file_id
stringlengths
6
9
content
stringlengths
1.13k
279k
local_path
stringlengths
67
70
kaggle_dataset_name
stringclasses
28 values
kaggle_dataset_owner
stringclasses
24 values
kversion
stringlengths
508
571
kversion_datasetsources
stringlengths
78
322
dataset_versions
stringclasses
29 values
datasets
stringclasses
29 values
users
stringclasses
24 values
script
stringlengths
1.1k
279k
df_info
stringclasses
1 value
has_data_info
bool
1 class
nb_filenames
int64
0
2
retreived_data_description
stringclasses
1 value
script_nb_tokens
int64
300
71.7k
upvotes
int64
0
26
tokens_description
int64
6
2.5k
tokens_script
int64
300
71.7k
69393429
<kaggle_start><data_title>progresbar2-local<data_name>progresbar2local <code># # The Bernstein Bears CRP Submission 1 # install necessary libraries from input # import progressbar library for offline usage # import text stat library for additional ml data prep FAST_DEV_RUN = False USE_CHECKPOINT = True USE_HIDDEN_IN_RGR = False N_FEATURES_TO_USE_HEAD = 1 N_FEATURES_TO_USE_TAIL = None # in this kernel, run train on all data to maximize score on held out data but use what we learned about optimal parameters # set to 16 bit precision to cut compute requirements/increase batch size capacity USE_16_BIT_PRECISION = True # set a seed value for consistent experimentation; optional, else leave as None SEED_VAL = 42 # set a train-validation split, .7 means 70% of train data and 30% to validation set TRAIN_VALID_SPLIT = 0.8 # if None, then don't split # set hyperparameters learned from tuning: https://www.kaggle.com/justinchae/tune-roberta-pytorch-lightning-optuna MAX_EPOCHS = 4 BATCH_SIZE = 16 GRADIENT_CLIP_VAL = 0.18318092164684585 LEARNING_RATE = 3.613894271216525e-05 TOKENIZER_MAX_LEN = 363 WARMUP_STEPS = 292 WEIGHT_DECAY = 0.004560699842170359 import kaggle_config from kaggle_config import ( WORKFLOW_ROOT, DATA_PATH, CACHE_PATH, FIG_PATH, MODEL_PATH, ANALYSIS_PATH, KAGGLE_INPUT, CHECKPOINTS_PATH, LOGS_PATH, ) INPUTS, DEVICE = kaggle_config.run() KAGGLE_TRAIN_PATH = kaggle_config.get_train_path(INPUTS) KAGGLE_TEST_PATH = kaggle_config.get_test_path(INPUTS) import pytorch_lightning as pl from pytorch_lightning import loggers as pl_loggers from pytorch_lightning import seed_everything from pytorch_lightning.callbacks import ModelCheckpoint, EarlyStopping from pytorch_lightning.tuner.batch_size_scaling import scale_batch_size from pytorch_lightning.tuner.lr_finder import _LRFinder, lr_find import torchmetrics import optuna from optuna.integration import PyTorchLightningPruningCallback from optuna.samplers import TPESampler, RandomSampler, CmaEsSampler from optuna.visualization import ( plot_intermediate_values, plot_optimization_history, plot_param_importances, ) import optuna.integration.lightgbm as lgb import lightgbm as lgm from sklearn.model_selection import ( KFold, cross_val_score, RepeatedKFold, train_test_split, ) from sklearn.ensemble import ExtraTreesClassifier from sklearn.decomposition import PCA from sklearn.feature_selection import ( RFE, f_regression, mutual_info_regression, SequentialFeatureSelector, ) from sklearn.linear_model import LogisticRegression from sklearn.preprocessing import StandardScaler from sklearn.svm import SVR from sklearn.metrics import mean_squared_error import math import textstat import torch import torch.nn.functional as F from torch.utils.data import Dataset, DataLoader from torch.utils.data.dataset import random_split import tensorflow as tf from transformers import ( RobertaForSequenceClassification, RobertaTokenizer, AdamW, get_linear_schedule_with_warmup, ) import os import pandas as pd import numpy as np import gc from functools import partial from typing import List, Dict from typing import Optional from argparse import ArgumentParser import random if SEED_VAL: random.seed(SEED_VAL) np.random.seed(SEED_VAL) seed_everything(SEED_VAL) NUM_DATALOADER_WORKERS = os.cpu_count() try: resolver = tf.distribute.cluster_resolver.TPUClusterResolver(tpu="") tf.config.experimental_connect_to_cluster(resolver) tf.tpu.experimental.initialize_tpu_system(resolver) n_tpus = len(tf.config.list_logical_devices("TPU")) except ValueError: n_tpus = 0 ACCELERATOR_TYPE = {} ACCELERATOR_TYPE.update( {"gpus": torch.cuda.device_count() if torch.cuda.is_available() else None} ) ACCELERATOR_TYPE.update({"tpu_cores": n_tpus if n_tpus > 0 else None}) # still debugging how to best toggle between tpu and gpu; there's too much code to configure to work simply print("ACCELERATOR_TYPE:\n", ACCELERATOR_TYPE) PRETTRAINED_ROBERTA_BASE_MODEL_PATH = "/kaggle/input/pre-trained-roberta-base" PRETRAINED_ROBERTA_BASE_TOKENIZER_PATH = "/kaggle/input/tokenizer-roberta" PRETRAINED_ROBERTA_BASE_TOKENIZER = RobertaTokenizer.from_pretrained( PRETRAINED_ROBERTA_BASE_TOKENIZER_PATH ) TUNED_CHECKPOINT_PATH = "/kaggle/input/best-crp-ckpt-4/crp_roberta_trial_4.ckpt" # from: https://www.kaggle.com/justinchae/crp-regression-with-roberta-and-lightgbm TUNED_BEST_ROBERTA_PATH = "/kaggle/input/my-best-tuned-roberta" """Implementing Lightning instead of torch.nn.Module """ class LitRobertaLogitRegressor(pl.LightningModule): def __init__( self, pre_trained_path: str, output_hidden_states: bool = False, num_labels: int = 1, layer_1_output_size: int = 64, layer_2_output_size: int = 1, learning_rate: float = 1e-5, task_name: Optional[str] = None, warmup_steps: int = 100, weight_decay: float = 0.0, adam_epsilon: float = 1e-8, batch_size: Optional[int] = None, train_size: Optional[int] = None, max_epochs: Optional[int] = None, n_gpus: Optional[int] = 0, n_tpus: Optional[int] = 0, accumulate_grad_batches=None, tokenizer=None, do_decode=False, ): """refactored from: https://www.kaggle.com/justinchae/my-bert-tuner and https://www.kaggle.com/justinchae/roberta-tuner""" super(LitRobertaLogitRegressor, self).__init__() # this saves class params as self.hparams self.save_hyperparameters() self.model = RobertaForSequenceClassification.from_pretrained( self.hparams.pre_trained_path, output_hidden_states=self.hparams.output_hidden_states, num_labels=self.hparams.num_labels, ) self.accelerator_multiplier = n_gpus if n_gpus > 0 else 1 self.config = self.model.config self.parameters = self.model.parameters self.save_pretrained = self.model.save_pretrained # these layers are not currently used, tbd in future iteration self.layer_1 = torch.nn.Linear(768, layer_1_output_size) self.layer_2 = torch.nn.Linear(layer_1_output_size, layer_2_output_size) self.tokenizer = tokenizer self.do_decode = do_decode self.output_hidden_states = output_hidden_states def rmse_loss(x, y): criterion = F.mse_loss loss = torch.sqrt(criterion(x, y)) return loss # TODO: enable toggle for various loss funcs and torchmetrics package self.loss_func = rmse_loss # self.eval_func = rmse_loss def setup(self, stage=None) -> None: if stage == "fit": # when this class is called by trainer.fit, this stage runs and so on # Calculate total steps tb_size = self.hparams.batch_size * self.accelerator_multiplier ab_size = self.hparams.accumulate_grad_batches * float( self.hparams.max_epochs ) self.total_steps = (self.hparams.train_size // tb_size) // ab_size def extract_logit_only(self, input_ids, attention_mask) -> float: output = self.model(input_ids=input_ids, attention_mask=attention_mask) logit = output.logits logit = logit.cpu().numpy().astype(float) return logit def extract_hidden_only(self, input_ids, attention_mask) -> np.array: output = self.model(input_ids=input_ids, attention_mask=input_ids) hidden_states = output.hidden_states x = torch.stack(hidden_states[-4:]).sum(0) m1 = torch.nn.Sequential(self.layer_1, self.layer_2, torch.nn.Flatten()) x = m1(x) x = torch.squeeze(x).cpu().numpy() return x def forward(self, input_ids, attention_mask) -> torch.Tensor: output = self.model(input_ids=input_ids, attention_mask=attention_mask) x = output.logits return x def training_step(self, batch, batch_idx: int) -> float: # refactored from: https://www.kaggle.com/justinchae/epoch-utils labels, encoded_batch, kaggle_ids = batch input_ids = encoded_batch["input_ids"] attention_mask = encoded_batch["attention_mask"] # per docs, keep train step separate from forward call output = self.model(input_ids=input_ids, attention_mask=attention_mask) y_hat = output.logits # quick reshape to align labels to predictions labels = labels.view(-1, 1) loss = self.loss_func(y_hat, labels) self.log("train_loss", loss) return loss def validation_step(self, batch, batch_idx: int) -> float: # refactored from: https://www.kaggle.com/justinchae/epoch-utils labels, encoded_batch, kaggle_ids = batch input_ids = encoded_batch["input_ids"] attention_mask = encoded_batch["attention_mask"] # this self call is calling the forward method y_hat = self(input_ids, attention_mask) # quick reshape to align labels to predictions labels = labels.view(-1, 1) loss = self.loss_func(y_hat, labels) self.log("val_loss", loss) return loss def predict(self, batch, batch_idx: int, dataloader_idx: int = None): # creating this predict method overrides the pl predict method target, encoded_batch, kaggle_ids = batch input_ids = encoded_batch["input_ids"] attention_mask = encoded_batch["attention_mask"] # this self call is calling the forward method y_hat = self(input_ids, attention_mask) # convert to numpy then list like struct to zip with ids y_hat = y_hat.cpu().numpy().ravel() # customizing the predict behavior to account for unique ids if self.tokenizer is not None and self.do_decode: target = target.cpu().numpy().ravel() if len(target) > 0 else None excerpt = self.tokenizer.batch_decode( input_ids.cpu().numpy(), skip_special_tokens=True, clean_up_tokenization_spaces=True, ) if self.output_hidden_states: hidden_states = self.extract_hidden_only( input_ids=input_ids, attention_mask=attention_mask ) else: hidden_states = None if target is not None: predictions = list( zip( kaggle_ids, target, y_hat # , hidden_states ) ) predictions = pd.DataFrame( predictions, columns=[ "id", "target", "logit" # , 'hidden_states' ], ) else: predictions = list( zip( kaggle_ids, y_hat # , hidden_states ) ) predictions = pd.DataFrame( predictions, columns=[ "id", "logit" # , 'hidden_states' ], ) else: predictions = list(zip(kaggle_ids, y_hat)) predictions = pd.DataFrame(predictions, columns=["id", "target"]) return predictions def configure_optimizers(self) -> torch.optim.Optimizer: # Reference: https://pytorch-lightning.readthedocs.io/en/latest/notebooks/lightning_examples/text-transformers.html model = self.model no_decay = ["bias", "LayerNorm.weight"] optimizer_grouped_parameters = [ { "params": [ p for n, p in model.named_parameters() if not any(nd in n for nd in no_decay) ], "weight_decay": self.hparams.weight_decay, }, { "params": [ p for n, p in model.named_parameters() if any(nd in n for nd in no_decay) ], "weight_decay": 0.0, }, ] optimizer = AdamW( optimizer_grouped_parameters, lr=self.hparams.learning_rate, eps=self.hparams.adam_epsilon, ) scheduler = get_linear_schedule_with_warmup( optimizer, num_warmup_steps=self.hparams.warmup_steps, num_training_steps=self.total_steps, ) scheduler = {"scheduler": scheduler, "interval": "step", "frequency": 1} return [optimizer], [scheduler] def my_collate_fn( batch, tokenizer, max_length: int = 100, return_tensors: str = "pt", padding: str = "max_length", truncation: bool = True, ): # source: https://www.kaggle.com/justinchae/nn-utils labels = [] batch_texts = [] kaggle_ids = [] for _label, batch_text, kaggle_id in batch: if _label is not None: labels.append(_label) batch_texts.append(batch_text) kaggle_ids.append(kaggle_id) if _label is not None: labels = torch.tensor(labels, dtype=torch.float) encoded_batch = tokenizer( batch_texts, return_tensors=return_tensors, padding=padding, max_length=max_length, truncation=truncation, ) return labels, encoded_batch, kaggle_ids class CommonLitDataset(Dataset): def __init__( self, df, text_col: str = "excerpt", label_col: str = "target", kaggle_id: str = "id", sample_size: Optional[str] = None, ): self.df = df if sample_size is None else df.sample(sample_size) self.text_col = text_col self.label_col = label_col self.kaggle_id = kaggle_id self.num_labels = ( len(df[label_col].unique()) if label_col in df.columns else None ) # source: https://www.kaggle.com/justinchae/nn-utils def __len__(self): return len(self.df) def __getitem__(self, idx): result = None text = self.df.iloc[idx][self.text_col] kaggle_id = self.df.iloc[idx][self.kaggle_id] if "target" in self.df.columns: target = self.df.iloc[idx][self.label_col] return target, text, kaggle_id else: return None, text, kaggle_id class CommonLitDataModule(pl.LightningDataModule): def __init__( self, tokenizer, train_path, collate_fn=None, max_length: int = 280, batch_size: int = 16, valid_path: Optional[str] = None, test_path: Optional[str] = None, train_valid_split: float = 0.6, dtypes=None, shuffle_dataloader: bool = True, num_dataloader_workers: int = NUM_DATALOADER_WORKERS, kfold: Optional[dict] = None, ): super(CommonLitDataModule, self).__init__() self.tokenizer = tokenizer self.train_path = train_path self.valid_path = valid_path self.test_path = test_path self.train_valid_split = train_valid_split self.dtypes = {"id": str} if dtypes is None else dtypes self.train_size = None self.train_df, self.train_data = None, None self.valid_df, self.valid_data = None, None self.test_df, self.test_data = None, None if collate_fn is not None: self.collate_fn = partial( collate_fn, tokenizer=tokenizer, max_length=max_length ) else: self.collate_fn = partial( my_collate_fn, batch=batch_size, tokenizer=tokenizer ) self.shuffle_dataloader = shuffle_dataloader self.batch_size = batch_size self.num_dataloader_workers = num_dataloader_workers # refactored from: https://www.kaggle.com/justinchae/nn-utils def _strip_extraneous(self, df): strip_cols = ["url_legal", "license"] if all(col in df.columns for col in strip_cols): extraneous_data = strip_cols return df.drop(columns=extraneous_data) else: return df def prepare(self, prep_type=None): if prep_type == "train": # creates just an instance of the train data as a pandas df self.train_df = ( self.train_path if isinstance(self.train_path, pd.DataFrame) else pd.read_csv(self.train_path, dtype=self.dtypes) ) self.train_df = self._strip_extraneous(self.train_df) if prep_type == "train_stage_2": self.train_df = ( self.train_path if isinstance(self.train_path, pd.DataFrame) else pd.read_csv(self.train_path, dtype=self.dtypes) ) self.train_df = self._strip_extraneous(self.train_df) self.train_size = int(len(self.train_df)) self.train_data = CommonLitDataset(df=self.train_df) def setup(self, stage: Optional[str] = None) -> None: if stage == "fit": # when this class is called by trainer.fit, this stage runs and so on self.train_df = ( self.train_path if isinstance(self.train_path, pd.DataFrame) else pd.read_csv(self.train_path, dtype=self.dtypes) ) self.train_df = self._strip_extraneous(self.train_df) self.train_size = int(len(self.train_df)) self.train_data = CommonLitDataset(df=self.train_df) if self.train_valid_split is not None and self.valid_path is None: self.train_size = int(len(self.train_df) * self.train_valid_split) self.train_data, self.valid_data = random_split( self.train_data, [self.train_size, len(self.train_df) - self.train_size], ) elif self.valid_path is not None: self.valid_df = ( self.valid_path if isinstance(self.valid_path, pd.DataFrame) else pd.read_csv(self.valid_path, dtype=self.dtypes) ) self.valid_data = CommonLitDataset(df=self.valid_df) if stage == "predict": self.test_df = ( self.test_path if isinstance(self.test_path, pd.DataFrame) else pd.read_csv(self.test_path, dtype=self.dtypes) ) self.test_df = self._strip_extraneous(self.test_df) self.test_data = CommonLitDataset(df=self.test_df) self.train_df = ( self.train_path if isinstance(self.train_path, pd.DataFrame) else pd.read_csv(self.train_path, dtype=self.dtypes) ) self.train_df = self._strip_extraneous(self.train_df) self.train_size = int(len(self.train_df)) self.train_data = CommonLitDataset(df=self.train_df) def kfold_data(self): # TODO: wondering how to integrate kfolds into the datamodule pass def train_dataloader(self) -> DataLoader: return DataLoader( self.train_data, batch_size=self.batch_size, shuffle=self.shuffle_dataloader, collate_fn=self.collate_fn, num_workers=self.num_dataloader_workers, pin_memory=True, ) def val_dataloader(self) -> DataLoader: if self.valid_data is None: return None else: return DataLoader( self.valid_data, batch_size=self.batch_size, shuffle=False, collate_fn=self.collate_fn, num_workers=self.num_dataloader_workers, pin_memory=True, ) def predict_dataloader(self) -> DataLoader: if self.test_data is None: return None else: return DataLoader( self.test_data, batch_size=self.batch_size, shuffle=False, collate_fn=self.collate_fn, num_workers=self.num_dataloader_workers, pin_memory=True, ) def add_textstat_features(df): # adding the text standard seems to boost the accuracy score a bit df["text_standard"] = df["excerpt"].apply(lambda x: textstat.text_standard(x)) df["text_standard_category"] = df["text_standard"].astype("category").cat.codes # counting ratio of difficult words by lexicon count df["difficult_words_ratio"] = df["excerpt"].apply( lambda x: textstat.difficult_words(x) ) df["difficult_words_ratio"] = df.apply( lambda x: x["difficult_words_ratio"] / textstat.lexicon_count(x["excerpt"]), axis=1, ) df["syllable_ratio"] = df["excerpt"].apply(lambda x: textstat.syllable_count(x)) df["syllable_ratio"] = df.apply( lambda x: x["syllable_ratio"] / textstat.lexicon_count(x["excerpt"]), axis=1 ) ### You can add/remove any feature below and it will be used in training and test df["coleman_liau_index"] = df["excerpt"].apply( lambda x: textstat.coleman_liau_index(x) ) df["flesch_reading_ease"] = df["excerpt"].apply( lambda x: textstat.flesch_reading_ease(x) ) df["smog_index"] = df["excerpt"].apply(lambda x: textstat.smog_index(x)) df["gunning_fog"] = df["excerpt"].apply(lambda x: textstat.gunning_fog(x)) df["flesch_kincaid_grade"] = df["excerpt"].apply( lambda x: textstat.flesch_kincaid_grade(x) ) df["automated_readability_index"] = df["excerpt"].apply( lambda x: textstat.automated_readability_index(x) ) df["dale_chall_readability_score"] = df["excerpt"].apply( lambda x: textstat.dale_chall_readability_score(x) ) df["linsear_write_formula"] = df["excerpt"].apply( lambda x: textstat.linsear_write_formula(x) ) ### df = df.drop(columns=["excerpt", "text_standard"]) return df def process_hidden_states(df, drop_hidden_states=False): # for convenience, moving hidden states to the far right of the df if drop_hidden_states: df.drop(columns=["hidden_states"], inplace=True) return df elif "hidden_states" in df.columns: df["hidden_state"] = df["hidden_states"] df.drop(columns=["hidden_states"], inplace=True) temp = df["hidden_state"].apply(pd.Series) temp = temp.rename(columns=lambda x: "hidden_state_" + str(x)) df = pd.concat([df, temp], axis=1) df.drop(columns=["hidden_state"], inplace=True) return df else: print("hidden_states not found in dataframe, skipping process_hidden_states") return df datamodule = CommonLitDataModule( collate_fn=my_collate_fn, tokenizer=PRETRAINED_ROBERTA_BASE_TOKENIZER, train_path=KAGGLE_TRAIN_PATH, test_path=KAGGLE_TEST_PATH, max_length=TOKENIZER_MAX_LEN, batch_size=BATCH_SIZE, train_valid_split=TRAIN_VALID_SPLIT, ) # manually calling this stage since we need some params to set up model initially datamodule.setup(stage="fit") if USE_CHECKPOINT: # model = LitRobertaLogitRegressor.load_from_checkpoint(TUNED_CHECKPOINT_PATH) trainer = pl.Trainer( gpus=ACCELERATOR_TYPE["gpus"], tpu_cores=ACCELERATOR_TYPE["tpu_cores"] ) model = LitRobertaLogitRegressor( pre_trained_path=TUNED_BEST_ROBERTA_PATH, train_size=datamodule.train_size, batch_size=datamodule.batch_size, output_hidden_states=USE_HIDDEN_IN_RGR, n_gpus=ACCELERATOR_TYPE["gpus"], accumulate_grad_batches=trainer.accumulate_grad_batches, learning_rate=LEARNING_RATE, warmup_steps=WARMUP_STEPS, max_epochs=MAX_EPOCHS, tokenizer=datamodule.tokenizer, ) trainer = pl.Trainer( gpus=ACCELERATOR_TYPE["gpus"], tpu_cores=ACCELERATOR_TYPE["tpu_cores"] ) else: checkpoint_filename = f"crp_roberta_trial_main" checkpoint_save = ModelCheckpoint( dirpath=CHECKPOINTS_PATH, filename=checkpoint_filename ) early_stopping_callback = EarlyStopping(monitor="val_loss", patience=2) trainer = pl.Trainer( max_epochs=MAX_EPOCHS, gpus=ACCELERATOR_TYPE["gpus"], tpu_cores=ACCELERATOR_TYPE["tpu_cores"], precision=16 if USE_16_BIT_PRECISION else 32, default_root_dir=CHECKPOINTS_PATH, gradient_clip_val=GRADIENT_CLIP_VAL, stochastic_weight_avg=True, callbacks=[checkpoint_save, early_stopping_callback], fast_dev_run=FAST_DEV_RUN, ) model = LitRobertaLogitRegressor( pre_trained_path=PRETTRAINED_ROBERTA_BASE_MODEL_PATH, train_size=datamodule.train_size, batch_size=datamodule.batch_size, n_gpus=trainer.gpus, n_tpus=trainer.tpu_cores, max_epochs=trainer.max_epochs, accumulate_grad_batches=trainer.accumulate_grad_batches, learning_rate=LEARNING_RATE, warmup_steps=WARMUP_STEPS, tokenizer=datamodule.tokenizer, ) trainer.fit(model, datamodule=datamodule) # let's also save the tuned roberta state which our model wraps around model_file_name = f"tuned_roberta_model" model_file_path = os.path.join(MODEL_PATH, model_file_name) model.save_pretrained(model_file_path) # clean up memory torch.cuda.empty_cache() gc.collect() # freeze the model for prediction model.eval() model.freeze() datamodule.setup(stage="predict") model.do_decode = True # run predict on the test data train_data_stage_two = trainer.predict( model=model, dataloaders=datamodule.train_dataloader() ) train_data_stage_two = pd.concat(train_data_stage_two).reset_index(drop=True) train_data_stage_two = pd.merge( left=train_data_stage_two, right=datamodule.train_df.drop(columns=["standard_error", "target"]), left_on="id", right_on="id", ) print(train_data_stage_two) # TODO: test whether we need to save and upload the fine-tuned state of roberta or if pytorch lightning checkpoints take care of it all train_data_stage_three = add_textstat_features(train_data_stage_two) label_data = train_data_stage_three[["id"]].copy(deep=True) train_data = train_data_stage_three.drop( columns=["id", "target", "text_standard_category"] ).copy(deep=True) train_data_cols = list(train_data.columns) target_data = train_data_stage_three[["target"]].copy(deep=True) scaler = StandardScaler() train_data_scaled = scaler.fit_transform(train_data) train_data_scaled = pd.DataFrame(train_data_scaled, columns=train_data_cols) TARGET_SCALER = StandardScaler() target_data_scaled = TARGET_SCALER.fit_transform(target_data) target_data_scaled = pd.DataFrame(target_data_scaled, columns=["target"]) regr = SVR(kernel="linear") regr.fit(train_data_scaled, target_data_scaled["target"]) print(" Assessment of Features ") print("R2 Score: ", regr.score(train_data_scaled, target_data_scaled["target"])) print( "RSME Score: ", math.sqrt( mean_squared_error( target_data_scaled["target"], regr.predict(train_data_scaled) ) ), ) # regr.coef_ is a array of n, 1 feats_coef = list(zip(train_data_cols, regr.coef_[0])) feature_analysis = pd.DataFrame(feats_coef, columns=["feature_col", "coef_val"]) feature_analysis["coef_val"] = feature_analysis["coef_val"] # .abs() feature_analysis = feature_analysis.sort_values("coef_val", ascending=False) feature_analysis.plot.barh( x="feature_col", y="coef_val", title="Comparison of Features and Importance" ) # select the top n features for use in final regression approach best_n_features = feature_analysis.head(N_FEATURES_TO_USE_HEAD)["feature_col"].to_list() # the opposite if N_FEATURES_TO_USE_TAIL is not None: worst_n_features = feature_analysis.tail(N_FEATURES_TO_USE_TAIL)[ "feature_col" ].to_list() best_n_features.extend(worst_n_features) # manually adding this categorical feature in if "text_standard_category" not in best_n_features: best_n_features.append("text_standard_category") best_n_features = list(set(best_n_features)) train_data = train_data_stage_three[best_n_features] DATASET = train_data.copy(deep=True) DATASET["target"] = target_data_scaled["target"] DATASET["id"] = label_data["id"] temp_cols = list( DATASET.drop(columns=["id", "target", "text_standard_category"]).columns ) DATASET_scaled = DATASET[temp_cols] scaler = StandardScaler() DATASET_scaled = scaler.fit_transform(DATASET_scaled) DATASET_scaled = pd.DataFrame(DATASET_scaled, columns=temp_cols) DATASET_scaled[["id", "target", "text_standard_category"]] = DATASET[ ["id", "target", "text_standard_category"] ] print(DATASET_scaled) Dataset = DATASET_scaled # https://medium.com/optuna/lightgbm-tuner-new-optuna-integration-for-hyperparameter-optimization-8b7095e99258 # https://www.kaggle.com/corochann/optuna-tutorial-for-hyperparameter-optimization RGR_MODELS = [] def objective(trial: optuna.trial.Trial, n_folds=5, shuffle=True): params = { "metric": "rmse", "boosting_type": "gbdt", "verbose": -1, "num_leaves": trial.suggest_int("num_leaves", 4, 512), "max_depth": trial.suggest_int("max_depth", 4, 512), "max_bin": trial.suggest_int("max_bin", 4, 512), "min_data_in_leaf": trial.suggest_int("min_data_in_leaf", 64, 512), "bagging_fraction": trial.suggest_uniform("bagging_fraction", 0.1, 1.0), "bagging_freq": trial.suggest_int("max_bin", 5, 10), "feature_fraction": trial.suggest_uniform("feature_fraction", 0.4, 1.0), "learning_rate": trial.suggest_float("bagging_fraction", 0.0005, 0.01), "n_estimators": trial.suggest_int("num_leaves", 10, 10000), "lambda_l1": trial.suggest_loguniform("lambda_l1", 1e-8, 10.0), "lambda_l2": trial.suggest_loguniform("lambda_l2", 1e-8, 10.0), } fold = KFold( n_splits=n_folds, shuffle=shuffle, random_state=SEED_VAL if shuffle else None ) valid_score = [] best_model_tracker = {} for fold_idx, (train_idx, valid_idx) in enumerate(fold.split(range(len(DATASET)))): train_data = ( Dataset.iloc[train_idx].drop(columns=["id", "target"]).copy(deep=True) ) train_target = Dataset[["target"]].iloc[train_idx].copy(deep=True) valid_data = ( Dataset.iloc[valid_idx].drop(columns=["id", "target"]).copy(deep=True) ) valid_target = Dataset[["target"]].iloc[valid_idx].copy(deep=True) lgbm_train = lgm.Dataset( train_data, label=train_target, categorical_feature=["text_standard_category"], ) lgbm_valid = lgm.Dataset( valid_data, label=valid_target, categorical_feature=["text_standard_category"], ) curr_model = lgm.train( params, train_set=lgbm_train, valid_sets=[lgbm_train, lgbm_valid], verbose_eval=-1, ) valid_pred = curr_model.predict( valid_data, num_iteration=curr_model.best_iteration ) best_score = curr_model.best_score["valid_1"]["rmse"] best_model_tracker.update({best_score: curr_model}) valid_score.append(best_score) best_model_score = min([k for k, v in best_model_tracker.items()]) best_model = best_model_tracker[best_model_score] RGR_MODELS.append(best_model) # RGR_MODELS.append({best_model_score: best_model}) # worst_rgr_model_idx = max([d.keys[0] for d in RGR_MODELS]) # RGR_MODELS[worst_rgr_model_idx] = {best_model_score: None} score = np.mean(valid_score) return score study = optuna.create_study(storage="sqlite:///lgm-study.db") study.optimize(objective, n_trials=256) plot_optimization_history(study).show() print("Best Trial: ", study.best_trial, "\n") # use the study parameters to create and train a lgbm regressor lgm_train_data = DATASET_scaled.drop(columns=["id"]).copy(deep=True) x_features = lgm_train_data.loc[:, lgm_train_data.columns != "target"] y_train = lgm_train_data[["target"]] lgm_train_set_full = lgm.Dataset( data=x_features, categorical_feature=["text_standard_category"], label=y_train ) gbm = lgm.train( study.best_trial.params, lgm_train_set_full, ) model.do_decode = True trainer = pl.Trainer( gpus=ACCELERATOR_TYPE["gpus"], tpu_cores=ACCELERATOR_TYPE["tpu_cores"] ) # run predict on the test data submission_stage_1 = trainer.predict( model=model, dataloaders=datamodule.predict_dataloader() ) submission_stage_1 = pd.concat(submission_stage_1).reset_index(drop=True) print(" Submission Stage 1: After RoBERTA\n") print(submission_stage_1) submission_stage_2 = pd.merge( left=submission_stage_1, right=datamodule.test_df, left_on="id", right_on="id", how="left", ) submission_stage_2 = add_textstat_features(submission_stage_2) feature_cols = list(submission_stage_2.drop(columns=["id"]).copy(deep=True).columns) predict_data = submission_stage_2.drop(columns=["id"]).copy(deep=True) predict_data = predict_data[best_n_features] temp_cols = list(predict_data.drop(columns=["text_standard_category"]).columns) predict_data_scaled = predict_data[temp_cols] predict_data_scaled = scaler.transform(predict_data_scaled) predict_data_scaled = pd.DataFrame(predict_data_scaled, columns=temp_cols) predict_data_scaled["text_standard_category"] = predict_data["text_standard_category"] submission = submission_stage_2[["id"]].copy(deep=True) submission["target"] = gbm.predict(predict_data_scaled) submission["target"] = TARGET_SCALER.inverse_transform(submission["target"]) print(" Final Stage After LGBM\n") print(submission) submission.to_csv("submission.csv", index=False) <|endoftext|>
/fsx/loubna/kaggle_data/kaggle-code-data/data/0069/393/69393429.ipynb
progresbar2local
justinchae
[{"Id": 69393429, "ScriptId": 18638229, "ParentScriptVersionId": NaN, "ScriptLanguageId": 9, "AuthorUserId": 4319244, "CreationDate": "07/30/2021 12:40:32", "VersionNumber": 36.0, "Title": "The Bernstein Bears CRP Submission 1", "EvaluationDate": "07/30/2021", "IsChange": true, "TotalLines": 887.0, "LinesInsertedFromPrevious": 13.0, "LinesChangedFromPrevious": 0.0, "LinesUnchangedFromPrevious": 874.0, "LinesInsertedFromFork": 409.0, "LinesDeletedFromFork": 274.0, "LinesChangedFromFork": 0.0, "LinesUnchangedFromFork": 478.0, "TotalVotes": 0}]
[{"Id": 92503477, "KernelVersionId": 69393429, "SourceDatasetVersionId": 2311525}, {"Id": 92503478, "KernelVersionId": 69393429, "SourceDatasetVersionId": 2312589}, {"Id": 92503476, "KernelVersionId": 69393429, "SourceDatasetVersionId": 2311499}]
[{"Id": 2311525, "DatasetId": 1394642, "DatasourceVersionId": 2352908, "CreatorUserId": 4319244, "LicenseName": "Unknown", "CreationDate": "06/07/2021 14:51:02", "VersionNumber": 1.0, "Title": "progresbar2-local", "Slug": "progresbar2local", "Subtitle": "Downloaded for offline use in kaggle \"no internet\" kernels", "Description": NaN, "VersionNotes": "Initial release", "TotalCompressedBytes": 0.0, "TotalUncompressedBytes": 0.0}]
[{"Id": 1394642, "CreatorUserId": 4319244, "OwnerUserId": 4319244.0, "OwnerOrganizationId": NaN, "CurrentDatasetVersionId": 2311525.0, "CurrentDatasourceVersionId": 2352908.0, "ForumId": 1413893, "Type": 2, "CreationDate": "06/07/2021 14:51:02", "LastActivityDate": "06/07/2021", "TotalViews": 934, "TotalDownloads": 4, "TotalVotes": 1, "TotalKernels": 3}]
[{"Id": 4319244, "UserName": "justinchae", "DisplayName": "Justin Chae", "RegisterDate": "01/12/2020", "PerformanceTier": 1}]
# # The Bernstein Bears CRP Submission 1 # install necessary libraries from input # import progressbar library for offline usage # import text stat library for additional ml data prep FAST_DEV_RUN = False USE_CHECKPOINT = True USE_HIDDEN_IN_RGR = False N_FEATURES_TO_USE_HEAD = 1 N_FEATURES_TO_USE_TAIL = None # in this kernel, run train on all data to maximize score on held out data but use what we learned about optimal parameters # set to 16 bit precision to cut compute requirements/increase batch size capacity USE_16_BIT_PRECISION = True # set a seed value for consistent experimentation; optional, else leave as None SEED_VAL = 42 # set a train-validation split, .7 means 70% of train data and 30% to validation set TRAIN_VALID_SPLIT = 0.8 # if None, then don't split # set hyperparameters learned from tuning: https://www.kaggle.com/justinchae/tune-roberta-pytorch-lightning-optuna MAX_EPOCHS = 4 BATCH_SIZE = 16 GRADIENT_CLIP_VAL = 0.18318092164684585 LEARNING_RATE = 3.613894271216525e-05 TOKENIZER_MAX_LEN = 363 WARMUP_STEPS = 292 WEIGHT_DECAY = 0.004560699842170359 import kaggle_config from kaggle_config import ( WORKFLOW_ROOT, DATA_PATH, CACHE_PATH, FIG_PATH, MODEL_PATH, ANALYSIS_PATH, KAGGLE_INPUT, CHECKPOINTS_PATH, LOGS_PATH, ) INPUTS, DEVICE = kaggle_config.run() KAGGLE_TRAIN_PATH = kaggle_config.get_train_path(INPUTS) KAGGLE_TEST_PATH = kaggle_config.get_test_path(INPUTS) import pytorch_lightning as pl from pytorch_lightning import loggers as pl_loggers from pytorch_lightning import seed_everything from