@ninebix/nmt-system 1.0.4 → 2.0.0

package/dist/src/core/neuron-graph.d.ts

@@ -2,7 +2,7 @@
  * Neuron Graph Manager - Graph operations and traversal
  * @module core/neuron-graph
  */
-import type { UUID, NeuronNode, Synapse, SynapseType, Embedding384, TraversalStrategy, NeuronPath, INeuronStore } from '../types/index.js';
+import type { UUID, NeuronNode, Synapse, SynapseType, Embedding384, TraversalStrategy, NeuronPath, INeuronStore, SourceColumnSchema, SourceForeignKey, SourceIndex, SourceCheckConstraint, SourceTrigger } from '../types/index.js';
 import { HNSWIndex } from './hnsw-index.js';
 /**
  * Neuron Graph Manager options
@@ -24,6 +24,17 @@ export interface CreateNeuronInput {
     tags?: string[];
     autoConnect?: boolean;
     connectionThreshold?: number;
+    sourceRow?: Record<string, unknown>;
+    sourceColumns?: SourceColumnSchema[];
+    sourceForeignKeys?: SourceForeignKey[];
+    sourceIndexes?: SourceIndex[];
+    sourceChecks?: SourceCheckConstraint[];
+    sourceTriggers?: SourceTrigger[];
+    sourceTable?: string;
+    sourceEngine?: string;
+    sourceCharset?: string;
+    sourcePath?: string;
+    sourceName?: string;
 }
 /**
  * Traversal result
@@ -74,6 +85,16 @@ export declare class NeuronGraphManager {
         neuron: NeuronNode;
         score: number;
     }>>;
+    /**
+     * Find a near-duplicate neuron by embedding similarity.
+     * Returns the closest existing neuron if its score meets the threshold, null otherwise.
+     */
+    findDuplicate(embedding: Embedding384, threshold?: number): Promise<NeuronNode | null>;
+    /**
+     * Merge new tags into an existing neuron without overwriting existing ones.
+     * No-ops if the neuron is not found or there are no new tags to add.
+     */
+    mergeTags(neuronId: UUID, newTags: string[]): Promise<void>;
     /**
      * Find similar neurons to an existing neuron
      */
@@ -121,6 +142,114 @@ export declare class NeuronGraphManager {
      * Weaken synapse
      */
     weakenSynapse(synapseId: UUID, amount?: number): Promise<Synapse | null>;
+    /**
+     * Hebbian co-activation reinforcement.
+     *
+     * When a set of neurons are retrieved together in the same search query,
+     * the synapses connecting them are strengthened using the soft-ceiling rule:
+     *   w_new = w + η * (1 - w)
+     * This ensures weights approach 1.0 asymptotically and never exceed it.
+     *
+     * @param neuronIds  IDs of co-activated neurons (e.g. top-k search results)
+     * @param eta        Hebbian learning rate (default: 0.05)
+     */
+    reinforceCoActivation(neuronIds: UUID[], eta?: number): Promise<void>;
+    /**
+     * Compute the maximum synapse weight from a given neuron to any of the
+     * co-retrieved neurons. Used to boost search scores for well-connected results.
+     *
+     * @param neuronId      Source neuron
+     * @param peerIds       Set of peer neuron IDs in the same result set
+     * @returns             Max weight [0, 1], or 0 if no connecting synapses found
+     */
+    maxCoActivationWeight(neuronId: UUID, peerIds: Set<UUID>): Promise<number>;
+    /**
+     * Competitive inhibition: strengthen INHIBITORY synapses from higher-ranked
+     * neurons toward lower-ranked neurons that are semantically similar.
+     *
+     * Biological analogy: Winner-Take-All inhibition. When neuron A consistently
+     * outranks neuron B in the same search, A inhibits B to prevent redundant
+     * results. This promotes search result diversity over time.
+     *
+     * Formula (soft floor): w -= η * (1 - |w|)  →  weight approaches -1.0
+     *
+     * @param rankedNeuronIds  Neuron IDs sorted best-first (index 0 = winner)
+     * @param eta              Inhibitory learning rate (default: 0.03)
+     */
+    inhibitCoActivation(rankedNeuronIds: UUID[], eta?: number): Promise<void>;
+    /**
+     * Get the maximum absolute inhibitory weight targeting a neuron from any of
+     * the given peer neurons. Used to compute the inhibitory penalty in search.
+     *
+     * @param neuronId  Target neuron (potentially inhibited)
+     * @param peerIds   Set of peer neuron IDs (potential inhibitors)
+     * @returns         Max |weight| of INHIBITORY synapses from peers, or 0
+     */
+    maxInhibitoryWeight(neuronId: UUID, peerIds: Set<UUID>): Promise<number>;
+    /**
+     * Update a neuron's embedding vector (online learning).
+     * Deletes and re-inserts the node in the HNSW index to reflect the new vector.
+     *
+     * @param neuronId     Target neuron
+     * @param newEmbedding New (already L2-normalized) embedding
+     */
+    updateNeuronEmbedding(neuronId: UUID, newEmbedding: Embedding384): Promise<void>;
+    /**
+     * Synaptic pruning — remove structurally weak and unused synapses.
+     *
+     * Biological analogy: adolescent synaptic pruning — the brain eliminates
+     * ~50% of synapses formed in childhood, keeping only used pathways.
+     * This sharpens signal/noise ratio and reduces metabolic cost.
+     *
+     * Pruning criteria (both conditions must hold):
+     *   - Excitatory:  weight < minWeight   AND activationCount < minActivations
+     *   - Inhibitory:  |weight| < minWeight AND activationCount < minActivations
+     *
+     * @param minWeight        Minimum weight to keep (default: 0.05)
+     * @param minActivations   Minimum activation count to keep (default: 2)
+     * @param dryRun           If true, count candidates without deleting
+     * @returns                Number of synapses pruned (or candidates in dryRun)
+     */
+    pruneSynapses(options?: {
+        minWeight?: number;
+        minActivations?: number;
+        dryRun?: boolean;
+    }): Promise<{
+        pruned: number;
+        remaining: number;
+    }>;
+    /**
+     * Hopfield-style iterative pattern completion.
+     *
+     * Biological analogy: associative pattern completion in hippocampus/cortex.
+     * A partial or noisy cue converges to the stored memory by iteratively
+     * moving the query embedding toward the centroid of retrieved memories.
+     *
+     * Algorithm (per iteration):
+     *   1. Search top-k with current embedding
+     *   2. Compute score-weighted centroid of retrieved embeddings
+     *   3. Blend: q_new = normalize(α*q_old + (1-α)*centroid)
+     *   4. Repeat
+     *
+     * @param embedding   Initial (possibly noisy/partial) query embedding
+     * @param k           Number of candidates per iteration
+     * @param iterations  Refinement iterations (default: 3)
+     * @param alpha       Retention weight for original query (default: 0.3)
+     * @returns           Refined embedding and convergence delta
+     */
+    patternComplete(embedding: Embedding384, k?: number, iterations?: number, alpha?: number): Promise<{
+        refined: Embedding384;
+        delta: number;
+    }>;
+    /**
+     * Build episodic memory: create TEMPORAL synapses between neurons accessed
+     * together in the same search episode. This encodes the "context chain"
+     * of a reasoning session, analogous to hippocampal sequence encoding.
+     *
+     * @param episodeNeuronIds  Ordered list of neuron IDs in one episode
+     * @param maxDistance       Max positional distance to link (default: 2)
+     */
+    encodeEpisode(episodeNeuronIds: UUID[], maxDistance?: number): Promise<void>;
     private bfsTraverse;
     private dfsTraverse;
     private weightedTraverse;

package/dist/src/core/neuron-graph.d.ts.map

@@ -1 +1 @@
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package/dist/src/core/neuron-graph.js

@@ -2,6 +2,7 @@
  * Neuron Graph Manager - Graph operations and traversal
  * @module core/neuron-graph
  */
+import { normalize } from '../utils/similarity.js';
 /**
  * Neuron Graph Manager
  * Handles neuron creation, connection, and graph traversal
@@ -27,7 +28,18 @@ export class NeuronGraphManager {
             chunkHashes: input.chunkHashes,
             merkleRoot: input.merkleRoot,
             sourceType: input.sourceType,
-            tags: input.tags
+            tags: input.tags,
+            sourceRow: input.sourceRow,
+            sourceColumns: input.sourceColumns,
+            sourceForeignKeys: input.sourceForeignKeys,
+            sourceIndexes: input.sourceIndexes,
+            sourceChecks: input.sourceChecks,
+            sourceTriggers: input.sourceTriggers,
+            sourceTable: input.sourceTable,
+            sourceEngine: input.sourceEngine,
+            sourceCharset: input.sourceCharset,
+            sourcePath: input.sourcePath,
+            sourceName: input.sourceName,
         });
         // Add to HNSW index
         this.index.insert(neuron.id, neuron.embedding);
@@ -85,6 +97,40 @@ export class NeuronGraphManager {
         }
         return neurons;
     }
+    /**
+     * Find a near-duplicate neuron by embedding similarity.
+     * Returns the closest existing neuron if its score meets the threshold, null otherwise.
+     */
+    async findDuplicate(embedding, threshold = 0.95) {
+        const results = this.index.search(embedding, 1);
+        if (results.length === 0)
+            return null;
+        if (results[0].score < threshold)
+            return null;
+        return this.store.getNeuron(results[0].id);
+    }
+    /**
+     * Merge new tags into an existing neuron without overwriting existing ones.
+     * No-ops if the neuron is not found or there are no new tags to add.
+     */
+    async mergeTags(neuronId, newTags) {
+        if (newTags.length === 0)
+            return;
+        const neuron = await this.store.getNeuron(neuronId);
+        if (!neuron)
+            return;
+        const existing = new Set(neuron.metadata.tags);
+        if (!newTags.some(t => !existing.has(t)))
+            return; // nothing new
+        const mergedTags = [...new Set([...neuron.metadata.tags, ...newTags])];
+        await this.store.updateNeuron(neuronId, {
+            metadata: {
+                ...neuron.metadata,
+                tags: mergedTags,
+                updatedAt: new Date().toISOString(),
+            },
+        });
+    }
     /**
      * Find similar neurons to an existing neuron
      */
@@ -267,6 +313,258 @@ export class NeuronGraphManager {
         const newWeight = Math.max(0.0, synapse.weight - amount);
         return this.store.updateSynapseWeight(synapseId, newWeight);
     }
+    /**
+     * Hebbian co-activation reinforcement.
+     *
+     * When a set of neurons are retrieved together in the same search query,
+     * the synapses connecting them are strengthened using the soft-ceiling rule:
+     *   w_new = w + η * (1 - w)
+     * This ensures weights approach 1.0 asymptotically and never exceed it.
+     *
+     * @param neuronIds  IDs of co-activated neurons (e.g. top-k search results)
+     * @param eta        Hebbian learning rate (default: 0.05)
+     */
+    async reinforceCoActivation(neuronIds, eta = 0.05) {
+        if (neuronIds.length < 2)
+            return;
+        // Check all ordered pairs (i → j)
+        for (let i = 0; i < neuronIds.length; i++) {
+            for (let j = 0; j < neuronIds.length; j++) {
+                if (i === j)
+                    continue;
+                const synapse = await this.getConnection(neuronIds[i], neuronIds[j]);
+                if (!synapse)
+                    continue;
+                // Soft-ceiling Hebbian: w += η * (1 - w)
+                const newWeight = Math.min(1.0, synapse.weight + eta * (1 - synapse.weight));
+                await this.store.updateSynapseWeight(synapse.id, newWeight);
+                await this.store.recordSynapseActivation(synapse.id);
+            }
+        }
+    }
+    /**
+     * Compute the maximum synapse weight from a given neuron to any of the
+     * co-retrieved neurons. Used to boost search scores for well-connected results.
+     *
+     * @param neuronId      Source neuron
+     * @param peerIds       Set of peer neuron IDs in the same result set
+     * @returns             Max weight [0, 1], or 0 if no connecting synapses found
+     */
+    async maxCoActivationWeight(neuronId, peerIds) {
+        const outgoing = await this.store.getOutgoingSynapses(neuronId);
+        let max = 0;
+        for (const s of outgoing) {
+            if (s.type !== 'INHIBITORY' && peerIds.has(s.targetId) && s.weight > max) {
+                max = s.weight;
+            }
+        }
+        return max;
+    }
+    /**
+     * Competitive inhibition: strengthen INHIBITORY synapses from higher-ranked
+     * neurons toward lower-ranked neurons that are semantically similar.
+     *
+     * Biological analogy: Winner-Take-All inhibition. When neuron A consistently
+     * outranks neuron B in the same search, A inhibits B to prevent redundant
+     * results. This promotes search result diversity over time.
+     *
+     * Formula (soft floor): w -= η * (1 - |w|)  →  weight approaches -1.0
+     *
+     * @param rankedNeuronIds  Neuron IDs sorted best-first (index 0 = winner)
+     * @param eta              Inhibitory learning rate (default: 0.03)
+     */
+    async inhibitCoActivation(rankedNeuronIds, eta = 0.03) {
+        if (rankedNeuronIds.length < 2)
+            return;
+        // Winner → Loser: higher-rank inhibits lower-rank
+        for (let winner = 0; winner < rankedNeuronIds.length - 1; winner++) {
+            for (let loser = winner + 1; loser < rankedNeuronIds.length; loser++) {
+                const winnerId = rankedNeuronIds[winner];
+                const loserId = rankedNeuronIds[loser];
+                // Find existing INHIBITORY synapse (winner → loser)
+                const synapses = await this.store.getOutgoingSynapses(winnerId);
+                const existing = synapses.find((s) => s.targetId === loserId && s.type === 'INHIBITORY');
+                if (existing) {
+                    // Deepen inhibition: w -= η * (1 - |w|), floor at -1.0
+                    const newWeight = Math.max(-1.0, existing.weight - eta * (1 - Math.abs(existing.weight)));
+                    await this.store.updateSynapseWeight(existing.id, newWeight);
+                    await this.store.recordSynapseActivation(existing.id);
+                }
+                else {
+                    // Create new INHIBITORY synapse with small initial inhibition
+                    await this.store.createSynapse(winnerId, loserId, 'INHIBITORY', -0.05, false);
+                }
+            }
+        }
+    }
+    /**
+     * Get the maximum absolute inhibitory weight targeting a neuron from any of
+     * the given peer neurons. Used to compute the inhibitory penalty in search.
+     *
+     * @param neuronId  Target neuron (potentially inhibited)
+     * @param peerIds   Set of peer neuron IDs (potential inhibitors)
+     * @returns         Max |weight| of INHIBITORY synapses from peers, or 0
+     */
+    async maxInhibitoryWeight(neuronId, peerIds) {
+        const incoming = await this.store.getIncomingSynapses(neuronId);
+        let max = 0;
+        for (const s of incoming) {
+            if (s.type === 'INHIBITORY' && peerIds.has(s.sourceId)) {
+                const absW = Math.abs(s.weight);
+                if (absW > max)
+                    max = absW;
+            }
+        }
+        return max;
+    }
+    /**
+     * Update a neuron's embedding vector (online learning).
+     * Deletes and re-inserts the node in the HNSW index to reflect the new vector.
+     *
+     * @param neuronId     Target neuron
+     * @param newEmbedding New (already L2-normalized) embedding
+     */
+    async updateNeuronEmbedding(neuronId, newEmbedding) {
+        await this.store.updateNeuron(neuronId, { embedding: newEmbedding });
+        this.index.delete(neuronId);
+        this.index.insert(neuronId, newEmbedding);
+    }
+    /**
+     * Synaptic pruning — remove structurally weak and unused synapses.
+     *
+     * Biological analogy: adolescent synaptic pruning — the brain eliminates
+     * ~50% of synapses formed in childhood, keeping only used pathways.
+     * This sharpens signal/noise ratio and reduces metabolic cost.
+     *
+     * Pruning criteria (both conditions must hold):
+     *   - Excitatory:  weight < minWeight   AND activationCount < minActivations
+     *   - Inhibitory:  |weight| < minWeight AND activationCount < minActivations
+     *
+     * @param minWeight        Minimum weight to keep (default: 0.05)
+     * @param minActivations   Minimum activation count to keep (default: 2)
+     * @param dryRun           If true, count candidates without deleting
+     * @returns                Number of synapses pruned (or candidates in dryRun)
+     */
+    async pruneSynapses(options = {}) {
+        const { minWeight = 0.05, minActivations = 2, dryRun = false, } = options;
+        const allNeuronIds = await this.store.getAllNeuronIds();
+        const visitedSynapseIds = new Set();
+        let pruned = 0;
+        let remaining = 0;
+        for (const neuronId of allNeuronIds) {
+            const outgoing = await this.store.getOutgoingSynapses(neuronId);
+            for (const synapse of outgoing) {
+                if (visitedSynapseIds.has(synapse.id))
+                    continue;
+                visitedSynapseIds.add(synapse.id);
+                const absWeight = Math.abs(synapse.weight);
+                const activations = synapse.metadata.activationCount;
+                const shouldPrune = absWeight < minWeight && activations < minActivations;
+                if (shouldPrune) {
+                    if (!dryRun)
+                        await this.store.deleteSynapse(synapse.id);
+                    pruned++;
+                }
+                else {
+                    remaining++;
+                }
+            }
+        }
+        return { pruned, remaining };
+    }
+    /**
+     * Hopfield-style iterative pattern completion.
