Computational and Mathematical Research in Conservation Biology
Steven Phillips
This page describes my work on Computer Science applications in Conservation Biology, including links to papers
and software on the Maximum Entropy Method for
estimating a probability distribution from a limited number of
samples, and its application to modeling species distributions.
Please send mail to "phillips at-sign research.att.com"
with comments or suggestions.
Maxent Software for Modeling Species Distributions
Maxent is a self-contained Java
application for modeling species geographic distributions using the
Maximum Entropy Method. It has been developed in collaboration with
Rob Schapire and Miro Dudik, and is available for free download.
Papers involving Maxent
- Generative and Discriminative Learning with
Unknown Labeling Bias, M. Dudík and S. J. Phillips, Neural Information Processing Systems 2008 [pdf]
- Sample Selection Bias and
Presence-Only Species Distribution Models: Implications for Background
and Pseudo-absence data, S. J. Phillips, M. Dudík, J. Elith, C.H. Graham, A. Lehmann, J. Leathwich and S. Ferrier, Ecological Applications, 19(1), 2009, pp. 181-197. [pdf]
- Aligning Conservation Priorities Across Taxa in Madagascar with
High-Resolution Planning Tools, with C. Kremen, A. Cameron, A. Moilanen, S. J. Phillips, C. D. Thomas, H. Beentje, J. Dransfield, B. L. Fisher, F. Glaw, T. C. Good, G. J. Harper, R. J. Hijmans, D. C.
Lees, E. Louis Jr, R. A. Nussbaum, C. J. Raxworthy, A. Razafimpahanana, G. E.
Schatz, M. Vences, D. R. Vieites, P. C. Wright and M. L. Zjhra,
Science 320(5873), 2008, pp 222-226. [Full text available from Claire Kremen's website]
- Modeling of species distributions with Maxent: new extensions and
a comprehensive evaluation, S. J. Phillips and M. Dudík,
Ecography, Vol 31, 2008, pp
161-175. [pdf]
- Transferability, sample selection bias and background data in
presence-only modelling: a response to Peterson et al. (2007), S. J. Phillips,
Ecography, Vol 31, 2008, pp
272-278. [pdf]
- Maximum entropy density estimation with generalized regularization and an
application to species distrubtion modeling, M. Dudík, S. J. Phillips and R. E. Schapire,
Journal of Machine Learning Research, Vol 8, 2007, pp
1217-1260. [pdf]
- Maximum entropy modeling of species geographic
distributions, S. J. Phillips, R. P. Anderson and R. E. Schapire,
Ecological Modelling, Vol 190/3-4, 2006, pp
231-259. [pdf]
- Correcting sample selection bias in maximum entropy density estimation,
M. Dudík, S. J. Phillips and R. E. Schapire,
in Proceedings of Neural Information Processing Systems, 2005.
[pdf]
- Performance guarantees for regularized maximum entropy density
estimation, M. Dudík, S. J. Phillips and R. E. Schapire, in Proceedings of the
Seventeenth Annual Conference on Computational Learning Theory, 2004, pp 472-486.
[ps] [pdf]
- A maximum entropy approach to species distribution modeling,
S. J. Phillips, R. E. Schapire and M. Dudík, in Proceedings of the Twenty-First
International Conference on Machine Learning, 2004, pp 655-662.
[ps] [pdf]
Other Conservation Topics
The following paper describes and method for selecting an optimal set of sites that allows a group of species to migrate from their currently occupied areas to areas predicted to become suitable under climate change, with migration speed constained by the individual species' dispersal abilities. The method is based on "network flow", an optimization paradigm that is heavily used in modeling and optimizing telecom networks, among other applications.
- Optimizing Dispersal Corridors for the Cape Proteaceae Using Network Flow, S. J. Phillips, P. Williams, G. Midgley and A. Archer,
Ecological Applications 18(5), pp. 1200-1211. [pdf]
Once sites are protected, optimization methods can be useful for informing managament and trading off the needs of different species. This paper uses integer programming methods to optimize the configuration of managed ponds and restored tidal marsh in San Francisco Bay, formerly used as evaporative salt ponds, to simultaneously maximize predicted abundance of a set of marsh- and pond-associated bird species.
- Optimizing wetland restoration and management for avian
communities using a mixed integer programming approach, D. Stralberg, D.L. Applegate, S. J. Phillips, M.P. Herzog, N. Nur and N. Warnock, Biological
Conservation 142, pp 94-109. [pdf]
Species distribution models predict where suitable conditions for a species will be, but they do not directly say which suitable conditions are likely to be occupied. This paper integrates species distribution models with stochastic population models to model changes in a species' population size as suitable areas move under climate change:
- Predicting extinction risks under climate change: a new mechanistic
approach linking stochastic population models with dynamic bioclimatic
habitat models,
D. A. Keith, H. R. Akçakaya, W. Thuiller, G. F. Midgley, R. G. Pearson,
S. J. Phillips, H. M. Regan, M. B. Araújo and T. G. Rebelo,
Biology Letters 4, 2008, pp. 560-563. [pdf]
Other topics I'm currently working on include conservation planning and site
prioritization using both simple "irreplaceability"-style indices and
large-scale integer programming, and a new statistical tool for
measuring how well calibrated a species distribution model is.
Related topics
AT&T made a TV commercial highlighting my conservation work in Madagascar, as described in the Science article above. The commercial aired in Washington, DC in June, 2008. Mongabay.com featured my Madagascar work too.
Together with Richard Pearson from the American Museum of Natural History, I teach a biannual week-long course on Species Distribution Modeling for Conservation Biologists at the AMNH's Southwestern Research Station in the Chiricahua Mountains of Arizona.
I am a member of a cross-organizational "Green team" inside AT&T, investigating ways to reduce the company's electricity consumption and carbon footprint. I'm managing a wiki (internal AT&T link here) with information about wind and solar power technology, news and meteorological information on the distribution of clean energy resources.
In my spare time, I am a volunteer for Transportation Alternatives' campaign to close the loop road of Central Park to car traffic and return it to its original recreational use. As Edward Abbey put it, "we have agreed not to drive our automobiles into cathedrals, concert halls, art museums, private bedrooms and other sanctums of our culture; we should treat our parks with the same deference."
Last modified April 20, 2009.
