feat(embeddings): point size mapping and convex hulls for t-SNE

api/app/routes/projection.py

@@ -40,6 +40,7 @@ class ProjectionConceptResponse(BaseModel):
     ontology: Optional[str] = None  # Source ontology (for cross-ontology mode)
     item_type: Optional[str] = None  # Item type (for combined mode)
     cluster_id: Optional[int] = None  # DBSCAN cluster assignment (None = noise)
+    degree: Optional[int] = None  # Total edge count (in + out)
 
 
 class ProjectionParametersResponse(BaseModel):
@@ -142,6 +143,10 @@ class RegenerateRequest(BaseModel):
         default=False,
         description="Include diversity scores (slower)"
     )
+    include_degree: bool = Field(
+        default=True,
+        description="Include concept degree (edge count)"
+    )
     embedding_source: Literal["concepts", "sources", "vocabulary", "combined"] = Field(
         default="concepts",
         description="Which embeddings to project: concepts (default), sources, vocabulary, or combined"
@@ -287,6 +292,7 @@ async def regenerate_projection(
             include_grounding=body.include_grounding,
             refresh_grounding=body.refresh_grounding,
             include_diversity=body.include_diversity,
+            include_degree=body.include_degree,
             embedding_source=body.embedding_source
         )
 
@@ -316,6 +322,7 @@ async def regenerate_projection(
                     "center": body.center,
                     "include_grounding": body.include_grounding,
                     "include_diversity": body.include_diversity,
+                    "include_degree": body.include_degree,
                     "embedding_source": body.embedding_source
                 },
                 payload=dataset,
@@ -348,6 +355,7 @@ async def regenerate_projection(
             "include_grounding": body.include_grounding,
             "refresh_grounding": body.refresh_grounding,
             "include_diversity": body.include_diversity,
+            "include_degree": body.include_degree,
             "embedding_source": body.embedding_source,
             "create_artifact": body.create_artifact,
             "description": f"Regenerate {body.embedding_source} projection for '{ontology}'",

api/app/services/embedding_projection_service.py

@@ -590,6 +590,45 @@ def _add_diversity_scores(self, concepts: List[Dict]) -> List[Dict]:
 
         return concepts
 
+    def _add_degree_counts(self, concepts: List[Dict], ontology: str) -> List[Dict]:
+        """Add degree (total edge count) to concepts via bulk Cypher query."""
+        concept_ids = [c["concept_id"] for c in concepts if c.get("concept_id")]
+        if not concept_ids:
+            return concepts
+
+        try:
+            # Use _execute_cypher which handles AGE setup, query wrapping, and result parsing
+            results = self.client._execute_cypher(
+                """
+                MATCH (c:Concept)
+                WHERE c.concept_id IN $concept_ids
+                OPTIONAL MATCH (c)-[r_out]->(:Concept)
+                OPTIONAL MATCH (:Concept)-[r_in]->(c)
+                RETURN c.concept_id as concept_id,
+                       count(DISTINCT r_out) + count(DISTINCT r_in) as degree
+                """,
+                params={"concept_ids": concept_ids}
+            )
+
+            degree_map = {}
+            for row in results:
+                cid = row.get("concept_id")
+                deg = row.get("degree", 0)
+                if cid:
+                    degree_map[str(cid)] = int(deg) if deg is not None else 0
+
+            for concept in concepts:
+                concept["degree"] = degree_map.get(concept["concept_id"], 0)
+
+            logger.info(f"Added degree counts for {len(degree_map)}/{len(concept_ids)} concepts")
+
+        except Exception as e:
+            logger.error(f"Error adding degree counts: {e}", exc_info=True)
+            for concept in concepts:
+                concept["degree"] = None
+
+        return concepts
+
     def compute_projection(
         self,
         embeddings: np.ndarray,
@@ -867,6 +906,7 @@ def generate_projection_dataset(
         include_grounding: bool = True,
         refresh_grounding: bool = False,
         include_diversity: bool = False,  # Off by default for performance
+        include_degree: bool = True,  # On by default (cheap bulk query)
         embedding_source: Literal["concepts", "sources", "vocabulary", "combined"] = "concepts"
     ) -> Dict[str, Any]:
         """
@@ -1005,6 +1045,10 @@ def generate_projection_dataset(
                     if cid and cid in fresh_groundings:
                         item["grounding_strength"] = fresh_groundings[cid]
 
+        # Add degree counts if requested (bulk Cypher, cheap)
+        if include_degree and embedding_source in ("concepts", "combined"):
+            self._add_degree_counts(items, ontology)
+
         # Build result dataset
         result_items = []
         grounding_values = []
@@ -1044,6 +1088,9 @@ def generate_projection_dataset(
                 if item.get("diversity_score") is not None:
                     diversity_values.append(item["diversity_score"])
 
