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Short-Term Effects of Ambient Air Pollutants on Outpatient Visits for Childhood Allergic Diseases in Shanghai,China

Journal of Shanghai Jiaotong university(science) 2024年第6期29卷 979-994页

作者： HU Yi GU Jianlei WU Dan WANG Xiaolei LU Hui YU Guangjun Center for Biomedical Informatics Shanghai Children’s HospitalShanghai Jiao Tong University School of MedicineShanghai 200040China SJTU-Yale Joint Center for Biostatistics and Data Science Department of Bioinformatics and BiostatisticsShanghai Jiao Tong UniversityShanghai 200240China Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine Shanghai 200040China

This study aims to investigate the short-term effects of ambient air pollutants on outpatient visits for childhood allergic *** data on ambient air pollutants(NO2,SO2,CO and PM2.5)and outpatient visits for childhood allergic diseases(asthma,atopic dermatitis and allergic rhinitis)were obtained in Shanghai,China from 2013 to *** effects of ambient air pollutants were estimated for total outpatient visits for childhood allergic diseases,gender and age stratification and disease classification by using distributed lag non-linear model(DLNM).We found positive associations between short-term exposure to air pollutants and childhood allergic *** and children aged 7 years old were more likely to be sensitive to ambient air ***2 and SO2 showed stronger effects on asthma and atopic dermatitis,*** study provides evidence that short-term exposure to ambient air pollutants can increase the risk of childhood allergic diseases.

关键词： childhood allergic diseases ambient air pollutant nitrogen dioxide(NO2) sulfur dioxide(SO2) particulate matter<2.5μm in diameter(PM2.5)

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A Systematic Literature Review of CNN Approaches in Classifying Brain Tumor 6

A Systematic Literature Review of CNN Approaches in Classify...

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6th International Conference on Computer and Informatics Engineering, IC2IE 2023

作者： Paulindino, Aedentrisa Yasmanda Pardamean, Bens Elwirehardja, Gregorius Natanael Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9798350345162

The ability of Convolutional Neural Networks (CNNs) to accurately discriminate between normal and tumorous brain tissues has been promising. The review focuses on the different CNN models, pre-processing methods, data augmentation, and Transfer Learning (TL) strategies used in this research. This Systematic Literature Review (SLR) collected the data from Google Scholar. The results of this study indicate that open-source datasets from Kaggle and Brain MRI Images for Brain Tumor Detection are the most used datasets. However, limited data and imbalanced class problems remain common challenges across various datasets. To overcome those challenges, using a larger dataset, oversampling, Generative Adversarial Network (GAN), federated learning, and Self-Supervised Learning (SSL) to handle the imbalance are the potential solution. Additionally, popular CNN architectures for brain tumor classification extensively use pre-trained models such as VGG16, VGG19, DenseNet121, DenseNet201, GoogleNet, ResNet-50, and Inception-v3. TL strategies are preferred, allowing CNNs to leverage knowledge from large datasets, improving generalization even with limited labeled data. © 2023 IEEE.

关键词： brain tumor classification cnn mri pre-trained transfer learning

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Systematic Literature Review of Transformer Model Implementations in Detecting Depression 6

Systematic Literature Review of Transformer Model Implementa...

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6th International Conference on Computer and Informatics Engineering, IC2IE 2023

作者： Nanggala, Kenjovan Pardamean, Bens Elwirehardja, Gregorius Natanael Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9798350345162

This systematic literature review explores the application of transformer models in early detection of human depression, encompassing text, audio, and video data modalities. Transformer architectures, notably BERT for text, have proven adept at capturing crucial contextual and linguistic patterns associated with depression. For audio and video data, hybrid approaches that combine transformer models with other architectures are prevalent. Key features considered include eye gaze, head pose, facial muscle movements, and audio characteristics such as MFCC and Log-mel Spectrogram, along with text embeddings. Performance comparisons underscore the superiority of text-based data in consistently delivering the most promising results, followed by audio and video modalities when utilizing transformer models. The fusion of multiple modalities emerges as an effective strategy for enhancing predictive accuracy, with the amalgamation of audio, video, and text data yielding the most precise outcomes. However, it is noteworthy that unimodal approaches also exhibit potential, with text data exhibiting superior performance over audio and video data. Nevertheless, several challenges persist in this research domain, including imbalanced datasets, the limited availability of comprehensive and diverse samples, and the inherent complexities in interpreting visual cues. Addressing these challenges remains imperative for the continued advancement of depression detection using transformer-based models across various modalities. © 2023 IEEE.

