Mongodb Search And AI

Automated Embedding

Scope: This guide covers configuring MongoDB Vector Search to automatically generate and manage vector embeddings — no embedding code or model infrastructure required (queries still run through a $vectorSearch aggregation pipeline). It documents the autoEmbed index type and text-query $vectorSearch syntax. For manual vector search (bring your own embeddings), see vector-search.md. For combining with lexical search, see hybrid-search.md.

Table of Contents

• Prerequisites

• Model Selection

• Index Definition

• Query Construction

• Item-to-Item Similarity

• How It Works Internally

• Billing and Free Tokens

• Rate Limits

• Management and Monitoring

• Troubleshooting

Prerequisites

Verify these prerequisites before creating an autoEmbed index or query. Tier and auto-scaling prerequisites can change across Atlas releases — confirm the current requirements in the official docs before acting.

Atlas Clusters

Automated Embedding is supported on all Atlas cluster tiers: M0 (free), Flex, and M10+ dedicated.

M10+ dedicated clusters require storage auto-scaling to be enabled. If the user is on M10+ without storage auto-scaling, explain how to enable it in Atlas and wait for confirmation before proceeding to index creation.

Self-Managed Deployments

Requires:

1. MongoDB 8.3+ with mongot

2. A Voyage AI API key for indexing

3. A Voyage AI API key for querying (recommended to use separate keys)

4. Keys configured in mongot during deployment

If the user is on a self-managed deployment without Voyage AI configured, offer an alternative: "You can still do semantic search by generating embeddings yourself and storing them in your documents — this works on any deployment. Want to go that route instead?" If yes, proceed with manual Vector Search using vector-search.md.

Model Selection

All models use Voyage AI, hosted and managed by MongoDB (multi-tenant, US region, Google Cloud). Context window is 32,000 tokens for all models. Text exceeding this is truncated at index time; queries exceeding it return a context-limit-exceeded error. (Pricing and rate limits can change—confirm current values in Atlas or official MongoDB documentation.)

Decision guide:

• Default / unknown use case → voyage-4

• Large collection, cost is a concern → voyage-4-lite

• High-stakes retrieval where accuracy matters most → voyage-4-large

• Codebase or technical docs search → voyage-code-4

voyage-code-4 requires an Atlas deployment. On self-managed deployments, use voyage-code-3 for code and technical documentation.

Free tokens: 200 million tokens per model, one-time, shared across the entire Atlas organization. Does not refresh. See Billing and Free Tokens below for how consumption and invoicing work.

Index Definition

Syntax

{
  "fields": [
    {
      "type": "autoEmbed",
      "modality": "text",
      "path": "<text-field-to-embed>",
      "model": "<embedding-model>"
    },
    {
      "type": "filter",    // Optional: index one or more fields as filters to enable pre-filtering / scoped search
      "path": "<field-to-filter-on>"
    }
  ]
}

Fields

The embedding field (type: "autoEmbed") is required. To pre-filter queries, add one or more optional filter fields (each with its own type and path):

Examples

Minimal index (no filters):

{
  "fields": [
    {
      "type": "autoEmbed",
      "modality": "text",
      "path": "description",
      "model": "voyage-4"
    }
  ]
}

With filter fields (recommended for scoped search):

{
  "fields": [
    {
      "type": "autoEmbed",
      "modality": "text",
      "path": "description",
      "model": "voyage-4"
    },
    {
      "type": "filter",
      "path": "category"
    },
    {
      "type": "filter",
      "path": "year"
    }
  ]
}

Creating the Index (mongosh)

db.movies.createSearchIndex(
  "<index-name>",
  "vectorSearch",
  {
    "fields": [
      {
        "type": "autoEmbed",
        "modality": "text",
        "path": "<text-field>",
        "model": "voyage-4"
      }
    ]
  }
)

Note: After creation, MongoDB performs an initial sync — generating embeddings for all existing documents. This can take several hours for large collections. Monitor progress via Atlas → Search & Vector Search.

