veloVI application on murine neural crest data

veloVI application on murine neural crest data#

Library imports#

import scanpy as sc
import scvi
from velovi import VELOVI

from rgv_tools import DATA_DIR
from rgv_tools.benchmarking import set_output

/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_csv from `anndata` is deprecated. Import anndata.io.read_csv instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_excel from `anndata` is deprecated. Import anndata.io.read_excel instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_hdf from `anndata` is deprecated. Import anndata.io.read_hdf instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_loom from `anndata` is deprecated. Import anndata.io.read_loom instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_mtx from `anndata` is deprecated. Import anndata.io.read_mtx instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_umi_tools from `anndata` is deprecated. Import anndata.io.read_umi_tools instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_csv from `anndata` is deprecated. Import anndata.io.read_csv instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_loom from `anndata` is deprecated. Import anndata.io.read_loom instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing CSCDataset from `anndata.experimental` is deprecated. Import anndata.abc.CSCDataset instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing CSRDataset from `anndata.experimental` is deprecated. Import anndata.abc.CSRDataset instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_elem from `anndata.experimental` is deprecated. Import anndata.io.read_elem instead.
  warnings.warn(msg, FutureWarning)

General settings#

scvi.settings.seed = 0

[rank: 0] Seed set to 0

Constants#

DATASET = "mouse_neural_crest"

SAVE_DATA = True
if SAVE_DATA:
    (DATA_DIR / DATASET / "processed").mkdir(parents=True, exist_ok=True)

Velocity pipline#

for i in range(1, 5):
    adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / f"adata_stage{i}_processed_velo_all_regulons.h5ad")

    scvi.settings.seed = 0
    VELOVI.setup_anndata(adata, spliced_layer="Ms", unspliced_layer="Mu")
    vae = VELOVI(adata)
    vae.train()

    set_output(adata, vae, n_samples=30)

    if SAVE_DATA:
        adata.write_h5ad(DATA_DIR / DATASET / "processed" / f"adata_run_stage_{i}_velovi_all_regulons.h5ad")

[rank: 0] Seed set to 0
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
You are using a CUDA device ('NVIDIA A100 80GB PCIe') that has Tensor Cores. To properly utilize them, you should set `torch.set_float32_matmul_precision('medium' | 'high')` which will trade-off precision for performance. For more details, read https://pytorch.org/docs/stable/generated/torch.set_float32_matmul_precision.html#torch.set_float32_matmul_precision
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]

`Trainer.fit` stopped: `max_epochs=500` reached.
[rank: 0] Seed set to 0
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]

Monitored metric elbo_validation did not improve in the last 45 records. Best score: -5127.889. Signaling Trainer to stop.

[rank: 0] Seed set to 0
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]

`Trainer.fit` stopped: `max_epochs=500` reached.
[rank: 0] Seed set to 0
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]

Monitored metric elbo_validation did not improve in the last 45 records. Best score: -5689.659. Signaling Trainer to stop.
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