This paper introduced the first machine learned ``encyclopedia''
of the common protein-fold structures. The Journal of Molecular
Biology is the premier journal in this area.
Previous papers have studied learning of Stochastic Logic Programs (SLPs) either as a purely parametric estimation problem or separated structure learning and parameter estimation into separate phases. In this paper we consider ways in which both the structure and the parameters of an SLP can be learned simultaneously. The paper assumes an ILP algorithm, such as Progol or FOIL, in which clauses are constructed independently. We derive analytical and numerical methods for efficient computation of the optimal probability parameters for a single clause choice within such a search. An implementation of this approach in Progol4.5 is demonstrated.
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