Merge pull request #23 from ECRL/dev

Bug fixes, GA improvements, data sorting options, optimizations

README.md

@@ -12,7 +12,7 @@
 [T. Sennott et al.](https://doi.org/10.1115/ICEF2013-19185) have shown that neural networks can be applied to cetane number prediction with relatively little error. ECNet provides scientists an open source tool for predicting key fuel properties of potential next-generation biofuels, reducing the need for costly fuel synthesis and experimentation.
 
 <p align="center">
-  <img align="center" src="docs/workflow_diagram.png" width="50%" height="50%">
+  <img align="center" src="docs/img/workflow_diagram.png" width="50%" height="50%">
 </p>
 
 Using ECNet, [T. Kessler et al.](https://doi.org/10.1016/j.fuel.2017.06.015) have increased the generalizability of neural networks to predict the cetane number for a variety of molecular classes represented in our [cetane number database](https://github.com/TJKessler/ECNet/tree/master/databases), and have increased the accuracy of neural networks for predicting the cetane number of underrepresented molecular classes through targeted database expansion.

docs/tutorials/Getting Started/scripts/limit_input_descriptors.py

@@ -0,0 +1,25 @@
+from ecnet import Server
+
+
+def main():
+
+    sv = Server(log_level='debug', num_processes=4)
+    sv.import_data(
+        '../kv_model_v1.0_full.csv',
+        sort_type='random',
+        data_split=[0.6, 0.2, 0.2]
+    )
+    sv.limit_input_parameters(
+        limit_num=15,
+        output_filename='../kv_model_v1.0.csv',
+        use_genetic=True,
+        population_size=30,
+        num_generations=10,
+        mut_rate=0.2,
+        max_mut_amt=1
+    )
+
+
+if __name__ == '__main__':
+
+    main()

docs/tutorials/Getting Started/scripts/train_select_candidates.py

@@ -0,0 +1,29 @@
+from ecnet import Server
+
+
+def main():
+
+    sv = Server(log_level='debug', num_processes=4)
+    sv.import_data(
+        '../kv_model_v1.0.csv',
+        sort_type='random',
+        data_split=[0.6, 0.2, 0.2]
+    )
+    sv.create_project(
+        'kinetic_viscosity',
+        num_builds=1,
+        num_nodes=5,
+        num_candidates=25
+    )
+    sv.train_model(
+        validate=True,
+        shuffle='train',
+        data_split=[0.6, 0.2, 0.2]
+    )
+    sv.select_best(dset='test')
+    sv.save_project(clean_up=True)
+
+
+if __name__ == '__main__':
+
+    main()

docs/tutorials/Getting Started/scripts/tune_hyperparameters.py

@@ -0,0 +1,20 @@
+from ecnet import Server
+
+
+def main():
+
+    sv = Server(log_level='debug', num_processes=4)
+    sv.import_data(
+        '../kv_model_v1.0.csv',
+        sort_type='random',
+        data_split=[0.6, 0.2, 0.2]
+    )
+    sv.tune_hyperparameters(
+        num_employers=30,
+        num_iterations=10
+    )
+
+
+if __name__ == '__main__':
+
+    main()

docs/tutorials/Getting Started/scripts/use_project.py

@@ -0,0 +1,25 @@
+from ecnet import Server
+
+
+def main():
+
+    sv = Server(
+        project_file='kinetic_viscosity.prj',
+        log_level='debug'
+    )
+    sv.use_model(
+        dset='test',
+        output_filename='../kv_test_results.csv'
+    )
+    sv.calc_error(
+        'rmse',
+        'mean_abs_error',
+        'med_abs_error',
+        'r2',
+        dset='test'
+    )
+
+
+if __name__ == '__main__':
+
+    main()

ecnet/__init__.py

@@ -3,4 +3,4 @@
 import ecnet.error_utils
 import ecnet.model
 import ecnet.limit_parameters
-__version__ = '2.1.0'
+__version__ = '2.1.1'

ecnet/data_utils.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 #
 # ecnet/data_utils.py
-# v.2.1.0
+# v.2.1.1
 # Developed in 2019 by Travis Kessler <travis.j.kessler@gmail.com>
 #
 # Contains the "DataFrame" class, and functions for processing/importing/

ecnet/error_utils.py

@@ -2,47 +2,30 @@
 # -*- coding: utf-8 -*-
 #
 # ecnet/error_utils.py
-# v.2.1.0
+# v.2.1.1
 # Developed in 2019 by Travis Kessler <Travis_Kessler@student.uml.edu>
 #
 # Contains functions for error calculations
 #
 
