Fix Qwen3

See https://discuss.huggingface.co/t/why-are-my-benchmark-results-so-different-from-the-mteb-leaderboard/168305

.gitignore

@@ -1,2 +1,3 @@
 .direnv
 .envrc.local
+__pycache__

README.md

@@ -295,6 +295,25 @@ For high-level information about these models, see the [MTEB Leaderboard](https:
 
 *... and 522 more queries*
 
+### huggingface/Qwen-Qwen3-Embedding-8B (BSB)
+
+**Accuracy: 82.8%** (1322/1596 points across 532 queries)
+
+| Query | Expected | Top Result | Score | ✓ |
+|-------|----------|------------|-------|---|
+| isn't there a verse about god is love? | ['1 John 4:8', '1 John 4:16'] | 1 John 4:8 | 0.6020 | ✅ |
+| god is love | ['1 John 4:8', '1 John 4:16'] | 1 John 4:8 | 0.6260 | ✅ |
+| verse about they meant bad but god meant good (rou... | ['Genesis 50:20'] | Genesis 50:20 | 0.6016 | ✅ |
+| they meant bad but god meant good | ['Genesis 50:20'] | Genesis 50:20 | 0.6255 | ✅ |
+| isn't there a verse about god loves the world? | ['John 3:16'] | John 3:16 | 0.6166 | ✅ |
+| god loves the world | ['John 3:16'] | 1 John 4:8 | 0.6084 | ❌ |
+| isn't there a verse about god loved the whole worl... | ['John 3:16'] | John 3:16 | 0.6256 | ✅ |
+| god loved the whole world | ['John 3:16'] | John 3:16 | 0.6262 | ✅ |
+| isn't there a verse about in the beginning god cre... | ['Genesis 1:1'] | Genesis 1:1 | 0.6202 | ✅ |
+| in the beginning god created | ['Genesis 1:1'] | Genesis 1:1 | 0.6736 | ✅ |
+
+*... and 522 more queries*
+
 ### openai/text-embedding-3-small (BSB)
 
 **Accuracy: 81.0%** (1293/1596 points across 532 queries)
@@ -371,6 +390,25 @@ For high-level information about these models, see the [MTEB Leaderboard](https:
 
 *... and 522 more queries*
 
+### huggingface/Qwen-Qwen3-Embedding-0.6B (BSB)
+
+**Accuracy: 73.9%** (1179/1596 points across 532 queries)
+
+| Query | Expected | Top Result | Score | ✓ |
+|-------|----------|------------|-------|---|
+| isn't there a verse about god is love? | ['1 John 4:8', '1 John 4:16'] | 1 John 4:16 | 0.6455 | ✅ |
+| god is love | ['1 John 4:8', '1 John 4:16'] | 1 John 4:16 | 0.6461 | ✅ |
+| verse about they meant bad but god meant good (rou... | ['Genesis 50:20'] | Genesis 50:20 | 0.6596 | ✅ |
+| they meant bad but god meant good | ['Genesis 50:20'] | Genesis 50:20 | 0.6567 | ✅ |
+| isn't there a verse about god loves the world? | ['John 3:16'] | 1 John 2:15 | 0.6730 | ❌ |
+| god loves the world | ['John 3:16'] | 1 John 2:15 | 0.6744 | ❌ |
+| isn't there a verse about god loved the whole worl... | ['John 3:16'] | John 3:16 | 0.6674 | ✅ |
+| god loved the whole world | ['John 3:16'] | John 3:16 | 0.6288 | ✅ |
+| isn't there a verse about in the beginning god cre... | ['Genesis 1:1'] | Genesis 2:4 | 0.6557 | ❌ |
+| in the beginning god created | ['Genesis 1:1'] | Genesis 1:1 | 0.6935 | ✅ |
+
+*... and 522 more queries*
+
 ### huggingface/thenlper-gte-large (BSB)
 
 **Accuracy: 73.1%** (1166/1596 points across 532 queries)
@@ -409,6 +447,25 @@ For high-level information about these models, see the [MTEB Leaderboard](https:
 
