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Low-rank Tensor Estimation via Riemannian Gauss-Newton: Statistical Optimality and Second-Order Convergence

Journal of Machine Learning Research 2023年 24卷

作者： Luo, Yuetian Zhang, Anru R. Data Science Institute University of Chicago ChicagoIL60637 United States Departments of Biostatistics & Bioinformatics and Computer Science Duke University DurhamNC27710 United States

In this paper, we consider the estimation of a low Tucker rank tensor from a number of noisy linear measurements. The general problem covers many specific examples arising from applications, including tensor regression, tensor completion, and tensor PCA/SVD. We consider an efficient Riemannian Gauss-Newton (RGN) method for low Tucker rank tensor estimation. Different from the generic (super)linear convergence guarantee of RGN in the literature, we prove the first local quadratic convergence guarantee of RGN for low-rank tensor estimation in the noisy setting under some regularity conditions and provide the corresponding estimation error upper bounds. A deterministic estimation error lower bound, which matches the upper bound, is provided that demonstrates the statistical optimality of RGN. The merit of RGN is illustrated through two machine learning applications: tensor regression and tensor SVD. Finally, we provide the simulation results to corroborate our theoretical findings. ©2023 Yuetian Luo and Anru R. Zhang.

关键词： Tensors

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data Mining for the Global Multiplex Weekly Average Income Analysis

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Procedia Computer science 2023年 219卷 52-59页

作者： Nicholas Dominic Gregorius Natanael Elwirehardja Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

The box office (BO) income had significantly declined up to 80% in 2020, as the COVID-19 pandemic emerged. To minimize further financial risks, multiplex (multiple cinema complexes) owners need to analyze their potential income for each movie, each week. Therefore, we developed a proper data mining strategy that allows multiplex owners to analyze and discover insights on how successfully produced movies could be. The methodology comprises (1) data loading and exploration, (2) data cleaning, (3) data selection, integration, and transformation using Pentaho, (4) data mining in which the results were stored in the MySQL database, and (5) pattern evaluation and presentation using Qlik Sense as the Business Intelligence (BI) dashboard. Based on our data mining methodology, we revealed that drama, comedy, action, and thriller are favorite genres. We also found that DreamWorks Animation and Pixar Animation Studios are both the most popular production houses, even Apatow Productions and Escape Artists still have the biggest revenue on average.

关键词： movie multiplex income data mining Business Intelligence dashboard

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database Design for Pre-Eclampsia Case Administration 8

Database Design for Pre-Eclampsia Case Administration

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8th International Conference on Information Technology and Digital Applications, ICITDA 2023

作者： Asadi, Faisal Elwirehardja, Gregorius Natanael Trinugroho, Joko Pebrianto Rahutomo, Reza Pardamean, Bens School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia School of Information Systems Bina Nusantara University Information System Department Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798350344691

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. © 2023 IEEE.

关键词： Medical informatics

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Decision Theory and Risk Simulation Analysis for Optimizing Profit in PayLater Services

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Procedia Computer science 2023年 219卷 60-67页

作者： Nicholas Dominic Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

The projected increase in PayLater utilization reaches up to five million people by 2025. To optimize the yearly profit from their PayLater service, fintech companies must examine all possible risks before a unanimous decision is taken. Therefore, we proposed a unified decision framework derived from decision theory and the Monte Carlo simulation technique. Two schemes were coined: (1) a decision-making scheme, and (2) a risk simulation scheme. Throughout experiments, the framework was able to estimate several alternative decisions and their impacts, analyze the causes of failure and delays in the development of the PayLater service, and execute Monte Carlo simulations in up to 10,000 trials. Outputs of this study will benefit decision-makers in the fintech initiative before launching their PayLater products.

关键词： PayLater decision-making Bayesian analysis fault tree analysis critical path method Monte Carlo simulation

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Machine Learning Implementations in Childhood Stunting Research: A Systematic Literature Review 8

Machine Learning Implementations in Childhood Stunting Resea...

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8th International Conference on Information Management and Technology, ICIMTech 2023

作者： Rahutomo, Reza Elwirehardja, Gregorius Natanael Isnan, Mahmud Asadi, Faisal Pardamean, Bens School of Information Systems Bina Nusantara University Information Systems Department Jakarta11480 Indonesia School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Binus Graduate Program - Master of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798350326093

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. © 2023 IEEE.

