honicky.bsky.social

honicky.bsky.social

@honicky.bsky.social

10 followers32 following13 posts

honicky.bsky.social
@honicky.bsky.social

Just do: INSTALL anndata FROM community; -- first time only ATTACH "anndata:your_file.h5ad" AS ad; SELECT * from ad.obs; Blog post: learning-exhaust.hashnode.dev/introducing-... GitHub: github.com/honicky/annd...

learning-exhaust.hashnode.devIntroducing the AnnData DuckDB extensionAt MiraOmics we look at a lot of H5AD files. We have a database of over a thousand of them, not to mention several of the public data sources. Pretty much every time I have a new file, the first thin...
honicky.bsky.social
@honicky.bsky.social

Working with a large set of AnnData files on S3 is tough if you don't have the metadata indexed, so I created a tool to help. github.com/honicky/annd... It uses partial downloads to dramatically speed up extracting the metadata without downloading the whole file. `pip install anndata-metadata`

github.comGitHub - honicky/anndata-metadata: A Python library and CLI tool for extracting metadata from AnnData .h5ad files, both locally and on S3A Python library and CLI tool for extracting metadata from AnnData .h5ad files, both locally and on S3 - honicky/anndata-metadata
honicky.bsky.social
@honicky.bsky.social

First post to bsky: I've been trying to post a bit more frequently and in smaller bites, so I'm going to try to pick one interesting thing I've learned from papers I read, and then write a quick post about them. Here's my first one: learning-exhaust.hashnode.dev/one-thing-i-...

learning-exhaust.hashnode.devEmbeddings are task specificModern training techniques for embedding models mean that we should probably include a prompt or fine tune to a specific type of task.

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