In [79]:
%pylab inline
from snakebite.client import Client
import pyaml as yaml
import sys
import pythonrun
reload(pythonrun)
import os
import seaborn as sns
from sklearn import metrics
import scala_python_endive_wrapper
reload(scala_python_endive_wrapper)
from scala_python_endive_wrapper import *
import pandas as pd
import os
from sklearn.cluster import KMeans
Populating the interactive namespace from numpy and matplotlib
/home/eecs/vaishaal/anaconda2/lib/python2.7/site-packages/IPython/core/magics/pylab.py:161: UserWarning: pylab import has clobbered these variables: ['gamma', 'linalg', 'random', 'power', 'info', 'fft']
`%matplotlib` prevents importing * from pylab and numpy
"\n`%matplotlib` prevents importing * from pylab and numpy"
In [2]:
hdfsclient = Client("amp-spark-master.amp", 8020, use_trash=False)
notebook_stdout = sys.stdout
notebook_stderr = sys.stderr
terminal_stdout = open('/dev/stdout', 'w')
terminal_stderr = open('/dev/stderr', 'w')
logpath = "/tmp/log"
In [3]:
executor_mem = "200g"
cores_per_executor = 32
num_executors = 14
EGR1_PATH = '/user/vaishaal/endive-data/EGR1'
In [4]:
make_dnase_gaussian_filter_gen(1.0, 1.0)(100).shape
Out[4]:
(100, 232)
In [73]:
# this is where the magic happens
results = []
num_filters = 256
gammas = [0.1]
dnase_gammas = [0.1]
kmer_size = 8
dnase_kmer_sizes = [8]
In [74]:
chromosomes = map(lambda x: "chr{0}".format(x+1), range(23))
# CHANGE ME BASED ON ENUM + TF
egr1_cell_types = string_to_enum_celltypes(['GM12878', 'H1hESC', 'HCT116', 'MCF7'])
results_dfs = []
for gamma in gammas:
for dnase_gamma in dnase_gammas:
for dnase_kmer_size in dnase_kmer_sizes:
feat_out_loc = "/user/vaishaal/featurizedWindows/sequence/small/{0}-filters/{1}-gamma/{2}-dnase-gamma/{3}-kmers/{4}-dnase-kmers/replicate-0"\
.format(num_filters, gamma, dnase_gamma, kmer_size, dnase_kmer_size)
res = run_kitchensink_featurize_pipeline(EGR1_PATH,
"/tmp/filters.csv",
logpath,
seed=0,
cores_per_executor=cores_per_executor,
num_filters=num_filters,
sample=0.01,
alphabet_size=4,
kmer_size=kmer_size,
dnase_kmer_size=dnase_kmer_size,
gamma=gamma,
dnase_gamma=dnase_gamma,
executor_mem=executor_mem,
num_partitions=cores_per_executor*num_executors,
featuresOutput=feat_out_loc,
num_executors=num_executors)
meta = {}
meta['dnase_kmer_size'] = dnase_kmer_size
meta['dnase_gamma'] = dnase_gamma
meta['gamma'] = gamma
results_df = cross_validate(feat_out_loc,
hdfsclient,
chromosomes,
egr1_cell_types,
numHoldOutChr=1,
numHoldOutCell=1,
cores_per_executor = 32,
num_executors = 14,
executor_mem="150g",
num_folds=1,
negativeSamplingFreqs=[0.1],
regs=[1e-8],
other_meta=meta)
print(results_df)
results_dfs.append(results_df)
W SHAPE (256, 48)
{'kmerLength': 8, 'reference': '/home/eecs/akmorrow/ADAM/endive/workfiles/hg19.2bit', 'filtersPath': '/tmp/filters.csv', 'numPartitions': 448, 'dnaseBams': '/data/anv/DREAMDATA/dnase_bams/merged_coverage/', 'approxDim': 256, 'aggregatedSequenceOutput': '/user/vaishaal/endive-data/EGR1', 'featuresOutput': '/user/vaishaal/featurizedWindows/sequence/small/256-filters/0.1-gamma/0.1-dnase-gamma/8-kmers/8-dnase-kmers/replicate-0', 'seed': 0, 'dnaseNarrow': '/data/anv/DREAMDATA/DNASE/peaks/relaxed/', 'dnaseKmerLength': 8, 'featurizeSample': 0.01, 'alphabetSize': 4, 'readFiltersFromDisk': True}