+            if include_degree:
+                entry["degree"] = item.get("degree")
+
             # Add extra metadata for sources
             if "full_text" in item:
                 entry["full_text"] = item["full_text"]

api/app/workers/projection_worker.py

@@ -90,6 +90,7 @@ def run_projection_worker(
         include_grounding = job_data.get("include_grounding", True)
         refresh_grounding = job_data.get("refresh_grounding", False)
         include_diversity = job_data.get("include_diversity", False)
+        include_degree = job_data.get("include_degree", True)
         embedding_source = job_data.get("embedding_source", "concepts")
 
         logger.info(
@@ -128,6 +129,7 @@ def run_projection_worker(
             include_grounding=include_grounding,
             refresh_grounding=refresh_grounding,
             include_diversity=include_diversity,
+            include_degree=include_degree,
             embedding_source=embedding_source
         )
 

web/src/api/client.ts

@@ -1470,6 +1470,7 @@ class APIClient {
       include_grounding?: boolean;
       refresh_grounding?: boolean; // Compute fresh grounding values
       include_diversity?: boolean;
+      include_degree?: boolean;    // Include degree (edge count) per concept
       embedding_source?: 'concepts' | 'sources' | 'vocabulary' | 'combined';
     }
   ): Promise<{

web/src/components/blocks/AndBlock.tsx

@@ -16,7 +16,7 @@ export const AndBlock: React.FC<NodeProps<BlockData>> = ({ id }) => {
       <div className="flex flex-col items-center justify-center gap-1">
         <div className="flex items-center gap-2">
           <span className="font-bold text-base text-amber-700 dark:text-amber-300">AND</span>
-          <span className="px-1.5 py-0.5 bg-amber-100 dark:bg-amber-900/50 text-amber-700 dark:text-amber-300 rounded text-[10px] font-medium">
+          <span className="px-1.5 py-0.5 bg-amber-100 dark:bg-amber-900/50 text-amber-700 dark:text-amber-300 rounded text-[0.625rem] font-medium">
             LOGIC
           </span>
         </div>

web/src/components/blocks/BlockBuilder.tsx

@@ -1162,7 +1162,7 @@ export const BlockBuilder = forwardRef<BlockBuilderHandle, BlockBuilderProps>(({
                               {diagram.description}
                             </div>
                           )}
-                          <div className="text-[10px] text-muted-foreground dark:text-gray-500 mt-1">
+                          <div className="text-[0.625rem] text-muted-foreground dark:text-gray-500 mt-1">
                             {diagram.nodeCount} blocks, {diagram.edgeCount} connections
                           </div>
                         </div>

web/src/components/blocks/BlockHelpPopup.tsx

@@ -71,7 +71,7 @@ export const BlockHelpPopup: React.FC<BlockHelpPopupProps> = ({ blockType, posit
       <div className="px-4 py-3 border-b border-border dark:border-gray-700 flex items-center justify-between">
         <div className="flex items-center gap-2">
           <span className="font-semibold text-card-foreground dark:text-gray-100">{content.title}</span>
-          <span className={`px-1.5 py-0.5 rounded text-[10px] font-medium ${tagStyle.bg} ${tagStyle.text}`}>
+          <span className={`px-1.5 py-0.5 rounded text-[0.625rem] font-medium ${tagStyle.bg} ${tagStyle.text}`}>
             {content.tag}
           </span>
         </div>

web/src/components/blocks/BlockPalette.tsx

@@ -247,7 +247,7 @@ export const BlockPalette: React.FC<BlockPaletteProps> = ({ onAddBlock, classNam
               {section.title}
             </h4>
             {section.description && (
-              <p className="text-[10px] text-muted-foreground dark:text-gray-500">{section.description}</p>
+              <p className="text-[0.625rem] text-muted-foreground dark:text-gray-500">{section.description}</p>
             )}
           </div>
 

web/src/components/blocks/EdgeFilterBlock.tsx

@@ -74,7 +74,7 @@ export const EdgeFilterBlock: React.FC<NodeProps<BlockData>> = ({ data }) => {
               }}
               className="w-3 h-3 text-blue-500 dark:text-blue-400 rounded"
             />
-            <span className="text-[10px] text-muted-foreground dark:text-gray-500">Regex</span>
+            <span className="text-[0.625rem] text-muted-foreground dark:text-gray-500">Regex</span>
           </label>
         </div>
 
@@ -102,7 +102,7 @@ export const EdgeFilterBlock: React.FC<NodeProps<BlockData>> = ({ data }) => {
 
