Merge pull request #73 from AlessandroBregoli/13-feature-add-ctmp

13 feature add ctmp

reCTBN/src/lib.rs

@@ -3,10 +3,9 @@
 #[cfg(test)]
 extern crate approx;
 
-pub mod ctbn;
-pub mod network;
 pub mod parameter_learning;
 pub mod params;
+pub mod process;
 pub mod sampling;
 pub mod structure_learning;
 pub mod tools;

reCTBN/src/parameter_learning.rs

@@ -5,10 +5,10 @@ use std::collections::BTreeSet;
 use ndarray::prelude::*;
 
 use crate::params::*;
-use crate::{network, tools};
+use crate::{process, tools};
 
 pub trait ParameterLearning {
-    fn fit<T: network::Network>(
+    fn fit<T: process::NetworkProcess>(
         &self,
         net: &T,
         dataset: &tools::Dataset,
@@ -17,7 +17,7 @@ pub trait ParameterLearning {
     ) -> Params;
 }
 
-pub fn sufficient_statistics<T: network::Network>(
+pub fn sufficient_statistics<T: process::NetworkProcess>(
     net: &T,
     dataset: &tools::Dataset,
     node: usize,
@@ -73,7 +73,7 @@ pub fn sufficient_statistics<T: network::Network>(
 pub struct MLE {}
 
 impl ParameterLearning for MLE {
-    fn fit<T: network::Network>(
+    fn fit<T: process::NetworkProcess>(
         &self,
         net: &T,
         dataset: &tools::Dataset,
@@ -120,7 +120,7 @@ pub struct BayesianApproach {
 }
 
 impl ParameterLearning for BayesianApproach {
-    fn fit<T: network::Network>(
+    fn fit<T: process::NetworkProcess>(
         &self,
         net: &T,
         dataset: &tools::Dataset,
@@ -177,7 +177,7 @@ impl<P: ParameterLearning> Cache<P> {
             dataset,
         }
     }
-    pub fn fit<T: network::Network>(
+    pub fn fit<T: process::NetworkProcess>(
         &mut self,
         net: &T,
         node: usize,

reCTBN/src/params.rs

@@ -267,11 +267,13 @@ impl ParamsTrait for DiscreteStatesContinousTimeParams {
             )));
         }
 
+        let domain_size = domain_size as f64;
+
         // Check if each row sum up to 0
         if cim
             .sum_axis(Axis(2))
             .iter()
-            .any(|x| f64::abs(x.clone()) > f64::EPSILON * 3.0)
+            .any(|x| f64::abs(x.clone()) > f64::EPSILON * domain_size)
         {
             return Err(ParamsError::InvalidCIM(String::from(
                 "The sum of each row must be 0",

reCTBN/src/process.rs

@@ -1,5 +1,8 @@
 //! Defines methods for dealing with Probabilistic Graphical Models like the CTBNs
 
+pub mod ctbn;
+pub mod ctmp;
+
 use std::collections::BTreeSet;
 
 use thiserror::Error;
@@ -15,7 +18,7 @@ pub enum NetworkError {
 
 /// It defines the required methods for a structure used as a Probabilistic Graphical Models (such
 /// as a CTBN).
-pub trait Network {
+pub trait NetworkProcess {
     fn initialize_adj_matrix(&mut self);
     fn add_node(&mut self, n: params::Params) -> Result<usize, NetworkError>;
     /// Add an **directed edge** between a two nodes of the network.

reCTBN/src/process/ctbn.rs

@@ -4,8 +4,11 @@ use std::collections::BTreeSet;
 
 use ndarray::prelude::*;
 
-use crate::network;
+use crate::params::{DiscreteStatesContinousTimeParams, Params, ParamsTrait, StateType};
-use crate::params::{Params, ParamsTrait, StateType};
+use crate::process;
+
+use super::ctmp::CtmpProcess;
+use super::NetworkProcess;
 
