geraintpalmer / pattern_mining

pattern-mining

Code for running sequential pattern mining algorithm ALERGIA.

Input data

For an initial PPTA that looks like (instert picture) with three actions or an alphabet [0, 1, 2] and 7 states, [0, 1, 2, 3, 4, 5, 6], the example input would be:

states = ["S", 0, 1, 2, 3, 4, 5, 6]
alphabet = [0, 1, 2]
pathway_matrix = np.array([
    [
        [0, 30, 0, 0, 0, 0, 0, 0],
        [0, 0, 15, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 5, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
    ],
    [
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 15, 0, 0, 0],
        [0, 0, 0, 7, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 5, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
    ],
    [
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 2],
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
        [0, 0, 0, 0, 0, 0, 0, 0],
    ]
])

The states includes an extra state "S" representing the starting state. The pathway_matrix is a 3D matrix with the first dimension representing the action, the second dimension representing the state, and the third dimension representing the next state. For example, pathway_matrix[0, 1, 4] is the number of times that action 0 was taken from state 0 to state 3.

Note that we have assumed that you go from the starting state "S" to state 0 by using action 0. This is not true, but has no effect on the maths.

Running tests

$ python -m pytest tests.py