Atul Butte
@atulbutte.bsky.social
Chief Data Scientist U of CA Health・Director, Bakar Computational Health Sci Institute・Distinguished Prof af UCSF・Entrepreneur・He/him・Opinions ⇨ my own
Reposted by Atul Butte
Reposted by Atul Butte
Go look at our #data
Free and #FAIRsharing.
144 studies, 10,244 human participants and > 135,000 samples.
#systems #immunology
@immportdb.bsky.social
#IDsky #immunesky
Check our #analysis tools at immunespace.org
immport.org/resources/hipc
Free and #FAIRsharing.
144 studies, 10,244 human participants and > 135,000 samples.
#systems #immunology
@immportdb.bsky.social
#IDsky #immunesky
Check our #analysis tools at immunespace.org
immport.org/resources/hipc
February 24, 2025 at 6:12 PM
Go look at our #data
Free and #FAIRsharing.
144 studies, 10,244 human participants and > 135,000 samples.
#systems #immunology
@immportdb.bsky.social
#IDsky #immunesky
Check our #analysis tools at immunespace.org
immport.org/resources/hipc
Free and #FAIRsharing.
144 studies, 10,244 human participants and > 135,000 samples.
#systems #immunology
@immportdb.bsky.social
#IDsky #immunesky
Check our #analysis tools at immunespace.org
immport.org/resources/hipc
Yeah! All 10 campuses of the @UofCalifornia are now considered R1 research institutions!
UC Merced achieves R1 classification, bringing all UC campuses to the highest tier among research universities
Each UC campus now resides among the exclusive group of 187 accredited doctoral-granting universities in the United States designated R1 by the Carnegie Classification of Institutions of Higher…
buff.ly
February 16, 2025 at 8:47 AM
Yeah! All 10 campuses of the @UofCalifornia are now considered R1 research institutions!
Great new article showcasing how researchers across @UofCAHealth are using @UofCalifornia Health Data Warehouse to study endometriosis, glaucoma, rare disease, cirrhosis, and more! Includes the work of @ManishButte @msirota84 @DrJonWatanabe and many others! bit.ly/4h5lmrh
Data science is accelerating UC medical research, diagnosis and treatment in California
bit.ly
January 25, 2025 at 12:39 AM
Great new article showcasing how researchers across @UofCAHealth are using @UofCalifornia Health Data Warehouse to study endometriosis, glaucoma, rare disease, cirrhosis, and more! Includes the work of @ManishButte @msirota84 @DrJonWatanabe and many others! bit.ly/4h5lmrh
So awesome! “Daily ferry service is sailing toward Mission Bay.” Imagine commuting directly to @UCSF Mission Bay via high-speed zero-emissions boat! Scheduled to begin service in 2027. Now all we need is service to the South Bay! 😊
www.ucsf.edu/news/2025/01...
www.ucsf.edu/news/2025/01...
Ferry Service at Mission Bay: When You’ll Benefit From a New Commute Option
A new all-electric ferry to Mission Bay launches in 2027, supported by a $55M EPA grant, aiding UCSF commuters and patients.
www.ucsf.edu
January 16, 2025 at 5:51 PM
So awesome! “Daily ferry service is sailing toward Mission Bay.” Imagine commuting directly to @UCSF Mission Bay via high-speed zero-emissions boat! Scheduled to begin service in 2027. Now all we need is service to the South Bay! 😊
www.ucsf.edu/news/2025/01...
www.ucsf.edu/news/2025/01...
Use my starter pack to add about 90 accounts to follow in science, #AI, bioinformatics, and clinical informatics! go.bsky.app/97wmgsZ
January 13, 2025 at 10:05 PM
Use my starter pack to add about 90 accounts to follow in science, #AI, bioinformatics, and clinical informatics! go.bsky.app/97wmgsZ
Thinking of and praying for my friends, family, and colleagues in and around Santa Monica and @UCLA @UCLAHealth during these terrible fires…
January 9, 2025 at 1:19 AM
Thinking of and praying for my friends, family, and colleagues in and around Santa Monica and @UCLA @UCLAHealth during these terrible fires…
Whoa!! @HHSGov drops 125 page HIPAA update for comments: "update[s] HIPAA Security Rule for the first time since 2013"!
www.hhs.gov/hipaa/for-pr...
www.hhs.gov/hipaa/for-pr...
www.hhs.gov
January 7, 2025 at 10:26 PM
Whoa!! @HHSGov drops 125 page HIPAA update for comments: "update[s] HIPAA Security Rule for the first time since 2013"!
www.hhs.gov/hipaa/for-pr...
www.hhs.gov/hipaa/for-pr...