 /// It represents both the structure and the parameters of a CTBN.
 ///
@@ -20,9 +23,9 @@ use crate::params::{Params, ParamsTrait, StateType};
 ///
 /// ```rust
 /// use std::collections::BTreeSet;
-/// use reCTBN::network::Network;
+/// use reCTBN::process::NetworkProcess;
 /// use reCTBN::params;
-/// use reCTBN::ctbn::*;
+/// use reCTBN::process::ctbn::*;
 ///
 /// //Create the domain for a discrete node
 /// let mut domain = BTreeSet::new();
@@ -67,9 +70,78 @@ impl CtbnNetwork {
             nodes: Vec::new(),
         }
     }
+
+    ///Transform the **CTBN** into a **CTMP**
+    ///
+    /// # Return
+    ///
+    /// * The equivalent *CtmpProcess* computed from the current CtbnNetwork
+    pub fn amalgamation(&self) -> CtmpProcess {
+        let variables_domain =
+            Array1::from_iter(self.nodes.iter().map(|x| x.get_reserved_space_as_parent()));
+
+        let state_space = variables_domain.product();
+        let variables_set = BTreeSet::from_iter(self.get_node_indices());
+        let mut amalgamated_cim: Array3<f64> = Array::zeros((1, state_space, state_space));
+
+        for idx_current_state in 0..state_space {
+            let current_state = CtbnNetwork::idx_to_state(&variables_domain, idx_current_state);
+            let current_state_statetype: Vec<StateType> = current_state
+                .iter()
+                .map(|x| StateType::Discrete(*x))
+                .collect();
+            for idx_node in 0..self.nodes.len() {
+                let p = match self.get_node(idx_node) {
+                    Params::DiscreteStatesContinousTime(p) => p,
+                };
+                for next_node_state in 0..variables_domain[idx_node] {
+                    let mut next_state = current_state.clone();
+                    next_state[idx_node] = next_node_state;
+
+                    let next_state_statetype: Vec<StateType> =
+                        next_state.iter().map(|x| StateType::Discrete(*x)).collect();
+                    let idx_next_state = self.get_param_index_from_custom_parent_set(
+                        &next_state_statetype,
+                        &variables_set,
+                    );
+                    amalgamated_cim[[0, idx_current_state, idx_next_state]] +=
+                        p.get_cim().as_ref().unwrap()[[
+                            self.get_param_index_network(idx_node, &current_state_statetype),
+                            current_state[idx_node],
+                            next_node_state,
+                        ]];
+                }
+            }
+        }
+
+        let mut amalgamated_param = DiscreteStatesContinousTimeParams::new(
+            "ctmp".to_string(),
+            BTreeSet::from_iter((0..state_space).map(|x| x.to_string())),
+        );
+
+        println!("{:?}", amalgamated_cim);
+        amalgamated_param.set_cim(amalgamated_cim).unwrap();
+
+        let mut ctmp = CtmpProcess::new();
+
+        ctmp.add_node(Params::DiscreteStatesContinousTime(amalgamated_param))
+            .unwrap();
+        return ctmp;
+    }
+
+    pub fn idx_to_state(variables_domain: &Array1<usize>, state: usize) -> Array1<usize> {
+        let mut state = state;
+        let mut array_state = Array1::zeros(variables_domain.shape()[0]);
+        for (idx, var) in variables_domain.indexed_iter() {
+            array_state[idx] = state % var;
+            state = state / var;
+        }
+
+        return array_state;
+    }
 }
 
-impl network::Network for CtbnNetwork {
+impl process::NetworkProcess for CtbnNetwork {
     /// Initialize an Adjacency matrix.
     fn initialize_adj_matrix(&mut self) {
         self.adj_matrix = Some(Array2::<u16>::zeros(
@@ -78,7 +150,7 @@ impl network::Network for CtbnNetwork {
     }
 
     /// Add a new node.
-    fn add_node(&mut self, mut n: Params) -> Result<usize, network::NetworkError> {
+    fn add_node(&mut self, mut n: Params) -> Result<usize, process::NetworkError> {
         n.reset_params();
         self.adj_matrix = Option::None;
         self.nodes.push(n);