 # 3rd party imports
-from numpy import absolute, asarray, median, sqrt as nsqrt, sum as nsum
+from numpy import absolute, asarray, float64, isinf, isnan, median,\
+    nan_to_num, square, sqrt as nsqrt, sum as nsum
 
 
 def calc_rmse(y_hat, y):
 
-    try:
-        return(nsqrt(((y_hat-y)**2).mean()))
-    except:
-        try:
-            return(nsqrt(((asarray(y_hat)-asarray(y))**2).mean()))
-        except:
-            raise ValueError('Check input data format.')
+    return nsqrt((square(_get_diff(y_hat, y)).mean()))
 
 
 def calc_mean_abs_error(y_hat, y):
 
-    try:
-        return(abs(y_hat-y).mean())
-    except:
-        try:
-            return(abs(asarray(y_hat)-asarray(y)).mean())
-        except:
-            raise ValueError('Check input data format.')
+    return absolute(_get_diff(y_hat, y)).mean()
 
 
 def calc_med_abs_error(y_hat, y):
 
-    try:
-        return(median(absolute(y_hat-y)))
-    except:
-        try:
-            return(median(absolute(asarray(y_hat)-asarray(y))))
-        except:
-            raise ValueError('Check input data format.')
+    return median(absolute(_get_diff(y_hat, y)))
 
 
 def calc_r2(y_hat, y):
@@ -57,14 +40,12 @@ def calc_r2(y_hat, y):
             y_mean = sum(y_form)/len(y_form)
         except:
             raise ValueError('Check input data format.')
-    try:
-        s_res = nsum((y_hat-y)**2)
-        s_tot = nsum((y-y_mean)**2)
-        return(1 - (s_res/s_tot))
-    except:
-        try:
-            s_res = nsum((asarray(y_hat)-asarray(y))**2)
-            s_tot = nsum((asarray(y)-y_mean)**2)
-            return(1 - (s_res/s_tot))
-        except:
-            raise ValueError('Check input data format.')
+
+    s_res = nsum(square(_get_diff(y_hat, y)))
+    s_tot = nsum(square(_get_diff(y, y_mean)))
+    return(1 - (s_res / s_tot))
+
+
+def _get_diff(y_hat, y):
+
+    return asarray(y_hat, dtype=float64) - asarray(y, dtype=float64)

ecnet/fitness_functions.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 #
 # ecnet/fitness_functions.py
-# v.2.1.0
+# v.2.1.1
 # Developed in 2019 by Travis Kessler <travis.j.kessler@gmail.com>
 #
 # Contains fitness functions used for input dimensionality reduction,

ecnet/limit_parameters.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 #
 # ecnet/limit_parameters.py
-# v.2.1.0
+# v.2.1.1
 # Developed in 2019 by Travis Kessler <travis.j.kessler@gmail.com>
 #
 # Contains the functions necessary for reducing the input dimensionality of a
@@ -158,7 +158,7 @@ def limit_iterative_include(DataFrame, limit_num, vars, logger=None):
 
 def limit_genetic(DataFrame, limit_num, vars, population_size, num_generations,
                   num_processes, shuffle=False, data_split=[0.65, 0.25, 0.1],
-                  logger=None):
+                  mut_rate=0, max_mut_amt=0, logger=None):
     '''Limits the dimensionality of input data using a genetic algorithm
 
     Args:
@@ -171,6 +171,10 @@ def limit_genetic(DataFrame, limit_num, vars, population_size, num_generations,
         shuffle (bool): whether to shuffle the data sets for each population
             member
         data_split (list): [learn%, valid%, test%] if shuffle == True
+        mut_rate (float): probability that a population member is subject
+            to mutation
+        max_mut_amt (float): if mutating, how much a parameter can mutate
+            (proportionally)
         logger (ColorLogger): ColorLogger object; if not supplied, does not log
 
