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3rd International Conference on Eco Engineering Development, ICEED 2019

作者： Pardamean, Bens Cenggoro, Tjeng Wawan Chandra, Bloomest Jansen Rahutomo, Reza 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 Computer Science Department College of Letters and Science University of Wisconsin MadisonWI53706 United States Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

The concept of smart building includes the optimization of energy usage in a building. One of the possible solutions for this is to adaptively adjust appliances utilization according to activity level in the building. Thus, an intelligent activity estimation system needs to be developed. However, massive annotated dataset is necessary to train the system. Therefore, we propose a system that enables rapid data annotation to collect the massive dataset. With the proposed system, an image can be annotated within 4.8 seconds in average. © 2020 Published under licence by IOP Publishing Ltd.

关键词： Historic preservation

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CIWARS: A Web Server for Antibiotic Resistance Surveillance Using Longitudinal Metagenomic Data

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Journal of Molecular Biology 2025年第15期437卷

作者： Emon, Muhit Islam Cheung, Yat Fei Stoll, James Rumi, Monjura Afrin Brown, Connor Choi, Joung Min Moumi, Nazifa Ahmed Ahmed, Shafayat Song, Haoqiu Sein, Justin Yao, Shunyu Khan, Ahmad Gupta, Suraj Kulkarni, Rutwik Butt, Ali Vikesland, Peter Pruden, Amy Zhang, Liqing Department of Computer Science Virginia Tech Blacksburg 24060 VA United States Fralin Life Science Institute Virginia Tech Blacksburg 24060 VA United States Department of Civil and Environmental Engineering Virginia Tech Blacksburg 24060 VA United States The Interdisciplinary PhD Program in Genetics Bioinformatics and Computational Biology Virginia Tech Blacksburg 24060 VA United States

The rise of antibiotic resistance (AR) poses a substantial threat to human and animal health, food security, and economic stability. Wastewater-based surveillance (WBS) has emerged as a powerful strategy for population-level AR monitoring, providing valuable data to guide public health and policy decisions. Metagenomic sequencing is especially promising, as it can yield comprehensive profiles of antibiotic resistance genes (ARGs) and other genes relevant to AR in a single run. However, online analytical platforms to facilitate analysis of longitudinal metagenomic data are lacking. To address this, we introduce CyberInfrastructure for Waterborne Antibiotic Resistance Surveillance (CIWARS), a web server configured for characterizing key AR trends from longitudinal metagenomic WBS data. CIWARS offers comprehensive profiling of ARGs and taxonomic profiling of pathogen-associated bacterial taxonomic groups, identifies potential associations of ARGs with mobile genetic elements (MGEs) and pathogen-containing taxa, and assesses resistome risk based on the co-occurrence of ARGs, MGEs, and pathogen-like sequences. Additionally, it detects anomalous AR indicators over time, aiding in identifying potential events of concern, such as the emergence of resistant strains or outbreaks. Through interactive temporal data visualization, CIWARS enables AR monitoring and can serve as a tool to inform effective and timely interventions to mitigate the spread and transmission of AR. Here, CIWARS is demonstrated using longitudinal metagenomic data from a wastewater treatment plant (WWTP) influent and effluent, but it can be extended to any environment. CIWARS provides a valuable tool to support global efforts to combat the evolution and spread of AR, while also guiding agricultural and public health efforts aimed at optimizing antibiotic use. The web server is freely available at https://***/. © 2025 Elsevier Ltd

关键词： anomaly detection antibiotic resistance (AR) AR indicator profiling longitudinal metagenomics wastewater-based surveillance

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Bayesian Formulations for Graph Spectral Denoising

arXiv

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arXiv 2023年

作者： Leone, Sam Sun, Xingzhi Perlmutter, Michael Krishnaswamy, Smita Program for Applied Mathematics Yale University United States Department of Computer Science Yale University United States Department of Mathematics Boise State University United States Department of Genetics Yale School of Medicine United States Wu Tsai Institute Yale University United States FAIR Meta AI United States Computational Biology and Bioinformatics Program Yale University United States

Here we consider the problem of denoising features associated to complex data, modeled as signals on a graph, via a smoothness prior. This is motivated in part by settings such as single-cell RNA where the data is very high-dimensional, but its structure can be captured via an affinity graph. This allows us to utilize ideas from graph signal processing. In particular, we present algorithms for the cases where the signal is perturbed by Gaussian noise, dropout, and uniformly distributed noise. The signals are assumed to follow a prior distribution defined in the frequency domain which favors signals which are smooth across the edges of the graph. By pairing this prior distribution with our three models of noise generation, we propose Maximum A Posteriori (M.A.P.) estimates of the true signal in the presence of noisy data and provide algorithms for computing the M.A.P. Finally, we demonstrate the algorithms' ability to effectively restore signals from white noise on image data and from severe dropout in single-cell RNA sequence data. © 2023, CC BY.

