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International Conference of computer and Informatics Engineering (IC2IE)

作者： Philips Bens Pardamean Gregorius Natanael Elwirehardja Mahmud Isnan Computer Science Department BINUS Graduate Program - Master of Compuer Science Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia

Medical imaging abnormality detection is challenging, but deep learning approaches have shown promise. This paper reviews the current state of the art in deep learning approaches for detecting abnormalities in chest medical imaging. To discover the trends, opportunities, and challenges associated with this field, 18 studies were selected from Google Scholar based on their titles, abstracts, and contents for extensive review to answer two research questions. The study found that the National Institutes of Health (NIH) Chest X-ray 14 dataset is the most used dataset for this task. Most research uses a single-modal approach, considering only image data as input, with X-ray being the more popular instrument. There are 8 out of 18 studies leverage the transfer learning approach, with ResN et50 being the most popular network. MobileNetV2 has demonstrated competitive results compared to more robust networks. Preprocessing techniques such as image enhancement and data augmentation are leveraged by 61.1 % of the reviewed studies and are shown to improve model performance.

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Bayesian Spectral Graph Denoising with Smoothness Prior

Bayesian Spectral Graph Denoising with Smoothness Prior

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Annual Conference on Information sciences and Systems (CISS)

作者： Sam Leone Xingzhi Sun Michael Perlmutter Smita Krishnaswamy Program for Applied Mathematics Yale University Department of Computer Science Yale University Department of Mathematics Boise State University Department of Genetics Yale School of Medicine Wu Tsai Institute Yale University FAIR Meta AI Computational Biology and Bioinformatics Program Yale University

Here we consider the problem of denoising features associated to complex data, modeled as signals on a graph, via a smoothness prior. This is motivated in part by settings such as single-cell RNA where the data is very high-dimensional, but its structure can be captured via an affinity graph. This allows us to utilize ideas from graph signal processing. In particular, we present algorithms for the cases where the signal is perturbed by Gaussian noise, dropout, and uniformly distributed noise. The signals are assumed to follow a prior distribution defined in the frequency domain which favors signals which are smooth across the edges of the graph. By pairing this prior distribution with our three models of noise generation, we propose Maximum A Posteriori (M.A.P.) estimates of the true signal in the presence of noisy data and provide algorithms for computing the M.A.P. Finally, we demonstrate the algorithms’ ability to effectively restore signals from white noise on image data and from severe dropout in single-cell RNA sequence data.

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A Hydrodynamic Analysis of Water System in Dadahup Swamp Irrigation Area 1

A Hydrodynamic Analysis of Water System in Dadahup Swamp Irr...

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1st International Conference on computer science and Artificial Intelligence, ICCSAI 2021

作者： Purboseno, Sentot Suparyanto, Teddy Hidayat, Alam Ahmad Pardamean, Bens Institute of Agriculture STIPER Department of Agricultural Engineering Yogyakarta55283 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center BINUS Graduate Program-Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781728133331

Dadahup Swamp Irrigation Area (DIR) in Kapuas Regency, Central Kalimantan is developed for agricultural activities to provide food security after the pandemic. The water system consists of various channels, gates, and a flood embankment structure, which is also connected to three different rivers: Barito River, Mangkatif River, and Kapuas Mumpung River. To quantify flood risk assessments in the area, we perform a hydrodynamic analysis using the unsteady flow method via HEC-RAS software version 4.1.0. We use geometrical profiles from topography measurements and the outer boundary of the Dadahup DIR as input for the hydrologic model. Our results estimate the maximum surface water level from both cross and longitudinal sections in the channels and find that several points near the flood embankment area are prone to flood events. Our modeling approach provides a preliminary assessment for the local government to formulate a flood mitigation plan and policy in the area. © 2021 IEEE.

关键词： Rivers

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ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics

arXiv

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arXiv 2024年

作者： Viswanath, Siddharth Bhaskar, Dhananjay Johnson, David R. Rocha, João Felipe Castro, Egbert Grady, Jackson D. Grigas, Alex T. Perlmutter, Michael A. O’Hern, Corey S. Krishnaswamy, Smita Department of Computer Science Yale University United States Department of Genetics Yale University United States Program in Computing Boise State University United States Computational Biology and Bioinformatics Program Yale University United States Department of Mathematics Boise State University United States

Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to millisecond scales remains challenging. To address these challenges, we introduce a novel deep learning architecture, Protein Transformer with Scattering, Attention, and Positional Embedding (ProtSCAPE), which leverages the geometric scattering transform alongside transformer-based attention mechanisms to capture protein dynamics from molecular dynamics (MD) simulations. ProtSCAPE utilizes the multi-scale nature of the geometric scattering transform to extract features from protein structures conceptualized as graphs and integrates these features with dual attention structures that focus on residues and amino acid signals, generating latent representations of protein trajectories. Furthermore, ProtSCAPE incorporates a regression head to enforce temporally coherent latent representations. Importantly, we demonstrate that ProtSCAPE generalizes effectively from short to long trajectories and from wild-type to mutant proteins, surpassing traditional approaches by delivering more precise and interpretable upsampling of dynamics. © 2024, CC BY.

关键词： Molecular docking

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Database Design for Pre-Eclampsia Case Administration

Database Design for Pre-Eclampsia Case Administration

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Information Technology and Digital Applications (ICITDA), IEEE International Conference on

作者： Faisal Asadi Gregorius Natanael Elwirehardja Joko Pebrianto Trinugroho Reza Rahutomo Bens Pardamean Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Information System Department School of Information Systems Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta Indonesia

The Ministry of Health of Indonesia has referred to pre-eclampsia as one of the most severe diseases affecting women. As an urgency, it is crucial to administrate pre-eclampsia cases for disease prevention as a long-term national healthcare strategy. Regarding health science, case data was significant in developing research and innovation. However, the main problem regarding pre-eclampsia case administration is data handling, recording, and management incompetence. Hence, this research proposed a conceptual design of a database for pre-eclampsia case administration. The proposed design covered conceptual, logical, and physical design. We elaborate the concept into three concepts of pre-eclampsia disease: pre-treatment, treatment, and post-treatment. This study proposed a solution to gain more data and study pre-eclampsia disease in Indonesia.

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Systematic Literature Review On Machine Learning Predictive Models For Indoor Climate In Smart Solar Dryer Dome

Systematic Literature Review On Machine Learning Predictive ...

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International Conference on Cybernetics and Intelligent System (ICORIS)

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

ISBN: (纸本)9781665453967

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.

关键词： Support vector machines Systematics Recurrent neural networks Power demand Bibliographies Artificial neural networks Predictive models

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Machine Learning Implementations in Childhood Stunting Research: A Systematic Literature Review

Machine Learning Implementations in Childhood Stunting Resea...

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International Conference on Information Management and Technology (ICIMTech)

作者： Reza Rahutomo Gregorius Natanael Elwirehardja Mahmud Isnan Faisal Asadi Bens Pardamean Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 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

Childhood stunting is a condition anticipated to affect the growth potential of children under the age of five. With numerous stunting researches that have been conducted, stunting datasets are now widely available to facilitate stunting research. This provides an opportunity to implement machine learning (ML) principles to produce a broader insight or a novel technique in stunting prediction. A systematic literature review is necessary to discover the landscape of machine learning implementation in the application domain as a preliminary study for creating an effective research roadmap. This paper presents a systematic literature review (SLR) of 22 curated manuscripts that focuses on identifying the ML models applied in stunting research, as well as the datasets used in such studies that were published during 2017–2022. The SLR process found that ML principles have been applied in stunting research since 2017, and the diversity of ML implementation has become more varied in 2021–2022. In terms of ML models, XGBoost and Random Forest are recognized as the two most utilized models, and stunting prediction is the most common ML implementation. The majority of stunting research utilizing ML has been conducted in Indonesia. Although national survey data has been the most commonly utilized dataset in stunting research, researchers in Indonesia have shown a preference for utilizing data from regional or independent surveys. This study will be followed by developing a classifier model for stunted children using XGBoost and Random Forest algorithms. The model will be trained on a dataset generated from StuntingDB.

