Kolaczyk: Software.

Software

My collaborators and I have created prototype software implementations of many of the methodologies developed in our research work. Some of these are available through this webpage. Unless otherwise specified, all code is written in Matlab on a Unix platform.

Please note that while we have done our best to comment the code sufficiently and test it, this is being made available `as is'. There have been no attempts to maintain the software, for example in terms of compatability with successive releases of the Matlab or alternate operating systems. Nor is any promise of `support' being made in releasing the code, although of course I will answer any questions as best I can. Therefore, as the saying goes, caveat emptor.

Software for Network-Based Research

Network Integration
Jiang, X., Steffen, M., Kasif, S., and Kolaczyk, E.D. (2007). Integration of Relational and Hierarchical Network Information for Protein Function Prediction. (Submitted).
Zip-file with software and data for hierarchical binomial neighborhood (HBN) method introduced in this paper.
Co-Betweenness
Kolaczyk, E.D., Chua, D.B., and Barthelemy, M. (2007). Co-Betweenness: A Pairwise Notion of Centrality. (Submitted).
Zip-file with software for computing vertex co-betweenness.

Software for Multiscale Reseach

TIPSH:
Forthcoming.
Multiscale Methods for Poisson Count Data:
- Estimation:
  Kolaczyk, E.D. (1999). Bayesian Multi-Scale Models for Poisson Processes. Journal of the American Statistical Association, 94, 920-933.
  Tar-file with software for estimation algorithm described in paper.
- Deconvolution:
  Nowak, R.D. and Kolaczyk, E.D. (2000). A Bayesian multiscale framework for Poisson inverse problems. IEEE Transactions on Information Theory, 46:5, 1811-1825.
  Tar-file with software for one-dimensional implementation of deconvolution algorithm described in paper.
- Segmentation:
  Kolaczyk, E.D. (2003). Bayesian multiscale methods for Poisson count data. In Statistical Challenges in Modern Astronomy III (eds. G.J. Babu & E.D. Feigelson), New York:Springer-Verlag.
  Tar-file with software for one-dimensional implementation of segmentation algorithm described in paper.
Multiscale Generalized Linear Models (MS-GLMs)
Kolaczyk, E.D. and Nowak, R.D. (2005). Multiscale generalized linear models for nonparametric function estimation. Biometrika (to appear).
Zipped-file with software for Poisson and binomial time series.
Multiscale, Multigranular Image Segmentation (MSMG)
Kolaczyk, E.D., Ju, J., and Gopal, S. (2005). Multiscale, multigranular statistical image segmentation. Journal of the American Statistical Association, (to appear).
Zipped-file with software for multiscale, multigranular image segmentation.