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The Journal of Machine Learning Research 2022年第1期23卷 255-296页

作者： Justin D. Silverman Kimberly Roche Zachary C. Holmes Lawrence A. David Sayan Mukherjee College of Information Science and Technology Department of Statistics and Institute for Computational and Data Science Penn State University University Park PA Program in Computational Biology and Bioinformatics Duke University Durham NC Department of Molecular Genetics and Microbiology Duke University Durham NC Department of Molecular Genetics and Microbiology and Center for Genomic and Computational Biology Duke University Durham NC Departments of Statistical Science Mathematics Computer Science Biostatistics & Bioinformatics Duke University Durham NC

Bayesian multinomial logistic-normal (MLN) models are popular for the analysis of sequence count data (e.g., microbiome or gene expression data) due to their ability to model multivariate count data with complex covariance structure. However, existing implementations of MLN models are limited to small datasets due to the non-conjugacy of the multinomial and logistic-normal distributions. Motivated by the need to develop efficient inference for Bayesian MLN models, we develop two key ideas. First, we develop the class of Marginally Latent Matrix-T Process (Marginally LTP) models. We demonstrate that many popular MLN models, including those with latent linear, non-linear, and dynamic linear structure are special cases of this class. Second, we develop an efficient inference scheme for Marginally LTP models with specific accelerations for the MLN subclass. Through application to MLN models, we demonstrate that our inference scheme are both highly accurate and often 4-5 orders of magnitude faster than MCMC.

关键词： Bayesian statistics multivariate analysis count data microbiome gene expression

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Assessing Rice Phenological Features with Hyperspectral Imaging Insights from Earth Surface Mineral Dust Source Investigation (EMIT)

Assessing Rice Phenological Features with Hyperspectral Imag...

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IEEE International Symposium on Geoscience and Remote Sensing (IGARSS)

作者： Shahryar Fazli Wenzhao Li Surendra Maharjan Hesham El Askary Computational and Data Sciences Graduate Program Schmid College of Science and Technology Chapman University Orange CA USA Earth Systems Science and Data Solutions Lab Chapman University Orange CA USA Department of Environmental Sciences Faculty of Science Alexandria University Alexandria Egypt

ISBN: (数字)9798350360325

ISBN: (纸本)9798350360332

In California's Central Valley, water management and crop health, particularly in rice cultivation, are critical. This paper details the application of Earth surface Mineral dust source InvesTigation (EMIT) hyperspectral imaging, specifically employing Spectral Correlation Mapper (SCM) and Spectral Information Divergence (SID), for precise phenological analysis. By aligning EMIT data with Hyperion satellite references, we address spectral and geographical discrepancies. Our methodology includes seasonal sampling of spectral curves to capture the phenological stages of rice. Results show a strong correlation (R 2 = 0.86) between August EMIT and Reference dataset, emphasizing EMIT's utility in enhancing agricultural practices and water efficiency in the region, and highlighting the importance of understanding rice phenology for sustainable farming.

关键词： Earth Correlation Satellites Accuracy Uncertainty Phenology Minerals

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Identify Non-mutational p53 Functional Deficiency in Human Cancers

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Genomics, Proteomics & Bioinformatics 2024年第5期22卷 85-98页

作者： Qianpeng Li Yang Zhang Sicheng Luo Zhang Zhang Ann L.Oberg David E.Kozono Hua Lu Jann N.Sarkaria Lina Ma Liguo Wang National Genomics Data Center China National Center for BioinformationBeijing 100101China Beijing Institute of Genomics Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Division of Computational Biology Mayo Clinic College of Medicine and ScienceRochesterMN 55905USA Department of Radiation Oncology Dana-Farber Cancer Institute and Brigham and Women's HospitalBostonMA 02215USA Department of Biochemistry&Molecular Biology and Tulane Cancer Center Tulane University School of MedicineNew OrleansLA 70112USA Department of Radiation Oncology Mayo Clinic College of Medicine and ScienceRochesterMN 55905USA Department of Biochemistry and Molecular Biology Mayo Clinic College of Medicine and ScienceRochesterMN 55905USA Bioinformatics and Computational Biology Graduate Program University of Minnesota RochesterRochesterMN 55904USA

An accurate assessment of p53's functional statuses is critical for cancer genomic ***,there is a significant challenge in identifying tumors with non-mutational p53 inactivation which is not detectable through DNA *** undetected cases are often misclassified as p53-normal,leading to inaccurate prognosis and downstream association *** address this issue,we built the support vector machine(SVM)models to systematically reassess p53's functional statuses in TP53 wild-type(TP53^(WT))tumors from multiple The Cancer Genome Atlas(TCGA)***-validation demonstrated the good performance of the SVM models with a mean area under the receiver operating characteristic curve(AUROC)of 0.9822,precision of 0.9747,and recall of *** study revealed that a significant proportion(87%-99%)of TP53^(WT) tumors actually had compromised p53 *** analyses uncovered that these genetically intact but functionally impaired(termed as predictively reduced function of p53 or TP53^(WT)-pRF)tumors exhibited genomic and pathophysiologic features akin to TP53-mutant tumors:heightened genomic instability and elevated levels of ***,patients with TP53^(WT)-pRF tumors experienced significantly shortened overall survival or progression-free survival compared to those with predictively normal function of p53(TP53^(WT)-pN)tumors,and these patients also displayed increased sensitivity to platinum-based chemotherapy and radiation therapy.

