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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...

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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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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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Systematic Literature Review on Metaheuristic Algorithms in SNP Analysis for Diseases 6

Systematic Literature Review on Metaheuristic Algorithms in ...

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6th International Conference on Cybernetics and Intelligent System, ICORIS 2024

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

ISBN: (纸本)9798331539603

Single-nucleotide polymorphism (SNP) analysis has become a pivotal strategy for drug discovery within bioinformatics, especially for incurable diseases like cancer. With the increasing number of researchers starting to embrace metaheuristic methods, a review was done by gathering papers from the Google Scholar database from 2018 to 2023, which resulted in 20 papers after title, abstract, and content filtering. The findings show that the Genetic Algorithm and the Harmony Search Algorithm have become popular approaches in SNP analysis, particularly in studies on breast cancer, age-related macular degeneration, and colorectal cancer. However, the review shows that while researchers have proven most methods effective in finding disease-related SNPs, a more measurable study in SNP analysis is needed, due to the lack of elaboration on measurement metrics in the found studies. © 2024 IEEE.

关键词： metaheuristic algorithms single nucleotide polymorphisms

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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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Fast Cauchy Sum Algorithms for Polynomial Zeros and Matrix Eigenvalues 13th

Fast Cauchy Sum Algorithms for Polynomial Zeros and Matrix...

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13th International Symposium on Algorithms and Complexity, CIAC 2023

作者： Pan, Victor Y. Go, Soo Luan, Qi Zhao, Liang Department of Computer Science Lehman College of CUNY BronxNY United States Program in Computer Science The Graduate Center of the City University of New York New York United States Program in Mathematics The Graduate Center of the City University of New York New York United States

ISBN: (纸本)9783031304477

Given a black box oracle that evaluates a univariate polynomial p(x) of a degree d, we seek its zeros, aka the roots of the equation. At FOCS 2016, Louis and Vempala approximated within an absolutely largest zero of such a real-rooted polynomial at the cost of the evaluation of Newton’s ratio (formula presented) points x and then extended this algorithm to approximation of an absolutely largest eigenvalue of a symmetric matrix at a record Boolean cost. By applying distinct approach and techniques we obtain much more general results at the same computational cost. Our use of Cauchy integrals and randomization is non-trivial and pioneering in this field. Somewhat surprisingly, the Boolean complexity of the accelerated versions of our algorithms in [25, 26] reached below the known lower bounds on the Boolean complexity of polynomial root-finding. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Approximation algorithms

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Analyzing the Impacts of Dynamic Game Balancing in a Survival Roguelike Chess Game

Analyzing the Impacts of Dynamic Game Balancing in a Surviva...

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Advancement in Data science, E-learning and Information Systems (ICADEIS), International Conference on

作者： Mario Yulyani Arifin Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program – Doctor of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331513320

ISBN: (纸本)9798331513337

This research investigates the novel application of Dynamic Game Balancing (DGB) techniques in the context of a hybrid chess-survival roguelike game, a unique combination of genres not widely explored in previous studies. The study addresses two primary research questions: the identification of suitable DGB techniques for these genres and the enhancement of user experience through DGB. A game prototype was developed using Unity, where players control a chess knight in a turn-based system, facing increasingly challenging enemy pieces. The DGB system dynamically adjusts the game's difficulty based on player performance, utilizing various inputs such as damage received or dealt, health points, powerup usage, and decision speed. Preliminary results from 14 beta-testers show overall positive feedback, with players reporting higher engagement and enjoyment due to the seamless difficulty adjustments, as reflected by the high mean scores from surveys like the User Experience Questionnaire (UEQ). This research fills a gap in the literature by demonstrating the feasibility and benefits of integrating DGB in a chess-survival roguelike setting. These findings highlight the potential for DGB to significantly improve player experience in hybrid game genres, suggesting that its application can create more adaptive and immersive gaming environments in various other genres as well.

关键词： Surveys Video games Electronic learning Prototypes Games Data science User experience Information systems

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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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Indonesian Agricultural-crops Classification Using Transfer Learning Model 8

Indonesian Agricultural-crops Classification Using Transfer ...

