Here is a list of my recent publications related to graphical models and applications of machine learning.

Machine Learning (papers and proceedings):

P McKeigue, M Colombo, FV Agakov, I Datta, A Levin, D Favro, C Gray-Montgomery, MC Iannuzzi, BA Rybicki.
Extending admixture mapping to nuclear pedigrees: application to sarcoidosis.
 Genetic Epidemiology, 37(3), 2013:256-66, 11p. doi: 10.1002/gepi.21710.

FV Agakov, P Orchard, A Storkey.
Discriminative Mixtures of Sparse Latent Fields for Risk Management. (Mixtures of Latent Graphical LASSO).
In AISTATS 2012, The Society for Artificial Intelligence and Statistics, 8p. [pdf]

S Sivakumaran, FV Agakov, E Theodoratou, JG Prendergast, L Zgaga, T Manolio, I Rudan, PM McKeigue, JF Wilson, H Campbell.
Abundant Pleiotropy in Human Complex Diseases and Traits.
Am. J. of Hum. Gen., 89(5), 2011,  12p. [pdf]

FV Agakov, PM McKeigue, J Krohn, J Flint.
Inference of Causal Relationships between Biomarkers and Outcomes in High Dimensions.
Accepted to J of Sys. Cyb. and Inf., 8p. [pdf] Short version appeared in BMIC 2010. The abstract appeared in European Mathematical Genetics Meeting (EMGM) 2010.

FV Agakov, P. McKeigue, J. Krohn, A. Storkey.
Sparse Instrumental Variables (SPIV) for Genome-Wide Studies.
In Advances in Neural Information Processing Systems 23, 2010, 9p. [pdf]

EV Bonilla, FV Agakov, CKI Williams.
Kernel Multi-task Learning using Task-specific Features.
In AISTATS 2007, The Society for Artificial Intelligence and Statistics, 8p. [pdf]

J Cavazos, C Dubach, FV Agakov, EV Bonilla, MFP O'Boyle, G Fursin, O Temam.
Automatic Performance Model Construction for the Fast Software Exploration of New Hardware Designs.
In Proc. Int. Conf. on Compilers, Architecture, and Synthesis for Embedded Systems (CASES), ACM, 2006, 11p. [pdf]

EV Bonilla, CKI Williams, FV Agakov, J Cavazos, J Thomson, MFP O'Boyle.
Predictive Search Distributions.
In Proc. ICML, OmniPress, 2006, 8p. [pdf]

FV Agakov, EV Bonilla, J Cavazos, B Franke, G Fusin, MFP O'Boyle, J Thomson, M Toussaint, CKI Williams.
Using Machine Learning to Focus Iterative Optimization.
In the 4th Annual International Symposium on Code Generation and Optimization (CGO), IEEE Comp. Soc., 2006, 11p. [pdf]

FV Agakov and D Barber. Auxiliary Variational Information Maximization for Dimensionality Reduction.
In C Saunders, M Grobelnik, S Gunn, J Shawe-Taylor (Eds.),
Revised selected papers of Subspace, Latent Structure, and Feature Selection Workshop (SLSFS), LNCS 3940, Springer, 2006, 12p. [ps.gz, pdf]

FV Agakov and D Barber. Kernelized Infomax Clustering.
In Advances in Neural Information Processing Systems 18, MIT Press, 2006, 8p. [ps.gz, pdf]

FV Agakov and D Barber. Variational Information Maximization for Neural Coding.
In NR Pal, N Kasabov, RK Mudi et. al. (Eds.), LNCS 3316, Springer, 2004, 6p. [pdf]

FV Agakov and D. Barber. An Auxiliary Variational Method.
In NR Pal, N Kasabov, RK Mudi et. al. (Eds.), LNCS 3316, Springer, 2004, 6p. [pdf]

D Barber and FV Agakov. The IM Algorithm: A variational approach to Information Maximization.
In Advances in Neural Information Processing Systems 16, MIT Press, 2004, 8p. [ps.gz, pdf]

M Welling, FV Agakov and CKI Williams. Extreme Components Analysis.
In Advances in Neural Information Processing Systems 16, MIT Press, 2004, 8p. [ps.gz, pdf]

FV Agakov and D Barber. Approximate Learning in Temporal Hidden Hopfield Models.
In International Conference on Artificial Neural Networks, Springer-Verlag, 2003, 8p. [ps.gz, pdf].

