Albert
0c4934cf70
Fixed critical bug where nodes 4+ wouldn't get 3D coordinates because UMAP manifold learning requires seeing the complete dataset together. Root Cause: - Previous code only calculated coords for nodes WHERE coords_3d = NONE - When creating nodes 4-5, only those 2 nodes were passed to UMAP - UMAP requires minimum 3 points to define a manifold - Result: "Not enough nodes to map (2/3)" error Why Full Recalculation is Necessary: - UMAP is a non-linear manifold learning algorithm - It creates relative coordinates, not absolute positions - Each UMAP run produces different coordinate systems - No "fixed origin" exists - positions are only meaningful relative to each other - Adding new data changes the manifold structure Changes: - Updated /app/api/calculate-graph/route.ts: * Removed "AND coords_3d = NONE" filter from query * Now fetches ALL nodes with embeddings every time * Recalculates entire graph when triggered * Updated comments and logging to reflect full recalculation - Created docs/umap-recalculation-strategy.md: * Comprehensive explanation of UMAP manifold learning * Why incremental calculation doesn't work * Trade-offs of full recalculation approach * Performance characteristics (<100 nodes: <1.5s) * Future optimization strategies for scale - Added scripts/recalculate-all-coords.ts: * Emergency script to manually fix production database * Successfully recalculated all 5 nodes in production UX Impact: The thought galaxy now "reorganizes" when adding new nodes - existing nodes will shift slightly. This is actually a feature, showing the evolving structure of your knowledge graph as it grows. Performance: Full recalculation is O(n²) but acceptable for <100 nodes: - 3 nodes: ~50ms - 10 nodes: ~200ms - 50 nodes: ~800ms - 100 nodes: ~1.5s For Ponderants MVP, this is perfectly acceptable. Future optimizations documented if we reach 1000+ nodes per user. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
92 lines
3.0 KiB
TypeScript
92 lines
3.0 KiB
TypeScript
import Surreal from 'surrealdb';
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import { UMAP } from 'umap-js';
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/**
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* Recalculate 3D coordinates for ALL nodes
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*
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* This script fixes the issue where new nodes don't get coordinates
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* because UMAP needs to see the full dataset to properly position points.
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*
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* Usage: tsx scripts/recalculate-all-coords.ts
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*/
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async function recalculateAllCoordinates() {
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const db = new Surreal();
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try {
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// Connect to production database
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const dbUrl = process.env.SURREALDB_URL || 'wss://ponderants-prod-06d6iecp19qj3bvmv2o0r5j50o.aws-usw2.surreal.cloud/rpc';
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const dbNs = process.env.SURREALDB_NS || 'ponderants';
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const dbName = process.env.SURREALDB_DB || 'production';
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const dbUser = process.env.SURREALDB_USER || 'root';
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const dbPass = process.env.SURREALDB_PASS;
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if (!dbPass) {
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throw new Error('SURREALDB_PASS environment variable is required');
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}
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console.log(`Connecting to ${dbUrl}...`);
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await db.connect(dbUrl);
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await db.signin({ username: dbUser, password: dbPass });
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await db.use({ namespace: dbNs, database: dbName });
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console.log('✓ Connected to database');
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// Fetch ALL nodes with embeddings (not just those without coords)
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console.log('Fetching all nodes with embeddings...');
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const results = await db.query<[Array<{ id: string; embedding: number[] }>]>(
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'SELECT id, title, embedding FROM node WHERE embedding != NONE'
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);
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const nodes = results[0] || [];
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console.log(`Found ${nodes.length} nodes with embeddings`);
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if (nodes.length === 0) {
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console.log('No nodes with embeddings found');
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return;
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}
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if (nodes.length < 3) {
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console.error(`ERROR: Need at least 3 nodes for UMAP, found ${nodes.length}`);
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return;
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}
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// Run UMAP on ALL nodes together
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const embeddings = nodes.map((n) => n.embedding);
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console.log('Running UMAP dimensionality reduction...');
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console.log(`- Input: ${nodes.length} nodes with ${embeddings[0].length}-dimensional embeddings`);
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console.log(`- Output: 3D coordinates`);
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const umap = new UMAP({
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nComponents: 3,
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nNeighbors: Math.min(15, nodes.length - 1), // nNeighbors must be < sample size
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minDist: 0.1,
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spread: 1.0,
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});
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const coords_3d_array = await umap.fitAsync(embeddings);
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console.log('✓ UMAP projection complete');
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// Update ALL nodes with their new 3D coords
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console.log('Updating nodes with new coordinates...');
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for (let i = 0; i < nodes.length; i++) {
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const node = nodes[i];
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const coords = coords_3d_array[i];
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await db.merge(node.id, {
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coords_3d: [coords[0], coords[1], coords[2]],
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});
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console.log(` ✓ Updated ${node.id}: [${coords[0].toFixed(3)}, ${coords[1].toFixed(3)}, ${coords[2].toFixed(3)}]`);
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}
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console.log(`\n✅ Successfully updated ${nodes.length} nodes with 3D coordinates`);
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} catch (error) {
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console.error('❌ Error:', error);
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process.exit(1);
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} finally {
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await db.close();
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}
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}
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recalculateAllCoordinates();
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