Perturbation prediction on hematopoiesis dataset via RegVelo#
Using RegVelo to perform perturbation prediction, under soft_mode each run will repeat run 5 models and aggregate prediction results
Library imports#
import shutil
import numpy as np
import pandas as pd
import torch
import scanpy as sc
import scvi
from regvelo import REGVELOVI
from rgv_tools import DATA_DIR, FIG_DIR
from rgv_tools.perturbation import get_list_name, TFScanning
/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)
Matplotlib is building the font cache; this may take a moment.
2025-03-26 02:47:24.664186: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:477] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
E0000 00:00:1742953645.512133 497175 cuda_dnn.cc:8310] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
E0000 00:00:1742953645.927052 497175 cuda_blas.cc:1418] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
General settings#
scvi.settings.seed = 0
[rank: 0] Seed set to 0
Constants#
DATASET = "hematopoiesis_revision"
SAVE_DATA = True
if SAVE_DATA:
(DATA_DIR / DATASET / "processed").mkdir(parents=True, exist_ok=True)
(DATA_DIR / DATASET / "results").mkdir(parents=True, exist_ok=True)
SAVE_FIGURES = True
if SAVE_FIGURES:
(FIG_DIR / DATASET).mkdir(parents=True, exist_ok=True)
Data loading#
adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed.h5ad")
Perturbation screening#
## prepare skeleton
W = adata.uns["skeleton"].copy()
W = torch.tensor(np.array(W)).int()
## prepare TF
TF = adata.var_names[adata.var["tf"]]
### repeat run the model to get aggregate performance
terminal_states = ["Meg", "Mon", "Bas", "Ery", "Neu"]
for nrun in range(0, 15):
print("training model...")
REGVELOVI.setup_anndata(adata, spliced_layer="Ms", unspliced_layer="Mu")
vae = REGVELOVI(adata, W=W.T, regulators=TF, lam2=1)
torch.cuda.empty_cache()
vae.train()
print("save model...")
model_name = "rgv_model_" + str(nrun)
coef_name = "coef_" + str(nrun)
pval_name = "pval_" + str(nrun)
model = DATA_DIR / DATASET / "processed" / "perturb_repeat_runs" / model_name
coef_save = DATA_DIR / DATASET / "results" / coef_name
pval_save = DATA_DIR / DATASET / "results" / pval_name
vae.save(model)
print("inferring perturbation...")
while True:
try:
perturb_screening = TFScanning(model, adata, 7, "cell_type", terminal_states, TF, 0)
coef = pd.DataFrame(np.array(perturb_screening["coefficient"]))
coef.index = perturb_screening["TF"]
coef.columns = get_list_name(perturb_screening["coefficient"][0])
pval = pd.DataFrame(np.array(perturb_screening["pvalue"]))
pval.index = perturb_screening["TF"]
pval.columns = get_list_name(perturb_screening["pvalue"][0])
rows_with_nan = coef.isna().any(axis=1)
# Set all values in those rows to NaN
coef.loc[rows_with_nan, :] = np.nan
pval.loc[rows_with_nan, :] = np.nan
coef.to_csv(coef_save)
pval.to_csv(pval_save)
break
except: # noqa E722
# If an error is raised, increment a and try again, and need to recompute double knock-out reults
print("perturbation screening has error, retraining model...")
shutil.rmtree(model)
REGVELOVI.setup_anndata(adata, spliced_layer="Ms", unspliced_layer="Mu")
vae = REGVELOVI(adata, W=W.T, regulators=TF, lam2=1)
vae.train()
print("save model...")
vae.save(model)
training model...
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: -340.831. Signaling Trainer to stop.
save model...
inferring perturbation...