CKI Williams and FV Agakov. Products of Gaussians and Probabilistic Minor Component Analysis.
Neural Computation, Vol. 14, No. 5, MIT Press, 2002. [ps.gz]

CKI Williams, FV Agakov and SN Felderhof. Products of Gaussians.
In Advances in Neural Information Processing Systems 14, MIT Press, 2002, 8p. [ps.gz]

Miscellaneous Applications (papers and proceedings)

Zgaga L, Agakov FV, Theodoratou E, Farrington SM, Tenesa A, Dunlop MG, McKeigue P, Campbell H.
Model Selection Approach Suggests Causal Association between 25-Hydroxyvitamin D and Colorectal Cancer.
PLoS One. 2013 May 24;8(5):e63475. doi: 10.1371/journal.pone.0063475. Print 2013.
PMID: 23717431

McKeigue PM, Colombo M, Agakov FV, Datta I, Levin A, Favro D, Gray-Montgomery C, Iannuzzi MC, Rybicki BA.
Extending admixture mapping to nuclear pedigrees: application to sarcoidosis.
Genet Epidemiol. 2013 Apr;37(3):256-66. doi: 10.1002/gepi.21710. Epub 2013 Jan 31. PMID: 23371909

Zgaga L, Theodoratou E, Kyle J, Farrington SM, Agakov FV, Tenesa A, Walker M, McNeill G, Wright AF, Rudan I, Dunlop MG, Campbell H.
The association of dietary intake of purine-rich vegetables, sugar-sweetened beverages and dairy with plasma urate, in a cross-sectional study.
PLoS One. 2012;7(6):e38123. doi: 10.1371/journal.pone.0038123. Epub 2012 Jun 6. PMID: 22701608

Sivakumaran S, Agakov FV, Theodoratou E, Prendergast JG, Zgaga L, Manolio T, Rudan I, McKeigue P, Wilson JF, Campbell H.
Abundant pleiotropy in human complex diseases and traits.
Am J Hum Genet. 2011 Nov 11;89(5):607-18. doi: 10.1016/j.ajhg.2011.10.004. PMID: 22077970

Zgaga L, Theodoratou E, Farrington SM, Agakov FV, Tenesa A, Walker M, Knox S, Wallace AM, Cetnarskyj R, McNeill G, Kyle J, Porteous ME, Dunlop MG, Campbell H.
Diet, environmental factors, and lifestyle underlie the high prevalence of vitamin D deficiency in healthy adults in Scotland, and supplementation reduces the proportion that are severely deficient.
J Nutr. 2011 Aug;141(8):1535-42. doi: 10.3945/jn.111.140012. PMID: 21697298

J Cavazos, C Dubach, FV Agakov, E Bonilla, MFP O'Boyle, G Fursin, O Temam.
Automatic performance model construction for the fast software exploration of new hardware designs.
Proceedings of the 2006 international conference on Compilers, architecture and synthesis for embedded systems: 24-34.

J Cavazos, G Fursin, FV Agakov, E Bonilla, MFP O'Boyle, O Temam.
Rapidly selecting good compiler optimizations using performance counters Code Generation and Optimization.
CGO 2007, 185-97.

 

Research and Technical reports:

F. V. Agakov and D. Barber. Variational Information Maximization in Gaussian Channels.
UoE, IANC, Technical Report, EDI-INF-RR-0206, Apr. 2004, 12p. [ps.gz, pdf]

F. V. Agakov and D. Barber. An Auxiliary Variational Method.
UoE, IANC. Technical Report, EDI-INF-RR-0205, Apr 2004, 10p. [ps.gz, pdf]

F. V. Agakov and D. Barber. Temporal Hidden Hopfield Models.
UoE, IANC. Technical Report, EDI-INF-RR-0156, Nov 2002, 18p. [ps.gz, pdf]
(Here are the slides for the related talk I gave at the Probabilistic Brain symposium in Cambridge, UK '03).

D. Barber and F. V. Agakov. Correlated sequence learning in a network
of spiking neurons using maximum likelihood.
UoE, IANC. Technical Report, EDI-INF-RR-0149, Apr 2002, 13p. [ps.gz]

C. K. I. Williams and F. V. Agakov. An Analysis of Contrastive Divergence
Learning in Gaussian Boltzmann Machines.
UoE, IANC. Technical Report, EDI-INF-RR-0120, May 2002, 14p. [ps.gz]

C. K. I. Williams and F. V. Agakov. Products of Gaussians and Probabilistic Minor Component Analysis.
UoE, Institute of Adaptive and Neural Computation. Technical Report, EDI-INF-RR-0043, July 2001, 11p.
[ps.gz]

Theses:

F. V. Agakov. Variational Information Maximization in Stochastic Environments.
PhD Thesis, School of Informatics, The University of Edinburgh, 2005, 205p. [pdf]

F. V. Agakov, Investigations of Gaussian Products-of-Experts Models.
Master's Thesis, Division of Informatics, The University of Edinburgh, 2000, 169p. [ps.gz]

Here is the list of older publications.

Back to the main page.


This page is maintained by Felix Agakov

Page last updated: Jun. 12, 2013