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"""Evaluating models for BibleBERT |
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Copyright 2021 © Javier de la Rosa |
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""" |
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import argparse |
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import logging |
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import os |
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import random |
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import sys |
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from dataclasses import dataclass |
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from dataclasses import field |
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from pathlib import Path |
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from typing import Optional |
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import datasets |
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import numpy as np |
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import pandas as pd |
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from datasets import load_dataset |
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from nltk.tokenize import word_tokenize |
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from nltk.tokenize.treebank import TreebankWordDetokenizer |
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from seqeval.metrics.sequence_labeling import accuracy_score as seq_accuracy_score |
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from seqeval.metrics.sequence_labeling import f1_score as seq_f1_score |
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from seqeval.metrics.sequence_labeling import precision_score as seq_precision_score |
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from seqeval.metrics.sequence_labeling import recall_score as seq_recall_score |
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from seqeval.metrics.sequence_labeling import classification_report as seq_classification_report |
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from sklearn.metrics import accuracy_score as sk_accuracy_score |
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from sklearn.metrics import f1_score as sk_f1_score |
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from sklearn.metrics import precision_score as sk_precision_score |
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from sklearn.metrics import recall_score as sk_recall_score |
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from sklearn.metrics import classification_report as sk_classification_report |
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from tqdm import tqdm |
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from transformers import ( |
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AutoConfig, |
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AutoModelForTokenClassification, |
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AutoModelForSequenceClassification, |
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AutoTokenizer, |
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RobertaTokenizer, |
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RobertaTokenizerFast, |
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DataCollatorForTokenClassification, |
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DataCollatorWithPadding, |
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PreTrainedTokenizerFast, |
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Trainer, |
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TrainingArguments, |
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pipeline, |
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set_seed, |
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) |
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import wandb |
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BIBLES_BASE_URI = "https://huggingface.co/datasets/linhd-postdata/stanzas/resolve/main" |
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BIBLES = { |
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"validation": f"{BIBLES_BASE_URI}/eval.csv", |
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"test": f"{BIBLES_BASE_URI}/test.csv", |
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"train": f"{BIBLES_BASE_URI}/train.csv" |
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} |
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def printm(string): |
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print(str(string)) |
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def tokenize_and_align_labels( |
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tokenizer, examples, text_column_name, max_length, padding, |
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label_column_name, label_to_id, label_all_tokens |
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): |
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tokenized_inputs = tokenizer( |
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examples[text_column_name], |
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max_length=max_length, |
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padding=padding, |
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truncation=True, |
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is_split_into_words=True, |
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) |
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labels = [] |
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for i, label in enumerate(examples[label_column_name]): |
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word_ids = tokenized_inputs.word_ids(batch_index=i) |
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previous_word_idx = None |
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label_ids = [] |
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for word_idx in word_ids: |
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if word_idx is None: |
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label_ids.append(-100) |
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elif word_idx != previous_word_idx: |
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label_ids.append(label_to_id[label[word_idx]]) |
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else: |
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label_ids.append(label_to_id[label[word_idx]] if label_all_tokens else -100) |
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previous_word_idx = word_idx |
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labels.append(label_ids) |
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tokenized_inputs["labels"] = labels |
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return tokenized_inputs |
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def token_compute_metrics(pairs, label_list): |
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"""Token metrics based on seqeval""" |
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raw_predictions, labels = pairs |
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predictions = np.argmax(raw_predictions, axis=2) |
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true_predictions = [ |
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[label_list[p] for (p, l) in zip(prediction, label) if l != -100] |
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for prediction, label in zip(predictions, labels) |
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] |
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true_probas = [ |
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[label_list[p] for (p, l) in zip(prediction, label) if l != -100] |
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for prediction, label in zip(predictions, labels) |
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] |
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true_labels = [ |
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[label_list[l] for (p, l) in zip(prediction, label) if l != -100] |
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for prediction, label in zip(predictions, labels) |
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] |
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raw_scores = ( |
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np.exp(raw_predictions) / np.exp(raw_predictions).sum(-1, keepdims=True) |
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) |
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scores = raw_scores.max(axis=2) |
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true_scores = [ |
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[(s, l) for (s, l) in zip(score, label) if l != -100] |
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for score, label in zip(scores, labels) |
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] |
