@justaddcoffee

Justin Reese, PhD | computational biology | machine learning | biomedical data | knowledge graphs | running

 Berkeley, CA
github.com/justaddcoffee
Joined March 2008
  • Tweets68
  • Following341
  • Followers116
justaddcoffee retweeted
mhackeroni@mhackeroni14 Aug 2023
This guy is the reason why we played Hack-a-Sat to begin with. Thanks @chqmatteo 🙏
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justaddcoffee retweeted
Chris Mungall@chrismungall7 Apr 2023
Here's our pre-print describing our GPT-3 based knowledge extraction tool SPIRES: arxiv.org/abs/2304.02711. Great work from @harry_caufield et al! SPIRES allows you to specify a knowledge schema (in @linkml_data) and then populate instances of that schema from unstructured text
depiction of SPIRES approach: input is a schema and text, the OntoGPT engine will run SPIRES by recursively querying GPT-3 for prompt completions, the end result is grounded using public databases and ontologies

ALT depiction of SPIRES approach: input is a schema and text, the OntoGPT engine will run SPIRES by recursively querying GPT-3 for prompt completions, the end result is grounded using public databases and ontologies

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justaddcoffee retweeted
Peter Robinson@pnrobins2 Feb 2023
A pleasure to collaborate with Elena Casiraghi on so many cool projects! Here's the latest: A method for comparing multiple imputation techniques: a case study on the U.S. National COVID Cohort Collaborative sciencedirect.com/science/ar…
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justaddcoffee retweeted
Cmckenna@McKennaGenetics23 Jan 2023
If you work in a Clinical Genetics department that recruited to the 100k Genome Project I *highly* recommend encouraging one of your clinical genetics trainees to review the top 5 exomiser results in your undiagnosed patients (particularly the trios). – at Belfast, Northern Ireland
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Thanks @SecGranholm for sharing our work!
Secretary Jennifer Granholm
@SecGranholm10 Jan 2023
This crucial research will help fill the gaps in our understanding of how #LongCOVID works and develop more effective treatments for those still suffering. newscenter.lbl.gov/2023/01/0…

Machine Learning Tackles Long COVID

We’re untangling long COVID using machine learning on real-world patient data to accelerate the path to treatment

newscenter.lbl.gov
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Interesting statistical problem I hadn't heard of: en.wikipedia.org/wiki/German…
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justaddcoffee retweeted
GRAPE@GRAPElib7 Dec 2022
Woohoo! #GRAPE just hit 100 stars on GitHub! Thank you to all the amazing developers who have supported our graph representation learning library. We couldn't have done it without you! 🍇💜🍇 #opensource #machinelearning
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Scientific #publications are a treasure trove, but integrating their knowledge into #graph #machinelearning is more challenging than it needs to be! 🧵 1/4
PS: I made a BERT/Einstein muppet for SciBERT using Stable Diffusion!

ALT PS: I made a BERT/Einstein muppet for SciBERT using Stable Diffusion!

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justaddcoffee retweeted
GRAPE@GRAPElib8 Oct 2022
Pushing the ✉️ of 🍇's @psresnik score implementation by computing 3T, i.e. 3*10^12, scores from @NCBI Taxonomy (2438821 nodes) upper triangular matrix. This is heavily parallelized and takes ≈3h on a 💻 with 8GBs of RAM and 96 cores.
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Our preprint demonstrating the association of metformin with reduced COVID-19 severity in patients with prediabetes: medrxiv.org/content/10.1101/…

Metformin is Associated with Reduced COVID-19 Severity in Patients with Prediabetes

Background With the continuing COVID-19 pandemic, identifying medications that improve COVID-19 outcomes is crucial. Studies suggest that use of metformin, an oral antihyperglycemic, is associated...

medrxiv.org
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justaddcoffee retweeted
GRAPE@GRAPElib18 Aug 2022
#GraphML 🍇 preprint is on @arxiv! ❤️ to @LucaCappellett6, @Zommiommy, Casiraghi, @RavanmehrVida, @Tiff_callahan, @realmarcin, @chrismungall, @pnrobins, @justaddcoffee & Valentini 📍@MonarchInit, @ConsorzioCINI, @LaStatale, @jacksonlab & @BerkeleyLab 📜:arxiv.org/pdf/2110.06196.pdf
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justaddcoffee retweeted
GRAPE@GRAPElib10 Aug 2022
Animations >> Words! Here's @justaddcoffee's KGCOVID19 embedding (~574k nodes, ~18M edges), animated in ~4m on my desktop using 🍇's @rustlang implementation (with #Python bindings) of @tangjianpku's First-order LINE. Use it with @googleslides! 💻: github.com/AnacletoLAB/grape…
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justaddcoffee retweeted
GRAPE@GRAPElib3 Aug 2022
The new version of 🍇, 0.1.10, is out! We introduce support for 14 MMAP-ed graph embedding algorithms, plus a significantly extended set of tutorials! E.g. TSNEs of 36 node embeddings of Cora, find the code here: github.com/AnacletoLAB/grape…
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Our latest paper identifying subtypes of #longcovid using machine learning on EHR data from the National COVID Cohort Collaborative (N3C): medrxiv.org/content/10.1101/…
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After a lot of hard work by many people it’s finally done: Simple Standard for Sharing Ontological Mappings (SSSOM). Thank you to all contributors! academic.oup.com/database/ar…

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Abstract. Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapp

academic.oup.com
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justaddcoffee retweeted
Peter Robinson@pnrobins15 May 2022
An algorithmic framework for isoform-specific functional analysis biorxiv.org/content/10.1101/… @MonarchInit

An algorithmic framework for isoform-specific functional analysis

Gene Ontology (GO) overrepresentation analysis characterizes the biological mechanisms common to sets of differentially expressed genes identified by high-throughput experiments. To date, GO overre...

biorxiv.org
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Biolink Model is our proposed standard for biological #KnowledgeGraphs, created by the @ncats_nih_gov #BiomedicalDataTranslator team arxiv.org/abs/2203.13906

Biolink Model: A Universal Schema for Knowledge Graphs in...

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph-based data models elucidate the interconnectedness...

arxiv.org
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who.int/news/item/26-11-2021…
justaddcoffee retweeted
Peter Robinson@pnrobins25 Nov 2021
Translating long COVID manifestations into computable HPO terms: authors.elsevier.com/sd/arti… @hp_ontology @MonarchInit
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Quick! Stop scrolling. What you see here aren’t just any clouds, they’re Martian clouds. Take a moment out of your day to look at the sky of another world. 📸 taken by my right Navigation Camera. go.nasa.gov/2QSoqja
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