Seedable

.github/ISSUE_TEMPLATE/meta_request.md

@@ -0,0 +1,26 @@
+---
+name: 📑 Meta request
+about: Suggest an idea or a change for this same repository
+title: '[Meta] '
+labels: 'meta'
+assignees: ''
+
+---
+
+## Description
+
+As a X, I want to Y, so Z.
+
+## Acceptance Criteria
+
+* Criteria 1
+* Criteria 2
+
+## Checklist
+
+* [ ] Element 1
+* [ ] Element 2
+
+## (Optional) Extra info
+
+None

.github/ISSUE_TEMPLATE/refactor_request.md

@@ -0,0 +1,26 @@
+---
+name: ⚙️ Refactor request
+about: Suggest a refactor for this project
+title: '[Refactor] '
+labels: 'enhancement'
+assignees: ''
+
+---
+
+## Description
+
+As a X, I want to Y, so Z.
+
+## Acceptance Criteria
+
+* Criteria 1
+* Criteria 2
+
+## Checklist
+
+* [ ] Element 1
+* [ ] Element 2
+
+## (Optional) Extra info
+
+None

.gitignore

@@ -1,2 +1,3 @@
 /target
 Cargo.lock
+.vscode

Cargo.toml

@@ -13,6 +13,7 @@ rand = "*"
 bimap = "*"
 enum_dispatch = "*"
 statrs = "*"
+rand_chacha = "*"
 
 [dev-dependencies]
 approx = "*"

src/parameter_learning.rs

@@ -114,8 +114,8 @@ impl ParameterLearning for MLE {
 }
 
 pub struct BayesianApproach {
-    pub default_alpha: usize,
+    pub alpha: usize,
-    pub default_tau: f64
+    pub tau: f64
 }
 
 impl ParameterLearning for BayesianApproach {
@@ -135,13 +135,15 @@ impl ParameterLearning for BayesianApproach {
         };
         
         let (mut M, mut T) = sufficient_statistics(net, dataset, node.clone(), &parent_set);
-        M.mapv_inplace(|x|{x + self.default_alpha});
+
-        T.mapv_inplace(|x|{x + self.default_tau});
+        let alpha: f64 = self.alpha as f64 / M.shape()[0] as f64;
+        let tau: f64 = self.tau as f64 / M.shape()[0] as f64;
+
         //Compute the CIM as M[i,x,y]/T[i,x]  
         let mut CIM: Array3<f64> = Array::zeros((M.shape()[0], M.shape()[1], M.shape()[2]));
         CIM.axis_iter_mut(Axis(2))
             .zip(M.mapv(|x| x as f64).axis_iter(Axis(2)))
-            .for_each(|(mut C, m)| C.assign(&(&m/&T)));
+            .for_each(|(mut C, m)| C.assign(&(&m.mapv(|y| y + alpha)/&T.mapv(|y| y + tau))));
 
         //Set the diagonal of the inner matrices to the the row sum multiplied by -1
         let tmp_diag_sum: Array2<f64> = CIM.sum_axis(Axis(2)).mapv(|x| x * -1.0);

src/params.rs

@@ -3,6 +3,7 @@ use ndarray::prelude::*;
 use rand::Rng;
 use std::collections::{BTreeSet, HashMap};
 use thiserror::Error;
+use rand_chacha::ChaCha8Rng;
 
 /// Error types for trait Params
 #[derive(Error, Debug, PartialEq)]
@@ -30,15 +31,15 @@ pub trait ParamsTrait {
 
     /// Randomly generate a possible state of the node disregarding the state of the node and it's
     /// parents.
-    fn get_random_state_uniform(&self) -> StateType;
+    fn get_random_state_uniform(&self, rng: &mut ChaCha8Rng) -> StateType;
 
     /// Randomly generate a residence time for the given node taking into account the node state
     /// and its parent set.
-    fn get_random_residence_time(&self, state: usize, u: usize) -> Result<f64, ParamsError>;
+    fn get_random_residence_time(&self, state: usize, u: usize, rng: &mut ChaCha8Rng) -> Result<f64, ParamsError>;
 
