What Makes a Good Vector Database? Comparing Pinecone and LanceDB

Published: May 22, 2024
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Which vector database is best to use? It depends. Based on our experiences using them, there is no one-size-fits-all "best" database. Rather, a Superior Vector Database is one that is well-matched with its use case, meeting the unique requirements of that scenario. Read our comparative analysis to discover why.

  • Alex HuAlex Hu / Machine Learning Engineer
  • Steven ZhangSteven Zhang / Backend Software Engineer
  • Anjing WangAnjing Wang / AI Lead

1. The Hallmarks of a Superior Vector Database

In our data-driven age where processing high-dimensional vectors efficiently marks the difference between industry leaders and the competition, the significance of a top-tier vector database cannot be overstated. Such a database must possess a definitive set of characteristics that not only address the immense complexity of big data but also cater to the refined demands of advanced analytics.

Vector database funtions

Search performance

At the core, search speed stands as the linchpin of vector database performance, impacting user experience and real-time decision-making. Superior vector databases must offer flexibility in utilizing a range of similarity algorithms, including but not limited to Euclidean distance and cosine similarity, crucial for conducting Approximate Nearest Neighbor (ANN) searches with precision across extensive datasets. It's not solely about rapid execution; it involves consistently delivering quick and precise vector similarity searches scalable with data growth.

Storage efficiency

Storage efficiency is equally integral to a database's prowess. Ideal vector databases minimize the latency between data insertion and query processing, aiming for millisecond-level turnaround times. This is realized through advanced encoding and indexing technologies like inverted indexes, hierarchical clustering, and quantization, all tailored to conserve storage space without compromising accessibility or performance.

Data migration

Data migration capabilities are also vital, facilitating smooth transitions and scaling by allowing efficient replication of tables-even those with considerable volumes of data. This ensures that the database remains adaptable and responsive as organizational needs evolve, without interrupting existing processes.

Usability and scalability

Usability and scalability come down to the clarity of APIs and user interfaces, simplifying integration and deployment for developers. However, such simplicity must be compounded with robust scalability options, both horizontally and vertically. A model vector database would not only adapt performance as datasets expand but also seamlessly transition between single-node configurations and cluster-based deployments.

Persistence and reliability

Features that assure data persistence and reliability are indicative of a vector database's caliber. Leading databases provide secure data storage with resilience against system failures, maintaining consistent performance and response times even under high demand–a requirement for enterprise-grade applications.

In today's diverse technological ecosystem, a vector database's integration capabilities must be broad. Compatibility becomes critical–it should align with a variety of data formats and integrate smoothly with the prevailing data science and machine learning ecosystems.

Security

A vector database should include features for encryption, access control, and audit logging. These features are paramount for safeguarding data integrity and confidentiality, increasingly important in an era where data privacy concerns are more pronounced.

Automation

Moreover, automation and operational simplicity are crucial for mitigating cognitive loads on users. Features that allow hands-off maintenance, backups, recoveries, and optimizations demonstrate a database solution that values modern operational efficiency.

Cost-effectiveness

Cost-effectiveness should not be overlooked when evaluating a vector database. A transparent and predictable cost structure allows users to plan their expenses relative to their scale of operations and patterns of usage.

Supportive community and dependable support

Lastly, the importance of a supportive community and reliable customer service is indisputable. For open-source platforms, the community drives innovation and troubleshooting, while proprietary databases must offer excellent and dependable support.

To sum it up, a vector database that harmonizes these attributes not only excels in its field but also emerges as an indispensable ally in harnessing the full potential of vector data.

2. Introduction

2.1 What is Pinecone

Pinecone is a closed source, fully-managed, cloud-native vector database specifically designed for high-performance Artificial Intelligence (AI) applications. Its main features include offering a simple API that allows users to effortlessly provide a long-term memory function for AI applications without the need to manage the underlying infrastructure. It allows you to search and retrieve the most similar items in a high-dimensional vector space efficiently. Pinecone is particularly useful for applications such as recommendation systems, image search, and natural language processing tasks, where similarity search plays a vital role.

2.2 What is LanceDB

LanceDB is an open-source vector database that excels in handling multimodal data including text, images, and video. It employs a serverless architecture with hard disk drives (HDD) for persistent storage. Additionally, at its data storage layer, LanceDB utilizes Lance, a novel and faster columnar format than parquet, specifically designed for highly efficient lookups.

