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Interplay between morphology and competition in two-dimensional colony expansion

Physical Review E 2023年第3期108卷 L032301-L032301页

作者： Daniel W. Swartz Hyunseok Lee Mehran Kardar Kirill S. Korolev Department of Physics Graduate Program in Bioinformatics and Biological Design Center Boston University Boston Massachusetts 02215 USA

In growing populations, the fate of mutations depends on their competitive ability against the ancestor and their ability to colonize new territory. Here we present a theory that integrates both aspects of mutant fitness by coupling the classic description of one-dimensional competition (Fisher equation) to the minimal model of front shape (Kardar-Parisi-Zhang equation). We solve these equations and find three regimes, which are controlled solely by the expansion rates, solely by the competitive abilities, or by both. Collectively, our results provide a simple framework to study spatial competition.

关键词： Ecological population dynamics Front propagation Surface growth Coarse graining

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Variational quantum neural network with optimized ansatz for predicting malignant ventricular arrhythmias 9th

Variational quantum neural network with optimized ansatz for...

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

作者： Dominic, Nicholas Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

Preventive strategies should be the utmost priority when dealing with diverse patients suffering from malignant ventricular arrhythmia (MVA) that can lead to sudden cardiac death (SCD). Electrocardiogram (ECG) data is commonly used as a predictor for MVA predictive models. In this study, all ECG signals from MIT-BIH databases were fragmented into five-minute durations with a frequency sampling of 128 Hz. To solve the absence of hybrid optimizations in Machine Learning (ML) models, a novel Variational Quantum Neural Network (VQNN) was invented. Empowered by deep learning capabilities and optimized quantum circuits design, VQNN achieved remarkable performances designated by an accuracy of up to 95.1%, a perfect 100% recall, and a 95.2% score of the area under the Receiver Operating Characteristic curve (AUC ROC) with Conjugate Gradient as an optimizer and EfficientSU2 as a quantum ansatz. Despite the susceptibility to quantum noise, this research settles a new trajectory of utilizing quantum variational algorithms to predict and expand its applicability for MVA cases. © 2024 The Authors.

关键词： Quantum computers

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Sequence to Sequence Deep Learning Architecture for Forecasting Temperature and Humidity inside Closed Space 10

Sequence to Sequence Deep Learning Architecture for Forecast...

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10th International Conference on Cyber and IT Service Management, CITSM 2022

作者： Setiawan, Karli Eka Elwirehardja, Gregorius Natanael Pardamean, Bens Bina Nusantara University Binus Graduate Program Computer Science Program Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia

ISBN: (数字)9781665460743

ISBN: (纸本)9781665460743

Solar Dryer Dome (SDD), an agricultural facility for drying and preserving agricultural products, needs a smart ability to predict the future indoor climate accurately, including indoor temperature and indoor humidity, in order to optimize electricity usage. To overcome these challenges, deep learning has been a widely adopted method. This research aims to forecast the future indoor climate using time series data by implementing a sequence-to-sequence (seq2seq) architecture, which is mostly used in Natural Language Processing (NLP) tasks. The two proposed seq2seq models, Long Short-Term Memory (LSTM) seq2seq and Gated Recurrent Unit (GRU) seq2seq, have proven to be superior to the adapted LSTM and GRU. The results show that the seq2seq GRU model outperforms the adapted GRU baseline model by an average difference of 0.03013 in MAE and the seq2seq LSTM model outperforms the adapted LSTM baseline model by an average difference of 0.00941 in MAE. To the best of our knowledge, this is the first implementation of seq2seq models for indoor climate forecasting on the Room Climate dataset. © 2022 IEEE.

关键词： Long short-term memory

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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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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...

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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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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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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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Systematic Literature Review on Machine Learning Predictive Models for Indoor Climate in Smart Solar Dryer Dome 4

Systematic Literature Review on Machine Learning Predictive ...

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4th International Conference on Cybernetics and Intelligent System, ICORIS 2022

作者： Setiawan, Karli Eka Elwirehardja, Gregorius Natanael Pardamean, Bens Bina Nusantara University BINUS Graduate Program Master of Computer Science Program Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia

ISBN: (纸本)9781665453950

Precise predictions of indoor climate conditions are required in the implementation of Smart Solar Dryer Dome (SDD). Trend development of prediction models is discussed in this review from 15 selected research papers (2018-2022) on indoor climate prediction which was obtained from research paper databases The output shows that the most used model for predicting indoor climate is Artificial Neural Network (ANN), especially Recurrent Neural Network (RNN) such as LSTM and GRU. However, there are some potential methods such as Transformer, Combined Support Vector Machines (SVM)-Deep Learning, and sequence-to-sequence which could outperform other commonly used models. Based on findings various opportunities exist to improve the precision of indoor climate prediction, which can bring power consumption efficiency and others benefit to Smart SDD users. Such studies may further be explored to produce more accurate machine learning models. © 2022 IEEE.

关键词： Domes

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