     /// Randomly generate a possible state for the given node taking into account the node state
     /// and its parent set.
-    fn get_random_state(&self, state: usize, u: usize) -> Result<StateType, ParamsError>;
+    fn get_random_state(&self, state: usize, u: usize, rng: &mut ChaCha8Rng) -> Result<StateType, ParamsError>;
 
     /// Used by childern of the node described by this parameters to reserve spaces in their CIMs.
     fn get_reserved_space_as_parent(&self) -> usize;
@@ -137,18 +138,16 @@ impl ParamsTrait for DiscreteStatesContinousTimeParams {
         self.residence_time = Option::None;
     }
 
-    fn get_random_state_uniform(&self) -> StateType {
+    fn get_random_state_uniform(&self, rng: &mut ChaCha8Rng) -> StateType {
-        let mut rng = rand::thread_rng();
         StateType::Discrete(rng.gen_range(0..(self.domain.len())))
     }
 
-    fn get_random_residence_time(&self, state: usize, u: usize) -> Result<f64, ParamsError> {
+    fn get_random_residence_time(&self, state: usize, u: usize, rng: &mut ChaCha8Rng) -> Result<f64, ParamsError> {
         // Generate a random residence time given the current state of the node and its parent set.
         // The method used is described in:
         // https://en.wikipedia.org/wiki/Exponential_distribution#Generating_exponential_variates
         match &self.cim {
             Option::Some(cim) => {
-                let mut rng = rand::thread_rng();
                 let lambda = cim[[u, state, state]] * -1.0;
                 let x: f64 = rng.gen_range(0.0..=1.0);
                 Ok(-x.ln() / lambda)
@@ -159,13 +158,12 @@ impl ParamsTrait for DiscreteStatesContinousTimeParams {
         }
     }
 
-    fn get_random_state(&self, state: usize, u: usize) -> Result<StateType, ParamsError> {
+    fn get_random_state(&self, state: usize, u: usize, rng: &mut ChaCha8Rng) -> Result<StateType, ParamsError> {
         // Generate a random transition given the current state of the node and its parent set.
         // The method used is described in:
         // https://en.wikipedia.org/wiki/Multinomial_distribution#Sampling_from_a_multinomial_distribution
         match &self.cim {
             Option::Some(cim) => {
-                let mut rng = rand::thread_rng();
                 let lambda = cim[[u, state, state]] * -1.0;
                 let urand: f64 = rng.gen_range(0.0..=1.0);
 

src/tools.rs

@@ -3,6 +3,8 @@ use crate::node;
 use crate::params;
 use crate::params::ParamsTrait;
 use ndarray::prelude::*;
+use rand_chacha::ChaCha8Rng;
+use rand_chacha::rand_core::SeedableRng;
 
 pub struct Trajectory {
     pub time: Array1<f64>,
@@ -17,11 +19,16 @@ pub fn trajectory_generator<T: network::Network>(
     net: &T,
     n_trajectories: u64,
     t_end: f64,
+    seed: Option<u64>,
 ) -> Dataset {
     let mut dataset = Dataset {
         trajectories: Vec::new(),
     };
 
+    let seed = seed.unwrap_or_else(rand::random);
+
+    let mut rng = ChaCha8Rng::seed_from_u64(seed);
+
     let node_idx: Vec<_> = net.get_node_indices().collect();
     for _ in 0..n_trajectories {
         let mut t = 0.0;
@@ -29,7 +36,7 @@ pub fn trajectory_generator<T: network::Network>(
         let mut events: Vec<Array1<usize>> = Vec::new();
         let mut current_state: Vec<params::StateType> = node_idx
             .iter()
-            .map(|x| net.get_node(*x).params.get_random_state_uniform())
+            .map(|x| net.get_node(*x).params.get_random_state_uniform(&mut rng))
             .collect();
         let mut next_transitions: Vec<Option<f64>> =
             (0..node_idx.len()).map(|_| Option::None).collect();
@@ -51,6 +58,7 @@ pub fn trajectory_generator<T: network::Network>(
                             .get_random_residence_time(
                                 net.get_node(idx).params.state_to_index(&current_state[idx]),
                                 net.get_param_index_network(idx, &current_state),
+                                &mut rng,
                             )
                             .unwrap()
                             + t,
@@ -78,6 +86,7 @@ pub fn trajectory_generator<T: network::Network>(
                         .params
                         .state_to_index(&current_state[next_node_transition]),
                     net.get_param_index_network(next_node_transition, &current_state),
+                    &mut rng,
                 )
                 .unwrap();
 

tests/parameter_learning.rs

@@ -40,14 +40,14 @@ fn learn_binary_cim<T: ParameterLearning> (pl: T) {
         }
     }
 