reCTBN/src/process/ctmp.rs

@@ -0,0 +1,118 @@
+use std::collections::BTreeSet;
+
+use crate::{
+    params::{Params, StateType},
+    process,
+};
+
+use super::NetworkProcess;
+
+pub struct CtmpProcess {
+    param: Option<Params>,
+}
+
+impl CtmpProcess {
+    pub fn new() -> CtmpProcess {
+        CtmpProcess { param: None }
+    }
+}
+
+impl NetworkProcess for CtmpProcess {
+    fn initialize_adj_matrix(&mut self) {
+        unimplemented!("CtmpProcess has only one node")
+    }
+
+    fn add_node(&mut self, n: crate::params::Params) -> Result<usize, process::NetworkError> {
+        match self.param {
+            None => {
+                self.param = Some(n);
+                Ok(0)
+            }
+            Some(_) => Err(process::NetworkError::NodeInsertionError(
+                "CtmpProcess has only one node".to_string(),
+            )),
+        }
+    }
+
+    fn add_edge(&mut self, _parent: usize, _child: usize) {
+        unimplemented!("CtmpProcess has only one node")
+    }
+
+    fn get_node_indices(&self) -> std::ops::Range<usize> {
+        match self.param {
+            None => 0..0,
+            Some(_) => 0..1,
+        }
+    }
+
+    fn get_number_of_nodes(&self) -> usize {
+        match self.param {
+            None => 0,
+            Some(_) => 1,
+        }
+    }
+
+    fn get_node(&self, node_idx: usize) -> &crate::params::Params {
+        if node_idx == 0 {
+            self.param.as_ref().unwrap()
+        } else {
+            unimplemented!("CtmpProcess has only one node")
+        }
+    }
+
+    fn get_node_mut(&mut self, node_idx: usize) -> &mut crate::params::Params {
+        if node_idx == 0 {
+            self.param.as_mut().unwrap()
+        } else {
+            unimplemented!("CtmpProcess has only one node")
+        }
+    }
+
+    fn get_param_index_network(
+        &self,
+        node: usize,
+        current_state: &Vec<crate::params::StateType>,
+    ) -> usize {
+        if node == 0 {
+            match current_state[0] {
+                StateType::Discrete(x) => x,
+            }
+        } else {
+            unimplemented!("CtmpProcess has only one node")
+        }
+    }
+
+    fn get_param_index_from_custom_parent_set(
+        &self,
+        _current_state: &Vec<crate::params::StateType>,
+        _parent_set: &std::collections::BTreeSet<usize>,
+    ) -> usize {
+        unimplemented!("CtmpProcess has only one node")
+    }
+
+    fn get_parent_set(&self, node: usize) -> std::collections::BTreeSet<usize> {
+        match self.param {
+            Some(_) => {
+                if node == 0 {
+                    BTreeSet::new()
+                } else {
+                    unimplemented!("CtmpProcess has only one node")
+                }
+            }
+            None => panic!("Uninitialized CtmpProcess"),
+        }
+    }
+
+    fn get_children_set(&self, node: usize) -> std::collections::BTreeSet<usize> {
+        match self.param {
+            Some(_) => {
+                if node == 0 {
+                    BTreeSet::new()
+                } else {
+                    unimplemented!("CtmpProcess has only one node")
+                }
+            }
+            None => panic!("Uninitialized CtmpProcess"),
+        }
+    }
+}

reCTBN/src/sampling.rs

@@ -1,8 +1,8 @@
 //! Module containing methods for the sampling.
 
 use crate::{
-    network::Network,
     params::{self, ParamsTrait},
+    process::NetworkProcess,
 };
 use rand::SeedableRng;
 use rand_chacha::ChaCha8Rng;
@@ -13,7 +13,7 @@ pub trait Sampler: Iterator {
 
 pub struct ForwardSampler<'a, T>
 where
-    T: Network,
+    T: NetworkProcess,
 {
     net: &'a T,
     rng: ChaCha8Rng,
@@ -22,7 +22,7 @@ where
     next_transitions: Vec<Option<f64>>,
 }
 
-impl<'a, T: Network> ForwardSampler<'a, T> {
+impl<'a, T: NetworkProcess> ForwardSampler<'a, T> {
     pub fn new(net: &'a T, seed: Option<u64>) -> ForwardSampler<'a, T> {
         let rng: ChaCha8Rng = match seed {
             //If a seed is present use it to initialize the random generator.
@@ -42,7 +42,7 @@ impl<'a, T: Network> ForwardSampler<'a, T> {
     }
 }
 
