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Flexible dual-branched message passing neural network for quantum mechanical property prediction with molecular conformation

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arXiv 2021年

作者： Jo, Jeonghee Kwak, Bumju Lee, Byunghan Yoon, Sungroh Interdisciplinary Program in Bioinformatics Seoul National University Recommendation Team Kakao Corporation Department of Electronic and IT Media Engineering Seoul National University of Science and Technology Department of Electrical and Computer Engineering Seoul National University

A molecule is a complex of heterogeneous components, and the spatial arrangements of these components determine the whole molecular properties and characteristics. With the advent of deep learning in computational chemistry, several studies have focused on how to predict molecular properties based on molecular configurations. Message passing neural network provides an effective framework for capturing molecular geometric features with the perspective of a molecule as a graph. However, most of these studies assumed that all heterogeneous molecular features, such as atomic charge, bond length, or other geometric features always contribute equivalently to the target prediction, regardless of the task type. In this study, we propose a dual-branched neural network for molecular property prediction based on message-passing framework. Our model learns heterogeneous molecular features with different scales, which are trained flexibly according to each prediction target. In addition, we introduce a discrete branch to learn single atom features without local aggregation, apart from message-passing steps. We verify that this novel structure can improve the model performance with faster convergence in most targets. The proposed model outperforms other recent models with sparser representations. Our experimental results indicate that in the chemical property prediction tasks, the diverse chemical nature of targets should be carefully considered for both model performance and generalizability. © 2021, CC BY.

关键词： Deep learning

Application for sugarcane plantation: Manpower and transportation planning

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AIP Conference Proceedings 2023年第1期2594卷

作者： H. G. Mawandha D. Sudigyo T. Suparyanto B. Pardamean Department of Agrotechnology Institute of Agriculture STIPER Yogyakarta Indonesia 55281 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

Sugarcane plantations in Indonesia are still managed in a labor-intensive manner, especially plantation-owned by farmers. Labor intensive means that every stage of work in sugarcane plantation management still uses manpower. One of the jobs in sugarcane plantations that requires a lot of labor is sugar cane harvesting. Trend changing in the workforce gender would affect the quantity and quality of jobs, which is determined by the workforce's capacity and the workload of the work performed. The result of this research was a sugarcane agricultural calculator that made it simple for farmers to measure manpower and transportation requirements in estimating harvest costs. Manpower and transportation of harvested sugarcane commodities were estimated through the workload approach, namely, crop production and manpower's ability to carry a load. These two components helped sugarcane farmers to determine manpower and transportation during the harvest. The final yield produced by the projected harvest labor cost would be known immediately.

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SRAMM: Short read alignment mapping metrics

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arXiv 2021年

作者： Chon, Alvin Huang, Xiaoqiu Bioinformatics and Computational Biology Graduate Program Iowa State University AmesIA50010 United States Department of Computer Science Iowa State University AmesIA50010 United States

Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods generally are neither standardized nor well described in literature or software manuals. Additionally, third party mapping quality programs are typically computationally intensive or designed for specific applications. SRAMM efficiently generates multiple different concept-based mapping scores to provide for an informative post alignment examination and filtering process of aligned short reads for various downstream applications. SRAMM is compatible with Python 2.6+ and Python 3.6+ on all operating systems. It works with any short read aligner that generates SAM/BAM/CRAM file outputs and reports 'AS' tags. It is freely available under the MIT license at http://***/achon/sramm. © 2021, CC BY.

关键词： Mapping

SPGP: Structure Prototype Guided Graph Pooling

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arXiv 2022年

作者： Lee, Sangseon Lee, Dohoon Piao, Yinhua Kim, Sun Institute of Computer Technology Seoul National University Korea Republic of BK21 FOUR Intelligence Computing Seoul National University Korea Republic of Department of Computer Science and Engineering Seoul National University Korea Republic of Interdisciplinary Program in Bioinformatics Seoul National University Korea Republic of Interdisciplinary Program in Artificial Intelligence Seoul National University Korea Republic of AIGENDRUG Co. Ltd. Korea Republic of

While graph neural networks (GNNs) have been successful for node classification tasks and link prediction tasks in graph, learning graph-level representations still remains a challenge. For the graph-level representation, it is important to learn both representation of neighboring nodes, i.e., aggregation, and graph structural information. A number of graph pooling methods have been developed for this goal. However, most of the existing pooling methods utilize k-hop neighborhood without considering explicit structural information in a graph. In this paper, we propose Structure Prototype Guided Pooling (SPGP) that utilizes prior graph structures to overcome the limitation. SPGP formulates graph structures as learnable prototype vectors and computes the affinity between nodes and prototype vectors. This leads to a novel node scoring scheme that prioritizes informative nodes while encapsulating the useful structures of the graph. Our experimental results show that SPGP outperforms state-of-the-art graph pooling methods on graph classification benchmark datasets in both accuracy and scalability. Copyright © 2022, The Authors. All rights reserved.

关键词： Graph neural networks

Missing Value Recovery for Single Cell RNA Sequencing Data

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Missing Value Recovery for Single Cell RNA Sequencing Data

International Conference on Computational science and Computational Intelligence (CSCI)

作者： Wenjuan Zhang William Yang John Talburt Sherman Weissman Mary Qu Yang MidSouth Bioinformatics Center and Bioinformatics Graduate Program University of Arkansas Little Rock and Univ. of Arkansas for Medical Sciences Little Rock USA Computer Science Department Princeton University Princeton USA Information Science Department University of Arkansas Little Rock Little Rock USA Department of Genetics Yale University New Haven USA

ISBN: (纸本)9781665458429

The emergence of single-cell sequencing technologies has enabled the production of high-resolution data at the individual cell level, providing unprecedented opportunities to capture cell population diversity and dissect the cellular heterogeneity of complex diseases. At the same time, relatively high biological and technical noise poses new challenges for single-cell data analysis. The single-cell RNA sequencing (scRNA-seq) data often contains substantial missing values due to gene dropout events. Here, we developed a convolutional neural network based model to recover missing values for scRNA-seq data. We first calculated the probability of dropout employing gamma-normal expectation maximum algorithm. Unlike most existing approaches, our model only recovered the expression values that have a dropout probability larger than a threshold. The mean square error and Pearson correlation coefficient were used to assess the accuracy of predicted expression values. The purity and entropy were computed to measure the homogeneity of cell clusters using imputed gene expression profiles. Across various scRNAseq datasets, our model demonstrated robust performance and achieved comparable or better results compared to the other imputation methods.

关键词： Sequential analysis Scientific computing Computational modeling RNA Sociology Production Mean square error methods

ReLSO: A Transformer-based Model for Latent Space Optimization and Generation of Proteins

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arXiv 2022年

作者： Castro, Egbert Godavarthi, Abhinav Rubinfien, Julian Givechian, Kevin Bhaskar, Dhananjay Krishnaswamy, Smita Computational Biology and Bioinformatics Program Yale University New HavenCT06511 United States Department of Applied Mathematics Yale University New HavenCT06511 United States Department of Genetics Yale University New HavenCT06511 United States Department of Computer Science Yale University New HavenCT06511 United States

The development of powerful natural language models have increased the ability to learn meaningful representations of protein sequences. In addition, advances in high-throughput mutagenesis, directed evolution, and next-generation sequencing have allowed for the accumulation of large amounts of labeled fitness data. Leveraging these two trends, we introduce Regularized Latent Space Optimization (ReLSO), a deep transformer-based autoencoder which features a highly structured latent space that is trained to jointly generate sequences as well as predict fitness. Through regularized prediction heads, ReLSO introduces a powerful protein sequence encoder and novel approach for efficient fitness landscape traversal. Using ReLSO, we explicitly model the sequence-function landscape of large labeled datasets and generate new molecules by optimizing within the latent space using gradient-based methods. We evaluate this approach on several publicly-available protein datasets, including variant sets of anti-ranibizumab and GFP. We observe a greater sequence optimization efficiency (increase in fitness per optimization step) by ReLSO compared to other approaches, where ReLSO more robustly generates high-fitness sequences. Furthermore, the attention-based relationships learned by the jointly-trained ReLSO models provides a potential avenue towards sequence-level fitness attribution information. © 2022, CC BY-NC-ND.

关键词： Proteins

Maintaining the Quality and Aroma of Coffee with Fuzzy Logic Coffee Roasting Machine 3

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Maintaining the Quality and Aroma of Coffee with Fuzzy Logic...

3rd International Conference on Eco Engineering Development, ICEED 2019

作者： Harsawardana Samodro, Bayu Mahesworo, Bharuno Suparyanto, Teddy Surya Atmaja, Don Bosco Pardamean, Bens Institut Pertanian STIPER Yogyakarta55281 Indonesia Mechatronics and AI Research and Development Center Biotechnic Innovation Yogyakarta55281 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia

With the increasing global demands of coffee, Indonesia need to increase their coffee beans supply and improve the quality to maintain its position in the international coffee industry. One of the most important coffeepre-processing, coffee bean roasting, is under developed in Indonesia. Indonesia coffee farmers prefer to use the traditional cauldron to roast their coffee beans. Roasting coffee beans using traditional cauldron is inefficient and resulting unequal roasted level for the coffee beans. In this study, we proposed atemperature control system based on fuzzy logic for coffee roaster machine. The system controls the temperature in accordance with the demanded roasting level. A thermal camera is attached inside the roasting chamber to monitor the heaton the roasted coffee beans. The thermal camera is integrated with a stirring mechanism to equalise the heat among the beans. © 2020 Published under licence by IOP Publishing Ltd.

关键词： Fuzzy logic

Beyond predictive R 2 : Quantile regression and non-equivalence tests reveal complex relationships of traits and polygenic scores

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The American Journal of Human Genetics 2025年第6期112卷 1363-1375页

作者： Joel Mefford Molly Smullen Felix Zhang Michal Sadowski Richard Border Andy Dahl Jonathan Flint Noah Zaitlen Semel Institute for Neuroscience and Human Behavior University of California Los Angeles Los Angeles CA USA Chan Medical School University of Massachusetts Worcester MA USA Department of Computer Science University of California Los Angeles Los Angeles CA USA Bioinformatics Interdepartmental Program University of California Los Angeles Los Angeles CA USA Department of Neurology University of California Los Angeles Los Angeles CA USA Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA Section of Genetic Medicine Department of Medicine University of Chicago Chicago IL USA Department of Psychiatry and Biobehavioral Sciences David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA

Polygenic scores (PGSs) are genetic predictions of trait values or disease risk that are increasingly finding applications in clinical predictive models and basic genetics research. However, the predictive value of a PGS can vary within similar population groups, depending on characteristics such as the environmental exposures, sex, age, or socioeconomic status of the individuals. To maximize the value of a PGS, approaches to screen trait-PGS pairs for evidence of such heterogeneity without having to specify the relevant exposure or individual characteristics would be useful. Here, in analyses from the UK Biobank, we show that a PGS’s predictive accuracy depends on the quantile of the phenotypic distribution to which the PGS is being applied. We quantify differences in predictive value across the phenotypic range using quantile regression linear models to estimate quantile-specific effect sizes for linear models of phenotype values as a function of PGS. Of 25 continuous traits, only three have no quantile-specific effect sizes that varied by at least 1.2-fold from the ordinary least squares estimate. Through simulation, we demonstrate that this heterogeneity of PGS predictive value can arise from gene-by-environment interactions. Our approach can be used to flag traits where the use of PGSs warrants extra caution, and perhaps stratification variables should be sought and used because PGSs perform substantially differently in portions of the sampled population than expected from quoted predictive R 2 or incremental R 2 values that represent average performance across a dataset.

