lineage.Viterbi

This file contains the methods for the Viterbi algorithm implemented in an a upward recursion.

Module Contents

lineage.Viterbi.get_deltas(X: list, E: list, T: np.ndarray) → Tuple[list[np.ndarray], list]

Delta matrix and base case at the leaves. Each element in this N by K matrix is the probability for the leaves \(P(x_n = x | z_n = k)\).

Then calculates delta values for non-leaf cells by filling out the delta matrix.

Parameters

tHMMobj – the tHMM object

Returns

a list of N by K matrices for each lineage, initialized from the leaf cells by EL(n,k).

lineage.Viterbi.get_delta_parent_child_prod(linObj, delta_array: np.ndarray, T: np.ndarray, node_parent_m_idx: int) → Tuple[np.ndarray, list]

Calculates the delta coefficient for every parent-child relationship of a given parent cell in a given state. In these set of functions state pointer is an array of size K, that holds the state number with the highest probability in each row of the max_holder. max_holder is a matrix of size K x K that initially starts from T, and gets updated. delta_m_n_holder is a vector of size K that has the highest of those probabilities.

Parameters

  • lineage – A list containing cells (which are objects with their own properties).

  • delta_array – A N by K matrix containing the delta values that will be used in Viterbi.

  • T – The K by K transition matrix.

  • node_parent_m_index – The index of the parent to the currently-intended-cell.

Return delta_m_n_holder

A list to hold the factors in the product.

Return max_state_ptr

A list of tuples of daughter cell indexes and their state pointers.

lineage.Viterbi.Viterbi(tHMMobj) → list[np.ndarray]

Runs the viterbi algorithm and returns a list of arrays containing the optimal state of each cell. This function returns the most likely sequence of states for each lineage.

Parameters

  • tHMMobj – a class object with properties of the lineages of cells

  • deltas – a list of N by K matrices containing the delta values for each lineage

  • state_ptrs – a list of tuples of daughter cell indexes and their state pointers

Returns

assigned states to each cell in all lineages