Instructions to use apps1/medical_studentv2 with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use apps1/medical_studentv2 with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("text-classification", model="apps1/medical_studentv2", trust_remote_code=True)# Load model directly from transformers import AutoModelForSequenceClassification model = AutoModelForSequenceClassification.from_pretrained("apps1/medical_studentv2", trust_remote_code=True, dtype="auto") - Notebooks
- Google Colab
- Kaggle
| from typing import Optional, Union | |
| import torch | |
| from torch import nn | |
| from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss | |
| from transformers.cache_utils import Cache | |
| from transformers.models.bert.modeling_bert import BertEncoder, BertPooler, BertPreTrainedModel, BertOnlyMLMHead | |
| from transformers.modeling_attn_mask_utils import _prepare_4d_attention_mask_for_sdpa, _prepare_4d_causal_attention_mask_for_sdpa | |
| from transformers.modeling_outputs import ( | |
| BaseModelOutputWithPoolingAndCrossAttentions, | |
| MaskedLMOutput, | |
| SequenceClassifierOutput, | |
| ) | |
| from transformers.utils import auto_docstring, logging | |
| from .configuration_bert_hash import BertHashConfig | |
| logger = logging.get_logger(__name__) | |
| class BertHashTokens(nn.Module): | |
| """ | |
| Module that embeds token vocabulary to an intermediate embeddings layer then projects those embeddings to the | |
| hidden size. | |
| The number of projections is like a hash. Setting the projections parameter to 5 is like generating a | |
| 160-bit hash (5 x float32) for each token. That hash is then projected to the hidden size. | |
| This significantly reduces the number of parameters necessary for token embeddings. | |
| For example: | |
| Standard token embeddings: | |
| 30,522 (vocab size) x 768 (hidden size) = 23,440,896 parameters | |
| 23,440,896 x 4 (float32) = 93,763,584 bytes | |
| Hash token embeddings: | |
| 30,522 (vocab size) x 5 (hash buckets) + 5 x 768 (projection matrix)= 156,450 parameters | |
| 156,450 x 4 (float32) = 625,800 bytes | |
| """ | |
| def __init__(self, config): | |
| super().__init__() | |
| self.config = config | |
| # Token embeddings | |
| self.embeddings = nn.Embedding(config.vocab_size, config.projections, padding_idx=config.pad_token_id) | |
| # Token embeddings projections | |
| self.projections = nn.Linear(config.projections, config.hidden_size) | |
| def forward(self, input_ids): | |
| # Project embeddings to hidden size | |
| return self.projections(self.embeddings(input_ids)) | |
| class BertHashEmbeddings(nn.Module): | |
| """Construct the embeddings from word, position and token_type embeddings.""" | |
| def __init__(self, config): | |
| super().__init__() | |
| self.word_embeddings = BertHashTokens(config) | |
| self.position_embeddings = nn.Embedding(config.max_position_embeddings, config.hidden_size) | |
| self.token_type_embeddings = nn.Embedding(config.type_vocab_size, config.hidden_size) | |
| # self.LayerNorm is not snake-cased to stick with TensorFlow model variable name and be able to load | |
| # any TensorFlow checkpoint file | |
| self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps) | |
| self.dropout = nn.Dropout(config.hidden_dropout_prob) | |
| # position_ids (1, len position emb) is contiguous in memory and exported when serialized | |
| self.position_embedding_type = getattr(config, "position_embedding_type", "absolute") | |
| self.register_buffer( | |
| "position_ids", torch.arange(config.max_position_embeddings).expand((1, -1)), persistent=False | |
| ) | |
| self.register_buffer( | |
| "token_type_ids", torch.zeros(self.position_ids.size(), dtype=torch.long), persistent=False | |
| ) | |
| def forward( | |
| self, | |
| input_ids: Optional[torch.LongTensor] = None, | |
| token_type_ids: Optional[torch.LongTensor] = None, | |
| position_ids: Optional[torch.LongTensor] = None, | |
| inputs_embeds: Optional[torch.FloatTensor] = None, | |
| past_key_values_length: int = 0, | |
| ) -> torch.Tensor: | |
| if input_ids is not None: | |
| input_shape = input_ids.size() | |
| else: | |
| input_shape = inputs_embeds.size()[:-1] | |
| seq_length = input_shape[1] | |
| if position_ids is None: | |
| position_ids = self.position_ids[:, past_key_values_length : seq_length + past_key_values_length] | |
| # Setting the token_type_ids to the registered buffer in constructor where it is all zeros, which usually occurs | |
| # when its auto-generated, registered buffer helps users when tracing the model without passing token_type_ids, solves | |
| # issue #5664 | |
| if token_type_ids is None: | |
| if hasattr(self, "token_type_ids"): | |
| buffered_token_type_ids = self.token_type_ids[:, :seq_length] | |
| buffered_token_type_ids_expanded = buffered_token_type_ids.expand(input_shape[0], seq_length) | |
| token_type_ids = buffered_token_type_ids_expanded | |
| else: | |
| token_type_ids = torch.zeros(input_shape, dtype=torch.long, device=self.position_ids.device) | |
| if inputs_embeds is None: | |
| inputs_embeds = self.word_embeddings(input_ids) | |
| token_type_embeddings = self.token_type_embeddings(token_type_ids) | |
| embeddings = inputs_embeds + token_type_embeddings | |
| if self.position_embedding_type == "absolute": | |
| position_embeddings = self.position_embeddings(position_ids) | |
| embeddings += position_embeddings | |
| embeddings = self.LayerNorm(embeddings) | |
| embeddings = self.dropout(embeddings) | |
| return embeddings | |
| class BertHashModel(BertPreTrainedModel): | |
| config_class = BertHashConfig | |
| _no_split_modules = ["BertEmbeddings", "BertLayer"] | |
| def __init__(self, config, add_pooling_layer=True): | |
| r""" | |
| add_pooling_layer (bool, *optional*, defaults to `True`): | |
| Whether to add a pooling layer | |
| """ | |
| super().__init__(config) | |
| self.config = config | |
| self.embeddings = BertHashEmbeddings(config) | |
| self.encoder = BertEncoder(config) | |
| self.pooler = BertPooler(config) if add_pooling_layer else None | |
| self.attn_implementation = config._attn_implementation | |
| self.position_embedding_type = config.position_embedding_type | |
| # Initialize weights and apply final processing | |
| self.post_init() | |
| def get_input_embeddings(self): | |
| return self.embeddings.word_embeddings.embeddings | |
| def set_input_embeddings(self, value): | |
| self.embeddings.word_embeddings.embeddings = value | |
| def _prune_heads(self, heads_to_prune): | |
| """ | |
| Prunes heads of the model. heads_to_prune: dict of {layer_num: list of heads to prune in this layer} See base | |
| class PreTrainedModel | |
| """ | |
| for layer, heads in heads_to_prune.items(): | |
| self.encoder.layer[layer].attention.prune_heads(heads) | |
| def forward( | |
| self, | |
| input_ids: Optional[torch.Tensor] = None, | |
| attention_mask: Optional[torch.Tensor] = None, | |
| token_type_ids: Optional[torch.Tensor] = None, | |
| position_ids: Optional[torch.Tensor] = None, | |
| head_mask: Optional[torch.Tensor] = None, | |
| inputs_embeds: Optional[torch.Tensor] = None, | |
| encoder_hidden_states: Optional[torch.Tensor] = None, | |
| encoder_attention_mask: Optional[torch.Tensor] = None, | |
| past_key_values: Optional[list[torch.FloatTensor]] = None, | |
| use_cache: Optional[bool] = None, | |
| output_attentions: Optional[bool] = None, | |
| output_hidden_states: Optional[bool] = None, | |
| return_dict: Optional[bool] = None, | |
| cache_position: Optional[torch.Tensor] = None, | |
| ) -> Union[tuple[torch.Tensor], BaseModelOutputWithPoolingAndCrossAttentions]: | |
| output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions | |
| output_hidden_states = ( | |
| output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states | |
| ) | |
| return_dict = return_dict if return_dict is not None else self.config.use_return_dict | |
| if self.config.is_decoder: | |
| use_cache = use_cache if use_cache is not None else self.config.use_cache | |
| else: | |
| use_cache = False | |
| if input_ids is not None and inputs_embeds is not None: | |
| raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time") | |
| elif input_ids is not None: | |
| self.warn_if_padding_and_no_attention_mask(input_ids, attention_mask) | |
| input_shape = input_ids.size() | |
| elif inputs_embeds is not None: | |
| input_shape = inputs_embeds.size()[:-1] | |
| else: | |
| raise ValueError("You have to specify either input_ids or inputs_embeds") | |
| batch_size, seq_length = input_shape | |
| device = input_ids.device if input_ids is not None else inputs_embeds.device | |
| past_key_values_length = 0 | |
| if past_key_values is not None: | |
| past_key_values_length = ( | |
| past_key_values[0][0].shape[-2] | |
| if not isinstance(past_key_values, Cache) | |
| else past_key_values.get_seq_length() | |
| ) | |
| if token_type_ids is None: | |
| if hasattr(self.embeddings, "token_type_ids"): | |
| buffered_token_type_ids = self.embeddings.token_type_ids[:, :seq_length] | |
| buffered_token_type_ids_expanded = buffered_token_type_ids.expand(batch_size, seq_length) | |
| token_type_ids = buffered_token_type_ids_expanded | |
| else: | |
| token_type_ids = torch.zeros(input_shape, dtype=torch.long, device=device) | |
| embedding_output = self.embeddings( | |
| input_ids=input_ids, | |
| position_ids=position_ids, | |
| token_type_ids=token_type_ids, | |
| inputs_embeds=inputs_embeds, | |
| past_key_values_length=past_key_values_length, | |
| ) | |
| if attention_mask is None: | |
| attention_mask = torch.ones((batch_size, seq_length + past_key_values_length), device=device) | |
| use_sdpa_attention_masks = ( | |
| self.attn_implementation == "sdpa" | |
| and self.position_embedding_type == "absolute" | |
| and head_mask is None | |
| and not output_attentions | |
| ) | |
| # Expand the attention mask | |
| if use_sdpa_attention_masks and attention_mask.dim() == 2: | |
| # Expand the attention mask for SDPA. | |
| # [bsz, seq_len] -> [bsz, 1, seq_len, seq_len] | |
| if self.config.is_decoder: | |
| extended_attention_mask = _prepare_4d_causal_attention_mask_for_sdpa( | |
| attention_mask, | |
| input_shape, | |
| embedding_output, | |
| past_key_values_length, | |
| ) | |
| else: | |
| extended_attention_mask = _prepare_4d_attention_mask_for_sdpa( | |
| attention_mask, embedding_output.dtype, tgt_len=seq_length | |
| ) | |
| else: | |
| # We can provide a self-attention mask of dimensions [batch_size, from_seq_length, to_seq_length] | |
| # ourselves in which case we just need to make it broadcastable to all heads. | |
| extended_attention_mask = self.get_extended_attention_mask(attention_mask, input_shape) | |
| # If a 2D or 3D attention mask is provided for the cross-attention | |
| # we need to make broadcastable to [batch_size, num_heads, seq_length, seq_length] | |
| if self.config.is_decoder and encoder_hidden_states is not None: | |
| encoder_batch_size, encoder_sequence_length, _ = encoder_hidden_states.size() | |
| encoder_hidden_shape = (encoder_batch_size, encoder_sequence_length) | |
| if encoder_attention_mask is None: | |
| encoder_attention_mask = torch.ones(encoder_hidden_shape, device=device) | |
| if use_sdpa_attention_masks and encoder_attention_mask.dim() == 2: | |
| # Expand the attention mask for SDPA. | |
| # [bsz, seq_len] -> [bsz, 1, seq_len, seq_len] | |
| encoder_extended_attention_mask = _prepare_4d_attention_mask_for_sdpa( | |
| encoder_attention_mask, embedding_output.dtype, tgt_len=seq_length | |
| ) | |
| else: | |
| encoder_extended_attention_mask = self.invert_attention_mask(encoder_attention_mask) | |
| else: | |
| encoder_extended_attention_mask = None | |
| # Prepare head mask if needed | |
| # 1.0 in head_mask indicate we keep the head | |
| # attention_probs has shape bsz x n_heads x N x N | |
| # input head_mask has shape [num_heads] or [num_hidden_layers x num_heads] | |
| # and head_mask is converted to shape [num_hidden_layers x batch x num_heads x seq_length x seq_length] | |
| head_mask = self.get_head_mask(head_mask, self.config.num_hidden_layers) | |
| encoder_outputs = self.encoder( | |
| embedding_output, | |
| attention_mask=extended_attention_mask, | |
| head_mask=head_mask, | |
| encoder_hidden_states=encoder_hidden_states, | |
| encoder_attention_mask=encoder_extended_attention_mask, | |
| past_key_values=past_key_values, | |
| use_cache=use_cache, | |
| output_attentions=output_attentions, | |
| output_hidden_states=output_hidden_states, | |
| return_dict=return_dict, | |
| cache_position=cache_position, | |
| ) | |
| sequence_output = encoder_outputs[0] | |
| pooled_output = self.pooler(sequence_output) if self.pooler is not None else None | |
| if not return_dict: | |
| return (sequence_output, pooled_output) + encoder_outputs[1:] | |
| return BaseModelOutputWithPoolingAndCrossAttentions( | |
| last_hidden_state=sequence_output, | |
| pooler_output=pooled_output, | |
| past_key_values=encoder_outputs.past_key_values, | |
| hidden_states=encoder_outputs.hidden_states, | |
| attentions=encoder_outputs.attentions, | |
| cross_attentions=encoder_outputs.cross_attentions, | |
| ) | |
| class BertHashForMaskedLM(BertPreTrainedModel): | |
| _tied_weights_keys = ["predictions.decoder.bias", "cls.predictions.decoder.weight"] | |
| config_class = BertHashConfig | |
| def __init__(self, config): | |
| super().__init__(config) | |
| if config.is_decoder: | |
| logger.warning( | |
| "If you want to use `BertForMaskedLM` make sure `config.is_decoder=False` for " | |
| "bi-directional self-attention." | |
| ) | |
| self.bert = BertHashModel(config, add_pooling_layer=False) | |
| self.cls = BertOnlyMLMHead(config) | |
| # Initialize weights and apply final processing | |
| self.post_init() | |
| def forward( | |
| self, | |
| input_ids: Optional[torch.Tensor] = None, | |
| attention_mask: Optional[torch.Tensor] = None, | |
| token_type_ids: Optional[torch.Tensor] = None, | |
| position_ids: Optional[torch.Tensor] = None, | |
| head_mask: Optional[torch.Tensor] = None, | |
| inputs_embeds: Optional[torch.Tensor] = None, | |
| encoder_hidden_states: Optional[torch.Tensor] = None, | |
| encoder_attention_mask: Optional[torch.Tensor] = None, | |
| labels: Optional[torch.Tensor] = None, | |
| output_attentions: Optional[bool] = None, | |
| output_hidden_states: Optional[bool] = None, | |
| return_dict: Optional[bool] = None, | |
| ) -> Union[tuple[torch.Tensor], MaskedLMOutput]: | |
| r""" | |
| labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*): | |
| Labels for computing the masked language modeling loss. Indices should be in `[-100, 0, ..., | |
| config.vocab_size]` (see `input_ids` docstring) Tokens with indices set to `-100` are ignored (masked), the | |
| loss is only computed for the tokens with labels in `[0, ..., config.vocab_size]` | |
| """ | |
| return_dict = return_dict if return_dict is not None else self.config.use_return_dict | |
| outputs = self.bert( | |
| input_ids, | |
| attention_mask=attention_mask, | |
| token_type_ids=token_type_ids, | |
| position_ids=position_ids, | |
| head_mask=head_mask, | |
| inputs_embeds=inputs_embeds, | |
| encoder_hidden_states=encoder_hidden_states, | |
| encoder_attention_mask=encoder_attention_mask, | |
| output_attentions=output_attentions, | |
| output_hidden_states=output_hidden_states, | |
| return_dict=return_dict, | |
| ) | |
| sequence_output = outputs[0] | |
| prediction_scores = self.cls(sequence_output) | |
| masked_lm_loss = None | |
| if labels is not None: | |
| loss_fct = CrossEntropyLoss() # -100 index = padding token | |
| masked_lm_loss = loss_fct(prediction_scores.view(-1, self.config.vocab_size), labels.view(-1)) | |
| if not return_dict: | |
| output = (prediction_scores,) + outputs[2:] | |
| return ((masked_lm_loss,) + output) if masked_lm_loss is not None else output | |
| return MaskedLMOutput( | |
| loss=masked_lm_loss, | |
| logits=prediction_scores, | |
| hidden_states=outputs.hidden_states, | |
| attentions=outputs.attentions, | |
| ) | |
| def prepare_inputs_for_generation(self, input_ids, attention_mask=None, **model_kwargs): | |
| input_shape = input_ids.shape | |
| effective_batch_size = input_shape[0] | |
| # add a dummy token | |
| if self.config.pad_token_id is None: | |
| raise ValueError("The PAD token should be defined for generation") | |
| attention_mask = torch.cat([attention_mask, attention_mask.new_zeros((attention_mask.shape[0], 1))], dim=-1) | |
| dummy_token = torch.full( | |
| (effective_batch_size, 1), self.config.pad_token_id, dtype=torch.long, device=input_ids.device | |
| ) | |
| input_ids = torch.cat([input_ids, dummy_token], dim=1) | |
| return {"input_ids": input_ids, "attention_mask": attention_mask} | |
| def can_generate(cls) -> bool: | |
| """ | |
| Legacy correction: BertForMaskedLM can't call `generate()` from `GenerationMixin`, even though it has a | |
| `prepare_inputs_for_generation` method. | |
| """ | |
| return False | |
| class BertHashForSequenceClassification(BertPreTrainedModel): | |
| config_class = BertHashConfig | |
| def __init__(self, config): | |
| super().__init__(config) | |
| self.num_labels = config.num_labels | |
| self.config = config | |
| self.bert = BertHashModel(config) | |
| classifier_dropout = ( | |
| config.classifier_dropout if config.classifier_dropout is not None else config.hidden_dropout_prob | |
| ) | |
| self.dropout = nn.Dropout(classifier_dropout) | |
| self.classifier = nn.Linear(config.hidden_size, config.num_labels) | |
| # Initialize weights and apply final processing | |
| self.post_init() | |
| def forward( | |
| self, | |
| input_ids: Optional[torch.Tensor] = None, | |
| attention_mask: Optional[torch.Tensor] = None, | |
| token_type_ids: Optional[torch.Tensor] = None, | |
| position_ids: Optional[torch.Tensor] = None, | |
| head_mask: Optional[torch.Tensor] = None, | |
| inputs_embeds: Optional[torch.Tensor] = None, | |
| labels: Optional[torch.Tensor] = None, | |
| output_attentions: Optional[bool] = None, | |
| output_hidden_states: Optional[bool] = None, | |
| return_dict: Optional[bool] = None, | |
| ) -> Union[tuple[torch.Tensor], SequenceClassifierOutput]: | |
| r""" | |
| labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*): | |
| Labels for computing the sequence classification/regression loss. Indices should be in `[0, ..., | |
| config.num_labels - 1]`. If `config.num_labels == 1` a regression loss is computed (Mean-Square loss), If | |
| `config.num_labels > 1` a classification loss is computed (Cross-Entropy). | |
| """ | |
| return_dict = return_dict if return_dict is not None else self.config.use_return_dict | |
| outputs = self.bert( | |
| input_ids, | |
| attention_mask=attention_mask, | |
| token_type_ids=token_type_ids, | |
| position_ids=position_ids, | |
| head_mask=head_mask, | |
| inputs_embeds=inputs_embeds, | |
| output_attentions=output_attentions, | |
| output_hidden_states=output_hidden_states, | |
| return_dict=return_dict, | |
| ) | |
| pooled_output = outputs[1] | |
| pooled_output = self.dropout(pooled_output) | |
| logits = self.classifier(pooled_output) | |
| loss = None | |
| if labels is not None: | |
| if self.config.problem_type is None: | |
| if self.num_labels == 1: | |
| self.config.problem_type = "regression" | |
| elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int): | |
| self.config.problem_type = "single_label_classification" | |
| else: | |
| self.config.problem_type = "multi_label_classification" | |
| if self.config.problem_type == "regression": | |
| loss_fct = MSELoss() | |
| if self.num_labels == 1: | |
| loss = loss_fct(logits.squeeze(), labels.squeeze()) | |
| else: | |
| loss = loss_fct(logits, labels) | |
| elif self.config.problem_type == "single_label_classification": | |
| loss_fct = CrossEntropyLoss() | |
| loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1)) | |
| elif self.config.problem_type == "multi_label_classification": | |
| loss_fct = BCEWithLogitsLoss() | |
| loss = loss_fct(logits, labels) | |
| if not return_dict: | |
| output = (logits,) + outputs[2:] | |
| return ((loss,) + output) if loss is not None else output | |
| return SequenceClassifierOutput( | |
| loss=loss, | |
| logits=logits, | |
| hidden_states=outputs.hidden_states, | |
| attentions=outputs.attentions, | |
| ) | |