Philip Bradley

Thanks! You could try replacing " --all " with " --tcr_clumping " but it will still take a little while, I'm afraid. That is a lot of convergent TCR clusters!...

Hi Mark, Thanks for your interest in CONGA! Right now, the iMHC scores are not written out or explicitly saved in the AnnData (adata) object. They are computed on the...

Hi there, That looks like the production command line to me. For our parameter set, we stopped training after 2 epochs (2 times through all the training examples). Let me...

Hi there, Can you tell how far the command has gotten, for example by looking at some of the log messages? It will run for 10 epochs by default, but...

Thanks for the heads up! Let me see if I can reproduce this and try to figure out what's going on. I bet you are right that it's a GPU...

Hi Bear, Thanks for trying this out! THese are all great questions. As you can see, TCR specificity prediction is a very hard problem. Here are a few thoughts: *...

Hi Bear, Right, it would be generating (and finding!) more binding data for training the models. Though more structure would certainly help, too. They are just harder to come by......

Hi there, Thanks for the positive feedback, and apologies for my slowness replying (travel). I added a new answer to the 'Frequently Asked Questions' section of the CoNGA README. Let...

Right now the main thing is visualizing the batch composition of the conga clusters, tcr clumping groups, and g-v-f and hotspot clustermaps. If the list of `adata.obs` batch column names...

Thanks for the update! The batch column names do need to be set in adata.uns['batch_keys'] before reducing to a single cell per TCR, so that the batch composition of clonotypes...