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_0/model.pt already downloaded
2025-03-26 02:56:41,166 - INFO - Using pre-computed Schur decomposition
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_0/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 13 Broken Pipe: Likely while reading or writing to a socket
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
2025-03-26 02:56:51,696 - INFO - Using pre-computed Schur decomposition
Done ARID5B
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_0/model.pt already downloaded
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 13 Broken Pipe: Likely while reading or writing to a socket
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
Abort(59) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 13 Broken Pipe: Likely while reading or writing to a socket
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
Abort(59) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
2025-03-26 02:57:04,254 - INFO - Using pre-computed Schur decomposition
Done ATF6
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_0/model.pt already downloaded
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 13 Broken Pipe: Likely while reading or writing to a socket
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
Abort(59) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
2025-03-26 03:23:03,244 - INFO - Using pre-computed Schur decomposition
Done SPI1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_1/model.pt already downloaded
2025-03-26 03:23:13,824 - INFO - Using pre-computed Schur decomposition
Done STAT2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_1/model.pt already downloaded
2025-03-26 03:23:24,707 - INFO - Using pre-computed Schur decomposition
Done STAT6
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_1/model.pt already downloaded
2025-03-26 03:23:36,927 - INFO - Using pre-computed Schur decomposition
Done TAF1
INFO File
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2025-03-26 03:23:48,183 - INFO - Using pre-computed Schur decomposition
Done TAL1
INFO File
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2025-03-26 03:23:58,984 - INFO - Using pre-computed Schur decomposition
Done TCF4
INFO File
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2025-03-26 03:24:09,458 - INFO - Using pre-computed Schur decomposition
Done TFCP2
INFO File
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2025-03-26 03:24:20,256 - INFO - Using pre-computed Schur decomposition
Done TFDP1
INFO File
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v_model_1/model.pt already downloaded
2025-03-26 03:24:32,953 - INFO - Using pre-computed Schur decomposition
Done ZEB1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_1/model.pt already downloaded
2025-03-26 03:24:44,043 - INFO - Using pre-computed Schur decomposition
Done ZFHX3
INFO File
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v_model_1/model.pt already downloaded
2025-03-26 03:24:54,463 - INFO - Using pre-computed Schur decomposition
Done ZNF263
INFO File
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v_model_1/model.pt already downloaded
2025-03-26 03:25:07,258 - INFO - Using pre-computed Schur decomposition
Done ZNF274
training model...
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]
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
2025-03-26 03:57:40,631 - INFO - Using pre-computed Schur decomposition
Done LMO2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 03:57:51,488 - INFO - Using pre-computed Schur decomposition
Done MECP2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 03:58:01,971 - INFO - Using pre-computed Schur decomposition
Done MEF2A
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 03:58:12,713 - INFO - Using pre-computed Schur decomposition
Done MEF2C
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 03:58:23,203 - INFO - Using pre-computed Schur decomposition
Done NFATC3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 03:58:36,243 - INFO - Using pre-computed Schur decomposition
Done NFIA
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 03:58:46,793 - INFO - Using pre-computed Schur decomposition
Done NFIB
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 03:58:59,762 - INFO - Using pre-computed Schur decomposition
Done NFYA
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 03:59:10,309 - INFO - Using pre-computed Schur decomposition
Done NFYC
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 03:59:23,028 - INFO - Using pre-computed Schur decomposition
Done NR6A1
INFO File
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2025-03-26 03:59:34,517 - INFO - Using pre-computed Schur decomposition
Done NRF1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 03:59:47,147 - INFO - Using pre-computed Schur decomposition
Done POU2F1
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 03:59:57,593 - INFO - Using pre-computed Schur decomposition
Done PPARA
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:00:08,371 - INFO - Using pre-computed Schur decomposition
Done RAD21
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:00:18,883 - INFO - Using pre-computed Schur decomposition
Done RBPJ
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:00:29,622 - INFO - Using pre-computed Schur decomposition
Done RREB1
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 04:00:40,376 - INFO - Using pre-computed Schur decomposition
Done SMC3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:00:50,824 - INFO - Using pre-computed Schur decomposition
Done SPI1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:01:04,112 - INFO - Using pre-computed Schur decomposition
Done STAT2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:01:14,802 - INFO - Using pre-computed Schur decomposition
Done STAT6
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 04:01:25,400 - INFO - Using pre-computed Schur decomposition
Done TAF1
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 04:01:35,924 - INFO - Using pre-computed Schur decomposition
2025-03-26 04:01:39,020 - INFO - Using pre-computed Schur decomposition
perturbation screening has error, retraining model...
