Variational Inference CLI

See the examples for an example of how to run the variational inference CLI.

treeflow_vi

Perform fixed-topology variational Bayesian inference for a phylogenetic model with a given tree topology and multiple sequence alignment.

The tree prior and substitution model used can be specified using the TreeFlow YAML model definition format (see the package documentation).

Usage

treeflow_vi [OPTIONS]

Options

-i, --input <input>

Required Alignment file (FASTA format)

-t, --topology <topology>

Required Topology file

-m, --model-file <model_file>

YAML model definition file

-va, --variational-approximation <variational_approximation>

Required Variational approximation type

Default:

'mean_field'

Options:

mean_field | iaf

-n, --num-steps <num_steps>

Required Number of VI iterations

Default:

40000

-o, --optimizer <optimizer>

Required

Default:

'robust_adam'

Options:

adam | robust_adam

--init-values <init_values>

Initial values in the format ‘scalar_parameter=value1,vector_parameter=value2a|value2b’

-s, --seed <seed>

--trace-output <trace_output>

Path to save pickled optimization trace

--samples-output <samples_output>

Path to save parameter samples in CSV format

--tree-samples-output <tree_samples_output>

Path to save tree samples to in Nexus format

--n-output-samples <n_output_samples>

Required Number of samples to use for outputs

Default:

200

-r, --learning-rate <learning_rate>

Required

Default:

0.001

-c, --convergence-criterion <convergence_criterion>

Options:

nonfinite

--elbo-samples <elbo_samples>

Required Number of samples to use in displayed estimate of evidence lower bound

Default:

100

--progress-bar, --no-progress-bar

--alignment-format <alignment_format>

Required File format for alignment

Default:

'fasta'

Options:

fasta | nexus | nexml | phylip

--subnewick-format <subnewick_format>

Required Subnewick format (see ete3.Tree)

Default:

0