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Submodule RNABERT
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| project: scprint_ablation | ||
| seed_everything: 50 | ||
| set_float32_matmul_precision: True | ||
| wandblog: all | ||
| log_freq: 200 | ||
| log_graph: True | ||
| trainer: | ||
| precision: 16-mixed | ||
| strategy: ddp_find_unused_parameters_true | ||
| gradient_clip_val: 40 | ||
| log_every_n_steps: 100 | ||
| limit_train_batches: 5000 | ||
| gradient_clip_algorithm: norm | ||
| limit_val_batches: 4000 | ||
| limit_test_batches: 1 # we don't perform tests this way | ||
| reload_dataloaders_every_n_epochs: 20 | ||
| max_epochs: 21 | ||
| accumulate_grad_batches: 1 | ||
| logger: | ||
| - class_path: lightning.pytorch.loggers.WandbLogger | ||
| init_args: | ||
| project: ${project} | ||
| save_dir: /lustre/fswork/projects/rech/xeg/uat95fg/ #/pasteur/zeus/projets/p02/ml4ig_hot/Users/jkalfon/ #/data/log/ | ||
| offline: False | ||
| callbacks: | ||
| - class_path: lightning.pytorch.callbacks.StochasticWeightAveraging | ||
| init_args: | ||
| swa_lrs: 0.03 | ||
| - class_path: lightning.pytorch.callbacks.ModelCheckpoint | ||
| init_args: | ||
| monitor: val_loss | ||
| save_top_k: 3 | ||
| save_last: True | ||
| scprint_training: | ||
| run_full_forward: False | ||
| # noise: [0.6] | ||
| do_ecs: False | ||
| do_denoise: False | ||
| class_embd_diss_scale: 0.1 | ||
| do_generate: True | ||
| test_every: 5 | ||
| do_cce: False | ||
| mask_ratio: 0.3 #["TF"] | ||
| model: | ||
| dropout: 0.1 | ||
| num_heads_kv: 2 | ||
| transformer: flash | ||
| mvc_decoder: inner product | ||
| residual_in_fp32: True | ||
| checkpointing: True | ||
| cell_specific_blocks: True | ||
| fused_dropout_add_ln: False | ||
| prenorm: True | ||
| fused_mlp: False | ||
| fused_bias_fc: False | ||
| drop_path_rate: 0 | ||
| freeze_embeddings: True | ||
| normalization: log | ||
| pred_embedding: | ||
| - cell_type_ontology_term_id | ||
| data: | ||
| organisms: | ||
| - NCBITaxon:9606 | ||
| gene_position_tolerance: 10_000 | ||
| gene_embeddings: /lustre/fswork/projects/rech/xeg/uat95fg/gene_embeddings.parquet | ||
| collection_name: scPRINT-V2 (100 random humans) #scPRINT-V2 (good quality) | ||
| how: random expr | ||
| max_len: 2200 | ||
| pin_memory: True | ||
| prefetch_factor: 3 | ||
| # metacell_mode: 0.2 | ||
| weight_scaler: 200 | ||
| do_gene_pos: ./data/main/biomart_pos.parquet | ||
| add_zero_genes: 0 | ||
| train_oversampling_per_epoch: 0.15 | ||
| validation_split: 0.05 | ||
| test_split: 0.02 | ||
| batch_size: 32 | ||
| num_workers: 20 | ||
| hierarchical_clss: | ||
| - cell_type_ontology_term_id | ||
| - tissue_ontology_term_id | ||
| - disease_ontology_term_id | ||
| - age_group | ||
| - assay_ontology_term_id | ||
| - self_reported_ethnicity_ontology_term_id | ||
| clss_to_weight: | ||
| - clust_cell_type | ||
| - tissue_ontology_term_id | ||
| - disease_ontology_term_id | ||
| - age_group | ||
| - assay_ontology_term_id | ||
| - self_reported_ethnicity_ontology_term_id | ||
| - sex_ontology_term_id | ||
| - organism_ontology_term_id | ||
| - cell_culture | ||
| # - nnz | ||
| clss_to_predict: | ||
| - cell_type_ontology_term_id | ||