关键词： Machine learning

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A review: data pre-processing techniques used for diabetes prediction

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Procedia Computer science 2024年 245卷 667-676页

作者： Mahmud Isnan Gregorius Natanael Elwirehardja Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Cmputer Science Department BINUS Graduate Program – Master of Computer Science Program Bina Nusantara University Jakarta 11480 Indonesia

When processing datasets in diabetes classification, common problems included a large number of missing values, outliers, and dataset imbalance. To deal with those issues, this study analyzed 18 studies on diabetes classification with machine learning algorithms over the past 5 years. This revealed the important role of data pre-processing in creating effective classification models, as it was found that by using different data pre-processing techniques, the same model can provide different performance. The study identified K-Nearest Neighbor (KNN) and support vector machine (SVM) as superior methods for filling in missing values, achieving an accuracy of 98.49% and 94.89%, respectively. These approaches outperformed traditional methods such as median or mean replacement. However, the challenge of imbalanced data sets remains in all studies reviewed. The common evaluation metrics used to evaluate the created models in previous studies included accuracy, precision, specificity, sensitivity/recall, and F1 Score. Overall, this review showed that the role of data pre-processing is no less important than algorithm selection to improve the performance of machine learning models in diabetes classification.

关键词： Diabetes Classification data Pre-Processing Machine Learning Imbalanced dataset

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A bioinformatics Analysis and Homology 3D Modeling of Dihydroxy-orotate-dehydrogenase of Plasmodium ovale

A Bioinformatics Analysis and Homology 3D Modeling of Dihydr...

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

作者： Rudi Nirwantono Khoirunnisa Assidqi Alam Ahmad Hidayat Joko Pebrianto Trinugroho Bens Pardamean Biotechnology Department Faculty of Engineering Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Food Biotechnology Research Center Bina Nusantara University Jakarta Indonesia Mathematics Departement School of Computer Science Bioinformatics and Data Science Research Center 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 Program Bina Nusantara University Jakarta Indonesia

The infection of Plasmodium vivax is relatively less virulent than the deathliest Plasmodium falciparum. However, it still can lead to a fatal case and often induces recurring malaria due to dormant parasites in the liver. Thus, the research to study the drug to treat Plasmodium vivax is essential, where the enzyme dihydroorotate dehydrogenase (DHODH) has recently become a new drug target. However, the drug-enzyme interaction study has only recently been conducted in Plasmodium falciparum (pfDHODH) due to the lack of the 3D structure of enzyme DHODH from Plasmodium vivax that is crucial for the study. Therefore, this study aimed to perform the modelling study of Plasmodium vivax DHODH (PvDHODH) to create a 3D structure as a basis for drug-protein interaction study in upcoming studies. Sequence pvDHODH (Accession: SCO68359.1) was used in homology modelling using Modeller 10.2 with the crystal structure of DHODH from DHODH (Accession: 7KZY) as a template. Overall, the model generated from the homology modelling was considered a good model, and the 3D structure was close to the native state according to several parameters, including DOPE score, GA341 score, QMEAN4 value, 3D-1D score, ERRAT2 score, and ProSA score. Ramachandran plot also revealed that almost all amino acids were distributed in the desirable and allowed area (99.1%), and only 0.9% were in generously allowed regions. Superimposition of the model with the template also indicated that the model has an almost similar structure and amino acids positioning, including in the binding pocket and active site. Therefore, the model can be used for downstream analysis in drug-protein interaction studies. Nevertheless, some improvements can still be performed to upgrade the quality of the model by deleting unaligned residues on the C-terminal and realigning the residues at the doubting site.

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Artificial Intelligence and IBD: Where are We Now and Where Will We Be in the Future?

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Current Gastroenterology Reports 2024年第5期26卷 137-144页

作者： Ahmed, Mehwish Stone, Molly L. Stidham, Ryan W. Division of Gastroenterology Department of Internal Medicine Michigan Medicine Ann Arbor MI United States Department of Computational Medicine and Bioinformatics University of Michigan 3912 Taubman Center 1500 East Medical Center Drive Ann Arbor 48109 MI United States Michigan Institute for Data Science (MIDAS) University of Michigan Ann Arbor MI United States

