Aziz Zafar
@aziz-zafar.bsky.social
Ph.D. Student at Columbia University Biomedical Informatics | Machine Learning for Genomics.
Aspiring scientific educator with a love for writing and parks.
Aspiring scientific educator with a love for writing and parks.
How can we better understand pathogenic variants in intrinsically disordered regions (IDRs)? How do models such as AlphaMissense and ESM1b predict pathogenicity, when these regions typically exhibit lower genomic conservation than ordered regions? Read more:
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Molecular dynamics simulations of intrinsically disordered protein regions enable biophysical interpretation of variant effect predictors
Predictive models for missense variant pathogenicity offer little functional interpretation for intrinsically disordered regions, since they rely on conservation and coevolution across homologous sequ...
doi.org
May 13, 2025 at 2:15 PM
How can we better understand pathogenic variants in intrinsically disordered regions (IDRs)? How do models such as AlphaMissense and ESM1b predict pathogenicity, when these regions typically exhibit lower genomic conservation than ordered regions? Read more:
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Reposted by Aziz Zafar
Protein language model likelihood are better zero shot mutation effect predictions when they have perplexity 3-6 on the wildtype sequence.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 30, 2025 at 6:18 PM
Protein language model likelihood are better zero shot mutation effect predictions when they have perplexity 3-6 on the wildtype sequence.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Aziz Zafar
Why do large protein language models like ESM2-15B underperform compared to medium-sized ones like ESM2-650M in predicting mutation effects? 🤔
We dive into this issue in our new preprint—bringing insights into model scaling on mutation effect prediction. 🧬📉
We dive into this issue in our new preprint—bringing insights into model scaling on mutation effect prediction. 🧬📉
April 29, 2025 at 5:54 PM
Why do large protein language models like ESM2-15B underperform compared to medium-sized ones like ESM2-650M in predicting mutation effects? 🤔
We dive into this issue in our new preprint—bringing insights into model scaling on mutation effect prediction. 🧬📉
We dive into this issue in our new preprint—bringing insights into model scaling on mutation effect prediction. 🧬📉