semantica/docs/reference/deduplication.md

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Deduplication Module	Entity deduplication v1/v2 — similarity scoring, blocking, merging, and cluster-based batch processing.	copy

semantica.deduplication detects and merges duplicate entities across sources to produce a clean, single-source-of-truth knowledge graph. v2 strategies (blocking_v2, hybrid_v2, semantic_v2) are up to 7x faster than v1 with fine-grained result control.

What You Get

• DuplicateDetector — pairwise and batch duplicate detection with configurable strategies
• EntityMerger — merge duplicate groups with configurable property-level merge policies
• SimilarityCalculator — multi-factor similarity: Levenshtein, Jaro-Winkler, cosine, Jaccard, embedding
• ClusterBuilder — Union-Find and hierarchical clustering for large-scale batch deduplication
• Convenience functions — detect_duplicates, merge_entities, calculate_similarity

DuplicateDetector

Find duplicate entity pairs with configurable strategies and result filtering:

from semantica.deduplication import DuplicateDetector

detector = DuplicateDetector(similarity_threshold=0.85)
duplicates = detector.detect_duplicates(entities)

for dup in duplicates:
    print(f"{dup.entity_a} ≈ {dup.entity_b}  ({dup.similarity:.2f})")

Fine-grained control over strategy, thresholds, and result size:

duplicates = detector.detect_duplicates(
    entities,
    strategy="semantic_v2",    # see strategies table below
    min_similarity=0.85,        # minimum score to consider a match
    top_k_per_entity=3,         # max candidates per entity
    max_results=100,            # total result cap
    sort_by="similarity",       # "similarity" | "entity_id" | "cluster_size"
)

Detection Strategies

Strategy	Algorithm	Speed	Accuracy
jaro_winkler	String similarity (v1)	Fast	Medium
blocking_v2	Blocking + Jaro-Winkler (v2)	Very fast	Medium
hybrid_v2	Blocking + semantic + string (v2)	Fast	High
semantic_v2	Embedding similarity (v2)	Medium	Highest

**v0.5.0 fix:** `DuplicateDetector` no longer produces duplicate definition errors when the same entity appears in multiple sources with identical definitions.

EntityMerger

Merges detected duplicate groups into canonical entities, preserving provenance:

from semantica.deduplication import EntityMerger

merger = EntityMerger()
merged_entities = merger.merge_duplicates(
    entities,
    strategy="keep_most_complete",  # see strategies table below
    preserve_provenance=True,        # keep source references after merge
)

Merge Strategies

Strategy	Behavior
keep_first	Keep the first entity in each duplicate group
keep_last	Keep the most recently seen entity
keep_most_complete	Keep the entity with the most non-null properties
union	Merge all properties — non-conflicting fields combined
voting	Most common property value wins

Fine-grained per-property merge rules:

from semantica.deduplication import EntityMerger, PropertyMergeRule

merger = EntityMerger(
    property_rules={
        "name":        PropertyMergeRule.KEEP_FIRST,
        "aliases":     PropertyMergeRule.UNION,
        "description": PropertyMergeRule.KEEP_LONGEST,
    }
)

SimilarityCalculator

Compute multi-factor similarity scores between entity pairs:

from semantica.deduplication import SimilarityCalculator

calc = SimilarityCalculator()

score = calc.calculate_similarity(entity_a, entity_b)
# → SimilarityResult(score=0.91, components={...})

print(score.score)                    # overall score 0.0–1.0
print(score.components["label"])      # label similarity
print(score.components["embedding"])  # semantic similarity
print(score.components["property"])   # property overlap

Individual string and vector metrics:

lev  = calc.levenshtein("Apple Inc.", "Apple Inc")
jaro = calc.jaro_winkler("Steve Jobs", "Steven Jobs")
cos  = calc.cosine_similarity(embedding_a, embedding_b)
jacc = calc.jaccard({"founded", "tech"}, {"founded", "technology"})

ClusterBuilder

Build entity clusters for large-scale batch deduplication:

from semantica.deduplication import ClusterBuilder

builder = ClusterBuilder(algorithm="union_find")  # or "hierarchical"
result = builder.build_clusters(entities, similarity_threshold=0.85)

print(f"Clusters: {len(result.clusters)}")
for cluster in result.clusters:
    print(f"  [{cluster.id}] {cluster.members} — cohesion: {cluster.cohesion:.2f}")

Blocking Strategies

Blocking reduces the O(n²) pairwise comparison problem to a manageable candidate set:

detector = DuplicateDetector(
    blocking_strategy="token",     # "token" | "phonetic" | "ngram"
    blocking_threshold=0.6,
    similarity_threshold=0.85
)

Custom Similarity Functions

Register domain-specific similarity logic:

from semantica.deduplication import method_registry

def drug_name_similarity(entity_a, entity_b):
    # Match drug names by active compound
    return score  # 0.0 to 1.0

method_registry.register("similarity", "drug_name", drug_name_similarity)

detector = DuplicateDetector(similarity_method="drug_name")

Convenience Functions

from semantica.deduplication import detect_duplicates, merge_entities, calculate_similarity

# Quick detection
duplicates = detect_duplicates(entities, method="semantic_v2", similarity_threshold=0.85)

# Quick merge
merged = merge_entities(entities, duplicates, method="keep_most_complete")

# Quick similarity
score = calculate_similarity(entity_a, entity_b, method="hybrid_v2")

Detect value conflicts between non-duplicate entities. GraphBuilder uses deduplication during construction. Normalize entity names before deduplication. Track merged entity lineage.