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To train the model, we design a two-step maximum likelihood optimization procedure that ensures the orthogonality of the projection matrix by exploiting recent results on the Stiefel manifold, i.e., the manifold of matrices with orthogonal columns.
Then it goes through a maximum likelihood optimization of the tree [21], [22].
This function estimates ancestral character states by maximum likelihood optimization [ 45].
We derived a maximum likelihood optimization approach allowing the estimation of the relative amplification efficiency of each allele.
The trees resulting from maximum likelihood optimization for ORF5 and ORF7 respectively showed a strong clustering by farm.
Both normal-binomial model and inverted beta-binomial model belong to the class of hierarchical modeling for which maximum likelihood optimization is difficult because of the integrations involved.
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For example, MP-EST, which has been used in many biological dataset analyses [ 12- 15], uses a heuristic search to solve an NP-hard pseudo-maximum likelihood optimization problem (based on the triplet gene tree distribution).
Phylogenetic trees were inferred using maximum-likelihood optimization criteria.
The maximum entropy models were fit using a combination of the generalized iterative scaling algorithm (Darroch and Ratcliff, 1972), and a maximum-likelihood optimization using a variant of the gradient descent algorithm with line search (Nesterov, 2005).
Bud scale was scored as 0 (= margin free) or 1 (= margin connate), and stamen number as 0 (= more than two) or 1 (= two), and ancestral states were estimated using Mk1-model maximum-likelihood optimization in Mesquite v. 2.75 [ 85].
We then coded the data as unordered binary or multistate characters, and reconstructed ancestral states by single-rate (Mk1) maximum likelihood (ML) optimization in Mesquite v. 2.75 [ 63].
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maximum likelihood detection
maximum likelihood modeling
maximum parsimony optimization
maximum likelihood estimation/estimator
maximum likelihood reconstruction
maximum likelihood dendrogram
maximum likelihood ratio
maximum likelihood learning
maximum likelihood tree
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maximum likelihood approach
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maximum likelihood Estimation
maximum margin optimization
maximum likelihood expectation
maximum likelihood phylogram
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