检索结果-内蒙古大学图书馆

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

来源：评论

学校读者我要写书评

暂无评论

LDA Topic Modeling for bioinformatics Terms in arXiv Documents 9th

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

引用

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

来源：评论

学校读者我要写书评

暂无评论

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

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

引用

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

来源：评论

学校读者我要写书评

暂无评论

Implementation of Fine-Tuned BERT for Enzyme Classification Based on Gene Ontology 11

Implementation of Fine-Tuned BERT for Enzyme Classification ...

引用

11th International Conference on Advanced Informatics: Concept, Theory and Application, ICAICTA 2024

作者： Henry, Matthew Martianus Kenneth, Christian 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)9798331520311

Enzymes are biocatalysts with vital roles in biological functions and many industrial applications. Diverse enzymes are classified using Enzyme Commission (EC) nomenclature, making differentiation challenging. On the other hand, another biological information, gene ontology (GO), can describe the biological aspects of enzymes, covering related biological processes (BP), molecular functions (MF), and their locations within cells (CC). This study proposes a novel EC class and subclass classification of enzymes within the ontology subclass based on their GO semantics using a Bidirectional Encoder Representation of Transformer (BERT). The BERT model is first fine-tuned using the preprocessed GO term name and definition, with the enzymes in each ontology class (BP, MF, or CC) are also divided based on how the GO assigned, either through manual annotation (NONIEA) or electronically inferred (IEA). BERT successfully obtained 0.93, 0.60, 0.99, 0.90, 0.40, and 0.35 F1 scores during fine-tuning for BP IEA, BP NONIEA, MF IEA, MF NONIEA, CC IEA, and CC NONIEA, respectively. On the test set, the fine-tuned BERT significantly outperformed GOntoSim, a framework to calculate semantic similarity based on classical information theory, in EC class classification across all metrics with less inference time in all ontology subclass. Expanded further to the EC subclass, BERT can classify the enzyme on the EC subclass level in BP IEA and MF IEA ontology subclass. However, longer epochs are needed in fine-tuning. This result shows that the names and definitions of GO terms are distinguishable features in classifying enzymes as an alternative to the information content approach. © 2024 IEEE.

关键词： Gene Ontology

来源：评论

学校读者我要写书评

暂无评论

A bioinformatics Analysis and Homology 3D Modeling of Dihydroxy-orotate-dehydrogenase of Plasmodium ovale

A Bioinformatics Analysis and Homology 3D Modeling of Dihydr...

引用

2023 International Conference on Informatics, Multimedia, Cyber and Information Systems, ICIMCIS 2023

作者： Nirwantono, Rudi Assidqi, Khoirunnisa Hidayat, Alam Ahmad Pebrianto Trinugroho, Joko Pardamean, Bens Bina Nusantara University Faculty of Engineering Bioinformatics and Data Science Research Center Biotechnology Department Jakarta11480 Indonesia Bina Nusantara University Faculty of Engineering Food Biotechnology Research Center Biotechnology Department Jakarta11480 Indonesia Bina Nusantara University School of Computer Science Bioinformatics and Data Science Research Center Mathematics Departement Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program - Computer Science Program Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798350307306

The infection of Plasmodium vivax is relatively less virulent than the deathliest Plasmodium falciparum. However, it still can lead to a fatal case and often induces recurring malaria due to dormant parasites in the liver. Thus, the research to study the drug to treat Plasmodium vivax is essential, where the enzyme dihydroorotate dehydrogenase (DHODH) has recently become a new drug target. However, the drug-enzyme interaction study has only recently been conducted in Plasmodium falciparum (pfDHODH) due to the lack of the 3D structure of enzyme DHODH from Plasmodium vivax that is crucial for the study. Therefore, this study aimed to perform the modelling study of Plasmodium vivax DHODH (PvDHODH) to create a 3D structure as a basis for drug-protein interaction study in upcoming studies. Sequence pvDHODH (Accession: SCO68359.1) was used in homology modelling using Modeller 10.2 with the crystal structure of DHODH from DHODH (Accession: 7KZY) as a template. Overall, the model generated from the homology modelling was considered a good model, and the 3D structure was close to the native state according to several parameters, including DOPE score, GA341 score, QMEAN4 value, 3D-1D score, ERRAT2 score, and ProSA score. Ramachandran plot also revealed that almost all amino acids were distributed in the desirable and allowed area (99.1%), and only 0.9% were in generously allowed regions. Superimposition of the model with the template also indicated that the model has an almost similar structure and amino acids positioning, including in the binding pocket and active site. Therefore, the model can be used for downstream analysis in drug-protein interaction studies. Nevertheless, some improvements can still be performed to upgrade the quality of the model by deleting unaligned residues on the C-terminal and realigning the residues at the doubting site. © 2023 IEEE.