pytorch_lightning.callbacks import ModelCheckpoint, EarlyStopping from pytorch_lightning.tuner.batch_size_scaling import scale_batch_size from pytorch_lightning.tuner.lr_finder import _LRFinder, lr_find import torchmetrics import optuna from optuna.integration import PyTorchLightningPruningCallback from optuna.samplers import TPESampler, RandomSampler, CmaEsSampler from optuna.visualization import ( plot_intermediate_values, plot_optimization_history, plot_param_importances, ) import optuna.integration.lightgbm as lgb import lightgbm as lgm from sklearn.model_selection import ( KFold, cross_val_score, RepeatedKFold, train_test_split, ) from sklearn.ensemble import ExtraTreesClassifier from sklearn.decomposition import PCA from sklearn.feature_selection import ( RFE, f_regression, mutual_info_regression, SequentialFeatureSelector, ) from sklearn.linear_model import LogisticRegression from sklearn.preprocessing import StandardScaler from sklearn.svm import SVR from sklearn.metrics import mean_squared_error import math import textstat import torch import torch.nn.functional as F from torch.utils.data import Dataset, DataLoader from torch.utils.data.dataset import random_split import tensorflow as tf from transformers import ( RobertaForSequenceClassification, RobertaTokenizer, AdamW, get_linear_schedule_with_warmup, ) import os import pandas as pd import numpy as np import gc from functools import partial from typing import List, Dict from typing import Optional from argparse import ArgumentParser import random if SEED_VAL: random.seed(SEED_VAL) np.random.seed(SEED_VAL) seed_everything(SEED_VAL) NUM_DATALOADER_WORKERS = os.cpu_count() try: resolver = tf.distribute.cluster_resolver.TPUClusterResolver(tpu="") tf.config.experimental_connect_to_cluster(resolver) tf.tpu.experimental.initialize_tpu_system(resolver) n_tpus = len(tf.config.list_logical_devices("TPU")) except ValueError: n_tpus = 0 ACCELERATOR_TYPE = {} ACCELERATOR_TYPE.update( {"gpus": torch.cuda.device_count() if torch.cuda.is_available() else None} ) ACCELERATOR_TYPE.update({"tpu_cores": n_tpus if n_tpus > 0 else None}) # still debugging how to best toggle between tpu and gpu; there's too much code to configure to work simply print("ACCELERATOR_TYPE:\n", ACCELERATOR_TYPE) PRETTRAINED_ROBERTA_BASE_MODEL_PATH = "/kaggle/input/pre-trained-roberta-base" PRETRAINED_ROBERTA_BASE_TOKENIZER_PATH = "/kaggle/input/tokenizer-roberta" PRETRAINED_ROBERTA_BASE_TOKENIZER = RobertaTokenizer.from_pretrained( PRETRAINED_ROBERTA_BASE_TOKENIZER_PATH ) TUNED_CHECKPOINT_PATH = "/kaggle/input/best-crp-ckpt-4/crp_roberta_trial_4.ckpt" # from: https://www.kaggle.com/justinchae/crp-regression-with-roberta-and-lightgbm TUNED_BEST_ROBERTA_PATH = "/kaggle/input/my-best-tuned-roberta" """Implementing Lightning instead of torch.nn.Module """ class LitRobertaLogitRegressor(pl.LightningModule): def __init__( self, pre_trained_path: str, output_hidden_states: bool = False, num_labels: int = 1, layer_1_output_size: int = 64, layer_2_output_size: int = 1, learning_rate: float = 1e-5, task_name: Optional[str] = None, warmup_steps: int = 100, weight_decay: float = 0.0, adam_epsilon: float = 1e-8, batch_size: Optional[int] = None, train_size: Optional[int] = None, max_epochs: Optional[int] = None, n_gpus: Optional[int] = 0, n_tpus: Optional[int] = 0, accumulate_grad_batches=None, tokenizer=None, do_decode=False, ): """refactored from: https://www.kaggle.com/justinchae/my-bert-tuner and https://www.kaggle.com/justinchae/roberta-tuner""" super(LitRobertaLogitRegressor, self).__init__() # this saves class params as self.hparams self.save_hyperparameters() self.model = RobertaForSequenceClassification.from_pretrained( self.hparams.pre_trained_path, output_hidden_states=self.hparams.output_hidden_states, num_labels=self.hparams.num_labels, ) self.accelerator_multiplier = n_gpus if n_gpus > 0 else 1 self.config = self.model.config self.parameters = self.model.parameters self.save_pretrained = self.model.save_pretrained # these layers are not currently used, tbd in future iteration self.layer_1 = torch.nn.Linear(768, layer_1_output_size) self.layer_2 = torch.nn.Linear(layer_1_output_size, layer_2_output_size) self.tokenizer = tokenizer self.do_decode = do_decode self.output_hidden_states = output_hidden_states def rmse_loss(x, y): criterion = F.mse_loss loss = torch.sqrt(criterion(x, y)) return loss # TODO: enable toggle for various loss funcs and torchmetrics package self.loss_func = rmse_loss # self.eval_func = rmse_loss def setup(self, stage=None) -> None: if stage == "fit": # when this class is called by trainer.fit, this stage runs and so on # Calculate total steps tb_size = self.hparams.batch_size * self.accelerator_multiplier ab_size = self.hparams.accumulate_grad_batches * float( self.hparams.max_epochs ) self.total_steps = (self.hparams.train_size // tb_size) // ab_size def extract_logit_only(self, input_ids, attention_mask) -> float: output = self.model(input_ids=input_ids, attention_mask=attention_mask) logit = output.logits logit = logit.cpu().numpy().astype(float) return logit def extract_hidden_only(self, input_ids, attention_mask) -> np.array: output = self.model(input_ids=input_ids, attention_mask=input_ids) hidden_states = output.hidden_states x = torch.stack(hidden_states[-4:]).sum(0) m1 = torch.nn.Sequential(self.layer_1, self.layer_2, torch.nn.Flatten()) x = m1(x) x = torch.squeeze(x).cpu().numpy() return x def forward(self, input_ids, attention_mask) -> torch.Tensor: output = self.model(input_ids=input_ids, attention_mask=attention_mask) x = output.logits return x def training_step(self, batch, batch_idx: int) -> float: # refactored from: https://www.kaggle.com/justinchae/epoch-utils labels, encoded_batch, kaggle_ids = batch input_ids = encoded_batch["input_ids"] attention_mask = encoded_batch["attention_mask"] # per docs, keep train step separate from forward call output = self.model(input_ids=input_ids, attention_mask=attention_mask) y_hat = output.logits # quick reshape to align labels to predictions labels = labels.view(-1, 1) loss = self.loss_func(y_hat, labels) self.log("train_loss", loss) return loss def validation_step(self, batch, batch_idx: int) -> float: # refactored from: https://www.kaggle.com/justinchae/epoch-utils labels, encoded_batch, kaggle_ids = batch input_ids = encoded_batch["input_ids"] attention_mask = encoded_batch["attention_mask"] # this self call is calling the forward method y_hat = self(input_ids, attention_mask) # quick reshape to align labels to predictions labels = labels.view(-1, 1) loss = self.loss_func(y_hat, labels) self.log("val_loss", loss) return loss def predict(self, batch, batch_idx: int, dataloader_idx: int = None): # creating this predict method overrides the pl predict method target, encoded_batch, kaggle_ids = batch input_ids = encoded_batch["input_ids"] attention_mask = encoded_batch["attention_mask"] # this self call is calling the forward method y_hat = self(input_ids, attention_mask) # convert to numpy then list like struct to zip with ids y_hat = y_hat.cpu().numpy().ravel() # customizing the predict behavior to account for unique ids if self.tokenizer is not None and self.do_decode: target = target.cpu().numpy().ravel() if len(target) > 0 else None excerpt = self.tokenizer.batch_decode( input_ids.cpu().numpy(), skip_special_tokens=True, clean_up_tokenization_spaces=True, ) if self.output_hidden_states: hidden_states = self.extract_hidden_only( input_ids=input_ids, attention_mask=attention_mask ) else: hidden_states = None if target is not None: predictions = list( zip( kaggle_ids, target, y_hat # , hidden_states ) ) predictions = pd.DataFrame( predictions, columns=[ "id", "target", "logit" # , 'hidden_states' ], ) else: predictions = list( zip( kaggle_ids, y_hat # , hidden_states ) ) predictions = pd.DataFrame( predictions, columns=[ "id", "logit" # , 'hidden_states' ], ) else: predictions = list(zip(kaggle_ids, y_hat)) predictions = pd.DataFrame(predictions, columns=["id", "target"]) return predictions def configure_optimizers(self) -> torch.optim.Optimizer: # Reference: https://pytorch-lightning.readthedocs.io/en/latest/notebooks/lightning_examples/text-transformers.html model = self.model no_decay = ["bias", "LayerNorm.weight"] optimizer_grouped_parameters = [ { "params": [ p for n, p in model.named_parameters() if not any(nd in n for nd in no_decay) ], "weight_decay": self.hparams.weight_decay, }, { "params": [ p for n, p in model.named_parameters() if any(nd in n for nd in no_decay) ], "weight_decay": 0.0, }, ] optimizer = AdamW( optimizer_grouped_parameters, lr=self.hparams.learning_rate, eps=self.hparams.adam_epsilon, ) scheduler = get_linear_schedule_with_warmup( optimizer, num_warmup_steps=self.hparams.warmup_steps, num_training_steps=self.total_steps, ) scheduler = {"scheduler": scheduler, "interval": "step", "frequency": 1} return [optimizer], [scheduler] def my_collate_fn( batch, tokenizer, max_length: int = 100, return_tensors: str = "pt", padding: str = "max_length", truncation: bool = True, ): # source: https://www.kaggle.com/justinchae/nn-utils labels = [] batch_texts = [] kaggle_ids = [] for _label, batch_text, kaggle_id in batch: if _label is not None: labels.append(_label) batch_texts.append(batch_text) kaggle_ids.append(kaggle_id) if _label is not None: labels = torch.tensor(labels, dtype=torch.float) encoded_batch = tokenizer( batch_texts, return_tensors=return_tensors, padding=padding, max_length=max_length, truncation=truncation, ) return labels, encoded_batch, kaggle_ids class CommonLitDataset(Dataset): def __init__( self, df, text_col: str = "excerpt", label_col: str = "target", kaggle_id: str = "id", sample_size: Optional[str] = None, ): self.df = df if sample_size is None else df.sample(sample_size) self.text_col = text_col self.label_col = label_col self.kaggle_id = kaggle_id self.num_labels = ( len(df[label_col].unique()) if label_col in df.columns else None ) # source: https://www.kaggle.com/justinchae/nn-utils def __len__(self): return len(self.df) def __getitem__(self, idx): result = None text = self.df.iloc[idx][self.text_col] kaggle_id = self.df.iloc[idx][self.kaggle_id] if "target" in self.df.columns: target = self.df.iloc[idx][self.label_col] return target, text, kaggle_id else: return None, text, kaggle_id class CommonLitDataModule(pl.LightningDataModule): def __init__( self, tokenizer, train_path, collate_fn=None, max_length: int = 280, batch_size: int = 16, valid_path: Optional[str] = None, test_path: Optional[str] = None, train_valid_split: float = 0.6, dtypes=None, shuffle_dataloader: bool = True, num_dataloader_workers: int = NUM_DATALOADER_WORKERS, kfold: Optional[dict] = None, ): super(CommonLitDataModule, self).__init__() self.tokenizer = tokenizer self.train_path = train_path self.valid_path = valid_path self.test_path = test_path self.train_valid_split = train_valid_split self.dtypes = {"id": str} if dtypes is None else dtypes self.train_size = None self.train_df, self.train_data = None, None self.valid_df, self.valid_data = None, None self.test_df, self.test_data = None, None if collate_fn is not None: self.collate_fn = partial( collate_fn, tokenizer=tokenizer, max_length=max_length ) else: self.collate_fn = partial( my_collate_fn, batch=batch_size, tokenizer=tokenizer ) self.shuffle_dataloader = shuffle_dataloader self.batch_size = batch_size self.num_dataloader_workers = num_dataloader_workers # refactored from: https://www.kaggle.com/justinchae/nn-utils def _strip_extraneous(self, df): strip_cols = ["url_legal", "license"] if all(col in df.columns for col in strip_cols): extraneous_data = strip_cols return df.drop(columns=extraneous_data) else: return df def prepare(self, prep_type=None): if prep_type == "train": # creates just an instance of the train data as a pandas df self.train_df = ( self.train_path if isinstance(self.train_path, pd.DataFrame) else pd.read_csv(self.train_path, dtype=self.dtypes) ) self.train_df = self._strip_extraneous(self.train_df) if prep_type == "train_stage_2": self.train_df = ( self.train_path if isinstance(self.train_path, pd.DataFrame) else pd.read_csv(self.train_path, dtype=self.dtypes) ) self.train_df = self._strip_extraneous(self.train_df) self.train_size = int(len(self.train_df)) self.train_data = CommonLitDataset(df=self.train_df) def setup(self, stage: Optional[str] = None) -> None: if stage == "fit": # when this class is called by trainer.fit, this stage runs and so on self.train_df = ( self.train_path if isinstance(self.train_path, pd.DataFrame) else pd.read_csv(self.train_path, dtype=self.dtypes) ) self.train_df = self._strip_extraneous(self.train_df) self.train_size = int(len(self.train_df)) self.train_data = CommonLitDataset(df=self.train_df) if self.train_valid_split is not None and self.valid_path is None: self.train_size = int(len(self.train_df) * self.train_valid_split) self.train_data, self.valid_data = random_split( self.train_data, [self.train_size, len(self.train_df) - self.train_size], ) elif self.valid_path is not None: self.valid_df = ( self.valid_path if isinstance(self.valid_path, pd.DataFrame) else pd.read_csv(self.valid_path, dtype=self.dtypes) ) self.valid_data = CommonLitDataset(df=self.valid_df) if stage == "predict": self.test_df = ( self.test_path if isinstance(self.test_path, pd.DataFrame) else pd.read_csv(self.test_path, dtype=self.dtypes) ) self.test_df = self._strip_extraneous(self.test_df) self.test_data = CommonLitDataset(df=self.test_df) self.train_df = ( self.train_path if isinstance(self.train_path, pd.DataFrame) else pd.read_csv(self.train_path, dtype=self.dtypes) ) self.train_df = self._strip_extraneous(self.train_df) self.train_size = int(len(self.train_df)) self.train_data = CommonLitDataset(df=self.train_df) def kfold_data(self): # TODO: wondering how to integrate kfolds into the datamodule pass def train_dataloader(self) -> DataLoader: return DataLoader( self.train_data, batch_size=self.batch_size, shuffle=self.shuffle_dataloader, collate_fn=self.collate_fn, num_workers=self.num_dataloader_workers, pin_memory=True, ) def val_dataloader(self) -> DataLoader: if self.valid_data is None: return None else: return DataLoader( self.valid_data, batch_size=self.batch_size, shuffle=False, collate_fn=self.collate_fn, num_workers=self.num_dataloader_workers, pin_memory=True, ) def predict_dataloader(self) -> DataLoader: if self.test_data is None: return None else: return DataLoader( self.test_data, batch_size=self.batch_size, shuffle=False, collate_fn=self.collate_fn, num_workers=self.num_dataloader_workers, pin_memory=True, ) def add_textstat_features(df): # adding the text standard seems to boost the accuracy score a bit df["text_standard"] = df["excerpt"].apply(lambda x: textstat.text_standard(x)) df["text_standard_category"] = df["text_standard"].astype("category").cat.codes # counting ratio of difficult words by lexicon count df["difficult_words_ratio"] = df["excerpt"].apply( lambda x: textstat.difficult_words(x) ) df["difficult_words_ratio"] = df.apply( lambda x: x["difficult_words_ratio"] / textstat.lexicon_count(x["excerpt"]), axis=1, ) df["syllable_ratio"] = df["excerpt"].apply(lambda x: textstat.syllable_count(x)) df["syllable_ratio"] = df.apply( lambda x: x["syllable_ratio"] / textstat.lexicon_count(x["excerpt"]), axis=1 ) ### You can add/remove any feature below and it will be used in training and test df["coleman_liau_index"] = df["excerpt"].apply( lambda x: textstat.coleman_liau_index(x) ) df["flesch_reading_ease"] = df["excerpt"].apply( lambda x: textstat.flesch_reading_ease(x) ) df["smog_index"] = df["excerpt"].apply(lambda x: textstat.smog_index(x)) df["gunning_fog"] = df["excerpt"].apply(lambda x: textstat.gunning_fog(x)) df["flesch_kincaid_grade"] = df["excerpt"].apply( lambda x: textstat.flesch_kincaid_grade(x) ) df["automated_readability_index"] = df["excerpt"].apply( lambda x: textstat.automated_readability_index(x) ) df["dale_chall_readability_score"] = df["excerpt"].apply( lambda x: textstat.dale_chall_readability_score(x) ) df["linsear_write_formula"] = df["excerpt"].apply( lambda x: textstat.linsear_write_formula(x) ) ### df = df.drop(columns=["excerpt", "text_standard"]) return df def