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]
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
2025-03-26 04:29:00,380 - INFO - Using pre-computed Schur decomposition
Done GATA2
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 04:29:13,223 - INFO - Using pre-computed Schur decomposition
Done GFI1B
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 04:29:24,093 - INFO - Using pre-computed Schur decomposition
Done GTF2I
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 04:29:34,836 - INFO - Using pre-computed Schur decomposition
Done HLTF
INFO File
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2025-03-26 04:29:45,695 - INFO - Using pre-computed Schur decomposition
Done HMBOX1
INFO File
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2025-03-26 04:29:56,471 - INFO - Using pre-computed Schur decomposition
Done HMGA1
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 04:30:09,408 - INFO - Using pre-computed Schur decomposition
Done IKZF1
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 04:30:21,342 - INFO - Using pre-computed Schur decomposition
Done IRF3
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 04:30:34,365 - INFO - Using pre-computed Schur decomposition
Done JDP2
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 04:30:45,411 - INFO - Using pre-computed Schur decomposition
Done KLF3
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 04:30:58,525 - INFO - Using pre-computed Schur decomposition
Done LMO2
INFO File
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v_model_3/model.pt already downloaded
2025-03-26 04:31:09,430 - INFO - Using pre-computed Schur decomposition
Done MECP2
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2025-03-26 04:31:20,171 - INFO - Using pre-computed Schur decomposition
Done MEF2A
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2025-03-26 04:31:31,289 - INFO - Using pre-computed Schur decomposition
Done MEF2C
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2025-03-26 04:31:44,405 - INFO - Using pre-computed Schur decomposition
Done NFATC3
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2025-03-26 04:31:57,299 - INFO - Using pre-computed Schur decomposition
Done NFIA
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2025-03-26 04:32:08,249 - INFO - Using pre-computed Schur decomposition
Done NFIB
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2025-03-26 04:32:19,268 - INFO - Using pre-computed Schur decomposition
Done NFYA
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2025-03-26 04:32:30,103 - INFO - Using pre-computed Schur decomposition
Done NFYC
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2025-03-26 04:32:40,754 - INFO - Using pre-computed Schur decomposition
Done NR6A1
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2025-03-26 04:32:51,645 - INFO - Using pre-computed Schur decomposition
Done NRF1
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2025-03-26 04:33:04,475 - INFO - Using pre-computed Schur decomposition
Done POU2F1
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2025-03-26 04:33:15,359 - INFO - Using pre-computed Schur decomposition
Done PPARA
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2025-03-26 04:33:28,628 - INFO - Using pre-computed Schur decomposition
Done RAD21
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2025-03-26 04:33:41,664 - INFO - Using pre-computed Schur decomposition
Done RBPJ
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2025-03-26 04:33:52,340 - INFO - Using pre-computed Schur decomposition
Done RREB1
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v_model_3/model.pt already downloaded
2025-03-26 04:34:05,252 - INFO - Using pre-computed Schur decomposition
Done SMC3
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:34:18,386 - INFO - Using pre-computed Schur decomposition
Done SPI1
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
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2025-03-26 04:34:29,035 - INFO - Using pre-computed Schur decomposition
Done STAT2
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
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2025-03-26 04:34:39,885 - INFO - Using pre-computed Schur decomposition
Done STAT6
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:34:50,319 - INFO - Using pre-computed Schur decomposition
Done TAF1
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:35:03,303 - INFO - Using pre-computed Schur decomposition
Done TAL1
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
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2025-03-26 04:35:16,490 - INFO - Using pre-computed Schur decomposition
Done TCF4
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:35:27,114 - INFO - Using pre-computed Schur decomposition
Done TFCP2
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:35:40,202 - INFO - Using pre-computed Schur decomposition
Done TFDP1
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:35:50,961 - INFO - Using pre-computed Schur decomposition
Done ZEB1
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:36:04,052 - INFO - Using pre-computed Schur decomposition
Done ZFHX3
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:36:16,251 - INFO - Using pre-computed Schur decomposition
Done ZNF263
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_3/model.pt already downloaded
2025-03-26 04:36:29,089 - INFO - Using pre-computed Schur decomposition
Done ZNF274
training model...
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]
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
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Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
2025-03-26 05:08:50,583 - INFO - Using pre-computed Schur decomposition
Done CHD2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_5/model.pt already downloaded
2025-03-26 05:09:02,227 - INFO - Using pre-computed Schur decomposition
Done CUX1
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_5/model.pt already downloaded
2025-03-26 05:09:15,551 - INFO - Using pre-computed Schur decomposition
Done DEAF1
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_5/model.pt already downloaded
