mediKanren VS wh40ksim

Not really production, but probably THE most impressive biomedicine research work I've seen (and I'm an academic MD):

https://github.com/webyrd/mediKanren

This is a FOL theorem prover that uses medical research articles as terms. They use it to do genetics and drug repurposing metaresearch. It's like the wet dream of all the biomed machine learning fanboys out there, except that:

1. it's not machine learning

and

2. it really works

And wow, he uses logic programming to deduce a diagnostic from the facts https://github.com/webyrd/mediKanren .. and used to find out what his son had https://www.statnews.com/2019/07/25/ai-expert-writing-code-save-son/

Hi Kamaal!

I know Cisco is using core.logic, which is David Nolen's Clojure variant of miniKanren, in their ThreatGrid product. I think the Enterprisey uses of mediKanren are a bit different than the purely relational programming that I find most interesting, though.

Having said that, we are now on our second generation of mediKanren, which is software that performs reasoning over large biomedical knowledge graphs:

https://github.com/webyrd/mediKanren/tree/master/medikanren2

mediKanren is being developed by the Hugh Kaul Precision Medicine Institute at the University of Alabama at Birmingham (HKPMI). HKPMI is run by Matt Might, who you may know from his work on abstract interpretation and parsing with derivatives, or from his more recent work on precision medicine. mediKanren is part of the NIH NCATS Biomedical Data Translator Project, and is funded by NCATS:

https://ncats.nih.gov/translator

Greg Rosenblatt, who sped up Barliman's relational interpreter many order of magnitude, has been hacking on dbKanren, which augments miniKanren with automatic goal reordering, stratified queries/aggregation, a graph database engine, and many other goodies. dbKanren is the heart of mediKanren 2.

I can imagine co-writing a book on mediKanren 2, and its uses for precision medicine...

Cheers,

--Will

The Precision Medicine Institute that I now run produces mediKanren: https://github.com/webyrd/mediKanren

It's an open source logical reasoning engine (read: 1960's AI) for drug repurposing that we deploy routinely to help patients.

There is always a need for better relationalization of biological data sets that feed such tools too.

For example, SemMedDB is really showing its age for NLP of the scientific literature and yet it is still astonishingly useful for helping patients even as is.

Here's some stuff I've written in Prolog, some for my own enjoyment, one for my degree project.

Most of the benefits I found come down to two things:

a) Prolog, like the various kanrens, is a relational language so a program is effectively a database. There's no need to do anything special to glue together a data layer and a logic layer, because you have both written in Prolog.

b) Prolog's declarative style makes translating rules and directives to code a breeze. The three projects below are all games and benefit heavily from this feature. I

1. Warhammer 40K simulation:

https://github.com/stassa/wh40ksim

Runs simulations of combat between WH40k units.

2. Gleemin, a Magic: the Gathering expert system:

https://github.com/stassa/Gleemin

Doesn't work anymore! Because backwards compatibility. Includes a) a parser for the rules text on M:tG cards written in Prolog's Definite Clause Grammars notation, b) a rules engine and c) a (primitive) AI player. The parser translates rules text from cards into rules engine calls. The cards themselves are Prolog predicates. Your data and your program are one and now you can also do stuff with them.

3. Nests & Insects, a roguelike TTRPG:

https://github.com/stassa/nests-and-insects

WIP! Here I use Prolog to keep the data about my tabletop rpg organised, and also to automatically fill-in the character sheets typeset in the rulebook. The Prolog code runs a character creation process and generates completed character sheets. I plan to do the same for enemies' stat blocks, various procedural generation tables, etc. I also use Prolog to typeset the ASCII-styled rulebook, but that's probably not a good application of Prolog.

You asked about "logic programming" in general and not miniKanren in particular. I haven't actually used miniKanren, so I commented about the logic programming language I've used the most, Prolog. I hope that's not a thread hijack!

All three of the projects above are basically games. I have more "serious" stuff on my github but I feel a certain shortfall of gravitas, I suppose.