Upload BertForSyntaxParsing.py with huggingface_hub

BertForSyntaxParsing.py

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+import math
+from transformers.utils import ModelOutput
+import torch
+from torch import nn
+from typing import Dict, List, Tuple, Optional, Union
+from dataclasses import dataclass
+from transformers import BertPreTrainedModel, BertModel, BertTokenizerFast
+
+ALL_FUNCTION_LABELS = ["nsubj", "nsubj:cop", "punct", "mark", "mark:q", "case", "case:gen", "case:acc", "fixed", "obl", "det", "amod", "acl:relcl", "nmod", "cc", "conj", "root", "compound:smixut", "cop", "compound:affix", "advmod", "nummod", "appos", "nsubj:pass", "nmod:poss", "xcomp", "obj", "aux", "parataxis", "advcl", "ccomp", "csubj", "acl", "obl:tmod", "csubj:pass", "dep", "dislocated", "nmod:tmod", "nmod:npmod", "flat", "obl:npmod", "goeswith", "reparandum", "orphan", "list", "discourse", "iobj", "vocative", "expl", "flat:name"]
+
+@dataclass
+class SyntaxLogitsOutput(ModelOutput):
+    dependency_logits: torch.FloatTensor = None
+    function_logits: torch.FloatTensor = None
+    dependency_head_indices: torch.LongTensor = None
+
+    def detach(self):
+        return SyntaxTaggingOutput(self.dependency_logits.detach(), self.function_logits.detach(), self.dependency_head_indices.detach())
+
+@dataclass
+class SyntaxTaggingOutput(ModelOutput):
+    loss: Optional[torch.FloatTensor] = None
+    logits: Optional[SyntaxLogitsOutput] = None
+    hidden_states: Optional[Tuple[torch.FloatTensor]] = None
+    attentions: Optional[Tuple[torch.FloatTensor]] = None
+
+@dataclass
+class SyntaxLabels(ModelOutput):
+    dependency_labels: Optional[torch.LongTensor] = None
+    function_labels: Optional[torch.LongTensor] = None
+
+    def detach(self):
+        return SyntaxLabels(self.dependency_labels.detach(), self.function_labels.detach())
+    
+    def to(self, device):
+        return SyntaxLabels(self.dependency_labels.to(device), self.function_labels.to(device))
+
+class BertSyntaxParsingHead(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+
+        # the attention query & key values
+        self.head_size = config.syntax_head_size# int(config.hidden_size / config.num_attention_heads * 2)
+        self.query = nn.Linear(config.hidden_size, self.head_size)
+        self.key = nn.Linear(config.hidden_size, self.head_size)
+        # the function classifier gets two encoding values and predicts the labels
+        self.num_function_classes = len(ALL_FUNCTION_LABELS)
+        self.cls = nn.Linear(config.hidden_size * 2, self.num_function_classes)
+
+    def forward(
+            self, 
+            hidden_states: torch.Tensor, 
+            extended_attention_mask: Optional[torch.Tensor],
+            labels: Optional[SyntaxLabels] = None,
+            compute_mst: bool = False) -> Tuple[torch.Tensor, SyntaxLogitsOutput]:
+        
+        # Take the dot product between "query" and "key" to get the raw attention scores.
+        query_layer = self.query(hidden_states)
+        key_layer = self.key(hidden_states)
+        attention_scores = torch.bmm(query_layer, key_layer.transpose(-1, -2)) / math.sqrt(self.head_size)
+
+        # add in the attention mask
+        if extended_attention_mask is not None:
+            if extended_attention_mask.ndim == 4:
+                extended_attention_mask = extended_attention_mask.squeeze(1)
+            attention_scores += extended_attention_mask# batch x seq x seq
+
+        # At this point take the hidden_state of the word and of the dependency word, and predict the function
+        # If labels are provided, use the labels.
+        if self.training and labels is not None:
+            # Note that the labels can have -100, so just set those to zero with a max
+            dep_indices = labels.dependency_labels.clamp_min(0)
+        # Otherwise - check if he wants the MST or just the argmax
+        elif compute_mst:
+            dep_indices = compute_mst_tree(attention_scores, extended_attention_mask)
+        else: 
+            dep_indices = torch.argmax(attention_scores, dim=-1)
+        
+        # After we retrieved the dependency indicies, create a tensor of teh batch indices, and and retrieve the vectors of the heads to calculate the function
+        batch_indices = torch.arange(dep_indices.size(0)).view(-1, 1).expand(-1, dep_indices.size(1)).to(dep_indices.device)
+        dep_vectors = hidden_states[batch_indices, dep_indices, :] # batch x seq x dim
+
+        # concatenate that with the last hidden states, and send to the classifier output
+        cls_inputs = torch.cat((hidden_states, dep_vectors), dim=-1)
+        function_logits = self.cls(cls_inputs)
+
+        loss = None
+        if labels is not None:
+            loss_fct = nn.CrossEntropyLoss()
+            # step 1: dependency scores loss - this is applied to the attention scores
+            loss = loss_fct(attention_scores.view(-1, hidden_states.size(-2)), labels.dependency_labels.view(-1))
+            # step 2: function loss
+            loss += loss_fct(function_logits.view(-1, self.num_function_classes), labels.function_labels.view(-1))
+        
+        return (loss, SyntaxLogitsOutput(attention_scores, function_logits, dep_indices))
+
+
+class BertForSyntaxParsing(BertPreTrainedModel):
+
+    def __init__(self, config):
+        super().__init__(config)
+
+        self.bert = BertModel(config, add_pooling_layer=False)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+        self.syntax = BertSyntaxParsingHead(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,
+        labels: Optional[SyntaxLabels] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.Tensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+        compute_syntax_mst: Optional[bool] = None,
+    ):
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        bert_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,
+        )
+        
+        extended_attention_mask = None
+        if attention_mask is not None:
+            extended_attention_mask = self.get_extended_attention_mask(attention_mask, input_ids.size())
+        # apply the syntax head
+        loss, logits = self.syntax(self.dropout(bert_outputs[0]), extended_attention_mask, labels, compute_syntax_mst)
+        
+        if not return_dict:
+            return (loss,(logits.dependency_logits, logits.function_logits)) + bert_outputs[2:]
+        
+        return SyntaxTaggingOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=bert_outputs.hidden_states,
+            attentions=bert_outputs.attentions,
+        )
+
+    def predict(self, sentences: Union[str, List[str]], tokenizer: BertTokenizerFast, compute_mst=True):
+        if isinstance(sentences, str):
+            sentences = [sentences]
+            
+        # predict the logits for the sentence
+        inputs = tokenizer(sentences, padding='longest', truncation=True, return_tensors='pt')
+        inputs = {k:v.to(self.device) for k,v in inputs.items()}
+        logits = self.forward(**inputs, return_dict=True, compute_syntax_mst=compute_mst).logits
+        return parse_logits(inputs['input_ids'].tolist(), sentences, tokenizer, logits)
+
+def parse_logits(input_ids: List[List[int]], sentences: List[str], tokenizer: BertTokenizerFast, logits: SyntaxLogitsOutput):
+    outputs = []        
+
+    special_toks = tokenizer.all_special_tokens
+    for i in range(len(sentences)):
+        deps = logits.dependency_head_indices[i].tolist()
+        funcs = logits.function_logits.argmax(-1)[i].tolist()
+        toks = [tok for tok in tokenizer.convert_ids_to_tokens(input_ids[i]) if tok not in special_toks]
+        
+        # first, go through the tokens and create a mapping between each dependency index and the index without wordpieces
+        # wordpieces. At the same time, append the wordpieces in
+        idx_mapping = {-1:-1} # default root 
+        real_idx = -1
+        for i in range(len(toks)):
+            if not toks[i].startswith('##'):
+                real_idx += 1
+            idx_mapping[i] = real_idx
+            
+        # build our tree, keeping tracking of the root idx
+        tree = []
+        root_idx = 0
+        for i in range(len(toks)):
+            if toks[i].startswith('##'):
+                tree[-1]['word'] += toks[i][2:]
+                continue 
+            
+            dep_idx = deps[i + 1] - 1 # increase 1 for cls, decrease 1 for cls
+            if dep_idx == len(toks): dep_idx = i - 1 # if he predicts sep, then just point to the previous word
+            
+            dep_head = 'root' if dep_idx == -1 else toks[dep_idx]
+            dep_func = ALL_FUNCTION_LABELS[funcs[i + 1]]
+
+            if dep_head == 'root': root_idx = len(tree)
+            tree.append(dict(word=toks[i], dep_head_idx=idx_mapping[dep_idx], dep_func=dep_func))
+        # append the head word
+        for d in tree:
+            d['dep_head'] = tree[d['dep_head_idx']]['word']
+        
+        outputs.append(dict(tree=tree, root_idx=root_idx))
+    return outputs
+
+
+def compute_mst_tree(attention_scores: torch.Tensor, extended_attention_mask: torch.LongTensor):
+    # attention scores should be 3 dimensions - batch x seq x seq (if it is 2 - just unsqueeze)
+    if attention_scores.ndim == 2: attention_scores = attention_scores.unsqueeze(0)
+    if attention_scores.ndim != 3 or attention_scores.shape[1] != attention_scores.shape[2]:
+        raise ValueError(f'Expected attention scores to be of shape batch x seq x seq, instead got {attention_scores.shape}')
+    
+    batch_size, seq_len, _ = attention_scores.shape
+    # start by softmaxing so the scores are comparable
+    attention_scores = attention_scores.softmax(dim=-1)
+    
+    batch_indices = torch.arange(batch_size, device=attention_scores.device)
+    seq_indices = torch.arange(seq_len, device=attention_scores.device)
+
+    seq_lens = torch.full((batch_size,), seq_len)
+    
+    if extended_attention_mask is not None:
+        seq_lens = torch.argmax((extended_attention_mask != 0).int(), dim=2).squeeze(1)     
+        # zero out any padding
+        attention_scores[extended_attention_mask.squeeze(1) != 0] = 0
+
+    # set the values for the CLS and sep to all by very low, so they never get chosen as a replacement arc
+    attention_scores[:, 0, :] = 0
+    attention_scores[batch_indices, seq_lens - 1, :] = 0
+    attention_scores[batch_indices, :, seq_lens - 1] = 0 # can never predict sep
+    # set the values for each token pointing to itself be 0
+    attention_scores[:, seq_indices, seq_indices] = 0
+    
+    # find the root, and make him super high so we never have a conflict
+    root_cands = torch.argsort(attention_scores[:, :, 0], dim=-1)
+    attention_scores[batch_indices.unsqueeze(1), root_cands, 0] = 0
+    attention_scores[batch_indices, root_cands[:, -1], 0] = 1.0
+
+    # we start by getting the argmax for each score, and then computing the cycles and contracting them
+    sorted_indices = torch.argsort(attention_scores, dim=-1, descending=True)
+    indices = sorted_indices[:, :, 0].clone() # take the argmax
+    
+    attention_scores = attention_scores.tolist()
+    seq_lens = seq_lens.tolist()
+    sorted_indices = [[sub_l[:slen] for sub_l in l[:slen]] for l,slen in zip(sorted_indices.tolist(), seq_lens)]
+
+
+    # go through each batch item and make sure our tree works
+    for batch_idx in range(batch_size):
+        # We have one root - detect the cycles and contract them. A cycle can never contain the root so really
+        # for every cycle, we look at all the nodes, and find the highest arc out of the cycle for any values. Replace that and tada
+        has_cycle, cycle_nodes = detect_cycle(indices[batch_idx], seq_lens[batch_idx])
+        contracted_arcs = set()
+        while has_cycle:
+            base_idx, head_idx = choose_contracting_arc(indices[batch_idx], sorted_indices[batch_idx], cycle_nodes, contracted_arcs, seq_lens[batch_idx], attention_scores[batch_idx])
+            indices[batch_idx, base_idx] = head_idx
+            contracted_arcs.add(base_idx)
+            # find the next cycle
+            has_cycle, cycle_nodes = detect_cycle(indices[batch_idx], seq_lens[batch_idx])
+
+    return indices
+
+def detect_cycle(indices: torch.LongTensor, seq_len: int):
+    # Simple cycle detection algorithm
+    # Returns a boolean indicating if a cycle is detected and the nodes involved in the cycle
+    visited = set()
+    for node in range(1, seq_len - 1): # ignore the CLS/SEP tokens
+        if node in visited:
+            continue
+        current_path = set()
+        while node not in visited:
+            visited.add(node)
+            current_path.add(node)
+            node = indices[node].item()
+            if node == 0: break # roots never point to anything
+            if node in current_path:
+                return True, current_path  # Cycle detected
+    return False, None
+
+def choose_contracting_arc(indices: torch.LongTensor, sorted_indices: List[List[int]], cycle_nodes: set, contracted_arcs: set, seq_len: int, scores: List[List[float]]):
+    # Chooses the highest-scoring, non-cycling arc from a graph. Iterates through 'cycle_nodes' to find
+    # the best arc based on 'scores', avoiding cycles and zero node connections.
+    # For each node, we only look at the next highest scoring non-cycling arc 
+    best_base_idx, best_head_idx = -1, -1
+    score = 0
+    
+    # convert the indices to a list once, to avoid multiple conversions (saves a few seconds)
+    currents = indices.tolist()
+    for base_node in cycle_nodes:
+        if base_node in contracted_arcs: continue
+        # we don't want to take anything that has a higher score than the current value - we can end up in an endless loop
+        # Since the indices are sorted, as soon as we find our current item, we can move on to the next. 
+        current = currents[base_node]
+        found_current = False
+        
+        for head_node in sorted_indices[base_node]:
+            if head_node == current:
+                found_current = True
+                continue
+            if head_node in contracted_arcs: continue
+            if not found_current or head_node in cycle_nodes or head_node == 0: 
+                continue
+            
+            current_score = scores[base_node][head_node]
+            if current_score > score:
+                best_base_idx, best_head_idx, score = base_node, head_node, current_score
+            break
+    
+    if best_base_idx == -1:
+        raise ValueError('Stuck in endless loop trying to compute syntax mst. Please try again setting compute_syntax_mst=False')
+
+    return best_base_idx, best_head_idx