Charles Tapley Hoyt

Add progress bar to encoder with `tqdm`

3

I'm encoding the [Rhea](https://www.rhea-db.org/) reactions with `drfp` right now and it's taking more than 10 seconds, so naturally I'd like to see how much longer it will take using a...

I'm running DRFP on the 30K reactions from Rhea and it takes about 20 minutes on my 2019 macbook pro on a single core. It would be great to add...

Is there a preferred way to store drfps?

1

I've just spent some time to automate generating drfps from the Rhea database (see [here](https://github.com/cthoyt/rhea-fingerprints)) and would like to save a pre-cached version for later use. The word2vec world has...

Pre-compiled CLIXO does not work

2

Having pre-compiled C++ code in the repository is a bit confusing, since it doesn't generally work on each person's system. This isn't obvious from using the python code, since using...

Tulip does not work on python37

1

Right now, there hasn't been a wheel added for py37 so it can't yet be used. It seems like they do not have their source code publicly available so I...

I saw this in several places. would be cool to set up here

Suggested by @jmuhlich: https://github.com/pypa/setuptools_scm

This PR adds the Bioregistry (https://github.com/biopragmatics/bioregistry / https://bioregistry.io) to the list of tools using Prefix.cc. Short summary: the Bioregistry is also keeping track of prefixes useful in the biomedical domain...

Use case: assessing goodness of fit between two PyKEEN models

1

If I have two different embedding spaces describing the same entities, like if I train two models on the same dataset in PyKEEN, how can I use Kiez to assess...