         {/* Regex error message */}
         {regexError && (
-          <div className="text-[10px] text-red-500 dark:text-red-400">
+          <div className="text-[0.625rem] text-red-500 dark:text-red-400">
             {regexError}
           </div>
         )}

web/src/components/blocks/EndBlock.tsx

@@ -21,13 +21,13 @@ export const EndBlock: React.FC<NodeProps<BlockData>> = ({ data }) => {
       <div className="flex items-center justify-center gap-2 mb-2">
         <Square className="w-4 h-4 text-red-600 dark:text-red-400 fill-current" />
         <span className="font-medium text-sm text-card-foreground dark:text-gray-100">END</span>
-        <span className="px-1.5 py-0.5 bg-red-100 dark:bg-red-900/50 text-red-700 dark:text-red-300 rounded text-[10px] font-medium">
+        <span className="px-1.5 py-0.5 bg-red-100 dark:bg-red-900/50 text-red-700 dark:text-red-300 rounded text-[0.625rem] font-medium">
           FLOW
         </span>
       </div>
 
       {/* Output Format Control */}
-      <div className="flex items-center justify-center gap-1 text-[10px]">
+      <div className="flex items-center justify-center gap-1 text-[0.625rem]">
         <button
           className={`flex items-center gap-1 px-2 py-1 rounded ${
             outputFormat === 'visualization'

web/src/components/blocks/EnrichBlock.tsx

@@ -59,7 +59,7 @@ export const EnrichBlock: React.FC<NodeProps<BlockData>> = ({ data }) => {
           />
           <div className="flex-1">
             <span className="text-sm text-card-foreground dark:text-gray-100">Ontology</span>
-            <p className="text-[10px] text-muted-foreground dark:text-gray-500">Color-code by source document</p>
+            <p className="text-[0.625rem] text-muted-foreground dark:text-gray-500">Color-code by source document</p>
           </div>
         </label>
 
@@ -72,7 +72,7 @@ export const EnrichBlock: React.FC<NodeProps<BlockData>> = ({ data }) => {
           />
           <div className="flex-1">
             <span className="text-sm text-card-foreground dark:text-gray-100">Grounding</span>
-            <p className="text-[10px] text-muted-foreground dark:text-gray-500">Confidence/reliability score</p>
+            <p className="text-[0.625rem] text-muted-foreground dark:text-gray-500">Confidence/reliability score</p>
           </div>
         </label>
 
@@ -85,7 +85,7 @@ export const EnrichBlock: React.FC<NodeProps<BlockData>> = ({ data }) => {
           />
           <div className="flex-1">
             <span className="text-sm text-card-foreground dark:text-gray-100">Search Terms</span>
-            <p className="text-[10px] text-muted-foreground dark:text-gray-500">Alternative labels/aliases</p>
+            <p className="text-[0.625rem] text-muted-foreground dark:text-gray-500">Alternative labels/aliases</p>
           </div>
         </label>
       </div>

web/src/components/blocks/EpistemicFilterBlock.tsx

@@ -54,7 +54,7 @@ export const EpistemicFilterBlock: React.FC<NodeProps<BlockData>> = ({ data }) =
       <div className="flex items-center gap-2 mb-3">
         <Snowflake className="w-4 h-4 text-indigo-600 dark:text-indigo-400" />
         <span className="font-medium text-sm text-card-foreground dark:text-gray-100">Epistemic Filter</span>
-        <span className="ml-auto px-1.5 py-0.5 bg-indigo-100 dark:bg-indigo-900/50 text-indigo-700 dark:text-indigo-300 rounded text-[10px] font-medium">
+        <span className="ml-auto px-1.5 py-0.5 bg-indigo-100 dark:bg-indigo-900/50 text-indigo-700 dark:text-indigo-300 rounded text-[0.625rem] font-medium">
           SMART
         </span>
       </div>
@@ -76,7 +76,7 @@ export const EpistemicFilterBlock: React.FC<NodeProps<BlockData>> = ({ data }) =
         >
           Include Only
           {includeStatuses.length > 0 && (
-            <span className="ml-1 px-1 bg-white/20 rounded text-[10px]">{includeStatuses.length}</span>
+            <span className="ml-1 px-1 bg-white/20 rounded text-[0.625rem]">{includeStatuses.length}</span>
           )}
         </button>
         <button
@@ -89,7 +89,7 @@ export const EpistemicFilterBlock: React.FC<NodeProps<BlockData>> = ({ data }) =
         >
           Exclude
           {excludeStatuses.length > 0 && (
-            <span className="ml-1 px-1 bg-white/20 rounded text-[10px]">{excludeStatuses.length}</span>
+            <span className="ml-1 px-1 bg-white/20 rounded text-[0.625rem]">{excludeStatuses.length}</span>
           )}
         </button>
       </div>
@@ -121,7 +121,7 @@ export const EpistemicFilterBlock: React.FC<NodeProps<BlockData>> = ({ data }) =
                 <span className="text-xs font-medium text-card-foreground dark:text-gray-200 block">
                   {status.label}
                 </span>
-                <span className="text-[10px] text-muted-foreground dark:text-gray-500 block truncate">
+                <span className="text-[0.625rem] text-muted-foreground dark:text-gray-500 block truncate">
                   {status.description}
                 </span>
               </div>
@@ -132,7 +132,7 @@ export const EpistemicFilterBlock: React.FC<NodeProps<BlockData>> = ({ data }) =
 
