Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
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143 lines
7.3 KiB
143 lines
7.3 KiB
import sys
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sys.path.append('../')
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import numpy as np
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from ..structure_graph.network_graph import NetworkGraph
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from ..structure_graph.set_of_cims import SetOfCims
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from ..structure_graph.trajectory import Trajectory
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class ParametersEstimator(object):
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"""Has the task of computing the cims of particular node given the trajectories and the net structure
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in the graph ``_net_graph``.
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:param trajectories: the trajectories
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:type trajectories: Trajectory
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:param net_graph: the net structure
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:type net_graph: NetworkGraph
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:_single_set_of_cims: the set of cims object that will hold the cims of the node
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"""
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def __init__(self, trajectories: Trajectory, net_graph: NetworkGraph):
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"""Constructor Method
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"""
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self._trajectories = trajectories
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self._net_graph = net_graph
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self._single_set_of_cims = None
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def fast_init(self, node_id: str) -> None:
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"""Initializes all the necessary structures for the parameters estimation for the node ``node_id``.
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:param node_id: the node label
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:type node_id: string
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"""
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p_vals = self._net_graph._aggregated_info_about_nodes_parents[2]
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node_states_number = self._net_graph.get_states_number(node_id)
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self._single_set_of_cims = SetOfCims(node_id, p_vals, node_states_number, self._net_graph.p_combs)
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def compute_parameters_for_node(self, node_id: str) -> SetOfCims:
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"""Compute the CIMS of the node identified by the label ``node_id``.
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:param node_id: the node label
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:type node_id: string
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:return: A SetOfCims object filled with the computed CIMS
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:rtype: SetOfCims
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"""
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node_indx = self._net_graph.get_node_indx(node_id)
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state_res_times = self._single_set_of_cims._state_residence_times
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transition_matrices = self._single_set_of_cims._transition_matrices
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ParametersEstimator.compute_state_res_time_for_node(self._trajectories.times,
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self._trajectories.trajectory,
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self._net_graph.time_filtering,
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self._net_graph.time_scalar_indexing_strucure,
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state_res_times)
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ParametersEstimator.compute_state_transitions_for_a_node(node_indx, self._trajectories.complete_trajectory,
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self._net_graph.transition_filtering,
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self._net_graph.transition_scalar_indexing_structure,
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transition_matrices)
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self._single_set_of_cims.build_cims(state_res_times, transition_matrices)
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return self._single_set_of_cims
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@staticmethod
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def compute_state_res_time_for_node(times: np.ndarray, trajectory: np.ndarray,
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cols_filter: np.ndarray, scalar_indexes_struct: np.ndarray,
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T: np.ndarray) -> None:
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"""Compute the state residence times for a node and fill the matrix ``T`` with the results
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:param node_indx: the index of the node
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:type node_indx: int
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:param times: the times deltas vector
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:type times: numpy.array
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:param trajectory: the trajectory
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:type trajectory: numpy.ndArray
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:param cols_filter: the columns filtering structure
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:type cols_filter: numpy.array
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:param scalar_indexes_struct: the indexing structure
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:type scalar_indexes_struct: numpy.array
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:param T: the state residence times vectors
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:type T: numpy.ndArray
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"""
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T[:] = np.bincount(np.sum(trajectory[:, cols_filter] * scalar_indexes_struct / scalar_indexes_struct[0], axis=1)
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.astype(np.int), \
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times,
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minlength=scalar_indexes_struct[-1]).reshape(-1, T.shape[1])
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@staticmethod
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def compute_state_transitions_for_a_node(node_indx: int, trajectory: np.ndarray, cols_filter: np.ndarray,
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scalar_indexing: np.ndarray, M: np.ndarray) -> None:
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"""Compute the state residence times for a node and fill the matrices ``M`` with the results.
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:param node_indx: the index of the node
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:type node_indx: int
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:param trajectory: the trajectory
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:type trajectory: numpy.ndArray
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:param cols_filter: the columns filtering structure
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:type cols_filter: numpy.array
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:param scalar_indexing: the indexing structure
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:type scalar_indexing: numpy.array
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:param M: the state transitions matrices
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:type M: numpy.ndArray
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"""
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diag_indices = np.array([x * M.shape[1] + x % M.shape[1] for x in range(M.shape[0] * M.shape[1])],
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dtype=np.int64)
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trj_tmp = trajectory[trajectory[:, int(trajectory.shape[1] / 2) + node_indx].astype(np.int) >= 0]
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M[:] = np.bincount(np.sum(trj_tmp[:, cols_filter] * scalar_indexing / scalar_indexing[0], axis=1).astype(np.int)
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, minlength=scalar_indexing[-1]).reshape(-1, M.shape[1], M.shape[2])
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M_raveled = M.ravel()
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M_raveled[diag_indices] = 0
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M_raveled[diag_indices] = np.sum(M, axis=2).ravel()
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def init_sets_cims_container(self):
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self.sets_of_cims_struct = acims.SetsOfCimsContainer(self.net_graph.nodes,
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self.net_graph.nodes_values,
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self.net_graph.get_ordered_by_indx_parents_values_for_all_nodes(),
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self.net_graph.p_combs)
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def compute_parameters(self):
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#print(self.net_graph.get_nodes())
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#print(self.amalgamated_cims_struct.sets_of_cims)
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#enumerate(zip(self.net_graph.get_nodes(), self.amalgamated_cims_struct.sets_of_cims))
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for indx, aggr in enumerate(zip(self.net_graph.nodes, self.sets_of_cims_struct.sets_of_cims)):
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#print(self.net_graph.time_filtering[indx])
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#print(self.net_graph.time_scalar_indexing_strucure[indx])
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self.compute_state_res_time_for_node(self.net_graph.get_node_indx(aggr[0]), self.sample_path.trajectories.times,
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self.sample_path.trajectories.trajectory,
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self.net_graph.time_filtering[indx],
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self.net_graph.time_scalar_indexing_strucure[indx],
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aggr[1]._state_residence_times)
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#print(self.net_graph.transition_filtering[indx])
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#print(self.net_graph.transition_scalar_indexing_structure[indx])
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self.compute_state_transitions_for_a_node(self.net_graph.get_node_indx(aggr[0]),
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self.sample_path.trajectories.complete_trajectory,
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self.net_graph.transition_filtering[indx],
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self.net_graph.transition_scalar_indexing_structure[indx],
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aggr[1]._transition_matrices)
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aggr[1].build_cims(aggr[1]._state_residence_times, aggr[1]._transition_matrices)
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