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justaddcoffee
68 posts
justaddcoffee
@justaddcoffee
Justin Reese, PhD | computational biology | machine learning | biomedical data | knowledge graphs | running
Berkeley, CA Katılım Mart 2008
348 Takip Edilen119 Takipçiler
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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
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@ontowonka @MonarchInit @hp_ontology @AMIAinformatics Many thanks @ontowonka for all your help making this project possible!
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With many kudos to @justaddcoffee for leading this truly innovative work! Slides are here: bit.ly/amia23clusteri… @MonarchInit @hp_ontology @AMIAinformatics #IS23 #ontologies #realWorldData
CTSA Data2Health@data2health
@ontowonka discussed a new way to analyze electronic health record (EHR) #data using the Human Phenotype Ontology method. In addition to Long COVID, this method was found to be extensible across other health systems and medical applications.
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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/articl…
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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).
Belfast, Northern Ireland 🇬🇧 English
Interesting statistical problem I hadn't heard of:
en.wikipedia.org/wiki/German_ta…
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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
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Our preprint demonstrating the association of metformin with reduced COVID-19 severity in patients with prediabetes:
medrxiv.org/content/10.110…
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#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…
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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/gr…
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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/gr…
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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/10.110…
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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/artic…
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An algorithmic framework for isoform-specific functional analysis biorxiv.org/content/10.110… @MonarchInit
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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
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Translating long COVID manifestations into computable HPO terms:
authors.elsevier.com/sd/article/S23… @hp_ontology @MonarchInit
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