关键词： deep learning major depressive disorder multimodal transformer unimodal

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A Systematic Literature Review of Deep Learning Application in Multiclass Anomaly Detection for Chest Medical Imaging 6

A Systematic Literature Review of Deep Learning Application ...

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6th International Conference on Computer and Informatics Engineering, IC2IE 2023

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

ISBN: (纸本)9798350345162

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. © 2023 IEEE.

关键词： abnormality detection attention mechanisms chest x-ray CT images deep learning transfer learning

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Pap Smear Medical Image Classification Using Deep Learning: A Systematic Review 6

Pap Smear Medical Image Classification Using Deep Learning: ...

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6th International Conference on Computer and Informatics Engineering, IC2IE 2023

作者： Selvano, Elvan Elwiehardja, Gregorius Natanael Pardamean, Bens Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta Indonesia

ISBN: (纸本)9798350345162

Cervical cancer has been known as one of the most prevalent medical disorders globally and a leading cause of death. Early detection, particularly through Pap tests, plays a vital role in its prevention. Previous studies have leveraged machine learning and deep learning techniques to classify the medical images obtained from Pap tests. In this study, a Systematic Literature Review methodology was used to examine 15 relevant papers that have been filtered from queries to Google Scholar which have gone through 4 stages of filtering that include: identification, screening, eligibility, and inclusion. This study addresses two research questions regarding the datasets and deep learning techniques for classifying pap smear images in recent years. The performance of the models was analyzed and potential areas for improvements are suggested. The findings of this study reveal that the Herlev University Hospital and SIPaKMed datasets are the most used. The methodologies used by researchers range from machine learning techniques, transfer learning using Convolutional Neural Networks, and utilize state-of-the-art models with novel optimizing methodology. While there are exciting opportunities in the field, challenges include model generalization and interpretability. © 2023 IEEE.

关键词： cervical cancer deep learning machine learning pap test

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Sentiment Analysis: Indonesia Netflix User's Comment Using Multiple Lexicon-Based Dictionaries 4

Sentiment Analysis: Indonesia Netflix User's Comment Using M...

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4th International Conference on Intelligent Cybernetics Technology and Applications, ICICyTA 2024

作者： Mola, Sebastianus Adi Santoso Widiastuti, Tiwuk Roma, Rosa V. K. Isabela Ohe Karnyoto, Andrea Stevens Pardamean, Bens University of Nusa Cendana Faculty of Science and Engineering Kupang Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798331506490

A subscription movie streaming service from the United States, Netflix, has been present in Indonesia since 2016 and provides a wide variety of films without showing any single advertisements that can be viewed from anywhere, as long as there is access to the internet. Despite these advantages, many users have complained through the Google Play Store's comments column. Some of the common complaints include frequent buffering and connectivity issues, dissatisfaction with the limited selection of Indonesian movies, lack of subtitles for specific languages, or pricing concerns have also been raised. In this study developed two combined scenario methods using the InSet and SentiStrength-id dictionary to obtain better performance and compare them against independent InSet and SentiStrength-id. This study collected users' comments for the Netflix app in the Google Play Store as a dataset using web scraping techniques through the Google Collaboration tool. The dataset contains 3250 rows spanning the period from January 22, 2024, through June 6, 2024. To ensure proper processing of the text, data cleaning, lowercasing, normalization, tokenization, stemming, and stopwords removal are conducted. The results show that most user opinions are negative. The InSet dictionary has an accuracy of 92%, SentiStrength-id 78%, Combined scenario 1 is 87%, and scenario 2 reaches the highest among others which is 92.52%. © 2024 IEEE.

