Show HN: HelixDB – Open-source vector-graph database for AI applications (Rust)
github.comHey HN, we want to share HelixDB (https://github.com/HelixDB/helix-db/), a project a college friend and I are working on. It’s a new database that natively intertwines graph and vector types, without sacrificing performance. It’s written in Rust and our initial focus is on supporting RAG. Here’s a video runthrough: https://screen.studio/share/szgQu3yq.
Why a hybrid? Vector databases are useful for similarity queries, while graph databases are useful for relationship queries. Each stores data in a way that’s best for its main type of query (e.g. key-value stores vs. node-and-edge tables). However, many AI-driven applications need both similarity and relationship queries. For example, you might use vector-based semantic search to retrieve relevant legal documents, and then use graph traversal to identify relationships between cases.
Developers of such apps have the quandary of needing to build on top of two different databases—a vector one and a graph one—plus you have to link them together and sync the data. Even then, your two databases aren't designed to work together—for example, there’s no native way to perform joins or queries that span both systems. You’ll need to handle that logic at the application level.
Helix started when we realized that there are ways to integrate vector and graph data that are both fast and suitable for AI applications, especially RAG-based ones. See this cool research paper: https://arxiv.org/html/2408.04948v1. After reading that and some other papers on graph and hybrid RAG, we decided to build a hybrid DB. Our aim was to make something better to use from a developer standpoint, while also making it fast as hell.
After a few months of working on this as a side project, our benchmarking shows that we are on par with Pinecone and Qdrant for vectors, and our graph is up to three orders of magnitude faster than Neo4j.
Problems where a hybrid approach works particularly well include:
- Indexing codebases: you can vectorize code-snippets within a function (connected by edges) based on context and then create an AST (in a graph) from function calls, imports, dependencies, etc. Agents can look up code by similarity or keyword and then traverse the AST to get only the relevant code, which reduces hallucinations and prevents the LLM from guessing object shapes or variable/function names.
- Molecule discovery: Model biological interactions (e.g., proteins → genes → diseases) using graph types and then embed molecule structures to find similar compounds or case studies.
- Enterprise knowledge management: you can represent organisational structure, projects, and people (e.g., employee → team → project) in graph form, then index internal documents, emails, or notes as vectors for semantic search and link them directly employees/teams/projects in the graph.
I naively assumed when learning about databases for the first time that queries would be compiled and executed like functions in traditional programming. Turns out I was wrong, but this creates unnecessary latency by sending extra data (the whole written query), compiling it at run time, and then executing it. With Helix, you write the queries in our query language (HelixQL), which is then transpiled into Rust code and built directly into the database server, where you can call a generated API endpoint.
Many people have a thing against “yet another query language” (doubtless for good reason!) but we went ahead and did it anyway, because we think it makes working with our database so much easier that it’s worth a bit of a learning curve. HelixQL takes from other query languages such as Gremlin, Cypher and SQL with some extra ideas added in. It is declarative while the traversals themselves are functional. This allows complete control over the traversal flow while also having a cleaner syntax. HelixQL returns JSON to make things easy for clients. Also, it uses a schema, so the queries are type-checked.
We took a crude approach to building the original graph engine as a way to get an MVP out, so we are now working on improving the graph engine by making traversals massively parallel and pipelined. This means data is only ever decoded from disk when it is needed, and parts of reads are all processed in parallel.
If you’d like to try it out in a simple RAG demo, you can follow this guide and run our Jupyter notebook: https://github.com/HelixDB/helix-db/tree/main/examples/rag_d...
Many thanks! Comments and feedback welcome!
Looks really interesting. A couple of questions: Can you explain how helix handles writes? What are you using for keys? UUIDs? I'm curious if you've done, or are thinking about, any optimizations here.
Feel free to point me to docs / code if these are lazy questions :)
We utilize some of LMDB's optimizations such as the APPEND put flags. We also make use of LMDB handling duplicates as a one-to-many key instead of duplicating keys. This means we can get all values for one key in one call rather than a call for each duplicate.
