paperai VS faiss

Nice project!

I've spent quite a lot of time in the medical/scientific literature space. With regards to LLMs, specifically RAG, how the data is chunked is quite important. With that, I have a couple projects that might be beneficial additions.

paperetl (https://github.com/neuml/paperetl) - supports parsing arXiv, PubMed and integrates with GROBID to handle parsing metadata and text from arbitrary papers.

paperai (https://github.com/neuml/paperai) - builds embeddings databases of medical/scientific papers. Supports LLM prompting, semantic workflows and vector search. Built with txtai (https://github.com/neuml/txtai).

While arbitrary chunking/splitting can work, I've found that integrating parsing that has knowledge of medical/scientific paper structure increases the overall accuracy and experience of downstream applications.

https://github.com/neuml/paperai

Disclaimer: I am the author of both

paperai | paperetl

action: translate input: txtai executes machine-learning workflows to transform data and build AI-powered semantic search applications. output: txtai exécute des workflows d'apprentissage automatique pour transformer les données et construire des applications de recherche sémantique alimentées par l'IA. action: translate input: Traditional search systems use keywords to find data output: Les systèmes de recherche traditionnels utilisent des mots-clés pour trouver des données action: summary input: https://github.com/neuml/txtai output: txtai executes machine-learning workflows to transform data and build AI-powered semantic search applications. Semantic search applications have an understanding of natural language and identify results that have the same meaning, not necessarily the same keywords. API bindings for JavaScript, Java, Rust and Go. Cloud-native architecture scales out with container orchestration systems (e. g. Kubernetes) action: summary input: https://github.com/neuml/paperai output: paperai is an AI-powered literature discovery and review engine for medical/scientific papers. Paperai was used to analyze the COVID-19 Open Research Dataset (CORD-19) paperai and NeuML have been recognized in the following articles: Cord-19 Kaggle Challenge Awards Machine-Learning Experts Delve Into 47,000 Papers on Coronavirus Family. real 0m22.478s user 0m13.776s sys 0m3.218s

Or just use FAISS https://github.com/facebookresearch/faiss

You can try txtai (https://github.com/neuml/txtai) with a Faiss backend.

This Faiss wiki article might help (https://github.com/facebookresearch/faiss/wiki/Indexing-1G-v...).

For example, a partial Faiss configuration with 4-bit PQ quantization and only using 5% of the data to train an IVF index is shown below.

faiss={"components": "IVF,PQ384x4fs", "sample": 0.05}

If you want to experiment with vector stores, you can do that locally with something like faiss which has good platform support: https://github.com/facebookresearch/faiss

Doing full retrieval-augmented generation (RAG) and getting LLMs to interpret the results has more steps but you get a lot of flexibility, and there's no standard best-practice. When you use a vector DB you get the most similar texts back (or an index integer in the case of faiss), you then feed those to an LLM like a normal prompt.

The codifer for the RAG workflow is LangChain, but their demo is substantially more complex and harder-to-use than even a homegrown implementation: https://news.ycombinator.com/item?id=36725982

According to this documentation page, faiss-gpu is only supported on Linux, not on Windows.

Indexes for vector databases in high dimensions are nowhere near are effective as the 2-d indexes used in GIS or the 1-d B-tree indexes that are commonly used in databases.

Back around 2005 I was interested in similarity search and read a lot of conference proceedings on the top and was basically depressed at the state of vector database indexes and felt that at least for the systems I was prototyping I was OK with a full scan and later in 2013 I had the assignment of getting a search engine for patents using vector embeddings in front of customers and we got performance we found acceptable with full scan.

My impression today is that the scene is not too different than it was in 2005 but I can't say I haven't missed anything. That is, you have tradeoffs between faster algorithms that miss some results and slower algorithms that are more correct.

I think it's already a competitive business. You have Pinecone which had the good fortune of starting before the gold rush. Many established databases are adding vector extension. I know so many engineering managers who love postgresql and they're just going to load a vector extension and go. My RSS reader YOShInOn uses SBERT embeddings to cluster and classify text and certainly More Like This and semantic search are on the agenda, I'd expect it to take about an hour to get

https://github.com/facebookresearch/faiss

up and working, I could spend more time stuck on some "little" front end problem like getting something to look right in Bootstrap than it would take to get working.

I can totally believe somebody could make a better vector db than what's out there but will it be better enough? A startup going through YC now could spend 2-3 to get a really good product and find customers and that is forever in a world where everybody wants to build AI applications right now.

As the size of the codebase grows, storing and searching through embeddings in memory becomes inefficient. This is where vector databases come into play. Tools like Milvus, Faiss, and others are designed to handle large-scale vector data and provide efficient similarity search capabilities. I've wrtten about how to also use sqlite to store vector embeddings. By integrating a vector database, you can scale your code search tool to handle much larger codebases without compromising on search speed.

But FAISS has their own version ("FastScan") https://github.com/facebookresearch/faiss/wiki/Fast-accumula...

https://github.com/facebookresearch/faiss

Not a model, but I would use this Dense Passage Retrieval for Open Domain QA simply fine-tuning two BERT models, one for questions and one for queries, and then fine-tuning using contrastive loss between positive key/value pairs of document embeddings (the [CLS]) token. You can then use a vector database (Like Faiss, Elasticsearch, Vespa or similar) for querying the question.