-    let data = trajectory_generator(&net, 100, 100.0);
+    let data = trajectory_generator(&net, 100, 100.0, Some(6347747169756259),);
     let (CIM, M, T) = pl.fit(&net, &data, 1, None);
     print!("CIM: {:?}\nM: {:?}\nT: {:?}\n", CIM, M, T);
     assert_eq!(CIM.shape(), [2, 2, 2]);
     assert!(CIM.abs_diff_eq(&arr3(&[
                 [[-1.0, 1.0], [4.0, -4.0]],
                 [[-6.0, 6.0], [2.0, -2.0]],
-            ]), 0.2));
+            ]), 0.1));
 }
 
 #[test]
@@ -60,8 +60,8 @@ fn learn_binary_cim_MLE() {
 #[test]
 fn learn_binary_cim_BA() {
     let ba = BayesianApproach{
-        default_alpha: 1,
+        alpha: 1,
-        default_tau: 1.0};
+        tau: 1.0};
     learn_binary_cim(ba);
 }
 
@@ -93,7 +93,7 @@ fn learn_ternary_cim<T: ParameterLearning> (pl: T) {
         }
     }
 
-    let data = trajectory_generator(&net, 100, 200.0);
+    let data = trajectory_generator(&net, 100, 200.0, Some(6347747169756259),);
     let (CIM, M, T) = pl.fit(&net, &data, 1, None);
     print!("CIM: {:?}\nM: {:?}\nT: {:?}\n", CIM, M, T);
     assert_eq!(CIM.shape(), [3, 3, 3]);
@@ -101,7 +101,7 @@ fn learn_ternary_cim<T: ParameterLearning> (pl: T) {
                 [[-1.0, 0.5, 0.5], [3.0, -4.0, 1.0], [0.9, 0.1, -1.0]],
                 [[-6.0, 2.0, 4.0], [1.5, -2.0, 0.5], [3.0, 1.0, -4.0]],
                 [[-1.0, 0.1, 0.9], [2.0, -2.5, 0.5], [0.9, 0.1, -1.0]],
-            ]), 0.2));
+            ]), 0.1));
 }
 
 
@@ -115,8 +115,8 @@ fn learn_ternary_cim_MLE() {
 #[test]
 fn learn_ternary_cim_BA() {
     let ba = BayesianApproach{
-        default_alpha: 1,
+        alpha: 1,
-        default_tau: 1.0};
+        tau: 1.0};
     learn_ternary_cim(ba);
 }
 
@@ -148,13 +148,13 @@ fn learn_ternary_cim_no_parents<T: ParameterLearning> (pl: T) {
         }
     }
 
-    let data = trajectory_generator(&net, 100, 200.0);
+    let data = trajectory_generator(&net, 100, 200.0, Some(6347747169756259),);
     let (CIM, M, T) = pl.fit(&net, &data, 0, None);
     print!("CIM: {:?}\nM: {:?}\nT: {:?}\n", CIM, M, T);
     assert_eq!(CIM.shape(), [1, 3, 3]);
     assert!(CIM.abs_diff_eq(&arr3(&[[[-3.0, 2.0, 1.0], 
                                   [1.5, -2.0, 0.5],
-                                  [0.4, 0.6, -1.0]]]), 0.2));
+                                  [0.4, 0.6, -1.0]]]), 0.1));
 }
 
 
@@ -168,8 +168,8 @@ fn learn_ternary_cim_no_parents_MLE() {
 #[test]
 fn learn_ternary_cim_no_parents_BA() {
     let ba = BayesianApproach{
-        default_alpha: 1,
+        alpha: 1,
-        default_tau: 1.0};
+        tau: 1.0};
     learn_ternary_cim_no_parents(ba);
 }
 