2025-03-26 05:09:28,538 - INFO - Using pre-computed Schur decomposition
Done E2F1
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2025-03-26 05:09:41,445 - INFO - Using pre-computed Schur decomposition
Done E2F2
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v_model_5/model.pt already downloaded
2025-03-26 05:09:52,302 - INFO - Using pre-computed Schur decomposition
Done ELF2
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_5/model.pt already downloaded
2025-03-26 05:10:05,303 - INFO - Using pre-computed Schur decomposition
Done ERG
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_5/model.pt already downloaded
2025-03-26 05:10:16,179 - INFO - Using pre-computed Schur decomposition
Done ETS2
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_5/model.pt already downloaded
2025-03-26 05:10:26,985 - INFO - Using pre-computed Schur decomposition
Done ETV6
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_5/model.pt already downloaded
2025-03-26 05:10:37,933 - INFO - Using pre-computed Schur decomposition
Done FOXJ3
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_5/model.pt already downloaded
2025-03-26 05:10:50,886 - INFO - Using pre-computed Schur decomposition
Done FOXM1
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_5/model.pt already downloaded
2025-03-26 05:11:01,884 - INFO - Using pre-computed Schur decomposition
Done FOXO3
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2025-03-26 05:11:12,753 - INFO - Using pre-computed Schur decomposition
Done FOXP1
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v_model_5/model.pt already downloaded
2025-03-26 05:11:23,809 - INFO - Using pre-computed Schur decomposition
Done GATA1
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v_model_5/model.pt already downloaded
2025-03-26 05:11:34,494 - INFO - Using pre-computed Schur decomposition
Done GATA2
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v_model_5/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
2025-03-26 05:34:26,930 - INFO - Using pre-computed Schur decomposition
Done SMC3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_6/model.pt already downloaded
2025-03-26 05:34:40,102 - INFO - Using pre-computed Schur decomposition
Done SPI1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_6/model.pt already downloaded
2025-03-26 05:34:53,662 - INFO - Using pre-computed Schur decomposition
Done STAT2
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_6/model.pt already downloaded
2025-03-26 05:35:04,363 - INFO - Using pre-computed Schur decomposition
Done STAT6
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
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2025-03-26 05:35:15,360 - INFO - Using pre-computed Schur decomposition
Done TAF1
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_6/model.pt already downloaded
2025-03-26 05:35:26,985 - INFO - Using pre-computed Schur decomposition
Done TAL1
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2025-03-26 05:35:40,507 - INFO - Using pre-computed Schur decomposition
Done TCF4
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_6/model.pt already downloaded
2025-03-26 05:35:53,800 - INFO - Using pre-computed Schur decomposition
Done TFCP2
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_6/model.pt already downloaded
2025-03-26 05:36:06,785 - INFO - Using pre-computed Schur decomposition
Done TFDP1
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v_model_6/model.pt already downloaded
2025-03-26 05:36:17,652 - INFO - Using pre-computed Schur decomposition
Done ZEB1
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_6/model.pt already downloaded
2025-03-26 05:36:28,615 - INFO - Using pre-computed Schur decomposition
Done ZFHX3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_6/model.pt already downloaded
2025-03-26 05:36:41,580 - INFO - Using pre-computed Schur decomposition
Done ZNF263
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_6/model.pt already downloaded
2025-03-26 05:36:54,375 - INFO - Using pre-computed Schur decomposition
Done ZNF274
training model...
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: -278.560. Signaling Trainer to stop.
save model...
inferring perturbation...
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_7/model.pt already downloaded
2025-03-26 05:40:37,427 - INFO - Using pre-computed Schur decomposition
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_7/model.pt already downloaded
2025-03-26 05:40:48,313 - INFO - Using pre-computed Schur decomposition
Done ARID5B
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_7/model.pt already downloaded
2025-03-26 05:40:58,808 - INFO - Using pre-computed Schur decomposition
Done ATF6
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_7/model.pt already downloaded
2025-03-26 05:41:09,635 - INFO - Using pre-computed Schur decomposition
Done BACH2
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_7/model.pt already downloaded
2025-03-26 05:41:20,380 - INFO - Using pre-computed Schur decomposition
Done BPTF
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_7/model.pt already downloaded
2025-03-26 05:41:31,287 - INFO - Using pre-computed Schur decomposition
Done BRCA1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_7/model.pt already downloaded
2025-03-26 05:41:42,400 - INFO - Using pre-computed Schur decomposition
Done CEBPZ
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_7/model.pt already downloaded
2025-03-26 05:41:53,323 - INFO - Using pre-computed Schur decomposition
Done CHD2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_7/model.pt already downloaded
2025-03-26 05:42:04,113 - INFO - Using pre-computed Schur decomposition
Done CUX1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_7/model.pt already downloaded
2025-03-26 05:42:17,075 - INFO - Using pre-computed Schur decomposition
Done DEAF1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_7/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
Monitored metric elbo_validation did not improve in the last 45 records. Best score: -321.133. Signaling Trainer to stop.
save model...