关键词： Frequency domain analysis

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A FLOW ARTIST FOR HIGH-DIMENSIONAL CELLULAR DATA

arXiv

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arXiv 2023年

作者： MacDonald, Kincaid Bhaskar, Dhananjay Thampakkul, Guy Nguyen, Nhi Zhang, Joia Perlmutter, Michael Adelstein, Ian Krishnaswamy, Smita Department of Mathematics Yale University United States Department of Genetics Yale School of Medicine United States Department of Computer Science Yale University United States Department of Mathematics Pomona College United States Applied Mathematics Program Yale University United States Department of Statistics University of Washington United States Department of Mathematics Boise State University United States Computational Biology and Bioinformatics Program Yale University United States

We consider the problem of embedding point cloud data sampled from an underlying manifold with an associated flow or velocity. Such data arises in many contexts where static snapshots of dynamic entities are measured, including in high-throughput biology such as single-cell transcriptomics. Existing embedding techniques either do not utilize velocity information or embed the coordinates and velocities independently, i.e., they either impose velocities on top of an existing point embedding or embed points within a prescribed vector field. Here we present FlowArtist, a neural network that embeds points while jointly learning a vector field around the points. The combination allows FlowArtist to better separate and visualize velocity-informed structures. Our results, on toy datasets and single-cell RNA velocity data, illustrate the value of utilizing coordinate and velocity information in tandem for embedding and visualizing high-dimensional data. © 2023, CC BY.

关键词： RNA

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Genome data mining approach to identify potential protein in crop plants

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AIP Conference Proceedings 2024年第1期3026卷

作者： Joko Pebrianto Trinugroho Faisal Asadi Bens Pardamean Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

There is a need to produce more crop plants to meet the future global demand. However, the climate change has affected the global crop yield. Consequently, finding an alternative approach to improve crop yield becomes essential. The development of sequencing techniques, as well as information technologies, have enabled us to perform genome data mining. Using genome data mining approach, it is possible to identify or discover a protein which has a particular characteristic. This study aims to identify a protein, which could potentially improve crop yield, using genome data mining approach. D1 protein was used as the target, as this protein is highly involved in photosynthesis. Then, protein sequences of various crop plants were collected from biological database. After conducting data trimming and filtering, sequence analysis was performed. The analysis was used to construct phylogenetic tree and create a 3D protein model. Sequence analysis displayed variation in amino acid sequence in D1 protein. Protein modelling located the variations, which scattered within D1 protein. Furthermore, we highlighted the amino acid residues that are the targets for genetic engineering. The research findings may provide a reference to improve crop production through genome mining approach.

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Dental Disease Detection based on CNN for Panoramic Dental Radiographs

Dental Disease Detection based on CNN for Panoramic Dental R...

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IEEE International Conference on Intelligent Computing and Information Systems (ICICIS)

作者： Manar El Bagoury Mirna Al-Shetairy Omar Ahmed Samah S Mehanny Tassneem Hamdy Gihan Omar Marwan Akram Rana Mohamed Hebatullah Amr Walaa Gad Bioinformatics Program Faculty of Computer and Information Sciences Ain Shams University Cairo Egypt Computer Science Department Faculty of Computer and Information Sciences Ain Shams University Cairo Egypt Oral Biology Department Faculty of Dentistry Cairo and Galala Universities Cairo Egypt Oral and Maxillofacial Radiology Department Faculty of Dentistry Cairo University Cairo Egypt Oral Radiology Department Faculty of Oral and Dental Medicine Future University in Egypt Cairo Egypt Information Systems Department Faculty of Computer and Information Sciences Ain Shams University Cairo Egypt

