diff --git a/packages/memory-graph/src/hooks/use-force-simulation.ts b/packages/memory-graph/src/hooks/use-force-simulation.ts
index e1d6b19e..3b5bfe97 100644
--- a/packages/memory-graph/src/hooks/use-force-simulation.ts
+++ b/packages/memory-graph/src/hooks/use-force-simulation.ts
@@ -114,16 +114,17 @@ export function useForceSimulation(
 		// eslint-disable-next-line react-hooks/exhaustive-deps
 	}, [enabled])
 
-	// Update simulation nodes when they change
+	// Update simulation nodes and edges together to prevent race conditions
 	useEffect(() => {
-		if (simulationRef.current && nodes.length > 0) {
+		if (!simulationRef.current) return
+
+		// Update nodes
+		if (nodes.length > 0) {
 			simulationRef.current.nodes(nodes)
 		}
-	}, [nodes])
 
-	// Update simulation edges when they change
-	useEffect(() => {
-		if (simulationRef.current && edges.length > 0) {
+		// Update edges
+		if (edges.length > 0) {
 			const linkForce = simulationRef.current.force<
 				d3.ForceLink<GraphNode, GraphEdge>
 			>("link")
@@ -131,7 +132,7 @@ export function useForceSimulation(
 				linkForce.links(edges)
 			}
 		}
-	}, [edges])
+	}, [nodes, edges])
 
 	// Reheat simulation (called on drag start)
 	const reheat = useCallback(() => {
diff --git a/packages/memory-graph/src/hooks/use-graph-data.ts b/packages/memory-graph/src/hooks/use-graph-data.ts
index d8c7e5b5..f0afab1d 100644
--- a/packages/memory-graph/src/hooks/use-graph-data.ts
+++ b/packages/memory-graph/src/hooks/use-graph-data.ts
@@ -5,7 +5,7 @@ import {
 	getConnectionVisualProps,
 	getMagicalConnectionColor,
 } from "@/lib/similarity"
-import { useMemo, useRef } from "react"
+import { useMemo, useRef, useEffect } from "react"
 import { colors, LAYOUT_CONSTANTS } from "@/constants"
 import type {
 	DocumentsResponse,
@@ -26,6 +26,27 @@ export function useGraphData(
 	// Cache nodes to preserve d3-force mutations (x, y, vx, vy, fx, fy)
 	const nodeCache = useRef<Map<string, GraphNode>>(new Map())
 
+	// Cleanup nodeCache to prevent memory leak
+	useEffect(() => {
+		if (!data?.documents) return
+
+		// Build set of current node IDs
+		const currentNodeIds = new Set<string>()
+		data.documents.forEach((doc) => {
+			currentNodeIds.add(doc.id)
+			doc.memoryEntries.forEach((mem) => {
+				currentNodeIds.add(`${mem.id}`)
+			})
+		})
+
+		// Remove stale nodes from cache
+		for (const [id] of nodeCache.current.entries()) {
+			if (!currentNodeIds.has(id)) {
+				nodeCache.current.delete(id)
+			}
+		}
+	}, [data, selectedSpace])
+
 	return useMemo(() => {
 		if (!data?.documents) return { nodes: [], edges: [] }
 
@@ -296,12 +317,16 @@ export function useGraphData(
 		})
 
 		// Document-to-document similarity edges
-		for (let i = 0; i < filteredDocuments.length; i++) {
-			const docI = filteredDocuments[i]
+		// Performance optimization: limit comparisons to prevent O(n²) scaling issues
+		const MAX_DOCS_FOR_SIMILARITY = 50
+		const docsToCompare = filteredDocuments.slice(0, MAX_DOCS_FOR_SIMILARITY)
+
+		for (let i = 0; i < docsToCompare.length; i++) {
+			const docI = docsToCompare[i]
 			if (!docI) continue
 
-			for (let j = i + 1; j < filteredDocuments.length; j++) {
-				const docJ = filteredDocuments[j]
+			for (let j = i + 1; j < docsToCompare.length; j++) {
+				const docJ = docsToCompare[j]
 				if (!docJ) continue
 
 				const sim = calculateSemanticSimilarity(