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| (** supporting functions for estimating the parameters of phylogenetic models by | |
| expectation-maximization (EM) *) | |
| (** {1 E-step} *) | |
| (** sufficient statistics for the E-step, composed of estimates of how many times each | |
| character-character substitution occurred on each branch of the tree (summed over all sites) *) | |
| type sufficient_statistics = float array array array | |
| val new_sufficient_statistics : PhyloModel.t -> sufficient_statistics | |
| (** compute the E-step statistics for one site, given the leaves (as would be given to | |
| {{:PhyloModel}PhyloModel.prepare_lik}). Update the given [sufficient_statistics] and return the | |
| probability of the leaves under the model. This should be called for each site to collect the | |
| statistics for the whole alignment. *) | |
| val collect_sufficient_statistics : ?workspace:PhyloLik.workspace -> PhyloModel.t -> PhyloLik.leaf array -> sufficient_statistics -> float | |
| (** any entry in the sufficient statistics less than [tol] is set to zero. useful if e.g. planning | |
| to compress the sufficient statistics for transport between compute nodes *) | |
| val clean_sufficient_statistics : ?tol:float -> sufficient_statistics -> unit | |
| (** {1 M-step} *) | |
| (** expected log-likelihood of the model, where the expectation is over the soft assignment of the | |
| ancestral characters represented by the sufficient statistics of the E-step. (objective function of | |
| the M-step, sometimes called the Q function) *) | |
| val ell : PhyloModel.t -> sufficient_statistics -> float | |
| (** compute the portion of the ell arising from the prior over the ancestral sequence *) | |
| val prior_ell : PhyloModel.t -> sufficient_statistics -> float | |
| (** compute the portion of the ell arising from the substitution process *) | |
| val branches_ell : PhyloModel.t -> sufficient_statistics -> float | |
| (** compute the portion of the ell arising from the substitutions on a specific branch*) | |
| val branch_ell : PhyloModel.t -> sufficient_statistics -> int -> float | |
| (** compute the gradient of the ell with respect to the variables in the model's rate matrix p14n, | |
| based on their symbolic expressions *) | |
| val d_ell_dQ_dx : PhyloModel.P14n.instance -> sufficient_statistics -> float array | |
| (** compute the partial derivative with respect to one specific rate matrix variable only *) | |
| val d_ell_dQ_dxi : PhyloModel.P14n.instance -> sufficient_statistics -> int -> float | |
| (** compute the gradient with respect to the variables in the model's p14n for branch lengths, based | |
| on their symbolic expressions*) | |
| val d_ell_dtree : PhyloModel.P14n.instance -> sufficient_statistics -> float array | |
| (** compute the derivative with respect to one specific branch length variable only *) | |
| val d_ell_dbranch : PhyloModel.P14n.instance -> int -> sufficient_statistics -> float array |