You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I am trying to pretrain scGPT for in a small dataset and I am using the pipeline in the dev-temp branch (I merged it with the main branch). After solving the issues related to library version\flash-attn I finally make the pretrain.py works! But I found the train loss is a little bit strange.
This is part of the training log:
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - | end of epoch 186 | time: 8.76s | valid loss/mse 157.0726 | mre 1.4009
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - Saving the best model to ./save/eval-Mar25-14-06-2024
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - | end of epoch 187 | time: 8.13s | valid loss/mse 158.1381 | mre 1.4314
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - | end of epoch 188 | time: 5.81s | valid loss/mse 157.6718 | mre 1.3989
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - | end of epoch 189 | time: 6.14s | valid loss/mse 158.9929 | mre 1.4236
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - | end of epoch 190 | time: 8.69s | valid loss/mse 158.0198 | mre 1.4282
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - | end of epoch 191 | time: 8.16s | valid loss/mse 158.5909 | mre 1.4189
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - | end of epoch 192 | time: 9.12s | valid loss/mse 158.4677 | mre 1.4159
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - | end of epoch 193 | time: 8.12s | valid loss/mse 158.7186 | mre 1.4422
scGPT - INFO - -----------------------------------------------------------------------------------------
scGPT - INFO - -----------------------------------------------------------------------------------------
You can see the valid loss is pretty large and the mre is increasing.
Hi, thank you for such wondorful work!
I am trying to pretrain scGPT for in a small dataset and I am using the pipeline in the dev-temp branch (I merged it with the main branch). After solving the issues related to library version\flash-attn I finally make the pretrain.py works! But I found the train loss is a little bit strange.
This is part of the training log:
You can see the valid loss is pretty large and the mre is increasing.
My training command is:
I was wondering how normal train looks like and any help are welcome!
The text was updated successfully, but these errors were encountered: