Niksa Praljak

icon company PhD student at the University of Chicago icon location Chicago, IL icon location PhD Student at the University of Chicago

Results 6 issues of Niksa Praljak

Is 'n_training_epochs' working for parameteric UMAP?

I set `n_training_epochs` to `args.epochs`, where `args.epochs` is 1. Of course, I plan to change this after I complete the fast development. However, it appears that parameteric_umap.fit_transform() leads to 10...

Question: how can we do profile alignment using FAMSA?

I see that FAMSA allows for straightforward profile-profile alignment between MSAs using the following command: ```bash # profile-profile alignment without refining output ./famsa -refine_mode off ./test/adeno_fiber/upgma.no_refine.part1.fasta ./test/adeno_fiber/upgma.no_refine.part2.fasta pp.fasta ``` It...

Where can I find the expression values reported in the paper?

Awesome work! In figure 4 of the paper, the plot compares synthetic and designed nanobodies in terms of their expression levels (fluorescence AU). Where can I find the synthetic and...

Is it possible to use Tecan Fluent as backend?

4 comment

I enjoyed reading the peer-reviewer paper on pylabrobot! Question: I noticed that the wrapper is OS-agnostic and even robot-agnostic. It can even handle Tecan Evo as the backend. However, is...

enhancement: is it possible to adapt DiT architecture with Flash Attention?

Great work! Out of curiosity, what will it take to adapter DiT architecture for protein sequence generation with FLASH attention or other similar memory efficient attention mechanism?

General Question on Classifier-Free Guidance

Awesome repo on Discrete Flow Matching! Q: Is it posisble to do classifier-free guidance with "discrete" flow matching? I know that there is implementation with conditional flow matching on continuous...