 *... and 522 more queries*
 
+### huggingface/Qwen-Qwen3-Embedding-4B (BSB)
+
+**Accuracy: 72.4%** (1156/1596 points across 532 queries)
+
+| Query | Expected | Top Result | Score | ✓ |
+|-------|----------|------------|-------|---|
+| isn't there a verse about god is love? | ['1 John 4:8', '1 John 4:16'] | 1 John 4:8 | 0.6945 | ✅ |
+| god is love | ['1 John 4:8', '1 John 4:16'] | 1 John 4:8 | 0.6686 | ✅ |
+| verse about they meant bad but god meant good (rou... | ['Genesis 50:20'] | Genesis 50:20 | 0.6868 | ✅ |
+| they meant bad but god meant good | ['Genesis 50:20'] | Genesis 50:20 | 0.6910 | ✅ |
+| isn't there a verse about god loves the world? | ['John 3:16'] | 1 John 4:7 | 0.6471 | ❌ |
+| god loves the world | ['John 3:16'] | 1 John 4:7 | 0.6258 | ❌ |
+| isn't there a verse about god loved the whole worl... | ['John 3:16'] | 1 John 4:7 | 0.6446 | ❌ |
+| god loved the whole world | ['John 3:16'] | 1 John 4:7 | 0.6103 | ❌ |
+| isn't there a verse about in the beginning god cre... | ['Genesis 1:1'] | Genesis 1:1 | 0.6311 | ✅ |
+| in the beginning god created | ['Genesis 1:1'] | Genesis 1:1 | 0.6547 | ✅ |
+
+*... and 522 more queries*
+
 ### huggingface/intfloat-e5-large-v2 (BSB)
 
 **Accuracy: 72.1%** (1150/1596 points across 532 queries)
@@ -428,25 +485,6 @@ For high-level information about these models, see the [MTEB Leaderboard](https:
 
 *... and 522 more queries*
 
-### huggingface/Qwen-Qwen3-Embedding-8B (BSB)
-
-**Accuracy: 71.5%** (1141/1596 points across 532 queries)
-
-| Query | Expected | Top Result | Score | ✓ |
-|-------|----------|------------|-------|---|
-| isn't there a verse about god is love? | ['1 John 4:8', '1 John 4:16'] | 1 John 4:8 | 0.7362 | ✅ |
-| god is love | ['1 John 4:8', '1 John 4:16'] | 1 John 4:8 | 0.7374 | ✅ |
-| verse about they meant bad but god meant good (rou... | ['Genesis 50:20'] | Romans 12:21 | 0.6828 | ⚠️ |
-| they meant bad but god meant good | ['Genesis 50:20'] | Romans 12:21 | 0.7262 | ❌ |
-| isn't there a verse about god loves the world? | ['John 3:16'] | 1 John 4:8 | 0.7306 | ❌ |
-| god loves the world | ['John 3:16'] | Psalms 67:7 | 0.7223 | ❌ |
-| isn't there a verse about god loved the whole worl... | ['John 3:16'] | Psalms 67:7 | 0.7155 | ⚠️ |
-| god loved the whole world | ['John 3:16'] | Psalms 145:9 | 0.7543 | ❌ |
-| isn't there a verse about in the beginning god cre... | ['Genesis 1:1'] | Genesis 1:1 | 0.8065 | ✅ |
-| in the beginning god created | ['Genesis 1:1'] | Genesis 1:1 | 0.8381 | ✅ |
-
-*... and 522 more queries*
-
 ### huggingface/nomic-ai-nomic-embed-text-v1.5 (BSB)
 
 **Accuracy: 70.0%** (1117/1596 points across 532 queries)
@@ -675,25 +713,6 @@ For high-level information about these models, see the [MTEB Leaderboard](https:
 