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metrics = { |
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"accuracy": seq_accuracy_score(true_labels, true_predictions), |
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"precision_micro": seq_precision_score(true_labels, true_predictions, average="micro"), |
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"recall_micro": seq_recall_score(true_labels, true_predictions, average="micro"), |
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"f1_micro": seq_f1_score(true_labels, true_predictions, average="micro"), |
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"precision_macro": seq_precision_score(true_labels, true_predictions, average="macro"), |
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"recall_macro": seq_recall_score(true_labels, true_predictions, average="macro"), |
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"f1_macro": seq_f1_score(true_labels, true_predictions, average="macro"), |
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} |
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reports = seq_classification_report( |
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true_labels, true_predictions, output_dict=True, zero_division=0, |
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) |
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for label, report in reports.items(): |
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for metric_key, metric_value in report.items(): |
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metric_title = metric_key.replace(" avg", "_avg", 1) |
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metrics.update({ |
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f"label_{label}_{metric_title}": metric_value, |
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}) |
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flat_true_labels = sum(true_labels, []) |
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flat_true_predictions = sum(true_predictions, []) |
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wandb.log({ |
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"matrix": wandb.sklearn.plot_confusion_matrix( |
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flat_true_labels, flat_true_predictions, label_list |
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) |
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}) |
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return metrics |
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def sequence_compute_metrics(pairs, label_list): |
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"""Sequence metrics based on sklearn""" |
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raw_predictions, labels = pairs |
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predictions = np.argmax(raw_predictions, axis=1) |
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metrics = { |
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"accuracy": sk_accuracy_score(labels, predictions), |
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"precision_micro": sk_precision_score(labels, predictions, average="micro"), |
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"recall_micro": sk_recall_score(labels, predictions, average="micro"), |
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"f1_micro": sk_f1_score(labels, predictions, average="micro"), |
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"precision_macro": sk_precision_score(labels, predictions, average="macro"), |
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"recall_macro": sk_recall_score(labels, predictions, average="macro"), |
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"f1_macro": sk_f1_score(labels, predictions, average="macro"), |
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} |
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reports = sk_classification_report( |
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labels, predictions, target_names=label_list, output_dict=True, |
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) |
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for label, report in reports.items(): |
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if not isinstance(report, dict): |
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report = {"": report} |
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for metric_key, metric_value in report.items(): |
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metric_title = metric_key.replace(" avg", "_avg", 1) |
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metrics.update({ |
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f"label_{label}_{metric_title}": metric_value, |
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}) |
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wandb.log({ |
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"roc": wandb.plot.roc_curve( |
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labels, raw_predictions, labels=label_list |
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), |
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"matrix": wandb.sklearn.plot_confusion_matrix( |
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labels, predictions, label_list |
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) |
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}) |
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return metrics |
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def write_file(kind, metrics, output_dir, save_artifact=False): |
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output_file = output_dir / f"{kind}_results.txt" |
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headers = [] |
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label_headers = [] |
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data = [] |
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label_data = [] |
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with open(output_file, "w") as writer: |
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printm(f"**{kind.capitalize()} results**") |
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for key, value in metrics.items(): |
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printm(f"\t{key} = {value}") |
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writer.write(f"{key} = {value}\n") |
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title = key.replace("eval_", "", 1) |
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if title.startswith("label_"): |
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label_headers.append(title.replace("label_", "", 1)) |
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label_data.append(value) |
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else: |
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headers.append(title) |
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data.append(value) |
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wandb.log({f"{kind}:{title}": value}) |
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wandb.log({kind: wandb.Table(data=[data], columns=headers)}) |
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if label_headers: |
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wandb.log({ |
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f"{kind}:labels": wandb.Table( |
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data=[label_data], columns=label_headers |
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) |
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}) |
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if save_artifact: |
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artifact = wandb.Artifact(kind, type="result") |
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artifact.add_file(str(output_file)) |
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wandb.log_artifact(artifact) |
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def dataset_select(dataset, size): |
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dataset_len = len(dataset) |
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if size < 0 or size > dataset_len: |
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return dataset |
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elif size <= 1: |
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return dataset.select(range(int(size * dataset_len))) |
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else: |
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return dataset.select(range(int(size))) |
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def main(args): |
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if args.run: |
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seed = random.randrange(10**3) |
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else: |
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seed = args.seed |
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set_seed(seed) |
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model_name = args.model_name |
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model_name = model_name[2:] if model_name.startswith("./") else model_name |
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model_name = model_name[1:] if model_name.startswith("/") else model_name |
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run_name = f"{model_name}_{args.task_name}" |
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run_name = f"{run_name}_{args.dataset_config or args.dataset_name}" |
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run_name = run_name.replace("/", "-") |
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run_name = f"{run_name}_l{str(args.dataset_language)}" |
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run_name = f"{run_name}_c{str(args.dataset_century)}" |
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run_name = f"{run_name}_e{str(args.num_train_epochs)}" |
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run_name = f"{run_name}_lr{str(args.learning_rate)}" |
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run_name = f"{run_name}_ws{str(args.warmup_steps)}" |
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run_name = f"{run_name}_wd{str(args.weight_decay)}" |
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run_name = f"{run_name}_s{str(seed)}" |
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run_name = f"{run_name}_eas{str(args.eval_accumulation_steps)}" |
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if args.max_length != 512: |
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run_name = f"{run_name}_seq{str(args.max_length)}" |
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if args.label_all_tokens: |
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run_name = f"{run_name}_labelall" |
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if args.run: |
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run_name = f"{run_name}_r{str(args.run)}" |
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output_dir = Path(args.output_dir) / run_name |
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padding = "longest" |
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max_length = args.max_length |
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weight_decay = args.weight_decay |
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adam_beta1 = 0.9 |
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adam_beta2 = 0.999 |
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adam_epsilon = 1e-08 |
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max_grad_norm = 1.0 |
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save_total_limit = 1 |
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load_best_model_at_end = False |
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wandb.init(name=run_name, project="postdata") |
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wandb.log({ |
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"seed": int(seed), |
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}) |
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print("\n\n#####################################") |
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print(args.model_name) |
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print(args.task_name) |
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print(args.dataset_config) |
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print(args.dataset_language) |
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print(args.dataset_century) |
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train_split = args.dataset_split_train |
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test_split = args.dataset_split_test |
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validation_split = args.dataset_split_validation |
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if ":" in args.dataset_name: |
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dataset_name, dataset_config = args.dataset_name.split(":") |
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else: |
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dataset_name = args.dataset_name |
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dataset_config = args.dataset_config |
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use_auth_token = os.environ.get("AUTH_TOKEN", None) |
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if dataset_config is None or len(dataset_config) == 0: |
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dataset = load_dataset(dataset_name, use_auth_token=use_auth_token) |
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elif dataset_name == "csv" and dataset_config: |
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dataset = load_dataset( |
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dataset_name, |
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data_files={ |
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"train": BIBLES["train"](dataset_config), |
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"validation": BIBLES["validation"](dataset_config), |
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"test": BIBLES["test"](dataset_config), |
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}, |
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use_auth_token=use_auth_token) |
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else: |
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dataset = load_dataset(dataset_name, dataset_config, use_auth_token=use_auth_token) |
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if args.dataset_language and args.dataset_language.lower() not in ("all", "balanced"): |
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dataset = dataset.filter(lambda x: x["language"] == args.dataset_language) |
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if args.dataset_century and args.dataset_century.lower() != "all": |
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dataset = dataset.filter(lambda x: x["century"] in args.dataset_century) |
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if dataset["train"].shape[0] == 0 or dataset["test"].shape[0] == 0 or dataset["validation"].shape[0] == 0: |
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print(f"Not enough data for {str(args.dataset_language)} on {str(args.dataset_century)}: {str(dataset.shape)}") |
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return |
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column_names = dataset[train_split].column_names |
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features = dataset[train_split].features |
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if "tokens" in column_names: |
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text_column_name = "tokens" |
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elif "text" in column_names: |
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text_column_name = "text" |
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else: |
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text_column_name = column_names[0] |
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if f"{args.task_name}_tags" in column_names: |
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label_column_name = f"{args.task_name}_tags" |
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elif "label" in column_names: |
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label_column_name = "label" |
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else: |
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label_column_name = column_names[1] |
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if dataset_name == "csv": |
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label_list = list(set(dataset[train_split][label_column_name])) |
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elif isinstance(features[label_column_name], datasets.features.Sequence): |
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label_list = features[label_column_name].feature.names |
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else: |
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label_list = features[label_column_name].names |
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label_to_id = {i: i for i in range(len(label_list))} |
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num_labels = len(label_list) |
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print(f"Number of labels: {num_labels}") |
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print({label.split("-")[-1] for label in label_list}) |
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config = AutoConfig.from_pretrained( |
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args.model_name, |
