Séminaire Donnees et APprentissage Artificiel
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Experiments with Probabilistic Logic Programming applied to Biological Sequence Analysis
Intervenant(s) : Ole Torp Lassen (Roskilde University, Danemark & LIP6 depuis 01/04/2013)Systems that combine logic programming and statistical inference in theory allow machine learning systems to deal with both relational and statistical information.In practice, however, such applications do not scale very well.The LoSt project was concerned with a compositional approach to overcome those challenges. In particular, we experimented with applying one probabilistic logic programming system, PRISM (Taisuke Sato & Yoshitaka Kameya), based on B-Prolog, to complex, large scale bio-informatical problems.Firstly, some important aspects of the PRISM system and its underlying implementation were optimised for application to large scale data.Secondly, we developed a compositional method of analysis, Bayesian Annotation Networks, where the complex overall task is approximated by identifying and negotiating interdependent constituent subtasks and, in turn, integrating their analytical results according to their interdependencies.Finally, we experimented extensively with the developed framework in the domain of procaryotic gene-finding. As part of the general domain of DNA-annotation, the task of gene-finding is characterized by large sets of extremely long and highly ambiguous sequences of data and, thus, represents a suitably challenging setting for efficient analysis.In general, we concluded that with the computing power of today, probabilistic logic programming systems, as exemplified by PRISM, can be applied efficiently - also in large scale domains. As such, probabilistic logic programming offers extremely expressive models with very clear semantics – facilitating increased focus on domain properties and less on programming complexity.
Adrien.Revault-d'Allonnes (at) null