For keys we are using UUIDs, but using the v6 timestamped uuids so that they are easily lexicographically ordered at creation time. This means keys inserted into LMDB are inserted using the APPEND flag, meaning LMDB shortcuts to the rightmost leaf in its B-Tree (rather than starting at the root) and appends the new record. It can do this because the records are ordered by creation time meaning each new record is guaranteed to be larger (in terms of big-endian byte order) than the previous record.
We also store the UUIDs as u128 values for two reasons. The first is that a u128 takes up 16 bytes where as a string UUID takes up 36 bytes. This means we store 56% less data and LMDB has to decode 56% less bytes when doing code accesses.
For the outgoing/incoming edges for nodes, we store them as fixed sizes which means LMDB packs them in, removing the 8 byte header per Key-Value pair.
In the future, we are also going to separate the properties from the stored value as empty property objects still take up 8 bytes of space. We will also make it so nothing is inserted if the properties are empty.
You can see most of this in action in the storage core file: https://github.com/HelixDB/helix-db/blob/main/helixdb/src/he...
Congrats on the launch! I'm one of the authors of that paper you cited, glad it was useful and inspiring to building this :) Let me know if we can support in any way!
Wow! I enjoyed reading it a lot and it was definitely inspiring for this project!
Would love to talk to you about it and make sure we capture all of the pain points if you're open to it? :)
Absolutely, will DM you on X!
I spent a bit of time reading up on the internals and had a question about a small design choice (I am new to DB internals, specifically as they relate to vector DBs).
I notice that in your core vector type (`HVector`), you choose to store the vector data as a `Vec<f64>`. Given what I have seen from most embedding endpoints, they return `f32`s. Is there a particular reason for picking `f64` vs `f32` here? Is the additional precision a way to avoid headaches down the line or is it something I am missing context for?
Really cool project, gonna keep reading the code.
thanks for the question! we chose f64 as a default for now as just to cover all cases and we believed that basic vector operations would not be our bottleneck initially. As we optimize our HNSW implementation, we are going to add support for f32 and binary vectors and drop using Vec<f64/f32> and instead use [f64/f32; {num_dimensions}] to avoid unnecessary heap allocation!
I was thinking about intertwining Vector and Graph, because I have one specific usecase that required this combination. But I am not courageos or competent enough to build such a DB. So I am very excited to see this project and I am certainly going to use it. One question is what kind of hardware do you think this would require ? I am asking it because from what I understand Graph database performance is directly proportional to the amount of RAM it has and Vectors also needs persistence and computational resources .
The fortunate thing about our vector DB, like I mentioned in the post, is that we store the HNSW on disk. So, it is much less intense on your memory. Similar thing to what turbo puffer has done.
With regard to the graph db, we mostly use our laptops to test it and haven't run into an issue with performance yet on any size dataset.
If you wanna chat DM me on X :)
Neo4j supports vector indexes
Neo4j first of all is very slow for vectors, so if performance is something that matters for your user experience they definitely aren't a viable option. This is probably why Neo4j themselves have released guides on how to build that middleman software I mentioned with Qdrant for viable performance.
Furthermore, the vectors is capped at 4k dimensions which although may be enough most of the time, is a problem for some of the users we've spoken to. Also, they don't allow pre filtering which is a problem for a few people we've spoken to including Zep AI. They are on the right track, but there are a lot of holes that we are hoping to fill :)
Edit: AND, it is super memory intensive. People have had problems using extremely small datasets and have had memory overflows.
How does this scale horizontally across multiple regions. Is this something on your roadmap?
It’s definitely on our roadmap, but not a priority because no one using us needs it. Is this something that would be useful to you?
Congrats! Any chance Helixdb can be run in the browser too, maybe via WASM? I'm looking for a vector db that can be pre-populated on the server and then be searched on the client so user queries (chat) stay on-device for privacy / compliance reasons.
