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Literature study of stunting supplementation in Indonesian utilizing text mining approach 7

Literature study of stunting supplementation in Indonesian u...

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7th International Conference on Computer Science and Computational Intelligence, CSCI 2022

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

Numerous research on stunting supplementation interventions in Indonesia have been published. The information can be extracted through data mining, especially from academic research databases. In this paper, we presented a text mining-based literature review strategy to create a pipeline that researchers can use to accelerate the development of stunting supplementation intervention research in Indonesia. Utilizing various NLP (Natural Language Processing) techniques, data were crawled, processed, and visualized using Python. The crawling dataset used a module from the Pubmed API (Application programming Interface) to collect literature papers. The NLTK (Natural Language Toolkit) module and itertools were used to process text data. The n-grams model was applied to process tokens into bigrams and trigrams. Text information was visualized using Matplotlib and Word cloud packages. There is an increasing number of publication in stunting supplementation intervention according to our result, which was observed from 2015 to 2021. West Java was the province where most of the stunting research has been conducted, as determined by research abstracts. Top occurrences obtained from the bigram and trigrams models calculation produced different terms. The word pairings that occurred the most frequently in the bigram and trigram model analyses were "child-aged" and "iron-folic-acid," respectively. The findings of this study are expected to help researchers to obtain the latest research topics related to stunting supplementation interventions in Indonesia. © 2022 Elsevier B.V.. All rights reserved.

关键词： Data mining

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Evaluating the Effectiveness of Transformer Models for Molecular Property Prediction: A Review 9

Evaluating the Effectiveness of Transformer Models for Molec...

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

作者： Imani, Alyssa Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Binus Graduate Program Bina Nusantara University Computer Science Departement Jakarta11480 Indonesia

ISBN: (纸本)9798331510732

Transformer models, originally successful in natural language processing, are now being applied to chemical and biological studies, excelling in areas such as molecular property prediction, material science, and drug discovery. BERT, a Transformer-based model, has become foundational in cheminformatics, particularly for QSAR (Quantitative Structure-Activity Relationship) modeling and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) evaluations in drug discovery. However, achieving higher accuracy often requires designing more complex models, which can compromise their interpretability. This posing a challenge for researchers who need to understand the reasoning behind the predictions. The trade-off between accuracy and interpretability presents a critical challenge in applying black box models to real-world problems in cheminformatics. This work compares Transformer-based models with traditional machine learning and deep learning approaches, focusing on both interpretability and performance. The goal is to highlight the strengths and limitations of each method, offering insights into their optimal use in drug discovery and material science. © 2024 IEEE.

关键词： Prediction models

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Exploring EfficientNet Variants for Image Encoding in Auxiliary Signal Guided Knowledge Encoder-Decoder Framework 9th

Exploring EfficientNet Variants for Image Encoding in Auxili...

引用

9th International Conference on Computer Science and Computational Intelligence, ICCSCI 2024

作者： Henry, Matthew Martianus Heryanto, Nur Adhianti Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

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. © 2024 The Authors.

关键词： Medical imaging

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Semi-automated meningioma segmentation with bounding boxes 9th

Semi-automated meningioma segmentation with bounding boxes

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9th International Conference on Computer Science and Computational Intelligence, ICCSCI 2024

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

Segmentation is manually performed by physicians, which takes considerable time and may be subject to observers. Automating this task can increase efficiency and consistency. Existing studies on meningioma segmentation used data from limited study centers, indicating the need for research on multi-center data to assess generalizability. In this work, two semi-automated methods with bounding box priors, LiteMedSAM and BBU-Net, are evaluated on the brain tumor segmentation (BraTS) 2023 meningioma dataset collected from five study-centers. Preprocessing included exclusion of small tumors, z-score normalization, and extraction of slices that contain tumors, generating 25,602 2D axial magnetic resonance imaging (MRI) scans. A fine-tuning strategy is adopted for LiteMedSAM while BBU-Net is trained from scratch. The models are evaluated using a five-fold cross-validation, with data split at the case level. Results show that while U-Net models can achieve performance close to LiteMedSAM, the foundation model has overall better performance, with more than 90% in all evaluation scores. © 2024 The Authors.