-impl<'a, T: Network> Iterator for ForwardSampler<'a, T> {
+impl<'a, T: NetworkProcess> Iterator for ForwardSampler<'a, T> {
     type Item = (f64, Vec<params::StateType>);
 
     fn next(&mut self) -> Option<Self::Item> {
@@ -100,7 +100,7 @@ impl<'a, T: Network> Iterator for ForwardSampler<'a, T> {
     }
 }
 
-impl<'a, T: Network> Sampler for ForwardSampler<'a, T> {
+impl<'a, T: NetworkProcess> Sampler for ForwardSampler<'a, T> {
     fn reset(&mut self) {
         self.current_time = 0.0;
         self.current_state = self

reCTBN/src/structure_learning.rs

@@ -4,10 +4,10 @@ pub mod constraint_based_algorithm;
 pub mod hypothesis_test;
 pub mod score_based_algorithm;
 pub mod score_function;
-use crate::{network, tools};
+use crate::{process, tools};
 
 pub trait StructureLearningAlgorithm {
     fn fit_transform<T>(&self, net: T, dataset: &tools::Dataset) -> T
     where
-        T: network::Network;
+        T: process::NetworkProcess;
 }

reCTBN/src/structure_learning/hypothesis_test.rs

@@ -6,7 +6,7 @@ use ndarray::{Array3, Axis};
 use statrs::distribution::{ChiSquared, ContinuousCDF};
 
 use crate::params::*;
-use crate::{network, parameter_learning};
+use crate::{parameter_learning, process};
 
 pub trait HypothesisTest {
     fn call<T, P>(
@@ -18,7 +18,7 @@ pub trait HypothesisTest {
         cache: &mut parameter_learning::Cache<P>,
     ) -> bool
     where
-        T: network::Network,
+        T: process::NetworkProcess,
         P: parameter_learning::ParameterLearning;
 }
 
@@ -135,7 +135,7 @@ impl HypothesisTest for ChiSquare {
         cache: &mut parameter_learning::Cache<P>,
     ) -> bool
     where
-        T: network::Network,
+        T: process::NetworkProcess,
         P: parameter_learning::ParameterLearning,
     {
         // Prendo dalla cache l'apprendimento dei parametri, che sarebbe una CIM

reCTBN/src/structure_learning/score_based_algorithm.rs

@@ -4,7 +4,7 @@ use std::collections::BTreeSet;
 
 use crate::structure_learning::score_function::ScoreFunction;
 use crate::structure_learning::StructureLearningAlgorithm;
-use crate::{network, tools};
+use crate::{process, tools};
 
 pub struct HillClimbing<S: ScoreFunction> {
     score_function: S,
@@ -23,7 +23,7 @@ impl<S: ScoreFunction> HillClimbing<S> {
 impl<S: ScoreFunction> StructureLearningAlgorithm for HillClimbing<S> {
     fn fit_transform<T>(&self, net: T, dataset: &tools::Dataset) -> T
     where
-        T: network::Network,
+        T: process::NetworkProcess,
     {
         //Check the coherence between dataset and network
         if net.get_number_of_nodes() != dataset.get_trajectories()[0].get_events().shape()[1] {

reCTBN/src/structure_learning/score_function.rs

@@ -5,7 +5,7 @@ use std::collections::BTreeSet;
 use ndarray::prelude::*;
 use statrs::function::gamma;
 
-use crate::{network, parameter_learning, params, tools};
+use crate::{parameter_learning, params, process, tools};
 
 pub trait ScoreFunction {
     fn call<T>(
@@ -16,7 +16,7 @@ pub trait ScoreFunction {
         dataset: &tools::Dataset,
     ) -> f64
     where
-        T: network::Network;
+        T: process::NetworkProcess;
 }
 
 pub struct LogLikelihood {
@@ -41,7 +41,7 @@ impl LogLikelihood {
         dataset: &tools::Dataset,
     ) -> (f64, Array3<usize>)
     where
-        T: network::Network,
+        T: process::NetworkProcess,
     {
         //Identify the type of node used
         match &net.get_node(node) {
@@ -100,7 +100,7 @@ impl ScoreFunction for LogLikelihood {
         dataset: &tools::Dataset,
     ) -> f64
     where
-        T: network::Network,
+        T: process::NetworkProcess,
     {
         self.compute_score(net, node, parent_set, dataset).0
     }
@@ -127,7 +127,7 @@ impl ScoreFunction for BIC {
         dataset: &tools::Dataset,
     ) -> f64
     where
-        T: network::Network,
+        T: process::NetworkProcess,
     {
         //Compute the log-likelihood
         let (ll, M) = self.ll.compute_score(net, node, parent_set, dataset);

