""" Utils for the fixation duration module. """ import torch from datasets import load_from_disk from typing import Dict, Any, List, Optional, Union import transformers from torch.utils.data import Dataset import datasets from tqdm import tqdm import random # def get_input_embeddings( # data_instance: Dict[str, Any], # tokenizer: transformers.GPT2TokenizerFast, # gpt2_model: transformers.GPT2Model, # aggregate: str = 'mean', # 'mean', 'sum' # #max_length: int = 128, # ): # # dummy code for now # sn_repr_len = data_instance['sn_repr_len'] # # the sentence # sn_words = data_instance['words_for_mapping'].split() # while sn_words[-1] == '[PAD]': # sn_words.pop() # # the scanpath # # remove the CLS token (already have a SEP token at the end of the sentence and the two will beconcatenated) # # the SEP token can stay # sp_ids = data_instance['sn_sp_repr'][sn_repr_len:][1:] # # cut off the trialing pad tokens # while sp_ids[-1] == 127: # sp_ids.pop() # # get the scanpath as fixated words # sp_words = list() # for sp_id in sp_ids: # sp_words.append(sn_words[sp_id]) # # TODO doesn't make sense to have CLS sn SEP sp SEP for auto-regressive model. BOS token # # join sentence and scanpath into strings and concatenate them # sn = ' '.join(sn_words) # sp = ' '.join(sp_words) # sn_sp = sn + ' ' + sp # encoded = tokenizer.encode_plus( # sn_sp, # add_special_tokens=False, # return_tensors='pt', # return_attention_mask=True, # ) # word_ids = torch.Tensor(encoded.word_ids()) # last_hidden = gpt2_model(encoded.input_ids).last_hidden_state # # aggregate the embeddings to word-level # embeddings = aggregate_input_embeddings( # embeddings=last_hidden, # word_ids=word_ids, # aggregate=aggregate, # ) # return embeddings, word_ids, sn_sp def get_embeddings_seq2seq( data_instance: Dict[str, Any], tokenizer: transformers.GPT2TokenizerFast, gpt2_model: transformers.GPT2Model, bert_embeddings: torch.nn.Embedding, instance_idx: int, aggregate: str = "mean", # 'mean', 'sum' max_length: int = 128, sp_pad_token: int = 127, ): """ Get the embeddings of the scanpath (fixated words) from the encoder. :param data_instance: the data instance from the dataset. :param tokenizer: the tokenizer. :param gpt2_model: the GPT2 model. :param bert_embeddings: the BERT embeddings. :param aggregate: the aggregation method, either summing or averaging the sub-word embeddings. :return: the embeddings of the scanpath, the padded fixation durations, and the attention mask. """ sn_repr_len = data_instance["sn_repr_len"] # the sentence sn_words = data_instance["words_for_mapping"].split() while sn_words[-1] == "[PAD]": sn_words.pop() # remove the CLS and SEP tokens sn_words = sn_words[1:-1] # chinese characters are one string in a list if sp_pad_token == 67: # chinese pad token sn_words = list(sn_words[0]) # the scanpath # remove the CLS token sp_ids = data_instance["sn_sp_repr"][sn_repr_len:][1:] # cut off the trailing pad tokens while sp_ids[-1] == sp_pad_token: sp_ids.pop() # remove the SEP token sp_ids = sp_ids[:-1] # make the scanpath ids start from 0 for re-ordering of the embeddings sp_ids = [sp_id - 1 for sp_id in sp_ids] # get the scanpath as fixated words sp_words = list() try: for sp_id in sp_ids: sp_words.append(sn_words[sp_id]) except: print(f"Error at index {instance_idx}") # breakpoint() return None, None, None # get the fixation durations fix_durs = data_instance["sn_sp_fix_dur"][sn_repr_len + 1 :] while fix_durs[-1] == 0: fix_durs.pop() # convert to tensor fix_durs = torch.Tensor(fix_durs) # get the sentence encoding sn_enc = tokenizer.encode_plus( sn_words, add_special_tokens=False, return_tensors="pt", is_split_into_words=True, ) sn_word_ids = torch.Tensor(sn_enc.word_ids()) # get the embeddings with torch.no_grad(): last_hidden = gpt2_model(sn_enc.input_ids).last_hidden_state # aggregate