From dc1fff23fccdd62860fe2fd93ec799ad24f16d85 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mario=20Sa=CC=88nger?= <mario.saenger@student.hu-berlin.de>
Date: Sat, 5 May 2018 21:09:56 +0200
Subject: [PATCH] Move common code to abstract class
---
code_mario/clef18_task1_base.py | 358 +++++++++++++++++++++++++++++++
code_mario/clef18_task1_emb1.py | 367 +++-----------------------------
code_mario/clef18_task1_emb2.py | 311 +--------------------------
3 files changed, 397 insertions(+), 639 deletions(-)
create mode 100644 code_mario/clef18_task1_base.py
diff --git a/code_mario/clef18_task1_base.py b/code_mario/clef18_task1_base.py
new file mode 100644
index 0000000..a16c72a
--- /dev/null
+++ b/code_mario/clef18_task1_base.py
@@ -0,0 +1,358 @@
+import os
+import pandas as pd
+import keras as k
+import pickle
+
+from numpy.core.records import ndarray
+
+from pandas import DataFrame
+from argparse import Namespace
+from typing import Callable, List, Tuple
+
+from sklearn.dummy import DummyClassifier
+from sklearn.ensemble import RandomForestClassifier
+from sklearn.linear_model import SGDClassifier
+from sklearn.neighbors import KNeighborsClassifier
+from sklearn.preprocessing import LabelEncoder
+from sklearn.metrics import f1_score, accuracy_score
+from sklearn.svm import LinearSVC
+from sklearn.tree import DecisionTreeClassifier
+from sklearn.externals import joblib
+from sklearn.model_selection import train_test_split
+
+from app_context import AppContext
+from util import LoggingMixin
+from dnn_classifiers import NeuralNetworkClassifiers as nnc
+from keras_extension import KerasUtil as ku
+
+
+class ICD10LabelEncoders(object):
+
+ def __init__(self, chapter_encoder: LabelEncoder, section_encoder: LabelEncoder,
+ subsection_encoder: LabelEncoder, code_encoder: LabelEncoder):
+ self.chapter_encoder = chapter_encoder
+ self.section_encoder = section_encoder
+ self.subsection_encoder = subsection_encoder
+ self.code_encoder = code_encoder
+
+
+class EvaluationConfiguration(object):
+
+ def __init__(self, target_labels: List[str], label_encoders: ICD10LabelEncoders, input_dim: int,
+ train_data: ndarray, train_df: ndarray, val_data: ndarray, val_df: ndarray,
+ test_data: ndarray, test_df: ndarray):
+ self.target_labels = target_labels
+ self.label_encoders = label_encoders
+ self.input_dim = input_dim
+ self.train_data = train_data
+ self.train_df = train_df
+ self.val_data = val_data
+ self.val_df = val_df
+ self.test_data = test_data
+ self.test_df = test_df
+
+
+class EvaluationResult(object):
+
+ def __init__(self, target_label: str, classifier_name: str, data_set_name: str, accuracy: float):
+ self.target_label = target_label
+ self.classifier_name = classifier_name
+ self.data_set_name = data_set_name
+ self.accuracy = accuracy
+
+
+class Clef18Task1Base(LoggingMixin):
+
+ def __init__(self):
+ LoggingMixin.__init__(self, self.__class__.__name__, AppContext.default().default_log_file)
+
+ def run_evaluation(self, conf: EvaluationConfiguration):
+
+ target_label_configs = self.get_label_configuration(conf.target_labels, conf.label_encoders)
+
+ test_sets = [
+ # ("dict", dict_embeddings, config.dict_df),
+ ("cert-train", conf.train_data, conf.train_df),
+ ("cert-val", conf.val_data, conf.val_df),
+ ("cert-test", conf.test_data, conf.test_df)
+ ]
+
+ named_classifiers = [
+ ("KNN", lambda label, input_dim, output_dim, val_data: KNeighborsClassifier()),
+ ("KNN-Cos", lambda label, input_dim, output_dim, val_data: KNeighborsClassifier(metric="cosine")),
+ ("SGD", lambda label, input_dim, output_dim, val_data: SGDClassifier(verbose=1, random_state=42)),
+ ("DT", lambda label, input_dim, output_dim, val_data: DecisionTreeClassifier(random_state=42)),
+ ("RF", lambda label, input_dim, output_dim, val_data: RandomForestClassifier(verbose=1, random_state=42)),
+ ("LinearSVM", lambda label, input_dim, output_dim, val_data: LinearSVC(max_iter=10000, verbose=1, random_state=42)),
+
+ ("DNN-200", lambda label, input_dim, output_dim, val_data:
+ self.create_dnn_classifier("dnn-200", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200],
+ batch_normalization=False, dropout_rate=0.0, epochs=10, batch_size=2)),
+ ("DNN-300", lambda label, input_dim, output_dim, val_data:
+ self.create_dnn_classifier("dnn-300", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[300],
+ batch_normalization=False, dropout_rate=0.0, epochs=50, batch_size=2)),
+
+ ("DNN-200-BN-DO", lambda label, input_dim, output_dim, val_data:
+ self.create_dnn_classifier("dnn-200-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200],
+ batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
+ ("DNN-300-BN-DO", lambda label, input_dim, output_dim, val_data:
+ self.create_dnn_classifier("dnn-300-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[300],
+ batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
+
+ ("DNN-200-100", lambda label, input_dim, output_dim, val_data:
+ self.create_dnn_classifier("dnn-200-100", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200, 100],
+ batch_normalization=False, dropout_rate=0.0, epochs=50, batch_size=2)),
+ ("DNN-200-200", lambda label, input_dim, output_dim, val_data:
+ self.create_dnn_classifier("dnn-200-200", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200, 200],
+ batch_normalization=False, dropout_rate=0.0, epochs=50, batch_size=2)),
+ ("DNN-300-200", lambda label, input_dim, output_dim, val_data:
+ self.create_dnn_classifier("dnn-300-200", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[300, 200],
+ batch_normalization=False, dropout_rate=0.0, epochs=50, batch_size=2)),
+
+ ("DNN-200-100-BN-DO", lambda label, input_dim, output_dim, val_data:
+ self.create_dnn_classifier("dnn-200-100-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200, 100],
+ batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
+ ("DNN-200-200-BN-DO", lambda label, input_dim, output_dim, val_data:
+ self.create_dnn_classifier("dnn-200-200-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200, 200],
+ batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
+ ("DNN-300-200-BN-DO", lambda label, input_dim, output_dim, val_data:
+ self.create_dnn_classifier("dnn-300-200-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim,hidden_layer_sizes=[300, 200],
+ batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
+
+ ('DU1', lambda label, input_dim, output_dim, val_data: DummyClassifier(strategy="stratified")),
+ ('DU2', lambda label, input_dim, output_dim, val_data: DummyClassifier(strategy="most_frequent"))
+ ]
+
+ num_experiments = len(target_label_configs) * len(test_sets) * len(named_classifiers)
+ cur_experiment = 1
+
+ models_dir = os.path.join(AppContext.default().output_dir, "models")
+ os.makedirs(models_dir, exist_ok=True)
+
+ results = []
+ for target_label, target_column, label_encoder in target_label_configs:
+ self.logger.info("Start evaluation experiments with label %s", target_label)
+ output_dim = len(label_encoder.classes_)
+ train_labels = conf.train_df[target_column].values
+
+ #complete_train_data = np.append(dict_embeddings, train_cert_embeddings, axis=0)
+ #complete_train_labels = np.append(config.dict_df[target_column].values, config.train_cert_df[target_column].values, axis=0)
+
+ self.logger.info("Build complete training samples (data: %s, labels: %s)", conf.train_data.shape, train_labels.shape)
+
+ for cl_name, classifier_factory in named_classifiers:
+ self.logger.info("Start training of classifier %s", cl_name)
+ classifier = classifier_factory(target_label, conf.input_dim, output_dim, conf.val_data)
+ classifier.fit(conf.train_data, train_labels)
+
+ classifier_file_name = "cl_{}_{}.model".format(cl_name, target_label).lower()