Interesting, we've had a few people ask about this. So essentially you'd call the server to retrieve the HNSW and then store it in the browser and use WASM to query it?
Currently the road block for that is the LMDB storage engine. We have on our own storage engine on our roadmap, which we want to include WASM support with. If you wanna talk about it reach out to my twitter: https://x.com/georgecurtiss
to add to George's reply, for helix to run on the browser with WASM the storage engine has to be completely in memory. At the moment we use LMDB which uses file based storage so that does't work with the browser. As George said, we plan on making our own storage engine and as part of that we aim to have an in-memory implementation.
Not entirely sure if you could use it, but wondering if you’ve heard about the origin private file system feature of modern browsers? https://developer.mozilla.org/en-US/docs/Web/API/File_System...
very interesting, will look into this. I know for a fact that you cannot compile the likes of LMDB and RocksDB to work with WASM but this looks promising for our custom storage engine to be able to make it work with the browser. Thanks for this!
> In-house graph-vector storage engine (to replace LMDB)
Not sure if it's possible. But why not use fjall, if it is? [0]
[0]: https://github.com/fjall-rs/fjall/
We went with LMDB because it was a lot faster. But will definitely look over this before we work on our own engine
Very interesting project. Would be curious of a comparison with memgraph. Will definitely give it to try for my knowledge graph use case.
I'll add memgraph to our benchmarking list! Make sure you join our discord. would love to help in any way we can and hear about any issues you run in to
This is very cool, and right up my alley. Hesitant to try it out because of the bespoke query language for now.
I wonder if you'd like to share your thoughts on GQL becoming an ISO standard? Also, have you looked into how Neptune Analytics handles vector embeddings?
This is very interesting, are there any examples of interacting with LLMs? If the queries are compiled and loaded into the database ahead of time the pattern of asking an LLM to generate a query from a natural language request seems difficult because current LLMs aren't going to know your query language yet and compiling each query for each prompt would add unnecessary overhead.
This is definitely a problem we want to work on fixing quickly. We're currently planning an MCP tool that can traverse the graph and decide for itself at each step where to go to next. As opposed to having to generate actual text written queries.
I mentioned in another comment that you can provide a grammar with constrained decoding to force the LLM to generate tokens that comply with the grammar. This ensures that only valid syntactic constructs are produced.
Can I run this as an embedded DB like sqlite?
Can I sidestep the DSL? I want my LLMs to generate queries and using a new language is going to make that hard or expensive.
Currently you can't run us embedded and I'm not sure how you could sidestep the DSL :/
We're working on putting our grammar in llama's cpp code so that it only outputs grammatically correct HQL. But, even without that it shouldn't be hard or expensive to do. I wrote a Claude wrapper that had our docs in its context window, it did a good job of writing queries most of the time.
Looks very interesting, but I've seen these kind of multi-paradigm databases like Gel, Helix and Surreal and I'm not sure that any of them quite hit the graph spot.
Does Helix support much of the graph algorithm world? For things like GrapgRAG.
Either way, I'd be all over it if there was a python SDK witch worked with the generated types!
Shameless plug: If you're exploring graph+vector databases, check out https://github.com/Pometry/Raphtory/ — with a full Python SDK and built-in support for most common graph algorithms.
It’s built in Rust with native vector support. The open-source version is in-memory, but the commercial version supports disk-based scaling (we tested it with a 3TB graph on an M1 MacBook + insert all 100x faster than existing GraphDBs).
Looking at your benchmarks you say for inserting 1k edges its around 500,000 ns/iteration. Is this 500,000 ns/per edge insertion or for all 1k of them?
We started as a graph database, so that's definitely the main thing we want to get right and we wan't to prioritise capturing all that functionality.
We have a python SDK already! What do you mean by generated types though?
I have been happily using Gel (formerly EdgeDB) for a few projects. I'm curious what you think it is missing in regards to hitting the "graph spot"?
gel is a relational database, have you been building with it under a graph type philosophy?
How does it compare with https://kuzudb.com/ ?