the embeddings to word-level sn_embeddings = aggregate_input_embeddings( embeddings=last_hidden, word_ids=sn_word_ids, aggregate=aggregate, ) # convert sp_ids to tensor sp_ids = torch.Tensor(sp_ids).long() # re-order the embeddings as scanpath sp_embeddings = sn_embeddings[:, sp_ids, :] # pad the embeddings and fixation durations to max input length # and get the attention mask sp_embeddings_padded, fix_durs_padded, attention_mask = padding_and_mask_seq2seq( sp_embeddings=sp_embeddings, fix_durs=fix_durs, bert_embeddings=bert_embeddings, max_length=max_length, ) return sp_embeddings_padded.squeeze(0), fix_durs_padded, attention_mask.squeeze(0) def padding_and_mask_seq2seq( sp_embeddings: torch.Tensor, bert_embeddings: torch.nn.Embedding, max_length: int, fix_durs: Optional[torch.Tensor] = None, inference: Optional[bool] = None, ): """ Add the BERT CLS token to the beginning of the scanpath embedding (needed for pooler output). Pad the scanpath embeddings and fixation durations to max input lenght. Use the PAD token embedding for padding. """ # get the embedding for the pad token pad_emb = bert_embeddings(torch.Tensor([0]).long()) cls_emb = bert_embeddings(torch.Tensor([101]).long()) # prepend the cls emb to the sp_embeddings sp_embeddings = torch.cat((cls_emb.unsqueeze(0), sp_embeddings), dim=1) # pad the embeddings current_length = sp_embeddings.size(1) padding_needed = max_length - current_length pad_tensor = pad_emb.unsqueeze(0).expand(1, padding_needed, -1) sp_embeddings_padded = torch.cat((sp_embeddings, pad_tensor), dim=1) # create attention mask sp_mask = torch.ones((1, current_length), dtype=torch.long) pad_mask = torch.zeros((1, padding_needed), dtype=torch.long) attention_mask = torch.cat((sp_mask, pad_mask), dim=1) if inference: return sp_embeddings_padded, attention_mask # prepend 0 to the fixation durations because the first word is the CLS token fix_durs = torch.cat((torch.Tensor([0]), fix_durs), dim=0) # pad the fixation durations fix_dur_pad = torch.zeros(padding_needed) fix_durs_padded = torch.cat((fix_durs, fix_dur_pad), dim=0) return sp_embeddings_padded, fix_durs_padded, attention_mask def aggregate_input_embeddings( embeddings: torch.Tensor, word_ids: torch.Tensor, aggregate: str = "mean", # 'mean', 'sum' ): """ Aggregate the embeddings that are input to the fixation module to word-level. :param embeddings: the last hidden state (contextualised embeddings) of the sentence-scanpath concatenation when passed through the GPT2 model. :param word_ids: the word ids of the sentence-scanpath concatenation. :param aggregate: the aggregation method, either summing or averaging the sub-word embeddings. :return: the aggregated word embeddings. """ # get the unique indices and inverse unique_indices, inverse_indices = torch.unique(word_ids, return_inverse=True) # sum the tensor along the dimension 1 (sequence length) for the same word ids summed_tensor = torch.zeros((1, unique_indices.size(0), embeddings.size(2))) summed_tensor = summed_tensor.scatter_add( 1, inverse_indices.unsqueeze(0).unsqueeze(-1).expand_as(embeddings), embeddings ) if aggregate == "sum": return summed_tensor elif aggregate == "mean": # count the occurrences of each word id (how many sub-words per word) counts = torch.zeros(unique_indices.size(0)).scatter_add( 0, inverse_indices, torch.ones_like(inverse_indices, dtype=torch.float) ) # average the summed tensor averaged_tensor = summed_tensor / counts.view(1, -1, 1) return averaged_tensor class Seq2SeqDataset(Dataset): def __init__( self, data: Dict[str, torch.Tensor], normalize: Optional[bool] = None, inference: Optional[bool] = None, ): super().