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

作者： Setiawan, Devin Karnyoto, Andrea Stevens Intan, Indo Pardamean, Bens Department of Electrical Engineering and Computer Science University of Kansas Lawrence United States Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Department of Informatics Engineering Universitas Dipa Makassar Makassar Indonesia Computer Science Department BINUS Graduate Program Computer Science Program Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9798331539603

Breast cancer is an occurrence of cancer that attacks breast tissue and is the most common cancer among women worldwide, affecting one in eight women. In this modern world, breast cancer image classification simplifies the process of analyzing, providing objective and accurate results. By leveraging machine learning algorithms and computer vision techniques, we developed breast cancer detection. The dataset is histopathology dataset from BreakHis and UNHAS Hospital. We chose the ConvNeXt-Tiny model then modified the classifier head as the proposed method. Before the dataset is processed by the model, we augment the images by applying random horizontal and vertical flips, adjustments to brightness, contrast, saturation, and hue using color jitter. The augmentation process simulates real-world variance and enhances the model's ability to generalize to unseen data. Our proposed model gained better performance (accuracy, F1-Score) results compared two other techniques to VGG16 and SVM. According to our experiments, the F1-Score for the ConvNeXt-Tiny model with classifier head modification is higher at 0.9516, than the gain for VGG16 at 0.9292, and the gain for the SVM at 0.83. © 2024 IEEE.

关键词： Lung cancer

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Pathway-Based Analysis Using SVM-RFE for Gene Selection and Classification 7th

Pathway-Based Analysis Using SVM-RFE for Gene Selection and ...

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7th International Conference on Artificial Intelligence and Virtual Reality, AIVR 2023

作者： Rahman, Nurazreen Afiqah A. Nasarudin, Nurul Athirah Mohamad, Mohd Saberi Artificial Intelligence and Bioinformatics Research Group Faculty of Computing Universiti Teknologi Malaysia Johor81310 Malaysia Health Data Science Lab Department of Genetics and Genomics College of Medicine and Health Science United Arab Emirates University Al Ain Abu Dhabi United Arab Emirates

ISBN: (纸本)9789819990177

The pathway-based analysis is one method for selecting and classifying genes by incorporating pathway information. Integration of pathway knowledge into microarray data significantly advances researchers in the analysis of complex diseases. Microarray data involves thousands of genes to be selected, and therefore, a suitable method to eliminate noisy and uninformative genes is needed. Selecting significant genes for a specific disease is crucial to identifying genes highly related to disease production. Previous research shows that using both pathway information and gene expression data is more significant in disease identification. Therefore, pathway-based analysis using Support Vector Machine Recursive Feature Elimination (SVM-RFE) is introduced in this research to identify significant genes associated with analyzing the targeted phenotype. The datasets involved in this research are lung cancer and gender dataset. The results from the proposed method performed better than previous work as the significant genes are selected from the highest rank of genes in the highest rank of the pathway. The performance of the proposed method was evaluated using 10-fold cross-validation in terms of accuracy. Finally, a biological validation was conducted on selected genes in the top 5 pathways based on biological literature. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2024.

关键词： Gene expression

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LLM2Vec Sentence Embeddings Analysis in Sentiment Classification

LLM2Vec Sentence Embeddings Analysis in Sentiment Classifica...

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2024 IEEE International Conference on data and Software Engineering, ICoDSE 2024

作者： Henry, Matthew Martianus Heryanto, Nur Adhianti Isnan, Mahmud Kurnianingrum, Dian Ratnapuri, Chyntia Ika Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Entrepreneurship Department Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