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num_labels=num_labels, |
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finetuning_task=args.task_name, |
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cache_dir=args.cache_dir, |
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force_download=args.force_download, |
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) |
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tokenizer = AutoTokenizer.from_pretrained( |
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args.model_name, |
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cache_dir=args.cache_dir, |
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use_fast=True, |
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force_download=args.force_download, |
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) |
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if isinstance(tokenizer, (RobertaTokenizer, RobertaTokenizerFast)): |
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tokenizer = AutoTokenizer.from_pretrained( |
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args.model_name, |
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cache_dir=args.cache_dir, |
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use_fast=True, |
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force_download=args.force_download, |
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add_prefix_space=True, |
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) |
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tokenizer_test_sentence = """ |
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Ya que el Ángel del Señor tiene nombre propio, y su nombre es Yahveh. |
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""".strip() |
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printm("""Tokenizer test""") |
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printm(f"> {tokenizer_test_sentence}") |
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printm(tokenizer.tokenize(tokenizer_test_sentence)) |
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printm(tokenizer(tokenizer_test_sentence).input_ids) |
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is_stilt = args.model_name in args.stilt.split(",") or args.stilt == "all" |
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model_config = dict( |
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from_tf=bool(".ckpt" in args.model_name), |
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config=config, |
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cache_dir=args.cache_dir, |
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force_download=args.force_download, |
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) |
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if args.task_name in ("pos", "ner"): |
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if is_stilt: |
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model_config.pop("config") |
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model = AutoModelForTokenClassification.from_pretrained( |
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args.model_name, num_labels=num_labels, ignore_mismatched_sizes=True, **model_config, |
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) |
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else: |
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model = AutoModelForTokenClassification.from_pretrained( |
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args.model_name, **model_config, |
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) |
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tokenized_datasets = dataset.map( |
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lambda examples: tokenize_and_align_labels( |
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tokenizer, examples, text_column_name, max_length, padding, |
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label_column_name, label_to_id, args.label_all_tokens), |
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batched=True, |
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load_from_cache_file=not args.overwrite_cache, |
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num_proc=os.cpu_count(), |
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) |
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data_collator = DataCollatorForTokenClassification(tokenizer) |
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compute_metrics = token_compute_metrics |
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else: |
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if is_stilt: |
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model_config.pop("config") |
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model = AutoModelForSequenceClassification.from_pretrained( |
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args.model_name, num_labels=num_labels, ignore_mismatched_sizes=True, **model_config, |
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) |
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else: |
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model = AutoModelForSequenceClassification.from_pretrained( |
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args.model_name, **model_config, |
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) |
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tokenized_datasets = dataset.map( |
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lambda examples: tokenizer( |
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examples[text_column_name], |
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max_length=max_length, |
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padding=padding, |
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truncation=True, |
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is_split_into_words=False, |
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), |
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batched=True, |
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load_from_cache_file=not args.overwrite_cache, |
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num_proc=os.cpu_count(), |
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) |
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data_collator = DataCollatorWithPadding( |
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tokenizer, |
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max_length=max_length, |
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padding=padding, |
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) |
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compute_metrics = sequence_compute_metrics |
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train_dataset = dataset_select( |
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tokenized_datasets[train_split], args.max_train_size |
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) |
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test_dataset = dataset_select( |
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tokenized_datasets[test_split], args.max_test_size |
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) |
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validation_dataset = dataset_select( |
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tokenized_datasets[validation_split], args.max_validation_size |
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) |
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wandb.log({ |
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"train_size": len(train_dataset), |
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"test_size": len(test_dataset), |
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"validation_size": len(validation_dataset), |
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}) |
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samples_per_batch = ( |
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train_dataset.shape[0] / args.train_batch_size |
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) |
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total_steps = args.num_train_epochs * samples_per_batch |
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warmup_steps = int(args.warmup_steps * total_steps) |
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wandb.log({ |
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"total_steps": int(total_steps), |
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"total_warmup_steps": warmup_steps |
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}) |
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do_eval = args.do_eval and (validation_split in tokenized_datasets) |
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do_test = args.do_test and (test_split in tokenized_datasets) |