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_8/model.pt already downloaded
2025-03-26 06:12:40,590 - INFO - Using pre-computed Schur decomposition
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_8/model.pt already downloaded
2025-03-26 06:12:53,582 - INFO - Using pre-computed Schur decomposition
Done ARID5B
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_8/model.pt already downloaded
2025-03-26 06:13:04,239 - INFO - Using pre-computed Schur decomposition
Done ATF6
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_8/model.pt already downloaded
2025-03-26 06:13:16,804 - INFO - Using pre-computed Schur decomposition
Done BACH2
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_8/model.pt already downloaded
2025-03-26 06:13:27,459 - INFO - Using pre-computed Schur decomposition
Done BPTF
INFO File
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v_model_8/model.pt already downloaded
2025-03-26 06:13:38,839 - INFO - Using pre-computed Schur decomposition
Done BRCA1
INFO File
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v_model_8/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
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To change this limit, set the config variable
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ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
2025-03-26 06:39:47,046 - INFO - Using pre-computed Schur decomposition
Done MEF2C
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_9/model.pt already downloaded
2025-03-26 06:39:57,525 - INFO - Using pre-computed Schur decomposition
Done NFATC3
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v_model_9/model.pt already downloaded
2025-03-26 06:40:10,599 - INFO - Using pre-computed Schur decomposition
Done NFIA
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_9/model.pt already downloaded
2025-03-26 06:40:23,413 - INFO - Using pre-computed Schur decomposition
Done NFIB
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_9/model.pt already downloaded
2025-03-26 06:40:36,400 - INFO - Using pre-computed Schur decomposition
Done NFYA
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_9/model.pt already downloaded
2025-03-26 06:40:47,081 - INFO - Using pre-computed Schur decomposition
Done NFYC
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_9/model.pt already downloaded
2025-03-26 06:40:58,547 - INFO - Using pre-computed Schur decomposition
Done NR6A1
INFO File
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v_model_9/model.pt already downloaded
2025-03-26 06:41:11,559 - INFO - Using pre-computed Schur decomposition
Done NRF1
INFO File
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2025-03-26 06:41:24,373 - INFO - Using pre-computed Schur decomposition
Done POU2F1
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2025-03-26 06:41:37,862 - INFO - Using pre-computed Schur decomposition
Done PPARA
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2025-03-26 06:41:49,311 - INFO - Using pre-computed Schur decomposition
Done RAD21
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2025-03-26 06:41:59,775 - INFO - Using pre-computed Schur decomposition
Done RBPJ
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2025-03-26 06:42:12,925 - INFO - Using pre-computed Schur decomposition
Done RREB1
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2025-03-26 06:42:25,644 - INFO - Using pre-computed Schur decomposition
Done SMC3
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2025-03-26 06:42:38,305 - INFO - Using pre-computed Schur decomposition
Done SPI1
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2025-03-26 06:42:49,181 - INFO - Using pre-computed Schur decomposition
Done STAT2
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2025-03-26 06:43:00,083 - INFO - Using pre-computed Schur decomposition
Done STAT6
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2025-03-26 06:43:12,191 - INFO - Using pre-computed Schur decomposition
Done TAF1
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2025-03-26 06:43:23,756 - INFO - Using pre-computed Schur decomposition
Done TAL1
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2025-03-26 06:43:36,804 - INFO - Using pre-computed Schur decomposition
Done TCF4
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2025-03-26 06:43:47,869 - INFO - Using pre-computed Schur decomposition
Done TFCP2
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2025-03-26 06:44:00,727 - INFO - Using pre-computed Schur decomposition
Done TFDP1
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2025-03-26 06:44:11,693 - INFO - Using pre-computed Schur decomposition
Done ZEB1
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2025-03-26 06:44:22,765 - INFO - Using pre-computed Schur decomposition
Done ZFHX3
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2025-03-26 06:44:36,048 - INFO - Using pre-computed Schur decomposition
Done ZNF263
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v_model_9/model.pt already downloaded
2025-03-26 06:44:47,462 - INFO - Using pre-computed Schur decomposition
Done ZNF274
training model...
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]
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
2025-03-26 07:10:50,687 - INFO - Using pre-computed Schur decomposition
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
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2025-03-26 07:11:03,731 - INFO - Using pre-computed Schur decomposition
Done ARID5B
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2025-03-26 07:11:14,610 - INFO - Using pre-computed Schur decomposition
Done ATF6
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2025-03-26 07:11:27,514 - INFO - Using pre-computed Schur decomposition
Done BACH2
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2025-03-26 07:11:40,300 - INFO - Using pre-computed Schur decomposition
Done BPTF
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2025-03-26 07:11:51,058 - INFO - Using pre-computed Schur decomposition
Done BRCA1
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2025-03-26 07:12:04,232 - INFO - Using pre-computed Schur decomposition
Done CEBPZ
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2025-03-26 07:12:14,932 - INFO - Using pre-computed Schur decomposition
Done CHD2
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2025-03-26 07:12:28,108 - INFO - Using pre-computed Schur decomposition
Done CUX1