reCTBN/src/tools.rs

@@ -3,7 +3,7 @@
 use ndarray::prelude::*;
 
 use crate::sampling::{ForwardSampler, Sampler};
-use crate::{network, params};
+use crate::{params, process};
 
 pub struct Trajectory {
     time: Array1<f64>,
@@ -51,7 +51,7 @@ impl Dataset {
     }
 }
 
-pub fn trajectory_generator<T: network::Network>(
+pub fn trajectory_generator<T: process::NetworkProcess>(
     net: &T,
     n_trajectories: u64,
     t_end: f64,

reCTBN/tests/ctbn.rs

@@ -1,9 +1,12 @@
 mod utils;
 use std::collections::BTreeSet;
 
-use reCTBN::ctbn::*;
+
-use reCTBN::network::Network;
+use approx::AbsDiffEq;
+use ndarray::arr3;
 use reCTBN::params::{self, ParamsTrait};
+use reCTBN::process::NetworkProcess;
+use reCTBN::process::{ctbn::*};
 use utils::generate_discrete_time_continous_node;
 
 #[test]
@@ -129,3 +132,245 @@ fn compute_index_from_custom_parent_set() {
     );
     assert_eq!(2, idx);
 }
+
+#[test]
+fn simple_amalgamation() {
+    let mut net = CtbnNetwork::new();
+    let n1 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n1"), 2))
+        .unwrap();
+
+    net.initialize_adj_matrix();
+
+    match &mut net.get_node_mut(n1) {
+        params::Params::DiscreteStatesContinousTime(param) => {
+            assert_eq!(Ok(()), param.set_cim(arr3(&[[[-3.0, 3.0], [2.0, -2.0]]])));
+        }
+    }
+
+    let ctmp = net.amalgamation();
+    let params::Params::DiscreteStatesContinousTime(p_ctbn) = &net.get_node(0);
+    let p_ctbn = p_ctbn.get_cim().as_ref().unwrap();
+    let params::Params::DiscreteStatesContinousTime(p_ctmp) = &ctmp.get_node(0);
+    let p_ctmp = p_ctmp.get_cim().as_ref().unwrap();
+
+    assert!(p_ctmp.abs_diff_eq(p_ctbn, std::f64::EPSILON));
+}
+
+#[test]
+fn chain_amalgamation() {
+    let mut net = CtbnNetwork::new();
+    let n1 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n1"), 2))
+        .unwrap();
+    let n2 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n2"), 2))
+        .unwrap();
+    let n3 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n3"), 2))
+        .unwrap();
+
+    net.add_edge(n1, n2);
+    net.add_edge(n2, n3);
+
+    match &mut net.get_node_mut(n1) {
+        params::Params::DiscreteStatesContinousTime(param) => {
+            assert_eq!(Ok(()), param.set_cim(arr3(&[[[-0.1, 0.1], [1.0, -1.0]]])));
+        }
+    }
+
+    match &mut net.get_node_mut(n2) {
+        params::Params::DiscreteStatesContinousTime(param) => {
+            assert_eq!(
+                Ok(()),
+                param.set_cim(arr3(&[
+                    [[-0.01, 0.01], [5.0, -5.0]],
+                    [[-5.0, 5.0], [0.01, -0.01]]
+                ]))
+            );
+        }
+    }
+
+    match &mut net.get_node_mut(n3) {
+        params::Params::DiscreteStatesContinousTime(param) => {
+            assert_eq!(
+                Ok(()),
+                param.set_cim(arr3(&[
+                    [[-0.01, 0.01], [5.0, -5.0]],
+                    [[-5.0, 5.0], [0.01, -0.01]]
+                ]))
+            );
+        }
+    }
+
+    let ctmp = net.amalgamation();
+
+
+
+    let params::Params::DiscreteStatesContinousTime(p_ctmp) = &ctmp.get_node(0);
+    let p_ctmp = p_ctmp.get_cim().as_ref().unwrap();
+
+    let p_ctmp_handmade = arr3(&[[
