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Analysis of presence-only data via semi-supervised learning approaches


  • Wang, Junhui
  • Fang, Yixin


Presence-only data occur in a classification, which consist of a sample of observations from the presence class and a large number of background observations with unknown presence/absence. Since absence data are generally unavailable, conventional semi-supervised learning approaches are no longer appropriate as they tend to degenerate and assign all observations to the presence class. In this article, we propose a generalized class balance constraint, which can be equipped with semi-supervised learning approaches to prevent them from degeneration. Furthermore, to circumvent the difficulty of model tuning with presence-only data, a selection criterion based on classification stability is developed, which measures the robustness of any given classification algorithm against the sampling randomness. The effectiveness of the proposed approach is demonstrated through a variety of simulated examples, along with an application to gene function prediction.

Suggested Citation

  • Wang, Junhui & Fang, Yixin, 2013. "Analysis of presence-only data via semi-supervised learning approaches," Computational Statistics & Data Analysis, Elsevier, vol. 59(C), pages 134-143.
  • Handle: RePEc:eee:csdana:v:59:y:2013:i:c:p:134-143
    DOI: 10.1016/j.csda.2012.10.007

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    References listed on IDEAS

    1. Junhui Wang & Xiaotong Shen & Yufeng Liu, 2008. "Probability estimation for large-margin classifiers," Biometrika, Biometrika Trust, vol. 95(1), pages 149-167.
    2. Nicolai Meinshausen & Peter B├╝hlmann, 2010. "Stability selection," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 72(4), pages 417-473.
    3. Gill Ward & Trevor Hastie & Simon Barry & Jane Elith & John R. Leathwick, 2009. "Presence-Only Data and the EM Algorithm," Biometrics, The International Biometric Society, vol. 65(2), pages 554-563, June.
    4. Junhui Wang, 2010. "Consistent selection of the number of clusters via crossvalidation," Biometrika, Biometrika Trust, vol. 97(4), pages 893-904.
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