How to improve integration

[fe4960]

Hello,

Thanks for developing this great software. It has helped me a lot for integration of unpaired snRNA and snATAC. I recently run another dataset with my previous script following the scglue tutorial. The only difference between my script and the tutorial is that I used the 20% of top ranking variable peaks identified by episcanpy and 5000 hvg, which work quite well for all my previous scGlue analysis, since I have many cells and peaks. However, the result from the most recent analysis seems not optimal.

In the plot above, the "Unknown" label indicates the snATAC cells, while the rest labels are the snRNA cell types. It looks like snATAC doesn't integrate with snRNA well.

Here is the output of integration steps. Could you help take a look and suggest how to improve the integration? Thanks very much! @Jeff1995

[INFO] fit_SCGLUE: Pretraining SCGLUE model... [INFO] autodevice: Using GPU 1 as computation device. [INFO] check_graph: Checking variable coverage... [INFO] check_graph: Checking edge attributes... [INFO] check_graph: Checking self-loops... [INFO] check_graph: Checking graph symmetry... [INFO] SCGLUEModel: Setting graph_batch_size = 156794 [INFO] SCGLUEModel: Setting max_epochs = 48 [INFO] SCGLUEModel: Setting patience = 4 [INFO] SCGLUEModel: Setting reduce_lr_patience = 2 [INFO] SCGLUETrainer: Using training directory: "glue/pretrain" [INFO] SCGLUETrainer: [Epoch 10] train={'g_nll': 0.418, 'g_kl': 0.001, 'g_elbo': 0.419, 'x_rna_nll': 0.254, 'x_rna_kl': 0.005, 'x_rna_elbo': 0.259, 'x_atac_nll': 0.056, 'x_atac_kl': 0.0, 'x_atac_elbo': 0.056, 'dsc_loss': 0.693, 'vae_loss': 0.332, 'gen_loss': 0.298}, val={'g_nll': 0.417, 'g_kl': 0.001, 'g_elbo': 0.418, 'x_rna_nll': 0.254, 'x_rna_kl': 0.005, 'x_rna_elbo': 0.259, 'x_atac_nll': 0.057, 'x_atac_kl': 0.0, 'x_atac_elbo': 0.057, 'dsc_loss': 0.694, 'vae_loss': 0.333, 'gen_loss': 0.298}, 648.6s elapsed Epoch 00012: reducing learning rate of group 0 to 2.0000e-04. Epoch 00012: reducing learning rate of group 0 to 2.0000e-04. [INFO] LRScheduler: Learning rate reduction: step 1 Epoch 00019: reducing learning rate of group 0 to 2.0000e-05. Epoch 00019: reducing learning rate of group 0 to 2.0000e-05. [INFO] LRScheduler: Learning rate reduction: step 2 [INFO] SCGLUETrainer: [Epoch 20] train={'g_nll': 0.416, 'g_kl': 0.001, 'g_elbo': 0.417, 'x_rna_nll': 0.253, 'x_rna_kl': 0.005, 'x_rna_elbo': 0.258, 'x_atac_nll': 0.056, 'x_atac_kl': 0.0, 'x_atac_elbo': 0.056, 'dsc_loss': 0.692, 'vae_loss': 0.331, 'gen_loss': 0.296}, val={'g_nll': 0.416, 'g_kl': 0.001, 'g_elbo': 0.417, 'x_rna_nll': 0.253, 'x_rna_kl': 0.005, 'x_rna_elbo': 0.258, 'x_atac_nll': 0.057, 'x_atac_kl': 0.0, 'x_atac_elbo': 0.057, 'dsc_loss': 0.691, 'vae_loss': 0.332, 'gen_loss': 0.297}, 651.7s elapsed Epoch 00022: reducing learning rate of group 0 to 2.0000e-06. Epoch 00022: reducing learning rate of group 0 to 2.0000e-06. [INFO] LRScheduler: Learning rate reduction: step 3 Epoch 00025: reducing learning rate of group 0 to 2.0000e-07. Epoch 00025: reducing learning rate of group 0 to 2.0000e-07. [INFO] LRScheduler: Learning rate reduction: step 4 [INFO] EarlyStopping: Restoring checkpoint "21"... [INFO] EarlyStopping: Restoring checkpoint "21"... [INFO] fit_SCGLUE: Estimating balancing weight... [INFO] estimate_balancing_weight: Clustering cells... [INFO] estimate_balancing_weight: Matching clusters... [INFO] estimate_balancing_weight: Matching array shape = (28, 29)... [INFO] estimate_balancing_weight: Estimating balancing weight... [INFO] fit_SCGLUE: Fine-tuning SCGLUE model... [INFO] check_graph: Checking variable coverage... [INFO] check_graph: Checking edge attributes... [INFO] check_graph: Checking self-loops... [INFO] check_graph: Checking graph symmetry... [INFO] SCGLUEModel: Setting graph_batch_size = 156794 [INFO] SCGLUEModel: Setting align_burnin = 8 [INFO] SCGLUEModel: Setting max_epochs = 48 [INFO] SCGLUEModel: Setting patience = 4 [INFO] SCGLUEModel: Setting reduce_lr_patience = 2 [INFO] SCGLUETrainer: Using training directory: "glue/fine-tune" [INFO] SCGLUETrainer: [Epoch 10] train={'g_nll': 0.423, 'g_kl': 0.001, 'g_elbo': 0.424, 'x_rna_nll': 0.255, 'x_rna_kl': 0.005, 'x_rna_elbo': 0.26, 'x_atac_nll': 0.056, 'x_atac_kl': 0.0, 'x_atac_elbo': 0.056, 'dsc_loss': 0.675, 'vae_loss': 0.333, 'gen_loss': 0.3}, val={'g_nll': 0.422, 'g_kl': 0.001, 'g_elbo': 0.423, 'x_rna_nll': 0.254, 'x_rna_kl': 0.005, 'x_rna_elbo': 0.259, 'x_atac_nll': 0.057, 'x_atac_kl': 0.0, 'x_atac_elbo': 0.057, 'dsc_loss': 0.684, 'vae_loss': 0.333, 'gen_loss': 0.299}, 665.4s elapsed Epoch 00012: reducing learning rate of group 0 to 2.0000e-04. Epoch 00012: reducing learning rate of group 0 to 2.0000e-04. [INFO] LRScheduler: Learning rate reduction: step 1 Epoch 00018: reducing learning rate of group 0 to 2.0000e-05. Epoch 00018: reducing learning rate of group 0 to 2.0000e-05. [INFO] LRScheduler: Learning rate reduction: step 2 [INFO] EarlyStopping: Restoring checkpoint "16"... [INFO] EarlyStopping: Restoring checkpoint "16"...

[Jeff1995]

Hi @fe4960! What are the specific difference data-wise between the recent run and the previous runs? Does it contain a significantly larger number of cells and peaks?

Based on the training log only, it appears that the model is converging pretty fast (learning rate reduction in just 12 epochs, but this could also be due to large cell number). Could you compare the training log with previous runs that worked better and see if this is a premature convergence problem? If that was the case setting a larger patience value could be helpful.

[fe4960]

Hi @Jeff1995 , Thanks a lot for the suggestion! I am wondering what is the difference between the parameter "patience" and "reduce_lr_patience" . Indeed, the number of cells significant increased. Should I increase both "patience" and "reduce_lr_patience" values, e.g. "patience" : 20, "reduce_lr_patience" : 16, ? Thanks again.

Additionally, here are tensorbroad plot of glue for another dataset, which contain a large number of cells and did not integrated well.