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2025-03-26 07:12:41,062 - INFO - Using pre-computed Schur decomposition
Done DEAF1
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2025-03-26 07:12:52,056 - INFO - Using pre-computed Schur decomposition
Done E2F1
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2025-03-26 07:13:02,812 - INFO - Using pre-computed Schur decomposition
Done E2F2
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2025-03-26 07:13:15,674 - INFO - Using pre-computed Schur decomposition
Done ELF2
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2025-03-26 07:13:29,416 - INFO - Using pre-computed Schur decomposition
Done ERG
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2025-03-26 07:13:40,205 - INFO - Using pre-computed Schur decomposition
Done ETS2
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2025-03-26 07:13:51,029 - INFO - Using pre-computed Schur decomposition
Done ETV6
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2025-03-26 07:14:02,033 - INFO - Using pre-computed Schur decomposition
Done FOXJ3
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2025-03-26 07:14:15,006 - INFO - Using pre-computed Schur decomposition
Done FOXM1
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2025-03-26 07:14:27,260 - INFO - Using pre-computed Schur decomposition
Done FOXO3
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2025-03-26 07:14:40,173 - INFO - Using pre-computed Schur decomposition
Done FOXP1
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2025-03-26 07:14:51,047 - INFO - Using pre-computed Schur decomposition
Done GATA1
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v_model_11/model.pt already downloaded
WARNING: Using `7` components would split a block of complex conjugate eigenvalues. Using `n_components=8`
WARNING: Unable to compute macrostates with `n_states=7` because it will split complex conjugate eigenvalues. Using `n_states=8`
2025-03-26 07:15:04,149 - INFO - Using pre-computed Schur decomposition
Done GATA2
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
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2025-03-26 07:15:15,534 - INFO - Using pre-computed Schur decomposition
Done GFI1B
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2025-03-26 07:15:28,354 - INFO - Using pre-computed Schur decomposition
Done GTF2I
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2025-03-26 07:15:41,422 - INFO - Using pre-computed Schur decomposition
Done HLTF
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2025-03-26 07:15:54,461 - INFO - Using pre-computed Schur decomposition
Done HMBOX1
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2025-03-26 07:16:06,522 - INFO - Using pre-computed Schur decomposition
Done HMGA1
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2025-03-26 07:16:19,360 - INFO - Using pre-computed Schur decomposition
Done IKZF1
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2025-03-26 07:16:30,254 - INFO - Using pre-computed Schur decomposition
Done IRF3
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2025-03-26 07:16:42,851 - INFO - Using pre-computed Schur decomposition
Done JDP2
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2025-03-26 07:16:56,999 - INFO - Using pre-computed Schur decomposition
Done KLF3
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2025-03-26 07:17:07,863 - INFO - Using pre-computed Schur decomposition
Done LMO2
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2025-03-26 07:17:20,823 - INFO - Using pre-computed Schur decomposition
Done MECP2
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2025-03-26 07:17:31,621 - INFO - Using pre-computed Schur decomposition
Done MEF2A
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2025-03-26 07:17:42,378 - INFO - Using pre-computed Schur decomposition
Done MEF2C
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2025-03-26 07:17:55,743 - INFO - Using pre-computed Schur decomposition
Done NFATC3
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2025-03-26 07:18:06,785 - INFO - Using pre-computed Schur decomposition
Done NFIA
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2025-03-26 07:18:19,878 - INFO - Using pre-computed Schur decomposition
Done NFIB
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2025-03-26 07:18:30,952 - INFO - Using pre-computed Schur decomposition
Done NFYA
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2025-03-26 07:18:44,382 - INFO - Using pre-computed Schur decomposition
Done NFYC
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2025-03-26 07:18:55,344 - INFO - Using pre-computed Schur decomposition
Done NR6A1
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2025-03-26 07:19:06,155 - INFO - Using pre-computed Schur decomposition
Done NRF1
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2025-03-26 07:19:17,185 - INFO - Using pre-computed Schur decomposition
Done POU2F1
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2025-03-26 07:19:27,977 - INFO - Using pre-computed Schur decomposition
Done PPARA
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
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2025-03-26 07:19:39,236 - INFO - Using pre-computed Schur decomposition
Done RAD21
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2025-03-26 07:19:50,260 - INFO - Using pre-computed Schur decomposition
Done RBPJ
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2025-03-26 07:20:01,099 - INFO - Using pre-computed Schur decomposition
Done RREB1
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2025-03-26 07:20:14,187 - INFO - Using pre-computed Schur decomposition
Done SMC3
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2025-03-26 07:20:25,098 - INFO - Using pre-computed Schur decomposition
Done SPI1
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2025-03-26 07:20:38,087 - INFO - Using pre-computed Schur decomposition
Done STAT2
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2025-03-26 07:20:49,524 - INFO - Using pre-computed Schur decomposition
Done STAT6
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2025-03-26 07:21:00,566 - INFO - Using pre-computed Schur decomposition
Done TAF1
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IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
2025-03-26 07:44:38,657 - INFO - Using pre-computed Schur decomposition
Done ERG
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2025-03-26 07:44:51,485 - INFO - Using pre-computed Schur decomposition
