bdext 0.1.70__py3-none-any.whl → 0.1.71__py3-none-any.whl

bdeissct_dl/bdeissct_model.py

@@ -9,6 +9,7 @@ INFECTION_DURATION = 'd'
 
 MU = 'mu'
 INCUBATION_PERIOD = 'd_E'
+INCUBATION_FRACTION = 'f_E'
 
 F_S = 'f_S'
 X_S = 'X_S'
@@ -54,7 +55,7 @@ MODELS = (BD, BDCT, \
 
 
 TARGET_CT_COLUMNS = (UPSILON, X_C)
-TARGET_INCUBATION_COLUMNS = (INCUBATION_PERIOD,)
+TARGET_INCUBATION_COLUMNS = (INCUBATION_FRACTION,)
 TARGET_SS_COLUMNS = (F_S, X_S)
 TARGET_COLUMNS_BD = (REPRODUCTIVE_NUMBER, INFECTION_DURATION)
 TARGET_COLUMNS_BDCT = TARGET_COLUMNS_BD + TARGET_CT_COLUMNS

bdeissct_dl/dl_model.py

@@ -1,10 +1,10 @@
+from collections import defaultdict
+
 import tensorflow as tf
 from tensorflow.python.keras.utils.generic_utils import register_keras_serializable
 
 from bdeissct_dl.bdeissct_model import F_S, UPSILON, REPRODUCTIVE_NUMBER, \
-    INFECTION_DURATION, X_S, X_C, RHO, INCUBATION_PERIOD
-
-from collections import defaultdict
+    INFECTION_DURATION, X_S, X_C, INCUBATION_FRACTION
 
 LEARNING_RATE = 0.001
 
@@ -19,16 +19,6 @@ def relu_plus_one(x):
 
 
 LOSS_FUNCTIONS = defaultdict(lambda: "mean_squared_error")
-LOSS_FUNCTIONS.update({
-    REPRODUCTIVE_NUMBER: "mean_squared_error",
-    INFECTION_DURATION: "mean_squared_error",
-    INCUBATION_PERIOD: "mean_squared_error",
-    UPSILON: 'mean_squared_error',
-    RHO: 'mean_squared_error',
-    X_C: "mean_squared_error",
-    F_S: 'mean_squared_error',
-    X_S: "mean_squared_error",
-})
 
 
 def build_model(target_columns, n_x, optimizer=None, metrics=None):
@@ -59,8 +49,8 @@ def build_model(target_columns, n_x, optimizer=None, metrics=None):
         outputs[REPRODUCTIVE_NUMBER] = tf.keras.layers.Dense(1, activation="relu", name=REPRODUCTIVE_NUMBER)(x) # positive values only
     if INFECTION_DURATION in target_columns:
         outputs[INFECTION_DURATION] = tf.keras.layers.Dense(1, activation="relu", name=INFECTION_DURATION)(x) # positive values only
-    if INCUBATION_PERIOD in target_columns:
-        outputs[INCUBATION_PERIOD] = tf.keras.layers.Dense(1, activation="relu", name=INCUBATION_PERIOD)(x) # positive values only
+    if INCUBATION_FRACTION in target_columns:
+        outputs[INCUBATION_FRACTION] = tf.keras.layers.Dense(1, activation="sigmoid", name=INCUBATION_FRACTION)(x) # positive values only
     if F_S in target_columns:
         outputs[F_S] = tf.keras.layers.Dense(1, activation=half_sigmoid, name="FS_logits")(x)
     if X_S in target_columns:

bdeissct_dl/training.py

@@ -6,17 +6,17 @@ import pandas as pd
 import tensorflow as tf
 
 from bdeissct_dl import MODEL_PATH, BATCH_SIZE, EPOCHS
-from bdeissct_dl.bdeissct_model import MODEL2TARGET_COLUMNS, UPSILON, X_C, KAPPA, INCUBATION_PERIOD, F_S, \
+from bdeissct_dl.bdeissct_model import MODEL2TARGET_COLUMNS, UPSILON, X_C, KAPPA, INCUBATION_FRACTION, F_S, \
     X_S, TARGET_COLUMNS_BDCT, REPRODUCTIVE_NUMBER, INFECTION_DURATION
 from bdeissct_dl.dl_model import build_model
 from bdeissct_dl.model_serializer import save_model_keras, load_scaler_numpy, \
     load_model_keras
 from bdeissct_dl.tree_encoder import SCALING_FACTOR, STATS
 
-FEATURE_COLUMNS = [_ for _ in STATS if _ not in {'n_trees', 'n_tips', 'n_inodes', 'len_forest',
+FEATURE_COLUMNS = [_ for _ in STATS if _ not in {#'n_trees', 'n_tips', 'n_inodes', 'len_forest',
                                                  REPRODUCTIVE_NUMBER, INFECTION_DURATION,
                                                  UPSILON, X_C, KAPPA,
-                                                 INCUBATION_PERIOD,
+                                                 INCUBATION_FRACTION,
                                                  F_S, X_S,
                                                  SCALING_FACTOR}]
 
@@ -110,8 +110,8 @@ def get_train_data(target_columns, columns_x, columns_y, file_pattern=None, file
     if X_C in target_columns:
         train_labels[X_C] = Y[:, col_i]
         col_i += 1
-    if INCUBATION_PERIOD in target_columns:
-        train_labels[INCUBATION_PERIOD] = Y[:, col_i]
+    if INCUBATION_FRACTION in target_columns:
+        train_labels[INCUBATION_FRACTION] = Y[:, col_i]
         col_i += 1
     if F_S in target_columns:
         train_labels[F_S] = Y[:, col_i]

bdeissct_dl/tree_encoder.py

@@ -3,17 +3,19 @@ import os
 from glob import iglob
 
 import pandas as pd
+from treesimulator.mtbd_models import INCUBATION_FRACTION
 from treesumstats import FeatureCalculator, FeatureRegistry, FeatureManager
 from treesumstats.balance_sumstats import BalanceFeatureCalculator
 from treesumstats.basic_sumstats import BasicFeatureCalculator
 from treesumstats.branch_sumstats import BranchFeatureCalculator
 from treesumstats.event_time_sumstats import EventTimeFeatureCalculator
 from treesumstats.ltt_sumstats import LTTFeatureCalculator
+from treesumstats.resolution_sumstats import ResolutionFeatureCalculator
 from treesumstats.subtree_sumstats import SubtreeFeatureCalculator
 from treesumstats.transmission_chain_sumstats import TransmissionChainFeatureCalculator
 
 from bdeissct_dl.bdeissct_model import RHO, UPSILON, X_C, KAPPA, F_S, X_S, RATE_PARAMETERS, \
-    TIME_PARAMETERS, INFECTION_DURATION, REPRODUCTIVE_NUMBER, INCUBATION_PERIOD
+    TIME_PARAMETERS, INFECTION_DURATION, REPRODUCTIVE_NUMBER, INCUBATION_FRACTION, INCUBATION_PERIOD
 from bdeissct_dl.tree_manager import read_forest, rescale_forest_to_avg_brlen
 
 TARGET_AVG_BL = 1
@@ -88,7 +90,7 @@ class BDEISSCTFeatureCalculator(FeatureCalculator):
         pass
 
     def feature_names(self):
-        return [REPRODUCTIVE_NUMBER, INFECTION_DURATION, RHO, INCUBATION_PERIOD, F_S, X_S, UPSILON, X_C, KAPPA, \
+        return [REPRODUCTIVE_NUMBER, INFECTION_DURATION, RHO, INCUBATION_FRACTION, F_S, X_S, UPSILON, X_C, KAPPA, \
                 SCALING_FACTOR]
 
     def set_forest(self, forest, **kwargs):
@@ -116,8 +118,8 @@ class BDEISSCTFeatureCalculator(FeatureCalculator):
             return 'reproduction number.'
         if INFECTION_DURATION == feature_name:
             return 'infection duration.'
-        if INCUBATION_PERIOD == feature_name:
-            return 'incubation period.'
+        if INCUBATION_FRACTION == feature_name:
+            return 'incubation fraction.'
         return None
 
 
@@ -128,6 +130,7 @@ FeatureRegistry.register(TransmissionChainFeatureCalculator(CHAIN_LEN, percentil
 FeatureRegistry.register(LTTFeatureCalculator(N_LTT_COORDINATES))
 FeatureRegistry.register(BalanceFeatureCalculator())
 FeatureRegistry.register(SubtreeFeatureCalculator())
+FeatureRegistry.register(ResolutionFeatureCalculator())
 FeatureRegistry.register(BDEISSCTFeatureCalculator())
 
 BRLEN_STATS = ['brlen_inode_mean', 'brlen_inode_median', 'brlen_inode_var',
@@ -198,24 +201,29 @@ BALANCE_STATS = ['colless_normalized',
                  'frac_inodes_imbalanced', 'imbalance_avg']
 
 TOPOLOGY_STATS = ['frac_tips_in_2', 'frac_tips_in_3L', 'frac_tips_in_4L', 'frac_tips_in_4B', 'frac_tips_in_O',
+                  'frac_tips_in_3U', 'frac_tips_in_4U', 'frac_tips_in_4U3U1', 'frac_tips_in_4U211',
                   'frac_inodes_with_sibling_inodes']
 
-TIME_DIFF_STATS = ['time_diff_in_2_real_mean', 'time_diff_in_3L_real_mean', 'time_diff_in_I_real_mean',
-                   'time_diff_in_2_real_min', 'time_diff_in_3L_real_min', 'time_diff_in_I_real_min',
-                   'time_diff_in_2_real_max', 'time_diff_in_3L_real_max', 'time_diff_in_I_real_max',
-                   'time_diff_in_2_real_var', 'time_diff_in_3L_real_var', 'time_diff_in_I_real_var',
-                   'time_diff_in_2_real_median', 'time_diff_in_3L_real_median', 'time_diff_in_I_real_median',
+TIME_DIFF_STATS = ['time_diff_in_2_real_mean', 'time_diff_in_3L_real_mean', 'time_diff_in_3U_real_mean', 'time_diff_in_4U_real_mean', 'time_diff_in_I_real_mean',
+                   'time_diff_in_2_real_min', 'time_diff_in_3L_real_min', 'time_diff_in_3U_real_min', 'time_diff_in_4U_real_min', 'time_diff_in_I_real_min',
+                   'time_diff_in_2_real_max', 'time_diff_in_3L_real_max', 'time_diff_in_3U_real_max', 'time_diff_in_4U_real_max', 'time_diff_in_I_real_max',
+                   'time_diff_in_2_real_var', 'time_diff_in_3L_real_var', 'time_diff_in_3U_real_var', 'time_diff_in_4U_real_var', 'time_diff_in_I_real_var',
+                   'time_diff_in_2_real_median', 'time_diff_in_3L_real_median', 'time_diff_in_3U_real_median', 'time_diff_in_4U_real_median', 'time_diff_in_I_real_median',
                    #
-                   'time_diff_in_2_random_mean', 'time_diff_in_3L_random_mean', 'time_diff_in_I_random_mean',
-                   'time_diff_in_2_random_min', 'time_diff_in_3L_random_min', 'time_diff_in_I_random_min',
-                   'time_diff_in_2_random_max', 'time_diff_in_3L_random_max', 'time_diff_in_I_random_max',
-                   'time_diff_in_2_random_var', 'time_diff_in_3L_random_var', 'time_diff_in_I_random_var',
-                   'time_diff_in_2_random_median', 'time_diff_in_3L_random_median', 'time_diff_in_I_random_median',
+                   'time_diff_in_2_random_mean', 'time_diff_in_3L_random_mean', 'time_diff_in_3U_random_mean', 'time_diff_in_4U_random_mean', 'time_diff_in_I_random_mean',
+                   'time_diff_in_2_random_min', 'time_diff_in_3L_random_min', 'time_diff_in_3U_random_min', 'time_diff_in_4U_random_min', 'time_diff_in_I_random_min',
+                   'time_diff_in_2_random_max', 'time_diff_in_3L_random_max', 'time_diff_in_3U_random_max', 'time_diff_in_4U_random_max', 'time_diff_in_I_random_max',
+                   'time_diff_in_2_random_var', 'time_diff_in_3L_random_var', 'time_diff_in_3U_random_var', 'time_diff_in_4U_random_var', 'time_diff_in_I_random_var',
+                   'time_diff_in_2_random_median', 'time_diff_in_3L_random_median', 'time_diff_in_3U_random_median', 'time_diff_in_4U_random_median', 'time_diff_in_I_random_median',
                    #
                    'time_diff_in_2_real_perc1', 'time_diff_in_2_real_perc5', 'time_diff_in_2_real_perc10',
                    'time_diff_in_2_real_perc25',
                    'time_diff_in_3L_real_perc1', 'time_diff_in_3L_real_perc5', 'time_diff_in_3L_real_perc10',
                    'time_diff_in_3L_real_perc25',
+                   'time_diff_in_3U_real_perc1', 'time_diff_in_3U_real_perc5', 'time_diff_in_3U_real_perc10',
+                   'time_diff_in_3U_real_perc25',
+                   'time_diff_in_4U_real_perc1', 'time_diff_in_4U_real_perc5', 'time_diff_in_4U_real_perc10',
+                   'time_diff_in_4U_real_perc25',
                    'time_diff_in_I_real_perc75', 'time_diff_in_I_real_perc90', 'time_diff_in_I_real_perc95',
                    'time_diff_in_I_real_perc99',
                    #
@@ -223,22 +231,33 @@ TIME_DIFF_STATS = ['time_diff_in_2_real_mean', 'time_diff_in_3L_real_mean', 'tim
                    'time_diff_in_2_random_perc25',
                    'time_diff_in_3L_random_perc1', 'time_diff_in_3L_random_perc5', 'time_diff_in_3L_random_perc10',
                    'time_diff_in_3L_random_perc25',
+                   'time_diff_in_3U_random_perc1', 'time_diff_in_3U_random_perc5', 'time_diff_in_3U_random_perc10',
+                   'time_diff_in_3U_random_perc25',
+                   'time_diff_in_4U_random_perc1', 'time_diff_in_4U_random_perc5', 'time_diff_in_4U_random_perc10',
+                   'time_diff_in_4U_random_perc25',
                    'time_diff_in_I_random_perc75', 'time_diff_in_I_random_perc90', 'time_diff_in_I_random_perc95',
                    'time_diff_in_I_random_perc99',
                    #
                    'time_diff_in_2_random_vs_real_frac_less', 'time_diff_in_3L_random_vs_real_frac_less',
+                   'time_diff_in_3U_random_vs_real_frac_less', 'time_diff_in_4U_random_vs_real_frac_less',
                    'time_diff_in_I_random_vs_real_frac_more',
                    'time_diff_in_2_random_vs_real_pval_less', 'time_diff_in_3L_random_vs_real_pval_less',
+                   'time_diff_in_3U_random_vs_real_pval_less', 'time_diff_in_4U_random_vs_real_pval_less',
                    'time_diff_in_I_random_vs_real_pval_more']
 
+RESOLUTION_STATS = ['n_children_mean',
+                    'n_children_var',
+                    'frac_inodes_resolved',
+                    'frac_inodes_resolved_non_zero']
+
 EPI_STATS = [REPRODUCTIVE_NUMBER, INFECTION_DURATION, RHO,
              UPSILON, X_C, KAPPA,
-             INCUBATION_PERIOD,
+             INCUBATION_FRACTION,
              F_S, X_S]
 
-STATS = ['n_tips'] \
-        + BRLEN_STATS + TIME_STATS + CHAIN_STATS + LTT_STATS + BALANCE_STATS + TOPOLOGY_STATS + TIME_DIFF_STATS \
-        + EPI_STATS + [SCALING_FACTOR]
+STATS = ['n_tips', 'n_inodes'] \
+        + BRLEN_STATS + TIME_STATS + CHAIN_STATS + LTT_STATS + BALANCE_STATS + TOPOLOGY_STATS \
+        + TIME_DIFF_STATS + RESOLUTION_STATS + EPI_STATS + [SCALING_FACTOR]
 
 def forest2sumstat_df(forest, rho, R=0, d=0, x_c=0, upsilon=0, kappa=1, d_inc=0, f_ss=0, x_ss=1,
                       target_avg_brlen=TARGET_AVG_BL):
@@ -267,7 +286,7 @@ def forest2sumstat_df(forest, rho, R=0, d=0, x_c=0, upsilon=0, kappa=1, d_inc=0,
 
     kwargs = {SCALING_FACTOR: scaling_factor,
               REPRODUCTIVE_NUMBER: R, INFECTION_DURATION: d, RHO: rho,
-              INCUBATION_PERIOD: d_inc,
+              INCUBATION_FRACTION: d_inc / d,
               F_S: f_ss, X_S: x_ss,
               X_C: x_c, UPSILON: upsilon, KAPPA: kappa}
     scale(kwargs, scaling_factor)
@@ -322,7 +341,7 @@ def save_forests_as_sumstats(output, nwks=None, logs=None, patterns=None, target
                 kwargs = {SCALING_FACTOR: scaling_factor}
                 kwargs[REPRODUCTIVE_NUMBER], kwargs[INFECTION_DURATION], kwargs[RHO] = R, d, rho
                 kwargs[UPSILON], kwargs[KAPPA], kwargs[X_C] = upsilon, kappa, x_c
-                kwargs[INCUBATION_PERIOD] = d_inc
+                kwargs[INCUBATION_FRACTION] = d_inc / d
                 kwargs[F_S], kwargs[X_S] = f_ss, x_ss
 
                 scale(kwargs, scaling_factor)

{bdext-0.1.70.dist-info → bdext-0.1.71.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bdext
-Version: 0.1.70
+Version: 0.1.71
 Summary: Estimation of BDEISS-CT parameters from phylogenetic trees.
 Home-page: https://github.com/modpath/bdeissct
 Author: Anna Zhukova

bdext-0.1.71.dist-info/RECORD

@@ -0,0 +1,17 @@
+README.md,sha256=Ngj8bt0Yu3LUsvwblmMtUqqjvGyqxv6ku2_cYCb5_DQ,6539
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+bdext-0.1.71.dist-info/RECORD,,

bdext-0.1.70.dist-info/RECORD

@@ -1,17 +0,0 @@
-README.md,sha256=Ngj8bt0Yu3LUsvwblmMtUqqjvGyqxv6ku2_cYCb5_DQ,6539
-bdeissct_dl/__init__.py,sha256=QPEiIP-xVqGQgydeqN_9AZgT26IYWeJC4-JlHnd8Rjo,296
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-bdeissct_dl/estimator.py,sha256=QBWA8R0pBPZPd3JvItdJS2lN1J3VqvdJqBMzCi-NADs,3336
-bdeissct_dl/model_serializer.py,sha256=s1yBzQjhtr-w7eT8bTsNkG9_xnYRZrUc3HkeOzNZpQY,2464
-bdeissct_dl/scaler_fitting.py,sha256=9X0O7-Wc9xGTI-iF-Pfp1PPoW7j01wZUfJVZf8ky-IU,1752
-bdeissct_dl/sumstat_checker.py,sha256=TQ0nb86-BXmusqgMnOJusLpR4ul3N3Hi886IWUovrMI,1846
-bdeissct_dl/training.py,sha256=H5wA3V72nhc9Km7kvKmzjCYw0N1itMGDbj9c-Uat5BU,8350
-bdeissct_dl/tree_encoder.py,sha256=V-7_Kis9x9JacI_mF7rWRGGKvxn7AWFCto7LkgRawBw,18286
-bdeissct_dl/tree_manager.py,sha256=UXxUVmEkxwUhKpJeACVgiXZ8Kp1o_hiv8Qb80b6qmVU,11814
-bdext-0.1.70.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-bdext-0.1.70.dist-info/METADATA,sha256=USWAUX3zunofN9x2-6E63lFVrNAdRx2cZf2Sc8HKGe8,7479
-bdext-0.1.70.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
-bdext-0.1.70.dist-info/entry_points.txt,sha256=lcAwyk-Fc0G_w4Ex7KDivh7h1tzSA99PRMcy971b-nM,208
-bdext-0.1.70.dist-info/top_level.txt,sha256=z4dadFfcLghr4lwROy7QR3zEICpa-eCPT6mmcoHeEJY,12
-bdext-0.1.70.dist-info/RECORD,,