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arXiv 2022年

作者： Matsouaka, Roland A. Liu, Yi Zhou, Yunji Department of Biostatistics and Bioinformatics Duke University DurhamNC United States Program for Comparative Effectiveness Methodology Duke Clinical Research Institute DurhamNC United States

There has been a recent surge in statistical methods for handling the lack of adequate positivity when using inverse probability weights (IPW). However, these nascent developments have raised a number of questions. Thus, we demonstrate the ability of equipoise estimators (overlap, matching, and entropy weights) to handle the lack of positivity. Compared to IPW, the equipoise estimators have been shown to be flexible and easy to interpret. However, promoting their wide use requires that researchers know clearly why, when to apply them and what to expect. In this paper, we provide the rationale to use these estimators to achieve robust results. We specifically look into the impact imbalances in treatment allocation can have on the positivity and, ultimately, on the estimates of the treatment effect. We zero into the typical pitfalls of the IPW estimator and its relationship with the estimators of the average treatment effect on the treated (ATT) and on the controls (ATC). Furthermore, we also compare IPW trimming to the equipoise estimators. We focus particularly on two key points: What fundamentally distinguishes their estimands? When should we expect similar results? Our findings are illustrated through Monte-Carlo simulation studies and a data example on healthcare expenditure. Copyright © 2022, The Authors. All rights reserved.

关键词： Monte Carlo methods

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InDRI: Intelligent Diagnosis Radiology Images

InDRI: Intelligent Diagnosis Radiology Images

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International Conference on Cybernetics and Intelligent System (ICORIS)

作者： Mahmud Isnan Gregorius Natanael Elwirehardja Kuncahyo Setyo Nugroho Imelda Liana Ritonga Roby Pahala Januario Gultom Elida Afni Lubis 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 Undergraduate of Nursing Program Universitas Imelda Medan Indonesia Medan Indonesia Undergraduate Pharmacy Program Universitas Imelda Medan Indonesia Medan Indonesia Clinical Pathology Unit Rumah Sakit Imelda Pekerja Indonesia Medan Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331539603

ISBN: (纸本)9798331539610

The need for an early screening and Computer-Aided Diagnosis (CAD) system based on Artificial Intelligence (AI) for the field of radiology is essential to realize considering the large impact of lung diseases globally. However, developing AI requires a lot of data, which is a challenge because data in the health sector tends to be limited in quantity and has disparities between diagnostic categories (data imbalance). To overcome this issue, DINO ViT models was trained with the publicly available COVID-19 Radiography Database in our previous study. The model was subsequently implemented into a web application, with this study focusing on the development of a prototype for the application. The study found this application can be useful for medical personnel and doctors in carrying out early screening and CAD. Meanwhile, it also highlighted the general unfamiliarity with AI applications among medical staff, emphasizing the need for increased education and training on AI's role in healthcare.

关键词： Training Solid modeling Design automation Pulmonary diseases Prototypes Radiology Predictive models Computer aided diagnosis Artificial intelligence Medical diagnostic imaging

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Synthetic Control Removes Spurious Discoveries from Double Dipping in Single-Cell and Spatial Transcriptomics Data Analyses 29th

Synthetic Control Removes Spurious Discoveries from Double ...

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29th International Conference on Research in Computational Molecular Biology, RECOMB 2025

作者： Song, Dongyuan Chen, Siqi Lee, Christy Li, Kexin Ge, Xinzhou Li, Jingyi Jessica Department of Genetics and Genome Sciences University of Connecticut Health Center FarmingtonCT06032 United States Interdepartmental Program of Bioinformatics University of California Los Angeles Los AngelesCA90095-7246 United States Department of Statistics and Data Science University of California Los Angeles Los AngelesCA90095-1554 United States Department of Statistics Oregon State University CorvallisOR97331-4606 United States

ISBN: (纸本)9783031902512

Double dipping is a common analytical pitfall in single-cell and spatial transcriptomics data analysis: after a clustering algorithm finds clusters as putative cell types or spatial domains, statistical tests are applied to the same data to identify differentially expressed (DE) genes as potential cell-type or spatial-domain markers. Because the genes that contribute to clustering are inherently likely to be identified as DE genes, double dipping can result in false-positive markers, especially when clusters are spurious, leading to ambiguously defined cell types or spatial domains. To address this challenge, we propose ClusterDE, a statistical method designed to identify post-clustering DE genes as reliable markers of cell types and spatial domains, while controlling the false discovery rate (FDR) regardless of clustering quality. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2025.

关键词： Biomolecules

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Automatic Multiple Choice Question Generation: A Systematic Literature Review

Automatic Multiple Choice Question Generation: A Systematic ...