+ classifier_file = os.path.join(models_dir, classifier_file_name)
+ try:
+ joblib.dump(classifier, classifier_file)
+ except:
+ self.logger.error("Error while saving classifier %s to %s", cl_name, classifier_file)
+
+ self.logger.info("Start evaluation of %s", cl_name)
+ for ts_name, inputs, data_frame in test_sets:
+ gold_labels = data_frame[target_column].values
+
+ self.logger.info("Evaluate data set %s", ts_name)
+ prediction = classifier.predict(inputs)
+ acc_score = accuracy_score(gold_labels, prediction)
+
+ self.logger.info("Evaluation result: label=%s | classifier=%s | data_set=%s | acc_score=%s",
+ target_label, cl_name, ts_name, acc_score)
+ results.append(EvaluationResult(target_label, cl_name, ts_name, acc_score))
+
+ self.logger.info("Finished experiment %s out of %s", cur_experiment, num_experiments)
+ cur_experiment += 1
+
+ return results
+
+ def prepare_label_encoders(self, dict_df: DataFrame, cert_df: DataFrame) -> ICD10LabelEncoders:
+ self.logger.info("Fitting label encoder to ICD10 codes")
+ icd10_code_encoder = LabelEncoder()
+ icd10_code_encoder.fit(list([icd10.strip() for icd10 in dict_df["ICD10"].values]) +
+ list([icd10.strip() for icd10 in cert_df["ICD10"].values]))
+ self.logger.info("Found %s distinct ICD10 codes within the data set", len(icd10_code_encoder.classes_))
+
+ self.logger.info("Fitting label encoder to ICD10 chapters")
+ icd10_chapter_encoder = LabelEncoder()
+ icd10_chapter_encoder.fit(list([icd10.strip().lower()[0] for icd10 in dict_df["ICD10"].values]) +
+ list([icd10.strip().lower()[0] for icd10 in cert_df["ICD10"].values]))
+ self.logger.info("Found %s distinct ICD10 chapters within the data set", len(icd10_chapter_encoder.classes_))
+
+ self.logger.info("Fitting label encoder to ICD10 section")
+ icd10_section_encoder = LabelEncoder()
+ icd10_section_encoder.fit(list([icd10.strip().lower()[0:2] for icd10 in dict_df["ICD10"].values]) +
+ list([icd10.strip().lower()[0:2] for icd10 in cert_df["ICD10"].values]))
+ self.logger.info("Found %s distinct ICD10 sections within the data set", len(icd10_section_encoder.classes_))
+
+ self.logger.info("Fitting label encoder to ICD10 subsection")
+ icd10_subsection_encoder = LabelEncoder()
+ icd10_subsection_encoder.fit(list([icd10.strip().lower()[0:3] for icd10 in dict_df["ICD10"].values]) +
+ list([icd10.strip().lower()[0:3] for icd10 in cert_df["ICD10"].values]))
+ self.logger.info("Found %s distinct ICD10 subsections within the data set", len(icd10_subsection_encoder.classes_))
+
+ return ICD10LabelEncoders(icd10_chapter_encoder, icd10_section_encoder, icd10_subsection_encoder, icd10_code_encoder)
+
+ def get_label_configuration(self, target_labels: List[str], icd10_encoders: ICD10LabelEncoders) -> List:
+ label_configs = []
+
+ for target_label in target_labels:
+ if target_label == "chap" or target_label == "chapter":
+ label_configs.append((target_label, "ICD10_chapter_encoded", icd10_encoders.chapter_encoder))
+ elif target_label == "sect" or target_label == "section":
+ label_configs.append((target_label, "ICD10_section_encoded", icd10_encoders.section_encoder))
+ elif target_label == "subs" or target_label == "subsection":
+ label_configs.append((target_label, "ICD10_subsection_encoded", icd10_encoders.subsection_encoder))
+ elif target_label == "code" or target_label == "icd10":
+ label_configs.append((target_label, "ICD10_encoded", icd10_encoders.code_encoder))
+ else:
+ self.logger.error("Can't create label configuration for label " + target_label)
+
+ return label_configs
+
+ def split_train_test(self, certificate_df: DataFrame, train_size: float,
+ stratified_splits: bool, label_column: str) -> Tuple[DataFrame, DataFrame]:
+ if stratified_splits:
+ self.logger.info("Creating stratified splits for column %s", label_column)
+ training_data, test_data = train_test_split(certificate_df, train_size=train_size, stratify=certificate_df[label_column])
+ else:
+ self.logger.info("Creating non-stratified splits")
+ training_data, test_data = train_test_split(certificate_df, train_size=train_size)
+
+ return training_data, test_data
+
+ def save_evaluation_results(self, eval_results: List[EvaluationResult]):
+ result_configurations = [
+ ("results.csv", None),
+ ("results_by_classifier.csv", lambda result: result.classifier_name),
+ ("results_by_data_set.csv", lambda result: result.data_set_name),
+ ("results_by_label.csv", lambda result: result.target_label)
+ ]
+
+ for file_name, sort_key in result_configurations:
+ results_file = os.path.join(AppContext.default().output_dir, file_name)
+ with open(results_file, "w", encoding="utf8") as result_writer:
+ if sort_key:
+ eval_results = sorted(eval_results, key=sort_key)
+
+ for r in eval_results:
+ result_writer.write("%s\t%s\t%s\t%s\n" % (r.target_label, r.classifier_name, r.data_set_name, r.accuracy))
+ result_writer.close()
+
+ def save_arguments(self, arguments: Namespace):
+ arguments_file = os.path.join(AppContext.default().log_dir, "arguments.txt")
+ self.logger.info("Saving arguments to " + arguments_file)
+
+ with open(arguments_file, 'w', encoding="utf8") as writer:
+ for key, value in arguments.__dict__.items():
+ writer.write("%s=%s\n" % (str(key), str(value)))
+ writer.close()
+
+ def reload_embedding_model(self, emb_model_file: str):
+ self.logger.info("Reloading embedding model from " + emb_model_file)
+ return k.models.load_model(emb_model_file)
+
+ def create_dnn_classifier(self, model_name, label: str, val_data: Tuple, **kwargs):
+ if val_data is not None:
+ monitor_loss = "val_loss"
+ else:
+ monitor_loss = "loss"
+
+ callbacks = [
+ ku.best_model_checkpointing_by_model_name(model_name),
+ ku.csv_logging_callback(model_name, label),
+ ku.early_stopping(monitor_loss, 5)
+ ]
+
+ kwargs["callbacks"] = callbacks
+ return nnc.dense_network(**kwargs)
+
+ def save_configuration(self, configuration):
+ label_encoder_file = os.path.join(AppContext.default().output_dir, "label_encoder.pk")
+ self.logger.info("Saving label encoder to " + label_encoder_file)
+ with open(label_encoder_file, 'wb') as encoder_writer:
+ pickle.dump(configuration.label_encoders, encoder_writer)
+ encoder_writer.close()
+
+ keras_tokenizer_file = os.path.join(AppContext.default().output_dir, "keras_tokenizer.pk")
+ self.logger.info("Saving keras sequencer to " + keras_tokenizer_file)
+ with open(keras_tokenizer_file, 'wb') as keras_sequencer_writer:
+ pickle.dump(configuration.keras_tokenizer, keras_sequencer_writer)
+ keras_sequencer_writer.close()
+
+ configuration_file = os.path.join(AppContext.default().output_dir, "configuration.pk")
+ self.logger.info("Saving configuration to " + configuration_file)
+ with open(configuration_file, 'wb') as train_conf_writer:
+ pickle.dump(configuration, train_conf_writer)
+ train_conf_writer.close()
+
+ def reload_configuration(self, file_path: str):
+ self.logger.info("Reloading configuration from " + file_path)
+ with open(file_path, 'rb') as train_conf_reader:
+ configuration = pickle.load(train_conf_reader)
+ train_conf_reader.close()
+
+ return configuration
+
+
+class NegativeSampling(LoggingMixin):
+
+ def __init__(self):
+ LoggingMixin.__init__(self, self.__class__.__name__, AppContext.default().default_log_file)
+
+ def get_strategy_by_name(self, name: str, args: Namespace) -> Callable:
+ #FIXME: Make args to dictionary
+
+ if name == "def":
+ return self.default_strategy(args.num_neg_samples)
+ elif name == "ext1":
+ return self.extended1_strategy(args.num_neg_cha, args.num_neg_sec, args.num_neg_sub, args.num_neg_oth)
+ else:
+ raise AssertionError("Unsupported negative sampling strategy: " + name)
+
+ def default_strategy(self, num_negative_samples: int) -> Callable:
+ def _sample(dictionary_df: DataFrame, line_icd10_code: str):
+ negative_samples = dictionary_df.query("ICD10 != '%s'" % line_icd10_code)
+
+ # Only necessary during development and tests with only very few examples
+ if len(negative_samples) > 0:
+ negative_samples = negative_samples.sample(min(num_negative_samples, len(negative_samples)))
+
+ return negative_samples
+
+ return _sample
+
+ def extended1_strategy(self, num_chapter_samples, num_section_samples, num_subsection_samples, num_other_samples):
+ def _sample(dictionary_df: DataFrame, icd10_code: str):
+ icd10_chapter = icd10_code[0].lower()
+ icd10_section = icd10_code[0:2].lower()
+ icd10_subsection = icd10_code[0:3].lower()
+
+ chapter_samples = dictionary_df.query("ICD10 != '%s' & ICD10_chapter == '%s'" % (icd10_code, icd10_chapter))
+ if len(chapter_samples) > 0:
+ chapter_samples = chapter_samples.sample(min(num_chapter_samples, len(chapter_samples)))
+
+ section_samples = dictionary_df.query("ICD10 != '%s' & ICD10_section == '%s'" % (icd10_code, icd10_section))
+ if len(section_samples) > 0:
+ section_samples = section_samples.sample(min(num_section_samples, len(section_samples)))
+
+ subsection_samples = dictionary_df.query("ICD10 != '%s' & ICD10_subsection == '%s'" % (icd10_code, icd10_subsection))
+ if len(subsection_samples) > 0:
+ subsection_samples = subsection_samples.sample(min(num_subsection_samples, len(subsection_samples)))
+
+ exp_sim_samples = num_chapter_samples + num_section_samples + num_subsection_samples
+ act_sim_samples = len(chapter_samples) + len(section_samples) + len(subsection_samples)
+
+ other_samples = dictionary_df.query("ICD10 != '%s' & ICD10_chapter != '%s'" % (icd10_code, icd10_chapter))
+ other_samples = other_samples.sample(min(num_other_samples + (exp_sim_samples - act_sim_samples), len(other_samples)))
+
+ # print("#Chapter samples: ", len(chapter_samples))
+ # print("#Section samples: ", len(section_samples))
+ # print("#Subsection samples: ", len(subsection_samples))
+ # print("#Other samples: ", len(other_samples))
+
+ return pd.concat([chapter_samples, section_samples, subsection_samples, other_samples])
+ return _sample
diff --git a/code_mario/clef18_task1_emb1.py b/code_mario/clef18_task1_emb1.py
index c5b380e..9f933e7 100644
--- a/code_mario/clef18_task1_emb1.py
+++ b/code_mario/clef18_task1_emb1.py
@@ -1,55 +1,32 @@
from init import *
+from clef18_task1_base import ICD10LabelEncoders, Clef18Task1Base, EvaluationConfiguration, NegativeSampling
+from clef18_task1_emb2 import EvaluationResult
+
import argparse
import numpy as np
import pandas as pd
import keras as k
-import pickle
import os
-from argparse import Namespace
-from gensim.models import FastText
from keras import Input, Model
-from keras.callbacks import ModelCheckpoint, Callback, EarlyStopping, CSVLogger
from keras.layers import Bidirectional, Dense, Dot, LSTM, Embedding
from keras.preprocessing.sequence import pad_sequences
from keras.preprocessing.text import Tokenizer
from pandas import DataFrame
-from sklearn.dummy import DummyClassifier
-from sklearn.ensemble import RandomForestClassifier
-from sklearn.linear_model import SGDClassifier
from sklearn.metrics import f1_score, accuracy_score
-from sklearn.model_selection import train_test_split
-from sklearn.neighbors import KNeighborsClassifier
from sklearn.pipeline import Pipeline
-from sklearn.preprocessing import LabelEncoder
-from sklearn.svm import LinearSVC
-from sklearn.tree import DecisionTreeClassifier
from tqdm import tqdm
from typing import Tuple, Dict, List, Callable
-from sklearn.externals import joblib
-import ft_embeddings
from app_context import AppContext
from clef18_task1_data import Clef18Task1Data
-from dnn_classifiers import NeuralNetworkClassifiers as nnc
from ft_embeddings import FastTextEmbeddings, FastTextModel
from preprocessing import DataPreparationUtil as pdu
from keras_extension import KerasUtil as ku
-from util import LoggingMixin
-
-
-class ICD10LabelEncoders(object):
- def __init__(self, chapter_encoder: LabelEncoder, section_encoder: LabelEncoder,
- subsection_encoder: LabelEncoder, code_encoder: LabelEncoder):
- self.chapter_encoder = chapter_encoder
- self.section_encoder = section_encoder
- self.subsection_encoder = subsection_encoder
- self.code_encoder = code_encoder
-
-class Configuration(object):
+class Emb1Configuration(object):
def __init__(self, train_cert_df: DataFrame, val_cert_df: DataFrame, test_cert_df: DataFrame, dict_df: DataFrame,
max_cert_length: int, max_dict_length: int, ft_embedding_size: int, label_column: str,
@@ -66,21 +43,12 @@ class Configuration(object):
self.keras_tokenizer = keras_tokenizer
-class EvaluationResult(object):
-
- def __init__(self, target_label: str, classifier_name: str, data_set_name: str, accuracy: float):
- self.target_label = target_label
- self.classifier_name = classifier_name
- self.data_set_name = data_set_name
- self.accuracy = accuracy
-
-
-class Clef18Task1Emb1(LoggingMixin):
+class Clef18Task1Emb1(Clef18Task1Base):
def __init__(self):
- LoggingMixin.__init__(self, self.__class__.__name__, AppContext.default().default_log_file)
+ Clef18Task1Base.__init__(self)
- def train_embedding_model(self, config: Configuration, ft_model: FastTextModel, neg_sampling_strategy: Callable, epochs: int, batch_size: int) -> Model:
+ def train_embedding_model(self, config: Emb1Configuration, ft_model: FastTextModel, neg_sampling_strategy: Callable, epochs: int, batch_size: int) -> Model:
self.logger.info("Start building training pairs")
train_pair_data = self.build_pairs(config.train_cert_df, config.dict_df, neg_sampling_strategy)
self.logger.info("Label distribution:\n%s", train_pair_data["Label"].value_counts())
@@ -142,7 +110,7 @@ class Clef18Task1Emb1(LoggingMixin):
return model
- def train_and_evaluate_classifiers(self, emb_model: Model, config: Configuration, target_labels: List) -> List[EvaluationResult]:
+ def train_and_evaluate_classifiers(self, emb_model: Model, config: Emb1Configuration, target_labels: List) -> List[EvaluationResult]:
self.logger.info("Start training and evaluation of classifier models")
self.logger.info("Building dictionary embeddings")
@@ -151,7 +119,7 @@ class Clef18Task1Emb1(LoggingMixin):
dict_inputs = pad_sequences(config.dict_df["Token_ids"].values, maxlen=config.max_dict_length)
dict_embeddings = dict_rnn.predict(dict_inputs, verbose=1, batch_size=1)
- self.logger.info("Building certificate embeddings")
+ self.logger.info("Building train certificate embeddings")
cert_input = emb_model.inputs[0]
cert_rnn = Model(inputs=cert_input, outputs=emb_model.get_layer("cert_rnn").output, name="Cert-RNN-Model")
@@ -159,142 +127,29 @@ class Clef18Task1Emb1(LoggingMixin):
train_cert_embeddings = cert_rnn.predict(train_cert_inputs, verbose=1)
self.logger.info("cert train input shape: %s", train_cert_embeddings.shape)
- val_cert_inputs = pad_sequences(config.val_cert_df["Token_ids"].values, maxlen=config.max_cert_length)
- val_cert_embeddings = cert_rnn.predict(val_cert_inputs, verbose=1)
- self.logger.info("cert val input shape: %s", val_cert_embeddings.shape)
+ self.logger.info("Building val certificate embeddings")
+ val_inputs = pad_sequences(config.val_cert_df["Token_ids"].values, maxlen=config.max_cert_length)
+ val_embeddings = cert_rnn.predict(val_inputs, verbose=1)
+ self.logger.info("cert val input shape: %s", val_embeddings.shape)
- test_cert_inputs = pad_sequences(config.test_cert_df["Token_ids"].values, maxlen=config.max_cert_length)
- test_cert_embeddings = cert_rnn.predict(test_cert_inputs, verbose=1)
- self.logger.info("cert test input shape: %s", test_cert_embeddings.shape)
+ self.logger.info("Building test certificate embeddings")
+ test_inputs = pad_sequences(config.test_cert_df["Token_ids"].values, maxlen=config.max_cert_length)
+ test_embeddings = cert_rnn.predict(test_inputs, verbose=1)
+ self.logger.info("cert test input shape: %s", test_embeddings.shape)
target_label_configs = self.get_label_configuration(target_labels, config.label_encoders)
+ target_label_columns = [label_column for _, label_column, _ in target_label_configs]
- test_sets = [
- #("dict", dict_embeddings, config.dict_df),
- ("cert-train", train_cert_embeddings, config.train_cert_df),
- ("cert-val", val_cert_embeddings, config.val_cert_df),
- ("cert-test", test_cert_embeddings, config.test_cert_df)
- ]
-
- named_classifiers = [
- ("KNN", lambda label, input_dim, output_dim, val_data: KNeighborsClassifier()),
- ("KNN-Cos", lambda label, input_dim, output_dim, val_data: KNeighborsClassifier(metric="cosine")),
- ("SGD", lambda label, input_dim, output_dim, val_data: SGDClassifier(verbose=1, random_state=42)),
- ("DT", lambda label, input_dim, output_dim, val_data: DecisionTreeClassifier(random_state=42)),
- ("RF", lambda label, input_dim, output_dim, val_data: RandomForestClassifier(verbose=1, random_state=42)),
- ("LinearSVM", lambda label, input_dim, output_dim, val_data: LinearSVC(max_iter=10000, verbose=1, random_state=42)),
-
- ("DNN-200", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-200", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200],
- batch_normalization=False, dropout_rate=0.0, epochs=10, batch_size=2)),
- ("DNN-300", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-300", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[300],
- batch_normalization=False, dropout_rate=0.0, epochs=50, batch_size=2)),
-
- ("DNN-200-BN-DO", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-200-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200],
- batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
- ("DNN-300-BN-DO", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-300-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[300],
- batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
-
- ("DNN-200-100", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-200-100", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200, 100],
- batch_normalization=False, dropout_rate=0.0, epochs=50, batch_size=2)),
- ("DNN-200-200", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-200-200", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200, 200],
- batch_normalization=False, dropout_rate=0.0, epochs=50, batch_size=2)),
- ("DNN-300-200", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-300-200", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[300, 200],
- batch_normalization=False, dropout_rate=0.0, epochs=50, batch_size=2)),
-
- ("DNN-200-100-BN-DO", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-200-100-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200, 100],
- batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
- ("DNN-200-200-BN-DO", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-200-200-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200, 200],
- batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
- ("DNN-300-200-BN-DO", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-300-200-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[300, 200],
- batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
-
- ('DU1', lambda label, input_dim, output_dim, val_data: DummyClassifier(strategy="stratified")),
- ('DU2', lambda label, input_dim, output_dim, val_data: DummyClassifier(strategy="most_frequent"))
- ]
-
- num_experiments = len(target_label_configs) * len(test_sets) * len(named_classifiers)
- cur_experiment = 1
+ train_labels = pd.concat([config.dict_df[target_label_columns], config.train_cert_df[target_label_columns]])
+ train_data = np.append(dict_embeddings, train_cert_embeddings, axis=0)
input_dim = cert_rnn.output.shape[1].value
- models_dir = os.path.join(AppContext.default().output_dir, "models")
- os.makedirs(models_dir, exist_ok=True)
-
- results = []
- for target_label, target_column, label_encoder in target_label_configs:
- self.logger.info("Start evaluation experiments with label %s", target_label)
- output_dim = len(label_encoder.classes_)
-
- complete_train_data = np.append(dict_embeddings, train_cert_embeddings, axis=0)
- complete_train_labels = np.append(config.dict_df[target_column].values, config.train_cert_df[target_column].values, axis=0)
- self.logger.info("Build complete training samples (data: %s, labels: %s)", complete_train_data.shape, complete_train_labels.shape)
-
- for cl_name, classifier_factory in named_classifiers:
- self.logger.info("Start training of classifier %s", cl_name)
- classifier = classifier_factory(target_label, input_dim, output_dim, val_cert_embeddings)
- classifier.fit(complete_train_data, complete_train_labels)
-
- classifier_file_name = "cl_{}_{}.model".format(cl_name, target_label).lower()
- classifier_file = os.path.join(models_dir, classifier_file_name)
- try:
- joblib.dump(classifier, classifier_file)
- except:
- self.logger.error("Error while saving classifier %s to %s", cl_name, classifier_file)
-
- self.logger.info("Start evaluation of %s", cl_name)
- for ts_name, inputs, data_frame in test_sets:
- gold_labels = data_frame[target_column].values
-
- self.logger.info("Evaluate data set %s", ts_name)
- prediction = classifier.predict(inputs)
- acc_score = accuracy_score(gold_labels, prediction)
-
- self.logger.info("Evaluation result: label=%s | classifier=%s | data_set=%s | acc_score=%s",
- target_label, cl_name, ts_name, acc_score)
- results.append(EvaluationResult(target_label, cl_name, ts_name, acc_score))
-
- self.logger.info("Finished experiment %s out of %s", cur_experiment, num_experiments)
- cur_experiment += 1
-
- return results
-
- def get_label_configuration(self, target_labels: List[str], icd10_encoders: ICD10LabelEncoders) -> List:
- label_configs = []
-
- for target_label in target_labels:
- if target_label == "chap" or target_label == "chapter":
- label_configs.append((target_label, "ICD10_chapter_encoded", icd10_encoders.chapter_encoder))
- elif target_label == "sect" or target_label == "section":
- label_configs.append((target_label, "ICD10_section_encoded", icd10_encoders.section_encoder))
- elif target_label == "subs" or target_label == "subsection":
- label_configs.append((target_label, "ICD10_subsection_encoded", icd10_encoders.subsection_encoder))
- elif target_label == "code" or target_label == "icd10":
- label_configs.append((target_label, "ICD10_encoded", icd10_encoders.code_encoder))
- else:
- self.logger.error("Can't create label configuration for label " + target_label)
-
- return label_configs
-
- def split_train_test(self, certificate_df: DataFrame, train_size: float,
- stratified_splits: bool, label_column: str) -> Tuple[DataFrame, DataFrame]:
- if stratified_splits:
- self.logger.info("Creating stratified splits for column %s", label_column)
- training_data, test_data = train_test_split(certificate_df, train_size=train_size, stratify=certificate_df[label_column])
- else:
- self.logger.info("Creating non-stratified splits")
- training_data, test_data = train_test_split(certificate_df, train_size=train_size)
+ eval_configuration = EvaluationConfiguration(target_labels, config.label_encoders, input_dim, train_data, train_labels,
+ val_embeddings, config.val_cert_df, test_embeddings, config.test_cert_df)
+ return self.run_evaluation(eval_configuration)
- return training_data, test_data
+ # ---------------------------------------------------------------------------------------------------------------------------------------
def build_embedding_model(self, word_index: Dict, ft_model: FastTextModel, max_cert_length: int, max_dict_length: int):
# TODO: Make hyper-parameter configurable!
@@ -334,7 +189,7 @@ class Clef18Task1Emb1(LoggingMixin):
return model
def prepare_data_set(self, cert_df: DataFrame, dict_df: DataFrame, ft_model: FastTextModel, train_ratio: float, val_ratio: float,
- strat_column: str, samples: int=None, stratified_splits: bool=False) -> Configuration:
+ strat_column: str, samples: int=None, stratified_splits: bool=False) -> Emb1Configuration:
if samples:
self.logger.info("Sampling %s instances", samples)
@@ -362,35 +217,8 @@ class Clef18Task1Emb1(LoggingMixin):
self.logger.info("Start preparation of dictionary data (%s instances)", len(dict_df))
dict_df, max_dict_length = self.prepare_dictionary_df(dict_df, "train", label_encoders, keras_tokenizer)
- return Configuration(train_cert_df, val_cert_df, test_cert_df, dict_df, max_cert_length, max_dict_length,
- ft_model.vector_size, strat_column, label_encoders, keras_tokenizer)
-
- def prepare_label_encoders(self, dict_df: DataFrame, cert_df: DataFrame) -> ICD10LabelEncoders:
- self.logger.info("Fitting label encoder to ICD10 codes")
- icd10_code_encoder = LabelEncoder()
- icd10_code_encoder.fit(list([icd10.strip() for icd10 in dict_df["ICD10"].values]) +
- list([icd10.strip() for icd10 in cert_df["ICD10"].values]))
- self.logger.info("Found %s distinct ICD10 codes within the data set", len(icd10_code_encoder.classes_))
-
- self.logger.info("Fitting label encoder to ICD10 chapters")
- icd10_chapter_encoder = LabelEncoder()
- icd10_chapter_encoder.fit(list([icd10.strip().lower()[0] for icd10 in dict_df["ICD10"].values]) +
- list([icd10.strip().lower()[0] for icd10 in cert_df["ICD10"].values]))
- self.logger.info("Found %s distinct ICD10 chapters within the data set", len(icd10_chapter_encoder.classes_))
-
- self.logger.info("Fitting label encoder to ICD10 section")
- icd10_section_encoder = LabelEncoder()
- icd10_section_encoder.fit(list([icd10.strip().lower()[0:2] for icd10 in dict_df["ICD10"].values]) +
- list([icd10.strip().lower()[0:2] for icd10 in cert_df["ICD10"].values]))
- self.logger.info("Found %s distinct ICD10 sections within the data set", len(icd10_section_encoder.classes_))
-
- self.logger.info("Fitting label encoder to ICD10 subsection")
- icd10_subsection_encoder = LabelEncoder()
- icd10_subsection_encoder.fit(list([icd10.strip().lower()[0:3] for icd10 in dict_df["ICD10"].values]) +
- list([icd10.strip().lower()[0:3] for icd10 in cert_df["ICD10"].values]))
- self.logger.info("Found %s distinct ICD10 subsections within the data set", len(icd10_subsection_encoder.classes_))
-
- return ICD10LabelEncoders(icd10_chapter_encoder, icd10_section_encoder, icd10_subsection_encoder, icd10_code_encoder)
+ return Emb1Configuration(train_cert_df, val_cert_df, test_cert_df, dict_df, max_cert_length, max_dict_length,
+ ft_model.vector_size, strat_column, label_encoders, keras_tokenizer)
def prepare_certificate_df(self, certificate_df: DataFrame, mode: str, icd10_encoders: ICD10LabelEncoders,
keras_tokenizer: Tokenizer) -> Tuple[DataFrame, int]:
@@ -496,139 +324,6 @@ class Clef18Task1Emb1(LoggingMixin):
return data_matrix
- def save_evaluation_results(self, eval_results: List[EvaluationResult]):
- result_configurations = [
- ("results.csv", None),
- ("results_by_classifier.csv", lambda result: result.classifier_name),
- ("results_by_data_set.csv", lambda result: result.data_set_name),
- ("results_by_label.csv", lambda result: result.target_label)
- ]
-
- for file_name, sort_key in result_configurations:
- results_file = os.path.join(AppContext.default().output_dir, file_name)
- with open(results_file, "w", encoding="utf8") as result_writer:
- if sort_key:
- eval_results = sorted(eval_results, key=sort_key)
-
- for r in eval_results:
- result_writer.write("%s\t%s\t%s\t%s\n" % (r.target_label, r.classifier_name, r.data_set_name, r.accuracy))
- result_writer.close()
-
- def save_arguments(self, arguments: Namespace):
- arguments_file = os.path.join(AppContext.default().log_dir, "arguments.txt")
- self.logger.info("Saving arguments to " + arguments_file)
-
- with open(arguments_file, 'w', encoding="utf8") as writer:
- for key, value in arguments.__dict__.items():
- writer.write("%s=%s\n" % (str(key), str(value)))
- writer.close()
-
- def save_configuration(self, configuration: Configuration):
- label_encoder_file = os.path.join(AppContext.default().output_dir, "label_encoder.pk")
- self.logger.info("Saving label encoder to " + label_encoder_file)
- with open(label_encoder_file, 'wb') as encoder_writer:
- pickle.dump(configuration.label_encoders, encoder_writer)
- encoder_writer.close()
-
- keras_tokenizer_file = os.path.join(AppContext.default().output_dir, "keras_tokenizer.pk")
- self.logger.info("Saving keras sequencer to " + keras_tokenizer_file)
- with open(keras_tokenizer_file, 'wb') as keras_sequencer_writer:
- pickle.dump(configuration.keras_tokenizer, keras_sequencer_writer)
- keras_sequencer_writer.close()
-
- configuration_file = os.path.join(AppContext.default().output_dir, "configuration.pk")
- self.logger.info("Saving configuration to " + configuration_file)
- with open(configuration_file, 'wb') as train_conf_writer:
- pickle.dump(configuration, train_conf_writer)
- train_conf_writer.close()
-
- def reload_configuration(self, file_path: str):
- self.logger.info("Reloading configuration from " + file_path)
- with open(args.train_conf, 'rb') as train_conf_reader:
- configuration = pickle.load(train_conf_reader)
- train_conf_reader.close()
-
- return configuration
-
- def reload_embedding_model(self, emb_model_file: str):
- self.logger.info("Reloading embedding model from " + emb_model_file)
- return k.models.load_model(args.emb_model)
-
- def create_dnn_classifier(self, model_name, label: str, val_data: Tuple, **kwargs):
- if val_data is not None:
- monitor_loss = "val_loss"
- else:
- monitor_loss = "loss"
-
- callbacks = [
- ku.best_model_checkpointing_by_model_name(model_name),
- ku.csv_logging_callback(model_name, label),
- ku.early_stopping(monitor_loss, 5)
- ]
-
- kwargs["callbacks"] = callbacks
- return nnc.dense_network(**kwargs)
-
-
-class NegativeSampling(LoggingMixin):
-
- def __init__(self):
- LoggingMixin.__init__(self, self.__class__.__name__, AppContext.default().default_log_file)
-
- def get_strategy_by_name(self, name: str, args: Namespace) -> Callable:
- #FIXME: Make args to dictionary
-
- if name == "def":
- return self.default_strategy(args.num_neg_samples)
- elif name == "ext1":
- return self.extended1_strategy(args.num_neg_cha, args.num_neg_sec, args.num_neg_sub, args.num_neg_oth)
- else:
- raise AssertionError("Unsupported negative sampling strategy: " + name)
-
- def default_strategy(self, num_negative_samples: int) -> Callable:
- def _sample(dictionary_df: DataFrame, line_icd10_code: str):
- negative_samples = dictionary_df.query("ICD10 != '%s'" % line_icd10_code)
-
- # Only necessary during development and tests with only very few examples
- if len(negative_samples) > 0:
- negative_samples = negative_samples.sample(min(num_negative_samples, len(negative_samples)))
-
- return negative_samples
-
- return _sample
-
- def extended1_strategy(self, num_chapter_samples, num_section_samples, num_subsection_samples, num_other_samples):
- def _sample(dictionary_df: DataFrame, icd10_code: str):
- icd10_chapter = icd10_code[0].lower()
- icd10_section = icd10_code[0:2].lower()
- icd10_subsection = icd10_code[0:3].lower()
-