关键词： Magnetic resonance imaging

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LDA Topic Modeling for bioinformatics Terms in arXiv Documents 9th

LDA Topic Modeling for Bioinformatics Terms in arXiv Documen...

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9th International Conference on Computer Science and Computational Intelligence, ICCSCI 2024

作者： Karnyoto, Andrea Stevens Henry, Matthew Martianus Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

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. © 2024 The Authors.

关键词： arXiv bioinformatics Latent Dirichlet Allocation

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Investigating the genomic basis of metabolic robustness through in silico flux analysis

Investigating the genomic basis of metabolic robustness thro...

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IEEE Conference on Decision and Control

作者： Marcin Imielinski Niels Klitgord Calin Belta N. Klitgord C. Belta University of Pennsylvania School of Medicine Philadelphia PA USA Boston University Graduate Program in Bioinformatics Boston MA USA Boston University Graduate Program in Bioinformatics MA 02115 USA

ISBN: (纸本)9781424431236

We employ a novel implementation of flux balance analysis to investigate the role of genome structure in the maintenance of metabolic robustness. We propose the hypothesis that the genomic organization of a bacterium buffers its metabolome against random gene deletion. To test this hypothesis, we use a novel implementation of producibility analysis to determine the metabolomic impact of gene deletions in the E. coli iJR904 genome-scale metabolic model. From these results, we determine metabolomic fragility, which we compute as the average number of metabolites knocked out across all gene deletions of a given size in a given nutrient media. We apply this analysis for three deletion window sizes (4000, 8000, 16000 bp) across the length of the E. coli genome. We compare these results to those obtained from several null distributions of permuted genomes to assess the impact of E. coli genome organization on its metabolic robustness. Our results strongly suggest that the arrangement of genes on the E. coli genome buffers metabolite producibility against random gene deletion. Our results have interesting implications for the understanding of metabolic network evolution. Future work includes examining our hypothesis for a wider range of deletion sizes and nutrient environments and extending our results to the metabolic networks of other species.

关键词： Genomics bioinformatics Robustness Biochemistry Metabolomics Biological system modeling Organisms Robust control Testing Biological systems

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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 Hybrid CNN-SVM Approach for Malaria in Blood Cell Detection 2

A Hybrid CNN-SVM Approach for Malaria in Blood Cell Detectio...

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2nd International Conference on Software Engineering and Information Technology, ICoSEIT 2024

作者： Karnyoto, Andrea Stevens Isnan, Mahmud Pardamean, Bens Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta Indonesia Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta Indonesia

ISBN: (纸本)9798350317503

There is still a severe malaria problem worldwide, particularly in regions with limited access to diagnostic tools. It is crucial to develop a system for detecting malaria in blood cells. This paper presents a hybrid Convolutional Neural Network (CNN), and as a classifier, we use a Support Vector Machine (SVM) framework for the automated detection of malaria parasites in blood cell images. The proposed system leverages the strengths of CNNs in feature extraction and representation learning from images, combined with the discriminative power of SVMs for classification. Initially, CNN extracts intricate features from blood cell images, capturing essential patterns indicative of malaria infection. Subsequently, the extracted features are used to train an SVM classifier, enabling accurate discrimination between parasitized and uninfected blood cells. Experimental dataset evaluations were obtained from the Lister Hill National Center for Biomedical Communications website of the National Library of Medicine. The proposed model achieves a better f1-score, outperforming individual CNN or SVM models, around 0.015 compared to individual CNN models and 0.27 compared to individual SVM models. This hybrid CNN-SVM methodology offers a promising solution for accurately and efficiently detecting malaria parasites in blood cell images. © 2024 IEEE.

关键词： Support vector machines

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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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