evalscope 1.1.0__py3-none-any.whl → 1.1.1__py3-none-any.whl

evalscope/utils/ner.py

@@ -0,0 +1,377 @@
+import re
+from typing import Any, Dict, List, Set, Tuple
+
+from evalscope.utils.logger import get_logger
+
+logger = get_logger()
+
+PROMPT_TEMPLATE = """
+You are a named entity recognition system that identifies the following entity types:
+{entities}
+
+Process the provided text and mark all named entities with XML-style tags.
+
+For example:
+<person>John Smith</person> works at <organization>Google</organization> in <location>Mountain View</location>.
+
+Available entity tags: {entity_list}
+
+INSTRUCTIONS:
+1. Wrap your entire response in <response>...</response> tags.
+2. Inside these tags, include the original text with entity tags inserted.
+3. Do not change the original text in any way (preserve spacing, punctuation, case, etc.).
+4. Tag ALL entities you can identify using the exact tag names provided.
+5. Do not include explanations, just the tagged text.
+6. If entity spans overlap, choose the most specific entity type.
+7. Ensure every opening tag has a matching closing tag.
+
+Text to process:
+{text}
+""".lstrip()
+
+FEWSHOT_TEMPLATE = """
+Here are some examples of named entity recognition:
+
+{fewshot}
+
+You are a named entity recognition system that identifies the following entity types:
+{entities}
+
+Process the provided text and mark all named entities with XML-style tags.
+
+For example:
+<person>John Smith</person> works at <organization>Google</organization> in <location>Mountain View</location>.
+
+Available entity tags: {entity_list}
+
+INSTRUCTIONS:
+1. Wrap your entire response in <response>...</response> tags.
+2. Inside these tags, include the original text with entity tags inserted.
+3. Do not change the original text in any way (preserve spacing, punctuation, case, etc.).
+4. Tag ALL entities you can identify using the exact tag names provided.
+5. Do not include explanations, just the tagged text.
+6. If entity spans overlap, choose the most specific entity type.
+7. Ensure every opening tag has a matching closing tag.
+
+Text to process:
+{text}
+""".lstrip()
+
+# Common error patterns to handle in XML predictions
+DEFAULT_TAG_FIX_PATTERNS = [
+    # Fix mismatched tags
+    (r'<(\w+)>(.*?)</\w+>', r'<\1>\2</\1>'),
+]
+
+
+def create_target_text(tokens: List[str], ner_tags: List[str], entity_type_map: Dict[str, str]) -> str:
+    """
+    Create annotated text from tokens and NER tags.
+    Handles BIO tagging scheme conversion to inline XML-style tags.
+
+    Args:
+        tokens: List of text tokens
+        ner_tags: List of BIO tags corresponding to tokens
+        entity_type_map: Mapping from BIO entity types to user-friendly tag names
+
+    Returns:
+        String with XML-style entity markup wrapped in <response> tags
+    """
+    result = []
+    current_entity = None
+    entity_tokens = []
+
+    for i, (token, tag) in enumerate(zip(tokens, ner_tags)):
+        if tag.startswith('B-'):  # Beginning of entity
+            # Close previous entity if exists
+            if current_entity:
+                entity_type = entity_type_map.get(current_entity, '')
+                if entity_type:
+                    result.append(f'<{entity_type.lower()}>{" ".join(entity_tokens)}</{entity_type.lower()}>')
+                else:
+                    result.append(' '.join(entity_tokens))
+                entity_tokens = []
+
+            current_entity = tag[2:]  # Remove B- prefix
+            entity_tokens.append(token)
+        elif tag.startswith('I-') and current_entity and tag[2:] == current_entity:  # Inside entity
+            entity_tokens.append(token)
+        else:  # Outside any entity (O tag)
+            if current_entity:  # Close previous entity
+                entity_type = entity_type_map.get(current_entity, '')
+                if entity_type:
+                    result.append(f'<{entity_type.lower()}>{" ".join(entity_tokens)}</{entity_type.lower()}>')
+                else:
+                    result.append(' '.join(entity_tokens))
+                current_entity = None
+                entity_tokens = []
+
+            result.append(token)
+
+    # Handle any remaining entity at end of sequence
+    if current_entity:
+        entity_type = entity_type_map.get(current_entity, '')
+        if entity_type:
+            result.append(f'<{entity_type.lower()}>{" ".join(entity_tokens)}</{entity_type.lower()}>')
+        else:
+            result.append(' '.join(entity_tokens))
+
+    # Wrap the entire response in <response> tags as required by the pipeline
+    return f'<response>{" ".join(result)}</response>'
+
+
+def clean_prediction(text: str, tag_fix_patterns: List[Tuple[str, str]] = None) -> str:
+    """
+    Clean and fix common XML errors in model predictions.
+
+    Args:
+        text: The prediction text to clean
+        tag_fix_patterns: List of regex patterns and replacements to fix common XML errors
+
+    Returns:
+        Cleaned text with fixed XML tags
+    """
+    if tag_fix_patterns is None:
+        tag_fix_patterns = DEFAULT_TAG_FIX_PATTERNS
+
+    cleaned = text
+
+    # Extract content from response tags if present
+    response_match = re.search(r'<response>(.*?)</response>', cleaned, re.DOTALL)
+    if response_match:
+        cleaned = response_match.group(1)
+
+    # Apply fix patterns for common XML errors
+    for pattern, replacement in tag_fix_patterns:
+        cleaned = re.sub(pattern, replacement, cleaned)
+
+    return cleaned
+
+
+def extract_entities_from_text(text: str, reverse_entity_map: Dict[str, str]) -> List[Tuple]:
+    """
+    Extract entities from tagged text with robust error handling.
+
+    Args:
+        text: Text with XML entity tags
+        reverse_entity_map: Mapping from user-friendly tag names to BIO entity types
+
+    Returns:
+        List of (entity_type, entity_text, start_idx, end_idx) tuples
+    """
+    entities = []
+
+    # Define regex pattern to find XML-style entity tags - handle potential errors
+    pattern = r'<(\w+)>(.*?)</\1>'
+
+    try:
+        for match in re.finditer(pattern, text):
+            entity_type = match.group(1).lower()  # Normalize type to lowercase
+            entity_text = match.group(2)
+            start_idx = match.start()
+            end_idx = match.end()
+
+            # Map back to entity types if possible
+            mapped_type = reverse_entity_map.get(entity_type)
+
+            if mapped_type:
+                entities.append((mapped_type, entity_text, start_idx, end_idx))
+            else:
+                # Unknown entity type but still count it for evaluation
+                entities.append((entity_type, entity_text, start_idx, end_idx))
+
+    except Exception as e:
+        logger.warning(f'Error parsing entities in text: {str(e)}')
+
+    # Handle malformed XML by trying to find additional tag patterns
+    # This is a fallback for when the model produces incorrect tags
+    unclosed_pattern = r'<(\w+)>(.*?)(?=<|$)'
+    try:
+        # Find potential unclosed tags
+        for match in re.finditer(unclosed_pattern, text):
+            # Skip if already part of a well-formed tag
+            if any(start_idx <= match.start() < end_idx for _, _, start_idx, end_idx in entities):
+                continue
+
+            entity_type = match.group(1).lower()
+            entity_text = match.group(2)
+            start_idx = match.start()
+            end_idx = match.end()
+
+            # Map back to entity types
+            mapped_type = reverse_entity_map.get(entity_type)
+            if mapped_type:
+                entities.append((mapped_type, entity_text, start_idx, end_idx))
+
+    except Exception as e:
+        logger.warning(f'Error handling malformed tags: {str(e)}')
+
+    return entities
+
+
+def xml_to_bio_tags(xml_text: str, original_tokens: List[str], reverse_entity_map: Dict[str, str]) -> List[str]:
+    """
+    Convert XML-annotated text back to BIO tags aligned with the original tokens.
+
+    Args:
+        xml_text: Text with XML entity annotations
+        original_tokens: Original tokens to align with
+        reverse_entity_map: Mapping from user-friendly tag names to BIO entity types
+
+    Returns:
+        List of BIO tags corresponding to the original tokens
+    """
+    # Extract entities with their character positions
+    entities = extract_entities_from_text(xml_text, reverse_entity_map)
+
+    # Initialize all tags as 'O'
+    bio_tags = ['O'] * len(original_tokens)
+
+    # Reconstruct the original text to find character positions for each token
+    original_text = ' '.join(original_tokens)
+
+    # Track token start positions in the original text
+    token_positions = []
+    pos = 0
+    for token in original_tokens:
+        token_pos = original_text.find(token, pos)
+        if token_pos == -1:
+            # Fallback: just use the current position if we can't find the exact match
+            token_positions.append(pos)
+        else:
+            token_positions.append(token_pos)
+            pos = token_pos + len(token)
+
+    # Add token end positions
+    token_ends = [pos + len(token) for pos, token in zip(token_positions, original_tokens)]
+
+    # Map entities to tokens based on character positions
+    for entity_type, entity_text, start_pos, end_pos in entities:
+        # Extract the context from the XML text to help locate the correct entity occurrence
+        # Get some context before and after the entity in the XML text
+        context_start = max(0, start_pos - 20)
+        context_end = min(len(xml_text), end_pos + 20)
+
+        # Extract context without XML tags
+        context_before = re.sub(r'<[^>]+>', '', xml_text[context_start:start_pos])
+        context_after = re.sub(r'<[^>]+>', '', xml_text[end_pos:context_end])
+
+        # Use context to find the correct entity position in original text
+        search_pos = 0
+        entity_start = -1
+
+        while search_pos < len(original_text):
+            # Find the next occurrence of the entity
+            potential_start = original_text.find(entity_text, search_pos)
+            if potential_start == -1:
+                break
+
+            # Check if the context matches
+            potential_context_start = max(0, potential_start - len(context_before))
+            potential_context_end = min(len(original_text), potential_start + len(entity_text) + len(context_after))
+
+            before_match = context_before.strip() in original_text[potential_context_start:potential_start].strip()
+            after_match = context_after.strip() in original_text[potential_start
+                                                                 + len(entity_text):potential_context_end].strip()
+
+            # If context matches or we can't find a better match, use this position
+            if before_match or after_match or search_pos > len(original_text) // 2:
+                entity_start = potential_start
+                break
+
+            # Move search position forward
+            search_pos = potential_start + 1
+
+        # If we couldn't find the entity with context, fall back to the first occurrence
+        if entity_start == -1:
+            entity_start = original_text.find(entity_text)
+            if entity_start == -1:
+                continue
+
+        entity_end = entity_start + len(entity_text)
+
+        # Find tokens that overlap with this entity
+        for i, (token_start, token_end) in enumerate(zip(token_positions, token_ends)):
+            if token_start <= entity_end and token_end >= entity_start:
+                # This token overlaps with the entity
+                if bio_tags[i] == 'O':
+                    # Start of entity
+                    if i == 0 or bio_tags[i - 1] == 'O' or not bio_tags[i - 1].endswith(entity_type):
+                        bio_tags[i] = f'B-{entity_type}'
+                    else:
+                        # Continuation of entity
+                        bio_tags[i] = f'I-{entity_type}'
+
+    return bio_tags
+
+
+def calculate_bio_metrics(pred_tags: List[str], gold_tags: List[str], tokens: List[str]) -> Tuple[int, int, int]:
+    """
+    Calculate metrics by comparing BIO tag sequences.
+
+    Args:
+        pred_tags: Predicted BIO tags
+        gold_tags: Gold standard BIO tags
+        tokens: Original tokens
+
+    Returns:
+        Tuple of (true_positives, false_positives, false_negatives)
+    """
+    # Extract entity spans from BIO tags
+    pred_spans = extract_spans_from_bio(pred_tags, tokens)
+    gold_spans = extract_spans_from_bio(gold_tags, tokens)
+
+    # Calculate metrics
+    true_positives = len(pred_spans.intersection(gold_spans))
+    false_positives = len(pred_spans - gold_spans)
+    false_negatives = len(gold_spans - pred_spans)
+
+    return true_positives, false_positives, false_negatives
+
+
+def extract_spans_from_bio(tags: List[str], tokens: List[str]) -> Set[Tuple]:
+    """
+    Extract entity spans from BIO tags.
+
+    Args:
+        tags: List of BIO tags
+        tokens: List of tokens corresponding to the tags
+
+    Returns:
+        Set of (entity_type, start_idx, end_idx, text) tuples
+    """
+    spans = set()
+    current_entity = None
+    start_idx = None
+    entity_tokens = []
+
+    for i, (token, tag) in enumerate(zip(tokens, tags)):
+        if tag.startswith('B-'):  # Beginning of entity
+            # Close previous entity if exists
+            if current_entity:
+                entity_type = current_entity
+                entity_text = ' '.join(entity_tokens)
+                spans.add((entity_type, start_idx, i - 1, entity_text))
+                entity_tokens = []
+
+            current_entity = tag[2:]  # Remove B- prefix
+            start_idx = i
+            entity_tokens.append(token)
+        elif tag.startswith('I-') and current_entity:  # Inside entity
+            entity_tokens.append(token)
+        elif tag == 'O':  # Outside any entity
+            if current_entity:  # Close previous entity
+                entity_type = current_entity
+                entity_text = ' '.join(entity_tokens)
+                spans.add((entity_type, start_idx, i - 1, entity_text))
+                current_entity = None
+                start_idx = None
+                entity_tokens = []
+
+    # Handle any remaining entity at end of sequence
+    if current_entity:
+        entity_type = current_entity
+        entity_text = ' '.join(entity_tokens)
+        spans.add((entity_type, start_idx, len(tokens) - 1, entity_text))
+
+    return spans

evalscope/version.py

@@ -1,4 +1,4 @@
 # Copyright (c) Alibaba, Inc. and its affiliates.
 
-__version__ = '1.1.0'
-__release_datetime__ = '2025-10-14 14:00:00'
+__version__ = '1.1.1'
+__release_datetime__ = '2025-10-27 17:00:00'