LanceDB is available in two flavors: OSS and Cloud.

LanceDB Cloud is a SaaS (software-as-a-service) solution that runs serverless in the cloud, making the storage clearly separated from compute. Currently in private beta with general availability coming soon.

3. Key Differences Between Pinecone and LanceDB

3.1 Workflow

The workflow in Pinecone starts with creating an index. This index must be established prior to uploading any vector data into the system, which thereafter becomes searchable. The index is the primary organizational structure within Pinecone for storing vectors, running queries, and executing other vector data-related tasks. Each Pinecone index is operated on at least one "pod", serving as its fundamental operational unit.

In contrast, LanceDB follows a traditional database workflow where the initial step involves defining a data table's schema (structure). Once the schema has been set, data can be added, and search operations can commence.

3.2 Data Type

Pinecone focuses on array vector types used in high-dimensional vector space, essential for applications involving similarity search and machine learning tasks.

LanceDB handles a wide array of data structures, including dict, lists of dicts, pd.DataFrame, pa.Table, iterable record batches, Pydantic models, and JavaScript objects. This adaptability makes it suitable for various structured and semi-structured data dealings.

LancdDB Overview

Pydantic integration with LanceDB enables the use of advanced features such as nested schemas and validators for building complex, valid table schemas, boosting data integrity and functionality. We can utilize the embedding function to annotate our model with the VectorField method, which instructs LanceDB to use a generic embedding technique to create embeddings for matching queries. Simultaneously, the SourceField ensures that when data is ingested, LanceDB automatically employs an appropriate embedding technique to encode the input images. This collaboration significantly streamlines the data handling process by enriching the vector column through the embedding function, and simplifies the data input and encoding process via the SourceField, without specifying any particular embedding model.

Example

The following example defines a Pydantic model named Pets for use with LanceDB, which includes a vector column for image embeddings that are generated using the specified embedding function from the clip module. This Pets model allows querying by leveraging both text and images, as demonstrated by its ability to search through the database using a text query as well as an image input for the search.

from PIL import Image
from lancedb.pydantic import LanceModel, Vector
from pathlib import Path


class Pets(LanceModel):
    vector: Vector(clip.ndims) = clip.VectorField()
    image_uri: str = clip.SourceField()

    @property
    def image(self):
        return Image.open(self.image_uri)

table = db.create_table("pets", schema=Pets)
result = table.search("dog")
p = Path("path/to/images/samoyed_100.jpg")
query_image = Image.open(p)
table.search(query_image)

Pinecone empowers users to perform scalable ANN searches quickly and accurately, excels with both sparse and dense vector support, allowing for mixed searches in a singular index. This hybrid approach combines semantic depth with keyword precision for improved relevance and accuracy in results. Additionally, Pinecone enables the attachment of metadata key-value pairs to indexed vectors, coupled with detailed filter expressions during queries, enabling tailored searches based on specific criteria. With support for up to 40 kb of metadata per vector, selective metadata indexing is advised to prevent unnecessary high-cardinality metadata from being indexed when not required for filtering. This adaptability allows users to create diverse search experiences, from simple text searches to complex queries.

Pinecone sparse-dense vectors have the following limitations:

  • Pinecone supports sparse vector values of sizes up to 1000 non-zero values.
  • Pinecone only supports upserting sparse-dense vectors to p1 and s1 indexes.
  • In order to query an index using sparse values, the index must use the dot product metric. Attempting to query any other index with sparse values returns an error.
  • Indexes created before February 22, 2023 do not support sparse values.

Pineone Record

LanceDB supports both vector search and full-text search via Tantivy, with full-text search currently available only in Python. When using the search method, if the query_type is set to 'auto', the system will automatically infer the type of query to perform. This means that if the query is a list or a NumPy array, it will be treated as a vector search. If the query is an image, the system may either perform a vector search or return an error if there is no corresponding embedding function available. If the query is a string, the query type can be either 'vector' or 'fts' (full-text search), depending on whether the table possesses an embedding function or not. In the absence of an index, LanceDB would need to exhaustively scan the entire vector column (via Flat Search) and compute the distance for every vector in order to identify the closest matches, which effectively constitutes a KNN (k-nearest neighbors) search. By constructing a vector index, LanceDB utilizes ANN search with a Vector Index for enhanced efficiency during query processing.

