Paulina Nuñez-Valencia
@paulinanunezv.bsky.social
PhD student - Machine Learning for Conservation.
Dias&Frazer Lab @crg.eu with Mafalda Días and @jonnyfrazer.bsky.social
Dias&Frazer Lab @crg.eu with Mafalda Días and @jonnyfrazer.bsky.social
Reposted by Paulina Nuñez-Valencia
Applications are open for the @crg_eu PhD Programme! 20 fully funded positions — including one in our group through the Evolutionary Medical Genomics ITN.
Join us to develop deep generative models of cross-species data to tackle open questions in disease genetics.
www.crg.eu/en/content/t...
Join us to develop deep generative models of cross-species data to tackle open questions in disease genetics.
www.crg.eu/en/content/t...
October 23, 2025 at 11:01 AM
Applications are open for the @crg_eu PhD Programme! 20 fully funded positions — including one in our group through the Evolutionary Medical Genomics ITN.
Join us to develop deep generative models of cross-species data to tackle open questions in disease genetics.
www.crg.eu/en/content/t...
Join us to develop deep generative models of cross-species data to tackle open questions in disease genetics.
www.crg.eu/en/content/t...
Check out our new preprint!
How can we get more out of existing protein/genome language models without retraining them?
How can we get more out of existing protein/genome language models without retraining them?
New preprint in collaboration with @paulinanunezv.bsky.social supervised by @jonnyfrazer.bsky.social and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models
Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biolog...
www.biorxiv.org
May 26, 2025 at 8:31 PM
Check out our new preprint!
How can we get more out of existing protein/genome language models without retraining them?
How can we get more out of existing protein/genome language models without retraining them?
Reposted by Paulina Nuñez-Valencia
Awesome paper. Simple post-hoc trick (averaging over homologs) with elegant evolution theory dramatically improves zero shot coding variant effect prediction in pLMs & actually delivers better results from the larger models (inverting the trend with raw likelihoods). 1/
From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models https://www.biorxiv.org/content/10.1101/2025.05.20.655154v1
May 26, 2025 at 9:40 AM
Awesome paper. Simple post-hoc trick (averaging over homologs) with elegant evolution theory dramatically improves zero shot coding variant effect prediction in pLMs & actually delivers better results from the larger models (inverting the trend with raw likelihoods). 1/
Reposted by Paulina Nuñez-Valencia
May 22, 2025 at 10:29 AM
Reposted by Paulina Nuñez-Valencia
Proud supervisor moment! Next up at #VariantEffect25: Charles Pugh @cwjpugh.bsky.social, PhD student in Mafalda’s and my group, presents: From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models #AI #ProteinML
May 22, 2025 at 10:10 AM
Proud supervisor moment! Next up at #VariantEffect25: Charles Pugh @cwjpugh.bsky.social, PhD student in Mafalda’s and my group, presents: From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models #AI #ProteinML
Reposted by Paulina Nuñez-Valencia
A lovely summary of what we have learnt about scaling from ProteinGym -- Have we reached a performance plateau? More on this later in the week from @cwjpugh.bsky.social
May 21, 2025 at 8:55 AM
A lovely summary of what we have learnt about scaling from ProteinGym -- Have we reached a performance plateau? More on this later in the week from @cwjpugh.bsky.social