Purpose of Review: Artificial intelligence (AI) is quickly demonstrating the ability to address problems and challenges in the care of IBD. This review with commentary will highlight today’s advancements in AI applications for IBD in image analysis, understanding text, and replicating clinical knowledge and experience. Recent Findings: Advancements in machine learning methods, availability of high-performance computing, and increasing digitization of medical data are providing opportunities for AI to assist in IBD care. Multiple groups have demonstrated the ability of AI to replicate expert endoscopic scoring in IBD, with expansion into automated capsule endoscopy, enterography, and histologic interpretations. Further, AI image analysis is being used to develop new endoscopic scoring with more granularity and detail than is possible using conventional methods. Advancements in natural language processing are proving to reduce laborious tasks required in the care of IBD, including documentation, information searches, and chart review. Finally, large language models and chatbots that can understand language and generate human-like replies are beginning to exhibit clinical intelligence that will revolutionize how we deliver IBD care. Summary: Today, AI is being deployed to replicate expert judgement in specific tasks where disagreement, subjectivity, and bias are common. However, the near future will herald contributions of AI doing what we cannot, including new detailed measures of IBD, enhanced analysis of images, and perhaps even fully automating care. As we speculate on future technologic capabilities that may improve how we care for IBD, this review will also consider how we will implement and fairly use AI in practice. © The Author(s), under exclusive licence to Springer science+Business Media, LLC, part of Springer Nature 2024.

关键词： Artificial intelligence Clinical trials Crohn’s disease Decision support Endoscopic scoring Inflammatory bowel disease Machine learning Prediction models Segmentation Ulcerative colitis

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Single-cell technologies: current and near future

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science China(Life sciences) 2025年第1期68卷 1-4页

作者： Chenfei Wang Qi Liu Xiaohui Fan Tieliu Shi KeyLaboratory of Spine and Spinal CordInjury Repairand Regeneration Ministry of EducationOrthopedics DepartmentTongji HospitalBioinformatics DepartmentSchoolofLifeSciencesandTechnologyTongji UniversityShanghai 200082China Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Key Laboratory of Advanced Theory and Application in Statistics and Data Science(MOE) School of StatisticsEast China Normal UniversityShanghai 200062China

Single-cell technologies enable the indepth exploration of multiple biological hierarchies at the scale of individual cells,which have deepened our knowledge of cellular diversity,tissue organization,and overall organism function(Sun et al.,2024).In 2009,single-cell RNA sequencing(scRNA-seq)was first developed as a powerful tool to dissect gene expression and uncover transcriptional *** the rapid advancement of technology,single-cell approaches have expanded to encompass other omics,such as genomics,epigenomics,proteomics,and ***,multimodal technologies including spatially resolved transcriptomics and clustered regularly interspaced short palindromic repeats(CRISPR)screening at the single-cell level further advanced our ability to comprehensively understand cellular ***-cell methods provide deeper insights into disease mechanisms across various conditions,including cancer,developmental disorders,and aging-associated *** this issue,we focus on topics related to single-cell methods,covering the following four aspects:(i)single-cell multi-omic sequencing technology;(ii)single-cell spatial technology;(iii)singlecell CRISPR screening technology;(iv)applications of single-cell technology.

关键词： expanded enable insight

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Integrated Graph Propagation and Optimization with Biological Applications 28

Integrated Graph Propagation and Optimization with Biologica...

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28th Pacific Symposium on Biocomputing, PSB 2023

作者： Krishnan, Krithika Shi, Tiange Yu, Han Hageman Blair, Rachael Institute Of Artificial Intelligence And Data Science University At Buffalo BuffaloNY14214 United States Department Of Biostatistics University At Buffalo BuffaloNY14214 United States Department Of Biostatistics And Bioinformatics Roswell Park Comprehensive Cancer Center BuffaloNY14263 United States

ISBN: (纸本)9789811270604

Mathematical models that utilize network representations have proven to be valuable tools for investigating biological systems. Often dynamic models are not feasible due to their complex functional forms that rely on unknown rate parameters. Network propagation has been shown to accurately capture the sensitivity of nodes to changes in other nodes;without the need for dynamic systems and parameter estimation. Node sensitivity measures rely solely on network structure and encode a sensitivity matrix that serves as a good approximation to the Jacobian matrix. The use of a propagation-based sensitivity matrix as a Jacobian has important implications for network optimization. This work develops Integrated Graph Propagation and OptimizatioN (IGPON), which aims to identify optimal perturbation patterns that can drive networks to desired target states. IGPON embeds propagation into an objective function that aims to minimize the distance between a current observed state and a target state. Optimization is performed using Broydens method with the propagationbased sensitivity matrix as the Jacobian. IGPON is applied to simulated random networks, DREAM4 in silico networks, and over-represented pathways from STAT6 knockout data and YBX1 knockdown data. Results demonstrate that IGPON is an effective way to optimize directed and undirected networks that are robust to uncertainty in the network structure. © 2022 The Authors.

关键词： Iterative methods

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