# %% import os os.environ['TOKENIZERS_PARALLELISM'] = 'false' import warnings warnings.filterwarnings("ignore") DEBUG=False USE_SIMPLIFIED_LABELS = True # <<< CHANGE THIS TO False TO USE ORIGINAL BIO LABELS # %% # !pip install -q seqeval # %% import gc import json import copy import time import pickle import numpy as np import pandas as pd from itertools import chain from transformers import AutoTokenizer from transformers import AutoModelForTokenClassification from transformers import get_cosine_schedule_with_warmup from tqdm import tqdm from seqeval.metrics import recall_score, precision_score from seqeval.metrics import f1_score import torch from torch import nn from torch.utils.data import Dataset, DataLoader from torch.nn.utils.rnn import pad_sequence from torch.nn import CrossEntropyLoss from torch.optim import AdamW import matplotlib.pyplot as plt from pylab import rcParams device = torch.device('cuda' if torch.cuda.is_available() else 'cpu') # %% [markdown] # # Config # %% exp_name_base = 'deberta_v3_large_w10_ado1_wd0_bs2_lr1e5_5epo' # Changed ado4 to ado1 exp_name = f"{exp_name_base}_{'simplified_labels' if USE_SIMPLIFIED_LABELS else 'original_bio_labels'}" backbone = 'microsoft/deberta-v3-large' TRAINING_MAX_LENGTH = 4096 batch_size = 2 lr = 1e-5 ds_rate = 0.3 attention_probs_dropout_prob = 0.4 hidden_dropout_prob = 0.1 wd = 0. pos_weight = 10 n_epochs = 5 use_amp = True # %% [markdown] # # Data # %% from sklearn.model_selection import train_test_split data = json.load(open('/export/home/acs/stud/t/tudor.farcasanu/SSL_Assignment/pii-data-detection-3rd-place-solution/datasets/train.json')) for sample in data: if len(set(sample['labels'])) > 1: sample['is_pos'] = 1 else: sample['is_pos'] = 0 print("original datapoints: ", len(data)) moredata = json.load(open('/export/home/acs/stud/t/tudor.farcasanu/SSL_Assignment/pii-data-detection-3rd-place-solution/datasets/moredata_dataset_fixed.json')) print("moredata datapoints: ", len(moredata)) # %% from sklearn.model_selection import GroupKFold import random random.seed(0) kf = GroupKFold(n_splits=5) folds = [] for i, (_, valid_index) in enumerate(kf.split(np.array(data), groups=[x['document'] for x in data])): folds.append([data[i]['document'] for i in valid_index]) # %% # Define simplified labels pii_types = [ 'EMAIL', 'ID_NUM', 'NAME_STUDENT', 'PHONE_NUM', 'STREET_ADDRESS', 'URL_PERSONAL', 'USERNAME' ] all_labels_simplified = sorted(pii_types + ['O']) label2id_simplified = {l: i for i, l in enumerate(all_labels_simplified)} id2label_simplified = {v: k for k, v in label2id_simplified.items()} # Original target BIO labels original_target_bio = sorted([ 'B-EMAIL', 'B-ID_NUM', 'B-NAME_STUDENT', 'B-PHONE_NUM', 'B-STREET_ADDRESS', 'B-URL_PERSONAL', 'B-USERNAME', 'I-ID_NUM', 'I-NAME_STUDENT', 'I-PHONE_NUM', 'I-STREET_ADDRESS', 'I-URL_PERSONAL', 'O' ]) if 'O' not in original_target_bio: original_target_bio_with_o = sorted(list(set(original_target_bio + ['O']))) else: original_target_bio_with_o = sorted(list(set(original_target_bio))) label2id_original_bio = {l: i for i, l in enumerate(original_target_bio_with_o)} id2label_original_bio = {v: k for k, v in label2id_original_bio.items()} if USE_SIMPLIFIED_LABELS: all_labels = all_labels_simplified label2id = label2id_simplified id2label = id2label_simplified print(f"Using SIMPLIFIED labels ({len(all_labels)}): {id2label}") else: all_labels = original_target_bio_with_o label2id = label2id_original_bio id2label = id2label_original_bio print(f"Using ORIGINAL BIO labels ({len(all_labels)}): {id2label}") # %% [markdown] # # Dataset # %% def tokenize(example, tokenizer, current_label2id, max_length, use_simplified): # Pass current_label2id and use_simplified flag # rebuild text from tokens text = [] char_labels = [] for t, l, ws in zip( example["tokens"], example["provided_labels"], example["trailing_whitespace"] ): text.append(t) current_label = l if use_simplified and l != "O": current_label = l[2:] # Strip "B-" or "I-" # Ensure current_label is in the target label set (either simplified or original BIO) # If a label from data isn't in the defined 'all_labels', map it to 'O'. if current_label not in current_label2id: current_label = "O" char_labels.extend([current_label] * len(t)) if ws: text.append(" ") char_labels.append("O") # Whitespace is always "O" tokenized = tokenizer("".join(text), return_offsets_mapping=True, truncation=False) if len(tokenized['input_ids']) > max_length: # "first N/2 + last N/2" truncation strategy first_half_len = max_length // 2 second_half_len = max_length - first_half_len keys_to_truncate = ['input_ids', 'attention_mask', 'offset_mapping'] for key in keys_to_truncate: if key in tokenized: original_list = tokenized[key] # takes the first 'first_half_len' elements and the last 'second_half_len' elements tokenized[key] = original_list[:first_half_len] + original_list[-second_half_len:] char_labels_arr = np.array(char_labels) text_str = "".join(text) token_labels = [] current_offset_mapping = tokenized["offset_mapping"] for start_idx, end_idx in current_offset_mapping: # Handle special tokens like [CLS], [SEP] which have (0,0) offset_mapping if start_idx == end_idx: token_labels.append(current_label2id["O"]) # Assign 'O' to special/empty tokens continue # Ensure indices are within the bounds of char_labels_arr and form a valid span # end_idx is exclusive for slicing, so it can be == len(char_labels_arr) if not (start_idx < end_idx and start_idx < len(char_labels_arr) and end_idx <= len(char_labels_arr)): token_labels.append(current_label2id["O"]) # Assign 'O' if token is outside char_labels range or invalid span continue char_span_labels = char_labels_arr[start_idx:end_idx] if not char_span_labels.size: token_labels.append(current_label2id["O"]) continue unique_labels, counts = np.unique(char_span_labels, return_counts=True) pii_labels_present_in_token = [] pii_counts_present_in_token = [] for lbl, count in zip(unique_labels, counts): # lbl is already simplified or original based on earlier logic if lbl != "O": pii_labels_present_in_token.append(lbl) pii_counts_present_in_token.append(count) if pii_labels_present_in_token: # If PII labels are present, choose the most frequent PII label most_frequent_pii_idx = np.argmax(pii_counts_present_in_token) most_frequent_pii_label = pii_labels_present_in_token[most_frequent_pii_idx] token_labels.append(current_label2id[most_frequent_pii_label]) else: # If only \'O\' is present or no PII labels found in the span token_labels.append(current_label2id["O"]) length = len(tokenized["input_ids"]) # Use dictionary-style access return {**tokenized, "labels": token_labels, "length": length} # %% tokenizer = AutoTokenizer.from_pretrained(backbone) class PIIDataset(Dataset): def __init__(self, tokenizer, data, current_label2id, max_length, use_simplified): # Pass current_label2id and use_simplified self.tokenizer = tokenizer self.data = copy.deepcopy(data) self.current_label2id = current_label2id # Store the active label2id self.max_length = max_length self.use_simplified = use_simplified for i in tqdm(range(len(self.data))): if self.data[i].get('input_ids') is None: self.data[i]['provided_labels'] = self.data[i]['labels'] self.data[i] = tokenize( self.data[i], self.tokenizer, self.current_label2id, # Pass the active label2id self.max_length, self.use_simplified # Pass the flag ) def __len__(self): return len(self.data) def __getitem__(self, idx): return self.data[idx] def collate_fn(batch): input_ids = [torch.tensor(x['input_ids']) for x in batch] attention_masks = [torch.tensor(x['attention_mask']) for x in batch] labels = [torch.tensor(x['labels']) for x in batch] input_ids_padded = pad_sequence(input_ids, batch_first=True, padding_value=tokenizer.pad_token_id if tokenizer.pad_token_id is not None else 0) attention_masks_padded = pad_sequence(attention_masks, batch_first=True, padding_value=0) labels_padded = pad_sequence(labels, batch_first=True, padding_value=-100) return { 'input_ids': input_ids_padded, 'attention_mask': attention_masks_padded, 'labels': labels_padded, } # Test with simplified labels ds = PIIDataset(tokenizer, data[:20], label2id, TRAINING_MAX_LENGTH, USE_SIMPLIFIED_LABELS) print(f"Example tokenized input IDs length: {len(ds[9]['input_ids'])}") print(f"Example tokenized labels: {ds[9]['labels']}") # %% [markdown] # # Model # %% model = AutoModelForTokenClassification.from_pretrained( backbone, attention_probs_dropout_prob=attention_probs_dropout_prob, hidden_dropout_prob=hidden_dropout_prob, num_labels=len(all_labels), # Use length of active labels id2label=id2label, # Use active id2label label2id=label2id, # Use active label2id ignore_mismatched_sizes=True ) # %% [markdown] # # Loss # %% weights = torch.ones(len(all_labels)) * pos_weight if 'O' in label2id: weights[label2id['O']] = 1 else: print(f"Warning: 'O' label not found in active label2id for weight assignment: {label2id}. Assuming last index for 'O'.") weights[-1] = 1 CE = nn.CrossEntropyLoss(weight=weights.to(device), ignore_index=-100) def criterion(logits, labels): return CE(logits.view(-1, len(all_labels)), labels.view(-1)) # %% [markdown] # # Metric # %% def compute_metrics(p, current_all_labels_list, th=0.5): predictions, labels = p o_label_str = "O" o_label_idx = -1 for i, lbl_str in enumerate(current_all_labels_list): if lbl_str == o_label_str: o_label_idx = i break if o_label_idx == -1: print(f"Warning: Could not find 'O' label in {current_all_labels_list} for metric thresholding. Using last index.") o_label_idx = len(current_all_labels_list) - 1 true_predictions = [] true_labels = [] for tmp, batch_l in zip(predictions, labels): batch_p_probs = torch.softmax(torch.from_numpy(tmp), dim=-1).numpy() o_column_probs_slice = batch_p_probs[:, :, o_label_idx] condition_mask = o_column_probs_slice < th o_column_probs_slice[condition_mask] = -9999 batch_p_final_ids = np.argmax(batch_p_probs, axis=-1) true_predictions.extend([current_all_labels_list[p_id] for (p_id, l_id) in zip(batch_p_final_ids.reshape(-1), batch_l.reshape(-1)) if l_id != -100]) true_labels.extend([current_all_labels_list[l_id] for l_id in batch_l.reshape(-1) if l_id != -100]) recall = recall_score([true_labels], [true_predictions], average='micro') # Use micro for overall precision = precision_score([true_labels], [true_predictions], average='micro') beta = 5 f5_score = (1 + beta**2) * precision * recall / ((beta**2 * precision) + recall + 1e-100) if precision + recall == 0: # Handle case where P and R are both zero f5_score = 0.0 results = { 'recall': recall, 'precision': precision, 'f1': f5_score } return results # %% [markdown] # # Train & Valid # %% def train_one_epoch(model, loader, optimizer, scheduler, scaler=None): model.train() running_loss = [] bar = tqdm(loader, total=len(loader)) for batch in bar: optimizer.zero_grad() input_ids = batch['input_ids'].to(device) attention_mask = batch['attention_mask'].to(device) labels = batch['labels'].to(device) if scaler is not None: with torch.cuda.amp.autocast(): outputs = model(input_ids, attention_mask=attention_mask, labels=labels) loss = criterion(outputs['logits'], labels) scaler.scale(loss).backward() scaler.step(optimizer) scaler.update() else: outputs = model(input_ids, attention_mask=attention_mask, labels=labels) loss = criterion(outputs['logits'], labels) loss.backward() optimizer.step() scheduler.step() running_loss.append(loss.item()) bar.set_description(f'train loss: {np.mean(running_loss[-20:]):.4f}') return np.mean(running_loss) def valid_one_epoch(model, loader): model.eval() running_loss = [] bar = tqdm(loader, total=len(loader)) predictions_logits = [] true_labels_list = [] with torch.no_grad(): for batch in bar: input_ids = batch['input_ids'].to(device) attention_mask = batch['attention_mask'].to(device) labels_batch = batch['labels'].to(device) outputs = model(input_ids, attention_mask=attention_mask) loss = criterion(outputs.logits, labels_batch) running_loss.append(loss.item()) predictions_logits.append(outputs.logits.cpu().numpy()) true_labels_list.append(labels_batch.cpu().numpy()) bar.set_description(f'valid loss: {np.mean(running_loss[-20:]):.4f}') # Pass the active all_labels (list of strings) to compute_metrics metrics_results = compute_metrics((predictions_logits, true_labels_list), all_labels) return np.mean(running_loss), metrics_results # %% [markdown] # # Scheduler # %% rcParams['figure.figsize'] = 20, 2 def get_scheduler(optimizer, num_training_steps, warmup_steps_ratio=0.1): return get_cosine_schedule_with_warmup( optimizer, int(num_training_steps * warmup_steps_ratio), num_training_steps ) opt = AdamW(model.parameters(), lr=lr) sch = get_scheduler(opt, 100, 0.1) lrs = [] for epoch in range(1, 100+1): sch.step() lrs.append(opt.param_groups[0]["lr"]) plt.plot(range(len(lrs)), lrs) # %% [markdown] # # Run # %% def run(fold,model_to_train): log_file = os.path.join('/export/home/acs/stud/t/tudor.farcasanu/SSL_Assignment/single_model/model/logs', f'{exp_name}.txt') model_save_dir_best = os.path.join('/export/home/acs/stud/t/tudor.farcasanu/SSL_Assignment/single_model/model', f'{exp_name}_fold{fold}_best_hf') model_save_dir_last = os.path.join('/export/home/acs/stud/t/tudor.farcasanu/SSL_Assignment/single_model/model', f'{exp_name}_fold{fold}_last_hf') os.makedirs(model_save_dir_best, exist_ok=True) os.makedirs(model_save_dir_last, exist_ok=True) optimizer_etc_file_last = os.path.join(model_save_dir_last, 'optimizer_etc_states.pth') valid_doc_ids = folds[fold] train_data = [x for x in data if (x['document'] not in valid_doc_ids) and ((x['is_pos'] == 1) or (x['is_pos'] == 0 and random.random() < ds_rate))] + moredata valid_data = [x for x in data if x['document'] in valid_doc_ids] dataset_train = PIIDataset(tokenizer, train_data, label2id, TRAINING_MAX_LENGTH, USE_SIMPLIFIED_LABELS) dataset_valid = PIIDataset(tokenizer, valid_data, label2id, TRAINING_MAX_LENGTH, USE_SIMPLIFIED_LABELS) print(len(dataset_train), len(dataset_valid)) loader_train = DataLoader(dataset_train, batch_size=batch_size, shuffle=True, num_workers=2, collate_fn=collate_fn) loader_valid = DataLoader(dataset_valid, batch_size=batch_size, shuffle=False, num_workers=2, collate_fn=collate_fn) current_model = model_to_train.to(device) optimizer = AdamW(current_model.parameters(), lr=lr, weight_decay=wd) scaler = torch.cuda.amp.GradScaler() if use_amp else None from_epoch = 0 metric_best = 0 scheduler = get_scheduler(optimizer, n_epochs*len(loader_train), 0.1) for epoch in range(1, n_epochs+1): print(time.ctime(), 'Epoch:', epoch) train_loss = train_one_epoch(current_model, loader_train, optimizer, scheduler, scaler) valid_loss, result = valid_one_epoch(current_model, loader_valid) metric = result["f1"] # F5 score on simplified labels content = time.ctime() + ' ' + \ f'Fold {fold}, Epoch {epoch}, lr: {optimizer.param_groups[0]["lr"]:.7f}, ' + \ f'train loss: {train_loss:.5f}, valid loss: {valid_loss:.5f}, ' + \ f'recall: {result["recall"]:.4f} precision: {result["precision"]:.4f} metric (F5 on simplified): {metric:.4f}.' print(content) with open(log_file, 'a') as appender: appender.write(content + '\n') if metric > metric_best: print(f'metric_best ({metric_best:.6f} --> {metric:.6f}). Saving model to {model_save_dir_best} ...') if not DEBUG: current_model.save_pretrained(model_save_dir_best, safe_serialization=True) tokenizer.save_pretrained(model_save_dir_best) metric_best = metric if not DEBUG: current_model.save_pretrained(model_save_dir_last, safe_serialization=True) tokenizer.save_pretrained(model_save_dir_last) torch.save( { 'epoch': epoch, 'optimizer_state_dict': optimizer.state_dict(), 'scheduler_state_dict': scheduler.state_dict(), 'scaler_state_dict': scaler.state_dict() if scaler else None, 'metric_best': metric_best, }, optimizer_etc_file_last ) del current_model torch.cuda.empty_cache() gc.collect() # %% run(0, model) # %%