FOLD 0
HOLDING OUT CHROMOSOMES ['chr12']
HOLDING OUT CELL TYPES [3]
RUNING SOLVER WITH REG=1e-08
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COMPUTING train metrics
COMPUTING val metrics
RUNING SOLVER WITH REG=0.1
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part-00853
part-00504
part-00168
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_SUCCESS
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part-00860
part-00098
part-00568
part-00210
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part-00486
part-00728
part-00876
part-00344
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part-00512
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COMPUTING train metrics
COMPUTING val metrics
dnase_gamma dnase_kmer_size gamma negativeSamplingFreq reg \
0 0.1 8 0.1 1 1.000000e-08
1 0.1 8 0.1 1 1.000000e-01
test_celltypes test_chromosomes train_auPRC train_auROC \
0 [3] [chr12] 0.286507 0.940043
1 [3] [chr12] 0.283020 0.941194
train_recall_at_05_fdr train_recall_at_10_fdr train_recall_at_25_fdr \
0 0.081238 0.104449 0.145390
1 0.076725 0.101547 0.142166
train_recall_at_50_fdr val_auPRC val_auROC val_recall_at_05_fdr \
0 0.221470 0.056017 0.900088 0.035714
1 0.215023 0.056503 0.899537 0.035714
val_recall_at_10_fdr val_recall_at_25_fdr val_recall_at_50_fdr
0 0.035714 0.035714 0.035714
1 0.035714 0.035714 0.035714
In [75]:
pd.concat(results_dfs)
Out[75]:
dnase_gamma
dnase_kmer_size
gamma
negativeSamplingFreq
reg
test_celltypes
test_chromosomes
train_auPRC
train_auROC
train_recall_at_05_fdr
train_recall_at_10_fdr
train_recall_at_25_fdr
train_recall_at_50_fdr
val_auPRC
val_auROC
val_recall_at_05_fdr
val_recall_at_10_fdr
val_recall_at_25_fdr
val_recall_at_50_fdr
0
0.1
8
0.1
1
1.000000e-08
[3]
[chr12]
0.286507
0.940043
0.081238
0.104449
0.145390
0.221470
0.056017
0.900088
0.035714
0.035714
0.035714
0.035714
1
0.1
8
0.1
1
1.000000e-01
[3]
[chr12]
0.283020
0.941194
0.076725
0.101547
0.142166
0.215023
0.056503
0.899537
0.035714
0.035714
0.035714
0.035714
In [ ]:
print(feat_out_loc)
results_df = cross_validate(feat_out_loc,
hdfsclient,
chromosomes,
egr1_cell_types,
numHoldOutChr=1,
numHoldOutCell=1,
cores_per_executor = 32,
num_executors = 14,
executor_mem="150g",
num_folds=1,
negativeSamplingFreqs=[0.001],
regs=[1e-8])
/user/vaishaal/featurizedWindows/sequence/small/256-filters/0.1-gamma/0.1-dnase-gamma/8-kmers/8-dnase-kmers/replicate-0
FOLD 0
HOLDING OUT CHROMOSOMES ['chr12']
HOLDING OUT CELL TYPES [3]
RUNING SOLVER WITH REG=1e-08
In [ ]:
results_df
In [67]:
Out[67]:
0.88036847526310447
In [35]:
feat_out_loc
Out[35]:
'/user/vaishaal/featurizedWindows/sequence/tiny/256-filters/1.0-gamma/1.0-dnase-gamma/8-kmers/100-dnase-kmers/replicate-0'
In [61]:
old_result_dfs = pd.concat(results_dfs)
In [ ]:
In [ ]:
In [ ]:
Content source: akmorrow13/endive
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