Done ETS2
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2025-03-26 07:45:04,218 - INFO - Using pre-computed Schur decomposition
Done ETV6
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2025-03-26 07:45:17,197 - INFO - Using pre-computed Schur decomposition
Done FOXJ3
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2025-03-26 07:45:29,986 - INFO - Using pre-computed Schur decomposition
Done FOXM1
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2025-03-26 07:45:43,143 - INFO - Using pre-computed Schur decomposition
Done FOXO3
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2025-03-26 07:45:54,024 - INFO - Using pre-computed Schur decomposition
Done FOXP1
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2025-03-26 07:46:04,824 - INFO - Using pre-computed Schur decomposition
Done GATA1
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2025-03-26 07:46:15,692 - INFO - Using pre-computed Schur decomposition
Done GATA2
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2025-03-26 07:46:28,725 - INFO - Using pre-computed Schur decomposition
Done GFI1B
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2025-03-26 07:46:42,273 - INFO - Using pre-computed Schur decomposition
Done GTF2I
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2025-03-26 07:46:55,854 - INFO - Using pre-computed Schur decomposition
Done HLTF
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2025-03-26 07:47:09,092 - INFO - Using pre-computed Schur decomposition
Done HMBOX1
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2025-03-26 07:47:22,258 - INFO - Using pre-computed Schur decomposition
Done HMGA1
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2025-03-26 07:47:35,219 - INFO - Using pre-computed Schur decomposition
Done IKZF1
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2025-03-26 07:47:48,502 - INFO - Using pre-computed Schur decomposition
Done IRF3
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2025-03-26 07:48:01,706 - INFO - Using pre-computed Schur decomposition
Done JDP2
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2025-03-26 07:48:14,788 - INFO - Using pre-computed Schur decomposition
Done KLF3
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2025-03-26 07:48:25,622 - INFO - Using pre-computed Schur decomposition
Done LMO2
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2025-03-26 07:48:36,663 - INFO - Using pre-computed Schur decomposition
Done MECP2
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2025-03-26 07:48:49,506 - INFO - Using pre-computed Schur decomposition
Done MEF2A
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2025-03-26 07:49:00,543 - INFO - Using pre-computed Schur decomposition
Done MEF2C
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2025-03-26 07:49:12,900 - INFO - Using pre-computed Schur decomposition
Done NFATC3
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2025-03-26 07:49:23,965 - INFO - Using pre-computed Schur decomposition
Done NFIA
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2025-03-26 07:49:35,065 - INFO - Using pre-computed Schur decomposition
Done NFIB
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2025-03-26 07:49:48,100 - INFO - Using pre-computed Schur decomposition
Done NFYA
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2025-03-26 07:49:58,821 - INFO - Using pre-computed Schur decomposition
Done NFYC
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2025-03-26 07:50:09,481 - INFO - Using pre-computed Schur decomposition
Done NR6A1
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2025-03-26 07:50:20,493 - INFO - Using pre-computed Schur decomposition
Done NRF1
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2025-03-26 07:50:34,133 - INFO - Using pre-computed Schur decomposition
Done POU2F1
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2025-03-26 07:50:44,981 - INFO - Using pre-computed Schur decomposition
Done PPARA
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2025-03-26 07:50:58,038 - INFO - Using pre-computed Schur decomposition
Done RAD21
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2025-03-26 07:51:10,925 - INFO - Using pre-computed Schur decomposition
Done RBPJ
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2025-03-26 07:51:24,080 - INFO - Using pre-computed Schur decomposition
Done RREB1
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2025-03-26 07:51:34,915 - INFO - Using pre-computed Schur decomposition
Done SMC3
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2025-03-26 07:51:45,869 - INFO - Using pre-computed Schur decomposition
Done SPI1
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2025-03-26 07:51:58,709 - INFO - Using pre-computed Schur decomposition
Done STAT2
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2025-03-26 07:52:09,659 - INFO - Using pre-computed Schur decomposition
Done STAT6
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2025-03-26 07:52:20,171 - INFO - Using pre-computed Schur decomposition
Done TAF1
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2025-03-26 07:52:33,179 - INFO - Using pre-computed Schur decomposition
Done TAL1
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2025-03-26 07:52:44,219 - INFO - Using pre-computed Schur decomposition
Done TCF4
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2025-03-26 07:52:55,039 - INFO - Using pre-computed Schur decomposition
Done TFCP2
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2025-03-26 07:53:08,403 - INFO - Using pre-computed Schur decomposition
Done TFDP1
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2025-03-26 07:53:19,403 - INFO - Using pre-computed Schur decomposition
Done ZEB1
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2025-03-26 07:53:30,432 - INFO - Using pre-computed Schur decomposition
Done ZFHX3
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2025-03-26 07:53:41,095 - INFO - Using pre-computed Schur decomposition
Done ZNF263
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v_model_12/model.pt already downloaded
2025-03-26 07:53:51,735 - INFO - Using pre-computed Schur decomposition
Done ZNF274
training model...
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]
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
Monitored metric elbo_validation did not improve in the last 45 records. Best score: -312.099. Signaling Trainer to stop.
save model...
inferring perturbation...