ISBN: (纸本)9798331506407

Sentiment analysis is crucial method in business intelligence to extract insights, which typically begin with sentiment classification. One of the latest frameworks for generating sentence embeddings for sentiment classification is LLM2Vec, which allows Transformer decoder-based models to generate sentence embeddings for text representation. Its capability is deemed language-agnostic, which, in this study, the framework is leveraged for Tokopedia tweet sentiment analysis to prove the claim. The base decoder models used in the LLM2Vec framework were Llama 3 8B, Llama 2 7B, Sheared Llama 1.3B, and Mistral 7B. Two BERT-based models, which are the Indonesian SBERT model and IndoBERT trained with the SimCSE approach, were employed as a comparison. The generated embeddings were classified using logistic regression, SVM, and MLP Classifier. Classifiers using embedding generated by LLM2Vec with Llama 3 8B and Mistral 7B achieves on-par performance with classifiers that utilize IndoBERT SimCSE embeddings, while classifiers using embeddings generated by LLM2Vec with Llama 2 7B and Sheared Llama 1.3B achieves much lower performance. Classifiers with Indonesian SBERT embeddings achieve the highest F1 score performance. Despite slightly lower performance, this study has proven the language-agnostic capability of LLM2Vec, especially with Llama 3 8B and Mistral 7B in colloquial Bahasa Indonesia sentiment analysis, since none of the base decoders were ever trained using the Bahasa Indonesia corpus. © 2024 IEEE.

关键词： Decoding

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Utilizing Semi-supervised Method in Predicting BRCA1 Pathogenicity Variants 8

Utilizing Semi-supervised Method in Predicting BRCA1 Pathoge...

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

作者： Hidayat, Alam Ahmad Trinugroho, Joko Pebrianto Nirwantono, Rudi Sudigyo, Digdo Pardamean, Bens Department of Mathematics School of Computer Science Bina Nusantara University 11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

Quantifying the effect of mutations in the BRCA1 gene is useful for understanding their clinical consequences on breast cancer. Machine learning models can be applied to predict the landscape of protein variant effects that might not be always accessible by experiments. In this work, we propose a simple semi-supervised learning method using a Gaussian mixture model to predict ~90% of the unlabeled missense variants of the BRCA1 gene collected from the ClinVar database. High-quality embeddings are used as a feature of the protein sequences, extracted using the latest pre-trained transformer-based language protein model. A statistical test show that the protein embeddings are effective and robust for predicting pathogenicity. Further, the lower representations of the features are then fed into the semi-supervised model. The prediction performance of the model only for the labeled testing data achieves an AUC score and an accuracy of 79.27% and 71.58%, respectively. Using our defined pathogenic probability score, we find that ~94% of variants in our unlabeled dataset are well-separated into either benign or pathogenic classes according to that scoring. Our scores obtain a moderate Spearman rank correlation with the results of established unsupervised variant effect models. Finally, our approach can potentially be developed for more accurate and biologically reliable predictions of the variant effects. © 2023 The Authors. Published by Elsevier B.V.

关键词： embeddings language model mutation effect protein sequence semi-supervised learning

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Systematic Literature Review on Statistics and Machine Learning Predictive Models for Rice Phenotypes 8

Systematic Literature Review on Statistics and Machine Learn...

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

作者： Dominic, Nicholas Cenggoro, Tjeng Wawan Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta11480 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. © 2023 The Authors. Published by Elsevier B.V.

关键词： machine learning rice phenotypes prediction statistics

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Asymptotics of Bayesian Uncertainty Estimation in Random Features Regression 37

Asymptotics of Bayesian Uncertainty Estimation in Random Fea...

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37th Conference on Neural Information Processing Systems, NeurIPS 2023

作者： Baek, Youngsoo Berchuck, Samuel I. Mukherjee, Sayan Department of Statistical Science Duke University DurhamNC27705 United States Department of Biostatistics & Bioinformatics Duke University DurhamNC27705 United States Center for Scalable Data Analysis and Artificial Intelligence Universität Leipzig Leipzig04105 Germany Deparments of Mathematics Computer Science Biostatistics & Bioinformatics Duke University NC United States

