Struct PhylogeneticKernel 

pub struct PhylogeneticKernel<State = Untrained> { /* private fields */ }

Kernel method for phylogenetic analysis using evolutionary distances

This kernel computes features based on phylogenetic tree structure and evolutionary distances between species.

References

• Vert (2002): “A tree kernel to analyze phylogenetic profiles”

Implementations

impl PhylogeneticKernel<Untrained>

pub fn new(n_components: usize, tree_depth: usize) -> Self

Create a new phylogenetic kernel

pub fn use_branch_lengths(self, use_branch_lengths: bool) -> Self

Set whether to use branch lengths for weighting

Trait Implementations

impl Default for PhylogeneticKernel<Untrained>

fn default() -> Self

Returns the “default value” for a type.

impl Fit<ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>, ()> for PhylogeneticKernel<Untrained>

type Fitted = PhylogeneticKernel<Trained>

The fitted model type

fn fit(self, x: &Array2<Float>, _y: &()) -> Result<Self::Fitted>

Fit the model to the provided data with validation

fn fit_with_validation( self, x: &X, y: &Y, _x_val: Option<&X>, _y_val: Option<&Y>, ) -> Result<(Self::Fitted, FitMetrics), SklearsError>

where Self: Sized,

Fit with custom validation and early stopping

impl Transform<ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>> for PhylogeneticKernel<Trained>

fn transform(&self, x: &Array2<Float>) -> Result<Array2<Float>>

Transform the input data