Reposted by Atul Butte
Join us for Post-Doctoral projects at @atulbutte.bsky.social on a newly funded FDA project on real-world analysis of onco-therapies! If you have a passion for epidemiology, causal inference, LLMs & scientific rigor, we'd love to hear from you. Please DM me. Spread the word. Thank you.
January 6, 2025 at 6:06 PM
Join us for Post-Doctoral projects at @atulbutte.bsky.social on a newly funded FDA project on real-world analysis of onco-therapies! If you have a passion for epidemiology, causal inference, LLMs & scientific rigor, we'd love to hear from you. Please DM me. Spread the word. Thank you.
I often wish the default iPad on screen keyboard had arrow keys to navigate in text…
January 2, 2025 at 8:47 AM
I often wish the default iPad on screen keyboard had arrow keys to navigate in text…
Reposted by Atul Butte
2024 saw another record for bioRxiv postings. Thanks to all the CSHL staff, affiliates, authors, funders, and everyone who advocates for the project. Happy New Year and #letsmakethisthenorm ! 🧪
January 1, 2025 at 2:16 PM
2024 saw another record for bioRxiv postings. Thanks to all the CSHL staff, affiliates, authors, funders, and everyone who advocates for the project. Happy New Year and #letsmakethisthenorm ! 🧪
Reposted by Atul Butte
I have a colleague (not on social media) who likes to say that works don't *fall* into the public domain, they *ascend* into the public domain. I really love that.
January 1, 2025 at 1:12 PM
I have a colleague (not on social media) who likes to say that works don't *fall* into the public domain, they *ascend* into the public domain. I really love that.
This ad seemed so hard to believe back in 1999… "all rooms have every movie ever made in any language anytime, day or night."
Qwest commercial 1999 - Every Movie
Remember how absurd this seemed in 1999 before the internet really took off? When the weary traveler asked the front desk what entertainment was available, t...
buff.ly
December 24, 2024 at 8:47 AM
This ad seemed so hard to believe back in 1999… "all rooms have every movie ever made in any language anytime, day or night."
Whoa! In @NEJM_AI:
A Multimodal Biomedical Foundation Model Trained from 15 Million Image–Text Pairs… fully open-access foundation model!
ai.nejm.org/doi/full/10....
A Multimodal Biomedical Foundation Model Trained from 15 Million Image–Text Pairs… fully open-access foundation model!
ai.nejm.org/doi/full/10....
A Multimodal Biomedical Foundation Model Trained from Fifteen Million Image–Text Pairs
Biomedical data are inherently multimodal, comprising physical measurements and natural-language
narratives. A generalist biomedical artificial intelligence (AI) model needs to simultaneously
proce...
ai.nejm.org
December 23, 2024 at 9:12 PM
Whoa! In @NEJM_AI:
A Multimodal Biomedical Foundation Model Trained from 15 Million Image–Text Pairs… fully open-access foundation model!
ai.nejm.org/doi/full/10....
A Multimodal Biomedical Foundation Model Trained from 15 Million Image–Text Pairs… fully open-access foundation model!
ai.nejm.org/doi/full/10....
Folks moving back to California!
“California nets large population increase in 2024 — nearly returning to pre-pandemic level”
https://buff.ly/4fxlMVs
“California nets large population increase in 2024 — nearly returning to pre-pandemic level”
https://buff.ly/4fxlMVs
California nets large population increase in 2024 — nearly returning to pre-pandemic level
It had the third most new residents of any state, by raw numbers.
buff.ly
December 22, 2024 at 8:47 AM
Folks moving back to California!
“California nets large population increase in 2024 — nearly returning to pre-pandemic level”
https://buff.ly/4fxlMVs
“California nets large population increase in 2024 — nearly returning to pre-pandemic level”
https://buff.ly/4fxlMVs
Reposted by Atul Butte
A great job for someone, for certain.
But I am re-posting this because this photo of the Geisel (of Dr. Seuss fame) Library at UC San Diego is a reminder of the twinned seriousness and surreality of my undergraduate education there--and the (re)imagining and (re)visioning it made possible for me.
But I am re-posting this because this photo of the Geisel (of Dr. Seuss fame) Library at UC San Diego is a reminder of the twinned seriousness and surreality of my undergraduate education there--and the (re)imagining and (re)visioning it made possible for me.
Great! @UCSD Biomedical Informatics is recruiting new tenure-track faculty!
Assistant Professor https://buff.ly/49LX6rf ; Associate or Full Professor
Assistant Professor https://buff.ly/49LX6rf ; Associate or Full Professor
Associate or Full Professor (Ladder/In-Residence) Biomedical Informatics Research
University of California, San Diego is hiring. Apply now!
buff.ly
December 21, 2024 at 4:18 PM
A great job for someone, for certain.
But I am re-posting this because this photo of the Geisel (of Dr. Seuss fame) Library at UC San Diego is a reminder of the twinned seriousness and surreality of my undergraduate education there--and the (re)imagining and (re)visioning it made possible for me.
But I am re-posting this because this photo of the Geisel (of Dr. Seuss fame) Library at UC San Diego is a reminder of the twinned seriousness and surreality of my undergraduate education there--and the (re)imagining and (re)visioning it made possible for me.
Great! @UCSD Biomedical Informatics is recruiting new tenure-track faculty!
Assistant Professor https://buff.ly/49LX6rf ; Associate or Full Professor
Assistant Professor https://buff.ly/49LX6rf ; Associate or Full Professor
Associate or Full Professor (Ladder/In-Residence) Biomedical Informatics Research
University of California, San Diego is hiring. Apply now!
buff.ly
December 21, 2024 at 4:06 PM
Great! @UCSD Biomedical Informatics is recruiting new tenure-track faculty!
Assistant Professor https://buff.ly/49LX6rf ; Associate or Full Professor
Assistant Professor https://buff.ly/49LX6rf ; Associate or Full Professor
Nearly 50 US #AI startups raised $100M+ in 2024!
Here’s the full list of 49 US AI startups that have raised $100M or more in 2024 | TechCrunch
AI startups continue to dominate the venture capital funding landscape. Here are the all the megarounds so far in 2024.
buff.ly
December 21, 2024 at 8:47 AM
Nearly 50 US #AI startups raised $100M+ in 2024!
$1 million dollars up for grabs from @NIH for the teams that come up with the best measures of research data sharing, also known as a Data Sharing Index (S-index)! www.freelancer.com/contest/nih-... HT @michaelfchiang.bsky.social
NIH Data Sharing Index (S-index) Challenge
Check out this contest and enter now!
www.freelancer.com
December 20, 2024 at 3:32 PM
$1 million dollars up for grabs from @NIH for the teams that come up with the best measures of research data sharing, also known as a Data Sharing Index (S-index)! www.freelancer.com/contest/nih-... HT @michaelfchiang.bsky.social
“When a measure becomes a target, it ceases to be a good measure." - Goodhart’s Law
en.m.wikipedia.org/wiki/Goodhar...
en.m.wikipedia.org/wiki/Goodhar...
Goodhart's law - Wikipedia
en.m.wikipedia.org
December 19, 2024 at 9:31 PM
“When a measure becomes a target, it ceases to be a good measure." - Goodhart’s Law
en.m.wikipedia.org/wiki/Goodhar...
en.m.wikipedia.org/wiki/Goodhar...
Reposted by Atul Butte
Here's a website that describes the NIH "s-index challenge" to promote data sharing by developing a robust metric to identify exemplary data sharers.
National Eye Institute is excited lead a large group of participating NIH institutes (shown on website).
www.freelancer.com/contest/NIH-...
National Eye Institute is excited lead a large group of participating NIH institutes (shown on website).
www.freelancer.com/contest/NIH-...