3.4 Index

Pinecone's index is a customized, optimized structure made for efficient vector similarity searches, known for bolstering the performance of ANN searches. Users can increase the number of replicas to enhance index availability and throughput, along with configuring the behavior of Pinecone's internal metadata index.

Pinecone supports partitioning records into namespaces within an index, allowing operations and queries to be restricted to specific, isolated segments. This facilitates differentiated search experiences tailored to particular subsets of data.

Indexes can be scaled horizontally-by adding "pods", which suspends upserts temporarily and increases general capacity, or by adding "replicas", which boosts throughput without disrupting upserts-and vertically for accommodating different load requirements.

It's important to be aware that the GCP starter environment doesn't support the advanced features mentioned here, such as pods, replicas, and collections. These options are reserved for more advanced Pinecone environments that allow such scalability and partitioning capabilities.

Example

The following example creates a vector index named "example-index" with a 1024-dimensional vector space, a copy, and the specified metadata configuration.

metadata_config = {
    'indexed': ['color']
}

pinecone.create_index('example-index', dimension=1024, replicas=1, metadata_config=metadata_config)

LanceDB supports various index types, among which IVF_PQ (Inverted File Index combined with Product Quantization) is the most commonly used. The dataset is partitioned into 'N' sections using IVF, and then each partition's vectors are compressed through Product Quantization (PQ). The parameters for IVF_PQ include 'num_partitions' (default: 256), determining the number of sections, and 'num_sub_vectors' (default: 96), which defines the count of sub-vectors 'M' for a 'D' dimensional vector, split into 'M' of 'D/M' sub-vectors, each represented by a single PQ code.

DISKANN (the DiskANN algorithm, presented at NeurIPS 2019, demonstrates the potential to be the fastest for disk-based searches across billion-scale datasets.) is an experimental index that structures the vector data on-disk as a graph with vertices representing vector neighbors.

Lance's Python SDK offers experimental GPU support for creating the IVF index which can significantly speed up the process. This feature requires PyTorch version above 2.0. Users can enable GPU acceleration by setting 'accelerator' to 'cuda' or 'mps' (for Apple Silicon devices) to facilitate GPU training.

Search refinement can be fine-tuned using two parameters: 'nprobes', which adjusts the number of partitions to search in, and 'refine_factor', influencing the refinement passes. These tools help in fine-tuning the search for a balance between speed and accuracy.

import lance


dataset = lance.dataset("/tmp/sift.lance")
dataset.create_index(
    "vector",
    "IVF_PQ",
    num_partitions=256,
    num_sub_vectors=16,
    accelerator="cuda"
)

tbl.search(np.random.random((1536))) 
    .limit(2) 
    .nprobes(20) 
    .refine_factor(10) 
    .to_pandas()

3.5 Versioning

In Pinecone, a collection captures a static snapshot of an index at a specific moment, preserving the complete set of vectors and metadata in a non-queryable form. It can serve as version control for data, enabling comparisons and historical rollbacks. Collections allow for the creation of new indices, providing the option to modify parameters such as pod count, pod type, or similarity metric relative to the original index.

Indexes in the gcp-starter environment do not support collections.

Example

The following example creates a collection named example-collection from an index named example-index and create an index named example-test from the collection named example-collection.

pinecone.create_collection("example-collection", "example-index")
pinecone.create_index('example-test', dimension=1024, replicas=1, source_collection="example-collection")

LanceDB eliminates the need for explicit version control management and the creation of costly and time-consuming snapshots. It automatically tracks the complete history of operations and supports quick rollbacks. In production, this capability is crucial for debugging issues and minimizing downtime by rapidly reverting to a previously successful state within seconds.

Example

The following example shows the current version and restoring to version 1.

table.list_versions()
[{'version': 1,
  'timestamp': datetime.datetime(2023, 10, 20, 14, 33, 39, 40549),
  'metadata': {}},
 {'version': 2,
  'timestamp': datetime.datetime(2023, 10, 20, 14, 33, 39, 63675),
  'metadata': {}}
]
table.restore(1)
table.list_versions()
[{'version': 1,
  'timestamp': datetime.datetime(2023, 10, 20, 14, 33, 39, 40549),
  'metadata': {}},
 {'version': 2,
  'timestamp': datetime.datetime(2023, 10, 20, 14, 33, 39, 63675),
  'metadata': {}},
 {'version': 3,
  'timestamp': datetime.datetime(2023, 10, 20, 14, 33, 53, 979216),
  'metadata': {}}
]

When we restore an old version, we're not deleting the version history, we're just creating a new version where the schema and data is equivalent to the restored old version. In this way, we can keep track of all of the changes and always rollback to a previous state.