+     *
+     * Biological analogy: associative pattern completion in hippocampus/cortex.
+     * A partial or noisy cue converges to the stored memory by iteratively
+     * moving the query embedding toward the centroid of retrieved memories.
+     *
+     * Algorithm (per iteration):
+     *   1. Search top-k with current embedding
+     *   2. Compute score-weighted centroid of retrieved embeddings
+     *   3. Blend: q_new = normalize(α*q_old + (1-α)*centroid)
+     *   4. Repeat
+     *
+     * @param embedding   Initial (possibly noisy/partial) query embedding
+     * @param k           Number of candidates per iteration
+     * @param iterations  Refinement iterations (default: 3)
+     * @param alpha       Retention weight for original query (default: 0.3)
+     * @returns           Refined embedding and convergence delta
+     */
+    async patternComplete(embedding, k = 10, iterations = 3, alpha = 0.3) {
+        let current = embedding;
+        let delta = 0;
+        for (let iter = 0; iter < iterations; iter++) {
+            const results = this.index.search(current, k);
+            if (results.length === 0)
+                break;
+            // Only use above-average scoring neurons for centroid.
+            // Using all k neurons in a small index would pull toward global mean,
+            // defeating convergence. Keeping the top half ensures the attractor
+            // is specific to the query cluster.
+            const meanScore = results.reduce((s, r) => s + r.score, 0) / results.length;
+            const topResults = results.filter(r => r.score >= meanScore);
+            // Score-weighted centroid of selected neurons
+            const centroid = new Float32Array(384);
+            let totalScore = 0;
+            for (const r of topResults) {
+                const neuron = await this.store.getNeuron(r.id);
+                if (!neuron)
+                    continue;
+                for (let d = 0; d < 384; d++) {
+                    centroid[d] += r.score * neuron.embedding[d];
+                }
+                totalScore += r.score;
+            }
+            if (totalScore === 0)
+                break;
+            for (let d = 0; d < 384; d++)
+                centroid[d] /= totalScore;
+            // Blend: retain alpha of original, pull (1-alpha) toward centroid
+            const blended = new Float32Array(384);
+            for (let d = 0; d < 384; d++) {
+                blended[d] = alpha * current[d] + (1 - alpha) * centroid[d];
+            }
+            const refined = normalize(blended);
+            // Measure convergence (L2 distance between iterations)
+            delta = Math.sqrt(Array.from(refined).reduce((s, v, i) => s + (v - current[i]) ** 2, 0));
+            current = refined;
+            if (delta < 1e-4)
+                break; // Converged
+        }
+        return { refined: current, delta };
+    }
+    /**
+     * Build episodic memory: create TEMPORAL synapses between neurons accessed
+     * together in the same search episode. This encodes the "context chain"
+     * of a reasoning session, analogous to hippocampal sequence encoding.
+     *
+     * @param episodeNeuronIds  Ordered list of neuron IDs in one episode
+     * @param maxDistance       Max positional distance to link (default: 2)
+     */
+    async encodeEpisode(episodeNeuronIds, maxDistance = 2) {
+        if (episodeNeuronIds.length < 2)
+            return;
+        for (let i = 0; i < episodeNeuronIds.length; i++) {
+            for (let j = i + 1; j <= Math.min(i + maxDistance, episodeNeuronIds.length - 1); j++) {
+                const srcId = episodeNeuronIds[i];
+                const tgtId = episodeNeuronIds[j];
+                // Skip if TEMPORAL synapse already exists
+                const existing = await this.getConnection(srcId, tgtId);
+                if (existing?.type === 'TEMPORAL') {
+                    // Strengthen existing temporal link
+                    const newW = Math.min(1.0, existing.weight + 0.05 * (1 - existing.weight));
+                    await this.store.updateSynapseWeight(existing.id, newW);
+                    await this.store.recordSynapseActivation(existing.id);
+                }
+                else if (!existing) {
+                    // Create new TEMPORAL synapse — initial weight decays with distance
+                    const initialWeight = 0.3 / j; // closer = stronger
+                    await this.store.createSynapse(srcId, tgtId, 'TEMPORAL', initialWeight, false);
+                }
+            }
+        }
+    }
     // ==================== Private Traversal Methods ====================
     async bfsTraverse(startId, maxDepth, visited, paths, filter) {
         const queue = [{ id: startId, depth: 0, path: [startId], synapses: [], weight: 0 }];

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package/dist/src/core/probabilistic-neuron.d.ts.map

@@ -1 +1 @@
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