__init__() self.data = data self.normalize = normalize self.inference = inference def __len__(self): return len(self.data["sp_embeddings"]) def __getitem__(self, idx): if self.inference: sample = { "sp_embeddings": self.data["sp_embeddings"][idx], "attention_masks": self.data["attention_masks"][idx], } return sample else: sample = { "sp_embeddings": self.data["sp_embeddings"][idx], "attention_masks": self.data["attention_masks"][idx], "fix_durs": self.data["fix_durs"][idx], } if self.normalize: sample["fix_durs_normalized"] = self.data["fix_durs_normalized"][idx] return sample def prepare_seq2seq_data( data: datasets.DatasetDict, tokenizer: transformers.GPT2TokenizerFast, gpt2_model: transformers.GPT2Model, bert_embeddings: torch.nn.Embedding, aggregate: str = "mean", max_length: int = 128, sp_pad_token: int = 127, ): """ Prepare the data for training the fixation duration module. :param data: the dataset. :param tokenizer: the tokenizer. :param gpt2_model: the GPT2 model. :param bert_embeddings: the BERT embeddings. :param aggregate: the aggregation method, either summing or averaging the sub-word embeddings. :param max_length: the maximum input length. :return: the data for training the fixation duration module. """ data_dict = { "sp_embeddings": [], "attention_masks": [], "fix_durs": [], } for idx, instance in tqdm(enumerate(data["train"])): sp_embeddings, fix_durs, attention_mask = get_embeddings_seq2seq( data_instance=instance, tokenizer=tokenizer, gpt2_model=gpt2_model, bert_embeddings=bert_embeddings, instance_idx=idx, aggregate=aggregate, max_length=max_length, sp_pad_token=sp_pad_token, ) if sp_embeddings is None: continue data_dict["sp_embeddings"].append(sp_embeddings) data_dict["attention_masks"].append(attention_mask) data_dict["fix_durs"].append(fix_durs) return data_dict def split_train_val_data( data: Dict[str, List[torch.Tensor]], val_size: float = 0.1, ): """ Split the train data into train and validation data. :param data: the data. :param val_size: the size of the validation data. :return: the train and validation data. """ num_samples = len(next(iter(data.values()))) # shuffle the indices indices = list(range(num_samples)) random.shuffle(indices) # compute the split point split_point = int(num_samples * val_size) train_indices = indices[split_point:] val_indices = indices[:split_point] train_data = {key: [value[i] for i in train_indices] for key, value in data.items()} val_data = {key: [value[i] for i in val_indices] for key, value in data.items()} return train_data, val_data def get_embeddings_seq2seq_hp( sn_repr_len: int, sn_words: List[str], sp_ids: List[int], tokenizer: transformers.GPT2TokenizerFast, gpt2_model: transformers.GPT2Model, bert_embeddings: torch.nn.Embedding, aggregate: str = "mean", max_length: int = 128, sp_pad_token: int = 127, ): """ Get the embeddings of the scanpath (fixated words) from the encoder. :param sn_repr_len: the length of the sentence representation. :param sn_words: the words of the sentence. :param sp_ids: the scanpath ids. :param tokenizer: the tokenizer. :param gpt2_model: the GPT2 model. :param bert_embeddings: the BERT embeddings. :param aggregate: the aggregation method, either summing or averaging the sub-word embeddings. :return: the embeddings of the scanpath, the padded fixation durations, and the attention mask. """ pad_idx = [i for i, word in enumerate(sn_words) if word == "[PAD]"] sep_idx = [sn_words.index("[SEP]")] all_remove_idx = [0] # for CLS all_remove_idx += sep_idx all_remove_idx += pad_idx # get rid of trailing pad tokens in sentence while sn_words[-1] == "[PAD]": sn_words.pop() # get rid of the CLS and SEP tokens sn_words = sn_words[1:-1] # the scanpath # get rid of predicted CLS, SEP and wrongly predicted PAD tokens (will throw error) sp_ids = [sp_id for sp_id in sp_ids if sp_id not in all_remove_idx] # make the scanpath ids start from 0 for re-ordering of the embeddings sp_ids = [sp_id - 1 for sp_id in sp_ids] # get the scanpath as fixated