| - tissue_ontology_term_id | ||
| - disease_ontology_term_id | ||
| - age_group | ||
| - assay_ontology_term_id | ||
| - self_reported_ethnicity_ontology_term_id | ||
| - sex_ontology_term_id | ||
| - organism_ontology_term_id |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,127 @@ | ||
| ###### | ||
| scprint_training: | ||
| run_full_forward: True | ||
| noise: [0.6] | ||
| do_denoise: True | ||
| class_embd_diss_scale: 0.1 | ||
| do_generate: True | ||
| do_cce: True | ||
|
|
||
| ###### TF masking | ||
| scprint_training: | ||
| mask_ratio: ["TF"] | ||
|
|
||
| ##### | ||
| scprint_training: | ||
| do_ecs: True | ||
|
|
||
| ##### Test cheap vs esm2 vs learnt | ||
|
|
||
|
|
||
| ##### untrained model’s performance | ||
| trainer: | ||
| limit_train_batches: 1 | ||
| limit_val_batches: 200 | ||
| limit_test_batches: 1 # we don't perform tests this way | ||
| max_epochs: 2 | ||
| scprint_training: | ||
| test_every: 1 | ||
|
|
||
| ##### Test attention bias faded vs none (MAKE SURE RIGHT DIR (T)) | ||
| model: | ||
| attn_bias: full | ||
|
|
||
| ##### | ||
| model: | ||
| dropout: 0 | ||
| num_heads_kv: 4 | ||
|
|
||
| ##### | ||
| model: | ||
| cell_specific_blocks: False | ||
|
|
||
| ##### | ||
| model: | ||
| freeze_embeddings: False | ||
|
|
||
| ##### | ||
| model: | ||
| normalization: sum | ||
|
|
||
| ##### no zinb vs mse vs both | ||
| model: | ||
| zinb: False | ||
|
|
||
| ##### no zinb vs mse vs both | ||
| scprint_training: | ||
| zinb_and_mse: True | ||
|
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||
| #### | ||
| model: | ||
| depth_atinput: True | ||
|
|
||
| #### | ||
| scprint_training: | ||
| do_mvc: True | ||
|
|
||
| ##### need to run them until the end | ||
| data: | ||
| organisms: | ||
| - NCBITaxon:9606 | ||
| - NCBITaxon:10090 | ||
| collection_name: scPRINT-V2 (good quality) | ||
|
|
||
| ##### need to run them until the end | ||
| data: | ||
| organisms: | ||
| - NCBITaxon:9606 | ||
| - NCBITaxon:10090 | ||
| collection_name: scPRINT-V2 full | ||
|
|
||
| ##### | ||
| data: | ||
| gene_position_tolerance: 1000 | ||
|
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||
| ##### | ||
| data: | ||
| do_gene_pos: False | ||
|
|
||
| ##### | ||
| data: | ||
| weight_scaler: 3000 | ||
|
|
||
| ##### Test multi context vs fixed | ||
| scprint_training: | ||
| var_context_length: True | ||
| data: | ||
| max_len: 3200 | ||
|
|
||
| ###### | ||
| data: | ||
| metacell_mode: 0.2 | ||
|
|
||
| ##### | ||
| data: | ||
| clss_to_weight: | ||
| - clust_cell_type | ||
| - tissue_ontology_term_id | ||
| - disease_ontology_term_id | ||
| - age_group | ||
| - assay_ontology_term_id | ||
| - self_reported_ethnicity_ontology_term_id | ||
| - sex_ontology_term_id | ||
| - organism_ontology_term_id | ||
| - cell_culture | ||
| - nnz | ||
|
|
||
| ##### | ||
| data: | ||
| clss_to_weight: | ||
| - cell_type_ontology_term_id | ||
| - tissue_ontology_term_id | ||
| - disease_ontology_term_id | ||
| - age_group | ||
| - assay_ontology_term_id | ||
| - self_reported_ethnicity_ontology_term_id | ||
| - sex_ontology_term_id | ||
| - organism_ontology_term_id |
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