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

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

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International Conference on Informatics, Multimedia, Cyber and Information System (ICIMCIS)

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

ISBN: (纸本)9781665473286

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.

关键词： Epidemics Temperature distribution Rain Meteorological factors Multimedia systems Time series analysis Weather forecasting

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Enhancing Interoperability of Digital Twin in the Maintenance phase of Lifecycle

Enhancing Interoperability of Digital Twin in the Maintenanc...

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International Conference on Information Technology, Information Systems and Electrical Engineering (ICITISEE)

作者： Dedy Ariansyah Bens Pardamean Bioinformatics and Data Science Research Centre Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta Indonesia

In today's digitalization era, asset management has evolved following the rapid adoption of information systems and digital technologies. In the maintenance phase of the asset, Digital Twin (DT) emerges as an effective approach to improve failure recognition and structural damage prediction through DT-driven Prognostic and Health Monitoring (PHM). As a result, DT allows asset manager to proactively plan maintenance strategy to improve the availability of the assets. However, to reduce asset downtime in a cost-effective and time efficient manner, DT for maintenance phase needs to be integrated with other software systems that manage the provision of maintenance service and spare part such as computerized maintenance management system (CMMS) or Enterprise Resource Planning (ERP). Nevertheless, many of the developed DT in PHM were not equipped with semantic data model and hence, lacks interoperability with other systems (e.g., other DT or non-DT system) and limits the effective use of the DT. To qualify as an effective DT, it needs a semantical-enabled interface to connect with data and models from various domain to enable DT-driven decision-making. This paper leverages a rule-based ontology reasoning model to enhance DT interoperability with other maintenance software systems. The results depicts that the developed model paves a way for an effective use of DT-driven system in asset maintenance management.

关键词： Ontologies Software systems Data models Enterprise resource planning Digital twins Prognostics and health management Interoperability

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Implementation of expert systems in potassium deficiency in cocoa plants using forward chaining method

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Procedia computer science 2023年 216卷 136-143页

作者： Muhammad Titan Hafizal Dian Pratama Putra Herry Wirianata Nanda Satya Nugraha Teddy Suparyanto Alam Ahmad Hidayat Bens Pardamean Faculty of Forestry STIPER Institute of Agriculture Yogyakarta 55282 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta 11480 Indonesia

As one of the largest exporters in the world, cocoa (Theobroma cacao L.) production in Indonesia provides an important contribution to the plantation sector that can, directly and indirectly, attribute to the national economic development. However, recent data shows a decline in cocoa productivity in Indonesia. This is arguably caused by various factors, including poor agricultural management and practices in cocoa plantations, that may lead to lower fertility in the soil and an increased risk of diseases and pests. Potassium deficiency is a major contributing factor to the low soil fertility that affects cocoa yields. Therefore, in this work, we implement an application with an expert system utilizing the forward chaining method to detect potassium deficiency in cocoa plants and then give a fertilization-based recommendation based on the plants’ condition. The system employs a set of rules to identify symptoms related to the deficiency on the sample photo of a cocoa leaf according to the channels of red, green, and blue of the image. The sample images of cocoa leaves are submitted to the application with an easy-to-use interface that can show the scanning result and proceed to display the suggested quantity of fertilizers to prevent potassium deficiency. Implementing the system can contribute constructive impacts to improve current practices in the overall cropping system of cocoa plants.

关键词： agriculture cocoa expert system forward chaining recommendation system

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