Raul Rodriguez-Esteban
@raulrod.bsky.social
Data science, text & data mining, machine learning, information science at Roche Pharmaceuticals research & development. Posts are mine.
Pinned
The lived experience of social anxiety disorder: A conceptual model based on published literature and social media listening
Social anxiety disorder (SAD) affects up to 1 in 8 individuals over their lifetime and is characterized by an intense fear of social situations where there may be exposure to unfamiliar people or poss...
www.medrxiv.org
How to understand patients who do not want to contact healthcare professionals? Our latest preprint deals with this topic: "The lived experience of social anxiety disorder: A conceptual model based on published literature and social media listening." www.medrxiv.org/content/10.1...
Reposted by Raul Rodriguez-Esteban
Just 1 week to go to the Annual General Meeting.
There'll be a short update on ISB business, followed by talks from our Early and Advanced Career Award Winners, Tiago Lubiana and Kimberly Van Auken.
All are welcome. You do not need to be an ISB member to attend.
Sign up: forms.gle/wDX7MGHQwgoz...
There'll be a short update on ISB business, followed by talks from our Early and Advanced Career Award Winners, Tiago Lubiana and Kimberly Van Auken.
All are welcome. You do not need to be an ISB member to attend.
Sign up: forms.gle/wDX7MGHQwgoz...
ISB 2025 Annual General Meeting Registration
The International Society for Biocuration (ISB) will hold its Annual General Meeting (AGM) on Monday, October 27th, 2025 along with presentations by our two biocurator career award winners, Tiago Lubi...
forms.gle
October 20, 2025 at 2:48 PM
Just 1 week to go to the Annual General Meeting.
There'll be a short update on ISB business, followed by talks from our Early and Advanced Career Award Winners, Tiago Lubiana and Kimberly Van Auken.
All are welcome. You do not need to be an ISB member to attend.
Sign up: forms.gle/wDX7MGHQwgoz...
There'll be a short update on ISB business, followed by talks from our Early and Advanced Career Award Winners, Tiago Lubiana and Kimberly Van Auken.
All are welcome. You do not need to be an ISB member to attend.
Sign up: forms.gle/wDX7MGHQwgoz...
Reposted by Raul Rodriguez-Esteban
DT-GPT: showing that LLMs can forecast patient trajectories (1/10)
Now in npj Digital Medicine www.nature.com/articles/s41...
Also in Doctor Penguin!
Big thanks to Maria Bordukova, @raulrod.bsky.social Papichaya Quengdaeng Daniel Garger @fschmich.bsky.social Michael Menden Helmholtz Munich Roche
Now in npj Digital Medicine www.nature.com/articles/s41...
Also in Doctor Penguin!
Big thanks to Maria Bordukova, @raulrod.bsky.social Papichaya Quengdaeng Daniel Garger @fschmich.bsky.social Michael Menden Helmholtz Munich Roche
October 7, 2025 at 7:36 AM
DT-GPT: showing that LLMs can forecast patient trajectories (1/10)
Now in npj Digital Medicine www.nature.com/articles/s41...
Also in Doctor Penguin!
Big thanks to Maria Bordukova, @raulrod.bsky.social Papichaya Quengdaeng Daniel Garger @fschmich.bsky.social Michael Menden Helmholtz Munich Roche
Now in npj Digital Medicine www.nature.com/articles/s41...
Also in Doctor Penguin!
Big thanks to Maria Bordukova, @raulrod.bsky.social Papichaya Quengdaeng Daniel Garger @fschmich.bsky.social Michael Menden Helmholtz Munich Roche
Reposted by Raul Rodriguez-Esteban
A new model, DT-GPT, uses LLMs to forecast patient health trajectories, enabling "digital twins." By processing raw EHR data, it outperformed state-of-the-art methods in cancer, ICU, and Alzheimer's cohorts and can even forecast untrained variables.
#MedSky #MedAI #MLSky
#MedSky #MedAI #MLSky
Large language models forecast patient health trajectories enabling digital twins - npj Digital Medicine
npj Digital Medicine - Large language models forecast patient health trajectories enabling digital twins
www.nature.com
October 2, 2025 at 2:47 PM
Reposted by Raul Rodriguez-Esteban
Ever-interesting Rod Brooks on how the challenges of touch are a barrier to achieving human-level dexterity in robots. Unlike language and sight, we can't get good training data for touch (nor, I might add, for olfaction, proprioception, pain, and interoception). rodneybrooks.com/why-todays-h...