- chapter_samples = dictionary_df.query("ICD10 != '%s' & ICD10_chapter == '%s'" % (icd10_code, icd10_chapter))
- if len(chapter_samples) > 0:
- chapter_samples = chapter_samples.sample(min(num_chapter_samples, len(chapter_samples)))
-
- section_samples = dictionary_df.query("ICD10 != '%s' & ICD10_section == '%s'" % (icd10_code, icd10_section))
- if len(section_samples) > 0:
- section_samples = section_samples.sample(min(num_section_samples, len(section_samples)))
-
- subsection_samples = dictionary_df.query("ICD10 != '%s' & ICD10_subsection == '%s'" % (icd10_code, icd10_subsection))
- if len(subsection_samples) > 0:
- subsection_samples = subsection_samples.sample(min(num_subsection_samples, len(subsection_samples)))
-
- exp_sim_samples = num_chapter_samples + num_section_samples + num_subsection_samples
- act_sim_samples = len(chapter_samples) + len(section_samples) + len(subsection_samples)
-
- other_samples = dictionary_df.query("ICD10 != '%s' & ICD10_chapter != '%s'" % (icd10_code, icd10_chapter))
- other_samples = other_samples.sample(min(num_other_samples + (exp_sim_samples - act_sim_samples), len(other_samples)))
-
- # print("#Chapter samples: ", len(chapter_samples))
- # print("#Section samples: ", len(section_samples))
- # print("#Subsection samples: ", len(subsection_samples))
- # print("#Other samples: ", len(other_samples))
-
- return pd.concat([chapter_samples, section_samples, subsection_samples, other_samples])
- return _sample
-
if __name__ == "__main__":
parser = argparse.ArgumentParser(prog="CLEF2018")
@@ -648,10 +343,10 @@ if __name__ == "__main__":
train_emb_parser.add_argument("--neg_sampling", help="Negative sampling strategy to use", default="ext1", choices=["def", "ext1"])
train_emb_parser.add_argument("--num_neg_samples", help="Number of negative samples to use (default strategy)", default=75, type=int)
- train_emb_parser.add_argument("--num_neg_cha", help="Number of negative chapter samples to use (ext1 strategy)", default=10, type=int)
- train_emb_parser.add_argument("--num_neg_sec", help="Number of negative section samples to use (ext1 strategy)", default=10, type=int)
- train_emb_parser.add_argument("--num_neg_sub", help="Number of negative subsection samples to use (ext1 strategy)", default=10, type=int)
- train_emb_parser.add_argument("--num_neg_oth", help="Number of negative other samples to use (ext1 strategy)", default=40, type=int)
+ train_emb_parser.add_argument("--num_neg_cha", help="Number of negative chapter samples to use (ext1 strategy)", default=20, type=int)
+ train_emb_parser.add_argument("--num_neg_sec", help="Number of negative section samples to use (ext1 strategy)", default=20, type=int)
+ train_emb_parser.add_argument("--num_neg_sub", help="Number of negative subsection samples to use (ext1 strategy)", default=20, type=int)
+ train_emb_parser.add_argument("--num_neg_oth", help="Number of negative other samples to use (ext1 strategy)", default=45, type=int)
eval_classifier_parser = subparsers.add_parser("eval-cl")
eval_classifier_parser.add_argument("emb_model", help="Path to the embedding model to use")
diff --git a/code_mario/clef18_task1_emb2.py b/code_mario/clef18_task1_emb2.py
index 1eeb7d8..f4ba77f 100644
--- a/code_mario/clef18_task1_emb2.py
+++ b/code_mario/clef18_task1_emb2.py
@@ -1,42 +1,28 @@
from init import *
+from clef18_task1_base import Clef18Task1Base, EvaluationConfiguration, NegativeSampling
import argparse
import numpy as np
import pandas as pd
import keras as k
-import pickle
import os
-from argparse import Namespace
-from gensim.models import FastText
from keras import Input, Model
-from keras.callbacks import ModelCheckpoint, Callback, EarlyStopping, CSVLogger
from keras.layers import Bidirectional, Dense, Dot, LSTM, Embedding, GlobalMaxPool1D
from keras.preprocessing.sequence import pad_sequences
from keras.preprocessing.text import Tokenizer
from pandas import DataFrame
-from sklearn.dummy import DummyClassifier
-from sklearn.ensemble import RandomForestClassifier
-from sklearn.linear_model import SGDClassifier
from sklearn.metrics import f1_score, accuracy_score
-from sklearn.model_selection import train_test_split
-from sklearn.neighbors import KNeighborsClassifier
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import LabelEncoder
-from sklearn.svm import LinearSVC
-from sklearn.tree import DecisionTreeClassifier
from tqdm import tqdm
from typing import Tuple, Dict, List, Callable
-from sklearn.externals import joblib
-import ft_embeddings
from app_context import AppContext
from clef18_task1_data import Clef18Task1Data
-from dnn_classifiers import NeuralNetworkClassifiers as nnc
from ft_embeddings import FastTextEmbeddings, FastTextModel
from preprocessing import DataPreparationUtil as pdu
from keras_extension import KerasUtil as ku
-from util import LoggingMixin
class ICD10LabelEncoders(object):
@@ -72,10 +58,10 @@ class EvaluationResult(object):
self.accuracy = accuracy
-class Clef18Task1Emb2(LoggingMixin):
+class Clef18Task1Emb2(Clef18Task1Base):
def __init__(self):
- LoggingMixin.__init__(self, self.__class__.__name__, AppContext.default().default_log_file)
+ Clef18Task1Base.__init__(self)
def train_embedding_model(self, config: Configuration, ft_model: FastTextModel, neg_sampling_strategy: Callable, epochs: int, batch_size: int) -> Model:
self.logger.info("Start building training pairs")
@@ -159,132 +145,15 @@ class Clef18Task1Emb2(LoggingMixin):
target_label_configs = self.get_label_configuration(target_labels, config.label_encoders)
- test_sets = [
- #("dict", dict_embeddings, config.dict_df),
- ("cert-train", train_embeddings, config.train_df),
- ("cert-val", val_embeddings, config.val_df),
- ("cert-test", test_embeddings, config.test_df)
- ]
-
- named_classifiers = [
- ("KNN", lambda label, input_dim, output_dim, val_data: KNeighborsClassifier()),
- ("KNN-Cos", lambda label, input_dim, output_dim, val_data: KNeighborsClassifier(metric="cosine")),
- ("SGD", lambda label, input_dim, output_dim, val_data: SGDClassifier(verbose=1, random_state=42)),
- ("DT", lambda label, input_dim, output_dim, val_data: DecisionTreeClassifier(random_state=42)),
- ("RF", lambda label, input_dim, output_dim, val_data: RandomForestClassifier(verbose=1, random_state=42)),
- ("LinearSVM", lambda label, input_dim, output_dim, val_data: LinearSVC(max_iter=10000, verbose=1, random_state=42)),
-
- ("DNN-200", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-200", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200],
- batch_normalization=False, dropout_rate=0.0, epochs=10, batch_size=2)),
- ("DNN-300", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-300", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[300],
- batch_normalization=False, dropout_rate=0.0, epochs=50, batch_size=2)),
-
- ("DNN-200-BN-DO", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-200-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200],
- batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
- ("DNN-300-BN-DO", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-300-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[300],
- batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
-
- ("DNN-200-100", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-200-100", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200, 100],
- batch_normalization=False, dropout_rate=0.0, epochs=50, batch_size=2)),