关键词： Cancer Composite expression DNA mutation Machine learning p53 deficiency

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Involution game with spatio-temporal heterogeneity of social resources

arXiv

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arXiv 2022年

作者： Wang, Chaoqian Szolnoki, Attila Program for Computational Social Science Department of Computational and Data Sciences George Mason University FairfaxVA22030 United States Institute of Technical Physics and Materials Science Centre for Energy Research P.O. Box 49 BudapestH-1525 Hungary

When group members claim a portion of limited resources, it is tempting to invest more effort to get a larger share. However, if everyone acts similarly, they all get the same piece they would obtain without extra effort. This is the involution game dilemma that can be detected in several real-life situations. It is also a realistic assumption that resources are not uniform in space and time, which may influence the system's resulting involution level. We here introduce spatio-temporal heterogeneity of social resources and explore their consequences on involution. When spatial heterogeneity is applied, network reciprocity can mitigate the involution for rich resources, which would be critical otherwise in a homogeneous population. Interestingly, when the resource level is modest, spatial heterogeneity causes more intensive involution in a system where most cooperator agents, who want to keep investment at a low level, are present. This picture is partly the opposite in the extreme case when more investment is less effective. Spatial heterogeneity can also produce a counterintuitive effect when the presence of alternative resource levels cannot explain the emergence of involution. If we apply temporal heterogeneity additionally, then the impact of spatial heterogeneity practically vanishes, and we turn back to the behavior observed in a homogeneous population earlier. Our observations are also supported by solving the corresponding replicator equations numerically. © 2022, CC BY.

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Adaptive coupling of a deep neural network potential to a classical force field

arXiv

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arXiv 2018年

作者： Zhang, Linfeng Wang, Han Weinan, E. Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Huayuan Road 6 Beijing100088 China Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Center for Data Science and Beijing International Center for Mathematical Research Peking University China Beijing Institute of Big Data Research Beijing100871 China

An adaptive modeling method (AMM) that couples a deep neural network potential and a classical force field is introduced to address the accuracy-efficiency dilemma faced by the molecular simulation community. The AMM simulated system is decomposed into three types of regions. The first type captures the important phenomena in the system and requires high accuracy, for which we use the Deep Potential Molecular Dynamics (DeePMD) model in this work. The DeePMD model is trained to accurately reproduce the statistical properties of the ab initio molecular dynamics. The second type does not require high accuracy and a classical force field is used to describe it in an efficient way. The third type is used for a smooth transition between the first and the second types of regions. By using a force interpolation scheme and imposing a thermodynamics force in the transition region, we make the DeePMD region embedded in the AMM simulated system as if it were embedded in a system that is fully described by the accurate potential. A representative example of the liquid water system is used to show the feasibility and promise of this method. Copyright © 2018, The Authors. All rights reserved.

关键词： Deep neural networks

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Pairwise Learning for Imbalanced data Classification

Pairwise Learning for Imbalanced Data Classification

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International Conference on computational science and computational Intelligence (CSCI)

作者： Shu Liu Qiang Wu Computational and Data Science PhD Program Middle Tennessee State University Murfreesboro TN USA Department of Mathematical Sciences Middle Tennessee State University Murfreesboro TN USA

ISBN: (纸本)9781665458429

Imbalanced data classification problems appear quite commonly in real-world applications and impose great challenges to traditional classification approaches which work well only on balanced data but usually perform poorly on the minority class when the data is imbalanced. Resampling preprocessing by oversampling the minority class or downsampling the majority class helps improve the performance but may suffer from overfitting or loss of information. In this paper we propose a novel method called pairwise robust support vector machine (PRSVM) to overcome the difficulty of imbalanced data classification. It adapts the non-convex robust support vector classification loss to the pairwise learning setting. In the training process, samples from the minority class and the majority class always appear as pairs. This automatically balances the impact of two classes. Simulations and real-world applications show that PRSVM is highly effective.

关键词： Training Adaptation models Scientific computing computational modeling Support vector machine classification computational intelligence

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Geospatial Intelligence for Individual Crop Detection and Anomaly Monitoring

Geospatial Intelligence for Individual Crop Detection and An...