Why Today’s Humanoids Won’t Learn Dexterity – Rodney Brooks
rodneybrooks.com
September 28, 2025 at 2:26 AM
Ever-interesting Rod Brooks on how the challenges of touch are a barrier to achieving human-level dexterity in robots. Unlike language and sight, we can't get good training data for touch (nor, I might add, for olfaction, proprioception, pain, and interoception). rodneybrooks.com/why-todays-h...
Reposted by Raul Rodriguez-Esteban
The ISB Annual General Meeting is coming up on October 27th. Register to hear what the society has been working on and to hear from our career award winners!
forms.gle/tC5TMZ2ZvFAD...
forms.gle/tC5TMZ2ZvFAD...
ISB 2025 Annual General Meeting Registration
The International Society for Biocuration (ISB) will hold its Annual General Meeting (AGM) on Monday, October 27th, 2025 along with presentations by our two biocurator career award winners, Tiago Lubi...
forms.gle
September 17, 2025 at 8:47 PM
The ISB Annual General Meeting is coming up on October 27th. Register to hear what the society has been working on and to hear from our career award winners!
forms.gle/tC5TMZ2ZvFAD...
forms.gle/tC5TMZ2ZvFAD...
Reposted by Raul Rodriguez-Esteban
Reposted by Raul Rodriguez-Esteban
The ISB Annual General Meeting is on October 27th at 4:00–6:00 pm CST / 3:00–5:00 pm GMT / 11:00 am–1:00 pm EDT / 8:00 am–10:00 am PDT We'll have an update on the society, followed by talks from our career award winners: Tiago Lubiana and Kimberly Van Auken
Register: forms.gle/sDVMzfrYBD7T...
Register: forms.gle/sDVMzfrYBD7T...
forms.gle
September 5, 2025 at 2:19 PM
The ISB Annual General Meeting is on October 27th at 4:00–6:00 pm CST / 3:00–5:00 pm GMT / 11:00 am–1:00 pm EDT / 8:00 am–10:00 am PDT We'll have an update on the society, followed by talks from our career award winners: Tiago Lubiana and Kimberly Van Auken
Register: forms.gle/sDVMzfrYBD7T...
Register: forms.gle/sDVMzfrYBD7T...
Reposted by Raul Rodriguez-Esteban
Late to share here on bsky, but so happy with this award!
Also: ISB is a beautiful society; if you care about organizing bio data/knowledge, you might benefit from joining it!
Also: ISB is a beautiful society; if you care about organizing bio data/knowledge, you might benefit from joining it!
Exceptional Contributions to Biocuration - Early Career Award winner: Tiago Lubiano.
Tiago's a passionate and motivated scientist interested in linked open data, ontologies, the semantic web, and their application in modeling cells and cell types. He is active in many curation projects & with ISB.
Tiago's a passionate and motivated scientist interested in linked open data, ontologies, the semantic web, and their application in modeling cells and cell types. He is active in many curation projects & with ISB.
August 25, 2025 at 4:54 PM
Late to share here on bsky, but so happy with this award!
Also: ISB is a beautiful society; if you care about organizing bio data/knowledge, you might benefit from joining it!
Also: ISB is a beautiful society; if you care about organizing bio data/knowledge, you might benefit from joining it!
Reposted by Raul Rodriguez-Esteban
What is happening to FlyBase and all the great people there is such a loss to the #Biocuration and #Bioinformatics community. Highly recommend anyone with openings to take the opportunity to employee these folks!
I just got the notice that all the FlyBase people at Harvard, including me, will be laid off on October 12. I'm devastated.
August 12, 2025 at 6:51 PM
What is happening to FlyBase and all the great people there is such a loss to the #Biocuration and #Bioinformatics community. Highly recommend anyone with openings to take the opportunity to employee these folks!
Reposted by Raul Rodriguez-Esteban
The 19th International Biocuration Conference is coming to 🌍 Cape Town, South Africa, April 20–24, 2026!
Hosted by:
@abinstitute.bsky.social
@biocurator.bsky.social
AfriGen-D & SADaCC
🔗 Info: bioinformaticsinstitute.africa/events/6/19t...
📬 Mailing list: bioinformaticsinstitute.africa/mailing-list
Hosted by:
@abinstitute.bsky.social
@biocurator.bsky.social
AfriGen-D & SADaCC
🔗 Info: bioinformaticsinstitute.africa/events/6/19t...
📬 Mailing list: bioinformaticsinstitute.africa/mailing-list
August 1, 2025 at 3:04 PM
The 19th International Biocuration Conference is coming to 🌍 Cape Town, South Africa, April 20–24, 2026!
Hosted by:
@abinstitute.bsky.social
@biocurator.bsky.social
AfriGen-D & SADaCC
🔗 Info: bioinformaticsinstitute.africa/events/6/19t...
📬 Mailing list: bioinformaticsinstitute.africa/mailing-list
Hosted by:
@abinstitute.bsky.social
@biocurator.bsky.social
AfriGen-D & SADaCC
🔗 Info: bioinformaticsinstitute.africa/events/6/19t...
📬 Mailing list: bioinformaticsinstitute.africa/mailing-list
Reposted by Raul Rodriguez-Esteban
Voting for the 2025 #Biocuration Career Awards has ended. We would like to thank all the nominees, nominators, and voters. These awards celebrate all of the hard work biocurators do everyday to make data FAIR. The winners are:
July 30, 2025 at 4:04 PM
Voting for the 2025 #Biocuration Career Awards has ended. We would like to thank all the nominees, nominators, and voters. These awards celebrate all of the hard work biocurators do everyday to make data FAIR. The winners are:
Reposted by Raul Rodriguez-Esteban
The 19th International Biocuration Conference is coming to 🌍 Cape Town, South Africa -April 20–24, 2026
Hosted by @abinstitute.bsky.social with @biocurator.bsky.social , AfriGen-D & SADaCC
🔗 Info: bioinformaticsinstitute.africa/news-events/6
📬Mailing list: bioinformaticsinstitute.africa/mailing-list
Hosted by @abinstitute.bsky.social with @biocurator.bsky.social , AfriGen-D & SADaCC
🔗 Info: bioinformaticsinstitute.africa/news-events/6
📬Mailing list: bioinformaticsinstitute.africa/mailing-list
July 7, 2025 at 12:59 PM
The 19th International Biocuration Conference is coming to 🌍 Cape Town, South Africa -April 20–24, 2026
Hosted by @abinstitute.bsky.social with @biocurator.bsky.social , AfriGen-D & SADaCC
🔗 Info: bioinformaticsinstitute.africa/news-events/6
📬Mailing list: bioinformaticsinstitute.africa/mailing-list
Hosted by @abinstitute.bsky.social with @biocurator.bsky.social , AfriGen-D & SADaCC
🔗 Info: bioinformaticsinstitute.africa/news-events/6
📬Mailing list: bioinformaticsinstitute.africa/mailing-list
Reposted by Raul Rodriguez-Esteban
I heard this morning that my informatics colleague Dr. Atul Butte passed after a battle with cancer. He was a giant in the field & inspired many of us over his distinguished career. He was a passionate champion of the power of big data & his impact on our field is immeasurable. RIP Atul & thanks.
June 14, 2025 at 1:20 PM
I heard this morning that my informatics colleague Dr. Atul Butte passed after a battle with cancer. He was a giant in the field & inspired many of us over his distinguished career. He was a passionate champion of the power of big data & his impact on our field is immeasurable. RIP Atul & thanks.
Reposted by Raul Rodriguez-Esteban
We've extended the nomination deadline for #Biocuration career awards until Friday, June 13. Nomination forms www.biocuration.org/nominations-...
Please nominate your favorite biocurator!
Please nominate your favorite biocurator!
Nominations Open for 2025 Biocuration Awards – International Society for Biocuration
www.biocuration.org
June 9, 2025 at 9:39 PM
We've extended the nomination deadline for #Biocuration career awards until Friday, June 13. Nomination forms www.biocuration.org/nominations-...
Please nominate your favorite biocurator!
Please nominate your favorite biocurator!
"This study compared fine-tuned LLMs (LLaMA2-13B and LLaMA3-8B) against BioMedICUS, a rule-based IE system, for extracting symptoms [...] BioMedICUS outperformed fine-tuned LLMs in most cases." journals.plos.org/plosone/arti...
A comparative analysis of large language models versus traditional information extraction methods for real-world evidence of patient symptomatology in acute and post-acute sequelae of SARS-CoV-2
Background Patient symptoms, crucial for disease progression and diagnosis, are often captured in unstructured clinical notes. Large language models (LLMs) offer potential advantages in extracting pat...
journals.plos.org
June 4, 2025 at 1:40 PM
"This study compared fine-tuned LLMs (LLaMA2-13B and LLaMA3-8B) against BioMedICUS, a rule-based IE system, for extracting symptoms [...] BioMedICUS outperformed fine-tuned LLMs in most cases." journals.plos.org/plosone/arti...
Reposted by Raul Rodriguez-Esteban
#drosophila @flybase.bsky.social request emergency funding:
"As it stands, by the end of July, 2025, there will be no future updates to FlyBase, and in the worst case scenario access to the website will also be lost" => please donate!
www.philanthropy.cam.ac.uk/give-to-camb...
"As it stands, by the end of July, 2025, there will be no future updates to FlyBase, and in the worst case scenario access to the website will also be lost" => please donate!
www.philanthropy.cam.ac.uk/give-to-camb...
Drosophila Genetic Database
The Drosophila Genetic Database, FlyBase, is on the brink of collapse due to the sudden termination of the FlyBase NIH grant, which includes salaries for 5 literature curators based at the University ...
www.philanthropy.cam.ac.uk
June 3, 2025 at 4:15 PM
#drosophila @flybase.bsky.social request emergency funding:
"As it stands, by the end of July, 2025, there will be no future updates to FlyBase, and in the worst case scenario access to the website will also be lost" => please donate!
www.philanthropy.cam.ac.uk/give-to-camb...
"As it stands, by the end of July, 2025, there will be no future updates to FlyBase, and in the worst case scenario access to the website will also be lost" => please donate!
www.philanthropy.cam.ac.uk/give-to-camb...
Reposted by Raul Rodriguez-Esteban
Just a few days left to nominate a deserving curator for one of the Biocuration Career Awards (1/6)
#Biocuration
#Biocuration
May 27, 2025 at 6:32 PM
Just a few days left to nominate a deserving curator for one of the Biocuration Career Awards (1/6)
#Biocuration
#Biocuration
Reposted by Raul Rodriguez-Esteban
Still time to submit your nominations! #biocuration
Nominations are open for the 2025 Excellence in Biocuration Awards
1. Early Career Award (forms.gle/pGABYnqSqPgi...)
2. Advanced Career Award (forms.gle/Tyfa25BcrM8e...)
3. Exceptional Contribution to Biocuration (i.e., lifetime award; forms.gle/3E2b85eSteao...)
1. Early Career Award (forms.gle/pGABYnqSqPgi...)
2. Advanced Career Award (forms.gle/Tyfa25BcrM8e...)
3. Exceptional Contribution to Biocuration (i.e., lifetime award; forms.gle/3E2b85eSteao...)
Excellence in Curation - Early Career Award Nominations
This award has been created to promote people who have been working in the field of biocuration for less than 7 years. The nominee will be in a non-leadership position and will have made a sustained c...
forms.gle
May 15, 2025 at 9:30 PM
Still time to submit your nominations! #biocuration
Reposted by Raul Rodriguez-Esteban
Don’t miss the Basel Computational Biology Conference [BC]2 8–10 Sept., 2025 Basel, Switzerland
Keynotes: Serena Nik-Zainal (Univ. of Cambridge, UK), Peer Bork (EMBL Heidelberg, Germany) & Julia Merkenschlager (Harvard Medical School, USA)
Early bird reg. ends 30 June!
www.bc2.ch/registration...
Keynotes: Serena Nik-Zainal (Univ. of Cambridge, UK), Peer Bork (EMBL Heidelberg, Germany) & Julia Merkenschlager (Harvard Medical School, USA)
Early bird reg. ends 30 June!
www.bc2.ch/registration...
April 23, 2025 at 4:11 PM
Don’t miss the Basel Computational Biology Conference [BC]2 8–10 Sept., 2025 Basel, Switzerland
Keynotes: Serena Nik-Zainal (Univ. of Cambridge, UK), Peer Bork (EMBL Heidelberg, Germany) & Julia Merkenschlager (Harvard Medical School, USA)
Early bird reg. ends 30 June!
www.bc2.ch/registration...
Keynotes: Serena Nik-Zainal (Univ. of Cambridge, UK), Peer Bork (EMBL Heidelberg, Germany) & Julia Merkenschlager (Harvard Medical School, USA)
Early bird reg. ends 30 June!
www.bc2.ch/registration...
Reposted by Raul Rodriguez-Esteban
Call for proposals to host the 2027 Biocuration conference is live! If you're in Asia/Oceania and interested in hosting please take a look. If you have questions please reach out to any member of the Executive Committee and we'll do our best to answer.
www.biocuration.org/call-for-pro...
www.biocuration.org/call-for-pro...
Call for Proposals to host the 2027 International Biocuration Conference. – International Society for Biocuration
www.biocuration.org
April 17, 2025 at 6:24 PM
Call for proposals to host the 2027 Biocuration conference is live! If you're in Asia/Oceania and interested in hosting please take a look. If you have questions please reach out to any member of the Executive Committee and we'll do our best to answer.
www.biocuration.org/call-for-pro...
www.biocuration.org/call-for-pro...
so the BERT/BART models are still better for text simplification, text summarization, document classification and entity recognition. But the GPT-type models are better at question answering
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Benchmarking large language models for biomedical natural language processing applications and recommendations - Nature Communications
Baseline performance, benchmarks, and guidance for LLMs in biomedicine are limited. The authors assess four LLMs on 12 tasks, establish baselines, examine hallucinations, and provide recommendations f...
www.nature.com
April 9, 2025 at 9:26 AM
so the BERT/BART models are still better for text simplification, text summarization, document classification and entity recognition. But the GPT-type models are better at question answering
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Raul Rodriguez-Esteban
can't really just use an LM as a surrogate for the world or a person. its internal causal model is pretty bespoke. GPT-2 and Llama have very different causal models of the world.
April 5, 2025 at 12:44 AM
can't really just use an LM as a surrogate for the world or a person. its internal causal model is pretty bespoke. GPT-2 and Llama have very different causal models of the world.
Reposted by Raul Rodriguez-Esteban
The 18th Annual International Biocuration Conference (stowers.org/events/biocu...) is just a few days away! 🎉 We’re excited to meet you at our upcoming:
-Workshop, 'AI and Biodata Resources: Implications for Sustainability and Best Practices in Biocuration' this weekend.
-Workshop, 'AI and Biodata Resources: Implications for Sustainability and Best Practices in Biocuration' this weekend.
18th Annual International Biocuration Conference
Organized by Sofia Robb, Chris Seidel, and Sue Bello Hosted by the Stowers Institute for Medical Research
stowers.org
April 2, 2025 at 7:30 PM
The 18th Annual International Biocuration Conference (stowers.org/events/biocu...) is just a few days away! 🎉 We’re excited to meet you at our upcoming:
-Workshop, 'AI and Biodata Resources: Implications for Sustainability and Best Practices in Biocuration' this weekend.
-Workshop, 'AI and Biodata Resources: Implications for Sustainability and Best Practices in Biocuration' this weekend.
Reposted by Raul Rodriguez-Esteban
We have a survey up collecting information about the field of biocuration. This information will be incorporated into the biocuration careers workshop during the #Biocuration2025 conference.
forms.gle/QGfRoC3caFcU...
forms.gle/QGfRoC3caFcU...
Biocuration Community Survey 2025
This survey aims to gather and analyze information about the field of biocuration.
This survey is being conducted by the International Society for Biocuration (ISB) to identify potential gaps or ineq...
forms.gle
March 6, 2025 at 4:51 PM
We have a survey up collecting information about the field of biocuration. This information will be incorporated into the biocuration careers workshop during the #Biocuration2025 conference.
forms.gle/QGfRoC3caFcU...
forms.gle/QGfRoC3caFcU...
Reposted by Raul Rodriguez-Esteban
PUBMED is down. This is disaster !!
We do not have the system and organization to replace it. (EuroPMC is great but not a replacement)
It is crystal clear that we cannot depend on critical systems provided by a single provider.
European reaction has to include science and science infrastructures.
We do not have the system and organization to replace it. (EuroPMC is great but not a replacement)
It is crystal clear that we cannot depend on critical systems provided by a single provider.
European reaction has to include science and science infrastructures.
March 2, 2025 at 10:18 AM
PUBMED is down. This is disaster !!
We do not have the system and organization to replace it. (EuroPMC is great but not a replacement)
It is crystal clear that we cannot depend on critical systems provided by a single provider.
European reaction has to include science and science infrastructures.
We do not have the system and organization to replace it. (EuroPMC is great but not a replacement)
It is crystal clear that we cannot depend on critical systems provided by a single provider.
European reaction has to include science and science infrastructures.