4. Conclusion

Selecting the ideal vector database hinges on the stark realization that there is no one-size-fits-all solution; the decision is intrinsically tied to how well the database aligns with the distinctive needs and specific use cases of a given project.

Here are some potential application scenarios for Pinecone and LanceDB:

1. Multimodal Data Analysis

  • Pinecone: Primarily optimized for efficient vector search, not specifically optimized for handling and analyzing diverse multimodal data.
  • LanceDB: Designed for integrating and analyzing diverse data types (such as images, text, audio), suitable for multimedia search engines, cross-modal retrieval, and smart recommendation systems.

2. Customizable Search and Analysis

  • Pinecone: Offers limited customization compared to LanceDB; mainly focusing on efficient default settings, which may be less flexible for scenarios requiring deeply customized search logic or workflows.
  • LanceDB: Supports deep customization of search algorithms and processing workflows, making it ideal for research institutions and corporate R&D departments that require specialized preprocessing, indexing, or querying of vector data.

3. Hybrid or Private Cloud Deployment

  • Pinecone: Primarily built as a cloud service; its support for private or hybrid cloud deployments is less flexible compared to LanceDB, with a focus on leveraging the convenience and scalability of cloud platforms.
  • LanceDB: Supports flexible storage with MinIO and S3 integration, suitable for secure and compliant data management in hybrid or private cloud environments.

4. Real-Time Recommendation Systems

  • Pinecone: Specially optimized for high-throughput real-time data processing, making it highly suitable for recommendation engines that require immediate and accurate similarity matching.
  • LanceDB: While capable of handling diverse data, it does not specifically emphasize optimization for high-concurrency data processing required by real-time recommendation systems.

5. High-Precision Similarity Search

  • Pinecone: Specifically optimized for high-precision, high-dimensional vector search, excelling in efficient scaling and resource management to minimize false positives, making it suitable for scenarios with very high accuracy requirements.
  • LanceDB: Although capable of handling high-dimensional vector search, its optimization and resource management strategies for high-precision search are less prominent compared to those of Pinecone.

6. Low Latency, High Throughput Situations

  • Pinecone: Optimized for low latency and high throughput scenarios, such as financial risk management, cybersecurity, smart homes, and security; offering a high-performance vector search solution that is quick to deploy and especially suitable for applications with strict response time and processing capacity requirements.
  • LanceDB: Not explicitly optimized for the extreme demands of low latency and high throughput.

LanceDB's extensive feature set is designed to manage a plethora of data types and complex queries adeptly. Nevertheless, in scenarios where pin-point accuracy in high-dimensional similarity searches is essential, LanceDB's approximate nearest neighbor search algorithms might necessitate improvements.

Both LanceDB and Pinecone showcase unique methodologies in scalability. LanceDB augments its data handling capabilities by integrating with external storage systems like MinIO and S3, whereas Pinecone advances with a seamless, resource-efficient scaling framework, empowered by its in-built resource and Pod management system.

Pinecone has earned preferences for its rapid query responses and its ability to process substantial volumes of real-time data within a user-friendly "plug-and-play" model. Conversely, LanceDB is particularly strong in handling multimodal data vectors and offers a more customized search experience. Despite its current data migration utilities having room for further development, it still presents valuable features that can be essential for certain applications.

Ultimately, the choice between Pinecone's operational simplicity and reliable performance and LanceDB's vast potential for customization through its open-source nature is a nuanced one. While both platforms facilitate machine learning integrations and LanceDB supports a wider variety of data types, the decision-making process should include consideration of LanceDB's advancement in data migration alongside other criteria.

Therefore, the best-suited vector database emerges not from a fixed archetype but from a process of discerning adaptation to your project's specificities and aspirations. Rigorous assessment of your project's requirements will decipher whether LanceDB's adaptability or Pinecone's streamlined efficiency and scalability will better serve your pursuit. As LanceDB and Pinecone evolve in the vector database sphere, they will continue to deepen their specialized capabilities to address a broad spectrum of user needs, collectively propelling forward the standards of excellence for vector database solutions.

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