Panoramic dental radiography is one of the examination tools frequently performed in dental clinics and hospitals as it captures a wide range of the dental region and its surroundings, but due to the complex structure of the dental area and lack of time, dentists focus on tiny parts of the images. With the help of Machine Learning, dentists can detect dental defects and anomalies faster and more accurately. In this study, a data set of 733 panoramic radiographs of adult patients was collected from the faculty of Oral and Dental Medicine, Future University, Egypt. Using a combination of pre-trained CNN architecture and a finetuned network, the collected panoramic radiographs were used to determine the optimal architecture. The purpose of this research was to develop a computer-aided detection system based on a finetuned CNN algorithm, and to evaluate the accuracy and usefulness of this system for the detection of proximal and occlusal caries, interdental and inter radicular alveolar bone loss, periapical lesions, and impacted teeth in panoramic radiographs. Different object detection models were tested to detect selected dental diseases that were found in the panoramic radiographs, and after a few experiments, the YOLOv5 architecture was proved to be the most optimal after achieving 0.61 mAP@0.5 and 0.28 mAP@ [0.5-0.95] for the total six classes. This is the best-achieved results to our knowledge.

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Towards High Generalization Performance on Electrocardiogram Classification

Towards High Generalization Performance on Electrocardiogram...

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2021 Computing in Cardiology, CinC 2021

作者： Han, Hyeongrok Park, Seongjae Min, Seonwoo Choi, Hyun-Soo Kim, Eunji Kim, Hyunki Park, Sangha Kim, Jinkook Park, Junsang An, Junho Lee, Kwanglo Jeong, Wonsun Chon, Sangil Ha, Kwonwoo Han, Myungkyu Yoon, Sungroh Department of Electrical and Computer Engineering Seoul National University Seoul Korea Republic of HUINNO Co. Ltd Seoul Korea Republic of LG AI Research Seoul Korea Republic of Department of Computer Science and Engineering Kangwon National University Chuncheon Korea Republic of Department of Biological Sciences Interdisciplinary Program in Bioinformatics Interdisciplinary Program in Artificial Intelligence ASRI INMC Institute of Engineering Research Seoul National University Seoul Korea Republic of

ISBN: (纸本)9781665479165

Recently, many electrocardiogram (ECG) classification algorithms using deep learning have been proposed. The characteristics of ECG vary from dataset to dataset for various reasons (i.e., hospital, race, etc.). Therefore, it is important for a model to have high generalization performance consistently over all datasets. In this paper, as part of the PhysioNet / Computing in Cardiology Challenge 2021, we present a model developed to classify cardiac abnormalities from 12 lead and reduced-lead ECGs. In particular, to upgrade our previous model for improving generalization performance, we newly adopt constant-weighted cross-entropy loss, additional features, Mixup augmentation, and squeeze/excitation block, OneCycle learning rate scheduler, which are selected via evaluation of generalization performance using leave-one-dataset-out cross-validation setting. With the present model, our DSAILSNU team has received challenge scores of 0.55, 0.58, 0.58, 0.57 and 0.57 (ranked 2nd, 1st, 1st, 2nd, 2nd out of 39 teams) for the 12-lead, 6-lead, 4-lead, 3-lead, and 2-lead versions of the hidden test set, respectively. The present model achieves higher generalization performance over all versions of the hidden test set than the model submitted last year. © 2021 Creative Commons.

关键词： Deep learning

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Cell2Sentence: teaching large language models the language of biology 24

Cell2Sentence: teaching large language models the language o...

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Proceedings of the 41st International Conference on Machine Learning

作者： Daniel Levine Syed Asad Rizvi Sacha Lévy Nazreen Pallikkavaliyaveetil David Zhang Xingyu Chen Sina Ghadermarzi Ruiming Wu Zihe Zheng Ivan Vrkic Anna Zhong Daphne Raskin Insu Han Antonio Henrique De Oliveira Fonseca Josue Ortega Caro Amin Karbasi Rahul M. Dhodapkar David Van Dijk Department of Computer Science Yale University New Haven CT School of Engineering Applied Science University of Pennsylvania Philadelphia PA School of Computer and Communication Sciences Swiss Federal Institute of Technology Lausanne Lausanne Switzerland Department of Computer Science Yale University New Haven CT and Department of Neuroscience Yale School of Medicine New Haven CT Department of Computer Science Yale University New Haven CT and Department of Neuroscience Yale School of Medicine New Haven CT and Wu Tsai Institute Yale University New Haven CT Google and Yale Institute for Foundations of Data Science New Haven CT and Department of Computer Science Yale University New Haven CT and Yale School of Engineering and Applied Science New Haven CT Roski Eye Institute University of Southern California Los Angeles CA and Department of Internal Medicine (Cardiology) Yale School of Medicine New Haven CT Department of Computer Science Yale University New Haven CT and Yale Institute for Foundations of Data Science New Haven CT and Wu Tsai Institute Yale University New Haven CT and Cardiovascular Research Center Yale School of Medicine New Haven CT and Interdepartmental Program in Computational Biology & Bioinformatics Yale University New Haven CT and Department of Internal Medicine (Cardiology) Yale School of Medicine New Haven CT