     Returns:
@@ -206,38 +210,47 @@ def limit_genetic(DataFrame, limit_num, vars, population_size, num_generations,
 
     population.generate_population()
     if logger is not None:
-        logger.log('debug', 'Generation: 0 - Population fitness: {}'.format(
-            sum(p.fitness_score for p in population.members) / len(population),
+        logger.log(
+            'debug',
+            'Generation: 0 - Population fitness: {:.5f}'.format(
+                float(population.med_cost_fn_val)
+            ), call_loc='LIMIT'
+        )
+        logger.log('debug', '\tBest fitness: {}'.format(
+            population.best_cost_fn_val
+        ), call_loc='LIMIT')
+        logger.log('debug', '\tBest parameters: {}'.format(
+            [DataFrame.input_names[val] for val in
+             population.best_parameters.values()]
         ), call_loc='LIMIT')
 
     for gen in range(num_generations):
-        population.next_generation()
+        population.next_generation(mut_rate, max_mut_amt)
         if logger is not None:
             logger.log(
                 'debug',
-                'Generation: {} - Population fitness: {}'.format(
+                'Generation: {} - Population fitness: {:.5f}'.format(
                     gen + 1,
-                    sum(
-                        p.fitness_score for p in population.members
-                    ) / len(population)
+                    float(population.med_cost_fn_val)
                 ),
                 call_loc='LIMIT'
             )
+            logger.log('debug', '\tBest fitness: {}'.format(
+                population.best_cost_fn_val
+            ), call_loc='LIMIT')
+            logger.log('debug', '\tBest parameters: {}'.format(
+                [DataFrame.input_names[val] for val in
+                 population.best_parameters.values()]
+            ), call_loc='LIMIT')
 
-    min_idx = 0
-    for new_idx, member in enumerate(population.members):
-        if member.fitness_score < population.members[min_idx].fitness_score:
-            min_idx = new_idx
-
-    input_list = []
-    for val in population.members[min_idx].parameters.values():
-        input_list.append(DataFrame.input_names[val])
+    input_list = [DataFrame.input_names[val] for val in
+                  population.best_parameters.values()]
 
     if logger is not None:
         logger.log(
             'debug',
             'Best member fitness score: {}'.format(
-                population.members[min_idx].fitness_score
+                population.best_cost_fn_val
             ),
             call_loc='LIMIT'
         )

ecnet/model.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 #
 # ecnet/error_utils.py
-# v.2.1.0
+# v.2.1.1
 # Developed in 2019 by Travis Kessler <travis.j.kessler@gmail.com>
 #
 # Contains functions necessary creating, training, saving, and reusing neural
@@ -17,14 +17,19 @@
 from random import uniform
 from multiprocessing import current_process
 from copy import deepcopy
+from warnings import filterwarnings
 
 # 3rd party imports
 from tensorflow import add, global_variables_initializer, matmul, nn
 from tensorflow import placeholder, random_normal, reset_default_graph
 from tensorflow import Session, square, train, Variable
-from numpy import asarray, sqrt as nsqrt
+from numpy import asarray, isinf, isnan, nan_to_num, seterr, sqrt as nsqrt
+
+# ECNet imports
+from ecnet.error_utils import calc_rmse
 
 environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
+# filterwarnings('ignore', category=RuntimeWarning)
 
 
 def __linear_fn(n):
@@ -214,9 +219,10 @@ def fit_validation(self, x_l, y_l, x_v, y_v, learning_rate=0.1,
                 sess.run(optimizer, feed_dict={x: x_l, y: y_l})
                 current_epoch += 1
                 if current_epoch % 250 == 0:
-                    valid_rmse = self.__calc_rmse(
-                        sess.run(pred, feed_dict={x: x_v}), y_v
-                    )
+                    valid_preds = sess.run(pred, feed_dict={x: x_v})
+                    if isnan(valid_preds).any() or isinf(valid_preds).any():
+                        valid_preds = nan_to_num(valid_preds)
+                    valid_rmse = calc_rmse(valid_preds, y_v)
                     if valid_rmse < valid_rmse_lowest:
                         valid_rmse_lowest = valid_rmse
                     elif valid_rmse > valid_rmse_lowest + (
@@ -243,6 +249,8 @@ def use(self, x):
             saver.restore(sess, self._filename)
             results = self.__feed_forward(x).eval()
         sess.close()
+        if isnan(results).any() or isinf(results).any():
+            results = nan_to_num(results)
         return results
 
     def save(self, filepath=None):
@@ -328,9 +336,13 @@ def __calc_rmse(self, y_hat, y):
         '''
 
         try:
-            return(nsqrt(((y_hat - y)**2).mean()))
+            diff = (y_hat - y)
         except:
-            return(nsqrt(((asarray(y_hat) - asarray(y))**2).mean()))
+            diff = (asarray(y_hat) - asarray(y))
+        for i, d in enumerate(diff):
+            if isnan(d):
+                diff[i] = nan_to_num(d)
+        return(nsqrt((diff**2).mean()))
 
 
 def train_model(validate, sets, vars, save_path=None, id=None):