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do_predict = args.do_predict and (test_split in tokenized_datasets) |
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training_args = TrainingArguments( |
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output_dir=output_dir.as_posix(), |
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overwrite_output_dir=args.overwrite_output_dir, |
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do_train=args.do_train, |
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do_eval=do_eval, |
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do_predict=do_test or do_predict, |
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per_device_train_batch_size=int(args.train_batch_size), |
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per_device_eval_batch_size=int(args.eval_batch_size or args.train_batch_size), |
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learning_rate=float(args.learning_rate), |
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weight_decay=weight_decay, |
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adam_beta1=adam_beta1, |
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adam_beta2=adam_beta2, |
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adam_epsilon=adam_epsilon, |
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max_grad_norm=max_grad_norm, |
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num_train_epochs=args.num_train_epochs, |
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warmup_steps=warmup_steps, |
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load_best_model_at_end=load_best_model_at_end, |
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seed=seed, |
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save_total_limit=save_total_limit, |
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run_name=run_name, |
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disable_tqdm=False, |
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eval_steps=1000, |
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eval_accumulation_steps=args.eval_accumulation_steps or None, |
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dataloader_num_workers=64, |
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) |
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trainer = Trainer( |
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model=model, |
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args=training_args, |
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train_dataset=train_dataset, |
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eval_dataset=validation_dataset if do_eval else None, |
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tokenizer=tokenizer, |
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data_collator=data_collator, |
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compute_metrics=lambda pairs: compute_metrics(pairs, label_list), |
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) |
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if args.do_train: |
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train_result = trainer.train() |
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trainer.save_model() |
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write_file("train", train_result.metrics, output_dir, save_artifact=args.save_artifacts) |
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trainer.state.save_to_json(output_dir / "trainer_state.json") |
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if do_eval: |
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printm(f"**Evaluate**") |
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results = trainer.evaluate() |
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write_file("eval", results, output_dir, save_artifact=args.save_artifacts) |
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if do_test or do_predict: |
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printm("**Test**") |
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predictions, labels, metrics = trainer.predict(test_dataset) |
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if not do_predict: |
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write_file("test", metrics, output_dir, save_artifact=args.save_artifacts) |
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if args.task_name in ("ner", "pos"): |
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predictions = np.argmax(predictions, axis=2) |
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true_predictions = [ |
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[label_list[p] for (p, l) in zip(prediction, label) if l != -100] |
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for prediction, label in zip(predictions, labels) |
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] |
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else: |
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predictions = np.argmax(predictions, axis=1) |
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true_predictions = [ |
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label_list[p] for (p, l) in zip(predictions, labels) if l != -100 |
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] |
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output_test_predictions_file = os.path.join(output_dir, "test_predictions.txt") |
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output_test_predictions = "\n".join(" ".join(map(str, p)) for p in true_predictions) |
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with open(output_test_predictions_file, "a+") as writer: |
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writer.write(output_test_predictions) |
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if args.save_artifacts: |
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artifact = wandb.Artifact("predictions", type="result") |
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artifact.add_file(output_test_predictions_file) |
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wandb.log_artifact(artifact) |
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if __name__ == "__main__": |
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parser = argparse.ArgumentParser(description=f"" |
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f"Evaluating BERT models for sequence classification on Bibles""" |
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f"", epilog=f"""Example usage: |
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{__file__} --task_name sequence --model_name "bert-base-multilingual-cased" |
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""", formatter_class=argparse.RawTextHelpFormatter) |
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parser.add_argument('--model_name', |
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metavar='model_name', help='Model name or path') |
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parser.add_argument('--dataset_name', default="csv", |
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metavar='dataset_name', help='Dataset name. It might enforce a config if added after a semicolon: "conll2002:es". This will ignore dataset_config, useful when run in grid search') |
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parser.add_argument('--dataset_config', |
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metavar='dataset_config', help='Dataset config name') |
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parser.add_argument('--dataset_language', default="all", |
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metavar='dataset_language', help='Dataset language name') |
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parser.add_argument('--dataset_century', default="all", |
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metavar='dataset_century', help='Dataset century') |
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parser.add_argument('--dataset_split_train', default="train", |
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metavar='dataset_split_train', help='Dataset train split name') |
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parser.add_argument('--dataset_split_test', default="test", |
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metavar='dataset_split_test', help='Dataset test split name') |
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parser.add_argument('--dataset_split_validation', default="validation", |
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metavar='dataset_split_validation', help='Dataset validation split name') |
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parser.add_argument('--max_train_size', type=float, default=-1.0, |
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metavar='max_train_size', help='Percentage of train dataset or number of rows to use') |
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parser.add_argument('--max_test_size', type=float, default=-1.0, |