We introduce Cell2Sentence (C2S), a novel method to directly adapt large language models to a biological context, specifically single-cell transcriptomics. By transforming gene expression data into "cell sentences," C2S bridges the gap between natural language processing and biology. We demonstrate cell sentences enable the fine-tuning of language models for diverse tasks in biology, including cell generation, complex cell-type annotation, and direct data-driven text generation. Our experiments reveal that GPT-2, when fine-tuned with C2S, can generate biologically valid cells based on cell type inputs, and accurately predict cell types from cell sentences. This illustrates that language models, through C2S fine-tuning, can acquire a significant understanding of single-cell biology while maintaining robust text generation capabilities. C2S offers a flexible, accessible framework to integrate natural language processing with transcriptomics, utilizing existing models and libraries for a wide range of biological applications.

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Gaussian Mixture Model Implementation for Population Stratification Estimation from Genomics Data

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Procedia computer science 2021年 179卷 202-210页

作者： Arif Budiarto Bharuno Mahesworo Alam Ahmad Hidayat Ika Nurlaila Bens Pardamean Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Information Systems Department BINUS Online Learning Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Genomics study, as opposed to socio-anthropology, has been demonstrated as an excellent tool to picture biological relatedness and disease risk factors. To analyze the data obtained from the study, Genome-wide Association Study (GWAS) has been more than decades known as the mainstay approach., is the most popular approach in analysing genomics data. The confounding variables selection, being that ancestry estimation or population stratification, is substantial to maintain the quality of GWAS. Researchers have developed various methods in extracting the population stratification information from high dimensional genomics data, especially Single Nucleotide Polymorphisms (SNPs) data. In the present study, we proposed an implementation of Principal Component Analysis (PCA)-complemented Gaussian Mixture Model (GMM) as an unsupervised model to estimate population stratification from samples. The results derived from this approach was further compared to that resulted from K-means and from the commonly used ancestry estimation software, fast STRUCTURE. We figured out that our recent improved approach outperformed the two later mentioned as shown by the average cluster and population scores. Furthermore, it was able to generate the probability distribution of each sample across all population, despite its limited quality. These intriguing results worth further investigations with much more comprehensive population coverage and more advanced algorithm.

关键词： Population Stratification Ancestry Estimation Gaussian Mixture Model Genomics SNPs

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Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter

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Scientific Reports 2023年第1期13卷 1-10页

作者： Kuo, Tzu-Yun Wang, Jen-Hung Huang, Yung-Wen Sung, Ting-Yi Chen, Ching-Tai Department of Biochemical Science and Technology National Taiwan University Taipei 10617 Taiwan Bioinformatics Program Taiwan International Graduate Program Institute of Statistical Science Academia Sinica Taipei 11529 Taiwan Institute of Information Science Academia Sinica Taipei 11529 Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei 11221 Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei 10617 Taiwan Department of Bioinformatics and Biomedical Engineering Asia University Taichung 41354 Taiwan Center for Precision Health Research Asia University Taichung 41354 Taiwan

Isobaric labeling relative quantitation is one of the dominating proteomic quantitation technologies. Traditional quantitation pipelines for isobaric-labeled mass spectrometry data are based on sequence database searching. In this study, we present a novel quantitation pipeline that integrates sequence database searching, spectral library searching, and a feature-based peptide-spectrum-match (PSM) filter using various spectral features for filtering. The combined database and spectral library searching results in larger quantitation coverage, and the filter removes PSMs with larger quantitation errors, retaining those with higher quantitation accuracy. Quantitation results show that the proposed pipeline can improve the overall quantitation accuracy at the PSM and protein levels. To our knowledge, this is the first study that utilizes spectral library searching to improve isobaric labeling-based quantitation. For users to conveniently perform the proposed pipeline, we have implemented the feature-based filter being executable on both Windows and Linux platforms;its executable files, user manual, and sample data sets are freely available at https://***/comics/Software_*** . Furthermore, with the developed filter, the proposed pipeline is fully compatible with the Trans-Proteomic Pipeline. © 2023, Springer Nature Limited.

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