关键词： Amino acids

来源：评论

学校读者我要写书评

暂无评论

Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A data-driven Perspective

引用

Genomics, Proteomics & bioinformatics 2023年第1期21卷 164-176页

作者： Jianlei Gu Jiawei Dai Hui Lu Hongyu Zhao SJTU-Yale Joint Center for Biostatistics and Data Science Department of Bioinformatics and BiostatisticsSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Center for Biomedical Informatics Shanghai Engineering Research Center for Big Data in Pediatric Precision MedicineShanghai Children’s HospitalShanghai 200040China Department of Biostatistics Yale UniversityNew HavenCT 06511USA

Comprehensive characterization of spatial and temporal gene expression patterns in humans is critical for uncovering the regulatory codes of the human genome and understanding the molecular mechanisms of human *** expressed genes(UEGs)refer to the genes expressed across a majority of,if not all,phenotypic and physiological conditions of an *** is known that many human genes are broadly expressed across ***,most previous UEG studies have only focused on providing a list of UEGs without capturing their global expression patterns,thus limiting the potential use of UEG *** this study,we proposed a novel data-driven framework to leverage the extensive collection of40,000 human transcriptomes to derive a list of UEGs and their corresponding global expression patterns,which offers a valuable resource to further characterize human *** results suggest that about half(12,234;49.01%)of the human genes are expressed in at least 80%of human transcriptomes,and the median size of the human transcriptome is 16,342 genes(65.44%).Through gene clustering,we identified a set of UEGs,named LoVarUEGs,which have stable expression across human transcriptomes and can be used as internal reference genes for expression *** further demonstrate the usefulness of this resource,we evaluated the global expression patterns for 16 previously predicted disallowed genes in islet beta cells and found that seven of these genes showed relatively more varied expression patterns,suggesting that the repression of these genes may not be unique to islet beta cells.

关键词： Ubiquitous expression Housekeeping gene Disallowed gene Expression specificity Expression variability

来源：评论

学校读者我要写书评

暂无评论

Solanaceae pangenomes are coming of graphical age to bring heritability back

引用

aBIOTECH 2022年第4期3卷 233-236页

作者： Björn Usadel Institute for Biological Data Science CEPLASHeinrich Heine UniversityDüsseldorfGermany IBG-4 Bioinformatics BioSCForschungszentrum JülichJülichGermany

Two recent articles describe a pangenome of potato and a graph-based pangenome for tomato,*** latter improves our understanding of the tomato genomics architecture even further and the use of this graph-based pangenom... 详细信息

关键词： Tomato Potato Pangenome Graph-based pangenome Heritability

来源：评论

学校读者我要写书评

暂无评论

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

Variational quantum neural network with optimized ansatz for...

引用

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

来源：评论

学校读者我要写书评

暂无评论

Knowledge Graph-Enhanced Semantic Cache for Low-Latency and Cost-Effective Inference in Large Language Models 9

Knowledge Graph-Enhanced Semantic Cache for Low-Latency and ...