Query Construction

Key Difference from Manual Vector Search

With Automated Embedding, you use query (a text string) instead of queryVector (an array of numbers). MongoDB generates the query embedding automatically.

Basic Query Syntax

db.collection.aggregate([
  {
    $vectorSearch: {
      index: "<index-name>",
      path: "<text-field>",
      query: "<your search text>",    // Plain text — no vector needed
      numCandidates: 100,
      limit: 10
    }
  },
  {
    $project: {
      _id: 0,
      description: 1,
      score: { $meta: "vectorSearchScore" }
    }
  }
])

Query with Pre-filtering

db.collection.aggregate([
  {
    $vectorSearch: {
      index: "<index-name>",
      path: "<text-field>",
      query: "your search text",
      filter: {
        $and: [
          { category: { $eq: "electronics" } },
          { year: { $gte: 2022 } }
        ]
      },
      numCandidates: 150,
      limit: 10
    }
  },
  {
    $project: {
      _id: 0,
      description: 1,
      category: 1,
      score: { $meta: "vectorSearchScore" }
    }
  }
])

Optional: Override the Query Model

You can specify a different (but compatible) embedding model at query time:

{
  $vectorSearch: {
    index: "<index-name>",
    path: "<text-field>",
    query: "your search text",
    model: "voyage-4-lite",    // Must be compatible with the index model
    numCandidates: 100,
    limit: 10
  }
}

Item-to-Item Similarity

For "given item A, find similar items" requests (e.g. "more movies like The Firm"), remember that query accepts only a plain text string — there is no raw-vector read path to reuse an existing document's stored embedding for an autoEmbed index.

Resolve the source item to its indexed text field first, then pass that text as the query:

// 1. Fetch the source item's text (the same field indexed as autoEmbed)
const source = db.movies.findOne(
  { title: "The Firm" },
  { projection: { plot: 1 } }
);

// 2. Use that text as the query
db.movies.aggregate([
  {
    $vectorSearch: {
      index: "<index-name>",
      path: "plot",
      query: source.plot,           // the source item's text, not its title
      filter: { _id: { $ne: source._id } },   // exclude the item itself
      numCandidates: 100,
      limit: 10
    }
  }
])

Filter fields must generally be indexed as type: "filter" (see the index definition above). _id is the one exception — it is implicitly filterable on every autoEmbed index, so the self-exclusion filter above works without declaring _id as a filter field.

Passing the item's name (e.g. query: "The Firm") searches for text semantically near that string, not near the item's actual content — pass the content field instead.

Query Parameters Reference

Note: Each query call counts against your Automated Embedding rate limits because it triggers an embedding API call.

How It Works Internally

Initial Sync

1. MongoDB scans all documents in the collection for the indexed text field

2. Sends text to the Voyage AI model in batches (uses Flex inference tier — no standard rate limits)

3. Stores embeddings in an internal reserved database: __mdb_internal_search

4. Builds the vector index from the stored embeddings

Ongoing Updates (via Change Streams)

• Insert: New doc detected → embedding generated → stored → index updated

• Update: Changed field detected → new embedding generated → old one replaced → index updated

• Delete: Doc deleted → embeddings removed → index updated

• Updates to non-indexed fields do not trigger embedding regeneration

Embeddings Storage

Stored in __mdb_internal_search (internal namespace — do not modify this database).

Each stored document has:

{
  _id: <same as source document>,
  <filter-field>: <copied from source>,
  _autoEmbed: {
    "<fieldPath>": [<embedding vector>]
  }
}

Billing and Free Tokens

Token consumption occurs during:

• Index creation (initial sync)

• Document inserts and updates

• Every query (embedding generated per query)

Free allocation: 200M tokens per model, per organization. One-time, does not refresh. Shared across all projects and clusters. See Model Selection above for per-model pricing after free tokens are used.

View usage: Atlas → Search & Vector Search → Automated Embedding → Usage

View invoices: Atlas → Billing → Invoices (broken down by model)

M0 clusters: When free tokens run out, MongoDB automatically invoices for additional usage — index builds and queries do not stop. M0 users can add a payment method without upgrading their cluster: Atlas → Billing → Payment Method. Charges are for embedding model usage only.