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metavar='max_test_size', help='Percentage of test dataset or number of rows to use') |
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parser.add_argument('--max_validation_size', type=float, default=-1.0, |
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metavar='max_validation_size', help='Percentage of validation dataset or number of rows to use') |
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parser.add_argument('--do_train', |
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metavar='do_train', default=True, type=bool, |
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help='Run training', |
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) |
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parser.add_argument('--do_eval', |
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metavar='do_eval', default=True, type=bool, |
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help='Run evaluation on validation test', |
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) |
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parser.add_argument('--do_test', |
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metavar='do_test', default=True, type=bool, |
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help='Run evaluation on test set', |
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) |
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parser.add_argument('--do_predict', |
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metavar='do_predict', default=False, type=bool, |
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help='Run prediction only on test set', |
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) |
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parser.add_argument('--task_name', |
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metavar='task_name', default="ner", |
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help='Task name (supported in the dataset), either ner or pos', |
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) |
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parser.add_argument('--num_train_epochs', |
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metavar='num_train_epochs', default=4, type=float, |
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help='Number of training epochs', |
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) |
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parser.add_argument('--eval_accumulation_steps', |
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metavar='eval_accumulation_steps', default=0, type=int, |
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help='Number of predictions steps to accumulate the output tensors for, before moving the results to the CPU.', |
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) |
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parser.add_argument('--cache_dir', |
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metavar='cache_dir', default="/var/ml/cache/", |
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help='Cache dir for the transformer library', |
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) |
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parser.add_argument('--overwrite_cache', |
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metavar='overwrite_cache', default=False, type=bool, |
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help='Overwrite cache dir if present', |
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) |
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parser.add_argument('--output_dir', |
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metavar='output_dir', default="/var/ml/output/", |
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help='Output dir for models and logs', |
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) |
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parser.add_argument('--overwrite_output_dir', |
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metavar='overwrite_output_dir', default=True, type=bool, |
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help='Overwrite output dir if present', |
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) |
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parser.add_argument('--seed', |
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metavar='seed', type=int, default=2021, |
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help='Seed for the experiments', |
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) |
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parser.add_argument('--run', |
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metavar='run', type=int, |
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help='Control variable for doing several runs of the same experiment. It will force random seeds even across the same set of parameters fo a grid search', |
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) |
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parser.add_argument('--train_batch_size', |
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metavar='train_batch_size', type=int, default=8, |
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help='Batch size for training', |
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) |
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parser.add_argument('--eval_batch_size', |
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metavar='eval_batch_size', type=int, |
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help='Batch size for evaluation. Defaults to train_batch_size', |
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) |
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parser.add_argument('--max_length', |
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metavar='max_length', type=int, default=512, |
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help='Maximum sequence length', |
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) |
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parser.add_argument('--learning_rate', |
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metavar='learning_rate', type=str, default="3e-05", |
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help='Learning rate', |
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) |
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parser.add_argument('--warmup_steps', |
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metavar='warmup_steps', type=float, default=0.0, |
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help='Warmup steps as percentage of the total number of steps', |
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) |
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parser.add_argument('--weight_decay', |
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metavar='weight_decay', type=float, default=0.0, |
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help='Weight decay', |
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) |
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parser.add_argument('--label_all_tokens', |
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metavar='label_all_tokens', type=bool, default=False, |
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help=('Whether to put the label for one word on all tokens of ' |
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'generated by that word or just on the one (in which case the ' |
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'other tokens will have a padding index).'), |
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) |
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parser.add_argument('--force_download', |
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metavar='force_download', type=bool, default=False, |
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help='Force the download of model, tokenizer, and config', |
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) |
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parser.add_argument('--save_artifacts', |
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metavar='save_artifacts', type=bool, default=False, |
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help='Save train, eval, and test files in Weight & Biases', |
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) |
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parser.add_argument('--stilt', |
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metavar='stilt', type=str, default="", |
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help='Specify models already fine-tuned for other tasks', |
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) |
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args = parser.parse_args() |
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main(args) |
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