Jake Lever
@jakelever.bsky.social
Lecturer at @uofgcompsci.bsky.social using machine learning to gather biomedical knowledge.
Pinned
Jake Lever
@jakelever.bsky.social
· Jul 15
Biomedical text mining for knowledge extraction @ ISMB 2025
A hands-on tutorial introducing biomedical natural language processing including named entity recognition, relation extraction and the power and limits of large language models.
ai4biomed.org
Had fun talking about biomedical information extraction with @javiersanzcruza.bsky.social today. Check out the materials from our #ISMBECCB2025 virtual tutorial. It's a mini intro course on #BioNLP! ai4biomed.org/ismb2025tuto...
Time for #BioNLP! @javiersanzcruza.bsky.social kicks off the workshop with our work on accelerating crossencoders for biomedical entity linking #acl2025
August 1, 2025 at 7:14 AM
Time for #BioNLP! @javiersanzcruza.bsky.social kicks off the workshop with our work on accelerating crossencoders for biomedical entity linking #acl2025
And that's the end of the text mining track at #ISMBECCB2025. So much cool work going on in this area
July 24, 2025 at 3:04 PM
And that's the end of the text mining track at #ISMBECCB2025. So much cool work going on in this area
Caralyn Reisle (@creisle.bsky.social) shows how language models can be used to verify claims in a big cancer knowledge base. A huge effort to create a fantastic benchmark set #ISMBECCB2025
July 24, 2025 at 1:12 PM
Caralyn Reisle (@creisle.bsky.social) shows how language models can be used to verify claims in a big cancer knowledge base. A huge effort to create a fantastic benchmark set #ISMBECCB2025
Lynn Schriml ( @diseaseontology.bsky.social ) gives a great talk on the Disease Ontology's philosophy of building a sustainable resource so that others can be confident to build upon it. 20+ years of the DO! academic.oup.com/nar/article/...
July 23, 2025 at 10:47 AM
Lynn Schriml ( @diseaseontology.bsky.social ) gives a great talk on the Disease Ontology's philosophy of building a sustainable resource so that others can be confident to build upon it. 20+ years of the DO! academic.oup.com/nar/article/...
Some beautiful and physically impossible predicted molecules from some AI models. Brilliant problems with AI from Charlotte Deane's keynote. The ring within a ring is particularly good! #ISMBECCB2025
July 23, 2025 at 8:34 AM
Some beautiful and physically impossible predicted molecules from some AI models. Brilliant problems with AI from Charlotte Deane's keynote. The ring within a ring is particularly good! #ISMBECCB2025
Creating a reasonable baseline (without fancy ML) is so important! Sometimes our ML methods aren't actually that good. Great example from Charlotte Deane in her Day 4 keynote #ISMBECCB2025
July 23, 2025 at 8:20 AM
Creating a reasonable baseline (without fancy ML) is so important! Sometimes our ML methods aren't actually that good. Great example from Charlotte Deane in her Day 4 keynote #ISMBECCB2025
Quick shout out for the Make Data Count challenge to improve data citation from @gigascience.bsky.social's Scott Edmunds. Looks cool and 💲prizes! #BOSC2025 #ISMBECCB2025 www.kaggle.com/competitions...
Make Data Count - Finding Data References
Identify scientific data use in papers and classify how they are mentioned.
www.kaggle.com
July 22, 2025 at 4:32 PM
Quick shout out for the Make Data Count challenge to improve data citation from @gigascience.bsky.social's Scott Edmunds. Looks cool and 💲prizes! #BOSC2025 #ISMBECCB2025 www.kaggle.com/competitions...
Keeping a data resource alive is a huge challenge. Lots of different guidelines being discussed in the #BOSC2025 panel for data resources including the O3 guidelines #ISMBECCB2025 www.nature.com/articles/s41...
The O3 guidelines: open data, open code, and open infrastructure for sustainable curated scientific resources - Scientific Data
Curated resources that support scientific research often go out of date or become inaccessible. This can happen for several reasons including lack of continuing funding, the departure of key personnel...
www.nature.com
July 22, 2025 at 4:15 PM
Keeping a data resource alive is a huge challenge. Lots of different guidelines being discussed in the #BOSC2025 panel for data resources including the O3 guidelines #ISMBECCB2025 www.nature.com/articles/s41...
Reposted by Jake Lever
Guy ending his talk telling the #BOSC2025 audience if they value global data infrastructure sign their open letter globalbiodata.org/open-letter-... #ISMBECCB2025
July 22, 2025 at 3:53 PM
Guy ending his talk telling the #BOSC2025 audience if they value global data infrastructure sign their open letter globalbiodata.org/open-letter-... #ISMBECCB2025
Biomedical data resources are essential for research but they're underfunded. Great to hear about the Global Biodata Coalition's mission to safeguard them. Time to sign their open letter! #ISMBECCB2025 globalbiodata.org/open-letter-...
OPEN LETTER CAMPAIGN - Global Biodata Coalition
Careers at the Global Biodata Coalition.
globalbiodata.org
July 22, 2025 at 3:58 PM
Biomedical data resources are essential for research but they're underfunded. Great to hear about the Global Biodata Coalition's mission to safeguard them. Time to sign their open letter! #ISMBECCB2025 globalbiodata.org/open-letter-...
Dystopian discussions about dealing with censorship in ontologies with the NCI deprecating transgender terms in the NCIT. Damien Goutte-Gattat gave a necessary but scary BOSC/BOKR talk about managing ontologies across borders. evsexplore.semantics.cancer.gov/evsexplore/c... #ISMBECCB2025
July 22, 2025 at 2:47 PM
Dystopian discussions about dealing with censorship in ontologies with the NCI deprecating transgender terms in the NCIT. Damien Goutte-Gattat gave a necessary but scary BOSC/BOKR talk about managing ontologies across borders. evsexplore.semantics.cancer.gov/evsexplore/c... #ISMBECCB2025
Ontologists do so much more than add new terms and curate papers! So many things to do, especially refactoring! Great BOSC/BOKR keynote from @cmungall.bsky.social #ISMBECCB2025
July 22, 2025 at 10:38 AM
Ontologists do so much more than add new terms and curate papers! So many things to do, especially refactoring! Great BOSC/BOKR keynote from @cmungall.bsky.social #ISMBECCB2025
Are AI agents having virtual lab meetings the future? Day 3 kicks off with a keynote from @jameszou.bsky.social. #ISMBECCB2025
July 22, 2025 at 8:08 AM
Are AI agents having virtual lab meetings the future? Day 3 kicks off with a keynote from @jameszou.bsky.social. #ISMBECCB2025
Some of the challenges in health data in the COALESCE study described by Angela Wood: people who died before they were born, pregnant men and having more patients registered at GPs than people in England #ISMBECCB2025 www.thelancet.com/journals/lan...
Undervaccination and severe COVID-19 outcomes: meta-analysis of national cohort studies in England, Northern Ireland, Scotland, and Wales
Rates of undervaccination against COVID-19 ranged from 32·8% to 49·8% across the four
UK nations in summer, 2022. Undervaccination was associated with an elevated risk
of severe COVID-19 outcomes.
www.thelancet.com
July 21, 2025 at 1:56 PM
Some of the challenges in health data in the COALESCE study described by Angela Wood: people who died before they were born, pregnant men and having more patients registered at GPs than people in England #ISMBECCB2025 www.thelancet.com/journals/lan...
Inspirational talk from @profbuchan.bsky.social on the amazing work going on in Liverpool, especially with the city's support for COVID work even in the face of fearmongering press news.liverpool.ac.uk/2025/03/07/5... #ISMBECCB2025
5 years since COVID-19: the University of Liverpool reflects - University of Liverpool News
5 years since COVID-19: the University of Liverpool reflects
news.liverpool.ac.uk
July 21, 2025 at 1:28 PM
Inspirational talk from @profbuchan.bsky.social on the amazing work going on in Liverpool, especially with the city's support for COVID work even in the face of fearmongering press news.liverpool.ac.uk/2025/03/07/5... #ISMBECCB2025
Brilliant results from DNA language models including an influence score that can differentiate benign and pathogenic variants from ClinVar. Great MLCSB talk from Julian Gagneur (@gagneurlab.bsky.social) #ISMBECCB2025
July 21, 2025 at 11:00 AM
Brilliant results from DNA language models including an influence score that can differentiate benign and pathogenic variants from ClinVar. Great MLCSB talk from Julian Gagneur (@gagneurlab.bsky.social) #ISMBECCB2025
Funding bioinformatics resources is getting even harder. Should we be charging industry for access? If we do, it needs to be seamless. Great keynote from Amos Bairoch to kick off Day 2 of #ISMBECCB2025
July 21, 2025 at 8:32 AM
Funding bioinformatics resources is getting even harder. Should we be charging industry for access? If we do, it needs to be seamless. Great keynote from Amos Bairoch to kick off Day 2 of #ISMBECCB2025
Had fun talking about biomedical information extraction with @javiersanzcruza.bsky.social today. Check out the materials from our #ISMBECCB2025 virtual tutorial. It's a mini intro course on #BioNLP! ai4biomed.org/ismb2025tuto...
Biomedical text mining for knowledge extraction @ ISMB 2025
A hands-on tutorial introducing biomedical natural language processing including named entity recognition, relation extraction and the power and limits of large language models.
ai4biomed.org
July 15, 2025 at 5:27 PM
Had fun talking about biomedical information extraction with @javiersanzcruza.bsky.social today. Check out the materials from our #ISMBECCB2025 virtual tutorial. It's a mini intro course on #BioNLP! ai4biomed.org/ismb2025tuto...