 *... and 522 more queries*
 
-### huggingface/Qwen-Qwen3-Embedding-4B (BSB)
-
-**Accuracy: 58.9%** (940/1596 points across 532 queries)
-
-| Query | Expected | Top Result | Score | ✓ |
-|-------|----------|------------|-------|---|
-| isn't there a verse about god is love? | ['1 John 4:8', '1 John 4:16'] | 1 John 4:8 | 0.7756 | ✅ |
-| god is love | ['1 John 4:8', '1 John 4:16'] | 1 John 4:8 | 0.7562 | ✅ |
-| verse about they meant bad but god meant good (rou... | ['Genesis 50:20'] | Genesis 50:20 | 0.7200 | ✅ |
-| they meant bad but god meant good | ['Genesis 50:20'] | Genesis 50:20 | 0.7370 | ✅ |
-| isn't there a verse about god loves the world? | ['John 3:16'] | 1 John 4:8 | 0.7019 | ❌ |
-| god loves the world | ['John 3:16'] | Job 20:5 | 0.7062 | ❌ |
-| isn't there a verse about god loved the whole worl... | ['John 3:16'] | 1 John 4:11 | 0.7045 | ❌ |
-| god loved the whole world | ['John 3:16'] | 1 Corinthians 16:14 | 0.7100 | ❌ |
-| isn't there a verse about in the beginning god cre... | ['Genesis 1:1'] | Genesis 1:1 | 0.7725 | ✅ |
-| in the beginning god created | ['Genesis 1:1'] | Genesis 1:1 | 0.8114 | ✅ |
-
-*... and 522 more queries*
-
 ### huggingface/BAAI-bge-base-en (BSB)
 
 **Accuracy: 56.9%** (908/1596 points across 532 queries)
@@ -713,25 +732,6 @@ For high-level information about these models, see the [MTEB Leaderboard](https:
 
 *... and 522 more queries*
 
-### huggingface/Qwen-Qwen3-Embedding-0.6B (BSB)
-
-**Accuracy: 56.8%** (907/1596 points across 532 queries)
-
-| Query | Expected | Top Result | Score | ✓ |
-|-------|----------|------------|-------|---|
-| isn't there a verse about god is love? | ['1 John 4:8', '1 John 4:16'] | 1 John 4:8 | 0.6569 | ✅ |
-| god is love | ['1 John 4:8', '1 John 4:16'] | Psalms 59:10 | 0.7234 | ❌ |
-| verse about they meant bad but god meant good (rou... | ['Genesis 50:20'] | Proverbs 16:4 | 0.6752 | ⚠️ |
-| they meant bad but god meant good | ['Genesis 50:20'] | Proverbs 16:4 | 0.6880 | ❌ |
-| isn't there a verse about god loves the world? | ['John 3:16'] | 1 John 2:15 | 0.6984 | ❌ |
-| god loves the world | ['John 3:16'] | Psalms 47:7 | 0.6723 | ❌ |
-| isn't there a verse about god loved the whole worl... | ['John 3:16'] | 1 John 2:15 | 0.6837 | ⚠️ |
-| god loved the whole world | ['John 3:16'] | Psalms 67:7 | 0.6642 | ❌ |
-| isn't there a verse about in the beginning god cre... | ['Genesis 1:1'] | Genesis 1:1 | 0.6984 | ✅ |
-| in the beginning god created | ['Genesis 1:1'] | John 1:2 | 0.7343 | ⚠️ |
-
-*... and 522 more queries*
-
 ### huggingface/BAAI-bge-large-en (BSB)
 
 **Accuracy: 47.4%** (756/1596 points across 532 queries)

main.py

@@ -49,6 +49,10 @@ class EmbeddingProvider(ABC):
         """Generate embeddings for a batch of texts."""
         pass
 
+    async def embed_query(self, query: str) -> List[float]:
+        """Generate embedding for a query. Base implementation falls back to embed_text."""
+        return await self.embed_text(query)
+
 
 class OpenAIProvider(EmbeddingProvider):
     """OpenAI embedding provider."""
@@ -246,10 +250,23 @@ class HuggingFaceProvider(EmbeddingProvider):
     def __init__(self, model_name: str):
         self.model_name = model_name
         self.model = None
+        self.query_prompt_config = self._get_query_prompt_config()
 
     def get_name(self) -> str:
         # Convert model path to filename-safe format
         return self.model_name.replace("/", "-").replace("_", "-")
+    
+    def _get_query_prompt_config(self) -> dict:
+        """Get query prompt configuration for specific models."""
+        # Model-specific query prompt configurations
+        if "Qwen3-Embedding" in self.model_name:
+            return {
+                "enabled": True,
+                "prompt_name": "query",
+                "instruction_template": "Instruct: Given a biblical passage, retrieve verses that are semantically related or answer the query\nQuery: {query}"
+            }
+        # Add other model-specific configurations here as needed
+        return {"enabled": False}
 