NIH Data Sharing Index (S-index) Challenge
Check out this contest and enter now!
www.freelancer.com
December 19, 2024 at 6:30 PM
Here's a website that describes the NIH "s-index challenge" to promote data sharing by developing a robust metric to identify exemplary data sharers.
National Eye Institute is excited lead a large group of participating NIH institutes (shown on website).
www.freelancer.com/contest/NIH-...
National Eye Institute is excited lead a large group of participating NIH institutes (shown on website).
www.freelancer.com/contest/NIH-...
Reposted by Atul Butte
There’s a lot to unpack in the Bipartisan House Task Force Report on AI. It’s clear that progress will require collaboration to ensure a healthy evaluation/adoption pipeline.
Glad to see @ucsdhealth.bsky.social’s work in sepsis AI highlighted in this report.
Link: www.speaker.gov/wp-content/u...
Glad to see @ucsdhealth.bsky.social’s work in sepsis AI highlighted in this report.
Link: www.speaker.gov/wp-content/u...
December 18, 2024 at 5:56 AM
There’s a lot to unpack in the Bipartisan House Task Force Report on AI. It’s clear that progress will require collaboration to ensure a healthy evaluation/adoption pipeline.
Glad to see @ucsdhealth.bsky.social’s work in sepsis AI highlighted in this report.
Link: www.speaker.gov/wp-content/u...
Glad to see @ucsdhealth.bsky.social’s work in sepsis AI highlighted in this report.
Link: www.speaker.gov/wp-content/u...
Reposted by Atul Butte
After nearly 15 years since its publication, #MANTRA (the tool for drug repositioning I designed during my PhD in Diego di Bernardo's lab at TIGEM) still goes strong! @atulbutte.bsky.social and colleagues using it for drug repurposing in skin inflammation here 👇 👍
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Repurposing an epithelial sodium channel inhibitor as a therapy for murine and human skin inflammation
Computational and molecular analysis identified benzamil as a potential treatment for skin inflammation in murine and human xenograft skin models.
www.science.org
December 16, 2024 at 12:42 PM
After nearly 15 years since its publication, #MANTRA (the tool for drug repositioning I designed during my PhD in Diego di Bernardo's lab at TIGEM) still goes strong! @atulbutte.bsky.social and colleagues using it for drug repurposing in skin inflammation here 👇 👍
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Woah! New Microsoft python packages convert from Office documents into Markdown! github.com/microsoft/ma...
GitHub - microsoft/markitdown: Python tool for converting files and office documents to Markdown.
Python tool for converting files and office documents to Markdown. - microsoft/markitdown
github.com
December 16, 2024 at 3:04 AM
Woah! New Microsoft python packages convert from Office documents into Markdown! github.com/microsoft/ma...
Reposted by Atul Butte
Excited to share our latest paper evaluating large language models in assessing oncology radiology reports. Led by superstars Travis Zack and CPH student Li-Cheng Chen!
@atulbutte.bsky.social
Annotated reports included
@ucsf-bcshi.bsky.social @ucsfcancer.bsky.social
ascopubs.org/doi/10.1200/...
@atulbutte.bsky.social
Annotated reports included
@ucsf-bcshi.bsky.social @ucsfcancer.bsky.social
ascopubs.org/doi/10.1200/...
Assessing Large Language Models for Oncology Data Inference From Radiology Reports | JCO Clinical Cancer Informatics
PURPOSEWe examined the effectiveness of proprietary and open large language models (LLMs)
in detecting disease presence, location, and treatment response in pancreatic cancer
from radiology reports.ME...
ascopubs.org
December 11, 2024 at 10:18 PM
Excited to share our latest paper evaluating large language models in assessing oncology radiology reports. Led by superstars Travis Zack and CPH student Li-Cheng Chen!
@atulbutte.bsky.social
Annotated reports included
@ucsf-bcshi.bsky.social @ucsfcancer.bsky.social
ascopubs.org/doi/10.1200/...
@atulbutte.bsky.social
Annotated reports included
@ucsf-bcshi.bsky.social @ucsfcancer.bsky.social
ascopubs.org/doi/10.1200/...