Kuzu don't support incremental indexing on the vectors. The vector index is completely separate and decoupled from the graph.
I.e: You have to re-index all of the vectors when you make an update to them.
Excellent work. Very exited to test this out. What are the limits or gotchas we should be aware of, or how do you want it pushed?
What other papers did you get inspiration from?
Thanks for the kind words! At the moment the query language transpilation is quite unstable but we are in the process of a large remodel which we aim to finish in the next day or so. This will make the query language compilation far more robust, and will return helpful error messages (like the rust compiler). The other thing is the core traversals are currently single threaded, so aggregating huge lists of graph items can take a bit of a hit. Note however, that we are also implementing parallel LMDB iterators with the help of the meilisearch guys to make aggregation of large results much faster.
How does it compare to SurrealDB and ChromaDB?
Graph DB OOMing 101. Can it do Erdős/Bacon numbers?
Graph DBs have been plagued with exploding complexity of queries as doing things like allowing recursion or counting paths isn't as trivial as it may sound. Do you have benchmarks and comparisons against other engines and query languages?
No, we are in the process of writing up some proper benchmarks. Our first user used us to build MuskMap and TrumpMap, which went viral on twitter. Not sure how it compared to other graph DBs at the time (bear in mind this was v1 and very bear bones), but it got latency of using Postgres >5s down to 50ms with us.
The fact that it's "backed by NVIDIA" and licensed under AGPL-3.0 makes me wonder about the cost(s) of using it in production.
Could you share any information on the pricing model?
We are open-source, so you can use and self host us for free. Our plan is to create a managed service (so long as all goes well) which shouldn't be priced any differently from other databases in the space.
We chose AGPL to make sure someone can't make a cloud hosted version of our product, think MongoDB on AWS a few years back.
What would be a typical/recommended server setup for using this for RAG? Would you typically have a separate server for the GPUs and the DB itself?
Assuming you are using GPUs for model inference, the best way to set it up would have the DB and a separate server to send inference requests. Note that we plan on support custom model endpoints and on the database side so you probably won't need the inference server in the future!
Nice "I'll have this name" when there's already the helix editor :)
First I'm hearing from it. The Beatles must've been super pissed when Apple took their name :(
https://crates.io/search?q=Helix
I'm surprised none in the team searched crates.io once before picking the name. Good luck!
I don't think `helix-editor` is even on crates.io, just placeholders.
https://github.com/helix-editor/helix/discussions/7038
That being said, when I saw `helix-db` I was thrown too. "What's a text editor doing writing a vector-graph database, I thought they were working on plugins?"
we just started off as a side project and thought the name fitted well. With the strands, graph type structure, connections...
We didn't think of getting people to use it until we found it was solving a real pain point for people, so weren't worried about trademarks or names. There was no other helix db so that was good enough for us at the time.
> There was no other helix db
https://en.wikipedia.org/wiki/Helix_(database)
There was no active one. We saw this and thought it would be a nice nod to history. We've actually spoken to some developers at apple who thought this was really neat :)
It's not the end of the world, just me being a bit grumpy. I mean it when I say good luck! :)
Thank you :)
I can't tell if this is droll sarcasm, but just in case not...
https://en.wikipedia.org/wiki/Apple_Corps_v_Apple_Computer
perhaps it’s a homage to the famous Helix database (see Wikipedia)
well noted
How do you think about building the graph relationships? Any special approaches you use?
Pretty much the same way you would with any graph DB, with the added benefit of being able to treat a vector as a node by creating those explicit relationships between them.
Does that answer your question properly?
It sounds very intriguing indeed. However, the README makes some claims. Are there any benchmarks to support them?
> Built for performance we're currently 1000x faster than Neo4j, 100x faster than TigerGraph
Those were actual benchmarks that we run, we didn't get a chance to write them out properly before posting. I'll get on it now and notify by replying to this comment when they're on the readme :)
Super cool!!! I'll try it this week and go back to give a feedback.
