In [1]:
import numpy as np
import h5py
#f = h5py.File("/oak/stanford/groups/akundaje/avsec/basepair/data/"
# +"processed/comparison/output/nexus,peaks,OSNK,0,10"
# +",1,FALSE,same,0.5,64,25,0.004,9,FALSE,[1,50],TRUE"
# +",FALSE,1/deeplift.imp_score.h5", "r")
f = h5py.File("deeplift.imp_score.h5","r")
nanog_mask = np.array(f['metadata']['interval_from_task'][:]=='Nanog')
nanog_profile_wn_hypimp = np.array(f["hyp_imp/Nanog/profile/wn"][:])[nanog_mask]
onehot_seq = np.array(f["inputs/seq"][:])[nanog_mask]
nanog_profile_wn_contribs = nanog_profile_wn_hypimp*onehot_seq
In [2]:
import modisco
FRAC_SEQS_TO_USE = 0.02
NUM_SEQS_TO_USE = int(FRAC_SEQS_TO_USE*len(nanog_profile_wn_contribs))
print("num seqs to use:", NUM_SEQS_TO_USE)
task_names=["Nanog_profile_wn"]
contrib_scores={'Nanog_profile_wn':
nanog_profile_wn_contribs[:NUM_SEQS_TO_USE]}
hypothetical_contribs={'Nanog_profile_wn':
nanog_profile_wn_hypimp[:NUM_SEQS_TO_USE]}
one_hot=onehot_seq[:NUM_SEQS_TO_USE]
TF-MoDISco is using the TensorFlow backend.
/users/avanti/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/users/avanti/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/users/avanti/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/users/avanti/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/users/avanti/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/users/avanti/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
/users/avanti/anaconda3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/users/avanti/anaconda3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/users/avanti/anaconda3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/users/avanti/anaconda3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/users/avanti/anaconda3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/users/avanti/anaconda3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
WARNING: Logging before flag parsing goes to stderr.
W1111 01:22:14.250214 140385681004352 deprecation.py:323] From /users/avanti/anaconda3/lib/python3.7/site-packages/tensorflow/python/compat/v2_compat.py:61: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
/users/avanti/anaconda3/lib/python3.7/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.neighbors.kde module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.neighbors. Anything that cannot be imported from sklearn.neighbors is now part of the private API.
warnings.warn(message, FutureWarning)
num seqs to use: 1104
In [3]:
np.save("nanog_profile_wn_contribs_fewerseqlets.npy", nanog_profile_wn_contribs[:NUM_SEQS_TO_USE])
np.save("nanog_profile_wn_hypimp_fewerseqlets.npy", nanog_profile_wn_hypimp[:NUM_SEQS_TO_USE])
np.save("onehot_seq_fewerseqlets.npy", onehot_seq[:NUM_SEQS_TO_USE])
In [4]:
#print modisco commit hash
%cd /users/avanti/tfmodisco
!git log -n 1
%cd /users/avanti/tfmodisco_bio_experiments/bpnet/trial1
from importlib import reload
%matplotlib inline
import h5py
import numpy as np
import modisco
import modisco.seqlet_embedding.advanced_gapped_kmer
reload(modisco.seqlet_embedding.advanced_gapped_kmer)
import modisco.seqlet_embedding
reload(modisco.seqlet_embedding)
import modisco
reload(modisco)
import modisco.cluster.phenograph.core
reload(modisco.cluster.phenograph.core)
import modisco.cluster.phenograph.cluster
reload(modisco.cluster.phenograph.cluster)
import modisco.cluster.phenograph
reload(modisco.cluster.phenograph)
import modisco.cluster.core
reload(modisco.cluster.core)
import modisco.cluster
reload(modisco.cluster)
import modisco.affinitymat.core
reload(modisco.affinitymat.core)
import modisco.affinitymat.transformers
reload(modisco.affinitymat.transformers)
import modisco.aggregator
reload(modisco.aggregator)
import modisco.nearest_neighbors
reload(modisco.nearest_neighbors)
import modisco.affinitymat
reload(modisco.affinitymat)
import modisco.value_provider
reload(modisco.value_provider)
import modisco.core
reload(modisco.core)
import modisco.coordproducers
reload(modisco.coordproducers)
import modisco.metaclusterers
reload(modisco.metaclusterers)
import modisco.clusterinit.memeinit
reload(modisco.clusterinit.memeinit)
import modisco.tfmodisco_workflow.seqlets_to_patterns
reload(modisco.tfmodisco_workflow.seqlets_to_patterns)
import modisco.tfmodisco_workflow.workflow
reload(modisco.tfmodisco_workflow.workflow)
%matplotlib inline
N_CORES = 10
workflow = modisco.tfmodisco_workflow.workflow.TfModiscoWorkflow(
sliding_window_size=21,
flank_size=10,
target_seqlet_fdr=0.2,
min_passing_windows_frac=0.03,
max_passing_windows_frac=0.2,
min_metacluster_size=2000,
min_metacluster_size_frac=0.02,
max_seqlets_per_metacluster=50000,
seqlets_to_patterns_factory=
modisco.tfmodisco_workflow.seqlets_to_patterns.TfModiscoSeqletsToPatternsFactory(
#initclusterer_factory=modisco.clusterinit.memeinit.MemeInitClustererFactory(
# meme_command="/software/meme/5.0.1/bin/meme",
# base_outdir="meme_out",
# num_seqlets_to_use=10000,
# nmotifs=20, n_jobs=4),
use_louvain=False,
trim_to_window_size=30,
initial_flank_to_add=10,
embedder_factory=modisco.seqlet_embedding
.advanced_gapped_kmer
.AdvancedGappedKmerEmbedderFactory(n_jobs=N_CORES),
#kmer_len=6,
#num_gaps=2,
#num_mismatches=0,
n_cores=N_CORES,
final_min_cluster_size=60
)
)
results = workflow(
task_names=["Nanog_profile_wn"],
contrib_scores=contrib_scores,
hypothetical_contribs=hypothetical_contribs,
one_hot=one_hot)
/mnt/lab_data2/avanti/tfmodisco commit 7b8febe0474f86be58181ce8b524db8d579ef018 (HEAD -> clustermergindev2, origin/clustermergindev2) Author: Avanti Shrikumar <avanti.shrikumar@gmail.com> Date: Wed Nov 11 01:20:56 2020 -0800 further speedups /mnt/lab_data2/avanti/tfmodisco_bio_experiments/bpnet/trial1 MEMORY 3.011002368 On task Nanog_profile_wn Computing windowed sums on original Generating null dist peak(mu)= 0.003840833756548818 Computing threshold Thresholds from null dist were -0.0166471004486084 and 0.10157325863838196 Final raw thresholds are -0.0166471004486084 and 0.10157325863838196 Final transformed thresholds are -0.519914596273292 and 0.8223334442472642
Got 9356 coords
After resolving overlaps, got 9356 seqlets
Across all tasks, the weakest transformed threshold used was: 0.519814596273292
MEMORY 3.111776256
9356 identified in total
Reducing weak_threshold_for_counting_sign to match weakest_transformed_thresh, from 0.8 to 0.519814596273292
1 activity patterns with support >= 2000 out of 2 possible patterns
Metacluster sizes: [8719]
Idx to activities: {0: '1'}
MEMORY 3.112534016
On metacluster 0
Metacluster size 8719
Relevant tasks: ('Nanog_profile_wn',)
Relevant signs: (1,)
TfModiscoSeqletsToPatternsFactory: seed=1234
(Round 1) num seqlets: 8719
(Round 1) Computing coarse affmat
MEMORY 3.112554496
Beginning embedding computation
[Parallel(n_jobs=10)]: Using backend LokyBackend with 10 concurrent workers. [Parallel(n_jobs=10)]: Done 30 tasks | elapsed: 4.0s [Parallel(n_jobs=10)]: Done 180 tasks | elapsed: 8.1s [Parallel(n_jobs=10)]: Done 430 tasks | elapsed: 14.3s [Parallel(n_jobs=10)]: Done 780 tasks | elapsed: 22.3s [Parallel(n_jobs=10)]: Done 1230 tasks | elapsed: 32.3s [Parallel(n_jobs=10)]: Done 1780 tasks | elapsed: 44.7s [Parallel(n_jobs=10)]: Done 2430 tasks | elapsed: 59.6s [Parallel(n_jobs=10)]: Done 3180 tasks | elapsed: 1.2min [Parallel(n_jobs=10)]: Done 4030 tasks | elapsed: 1.5min [Parallel(n_jobs=10)]: Done 4980 tasks | elapsed: 1.8min [Parallel(n_jobs=10)]: Done 6030 tasks | elapsed: 2.2min [Parallel(n_jobs=10)]: Done 7180 tasks | elapsed: 2.6min [Parallel(n_jobs=10)]: Done 8430 tasks | elapsed: 3.0min [Parallel(n_jobs=10)]: Done 8719 out of 8719 | elapsed: 3.2min finished [Parallel(n_jobs=10)]: Using backend LokyBackend with 10 concurrent workers. [Parallel(n_jobs=10)]: Done 40 tasks | elapsed: 1.4s [Parallel(n_jobs=10)]: Done 340 tasks | elapsed: 8.8s [Parallel(n_jobs=10)]: Done 840 tasks | elapsed: 20.5s [Parallel(n_jobs=10)]: Done 1540 tasks | elapsed: 37.3s [Parallel(n_jobs=10)]: Done 2440 tasks | elapsed: 56.8s [Parallel(n_jobs=10)]: Done 3540 tasks | elapsed: 1.3min [Parallel(n_jobs=10)]: Done 4840 tasks | elapsed: 1.8min [Parallel(n_jobs=10)]: Done 6340 tasks | elapsed: 2.2min [Parallel(n_jobs=10)]: Done 8040 tasks | elapsed: 2.8min [Parallel(n_jobs=10)]: Done 8700 out of 8719 | elapsed: 3.1min remaining: 0.4s [Parallel(n_jobs=10)]: Done 8719 out of 8719 | elapsed: 3.1min finished [Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers. [Parallel(n_jobs=1)]: Done 8719 out of 8719 | elapsed: 2.7min finished
Constructing csr matrix... csr matrix made in 12.94959282875061 s
[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers. [Parallel(n_jobs=1)]: Done 8719 out of 8719 | elapsed: 2.7min finished
Constructing csr matrix... csr matrix made in 12.955052137374878 s Finished embedding computation in 757.11 s Starting affinity matrix computations Batching in slices of size 500
100%|██████████| 18/18 [01:19<00:00, 4.42s/it]
Batching in slices of size 500
100%|██████████| 18/18 [01:18<00:00, 4.36s/it]
Finished affinity matrix computations in 161.47 s (Round 1) Compute nearest neighbors from coarse affmat MEMORY 8.095776768 Computed nearest neighbors in 7.01 s MEMORY 8.095776768 (Round 1) Computing affinity matrix on nearest neighbors MEMORY 8.095776768 Launching nearest neighbors affmat calculation job MEMORY 8.095780864 Parallel runs completed MEMORY 8.034615296 Job completed in: 71.14 s MEMORY 8.58191872 Launching nearest neighbors affmat calculation job MEMORY 8.58191872 Parallel runs completed MEMORY 8.61149184 Job completed in: 71.31 s MEMORY 9.219612672 (Round 1) Computed affinity matrix on nearest neighbors in 145.53 s MEMORY 8.6115328 Filtered down to 6862 of 8719 (Round 1) Retained 6862 rows out of 8719 after filtering MEMORY 8.611794944 (Round 1) Computing density adapted affmat MEMORY 7.772151808 [t-SNE] Computing 31 nearest neighbors... [t-SNE] Indexed 6862 samples in 0.080s... [t-SNE] Computed neighbors for 6862 samples in 0.483s... [t-SNE] Computed conditional probabilities for sample 1000 / 6862 [t-SNE] Computed conditional probabilities for sample 2000 / 6862 [t-SNE] Computed conditional probabilities for sample 3000 / 6862 [t-SNE] Computed conditional probabilities for sample 4000 / 6862 [t-SNE] Computed conditional probabilities for sample 5000 / 6862 [t-SNE] Computed conditional probabilities for sample 6000 / 6862 [t-SNE] Computed conditional probabilities for sample 6862 / 6862 [t-SNE] Mean sigma: 0.233649 (Round 1) Computing clustering MEMORY 7.772151808 Beginning preprocessing + Leiden
0%| | 0/50 [00:00<?, ?it/s]
Quality: 0.6951482852134592
4%|▍ | 2/50 [00:06<02:37, 3.27s/it]
Quality: 0.6955151158481995
6%|▌ | 3/50 [00:10<02:51, 3.65s/it]
Quality: 0.6955829561489105
14%|█▍ | 7/50 [00:29<03:04, 4.30s/it]
Quality: 0.6963400361673426
100%|██████████| 50/50 [03:58<00:00, 4.77s/it]
Got 23 clusters after round 1
Counts:
{14: 163, 4: 554, 9: 283, 13: 220, 7: 410, 8: 308, 11: 247, 1: 730, 0: 813, 10: 275, 6: 505, 3: 555, 15: 152, 16: 127, 2: 579, 19: 13, 17: 109, 5: 522, 20: 12, 12: 244, 22: 6, 18: 24, 21: 11}
MEMORY 7.395844096
(Round 1) Aggregating seqlets in each cluster
MEMORY 7.395844096
Aggregating for cluster 0 with 813 seqlets
MEMORY 7.395844096
Trimming eliminated 0 seqlets out of 813 Skipped 1 seqlets Removed 27 duplicate seqlets Removed 2 duplicate seqlets Aggregating for cluster 1 with 730 seqlets MEMORY 7.395856384 Trimming eliminated 0 seqlets out of 730 Skipped 1 seqlets Removed 20 duplicate seqlets Aggregating for cluster 2 with 579 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 579 Removed 11 duplicate seqlets Aggregating for cluster 3 with 555 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 555 Removed 4 duplicate seqlets Aggregating for cluster 4 with 554 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 554 Removed 3 duplicate seqlets Aggregating for cluster 5 with 522 seqlets MEMORY 7.39559424 Trimming eliminated 5 seqlets out of 522 Removed 5 duplicate seqlets Aggregating for cluster 6 with 505 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 505 Removed 19 duplicate seqlets Aggregating for cluster 7 with 410 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 410 Removed 10 duplicate seqlets Aggregating for cluster 8 with 308 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 308 Removed 9 duplicate seqlets Aggregating for cluster 9 with 283 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 283 Removed 3 duplicate seqlets Aggregating for cluster 10 with 275 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 275 Removed 3 duplicate seqlets Aggregating for cluster 11 with 247 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 247 Removed 4 duplicate seqlets Aggregating for cluster 12 with 244 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 244 Removed 1 duplicate seqlets Aggregating for cluster 13 with 220 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 220 Aggregating for cluster 14 with 163 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 163 Removed 1 duplicate seqlets Aggregating for cluster 15 with 152 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 152 Aggregating for cluster 16 with 127 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 127 Removed 12 duplicate seqlets Aggregating for cluster 17 with 109 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 109 Removed 1 duplicate seqlets Aggregating for cluster 18 with 24 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 24 Aggregating for cluster 19 with 13 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 13 Removed 5 duplicate seqlets Aggregating for cluster 20 with 12 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 12 Aggregating for cluster 21 with 11 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 11 Aggregating for cluster 22 with 6 seqlets MEMORY 7.39559424 Trimming eliminated 0 seqlets out of 6 (Round 2) num seqlets: 6692 (Round 2) Computing coarse affmat MEMORY 7.39559424 Beginning embedding computation
[Parallel(n_jobs=10)]: Using backend LokyBackend with 10 concurrent workers. [Parallel(n_jobs=10)]: Done 30 tasks | elapsed: 5.5s [Parallel(n_jobs=10)]: Done 180 tasks | elapsed: 8.0s [Parallel(n_jobs=10)]: Done 430 tasks | elapsed: 12.5s [Parallel(n_jobs=10)]: Done 980 tasks | elapsed: 20.7s [Parallel(n_jobs=10)]: Done 1880 tasks | elapsed: 31.6s [Parallel(n_jobs=10)]: Done 2980 tasks | elapsed: 45.9s [Parallel(n_jobs=10)]: Done 4280 tasks | elapsed: 1.1min [Parallel(n_jobs=10)]: Done 5780 tasks | elapsed: 1.4min [Parallel(n_jobs=10)]: Done 6673 out of 6692 | elapsed: 1.5min remaining: 0.3s [Parallel(n_jobs=10)]: Done 6692 out of 6692 | elapsed: 1.5min finished [Parallel(n_jobs=10)]: Using backend LokyBackend with 10 concurrent workers. [Parallel(n_jobs=10)]: Done 40 tasks | elapsed: 0.9s [Parallel(n_jobs=10)]: Done 340 tasks | elapsed: 7.4s [Parallel(n_jobs=10)]: Done 840 tasks | elapsed: 14.9s [Parallel(n_jobs=10)]: Done 1540 tasks | elapsed: 24.0s [Parallel(n_jobs=10)]: Done 2440 tasks | elapsed: 34.3s [Parallel(n_jobs=10)]: Done 3540 tasks | elapsed: 48.5s [Parallel(n_jobs=10)]: Done 4840 tasks | elapsed: 1.1min [Parallel(n_jobs=10)]: Done 6340 tasks | elapsed: 1.4min [Parallel(n_jobs=10)]: Done 6673 out of 6692 | elapsed: 1.5min remaining: 0.3s [Parallel(n_jobs=10)]: Done 6692 out of 6692 | elapsed: 1.5min finished [Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers. [Parallel(n_jobs=1)]: Done 6692 out of 6692 | elapsed: 1.3min finished
Constructing csr matrix... csr matrix made in 6.288353204727173 s
[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers. [Parallel(n_jobs=1)]: Done 6692 out of 6692 | elapsed: 1.3min finished
Constructing csr matrix... csr matrix made in 5.961185693740845 s Finished embedding computation in 362.13 s Starting affinity matrix computations Batching in slices of size 500
100%|██████████| 14/14 [00:30<00:00, 2.16s/it]
Batching in slices of size 500
100%|██████████| 14/14 [00:29<00:00, 2.07s/it]
Finished affinity matrix computations in 61.13 s (Round 2) Compute nearest neighbors from coarse affmat MEMORY 7.72149248 Computed nearest neighbors in 4.38 s MEMORY 7.72018176 (Round 2) Computing affinity matrix on nearest neighbors MEMORY 7.72018176 Launching nearest neighbors affmat calculation job MEMORY 7.72018176 Parallel runs completed MEMORY 7.730184192 Job completed in: 77.2 s MEMORY 7.988293632 Launching nearest neighbors affmat calculation job MEMORY 7.988293632 Parallel runs completed MEMORY 8.003936256 Job completed in: 76.89 s MEMORY 8.362184704 (Round 2) Computed affinity matrix on nearest neighbors in 156.33 s MEMORY 8.003944448 Not applying filtering for rounds above first round MEMORY 8.003944448 (Round 2) Computing density adapted affmat MEMORY 7.645679616 [t-SNE] Computing 31 nearest neighbors... [t-SNE] Indexed 6692 samples in 0.075s... [t-SNE] Computed neighbors for 6692 samples in 0.449s... [t-SNE] Computed conditional probabilities for sample 1000 / 6692 [t-SNE] Computed conditional probabilities for sample 2000 / 6692 [t-SNE] Computed conditional probabilities for sample 3000 / 6692 [t-SNE] Computed conditional probabilities for sample 4000 / 6692 [t-SNE] Computed conditional probabilities for sample 5000 / 6692 [t-SNE] Computed conditional probabilities for sample 6000 / 6692 [t-SNE] Computed conditional probabilities for sample 6692 / 6692 [t-SNE] Mean sigma: 0.252153 (Round 2) Computing clustering MEMORY 7.645679616 Beginning preprocessing + Leiden
0%| | 0/50 [00:00<?, ?it/s]
Quality: 0.6874693563873155
4%|▍ | 2/50 [00:07<03:17, 4.11s/it]
Quality: 0.688261494710417
6%|▌ | 3/50 [00:12<03:20, 4.27s/it]
Quality: 0.6882986076313621
10%|█ | 5/50 [00:21<03:14, 4.33s/it]
Quality: 0.6883395788609108
12%|█▏ | 6/50 [00:26<03:30, 4.79s/it]
Quality: 0.6884912950475355
14%|█▍ | 7/50 [00:32<03:32, 4.95s/it]
Quality: 0.6887325307101226
52%|█████▏ | 26/50 [02:13<02:02, 5.12s/it]
Quality: 0.6890034264550987
100%|██████████| 50/50 [04:05<00:00, 4.91s/it]
Got 26 clusters after round 2
Counts:
{0: 1008, 15: 108, 11: 255, 6: 371, 3: 559, 8: 296, 9: 289, 12: 252, 1: 708, 2: 610, 19: 37, 10: 259, 17: 52, 7: 365, 22: 10, 13: 241, 16: 94, 4: 517, 21: 19, 25: 2, 5: 426, 14: 140, 20: 26, 18: 43, 24: 2, 23: 3}
MEMORY 7.287156736