关键词： polygenic score polygenic risk score PRS PGS quantile regression non-equivalence test equivalence test trend test gene-by-environment interaction heterogeneity

Artificial intelligence for modelling infectious disease epidemics

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Nature 2025年第8051期638卷 623-635页

作者： Kraemer, Moritz U. G. Tsui, Joseph L.-H. Chang, Serina Y. Lytras, Spyros Khurana, Mark P. Vanderslott, Samantha Bajaj, Sumali Scheidwasser, Neil Curran-Sebastian, Jacob Liam Semenova, Elizaveta Zhang, Mengyan Unwin, H. Juliette T. Watson, Oliver J. Mills, Cathal Dasgupta, Abhishek Ferretti, Luca Scarpino, Samuel V. Koua, Etien Morgan, Oliver Tegally, Houriiyah Paquet, Ulrich Moutsianas, Loukas Fraser, Christophe Ferguson, Neil M. Topol, Eric J. Duchêne, David A. Stadler, Tanja Kingori, Patricia Parker, Michael J. Dominici, Francesca Shadbolt, Nigel Suchard, Marc A. Ratmann, Oliver Flaxman, Seth Holmes, Edward C. Gomez-Rodriguez, Manuel Schölkopf, Bernhard Donnelly, Christl A. Pybus, Oliver G. Cauchemez, Simon Bhatt, Samir Pandemic Sciences Institute University of Oxford Oxford United Kingdom Department of Biology University of Oxford Oxford United Kingdom Department of Electrical Engineering and Computer Science University of California Berkeley Berkeley CA United States UCSF UC Berkeley Joint Program in Computational Precision Health Berkeley CA United States Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan Section of Epidemiology Department of Public Health University of Copenhagen Copenhagen Denmark Oxford Vaccine Group University of Oxford and NIHR Oxford Biomedical Research Centre Oxford United Kingdom Department of Epidemiology and Biostatistics Imperial College London London United Kingdom Department of Computer Science University of Oxford Oxford United Kingdom School of Mathematics University of Bristol Bristol United Kingdom MRC Centre for Global Infectious Disease Analysis School of Public Health Imperial College London London United Kingdom Department of Statistics University of Oxford Oxford United Kingdom Doctoral Training Centre University of Oxford Oxford United Kingdom Institute for Experiential AI Northeastern University MA Boston Thailand Santa Fe Institute Santa Fe NM United States World Health Organization Regional Office for Africa Brazzaville Congo WHO Hub for Pandemic and Epidemic Intelligence Health Emergencies Programme World Health Organization Berlin Germany Centre for Epidemic Response and Innovation (CERI) School for Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa African Institute for Mathematical Sciences (AIMS) South Africa Muizenberg Cape Town South Africa Genomics England London United Kingdom Scripps Research La Jolla CA United States Department of Biosystems Science and Engineering ETH Zürich Basel Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland The Ethox Centre Nuffield

Infectious disease threats to individual and public health are numerous, varied and frequently unexpected. Artificial intelligence (AI) and related technologies, which are already supporting human decision making in economics, medicine and social science, have the potential to transform the scope and power of infectious disease epidemiology. Here we consider the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science. We first outline how recent advances in AI can accelerate breakthroughs in answering key epidemiological questions and we discuss specific AI methods that can be applied to routinely collected infectious disease surveillance data. Second, we elaborate on the social context of AI for infectious disease epidemiology, including issues such as explainability, safety, accountability and ethics. Finally, we summarize some limitations of AI applications in this field and provide recommendations for how infectious disease epidemiology can harness most effectively current and future developments in AI. © Springer Nature Limited 2025.

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