       {/* Active filters summary */}
       {activeCount > 0 && (
-        <div className="mt-2 pt-2 border-t border-border dark:border-gray-700 text-[10px] text-muted-foreground dark:text-gray-500">
+        <div className="mt-2 pt-2 border-t border-border dark:border-gray-700 text-[0.625rem] text-muted-foreground dark:text-gray-500">
           {includeStatuses.length > 0 && (
             <div>Include: {includeStatuses.join(', ')}</div>
           )}

web/src/components/blocks/FilterBlock.tsx

@@ -64,7 +64,7 @@ export const FilterBlock: React.FC<NodeProps<BlockData>> = ({ data }) => {
       <div className="flex items-center gap-2 mb-3">
         <Filter className="w-4 h-4 text-orange-600 dark:text-orange-400" />
         <span className="font-medium text-sm text-card-foreground dark:text-gray-100">Filter Results</span>
-        <span className="ml-auto px-1.5 py-0.5 bg-orange-100 dark:bg-orange-900/50 text-orange-700 dark:text-orange-300 rounded text-[10px] font-medium">
+        <span className="ml-auto px-1.5 py-0.5 bg-orange-100 dark:bg-orange-900/50 text-orange-700 dark:text-orange-300 rounded text-[0.625rem] font-medium">
           CYPHER
         </span>
       </div>
@@ -86,7 +86,7 @@ export const FilterBlock: React.FC<NodeProps<BlockData>> = ({ data }) => {
                 }}
                 className="w-3 h-3 text-orange-500 dark:text-orange-400 rounded"
               />
-              <span className="text-[10px] text-muted-foreground dark:text-gray-500">Regex</span>
+              <span className="text-[0.625rem] text-muted-foreground dark:text-gray-500">Regex</span>
             </label>
             {useRegex && (
               <div className="relative">
@@ -99,7 +99,7 @@ export const FilterBlock: React.FC<NodeProps<BlockData>> = ({ data }) => {
                   <HelpCircle className="w-3 h-3 text-muted-foreground dark:text-gray-500" />
                 </button>
                 {showRegexHelp && (
-                  <div className="absolute right-0 top-5 z-50 w-48 p-2 bg-card dark:bg-gray-800 border border-border dark:border-gray-600 rounded shadow-lg text-[10px]">
+                  <div className="absolute right-0 top-5 z-50 w-48 p-2 bg-card dark:bg-gray-800 border border-border dark:border-gray-600 rounded shadow-lg text-[0.625rem]">
                     <div className="font-medium text-card-foreground dark:text-gray-100 mb-1">Regex Examples</div>
                     <div className="space-y-0.5 text-muted-foreground dark:text-gray-400">
                       <div><code className="text-orange-600 dark:text-orange-400">.*</code> any characters</div>
@@ -139,7 +139,7 @@ export const FilterBlock: React.FC<NodeProps<BlockData>> = ({ data }) => {
 
         {/* Regex error message */}
         {regexError && (
-          <div className="text-[10px] text-red-500 dark:text-red-400">
+          <div className="text-[0.625rem] text-red-500 dark:text-red-400">
             {regexError}
           </div>
         )}

web/src/components/blocks/LimitBlock.tsx

@@ -27,7 +27,7 @@ export const LimitBlock: React.FC<NodeProps<BlockData>> = ({ data }) => {
       <div className="flex items-center gap-2 mb-3">
         <Hash className="w-4 h-4 text-gray-600 dark:text-gray-400" />
         <span className="font-medium text-sm text-card-foreground dark:text-gray-100">Limit Results</span>
-        <span className="ml-auto px-1.5 py-0.5 bg-gray-100 dark:bg-gray-900/50 text-gray-700 dark:text-gray-300 rounded text-[10px] font-medium">
+        <span className="ml-auto px-1.5 py-0.5 bg-gray-100 dark:bg-gray-900/50 text-gray-700 dark:text-gray-300 rounded text-[0.625rem] font-medium">
           CYPHER
         </span>
       </div>