Transformer model with the highest increased 2.40% accuracy and 3.02% on F1 score.

关键词： Seminars Sentiment analysis Analytical models Accuracy Law Soft sensors Transfer learning Medical services Transformers Long short term memory

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