Guido Sanguinetti

Research and PhD projects
CV & Publications
Software Downloads
Other Interests

School of Informatics
Informatics Forum
10 Crichton Street
Tel: +44 131 650 5136
Fax: +44 131 651 1426




I am a Reader in Machine Learning in the Institute for Adaptive and Neural Computation at the School of Informatics, University of Edinburgh. My interests focus on probabilistic modelling of biological systems, with particular emphasis on inference in dynamical systems. For more details of my research interests, including live projects and possible PhD projects, please see the research projects page. I'm also a potential supervisor on the newly funded EPSRC Centre for Doctoral Training in Data Science, see Data Science Ph.D. programme.


Some newly published papers

Gabriele Schweikert, Botond Cseke, Thomas Clouaire, Adrian Bird and Guido Sanguinetti, MMDiff: quantitative testing for shape changes in ChIP-Seq data sets, BMC Genomics 14:826, 2013, link

Botond Cseke, Manfred Opper and Guido Sanguinetti, Approximate Inference in Latent Diffusion Processes from Continuous Time Observations, to appear at NIPS 2013 camera-ready version and supplementary material

Robert I. Menzies, Andrew Zammit-Mangion, Lyam M. Hollis, Ross J. Lennen, Maurits A Jansen, David J. Webb, John J. Mullins, James W Dear, Guido Sanguinetti and Matthew Bailey, An antatomically-unbiased approach for analysis of renal BOLD magnetic resonance images, American Journal of Physiology, in press (2013)

Anastasis Georgoulas, Jane Hillston and Guido Sanguinetti, ABC-Fun: A Probabilistic Programming Language for Biology, in Computational Methods for Systems Biology (CMSB) 13

Luca Bortolussi and Guido Sanguinetti, Learning and designing stochastic processes from logical constraints, in Quantitative Evaluation of Systems (QEST) 13 pdf

Andrea Ocone, Andrew J. Millar and Guido Sanguinetti, Hybrid Regulatory Models: a statistically tractable approach to model regulatory network dynamics, Bioinformatics 29(7) (2013) journal link

Andrew Zammit-Mangion, Michael A. Dewar, Visakan Kadirkamanathan and Guido Sanguinetti, Point Process Modelling of the Afghan War Diary, Proceedings of the National Academy of Sciences of the USA (PNAS), Early Edition July 16th 2012 journal link. See also accompanying website here

Botond gets spotlight at NIPS!

Botond's paper "Approximate Inference in Latent Diffusion Processes from Continuous Time Observation" (joint with Manfred Opper and myself) is going to have a spotlight presentation at NIPS13. Only approx. 5% of submissions get spotlights, so very well done Botond!

Best paper award at QEST13

Luca Bortolussi's and my paper "Learning and designing stochastic processes from logical constraints" has been awarded the Best Paper Award at QEST13 (see press release by the University of Trieste here, in Italian). From my point of view, the interest of the paper is the attempt to perform learning directly from emerging properties of a stochastic process (in this sense, it is closely related to Botond's NIPS paper, item above).

Cozzarelli Prize 2012

Our PNAS paper "Point process Modelling of the Afghan War Diary" was awarded a Cozzarelli prize by the PNAS editorial board, an annual award to outstanding papers in the six main branches of the PNAS scope. Our paper won in the Engineering and Applied Science category. More details here

Andrew Zammit-Mangion wins IET Doctoral Prize in Control and Automation

Congratulations to Andrew, whom until recently worked with us as a postdoc and whose PhD was jointly supervised by Visakan Kadirkamanathan at Sheffield and myself. The IET Prize is a prestigious award for doctoral students at UK Universities, and deservedly acknowledges Andrew's great work during his doctorate. Well done Andrew!

ERC Starting Grant

I have been awarded an ERC Starting Independent Research Grant to investigate how machine learning techniques can be married with formal model descriptions of biological systems. This large project will run to 2017 and buy me out of teaching, as well as funding RAs and studentships. The official ads can be found here (postdoc) and here (studentship). If you are interested and would like some more info, do get in touch with me.

Arrivals and departures in the lab

Van Anh Huynh-Thu recently joined us to work on my ERC project from the University of Liege, where she worked on network reconstruction with Pierre Geurts and Louis Wehenkel.

David Schnoerr joined us and Ramon Grima's lab as a PhD student, after a theoretical physics degree in Heidelberg on renormalisation group techniques.

Daniel Trejo Banos arrived in February 2012 from the Universitad Nacional Autonoma de Mexico to pursue a PhD in computational systems biology. He will be looking to develop bioinformatics and machine learning methods to model plant oscillators.

Andrea Ocone submitted his thesis and is off to work in the Helmholtz Zentrum in Munich as a post doc with Fabian Theis.