Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Flaws in evaluation schemes for pair-input computational predictions

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Toy example (nine proteins) demonstrating prediction of protein-protein interactions and showing the shortcomings of a typical cross-validation scheme.

References

  1. 1

    Shen, J. et al. Proc. Natl. Acad. Sci. USA 104, 4337–4341 (2007).

    CAS  Article  Google Scholar 

  2. 2

    Wikberg, J.E. & Mutulis, F. Nat. Rev. Drug Discov. 7, 307–323 (2008).

    CAS  Article  Google Scholar 

  3. 3

    Yabuuchi, H. et al. Mol. Syst. Biol. 7, 472 (2011).

    CAS  Article  Google Scholar 

  4. 4

    Bellucci, M., Agostini, F., Masin, M. & Tartaglia, G.G. Nat. Methods 8, 444–445 (2011).

    CAS  Article  Google Scholar 

  5. 5

    Gottlieb, A., Stein, G.Y., Ruppin, E. & Sharan, R. Mol. Syst. Biol. 7, 496 (2011).

    Article  Google Scholar 

  6. 6

    Vert, J.-P. & Yamanishi, Y. Advances in Neural Information Processing Systems vol. 17 (eds. Saul, L., Weiss. Y. & Bottou, L.) 1433–1440 (MIT Press, Cambridge, Massachusetts, USA, 2005).

    Google Scholar 

  7. 7

    Flicek, P. et al. Nucleic Acids Res. 39, D800–D806 (2011).

    CAS  Article  Google Scholar 

  8. 8

    Schaefer, M.H. et al. PLoS ONE 7, e31826 (2012).

    CAS  Article  Google Scholar 

  9. 9

    Tropsha, A. & Golbraikh, A. Curr. Pharm. Des. 13, 3494–3504 (2007).

    CAS  Article  Google Scholar 

  10. 10

    Olah, M., Bologa, C. & Oprea, T.I. J. Comput. Aided Mol. Des. 18, 437–449 (2004).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank W.S. Noble, A. Ben-Hur, J.-P. Vert and V. Helms for stimulating discussions and critical comments on the manuscript. This work was supported by grants to E.M.M. from the US National Institutes of Health, the US Army (58343-MA), Cancer Prevention and Research in Texas and the Welch (F1515) Foundation. Y.P. acknowledges financial support from the Deutsche Forschungsgemeinschaft (DFG-Forschungsstipendium).

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Yungki Park or Edward M Marcotte.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–4, Supplementary Methods and Supplementary Discussion (PDF 534 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Park, Y., Marcotte, E. Flaws in evaluation schemes for pair-input computational predictions. Nat Methods 9, 1134–1136 (2012). https://doi.org/10.1038/nmeth.2259

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing