decoding life at scale
https://glcnd.io/transformers-propel-breakthroughs-in-genome-language-modeling/
#GenomicsAI #Transformers #BioNLP #LifeCode

includes 9 common datasets spanning four major BioNLP tasks. Our experimental results demonstrate consistent performance improvements across all tasks, highlighting the effectiveness of our approach in addressing the challenges associated with data [7/8 of https://arxiv.org/abs/2503.23673v1]

Today and tomorrow: a large number of workshops and colocated conferences. We still have three papers to present. Today I'll present in the poster session in REALM, tomorrow Lynn Greschner presents in BioNLP and Sean Papay in XLLM.

workload. On the BioNLP ACL'24 Discharge Me! Shared Task, we achieve new state-of-the-art results with simpler methods than prior submissions through more efficient training, yielding a 9\% relative improvement without [3/5 of https://arxiv.org/abs/2502.17571v1]

❗Stellenangebot:

Wir suchen eine:n wissenschaftliche:n Mitarbeiter:in (m/w/d) im Bereich biomedizinisches Machine Learning/Data Science/Natural Language Processing.

Alle Infos:
➡️https://www.zbmed.de/ueber-uns/karriere/stellenausschreibungen/wissenschaftlicher-mitarbeiterin-im-bereich-bionlp

#IJCAIworkshop The 9th BioCreative Challenge andWorkshop (BC9): Large Language Models for Clinical and Biomedical NLP #Regstration: 30 April #CFP Paper submission deadline: 5 May 2025 🌐https://www.ncbi.nlm.nih.gov/research/bionlp/biocreative9

#IJCAI2025 #Research #Innovation

We have five #nlproc papers accepted at @aclmeeting.bsky.social – after just one year in @uni-bamberg.de . Hope to meeting many of you in Vienna!

Hervorragende Fähigkeiten in der Entwicklung von KI-Programmen bewiesen die FH-Dortmund-Promovend*innen Tabea Pakull und Hendrik Damm beim BioNLP-Wettbewerb. Gleich zweimal belegten sie als Team des Graduiertenkollegs WisPerMed einen sehr guten Platz: www.fh-dortmund.de/news/wisperm...

Third is Das et. al https://aclanthology.org/2022.bionlp-1.27 who propose to expose psychologically vulnerable people to conversational bots trained on Reddit, which frankly is every bit as bad an idea as it sounds (the words "ethics" and "risk" do not occur in the paper 🤷)...

arXiv:2503.23673v1 Announce Type: new
Abstract: In Biomedical Natural Language Processing (BioNLP) tasks, such as Relation Extraction, Named Entity Recognition, and Text Classification, the scarcity of high-quality data remains a significant [1/8 of https://arxiv.org/abs/2503.23673v1]

“…our conclusion is that President Reagan had signs of Alzheimer’s sometime between 1983 and 1988. … corroborates results from other studies …

…was publicly disclosed only in November 1994.”

https://aclanthology.org/2020.bionlp-1.14.pdf https://aclanthology.org/2020.bionlp-1.14.pdf

If you’re at #IJCAI2025 / Biocreative, come see my talk at 2pm in room 524A.

BioNLP evaluation in the era of LLMs

coverage includes:

BC4CHEMD,
BC5CDR (chem + disease),
BC2GM,
JNLPBA,
BioNLP 2013 CG,
GELLUS,
FSU,
CLL,
Anatomy (AnatEM),
Linnaeus,
Species‑800,
NCBI‑Disease.

pick a size to match latency/accuracy needs and your deployment constraints.

🧵 (5/6)

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

#acl2022nlp #bionlp

🚨 New paper out! 🚨
We built a co-citation-based transformer model that supercharges scientific document embeddings — optimized for the complexity of biomedical literature.

📖: www.nature.com/articles/s41...

#AI4Science #BioNLP #Transformers #SemanticSearch #VectorDatabases #ML4Biomed

A Study of Calibration as a Measurement of Trustworthiness of Large Language Models in Biomedical Research [new]
BioNLP LLM trust calibration uses new metric. Post-hoc boosts biomed apps.

Here's the paper link: aclanthology.org/2025.bionlp-... #acl2025