Jamie Morton

Here is an example of this bug readout. ``` Traceback (most recent call last): File "/mnt/home/jmorton/miniconda3/envs/catvae/bin/linear-vae-train.py", line 7, in exec(compile(f.read(), __file__, 'exec')) File "/mnt/home/jmorton/research/catvae/scripts/linear-vae-train.py", line 56, in main(args) File "/mnt/home/jmorton/research/catvae/scripts/linear-vae-train.py",...

Hi @taylorreiter, thank you for reaching out - it sounds like a cool problem. 1. Could you clarify the input data type? Are you dealing with a count table of...

Right. When I refer to dimensionality, I typically refer to samples (rows) x microbes (columns) -- where the goal is to infer microbe-microbe correlations (aka column-column correlations). In order for...

Hi, you'll need to give more detail on what you are running. How many sequences are you inputting? And did you try the tutorial? On Mon, Jan 1, 2024 at...

Hi, those contain the vector embeddings, which can be used for downstream ML / search On Tue, Jan 2, 2024 at 7:40 AM Aurorajwy ***@***.***> wrote: > I used just...

Hmm, there should be alignments. Can you paste the command that you used and the full error message? You may need to specify the alignment flag. I’ll try to reproduce...

Hi, I've rerun the command on my end, had to change a few things to match the tutorial files (and to make it run within 1 hour) ``` head -n...

Hi, you need a couple of intermediate steps to do end-to-end training. I'd start with the training script https://github.com/flatironinstitute/deepblast/blob/master/scripts/deepblast-trai I"m not sure what you are trying to accomplish with your...

I see the confusion. The `aln` matrix here is the expected traceback matrix (i.e. the e matrix in algorithm 1 in the paper : https://www.nature.com/articles/s41587-023-01917-2#Sec10) Also see equation 11 here...

Hi yes this is by construction -- we zero out the first row / column to make autograd work ...