Rate Limits

Rate limits are enforced at the cluster level, shared across all autoEmbed indexes on that cluster. They are applied separately for queries, index inserts/updates, and initial builds.

Initial Index Build

No standard rate limits — uses a separate inference tier optimized for throughput, with dynamic scaling up to available GPU capacity, fair resource sharing between competing index builds, and safe ramp-up from low concurrency.

Best practice: create the index on a prepopulated collection rather than an empty one — the initial sync benefits from this unbounded throughput, while steady-state inserts/updates afterward are subject to the rate limits below.

Index Insert/Update Rate Limits (all tiers)

Best practice: space out bulk insert/update operations rather than sending them all at once — batching avoids hitting these per-minute limits.

Query Rate Limits

Free cluster (M0 without a payment method) — all models:

Paid cluster (M0 with a payment method, Flex, or M10+ dedicated):

Paid-tier limits increase automatically as usage grows over time — no action needed to benefit from that growth.

If rate limits are hit:

• Inserts/updates: queued and retried automatically with exponential backoff

• Queries: return an error — application must handle and retry

• Free cluster hitting the 3 RPM ceiling: add a payment method to upgrade to paid-tier limits (Atlas → Billing → Payment Method) — this alone raises the ceiling from 3 to 2,000 RPM (~667x), with a correspondingly higher TPM allowance

• Paid tier still hitting limits: contact MongoDB Support for a limit increase

Management and Monitoring

View Usage (Atlas)

Atlas → Search & Vector Search page → Automated Embedding → Usage

Shows:

• Total tokens used and remaining free tokens

• Usage breakdown by model

• Usage breakdown by operation (indexing vs querying)

View Rate Limits (Atlas)

Atlas → Search & Vector Search page → Automated Embedding → Rate Limits

View Organization-Level Usage

Atlas → Organization level → AI Models → Usage

Disable Automated Embedding (Organization Policy)

Use Atlas Resource Policies with Cedar syntax.

Disable entirely:

forbid (
  principal,
  action == ResourcePolicy::Action::"search.index.modify",
  resource
) when {
  context.search.index.isAutoEmbed
};

Disable with project-level exceptions (replace <project-id-1>/<project-id-2> with actual project IDs):

forbid (
  principal,
  action == ResourcePolicy::Action::"search.index.modify",
  resource
) when {
  context.search.index.isAutoEmbed
} unless {
  resource in ResourcePolicy::Project::"<project-id-1>" ||
  resource in ResourcePolicy::Project::"<project-id-2>"
};

Apply at: Atlas → Organization Settings → Resource Policies → Create policy

Note: this policy blocks new autoEmbed indexes going forward. Existing autoEmbed indexes must be deleted manually to bring a project into compliance.

Troubleshooting

Index stuck in Building state / initial sync taking a long time

• Normal for large collections — initial sync can take hours

• Monitor via Atlas → Search & Vector Search → index status

• Check token consumption hasn't exceeded rate limits

Query returns context-limit-exceeded error

• Your query text exceeds 32,000 tokens (the model context window)

• Truncate or shorten your query text before passing it to $vectorSearch

Queries return rate limit error

• You've exceeded your query RPM or TPM

• Free tier users: add a payment method to upgrade to paid limits

• Paid tier users: contact MongoDB Support for a limit increase

• Short term: implement retry with backoff in your application

No results returned

• Check the index status is READY (not Building or Failed)

• Verify the path in the query matches the path in the index definition

• Verify the index name matches exactly (typos return no results silently)

Missing embeddings for some documents

• Documents inserted before the index was created are synced during initial sync — check if sync is still in progress

• Documents without the indexed text field are skipped (no embedding generated)

__mdb_internal_search database appearing in Data Explorer

• This is normal — it's the internal storage for generated embeddings

• Do not modify or delete collections in this database