引用

9th International Conference on Information Management and Technology, ICIMTech 2024

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

ISBN: (纸本)9798350390025

In organizational knowledge management, Large Language Model (LLM) caches act as a semantic repository gathered from previous LLM responses. Due to intensive calls from multiple users, LLM may suffer from high inference latency. While there are many prior available approaches to solve this problem, most of them are inherently complex. This paper introduced a Knowledge Graph-enhanced Semantic Cache mechanism as an alternative, lightweight technique to boost retrieval for similar prompts. The latest state-of-the-art open-source LLM, named Google's Gemma-2B-it, was used to generate sample prompts and responses as a draft, while a knowledge graph (KG) was built from Wikipedia sentences. To create embeddings of prompts and KG, all-MiniLM-L6-v2 from SentenceTransformer was used. This new cache system resulted in up to 28% improvement over a standard model. In particular, reinforcement with KG cache embeddings yielded more than 85% semantic cache accuracy. To map the next trajectory of this pilot study, an overview of the extended framework for LLM knowledge management was also presented in this paper. The framework includes the new KG- enhanced cache system equipped with scalable security and fallback mechanisms that can promote green technology through substantial improvements in latency, throughput, and overall LLM costs. © 2024 IEEE.

关键词： Knowledge graph

来源：评论

学校读者我要写书评

暂无评论

UDCA,a novel strategy for preventing SARS-CoV-2 infection via FXR-mediated ACE2 downregulation

引用

生物化学与生物物理学报（英文版） 2023年第5期55卷 885-887页

作者： Mengjiao Chen Rongrong Zhu Min Zhang Institute of Cardiovascular Disease Key Laboratory for Arteriosclerology of Hunan ProvinceHunan International Scientific and Technological Cooperation Base of Arteriosclerotic DiseaseDepartment of Bioinformatics and Medical Big DataHengyang Medical SchoolUniversity of South ChinaHengyang 421001China

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has resulted in the current outbreak of coronavirus disease 2019(COVID-19)in humans,causing worldwide health issues[1].The periodic and unexpected consequences have made SARS-CoV-2 a severe threat to human beings,forcing researchers to explore the underlying mechanisms of *** converting enzyme 2(ACE2),a cell surface protein,acts as a specific functional receptor for SARS-CoV-2,as well as the earlier SARS-CoV,leading to viral entry into host cells[2].

关键词： "> UDCA a novel strategy for preventing SARS-CoV-2 infection via FXR-mediated ACE2 downregulation .MathJax_Hover_Frame {border-radius: .25em -webkit-border-radius: .25em -moz-border-radius: .25em -khtml-border-radius: .25em box-shadow: 0px 0px 15px #83A -webkit-box-shadow: 0px 0px 15px #83A -moz-box-shadow: 0px 0px 15px #83A -khtml-box-shadow: 0px 0px 15px #83A border: 1px solid #A6D ! important display: inline-block position: absolute} .MathJax_Menu_Button .MathJax_Hover_Arrow {position: absolute cursor: pointer display: inline-block border: 2px solid #AAA border-radius: 4px -webkit-border-radius: 4px -moz-border-radius: 4px -khtml-border-radius: 4px font-family: 'Courier New' Courier font-size: 9px color: #F0F0F0} .MathJax_Menu_Button .MathJax_Hover_Arrow span {display: block background-color: #AAA border: 1px solid border-radius: 3px line-height: 0 padding: 4px} .MathJax_Hover_Arrow:hover {color: white!important border: 2px solid #CCC!important} .MathJax_Hover_Arrow:hover span {background-color: #CCC!important} #MathJax_About {position: fixed left: 50% width: auto text-align: center border: 3px outset padding: 1em 2em background-color: #DDDDDD color: black cursor: default font-family: message-box font-size: 120% font-style: normal text-indent: 0 text-transform: none line-height: normal letter-spacing: normal word-spacing: normal word-wrap: normal white-space: nowrap float: none z-index: 201 border-radius: 15px -webkit-border-radius: 15px -moz-border-radius: 15px -khtml-border-radius: 15px box-shadow: 0px 10px 20px #808080 -webkit-box-shadow: 0px 10px 20px #808080 -moz-box-shadow: 0px 10px 20px #808080 -khtml-box-shadow: 0px 10px 20px #808080 filter: progid:DXImageTransform.Microsoft.dropshadow(OffX=2 OffY=2 Color='gray' Positive='true')} #MathJax_About.MathJax_MousePost {outline: none} .MathJax_Menu {position: absolute background-color: white color: black width: auto padding: 2px border: 1px solid #CCCCCC margin: 0 cursor: default font: menu text-align: left text-indent: 0 text-transform: none line-height: nor

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：