     def _get_model(self):
         if self.model is None:
@@ -288,6 +305,32 @@ class HuggingFaceProvider(EmbeddingProvider):
         model = self._get_model()
         embedding = model.encode([text], normalize_embeddings=True)[0]
         return embedding.tolist()
+    
+    async def embed_query(self, query: str) -> List[float]:
+        """Embed a query with model-specific prompting if needed."""
+        model = self._get_model()
+        
+        if self.query_prompt_config["enabled"]:
+            # Apply model-specific query prompting
+            if "prompt_name" in self.query_prompt_config:
+                # Use prompt_name parameter (for Qwen3)
+                embedding = model.encode(
+                    [query], 
+                    normalize_embeddings=True, 
+                    prompt_name=self.query_prompt_config["prompt_name"]
+                )[0]
+            elif "instruction_template" in self.query_prompt_config:
+                # Use instruction template formatting
+                formatted_query = self.query_prompt_config["instruction_template"].format(query=query)
+                embedding = model.encode([formatted_query], normalize_embeddings=True)[0]
+            else:
+                # Fallback to regular embedding
+                embedding = model.encode([query], normalize_embeddings=True)[0]
+        else:
+            # No special prompting needed
+            embedding = model.encode([query], normalize_embeddings=True)[0]
+        
+        return embedding.tolist()
 
     async def embed_batch(self, texts: List[str]) -> List[List[float]]:
         model = self._get_model()
@@ -295,8 +338,37 @@ class HuggingFaceProvider(EmbeddingProvider):
         embeddings = model.encode(texts, normalize_embeddings=True)
         return [emb.tolist() for emb in embeddings]
     
+    async def embed_queries_batch_internal(self, queries: List[str]) -> List[List[float]]:
+        """Embed a batch of queries with model-specific prompting if needed."""
+        model = self._get_model()
+        
+        if self.query_prompt_config["enabled"]:
+            # Apply model-specific query prompting
+            if "prompt_name" in self.query_prompt_config:
+                # Use prompt_name parameter (for Qwen3)
+                embeddings = model.encode(
+                    queries, 
+                    normalize_embeddings=True, 
+                    prompt_name=self.query_prompt_config["prompt_name"]
+                )
+            elif "instruction_template" in self.query_prompt_config:
+                # Use instruction template formatting
+                formatted_queries = [
+                    self.query_prompt_config["instruction_template"].format(query=query) 
+                    for query in queries
+                ]
+                embeddings = model.encode(formatted_queries, normalize_embeddings=True)
+            else:
+                # Fallback to regular embedding
+                embeddings = model.encode(queries, normalize_embeddings=True)
+        else:
+            # No special prompting needed
+            embeddings = model.encode(queries, normalize_embeddings=True)
+        
+        return [emb.tolist() for emb in embeddings]
+    
     async def embed_queries_batch(self, queries: List[str], batch_size: int = 500) -> List[List[float]]:
-        """Efficiently embed multiple queries using HuggingFace's batch capability."""
+        """Efficiently embed multiple queries using HuggingFace's batch capability with model-specific prompting."""
         all_embeddings = []
         
         # HuggingFace can handle larger batches efficiently since it's local
@@ -305,14 +377,14 @@ class HuggingFaceProvider(EmbeddingProvider):
             print(f"Embedding batch {i//batch_size + 1}/{(len(queries) + batch_size - 1)//batch_size} ({len(batch)} queries)")
             
             try:
-                batch_embeddings = await self.embed_batch(batch)
+                batch_embeddings = await self.embed_queries_batch_internal(batch)
                 all_embeddings.extend(batch_embeddings)
             except Exception as e:
                 print(f"Error in batch embedding: {e}")
                 # Fall back to individual embedding for this batch
                 for query in batch:
                     try:
-                        embedding = await self.embed_text(query)
+                        embedding = await self.embed_query(query)
                         all_embeddings.append(embedding)
                     except Exception as e2:
                         print(f"Error embedding query '{query}': {e2}")
@@ -1111,7 +1183,7 @@ async def search_embeddings(
 
     # Generate embedding for the query
     print(f"Generating embedding for query: '{query}'")
-    query_embedding = await provider.embed_text(query)
+    query_embedding = await provider.embed_query(query)
 
     # Use HNSW when explicitly requested
     if use_hnsw: