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pepembed

Overview

PEPembed is a Python package for computing text-embeddings of sample metadata stored in pephub for search-and-retrieval tasks. It provides both a CLI and a Python API. It handles the long-running job of downloading projects inside pephub, mining any relevant metadata from them, computing a rich text embedding on that data, and finally upserting it into a vector database. We use qdrant as our vector database for its performance and simplicity and payload capabilities.

Understand everything? Jump to running pepembed. Or view the quick start below.

Quick Start

pip install .
pepembed \
  --postgres-host $POSTGRES_HOST \
  --postgres-user $POSTGRES_USER \
  --postgres-password $POSTGRES_PASSWORD \
  --postgres-db $POSTGRES_DB \

Architecture

pepembed architecture

pepembed works in three steps: 1) Download PEPs from pephub, 2) Extract metadata from these PEPs and embeds them using a sentence transformer, and 3) inserts these PEPs into a qdrant instance.

1. Download PEPs:
pepembed downloads all PEPS from pephub. This is the most time-consuming process. Currently there is no way to parametrize this, but in the future we should. We should also allow for generating embeddings straight from files on disc.

2. Extract Metadata from PEPs adn embeddings:
Once the PEPs are downloaded, we then extract any relevant metadata from them. This is done by looking for keywords in the project-level attributes. For each PEP, a pseudo-description is built by looking for these keywords and building a string. Some example keyword attributes might be: cell_type, protocol, procedure, institution, etc. You can specify your own keywords to pepembed if you wish.

Sample modifiers in a configuration file

Once the pseudo-descriptions are mined, we can then utilize a sentence-transformer to generate low-dimensional representations of these descriptions. By defauly, we use a state-of-the-art transformer trained for the semantic textual similarity task (Reimers & Gurevych, 2019). The embeddings are linked back to the original PEP registry path, along with other information like the mined pseudo-description and the row id in the database.

3. Insert Embeddings:
Finally, we insert the embeddings into a qdrant instance. qdrant is a vector database that is designed to store embeddings as first-class data types as well as supporting native graph-based indexing of these embeddings. The allows for near-instant search and retrieval of nearest embeddings neighbors given a new embedding (say an encoded search query on a web application). qdrant supports arming the embeddings with a payload where we store basic information on that PEP like registry path, row id, and its description.

Install and Run

While simple to install and run, pepembed requires lots of information to function. There are three key aspects: 1) The pephub instance, 2) the qdrant instance, and 3) the keywords. Ensure the following before running the cli:

Setup

1. PEPhub instance:
Make sure you have access to a running pephub instance store with peps. Once complete, you can use the following environment variables to tell pepembed where to get data. Alternatively, you can pass these as command-line args:
* POSTGRES_HOST * POSTGRES_DB * POSTGRES_USER * POSTGRES_PASSWORD

2. Qdrant instance:
In addition to a pephub instance, you will need a running instance of qdrant. It is quite simple and instructions can be found here. The TL;DR is:

docker pull qdrant/qdrant
docker run -p 6333:6333 \
    -v $(pwd)/qdrant_storage:/qdrant/storage \
    qdrant/qdrant

This will give you a qdrant instance served at http://localhost:6333. You can pass this information to pepembed as environment variables. Alternatively, you may pass these as command-line args:
* QDRANT_HOST * QDRANT_PORT * QDRANT_API_KEY * QDRANT_COLLECTION_NAME

Unless you are running this for production, you most likely do not need to specify any of these.

3. Keywords:
Finally, we need a keywords file. This is technically optional, and pepembed comes with default keywords, but you may supply your own as a plain text file. This can be supplied only as command-line args: * KEYWORDS_FILE

There are many other options as well (like specifying the transformer model to use), but the defaults work great for a first try. Use pepembed --help to see all options. If you are like me, and like to keep your secrets in a .env file, you can export them easily to the environment with export $(cat .env | xargs)

Install

Clone this repository and install with pip:

pip install .

Run

pepembed \
  --keywords-file keywords.txt \
  --postgres-host $POSTGRES_HOST \
  --postgres-user $POSTGRES_USER \
  --postgres-password $POSTGRES_PASSWORD \
  --postgres-db $POSTGRES_DB \