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8th International Conference on computer science and Computational Intelligence, ICCSCI 2023

作者： Isnan, Mahmud Hidayat, Alam Ahmad Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Department of Mathematics School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

Classification of Indonesian crops is a critical task in developing farming and getting more understanding of agriculture. However, there is no clear task in classifying types of crops in Indonesia. Transfer learning has been used successfully in a variety of image classification applications. Thus, in this paper, we collected images of Indonesian crops from the internet randomly and proposed a classification by using transfer learning of deep learning with four pre-trained models: EffficientNetB0, ResNet18, VGG19, and AlexNet. In the experiment, augmentation techniques such as random horizontal flip, random vertical flip, and random affine were utilized to prevent the network from overfitting. The result found that EfficientNet-B0 outperformed other models with an accuracy of 82.55. Then, the model struggled to distinguish between crops in the same family. According to the results, although transfer learning can work well to classify images of Indonesian agricultural crops, some improvements are still required to address existing issues. © 2023 The Authors. Published by Elsevier B.V.

关键词： Agriculture Classification Crop Deep Learning Transfer learning

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Regional Classification of Indonesian Folk Songs Based on K-NN and PCC-LDA Model

Regional Classification of Indonesian Folk Songs Based on K-...

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2023 International Conference on computer science, Information Technology and Engineering, ICCoSITE 2023

作者： Mahardhika, Ferdinand Warnars, Harco Leslie Hendric Spits Nugroho, Anto Satriyo Budiharto, Widodo Bina Nusantara University BINUS Graduate Program Computer Science Computer Science Departement Jakarta11480 Indonesia Organisasi Riset Elektronika Dan Informatika Jakarta10340 Indonesia Bina Nusantara University School of Computer Science Computer Science Departement Jakarta11480 Indonesia

ISBN: (纸本)9798350320954

One of the biggest challenges in Music Information Retrieval (MIR) is classification. MIR is a subset of Machine Learning (ML), where the methods found in computer science can be used to solve problems in the music domain area. Indonesia is an archipelago country inhabited by around 1,340 ethnic groups spread across 38 provinces. This ethnic group has a variety of cultures, including folk songs, and almost every area in Indonesia has folk songs. In this study, we conducted a regional classification of 500 Indonesian folk songs from 10 regions in Indonesia. We build a model for regional classification tasks using the MIR approach. This model combines feature selection and dimension reduction capabilities. By using hyperparameter tunning and a cross- validation of 5 folds, the result of our proposed model for regional classification of Indonesian folk songs using K-NN with PCC-LDA can obtain an accuracy rate of 84.7%. © 2023 IEEE.

关键词： Music

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Count-Data Mixed Models of Topical Tweets: A Case of Indonesia Flood Events 8

Count-Data Mixed Models of Topical Tweets: A Case of Indones...

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8th International Conference on computer science and Computational Intelligence, ICCSCI 2023

作者： Hidayat, Alam Ahmad Pardamean, Bens Mathematics Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

Examining topic-level variability in modeling Twitter data can potentially yield more comprehensive insights into public perception during critical periods, thereby enhancing natural disaster mitigation and surveillance efforts. In this study, we utilized generalized linear mixed models (GLMMs) to illustrate the variability in tweet counts related to specific topics in Indonesia during the flood events that occurred in February 2021. The glmmTMB library in R was employed for this purpose. The data were assumed to follow two distinct exponential distributions: Poisson and Negative Binomial. To incorporate random effects, random intercepts and random slopes were introduced, allowing them to vary randomly across topics in the initial two models. Additionally, the final model addressed issues related to dispersion and zero-inflation. By evaluating the Akaike Information Criteria scores, we determined that a model based on the Negative Binomial distribution with random zero-inflation intercepts best fit the data. The chosen model formulation and the estimated parameters have the potential to forecast topic-specific trends in Indonesian flood-related Twitter data. © 2023 The Authors. Published by Elsevier B.V.

关键词： count data disaster surveillance floods mixed models Twitter

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