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

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

ISBN: (数字)9798331510732

ISBN: (纸本)9798331510749

Despite their drawbacks, multiple-choice questions (MCQ) have been widely used to assess the students' understanding of lectures through examinations. The development of automatic MCQ generation is beneficial, especially for educators. As a starting point for further development, a Systematic Literature Review (SLR) is conducted to uncover current trends, future challenges, and opportunities in automatic MCQ generation. Previously, an SLR was conducted, but it lacks coverage of the utilization of transformer-based models. This SLR covers the development of automatic MCQ generation using either traditional or advanced approaches such as Transformers. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework was used to gather the data from Scopus, IEEE Xplore, SpringerLink, arXiv, and Semantic Scholar. The included articles must be open-access computer science conference papers or journal articles and written in English less than five years ago. Four independent reviewers analyzed the research workflow, evaluation metric, and dataset used in each study. There are 18 included studies, where 17% (n = 3) studies are from 2024, 33% (n = 6) studies are from 2023, 22% (n = 4) studies are from 2022, 11% (n = 2) studies are from 2021, and 17% (n = 3) studies are from 2020. There are 33% (n = 6) of the studies used the traditional feature-based engineering approach, 39% (n = 7) of the studies used the Transformer-based model fine-tuning approach, and the remaining used novel approaches. The study found that BERT variants are the most utilized Transformer-based model in automatic MCQ. The research notes some challenges, but also open various opportunities for further research, including Large Language Model (LLM) utilization for automatic MCQ generation, the utilization BERT-based models for standardized machine-learned evaluation metrics, and the initiative for the creation of an MCQ dataset benchmark.

关键词： Measurement Semantics Reinforcement learning Benchmark testing Ontologies Transformers Question generation Prompt engineering Standards Systematic literature review

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Comparative Analysis of CNN Models for Multiclass Detection on Colon Disease

Comparative Analysis of CNN Models for Multiclass Detection ...

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

作者： Jason Sebastian Sulistyawan Kuncahyo Setyo Nugroho Mahmud Isnan 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 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331510732

ISBN: (纸本)9798331510749

Gastrointestinal diseases are significant health concerns that mostly affect the digestive and biliary tracts. These can only be observed internally through endoscopy, or a modern approach named Wireless Capsule Endoscopy. Though the approach has proven to work, the process relies heavily on medical experts, which is prone to error when given a considerably large load. The use of deep learning in detecting diseases with images has been proven to work in various cases and can be implemented for gastrointestinal diseases. This study compared four deep learning models based on Convolutional Neural Network architectures consisting of the VGG16, ResNet152V2, InceptionV3, and Xception for classifying colon disease images. The experiment showed that the ResNet152V2 performed the best, compared to the other three with a testing accuracy score of 0.9837. On the other hand, the VGG16 had the lowest performance with around accuracy score of 0.89 while the Xception and InceptionV3models yielded similar accuracy scores of 0.9587 and 0.9549, respectively. The results highlight the effectiveness of ResNet152V2 in handling the complexity of colon disease detection

关键词： Hands Deep learning Accuracy Endoscopes Real-time systems Gastrointestinal tract Data models Colon Medical diagnostic imaging Diseases

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Systematic Literature Review on Statistics and Machine Learning Predictive Models for Rice Phenotypes

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Procedia Computer Science 2023年 227卷 1054-1061页

作者： Nicholas Dominic Tjeng Wawan Cenggoro 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 Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta 11480 Indonesia

Predicting the best-quality of rice phenotypes is the priority among agricultural researchers to fulfill worldwide food security. Trend development of predictive models from statistics to machine learning is the subject of this review. Gathered from the Google Scholar database, 14 appropriate papers (2016-2020) related to the rice phenotypes prediction were selected through title and abstract content filtering. The outputs show that Support Vector Machine, Multi-layer Perceptron, and regression are the most used models, while yield is the priority prediction point besides tiller, panicle, and 1000-grain weight of rice. However, finding the accurate predictor is invariably challenging due to distinct rice varieties in the world and high confounding factors. Thus, developing an advanced deep learning model that accommodates these needs is worth considering further.

关键词： rice phenotypes prediction statistics machine learning

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PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion

arXiv

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arXiv 2024年

作者： Tang, Sophia Zhang, Yinuo Chatterjee, Pranam Department of Biomedical Engineering Duke University United States Management and Technology Program University of Pennsylvania United States Center of Computational Biology Duke-NUS Medical School Singapore Department of Computer Science Duke University United States Department of Biostatistics and Bioinformatics Duke University United States

Peptide therapeutics, a major class of medicines, have achieved remarkable success across diseases such as diabetes and cancer, with landmark examples such as GLP-1 receptor agonists revolutionizing the treatment of type-2 diabetes and obesity. Despite their success, designing peptides that satisfy multiple conflicting objectives, such as target binding affinity, solubility, and membrane permeability, remains a major challenge. Classical drug development and target structure-based design are ineffective for such tasks, as they fail to optimize global functional properties critical for therapeutic efficacy. Existing generative frameworks are largely limited to continuous spaces, unconditioned outputs, or single-objective guidance, making them unsuitable for discrete sequence optimization across multiple properties. To address this, we present PepTune, a multi-objective discrete diffusion model for the simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with bond-dependent masking schedules and penalty-based objectives. To guide the diffusion process, we propose a Monte Carlo Tree Search (MCTS)-based strategy that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTS integrates classifier-based rewards with search-tree expansion, overcoming gradient estimation challenges and data sparsity. Using PepTune, we generate diverse, chemically modified peptides optimized for multiple therapeutic properties, including target binding affinity, membrane permeability, solubility, hemolysis, and non-fouling for various disease-relevant targets. In total, our results demonstrate that MCTS-guided masked discrete diffusion is a powerful and modular approach for multi-objective sequence design in discrete state spaces. © 2024, CC BY-NC-ND.