- ("DNN-200-200", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-200-200", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200, 200],
- batch_normalization=False, dropout_rate=0.0, epochs=50, batch_size=2)),
- ("DNN-300-200", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-300-200", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[300, 200],
- batch_normalization=False, dropout_rate=0.0, epochs=50, batch_size=2)),
-
- ("DNN-200-100-BN-DO", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-200-100-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200, 100],
- batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
- ("DNN-200-200-BN-DO", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-200-200-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[200, 200],
- batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
- ("DNN-300-200-BN-DO", lambda label, input_dim, output_dim, val_data:
- self.create_dnn_classifier("dnn-300-200-bn-do", label, val_data, input_dim=input_dim, output_dim=output_dim, hidden_layer_sizes=[300, 200],
- batch_normalization=True, dropout_rate=0.5, epochs=50, batch_size=2)),
-
- ('DU1', lambda label, input_dim, output_dim, val_data: DummyClassifier(strategy="stratified")),
- ('DU2', lambda label, input_dim, output_dim, val_data: DummyClassifier(strategy="most_frequent"))
- ]
-
- num_experiments = len(target_label_configs) * len(test_sets) * len(named_classifiers)
- cur_experiment = 1
-
input_dim = text_rnn.output.shape[1].value
- models_dir = os.path.join(AppContext.default().output_dir, "models")
- os.makedirs(models_dir, exist_ok=True)
-
- results = []
- for target_label, target_column, label_encoder in target_label_configs:
- self.logger.info("Start evaluation experiments with label %s", target_label)
- output_dim = len(label_encoder.classes_)
-
- for cl_name, classifier_factory in named_classifiers:
- self.logger.info("Start training of classifier %s", cl_name)
- classifier = classifier_factory(target_label, input_dim, output_dim, val_embeddings)
- classifier.fit(train_embeddings, config.train_df[target_column].values)
-
- classifier_file_name = "cl_{}_{}.model".format(cl_name, target_label).lower()
- classifier_file = os.path.join(models_dir, classifier_file_name)
- try:
- joblib.dump(classifier, classifier_file)
- except:
- self.logger.error("Error while saving classifier %s to %s", cl_name, classifier_file)
-
- self.logger.info("Start evaluation of %s", cl_name)
- for ts_name, inputs, data_frame in test_sets:
- gold_labels = data_frame[target_column].values
-
- self.logger.info("Evaluate data set %s", ts_name)
- prediction = classifier.predict(inputs)
- acc_score = accuracy_score(gold_labels, prediction)
-
- self.logger.info("Evaluation result: label=%s | classifier=%s | data_set=%s | acc_score=%s",
- target_label, cl_name, ts_name, acc_score)
- results.append(EvaluationResult(target_label, cl_name, ts_name, acc_score))
-
- self.logger.info("Finished experiment %s out of %s", cur_experiment, num_experiments)
- cur_experiment += 1
-
- return results
-
- def get_label_configuration(self, target_labels: List[str], icd10_encoders: ICD10LabelEncoders) -> List:
- label_configs = []
-
- for target_label in target_labels:
- if target_label == "chap" or target_label == "chapter":
- label_configs.append((target_label, "ICD10_chapter_encoded", icd10_encoders.chapter_encoder))
- elif target_label == "sect" or target_label == "section":
- label_configs.append((target_label, "ICD10_section_encoded", icd10_encoders.section_encoder))
- elif target_label == "subs" or target_label == "subsection":
- label_configs.append((target_label, "ICD10_subsection_encoded", icd10_encoders.subsection_encoder))
- elif target_label == "code" or target_label == "icd10":
- label_configs.append((target_label, "ICD10_encoded", icd10_encoders.code_encoder))
- else:
- self.logger.error("Can't create label configuration for label " + target_label)
-
- return label_configs
-
- def split_train_test(self, certificate_df: DataFrame, train_size: float,
- stratified_splits: bool, label_column: str) -> Tuple[DataFrame, DataFrame]:
- if stratified_splits:
- self.logger.info("Creating stratified splits for column %s", label_column)
- training_data, test_data = train_test_split(certificate_df, train_size=train_size, stratify=certificate_df[label_column])
- else:
- self.logger.info("Creating non-stratified splits")
- training_data, test_data = train_test_split(certificate_df, train_size=train_size)
-
- return training_data, test_data
+ eval_config = EvaluationConfiguration(target_labels, config.label_encoders, input_dim, train_embeddings, config.train_df,
+ val_embeddings, config.val_df, test_embeddings, config.test_df)
+ return self.run_evaluation(eval_config)
def build_embedding_model(self, word_index: Dict, ft_model: FastTextModel, conf: Configuration):
# TODO: Make hyper-parameter configurable!
- # TODO: Think about using CNNs instead of RNNs since we can have multiple ICD-10 per line!
+ # TODO: Think about using CNNs instead of RNNs!
embedding_matrix = np.zeros((len(word_index) + 1, ft_model.vector_size))
for word, i in word_index.items():
@@ -359,33 +228,6 @@ class Clef18Task1Emb2(LoggingMixin):
return Configuration(train_df, val_df, test_df, max_length, ft_model.vector_size,
strat_column, label_encoders, keras_tokenizer)
- def prepare_label_encoders(self, dict_df: DataFrame, cert_df: DataFrame) -> ICD10LabelEncoders:
- self.logger.info("Fitting label encoder to ICD10 codes")
- icd10_code_encoder = LabelEncoder()
- icd10_code_encoder.fit(list([icd10.strip() for icd10 in dict_df["ICD10"].values]) +
- list([icd10.strip() for icd10 in cert_df["ICD10"].values]))
- self.logger.info("Found %s distinct ICD10 codes within the data set", len(icd10_code_encoder.classes_))
-
- self.logger.info("Fitting label encoder to ICD10 chapters")
- icd10_chapter_encoder = LabelEncoder()
- icd10_chapter_encoder.fit(list([icd10.strip().lower()[0] for icd10 in dict_df["ICD10"].values]) +
- list([icd10.strip().lower()[0] for icd10 in cert_df["ICD10"].values]))
- self.logger.info("Found %s distinct ICD10 chapters within the data set", len(icd10_chapter_encoder.classes_))
-
- self.logger.info("Fitting label encoder to ICD10 section")
- icd10_section_encoder = LabelEncoder()
- icd10_section_encoder.fit(list([icd10.strip().lower()[0:2] for icd10 in dict_df["ICD10"].values]) +
- list([icd10.strip().lower()[0:2] for icd10 in cert_df["ICD10"].values]))
- self.logger.info("Found %s distinct ICD10 sections within the data set", len(icd10_section_encoder.classes_))
-
- self.logger.info("Fitting label encoder to ICD10 subsection")
- icd10_subsection_encoder = LabelEncoder()
- icd10_subsection_encoder.fit(list([icd10.strip().lower()[0:3] for icd10 in dict_df["ICD10"].values]) +
- list([icd10.strip().lower()[0:3] for icd10 in cert_df["ICD10"].values]))
- self.logger.info("Found %s distinct ICD10 subsections within the data set", len(icd10_subsection_encoder.classes_))
-
- return ICD10LabelEncoders(icd10_chapter_encoder, icd10_section_encoder, icd10_subsection_encoder, icd10_code_encoder)
-
def prepare_cert_dict_df(self, cert_dict_df: DataFrame, mode: str, icd10_encoders: ICD10LabelEncoders,
keras_tokenizer: Tokenizer) -> Tuple[DataFrame, int]:
pipeline = Pipeline([
@@ -419,9 +261,7 @@ class Clef18Task1Emb2(LoggingMixin):
return data_prepared, max_length
def build_pairs(self, data_df: DataFrame, neg_sampling_strategy: Callable):
- # FIXME: This can be implemented more efficiently!
