mediKanren
scryer-prolog
mediKanren | scryer-prolog | |
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6 | 42 | |
316 | 1,895 | |
- | - | |
8.1 | 9.7 | |
15 days ago | 7 days ago | |
Racket | Rust | |
MIT License | BSD 3-clause "New" or "Revised" License |
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mediKanren
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Annotated implementation of microKanren: an embeddable logic language
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
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Human Knowledge and PhDs
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/
- With a nudge from AI, ketamine emerges as a potential rare disease treatment
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William Byrd on Logic and Relational Programming, MiniKanren (2014)
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
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Bertrand Might: Life, legacy and next steps
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.
scryer-prolog
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The Shen Programming Language
thank you! the scryer community deserves much of the credit too. everyone is welcome and encouraged to join us at https://github.com/mthom/scryer-prolog! some exciting plans in the pipe
- Appreciating Clpz_t/2
- Advent of Code 2023 is nigh
- Scryer Prolog version 0.9.3 is out
- Announcing Basic WebAssembly support in Scryer Prolog
- Basic WebAssembly Support in Scryer Prolog
- Scryer-Prolog 0.9.2
- Release v1.1.0 of PostgreSQL-Prolog
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Djot is a light markup syntax
Djot is the markup syntax that is used for the documentation of Scryer Prolog, using a parser written in Prolog:
https://github.com/aarroyoc/djota
It works well so far. One of the few limitations I noticed so far pertains to the formatting of tables. For instance, consider the table used in library(format) to describe control sequences:
https://github.com/mthom/scryer-prolog/blob/b0566e41503a6c8d...
It contains several entries that span multiple lines, yet are meant to denote only a single row of the table, such as:
% | `~Nr` | where N is an integer between 2 and 36: format the |
- The First Annual Scryer Prolog Meetup
What are some alternatives?
racketscript - Racket to JavaScript Compiler
swipl-devel - SWI-Prolog Main development repository
microKanren - The implementation of microKanren, a featherweight relational programming language
logica - Logica is a logic programming language that compiles to SQL. It runs on Google BigQuery, PostgreSQL and SQLite.
awesome-racket - A curated list of awesome Racket frameworks, libraries and software, maintained by Community
differential-datalog - DDlog is a programming language for incremental computation. It is well suited for writing programs that continuously update their output in response to input changes. A DDlog programmer does not write incremental algorithms; instead they specify the desired input-output mapping in a declarative manner.
gui
materialize - The data warehouse for operational workloads.
frog - Frog is a static blog generator implemented in Racket, targeting Bootstrap and able to use Pygments.
tau-prolog - An open source Prolog interpreter in JavaScript
iracket - Jupyter kernel for Racket
prolog - The only reasonable scripting engine for Go.