process_hidden_states(df, drop_hidden_states=False): # for convenience, moving hidden states to the far right of the df if drop_hidden_states: df.drop(columns=["hidden_states"], inplace=True) return df elif "hidden_states" in df.columns: df["hidden_state"] = df["hidden_states"] df.drop(columns=["hidden_states"], inplace=True) temp = df["hidden_state"].apply(pd.Series) temp = temp.rename(columns=lambda x: "hidden_state_" + str(x)) df = pd.concat([df, temp], axis=1) df.drop(columns=["hidden_state"], inplace=True) return df else: print("hidden_states not found in dataframe, skipping process_hidden_states") return df datamodule = CommonLitDataModule( collate_fn=my_collate_fn, tokenizer=PRETRAINED_ROBERTA_BASE_TOKENIZER, train_path=KAGGLE_TRAIN_PATH, test_path=KAGGLE_TEST_PATH, max_length=TOKENIZER_MAX_LEN, batch_size=BATCH_SIZE, train_valid_split=TRAIN_VALID_SPLIT, ) # manually calling this stage since we need some params to set up model initially datamodule.setup(stage="fit") if USE_CHECKPOINT: # model = LitRobertaLogitRegressor.load_from_checkpoint(TUNED_CHECKPOINT_PATH) trainer = pl.Trainer( gpus=ACCELERATOR_TYPE["gpus"], tpu_cores=ACCELERATOR_TYPE["tpu_cores"] ) model = LitRobertaLogitRegressor( pre_trained_path=TUNED_BEST_ROBERTA_PATH, train_size=datamodule.train_size, batch_size=datamodule.batch_size, output_hidden_states=USE_HIDDEN_IN_RGR, n_gpus=ACCELERATOR_TYPE["gpus"], accumulate_grad_batches=trainer.accumulate_grad_batches, learning_rate=LEARNING_RATE, warmup_steps=WARMUP_STEPS, max_epochs=MAX_EPOCHS, tokenizer=datamodule.tokenizer, ) trainer = pl.Trainer( gpus=ACCELERATOR_TYPE["gpus"], tpu_cores=ACCELERATOR_TYPE["tpu_cores"] ) else: checkpoint_filename = f"crp_roberta_trial_main" checkpoint_save = ModelCheckpoint( dirpath=CHECKPOINTS_PATH, filename=checkpoint_filename ) early_stopping_callback = EarlyStopping(monitor="val_loss", patience=2) trainer = pl.Trainer( max_epochs=MAX_EPOCHS, gpus=ACCELERATOR_TYPE["gpus"], tpu_cores=ACCELERATOR_TYPE["tpu_cores"], precision=16 if USE_16_BIT_PRECISION else 32, default_root_dir=CHECKPOINTS_PATH, gradient_clip_val=GRADIENT_CLIP_VAL, stochastic_weight_avg=True, callbacks=[checkpoint_save, early_stopping_callback], fast_dev_run=FAST_DEV_RUN, ) model = LitRobertaLogitRegressor( pre_trained_path=PRETTRAINED_ROBERTA_BASE_MODEL_PATH, train_size=datamodule.train_size, batch_size=datamodule.batch_size, n_gpus=trainer.gpus, n_tpus=trainer.tpu_cores, max_epochs=trainer.max_epochs, accumulate_grad_batches=trainer.accumulate_grad_batches, learning_rate=LEARNING_RATE, warmup_steps=WARMUP_STEPS, tokenizer=datamodule.tokenizer, ) trainer.fit(model, datamodule=datamodule) # let's also save the tuned roberta state which our model wraps around model_file_name = f"tuned_roberta_model" model_file_path = os.path.join(MODEL_PATH, model_file_name) model.save_pretrained(model_file_path) # clean up memory torch.cuda.empty_cache() gc.collect() # freeze the model for prediction model.eval() model.freeze() datamodule.setup(stage="predict") model.do_decode = True # run predict on the test data train_data_stage_two = trainer.predict( model=model, dataloaders=datamodule.train_dataloader() ) train_data_stage_two = pd.concat(train_data_stage_two).reset_index(drop=True) train_data_stage_two = pd.merge( left=train_data_stage_two, right=datamodule.train_df.drop(columns=["standard_error", "target"]), left_on="id", right_on="id", ) print(train_data_stage_two) # TODO: test whether we need to save and upload the fine-tuned state of roberta or if pytorch lightning checkpoints take care of it all train_data_stage_three = add_textstat_features(train_data_stage_two) label_data = train_data_stage_three[["id"]].copy(deep=True) train_data = train_data_stage_three.drop( columns=["id", "target", "text_standard_category"] ).copy(deep=True) train_data_cols = list(train_data.columns) target_data = train_data_stage_three[["target"]].copy(deep=True) scaler = StandardScaler() train_data_scaled = scaler.fit_transform(train_data) train_data_scaled = pd.DataFrame(train_data_scaled, columns=train_data_cols) TARGET_SCALER = StandardScaler() target_data_scaled = TARGET_SCALER.fit_transform(target_data) target_data_scaled = pd.DataFrame(target_data_scaled, columns=["target"]) regr = SVR(kernel="linear") regr.fit(train_data_scaled, target_data_scaled["target"]) print(" Assessment of Features ") print("R2 Score: ", regr.score(train_data_scaled, target_data_scaled["target"])) print( "RSME Score: ", math.sqrt( mean_squared_error( target_data_scaled["target"], regr.predict(train_data_scaled) ) ), ) # regr.coef_ is a array of n, 1 feats_coef = list(zip(train_data_cols, regr.coef_[0])) feature_analysis = pd.DataFrame(feats_coef, columns=["feature_col", "coef_val"]) feature_analysis["coef_val"] = feature_analysis["coef_val"] # .abs() feature_analysis = feature_analysis.sort_values("coef_val", ascending=False) feature_analysis.plot.barh( x="feature_col", y="coef_val", title="Comparison of Features and Importance" ) # select the top n features for use in final regression approach best_n_features = feature_analysis.head(N_FEATURES_TO_USE_HEAD)["feature_col"].to_list() # the opposite if N_FEATURES_TO_USE_TAIL is not None: worst_n_features = feature_analysis.tail(N_FEATURES_TO_USE_TAIL)[ "feature_col" ].to_list() best_n_features.extend(worst_n_features) # manually adding this categorical feature in if "text_standard_category" not in best_n_features: best_n_features.append("text_standard_category") best_n_features = list(set(best_n_features)) train_data = train_data_stage_three[best_n_features] DATASET = train_data.copy(deep=True) DATASET["target"] = target_data_scaled["target"] DATASET["id"] = label_data["id"] temp_cols = list( DATASET.drop(columns=["id", "target", "text_standard_category"]).columns ) DATASET_scaled = DATASET[temp_cols] scaler = StandardScaler() DATASET_scaled = scaler.fit_transform(DATASET_scaled) DATASET_scaled = pd.DataFrame(DATASET_scaled, columns=temp_cols) DATASET_scaled[["id", "target", "text_standard_category"]] = DATASET[ ["id", "target", "text_standard_category"] ] print(DATASET_scaled) Dataset = DATASET_scaled # https://medium.com/optuna/lightgbm-tuner-new-optuna-integration-for-hyperparameter-optimization-8b7095e99258 # https://www.kaggle.com/corochann/optuna-tutorial-for-hyperparameter-optimization RGR_MODELS = [] def objective(trial: optuna.trial.Trial, n_folds=5, shuffle=True): params = { "metric": "rmse", "boosting_type": "gbdt", "verbose": -1, "num_leaves": trial.suggest_int("num_leaves", 4, 512), "max_depth": trial.suggest_int("max_depth", 4, 512), "max_bin": trial.suggest_int("max_bin", 4, 512), "min_data_in_leaf": trial.suggest_int("min_data_in_leaf", 64, 512), "bagging_fraction": trial.suggest_uniform("bagging_fraction", 0.1, 1.0), "bagging_freq": trial.suggest_int("max_bin", 5, 10), "feature_fraction": trial.suggest_uniform("feature_fraction", 0.4, 1.0), "learning_rate": trial.suggest_float("bagging_fraction", 0.0005, 0.01), "n_estimators": trial.suggest_int("num_leaves", 10, 10000), "lambda_l1": trial.suggest_loguniform("lambda_l1", 1e-8, 10.0), "lambda_l2": trial.suggest_loguniform("lambda_l2", 1e-8, 10.0), } fold = KFold( n_splits=n_folds, shuffle=shuffle, random_state=SEED_VAL if shuffle else None ) valid_score = [] best_model_tracker = {} for fold_idx, (train_idx, valid_idx) in enumerate(fold.split(range(len(DATASET)))): train_data = ( Dataset.iloc[train_idx].drop(columns=["id", "target"]).copy(deep=True) ) train_target = Dataset[["target"]].iloc[train_idx].copy(deep=True) valid_data = ( Dataset.iloc[valid_idx].drop(columns=["id", "target"]).copy(deep=True) ) valid_target = Dataset[["target"]].iloc[valid_idx].copy(deep=True) lgbm_train = lgm.Dataset( train_data, label=train_target, categorical_feature=["text_standard_category"], ) lgbm_valid = lgm.Dataset( valid_data, label=valid_target, categorical_feature=["text_standard_category"], ) curr_model = lgm.train( params, train_set=lgbm_train, valid_sets=[lgbm_train, lgbm_valid], verbose_eval=-1, ) valid_pred = curr_model.predict( valid_data, num_iteration=curr_model.best_iteration ) best_score = curr_model.best_score["valid_1"]["rmse"] best_model_tracker.update({best_score: curr_model}) valid_score.append(best_score) best_model_score = min([k for k, v in best_model_tracker.items()]) best_model = best_model_tracker[best_model_score] RGR_MODELS.append(best_model) # RGR_MODELS.append({best_model_score: best_model}) # worst_rgr_model_idx = max([d.keys[0] for d in RGR_MODELS]) # RGR_MODELS[worst_rgr_model_idx] = {best_model_score: None} score = np.mean(valid_score) return score study = optuna.create_study(storage="sqlite:///lgm-study.db") study.optimize(objective, n_trials=256) plot_optimization_history(study).show() print("Best Trial: ", study.best_trial, "\n") # use the study parameters to create and train a lgbm regressor lgm_train_data = DATASET_scaled.drop(columns=["id"]).copy(deep=True) x_features = lgm_train_data.loc[:, lgm_train_data.columns != "target"] y_train = lgm_train_data[["target"]] lgm_train_set_full = lgm.Dataset( data=x_features, categorical_feature=["text_standard_category"], label=y_train ) gbm = lgm.train( study.best_trial.params, lgm_train_set_full, ) model.do_decode = True trainer = pl.Trainer( gpus=ACCELERATOR_TYPE["gpus"], tpu_cores=ACCELERATOR_TYPE["tpu_cores"] ) # run predict on the test data submission_stage_1 = trainer.predict( model=model, dataloaders=datamodule.predict_dataloader() ) submission_stage_1 = pd.concat(submission_stage_1).reset_index(drop=True) print(" Submission Stage 1: After RoBERTA\n") print(submission_stage_1) submission_stage_2 = pd.merge( left=submission_stage_1, right=datamodule.test_df, left_on="id", right_on="id", how="left", ) submission_stage_2 = add_textstat_features(submission_stage_2) feature_cols = list(submission_stage_2.drop(columns=["id"]).copy(deep=True).columns) predict_data = submission_stage_2.drop(columns=["id"]).copy(deep=True) predict_data = predict_data[best_n_features] temp_cols = list(predict_data.drop(columns=["text_standard_category"]).columns) predict_data_scaled = predict_data[temp_cols] predict_data_scaled = scaler.transform(predict_data_scaled) predict_data_scaled = pd.DataFrame(predict_data_scaled, columns=temp_cols) predict_data_scaled["text_standard_category"] = predict_data["text_standard_category"] submission = submission_stage_2[["id"]].copy(deep=True) submission["target"] = gbm.predict(predict_data_scaled) submission["target"] = TARGET_SCALER.inverse_transform(submission["target"]) print(" Final Stage After LGBM\n") print(submission) submission.to_csv("submission.csv", index=False)
false
0
9,748
0
27
9,748
69716135
"<kaggle_start><data_title>ResNet-50<data_description># ResNet-50\n\n---\n\n## Deep Residual Learnin(...TRUNCATED)
/fsx/loubna/kaggle_data/kaggle-code-data/data/0069/716/69716135.ipynb
resnet50
null
"[{\"Id\": 69716135, \"ScriptId\": 18933277, \"ParentScriptVersionId\": NaN, \"ScriptLanguageId\": 9(...TRUNCATED)
"[{\"Id\": 93188012, \"KernelVersionId\": 69716135, \"SourceDatasetVersionId\": 9900}, {\"Id\": 9318(...TRUNCATED)
"[{\"Id\": 9900, \"DatasetId\": 6209, \"DatasourceVersionId\": 9900, \"CreatorUserId\": 484516, \"Li(...TRUNCATED)
"[{\"Id\": 6209, \"CreatorUserId\": 484516, \"OwnerUserId\": NaN, \"OwnerOrganizationId\": 1202.0, \(...TRUNCATED)
null
"# # Title:Skin-Lesion Segmentation\n# ### Importing the Libraries\nfrom keras.models import Model, (...TRUNCATED)
false
0
23,035
0
608
23,035
69293649
"<kaggle_start><code># 生成data文件\nimport os\nfrom os.path import join, isfile\nimport numpy a(...TRUNCATED)
/fsx/loubna/kaggle_data/kaggle-code-data/data/0069/293/69293649.ipynb
null
null
"[{\"Id\": 69293649, \"ScriptId\": 18546956, \"ParentScriptVersionId\": NaN, \"ScriptLanguageId\": 9(...TRUNCATED)
null
null
null
null
"# 生成data文件\nimport os\nfrom os.path import join, isfile\nimport numpy as np\nimport h5py\nf(...TRUNCATED)
false
0
19,374
0
6
19,374
69955597
"<kaggle_start><code>from learntools.core import binder\n\nbinder.bind(globals())\nfrom learntools.p(...TRUNCATED)
/fsx/loubna/kaggle_data/kaggle-code-data/data/0069/955/69955597.ipynb
null
null
"[{\"Id\": 69955597, \"ScriptId\": 19129579, \"ParentScriptVersionId\": NaN, \"ScriptLanguageId\": 9(...TRUNCATED)
null
null
null
null
"from learntools.core import binder\n\nbinder.bind(globals())\nfrom learntools.python.ex7 import *\n(...TRUNCATED)
false
0
2,582
0
6
2,582
69728033
"<kaggle_start><data_title>mlb_unnested<data_description>ref: https://www.kaggle.com/naotaka1128/cre(...TRUNCATED)
/fsx/loubna/kaggle_data/kaggle-code-data/data/0069/728/69728033.ipynb
mlb-unnested
naotaka1128
"[{\"Id\": 69728033, \"ScriptId\": 19051813, \"ParentScriptVersionId\": NaN, \"ScriptLanguageId\": 9(...TRUNCATED)
[{"Id": 93200478, "KernelVersionId": 69728033, "SourceDatasetVersionId": 2323733}]
"[{\"Id\": 2323733, \"DatasetId\": 1402611, \"DatasourceVersionId\": 2365235, \"CreatorUserId\": 164(...TRUNCATED)
"[{\"Id\": 1402611, \"CreatorUserId\": 164146, \"OwnerUserId\": 164146.0, \"OwnerOrganizationId\": N(...TRUNCATED)
"[{\"Id\": 164146, \"UserName\": \"naotaka1128\", \"DisplayName\": \"ML_Bear\", \"RegisterDate\": \"(...TRUNCATED)
"# ## About this notebook\n# + train on 2021 regular season data(use update data\n# + cv on may,2021(...TRUNCATED)
false
1
15,688
2
56
15,688
87643680
"<kaggle_start><data_title>OCTant project<data_name>octant-project\n<code># # Enhancing an open-sour(...TRUNCATED)
/fsx/loubna/kaggle_data/kaggle-code-data/data/0087/643/87643680.ipynb
octant-project
nwheeler443
"[{\"Id\": 87643680, \"ScriptId\": 24617507, \"ParentScriptVersionId\": NaN, \"ScriptLanguageId\": 9(...TRUNCATED)
[{"Id": 117988798, "KernelVersionId": 87643680, "SourceDatasetVersionId": 3175055}]
"[{\"Id\": 3175055, \"DatasetId\": 1929287, \"DatasourceVersionId\": 3224540, \"CreatorUserId\": 359(...TRUNCATED)
"[{\"Id\": 1929287, \"CreatorUserId\": 359577, \"OwnerUserId\": 359577.0, \"OwnerOrganizationId\": N(...TRUNCATED)
"[{\"Id\": 359577, \"UserName\": \"nwheeler443\", \"DisplayName\": \"Nicole Wheeler\", \"RegisterDat(...TRUNCATED)
"# # Enhancing an open-source OCT segmentation tool with manual segmentation capabilities\n# ## Intr(...TRUNCATED)
false
0
24,379
0
23
24,379
87084457
"<kaggle_start><code># # Objective of first fast YOLO inspired network\n# The first network will gen(...TRUNCATED)
/fsx/loubna/kaggle_data/kaggle-code-data/data/0087/084/87084457.ipynb
null
null
"[{\"Id\": 87084457, \"ScriptId\": 24134606, \"ParentScriptVersionId\": NaN, \"ScriptLanguageId\": 9(...TRUNCATED)
null
null
null
null
"# # Objective of first fast YOLO inspired network\n# The first network will generate a square where(...TRUNCATED)
false
0
3,597
0
6
3,597
87964295
"<kaggle_start><code># !curl https://raw.githubusercontent.com/pytorch/xla/master/contrib/scripts/en(...TRUNCATED)
/fsx/loubna/kaggle_data/kaggle-code-data/data/0087/964/87964295.ipynb
null
null
"[{\"Id\": 87964295, \"ScriptId\": 24700958, \"ParentScriptVersionId\": NaN, \"ScriptLanguageId\": 9(...TRUNCATED)
null
null
null
null
"# !curl https://raw.githubusercontent.com/pytorch/xla/master/contrib/scripts/env-setup.py -o pytorc(...TRUNCATED)
false
0
3,368
0
6
3,368
87597153
"<kaggle_start><code># # HW2B: Neural Machine Translation\n# In this project, you will build a neura(...TRUNCATED)
/fsx/loubna/kaggle_data/kaggle-code-data/data/0087/597/87597153.ipynb
null
null
"[{\"Id\": 87597153, \"ScriptId\": 24604634, \"ParentScriptVersionId\": NaN, \"ScriptLanguageId\": 9(...TRUNCATED)
null
null
null
null
"# # HW2B: Neural Machine Translation\n# In this project, you will build a neural machine translatio(...TRUNCATED)
false
0
8,157
0
6
8,157
87030978
"<kaggle_start><code>import numpy as np # linear algebra\nimport pandas as pd # data processing, C(...TRUNCATED)
/fsx/loubna/kaggle_data/kaggle-code-data/data/0087/030/87030978.ipynb
null
null
"[{\"Id\": 87030978, \"ScriptId\": 23915017, \"ParentScriptVersionId\": NaN, \"ScriptLanguageId\": 9(...TRUNCATED)
null
null
null
null
"import numpy as np # linear algebra\nimport pandas as pd # data processing, CSV file I/O (e.g. pd(...TRUNCATED)
false
0
5,933
0
6
5,933

Dataset Card for "empty_function_kaggle"

More Information needed

Downloads last month
38
Edit dataset card