IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0061180.html
   My bibliography  Save this article

Empirical Mode Decomposition and k-Nearest Embedding Vectors for Timely Analyses of Antibiotic Resistance Trends

Author

Listed:
  • Douglas Teodoro
  • Christian Lovis

Abstract

Background: Antibiotic resistance is a major worldwide public health concern. In clinical settings, timely antibiotic resistance information is key for care providers as it allows appropriate targeted treatment or improved empirical treatment when the specific results of the patient are not yet available. Objective: To improve antibiotic resistance trend analysis algorithms by building a novel, fully data-driven forecasting method from the combination of trend extraction and machine learning models for enhanced biosurveillance systems. Methods: We investigate a robust model for extraction and forecasting of antibiotic resistance trends using a decade of microbiology data. Our method consists of breaking down the resistance time series into independent oscillatory components via the empirical mode decomposition technique. The resulting waveforms describing intrinsic resistance trends serve as the input for the forecasting algorithm. The algorithm applies the delay coordinate embedding theorem together with the k-nearest neighbor framework to project mappings from past events into the future dimension and estimate the resistance levels. Results: The algorithms that decompose the resistance time series and filter out high frequency components showed statistically significant performance improvements in comparison with a benchmark random walk model. We present further qualitative use-cases of antibiotic resistance trend extraction, where empirical mode decomposition was applied to highlight the specificities of the resistance trends. Conclusion: The decomposition of the raw signal was found not only to yield valuable insight into the resistance evolution, but also to produce novel models of resistance forecasters with boosted prediction performance, which could be utilized as a complementary method in the analysis of antibiotic resistance trends.

Suggested Citation

  • Douglas Teodoro & Christian Lovis, 2013. "Empirical Mode Decomposition and k-Nearest Embedding Vectors for Timely Analyses of Antibiotic Resistance Trends," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-14, April.
    • Handle: RePEc:plo:pone00:0061180
    DOI: 10.1371/journal.pone.0061180
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0061180
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0061180&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0061180?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Crone, Sven F. & Hibon, Michèle & Nikolopoulos, Konstantinos, 2011. "Advances in forecasting with neural networks? Empirical evidence from the NN3 competition on time series prediction," International Journal of Forecasting, Elsevier, vol. 27(3), pages 635-660.
    2. Albert C Yang & Jong-Ling Fuh & Norden E Huang & Ben-Chang Shia & Chung-Kang Peng & Shuu-Jiun Wang, 2011. "Temporal Associations between Weather and Headache: Analysis by Empirical Mode Decomposition," PLOS ONE, Public Library of Science, vol. 6(1), pages 1-6, January.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Barrow, Devon & Kourentzes, Nikolaos, 2018. "The impact of special days in call arrivals forecasting: A neural network approach to modelling special days," European Journal of Operational Research, Elsevier, vol. 264(3), pages 967-977.
    2. Alexander Vlasenko & Nataliia Vlasenko & Olena Vynokurova & Dmytro Peleshko, 2018. "A Novel Neuro-Fuzzy Model for Multivariate Time-Series Prediction," Data, MDPI, vol. 3(4), pages 1-14, December.
    3. Hewamalage, Hansika & Bergmeir, Christoph & Bandara, Kasun, 2021. "Recurrent Neural Networks for Time Series Forecasting: Current status and future directions," International Journal of Forecasting, Elsevier, vol. 37(1), pages 388-427.
    4. Petar Soric & Enric Monte & Salvador Torra & Oscar Claveria, 2022. ""Density forecasts of inflation using Gaussian process regression models"," IREA Working Papers 202210, University of Barcelona, Research Institute of Applied Economics, revised Jul 2022.
    5. Szafranek, Karol, 2019. "Bagged neural networks for forecasting Polish (low) inflation," International Journal of Forecasting, Elsevier, vol. 35(3), pages 1042-1059.
    6. Bojer, Casper Solheim & Meldgaard, Jens Peder, 2021. "Kaggle forecasting competitions: An overlooked learning opportunity," International Journal of Forecasting, Elsevier, vol. 37(2), pages 587-603.
    7. Zhidan Luo & Wei Guo & Qingfu Liu & Yiuman Tse, 2023. "A hybrid prediction model with time‐varying gain tracking differentiator in Taylor expansion: Evidence from precious metals," Journal of Forecasting, John Wiley & Sons, Ltd., vol. 42(5), pages 1138-1149, August.
    8. Rendon-Sanchez, Juan F. & de Menezes, Lilian M., 2019. "Structural combination of seasonal exponential smoothing forecasts applied to load forecasting," European Journal of Operational Research, Elsevier, vol. 275(3), pages 916-924.
    9. Huber, Jakob & Stuckenschmidt, Heiner, 2020. "Daily retail demand forecasting using machine learning with emphasis on calendric special days," International Journal of Forecasting, Elsevier, vol. 36(4), pages 1420-1438.
    10. Ruhnau, Oliver & Hennig, Patrick & Madlener, Reinhard, 2020. "Economic implications of forecasting electricity generation from variable renewable energy sources," Renewable Energy, Elsevier, vol. 161(C), pages 1318-1327.
    11. Arno de Caigny & Kristof Coussement & Koen W. de Bock & Stefan Lessmann, 2019. "Incorporating textual information in customer churn prediction models based on a convolutional neural network," Post-Print hal-02275958, HAL.
    12. Weifang Zhu & Heming Zhao & Dehui Xiang & Xinjian Chen, 2013. "A Flattest Constrained Envelope Approach for Empirical Mode Decomposition," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-12, April.
    13. Oscar Claveria & Enric Monte & Petar Soric & Salvador Torra, 2022. ""An application of deep learning for exchange rate forecasting"," IREA Working Papers 202201, University of Barcelona, Research Institute of Applied Economics, revised Jan 2022.
    14. Nghia Chu & Binh Dao & Nga Pham & Huy Nguyen & Hien Tran, 2022. "Predicting Mutual Funds' Performance using Deep Learning and Ensemble Techniques," Papers 2209.09649, arXiv.org, revised Jul 2023.
    15. Mergani A. Khairalla & Xu Ning & Nashat T. AL-Jallad & Musaab O. El-Faroug, 2018. "Short-Term Forecasting for Energy Consumption through Stacking Heterogeneous Ensemble Learning Model," Energies, MDPI, vol. 11(6), pages 1-21, June.
    16. Lessmann, Stefan & Voß, Stefan, 2017. "Car resale price forecasting: The impact of regression method, private information, and heterogeneity on forecast accuracy," International Journal of Forecasting, Elsevier, vol. 33(4), pages 864-877.
    17. De Caigny, Arno & Coussement, Kristof & De Bock, Koen W. & Lessmann, Stefan, 2020. "Incorporating textual information in customer churn prediction models based on a convolutional neural network," International Journal of Forecasting, Elsevier, vol. 36(4), pages 1563-1578.
    18. de Lucio, Juan, 2021. "Estimación adelantada del crecimiento regional mediante redes neuronales LSTM," INVESTIGACIONES REGIONALES - Journal of REGIONAL RESEARCH, Asociación Española de Ciencia Regional, issue 49, pages 45-64.
    19. Green, Kesten C. & Armstrong, J. Scott, 2015. "Simple versus complex forecasting: The evidence," Journal of Business Research, Elsevier, vol. 68(8), pages 1678-1685.
    20. Ioannis Nasios & Konstantinos Vogklis, 2023. "Blending gradient boosted trees and neural networks for point and probabilistic forecasting of hierarchical time series," Papers 2310.13029, arXiv.org.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0061180. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.