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IEEE International Symposium on Geoscience and Remote Sensing (IGARSS)

作者： Freda Elikem Dorbu Leila Hashemi-Beni Department of Computational Data Science and Engineering North Carolina A&T State University Department of Built Environment Geomatics Program North Carolina A&T State University

Acquisition of geospatial data by UAV has been acknowledged as an effective method of attaining reliable and quick high-resolution remote sensing data for analysis and decision-making in different applications such as agriculture as it produces timely results, and it is affordable. UAVs coupled with other technological applications such as robotics, computing and deep learning facilitate the execution of precision agriculture. The execution of individual tree identification enables vivid description of the crop peak height and canopy for accurate estimation of issues related to crop growth such as biomass reduction, lodging, and stunted growth. A geospatial intelligence algorithm was developed to determine the lodging state of the crops. First, the optical imagery (RGB) was automatically annotated using maximum likelihood classification algorithm for faster acquisition of ground truth and to verify with the manually annotated image data for deep learning training. The acquired images were split for training of fine-tuned three deep learning methods including U-net, U-net++ and attention-residual Unet. The results show that each model has the tendency to learn patterns in data and predict lodged crops. Results from the analysis were validated by visual assessment of the time-series aerial images and validation data acquired from the ground truth data using k-fold cross validation approach.

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Deciphering Water Quality and Algal Dynamics in Clear Lake Through Hyperspectral Analysis Using Emit data

Deciphering Water Quality and Algal Dynamics in Clear Lake T...

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IEEE International Symposium on Geoscience and Remote Sensing (IGARSS)

作者： Wenzhao Li Shahryar Fazli Surendra Maharjan Hesham El-Askary Earth Systems Science and Data Solutions Lab Schmid College of Science and Technology Chapman University Orange CA USA Computational and Data Sciences Graduate Program Schmid College of Science and Technology Chapman University Orange CA USA Department of Environmental Sciences Faculty of Science Alexandria University Alexandria Egypt

ISBN: (数字)9798350360325

ISBN: (纸本)9798350360332

This study evaluates the potential application of hyperspectral Earth Surface Mineral Dust Source Investigation (EMIT) remote sensing for monitoring harmful algal blooms (HABs) and water quality in Clear Lake, California. The research focuses on correlating the chlorophyll-a (Chl-a) concentrations with EMIT spectral signatures, using waterbody-wide statistical analysis of Chl-a and EMIT data sampling at various lake locations. Results demonstrate distinct spectral signatures associated with varying Chl-a levels, highlighting the potential of hyperspectral imaging in differentiating algae levels and assessing water quality variables. It also indicates the EMIT’s utility in filling data gaps and offering high-resolution monitoring. This study underscores the need for further research in hyperspectral imaging for aquatic ecosystems, especially under challenging atmospheric conditions, enhancing our understanding of water quality dynamics.

关键词： Satellites Statistical analysis Algae Water quality Lakes Filling Minerals

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End-to-end symmetry preserving inter-atomic potential energy model for finite and extended systems 18

End-to-end symmetry preserving inter-atomic potential energy...

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Proceedings of the 32nd International Conference on Neural Information Processing Systems

作者： Linfeng Zhang Jiequn Han Han Wang Wissam A. Saidi Roberto Car E. Weinan Program in Applied and Computational Mathematics Princeton University Institute of Applied Physics and Computational Mathematics China and CAEP Software Center for High Performance Numerical Simulation China Department of Mechanical Engineering and Materials Science University of Pittsburgh Program in Applied and Computational Mathematics Princeton University and Department of Chemistry and Department of Physics Princeton University and Princeton Institute for the Science and Technology of Materials Princeton University Program in Applied and Computational Mathematics Princeton University and Department of Mathematics Princeton University and Beijing Institute of Big Data Research China

Machine learning models are changing the paradigm of molecular modeling, which is a fundamental tool for material science, chemistry, and computational biology. Of particular interest is the inter-atomic potential energy surface (PES). Here we develop Deep Potential - Smooth Edition (DeepPot-SE), an end-to-end machine learning-based PES model, which is able to efficiently represent the PES of a wide variety of systems with the accuracy of ab initio quantum mechanics models. By construction, DeepPot-SE is extensive and continuously differentiable, scales linearly with system size, and preserves all the natural symmetries of the system. Further, we show that DeepPot-SE describes finite and extended systems including organic molecules, metals, semiconductors, and insulators with high fidelity.

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Parameter Optimization of Support Vector Regression Using Harris Hawks Optimization

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Procedia Computer science 2021年 179卷 17-24页

作者： I Nyoman Setiawan Robert Kurniawan Budi Yuniarto Rezzy Eko Caraka Bens Pardamean Computational Statistics Department Polytechnic of Statistics - STIS Jakarta 13330 Indonesia Department of Information Management College of Informatics Chaoyang University of Technology Taiwan (ROC) Bioinformatics and Data Science Research Center Bina Nusantara University Indonesia 11530 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia. 11530.

Support Vector Regression (SVR) is often used in forecasting. Adjustment of parameters in the SVR affects the results of forecasting. This study aims to analyze the SVR method that is optimized using Harris Hawks Optimization (HHO), hereinafter referred to as HHO-SVR. The HHO-SVR was evaluated using five benchmark datasets to determine the performance of this method. The HHO process is also compared based on the type of kernel and other metaheuristic algorithms. The results showed that the HHO-SVR has almost the same performance as other methods but is less efficient in terms of time. In addition, the type of kernel also affects the process and results.

关键词： SVR harris hawks optimization parameter optimization kernel forecasting

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