- # FIXME: Improve sampling of negative instances (especially if code is I-XXX sample other codes of the same class (e.g. I-YYY)
- # FIXME: Use negative sample ratio (depending on true dictionary entries), e.g. 0.5 or 1.2
+ # TODO: Think about to use a negative sample ratio (depending on true dictionary entries), e.g. 0.5 or 1.2
text_vectors = []
icd10_codes = []
@@ -445,139 +285,6 @@ class Clef18Task1Emb2(LoggingMixin):
data = {"Cert_input": text_vectors, "ICD10_input": icd10_codes, "Label": labels}
return pd.DataFrame(data)
- def save_evaluation_results(self, eval_results: List[EvaluationResult]):
- result_configurations = [
- ("results.csv", None),
- ("results_by_classifier.csv", lambda result: result.classifier_name),
- ("results_by_data_set.csv", lambda result: result.data_set_name),
- ("results_by_label.csv", lambda result: result.target_label)
- ]
-
- for file_name, sort_key in result_configurations:
- results_file = os.path.join(AppContext.default().output_dir, file_name)
- with open(results_file, "w", encoding="utf8") as result_writer:
- if sort_key:
- eval_results = sorted(eval_results, key=sort_key)
-
- for r in eval_results:
- result_writer.write("%s\t%s\t%s\t%s\n" % (r.target_label, r.classifier_name, r.data_set_name, r.accuracy))
- result_writer.close()
-
- def save_arguments(self, arguments: Namespace):
- arguments_file = os.path.join(AppContext.default().log_dir, "arguments.txt")
- self.logger.info("Saving arguments to " + arguments_file)
-
- with open(arguments_file, 'w', encoding="utf8") as writer:
- for key, value in arguments.__dict__.items():
- writer.write("%s=%s\n" % (str(key), str(value)))
- writer.close()
-
- def save_configuration(self, configuration: Configuration):
- label_encoder_file = os.path.join(AppContext.default().output_dir, "label_encoder.pk")
- self.logger.info("Saving label encoder to " + label_encoder_file)
- with open(label_encoder_file, 'wb') as encoder_writer:
- pickle.dump(configuration.label_encoders, encoder_writer)
- encoder_writer.close()
-
- keras_tokenizer_file = os.path.join(AppContext.default().output_dir, "keras_tokenizer.pk")
- self.logger.info("Saving keras sequencer to " + keras_tokenizer_file)
- with open(keras_tokenizer_file, 'wb') as keras_sequencer_writer:
- pickle.dump(configuration.keras_tokenizer, keras_sequencer_writer)
- keras_sequencer_writer.close()
-
- configuration_file = os.path.join(AppContext.default().output_dir, "configuration.pk")
- self.logger.info("Saving configuration to " + configuration_file)
- with open(configuration_file, 'wb') as train_conf_writer:
- pickle.dump(configuration, train_conf_writer)
- train_conf_writer.close()
-
- def reload_configuration(self, file_path: str):
- self.logger.info("Reloading configuration from " + file_path)
- with open(args.train_conf, 'rb') as train_conf_reader:
- configuration = pickle.load(train_conf_reader)
- train_conf_reader.close()
-
- return configuration
-
- def reload_embedding_model(self, emb_model_file: str):
- self.logger.info("Reloading embedding model from " + emb_model_file)
- return k.models.load_model(args.emb_model)
-
- def create_dnn_classifier(self, model_name, label: str, val_data: Tuple, **kwargs):
- if val_data is not None:
- monitor_loss = "val_loss"
- else:
- monitor_loss = "loss"
-
- callbacks = [
- ku.best_model_checkpointing_by_model_name(model_name),
- ku.csv_logging_callback(model_name, label),
- ku.early_stopping(monitor_loss, 5)
- ]
-
- kwargs["callbacks"] = callbacks
- return nnc.dense_network(**kwargs)
-
-
-class NegativeSampling(LoggingMixin):
-
- def __init__(self):
- LoggingMixin.__init__(self, self.__class__.__name__, AppContext.default().default_log_file)
-
- def get_strategy_by_name(self, name: str, args: Namespace) -> Callable:
- #FIXME: Make args to dictionary
-
- if name == "def":
- return self.default_strategy(args.num_neg_samples)
- elif name == "ext1":
- return self.extended1_strategy(args.num_neg_cha, args.num_neg_sec, args.num_neg_sub, args.num_neg_oth)
- else:
- raise AssertionError("Unsupported negative sampling strategy: " + name)
-
- def default_strategy(self, num_negative_samples: int) -> Callable:
- def _sample(dictionary_df: DataFrame, line_icd10_code: str):
- negative_samples = dictionary_df.query("ICD10 != '%s'" % line_icd10_code)
-
- # Only necessary during development and tests with only very few examples
- if len(negative_samples) > 0:
- negative_samples = negative_samples.sample(min(num_negative_samples, len(negative_samples)))
-
- return negative_samples
-
- return _sample
-
- def extended1_strategy(self, num_chapter_samples, num_section_samples, num_subsection_samples, num_other_samples):
- def _sample(dictionary_df: DataFrame, icd10_code: str):
- icd10_chapter = icd10_code[0].lower()
- icd10_section = icd10_code[0:2].lower()
- icd10_subsection = icd10_code[0:3].lower()
-
- chapter_samples = dictionary_df.query("ICD10 != '%s' & ICD10_chapter == '%s'" % (icd10_code, icd10_chapter))
- if len(chapter_samples) > 0:
- chapter_samples = chapter_samples.sample(min(num_chapter_samples, len(chapter_samples)))
-
- section_samples = dictionary_df.query("ICD10 != '%s' & ICD10_section == '%s'" % (icd10_code, icd10_section))
- if len(section_samples) > 0:
- section_samples = section_samples.sample(min(num_section_samples, len(section_samples)))
-
- subsection_samples = dictionary_df.query("ICD10 != '%s' & ICD10_subsection == '%s'" % (icd10_code, icd10_subsection))
- if len(subsection_samples) > 0:
- subsection_samples = subsection_samples.sample(min(num_subsection_samples, len(subsection_samples)))
-
- exp_sim_samples = num_chapter_samples + num_section_samples + num_subsection_samples
- act_sim_samples = len(chapter_samples) + len(section_samples) + len(subsection_samples)
-
- other_samples = dictionary_df.query("ICD10 != '%s' & ICD10_chapter != '%s'" % (icd10_code, icd10_chapter))
- other_samples = other_samples.sample(min(num_other_samples + (exp_sim_samples - act_sim_samples), len(other_samples)))
-
- # print("#Chapter samples: ", len(chapter_samples))
- # print("#Section samples: ", len(section_samples))
- # print("#Subsection samples: ", len(subsection_samples))
- # print("#Other samples: ", len(other_samples))
-
- return pd.concat([chapter_samples, section_samples, subsection_samples, other_samples])
- return _sample
-
if __name__ == "__main__":
parser = argparse.ArgumentParser(prog="CLEF2018")
@@ -651,5 +358,3 @@ if __name__ == "__main__":
eval_result = clef18_task1.train_and_evaluate_classifiers(embedding_model, configuration, args.target_labels)
clef18_task1.save_evaluation_results(eval_result)
-
-
--
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