@@ -228,7 +228,7 @@ fn learn_mixed_discrete_cim<T: ParameterLearning> (pl: T) {
     }
 
 
-    let data = trajectory_generator(&net, 300, 300.0);
+    let data = trajectory_generator(&net, 300, 300.0, Some(6347747169756259),);
     let (CIM, M, T) = pl.fit(&net, &data, 2, None);
     print!("CIM: {:?}\nM: {:?}\nT: {:?}\n", CIM, M, T);
     assert_eq!(CIM.shape(), [9, 4, 4]);
@@ -244,7 +244,7 @@ fn learn_mixed_discrete_cim<T: ParameterLearning> (pl: T) {
                 [[-2.0, 1.0, 0.6, 0.4], [2.6, -7.1, 1.4, 3.1], [5.0, 1.0, -8.0, 2.0], [1.4, 0.4, 0.2, -2.0]],
                 [[-3.0, 1.0, 1.5, 0.5], [3.0, -6.0, 1.0, 2.0], [0.3, 0.5, -1.9, 1.1], [5.0, 1.0, 2.0, -8.0]],
                 [[-2.6, 0.6, 0.2, 1.8], [2.0, -6.0, 3.0, 1.0], [0.1, 0.5, -1.3, 0.7], [0.8, 0.6, 0.2, -1.6]],
-            ]), 0.2));
+            ]), 0.1));
 }
 
 #[test]
@@ -257,7 +257,7 @@ fn learn_mixed_discrete_cim_MLE() {
 #[test]
 fn learn_mixed_discrete_cim_BA() {
     let ba = BayesianApproach{
-        default_alpha: 1,
+        alpha: 1,
-        default_tau: 1.0};
+        tau: 1.0};
     learn_mixed_discrete_cim(ba);
 }

tests/params.rs

@@ -1,6 +1,8 @@
 use ndarray::prelude::*;
 use rustyCTBN::params::*;
 use std::collections::BTreeSet;
+use rand_chacha::ChaCha8Rng;
+use rand_chacha::rand_core::SeedableRng;
 
 mod utils;
 
@@ -21,8 +23,10 @@ fn test_uniform_generation() {
     let param = create_ternary_discrete_time_continous_param();
     let mut states = Array1::<usize>::zeros(10000);
 
+    let mut rng = ChaCha8Rng::seed_from_u64(6347747169756259);
+
     states.mapv_inplace(|_| {
-        if let StateType::Discrete(val) = param.get_random_state_uniform() {
+        if let StateType::Discrete(val) = param.get_random_state_uniform(&mut rng) {
             val
         } else {
             panic!()
@@ -38,8 +42,10 @@ fn test_random_generation_state() {
     let param = create_ternary_discrete_time_continous_param();
     let mut states = Array1::<usize>::zeros(10000);
 
+    let mut rng = ChaCha8Rng::seed_from_u64(6347747169756259);
+
     states.mapv_inplace(|_| {
-        if let StateType::Discrete(val) = param.get_random_state(1, 0).unwrap() {
+        if let StateType::Discrete(val) = param.get_random_state(1, 0, &mut rng).unwrap() {
             val
         } else {
             panic!()
@@ -57,7 +63,9 @@ fn test_random_generation_residence_time() {
     let param = create_ternary_discrete_time_continous_param();
     let mut states = Array1::<f64>::zeros(10000);
 
-    states.mapv_inplace(|_| param.get_random_residence_time(1, 0).unwrap());
+    let mut rng = ChaCha8Rng::seed_from_u64(6347747169756259);
+
+    states.mapv_inplace(|_| param.get_random_residence_time(1, 0, &mut rng).unwrap());
 
     assert_relative_eq!(1.0 / 5.0, states.mean().unwrap(), epsilon = 0.01);
 }

tests/tools.rs

@@ -36,7 +36,7 @@ fn run_sampling() {
         }
     }
 
-    let data = trajectory_generator(&net, 4, 1.0);
+    let data = trajectory_generator(&net, 4, 1.0, Some(6347747169756259),);
 
     assert_eq!(4, data.trajectories.len());
     assert_relative_eq!(1.0, data.trajectories[0].time[data.trajectories[0].time.len()-1]);