+        [
+            -1.20e-01, 1.00e-01, 1.00e-02, 0.00e+00, 1.00e-02, 0.00e+00, 0.00e+00, 0.00e+00,
+        ],
+        [
+            1.00e+00, -6.01e+00, 0.00e+00, 5.00e+00, 0.00e+00, 1.00e-02, 0.00e+00, 0.00e+00,
+        ],
+        [
+            5.00e+00, 0.00e+00, -1.01e+01, 1.00e-01, 0.00e+00, 0.00e+00, 5.00e+00, 0.00e+00,
+        ],
+        [
+            0.00e+00, 1.00e-02, 1.00e+00, -6.01e+00, 0.00e+00, 0.00e+00, 0.00e+00, 5.00e+00,
+        ],
+        [
+            5.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, -5.11e+00, 1.00e-01, 1.00e-02, 0.00e+00,
+        ],
+        [
+            0.00e+00, 5.00e+00, 0.00e+00, 0.00e+00, 1.00e+00, -1.10e+01, 0.00e+00, 5.00e+00,
+        ],
+        [
+            0.00e+00, 0.00e+00, 1.00e-02, 0.00e+00, 5.00e+00, 0.00e+00, -5.11e+00, 1.00e-01,
+        ],
+        [
+            0.00e+00, 0.00e+00, 0.00e+00, 1.00e-02, 0.00e+00, 1.00e-02, 1.00e+00, -1.02e+00,
+        ],
+    ]]);
+
+    assert!(p_ctmp.abs_diff_eq(&p_ctmp_handmade, 1e-8));
+}
+
+#[test]
+fn chainfork_amalgamation() {
+    let mut net = CtbnNetwork::new();
+    let n1 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n1"), 2))
+        .unwrap();
+    let n2 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n2"), 2))
+        .unwrap();
+    let n3 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n3"), 2))
+        .unwrap();
+    let n4 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n4"), 2))
+        .unwrap();
+
+    net.add_edge(n1, n3);
+    net.add_edge(n2, n3);
+    net.add_edge(n3, n4);
+
+    match &mut net.get_node_mut(n1) {
+        params::Params::DiscreteStatesContinousTime(param) => {
+            assert_eq!(Ok(()), param.set_cim(arr3(&[[[-0.1, 0.1], [1.0, -1.0]]])));
+        }
+    }
+
+    match &mut net.get_node_mut(n2) {
+        params::Params::DiscreteStatesContinousTime(param) => {
+            assert_eq!(Ok(()), param.set_cim(arr3(&[[[-0.1, 0.1], [1.0, -1.0]]])));
+        }
+    }
+
+    match &mut net.get_node_mut(n3) {
+        params::Params::DiscreteStatesContinousTime(param) => {
+            assert_eq!(
+                Ok(()),
+                param.set_cim(arr3(&[
+                    [[-0.01, 0.01], [5.0, -5.0]],
+                    [[-0.01, 0.01], [5.0, -5.0]],
+                    [[-0.01, 0.01], [5.0, -5.0]],
+                    [[-5.0, 5.0], [0.01, -0.01]]
+                ]))
+            );
+        }
+    }
+
+    match &mut net.get_node_mut(n4) {
+        params::Params::DiscreteStatesContinousTime(param) => {
+            assert_eq!(
+                Ok(()),
+                param.set_cim(arr3(&[
+                    [[-0.01, 0.01], [5.0, -5.0]],
+                    [[-5.0, 5.0], [0.01, -0.01]]
+                ]))
+            );
+        }
+    }
+
+
+    let ctmp = net.amalgamation();
+
+    let params::Params::DiscreteStatesContinousTime(p_ctmp) = &ctmp.get_node(0); 
+
+    let p_ctmp = p_ctmp.get_cim().as_ref().unwrap();
+
+    let p_ctmp_handmade = arr3(&[[
+        [
+            -2.20e-01, 1.00e-01, 1.00e-01, 0.00e+00, 1.00e-02, 0.00e+00, 0.00e+00, 0.00e+00,
+            1.00e-02, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00,
+        ],
+        [
+            1.00e+00, -1.12e+00, 0.00e+00, 1.00e-01, 0.00e+00, 1.00e-02, 0.00e+00, 0.00e+00,
+            0.00e+00, 1.00e-02, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00,
+        ],
+        [
+            1.00e+00, 0.00e+00, -1.12e+00, 1.00e-01, 0.00e+00, 0.00e+00, 1.00e-02, 0.00e+00,
+            0.00e+00, 0.00e+00, 1.00e-02, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00,
+        ],
+        [
+            0.00e+00, 1.00e+00, 1.00e+00, -7.01e+00, 0.00e+00, 0.00e+00, 0.00e+00, 5.00e+00,
+            0.00e+00, 0.00e+00, 0.00e+00, 1.00e-02, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00,
+        ],
+        [
+            5.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, -1.02e+01, 1.00e-01, 1.00e-01, 0.00e+00,
+            0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 5.00e+00, 0.00e+00, 0.00e+00, 0.00e+00,
+        ],
+        [
+            0.00e+00, 5.00e+00, 0.00e+00, 0.00e+00, 1.00e+00, -1.11e+01, 0.00e+00, 1.00e-01,
+            0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 5.00e+00, 0.00e+00, 0.00e+00,
+        ],
+        [
+            0.00e+00, 0.00e+00, 5.00e+00, 0.00e+00, 1.00e+00, 0.00e+00, -1.11e+01, 1.00e-01,
+            0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 5.00e+00, 0.00e+00,
+        ],
+        [
+            0.00e+00, 0.00e+00, 0.00e+00, 1.00e-02, 0.00e+00, 1.00e+00, 1.00e+00, -7.01e+00,
+            0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 5.00e+00,
+        ],
+        [
+            5.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00,
+            -5.21e+00, 1.00e-01, 1.00e-01, 0.00e+00, 1.00e-02, 0.00e+00, 0.00e+00, 0.00e+00,
+        ],
+        [
+            0.00e+00, 5.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00,
+            1.00e+00, -6.11e+00, 0.00e+00, 1.00e-01, 0.00e+00, 1.00e-02, 0.00e+00, 0.00e+00,
+        ],
+        [
+            0.00e+00, 0.00e+00, 5.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00,
+            1.00e+00, 0.00e+00, -6.11e+00, 1.00e-01, 0.00e+00, 0.00e+00, 1.00e-02, 0.00e+00,
+        ],
+        [
+            0.00e+00, 0.00e+00, 0.00e+00, 5.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00,
+            0.00e+00, 1.00e+00, 1.00e+00, -1.20e+01, 0.00e+00, 0.00e+00, 0.00e+00, 5.00e+00,
+        ],
+        [
+            0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 1.00e-02, 0.00e+00, 0.00e+00, 0.00e+00,
+            5.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, -5.21e+00, 1.00e-01, 1.00e-01, 0.00e+00,
+        ],
+        [
+            0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 1.00e-02, 0.00e+00, 0.00e+00,
+            0.00e+00, 5.00e+00, 0.00e+00, 0.00e+00, 1.00e+00, -6.11e+00, 0.00e+00, 1.00e-01,
+        ],
+        [
+            0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 1.00e-02, 0.00e+00,
+            0.00e+00, 0.00e+00, 5.00e+00, 0.00e+00, 1.00e+00, 0.00e+00, -6.11e+00, 1.00e-01,
+        ],
+        [
+            0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 1.00e-02,
+            0.00e+00, 0.00e+00, 0.00e+00, 1.00e-02, 0.00e+00, 1.00e+00, 1.00e+00, -2.02e+00,
+        ],
+    ]]);
+
+    assert!(p_ctmp.abs_diff_eq(&p_ctmp_handmade, 1e-8));
+}