ISBN: (纸本)9781713899921

In this paper, we compare and contrast the behavior of the posterior predictive distribution to the risk of the maximum a posteriori (MAP) estimator for the random features regression model in the overparameterized regime. We will focus on the variance of the posterior predictive distribution (Bayesian model average) and compare its asymptotics to that of the risk of the MAP estimator. In the regime where the model dimensions grow faster than any constant multiple of the number of samples, asymptotic agreement between these two quantities is governed by the phase transition in the signal-to-noise ratio. They also asymptotically agree with each other when the number of samples grows faster than any constant multiple of model dimensions. Numerical simulations illustrate finer distributional properties of the two quantities for finite dimensions. We conjecture they have Gaussian fluctuations and exhibit similar properties as found by previous authors in a Gaussian sequence model, which is of independent theoretical interest. © 2023 Neural information processing systems foundation. All rights reserved.

关键词： Signal to noise ratio

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Machine Learning Approaches in Detecting Autism Spectrum Disorder 8

Machine Learning Approaches in Detecting Autism Spectrum Dis...

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

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

Early detection of Autism Spectrum Disorder (ASD) needs to be increased to prevent further adverse impacts. Thus, the classification between ASD and Typically Development (TD) individuals is an intriguing task. This review study has collected 26 related papers to answer four research questions, i.e., what are the most used data inputs, brain atlases, and machine learning models for ASD classification, as also to discover the significant parts of the brain correlated with the ASD. It was eventually found that functional connectivity matrix, Support Vector Machine, and CC200 are the most frequently used data input, model, and brain atlas, respectively. Researchers also concluded that the posterior temporal fusiform cortex, intracalcarine cortex, cuneal cortex, subcallosal cortex, occipital pole, and lateral occipital cortex are the brain regions highly correlated with ASD. © 2023 The Authors. Published by Elsevier B.V.

关键词： autism spectrum disorder brain atlas brain region machine learning

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Punctuated ancestral gene gains in streptophyte evolution

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Molecular Plant 2022年第5期15卷 799-801页

作者： Iker Irisarri Jan de Vries University of Goettingen Institute for Microbiology and GeneticsDepartment of Applied BioinformaticsGoldschmidtstr.137077 GöttingenGermany Campus Institute Data Science(CIDAS) GöttingenGermany University of Goettingen Goettingen Center for Molecular Biosciences(GZMB)Department of Applied BioinformaticsGoldschmidtstr.137077

Understanding the genomic substrate behind evolutionary change is a major endeavor in biology,shedding light on impor-tant aspects of the evolutionary history as well as unraveling the mechanisms of genome *** of the ... 详细信息

关键词： evolution evolution evolutionary

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A Bayesian-based approach for extracting the pion charge radius from electron-electron scattering data

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Chinese Physics C 2021年第8期45卷 12-27页

作者： Alam A Hidayat Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara UniversityJakarta 11480Indonesia Computer Science Department BINUS Graduate Program-Master of Computer ScienceBina Nusantara UniversityJakarta 11480Indonesia

In this study,we utilize a potentially versatile Bayesian parameter approach to compute the value of the pion charge radius and quantify its uncertainty from several experimental e^(+)e^(-) datasets for the pion vector form *** employ dispersion relations to model the pion vector form factor to extract the *** model selection is used to determine the order of polynomial appearing in the form factor formulation that can be supported by the data,adapting the computation of Bayes evidence and Bayesian effective complexity based on Occam's *** findings indicate that five out of six used datasets favor the nine-parameter model for radius extraction,and accordingly,we average the radii from the *** some inconsistencies with the most updated radius values,our approach may serve as a more intuitive method of addressing parameter estimations in dispersion theory.

关键词： Bayesian complexity dispersion hadron pion

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

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Procedia Computer science 2024年 245卷 391-398页

作者： Matthew Martianus Henry Nur Adhianti Heryanto Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

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.

关键词： Automated medical report generation DenseNet-121 EfficientNet Encoder-decoder framework

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