关键词： Trees (mathematics)

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In vitro and in vivo toxicity assessment of the senotherapeutic Peptide 14

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Toxicology Reports 2022年 9卷 1632-1638页

作者： Zonari, Alessandra Brace, Lear E. Alencar-Silva, Thuany Porto, William F. Foyt, Daniel Guiang, Mylieneth Cruz, Edgar Andres Ochoa Franco, Octavio L. Oliveira, Carolina R. Boroni, Mariana Carvalho, Juliana L. OneSkin Inc San Francisco 94107 CA United States Genomic Sciences and Biotechnology Program Catholic University of Brasilia DF Brasília 70790-160 Brazil DF Brasília 72236–011 Brazil Center of Proteomic Analyses and Biochemistry Genomic Sciences and Biotechnology Program Catholic University of Brasilia DF Brasilia 70790-160 Brazil S-Inova Biotech Biotechnology Program Catholic University Dom Bosco MS Campo Grande 79117-010 Brazil Molecular Pathology Program University of Brasilia DF Brasilia 70.910-900 Brazil Bioinformatics and Computational Biology Lab Brazilian National Cancer Institute (INCA) RJ Rio de Janeiro 20231-050 Brazil Interdisciplinary Biosciences Laboratory Faculty of Medicine University of Brasília DF Brasília 70.910–900 Brazil

Senotherapeutic molecules decrease cellular senescence burden, constituting promising approaches to combat the accumulation of senescent cells observed in chronological aging and age-related diseases. Numerous molecules have displayed senotherapeutic potential, but toxicity has been frequently observed. Recently, a new senotherapeutic compound, Peptide 14, was developed to modulate cellular senescence in the skin. In order to assess the potential toxic and genotoxic effects of the peptide, we observed the viability of human primary dermal fibroblasts and epidermal keratinocytes with Peptide 14 treatment, and show that it is mostly non-toxic in concentrations up to 100 μM. Cancer lines were also used to investigate its potential of modulating proliferation. Different concentrations of the peptide promoted a discrete reduction in the proliferation of cancerous cells of the MeWo and HeLa lineages. In full-thickness human skin equivalents, topically formulated Peptide 14 also failed to exert any significant irritation, nor cellular toxicity when added to the culture media. Genotoxic assays including the Ames, micronucleus, and karyotyping tests also indicate the safety of the peptide. Finally, the irritative potential of the peptide was assessed in human subjects in a repeated insult patch test executed using 1 mM peptide. No visible skin reactions were observed in any of the 54 participants. Taken together, the present data support that Peptide 14 is a senotherapeutic molecule with a positive safety profile as tested with cruelty-free models, justifying further studies involving the peptide. © 2022 The Authors

关键词： 3D skin equivalents Aging Cellular senescence In-vitro toxicology Peptide 14 RIPT

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Systematic Literature Review: An Intelligent Pulmonary TB Detection from Chest X-Rays 1

Systematic Literature Review: An Intelligent Pulmonary TB De...

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1st International Conference on Computer Science and Artificial Intelligence, ICCSAI 2021

作者： Jimmy Cenggoro, Tjeng Wawan Pardamean, Bens Bina Nusantara University BINUS Graduate Program-Master of Computer Science Program Computer Science Department Jakarta11480 Indonesia Bina Nusantara University School of Computer Science Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia

ISBN: (纸本)9781728133331

Tuberculosis (TB) is one of the top ten reasons for death from an infectious agent. Although TB is curable and preventable, delay in diagnosis and treatment can lead the patient to death. Advancements in computer-Aided diagnosis (CAD), particularly in medical images classification, significantly contribute to early TB detection. The current state-of-Art CAD for medical images classification applications using a method base on deep learning techniques. The problem faced in this deep learning technique is that, in general, it only uses a single modal for the model. In contrast, in medical practice, the data used for TB analysis not only focuses on images but also includes clinical data such as demographics, patient assessments, and lab test results. This systematic literature review describes different deep learning methods using single modal or multimodal techniques that combined images with other clinical data. We conducted a systematic search on Springer, PubMed, ResearchGate, and google scholar for original research leveraging deep learning for Pulmonary TB detection. © 2021 IEEE.

关键词： Computer aided diagnosis

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Web Development of Direct-to-consumer Genetics Testing 4

Web Development of Direct-to-consumer Genetics Testing

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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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