reCTBN/tests/ctmp.rs

@@ -0,0 +1,127 @@
+mod utils;
+
+use std::collections::BTreeSet;
+
+use reCTBN::{
+    params,
+    params::ParamsTrait,
+    process::{ctmp::*, NetworkProcess},
+};
+use utils::generate_discrete_time_continous_node;
+
+#[test]
+fn define_simple_ctmp() {
+    let _ = CtmpProcess::new();
+    assert!(true);
+}
+
+#[test]
+fn add_node_to_ctmp() {
+    let mut net = CtmpProcess::new();
+    let n1 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n1"), 2))
+        .unwrap();
+    assert_eq!(&String::from("n1"), net.get_node(n1).get_label());
+}
+
+#[test]
+fn add_two_nodes_to_ctmp() {
+    let mut net = CtmpProcess::new();
+    let _n1 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n1"), 2))
+        .unwrap();
+    let n2 = net.add_node(generate_discrete_time_continous_node(String::from("n1"), 2));
+
+    match n2 {
+        Ok(_) => assert!(false),
+        Err(_) => assert!(true),
+    };
+}
+
+#[test]
+#[should_panic]
+fn add_edge_to_ctmp() {
+    let mut net = CtmpProcess::new();
+    let _n1 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n1"), 2))
+        .unwrap();
+    let _n2 = net.add_node(generate_discrete_time_continous_node(String::from("n1"), 2));
+
+    net.add_edge(0, 1)
+}
+
+#[test]
+fn childen_and_parents() {
+    let mut net = CtmpProcess::new();
+    let _n1 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n1"), 2))
+        .unwrap();
+
+    assert_eq!(0, net.get_parent_set(0).len());
+    assert_eq!(0, net.get_children_set(0).len());
+}
+
+#[test]
+#[should_panic]
+fn get_childen_panic() {
+    let net = CtmpProcess::new();
+    net.get_children_set(0);
+}
+
+#[test]
+#[should_panic]
+fn get_childen_panic2() {
+    let mut net = CtmpProcess::new();
+    let _n1 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n1"), 2))
+        .unwrap();
+    net.get_children_set(1);
+}
+
+#[test]
+#[should_panic]
+fn get_parent_panic() {
+    let net = CtmpProcess::new();
+    net.get_parent_set(0);
+}
+
+#[test]
+#[should_panic]
+fn get_parent_panic2() {
+    let mut net = CtmpProcess::new();
+    let _n1 = net
+        .add_node(generate_discrete_time_continous_node(String::from("n1"), 2))
+        .unwrap();
+    net.get_parent_set(1);
+}
+
+#[test]
+fn compute_index_ctmp() {
+    let mut net = CtmpProcess::new();
+    let n1 = net
+        .add_node(generate_discrete_time_continous_node(
+            String::from("n1"),
+            10,
+        ))
+        .unwrap();
+
+    let idx = net.get_param_index_network(n1, &vec![params::StateType::Discrete(6)]);
+    assert_eq!(6, idx);
+}
+
+#[test]
+#[should_panic]
+fn compute_index_from_custom_parent_set_ctmp() {
+    let mut net = CtmpProcess::new();
+    let _n1 = net
+        .add_node(generate_discrete_time_continous_node(
+            String::from("n1"),
+            10,
+        ))
+        .unwrap();
+
+    let _idx = net.get_param_index_from_custom_parent_set(
+        &vec![params::StateType::Discrete(6)],
+        &BTreeSet::from([0])
+    );
+}

reCTBN/tests/parameter_learning.rs

@@ -2,8 +2,8 @@
 
 mod utils;
 use ndarray::arr3;
-use reCTBN::ctbn::*;
+use reCTBN::process::ctbn::*;
-use reCTBN::network::Network;
+use reCTBN::process::NetworkProcess;
 use reCTBN::parameter_learning::*;
 use reCTBN::params;
 use reCTBN::tools::*;

reCTBN/tests/structure_learning.rs

@@ -4,8 +4,8 @@ mod utils;
 use std::collections::BTreeSet;
 
 use ndarray::{arr1, arr2, arr3};
-use reCTBN::ctbn::*;
+use reCTBN::process::ctbn::*;
-use reCTBN::network::Network;
+use reCTBN::process::NetworkProcess;
 use reCTBN::parameter_learning::BayesianApproach;
 use reCTBN::parameter_learning::Cache;
 use reCTBN::params;

reCTBN/tests/tools.rs

@@ -1,6 +1,6 @@
 use ndarray::{arr1, arr2, arr3};
-use reCTBN::ctbn::*;
+use reCTBN::process::ctbn::*;
-use reCTBN::network::Network;
+use reCTBN::process::NetworkProcess;
 use reCTBN::params;
 use reCTBN::tools::*;