I look forward to it :)
What is the max number of dimensions supported for a vector?
There is currently no cap. We will probably impose a similar cap to Qdrant or Pinecone some time soon ~64k. There's obviously a performance trade off as you go up, but we hope to massively offset this by doing binary quantisation within the next couple of months.
there is also the fact that the more dimensions you have for embedded data the more diluted the embedding becomes so it is unusual to go anywhere near the limits of vector length!
"faster than Neo4j" How does it compare to Dgraph?
We don't have any benchmarks against them but from what I've just read about there bench marks, we should be just as good as them.
That is just heresy though, am interested myself now and will run some proper benchmarks
Congrats on the launch!
thank you! any feedback would be much appreciated
What method/model are you using for sparse search?
We're going to use BM25. Currently it is just dense search. Coming very soon
have you thought about SPALDE models? ex: https://arxiv.org/abs/2109.10086
Looks really interesting, I'll have a proper read. What would be your reasoning to incorporate this if we already have vector functionality and semantic search?
my project deals w/ non-english text, bm25 performance is middeling. Language specific sparse model helps.
We will definitely look into it. The SPLADE models look promising!
SPALDE*
How can I migrate neo4j to this?
We can build an ingestion engine for you :)
We've built SQL and PGVector ones already, just waiting for someone who could make use of other ones before we build them.
Let us know! Twitter in my bio
how did you get it 3 OOMs faster than neo4j?
Partly because they're working with a monolith that I imagine is difficult to iterate on and it's written in Java. We've had the benefit of working on this in Rust which lets us get really nitty and gritty with different optimisations.
My friend who I worked on this with is putting together a technical blog on those graph optimisations so I'll link it here when he's done
On comparable benchmarks with comparable guarantees? Comparable persistence levels? I’m very skeptical.
Looking forward to putting you at ease :) Working on some proper benchmarks over the next few days.
Can you do a compare/contrast with CozoDB?
https://github.com/cozodb/cozo
apart from the fact Cozo seems to be pretty dead, we use a different storage engine which makes our reads much faster. based on their benchmarks I estimate our most of our reads to be 10x faster. I think our query language is much simpler, and easy to understand than Datalog which is what they use.
How scalable is your DB in your tests? Could it be performent on graphs with 1B/10B/100B connections?
So far, we've tested it for up to ~10B connections and 50 odd million nodes. We didn't run in to any problems with it yet.
Looks nice! Are you looking to compete with https://www.falkordb.com or do something a bit different?
Pretty much, our biggest focus is on Graph and Hybrid RAG. They seem to have really honed in on Graph RAG since the last time I checked their website.
One of the problems I know people experience with them is that they're super slow at bulk reading.
Oh also, they aren't built in Rust haha
why not surrealdb?
General consensus is it's really slow, I like the concept of surreal though. Our first, and extremely bare bones, version of the graph db was 1-2 orders of magnitude faster than surreal (we haven't run benchmarks against surreal recently, but I'll put them here when we're done)
Hey George, Alexander from SurrealDB here.
Congratulations on the launch! This is a very exciting space, and it's great to see your take on it.
Running fair benchmarks, not benchmarketing, is a significant effort and we recently put in this effort to make things as fair and transparent as possible across a range of databases.
You can see the results and links to our code in the write-up here: https://surrealdb.com/blog/beginning-our-benchmarking-journe...
We'd be very interested in seeing the benchmarks you'd run and how we compare :)
You can sacrifice many things for faster performance, such as security, consistency levels or referential integrity.
I'm genuinely curious to learn what design decisions you will make as you continue building the database. There are so many options, each with its pros and cons.
If you would like to have a chat where we can exchange ideas, happy to do that :)
> so much easier that it’s worth a bit of a learning curve
I think you misspelled "vendor lock in"
You can literally use us for free haha. There's not a language that properly encapsulates graph and vector functionality, so we needed to make our own. Also, we thought it was dumb that query languages weren't type-safe... So we changed that