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_14/model.pt already downloaded
2025-03-26 08:18:59,671 - INFO - Using pre-computed Schur decomposition
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
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2025-03-26 08:19:12,593 - INFO - Using pre-computed Schur decomposition
Done ARID5B
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2025-03-26 08:19:25,437 - INFO - Using pre-computed Schur decomposition
Done ATF6
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2025-03-26 08:19:36,577 - INFO - Using pre-computed Schur decomposition
Done BACH2
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2025-03-26 08:19:47,423 - INFO - Using pre-computed Schur decomposition
Done BPTF
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2025-03-26 08:19:58,496 - INFO - Using pre-computed Schur decomposition
Done BRCA1
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2025-03-26 08:20:09,389 - INFO - Using pre-computed Schur decomposition
Done CEBPZ
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2025-03-26 08:20:22,626 - INFO - Using pre-computed Schur decomposition
Done CHD2
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2025-03-26 08:20:33,809 - INFO - Using pre-computed Schur decomposition
Done CUX1
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2025-03-26 08:20:44,817 - INFO - Using pre-computed Schur decomposition
Done DEAF1
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
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2025-03-26 08:20:55,616 - INFO - Using pre-computed Schur decomposition
Done E2F1
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2025-03-26 08:21:06,638 - INFO - Using pre-computed Schur decomposition
Done E2F2
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2025-03-26 08:21:17,733 - INFO - Using pre-computed Schur decomposition
Done ELF2
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
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2025-03-26 08:21:28,826 - INFO - Using pre-computed Schur decomposition
Done ERG
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2025-03-26 08:21:39,962 - INFO - Using pre-computed Schur decomposition
Done ETS2
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2025-03-26 08:21:54,183 - INFO - Using pre-computed Schur decomposition
Done ETV6
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2025-03-26 08:22:05,062 - INFO - Using pre-computed Schur decomposition
Done FOXJ3
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2025-03-26 08:22:15,813 - INFO - Using pre-computed Schur decomposition
Done FOXM1
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2025-03-26 08:22:28,606 - INFO - Using pre-computed Schur decomposition
Done FOXO3
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2025-03-26 08:22:39,390 - INFO - Using pre-computed Schur decomposition
Done FOXP1
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2025-03-26 08:22:50,351 - INFO - Using pre-computed Schur decomposition
Done GATA1
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2025-03-26 08:23:01,167 - INFO - Using pre-computed Schur decomposition
Done GATA2
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2025-03-26 08:23:12,098 - INFO - Using pre-computed Schur decomposition
Done GFI1B
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2025-03-26 08:23:25,248 - INFO - Using pre-computed Schur decomposition
Done GTF2I
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2025-03-26 08:23:36,390 - INFO - Using pre-computed Schur decomposition
Done HLTF
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2025-03-26 08:23:47,232 - INFO - Using pre-computed Schur decomposition
Done HMBOX1
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2025-03-26 08:23:58,408 - INFO - Using pre-computed Schur decomposition
Done HMGA1
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2025-03-26 08:24:09,425 - INFO - Using pre-computed Schur decomposition
Done IKZF1
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_14/model.pt already downloaded
2025-03-26 08:24:22,243 - INFO - Using pre-computed Schur decomposition
Done IRF3
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_14/model.pt already downloaded
2025-03-26 08:24:33,730 - INFO - Using pre-computed Schur decomposition
Done JDP2
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
v_model_14/model.pt already downloaded
2025-03-26 08:24:46,722 - INFO - Using pre-computed Schur decomposition
Done KLF3
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/hematopoiesis_revision/processed/perturb_repeat_runs/rg
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2025-03-26 08:24:57,593 - INFO - Using pre-computed Schur decomposition
Done LMO2
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v_model_14/model.pt already downloaded
2025-03-26 08:25:10,499 - INFO - Using pre-computed Schur decomposition
Done MECP2
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2025-03-26 08:25:23,754 - INFO - Using pre-computed Schur decomposition
Done MEF2A
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2025-03-26 08:25:37,138 - INFO - Using pre-computed Schur decomposition
Done MEF2C
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2025-03-26 08:25:50,235 - INFO - Using pre-computed Schur decomposition
Done NFATC3
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2025-03-26 08:26:01,252 - INFO - Using pre-computed Schur decomposition
Done NFIA
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2025-03-26 08:26:14,542 - INFO - Using pre-computed Schur decomposition
Done NFIB
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2025-03-26 08:26:27,509 - INFO - Using pre-computed Schur decomposition
Done NFYA
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2025-03-26 08:26:38,433 - INFO - Using pre-computed Schur decomposition
Done NFYC
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2025-03-26 08:26:49,212 - INFO - Using pre-computed Schur decomposition
Done NR6A1
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2025-03-26 08:27:01,330 - INFO - Using pre-computed Schur decomposition
Done NRF1
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2025-03-26 08:27:12,052 - INFO - Using pre-computed Schur decomposition
Done POU2F1
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v_model_14/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
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To change this limit, set the config variable
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Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
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