words sp_words = list() for sp_id in sp_ids: sp_words.append(sn_words[sp_id]) # get the sentence encoding sn_enc = tokenizer.encode_plus( sn_words, add_special_tokens=False, return_tensors="pt", is_split_into_words=True, ) sn_word_ids = torch.Tensor(sn_enc.word_ids()) # get the embeddings with torch.no_grad(): last_hidden = gpt2_model(sn_enc.input_ids).last_hidden_state # aggregate the embeddings to word-level sn_embeddings = aggregate_input_embeddings( embeddings=last_hidden, word_ids=sn_word_ids, aggregate=aggregate, ) # convert sp_ids to tensor sp_ids = torch.Tensor(sp_ids).long() # re-order the embeddings as scanpath sp_embeddings = sn_embeddings[:, sp_ids, :] # pad the embeddings to max input length and get the attention mask sp_embeddings_padded, attention_mask = padding_and_mask_seq2seq( sp_embeddings=sp_embeddings, bert_embeddings=bert_embeddings, max_length=max_length, inference=True, ) return sp_embeddings_padded.squeeze(0), attention_mask.squeeze(0) def prepare_seq2seq_data_hp( scandl_output: Dict[str, Any], tokenizer: transformers.GPT2TokenizerFast, gpt2_model: transformers.GPT2Model, bert_embeddings: torch.nn.Embedding, aggregate: str = "mean", max_length: int = 128, sp_pad_token: int = 127, ): """ Prepare the scandl output for inference of the hyper-parameter search of the Seq2Seq fixation duration model. :param scandl_output: the ScanDL output. :return: the data for inference. """ data_dict = { "sp_embeddings": [], "attention_masks": [], "original_fix_durs": [], "predicted_sp_ids": [], "reader_ids": [], "sn_ids": [], } for idx in tqdm(range(len(scandl_output["predicted_sp_ids"]))): sn_repr_len = scandl_output["sn_repr_len"][idx] if sp_pad_token == 67: # for Chinese: make sure the words are split correctly (chinese characters have no whitespace) sn_words = scandl_output["words_for_mapping"][idx].split() sn_words = [sn_words[0]] + list(sn_words[1]) + sn_words[2:] else: sn_words = scandl_output["words_for_mapping"][idx].split() sp_ids = scandl_output["predicted_sp_ids"][idx] try: sp_embeddings, attention_mask = get_embeddings_seq2seq_hp( sn_repr_len=sn_repr_len, sn_words=sn_words, sp_ids=sp_ids, tokenizer=tokenizer, gpt2_model=gpt2_model, bert_embeddings=bert_embeddings, aggregate=aggregate, max_length=max_length, sp_pad_token=sp_pad_token, ) # get the original fixation durations fix_durs = scandl_output["sn_sp_fix_dur"][idx][sn_repr_len:] while fix_durs[-1] == 0: fix_durs.pop() fix_durs.append(0) data_dict["sp_embeddings"].append(sp_embeddings) data_dict["attention_masks"].append(attention_mask) data_dict["original_fix_durs"].append(str(fix_durs)) data_dict["predicted_sp_ids"].append(str(sp_ids)) data_dict["reader_ids"].append(scandl_output["reader_ids"][idx]) data_dict["sn_ids"].append(scandl_output["sn_ids"][idx]) except: print(f"Error at index {idx}") continue return data_dict class Seq2SeqDatasetHP(Dataset): def __init__( self, data: Dict[str, Union[torch.Tensor, Any]], ): super().__init__() self.data = data def __len__(self): return len(self.data["sp_embeddings"]) def __getitem__(self, idx): sample = { "sp_embeddings": self.data["sp_embeddings"][idx], "attention_masks": self.data["attention_masks"][idx], #'predicted_sp_words': self.data['predicted_sp_words'][idx], #'original_sp_words': self.data['original_sp_words'][idx], "predicted_sp_ids": self.data["predicted_sp_ids"][idx], # 'original_sp_ids': self.data['original_sp_ids'][idx], # 'original_sn': self.data['original_sn'][idx], "sn_ids": self.data["sn_ids"][idx], "reader_ids": self.data["reader_ids"][idx], # 'sn_repr_len': self.data['sn_repr_len'][idx], # 'words_for_mapping': self.data['words_for_mapping'][idx], # 'sn_sp_repr': self.data['sn_sp_repr'][idx], # 'sn_sp_fix_dur': self.data['sn_sp_fix_dur'][idx], "original_fix_durs": self.data["original_fix_durs"][idx], } return sample