关键词： Video streaming

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Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis (vol 14, 3750, 2023)

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NATURE COMMUNICATIONS 2023年第1期14卷 1-16页

作者： Takada, Hitomi Sasagawa, Yohei Yoshimura, Mika Tanaka, Kaori Iwayama, Yoshimi Hayashi, Tetsutaro Isomura-Matoba, Ayako Nikaido, Itoshi Kurisaki, Akira Laboratory of Stem Cell Technologies Graduate School of Science and Technology Nara Institute of Science and Technology Takayama-cho Ikoma Nara Japan Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research Wako Saitama Japan Department of Functional Genome Informatics Biological Data Science Medical Research Institute Tokyo Medical and Dental University Bunkyo Tokyo Japan Master’s/Doctoral Program in Life Science Innovation (Bioinformatics) Degree Programs in Systems and Information Engineering Graduate School of Science and Technology University of Tsukuba Tsukuba Ibaraki Japan

Defects in gastric progenitor cell differentiation are associated with various gastric disorders, including atrophic gastritis, intestinal metaplasia, and gastric cancer. However, the mechanisms underlying the multilineage differentiation of gastric progenitor cells during healthy homeostasis remain poorly understood. Here, using a single-cell RNA sequencing method, Quartz-Seq2, we analyzed the gene expression dynamics of progenitor cell differentiation toward pit cell, neck cell, and parietal cell lineages in healthy adult mouse corpus tissues. Enrichment analysis of pseudotime-dependent genes and a gastric organoid assay revealed that EGFR-ERK signaling promotes pit cell differentiation, whereas NF-κB signaling maintains gastric progenitor cells in an undifferentiated state. In addition, pharmacological inhibition of EGFR in vivo resulted in a decreased number of pit cells. Although activation of EGFR signaling in gastric progenitor cells has been suggested as one of the major inducers of gastric cancers, our findings unexpectedly identified that EGFR signaling exerts a differentiation-promoting function, not a mitogenic function, in normal gastric homeostasis.

关键词： Adult stem cells Stem-cell differentiation Stem-cell niche

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Exploring Recurrent Neural Network Models for Depression Detection Through Facial Expressions: A Systematic Literature Review 6

Exploring Recurrent Neural Network Models for Depression Det...

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6th International Conference on Computer and Informatics Engineering, IC2IE 2023

作者： Rumahorbo, Brilyan Nathanael Pardamean, Bens Elwirehardja, Gregorius Natanael Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia

ISBN: (纸本)9798350345162

Major Depressive Disorder (MDD) is a prevalent mental disorder, affecting a significant number of individuals, with estimates reaching 300 million cases worldwide. Currently, the diagnosis of this condition relies heavily on subjective assessments based on the experience of medical professionals. Therefore, researchers have turned to deep learning models to explore the detection of depression. The objective of this review is to gather information on detecting depression based on facial expressions in videos using deep learning techniques. Overall, this research found that RNN models achieved 7.22 MAE for AVEC2014. LSTM models produced 4.83 MAE for DAIC-WOZ, while GRU models achieved an accuracy of 89.77% for DAIC-WOZ. Features like Facial Action Units (FAU), eye gaze, and landmarks show great potential and need to be further analyzed to improve results. Analysis can include applying feature engineering techniques. Aggregation methods, such as mean calculation, are recommended as effective approaches for data processing. This Systematic Literature Review found that facial expressions do have relevant patterns related to MDD. © 2023 IEEE.

关键词： deep learning facial expression GRU LSTM major depressive disorder

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Comparative Analysis of CNN Models for Multiclass Detection on Colon Disease 9

Comparative Analysis of CNN Models for Multiclass Detection ...

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9th International Conference on Information Technology and Digital Applications, ICITDA 2024

作者： Sulistyawan, Jason Sebastian Nugroho, Kuncahyo Setyo Isnan, Mahmud Pardamean, Bens Binus Graduate Program Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798331510732

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 © 2024 IEEE.

关键词： Convolutional neural networks

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Automatic Multiple Choice Question Generation: A Systematic Literature Review 9

Automatic Multiple Choice Question Generation: A Systematic ...

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9th International Conference on Information Technology and Digital Applications, ICITDA 2024

作者： Henry, Matthew Martianus Heryanto, Nur Adhianti Isnan, Mahmud Nugroho, Kuncahyo Setyo Pardamean, Bens Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798331510732

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. © 2024 IEEE.

关键词： Semantics

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