(Round 2) Aggregating seqlets in each cluster
MEMORY 7.286894592
Aggregating for cluster 0 with 1008 seqlets
MEMORY 7.286894592
Trimming eliminated 0 seqlets out of 1008 Removed 95 duplicate seqlets Aggregating for cluster 1 with 708 seqlets MEMORY 7.286894592 Trimming eliminated 0 seqlets out of 708 Removed 65 duplicate seqlets Aggregating for cluster 2 with 610 seqlets MEMORY 7.286894592 Trimming eliminated 0 seqlets out of 610 Removed 97 duplicate seqlets Aggregating for cluster 3 with 559 seqlets MEMORY 7.286894592 Trimming eliminated 0 seqlets out of 559 Removed 70 duplicate seqlets Aggregating for cluster 4 with 517 seqlets MEMORY 7.286894592 Trimming eliminated 0 seqlets out of 517 Removed 47 duplicate seqlets Aggregating for cluster 5 with 426 seqlets MEMORY 7.286894592 Trimming eliminated 0 seqlets out of 426 Removed 21 duplicate seqlets Aggregating for cluster 6 with 371 seqlets MEMORY 7.286894592 Trimming eliminated 0 seqlets out of 371 Removed 60 duplicate seqlets Aggregating for cluster 7 with 365 seqlets MEMORY 7.286894592 Trimming eliminated 0 seqlets out of 365 Skipped 1 seqlets Removed 48 duplicate seqlets Aggregating for cluster 8 with 296 seqlets MEMORY 7.286894592 Trimming eliminated 0 seqlets out of 296 Removed 33 duplicate seqlets Aggregating for cluster 9 with 289 seqlets MEMORY 7.286894592 Trimming eliminated 0 seqlets out of 289 Removed 21 duplicate seqlets Aggregating for cluster 10 with 259 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 259 Removed 24 duplicate seqlets Aggregating for cluster 11 with 255 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 255 Removed 25 duplicate seqlets Aggregating for cluster 12 with 252 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 252 Removed 32 duplicate seqlets Aggregating for cluster 13 with 241 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 241 Removed 8 duplicate seqlets Aggregating for cluster 14 with 140 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 140 Removed 19 duplicate seqlets Aggregating for cluster 15 with 108 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 108 Removed 10 duplicate seqlets Aggregating for cluster 16 with 94 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 94 Removed 4 duplicate seqlets Aggregating for cluster 17 with 52 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 52 Removed 2 duplicate seqlets Aggregating for cluster 18 with 43 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 43 Removed 1 duplicate seqlets Aggregating for cluster 19 with 37 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 37 Removed 10 duplicate seqlets Aggregating for cluster 20 with 26 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 26 Removed 2 duplicate seqlets Aggregating for cluster 21 with 19 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 19 Aggregating for cluster 22 with 10 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 10 Removed 1 duplicate seqlets Aggregating for cluster 23 with 3 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 3 Aggregating for cluster 24 with 2 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 2 Removed 1 duplicate seqlets Aggregating for cluster 25 with 2 seqlets MEMORY 7.286898688 Trimming eliminated 0 seqlets out of 2 Removed 1 duplicate seqlets Got 26 clusters Splitting into subclusters... MEMORY 7.286898688 Inspecting for spurious merging Wrote graph to binary file in 1.4457039833068848 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00451446 After 2 runs, maximum modularity is Q = 0.00552143 After 5 runs, maximum modularity is Q = 0.00552165 After 10 runs, maximum modularity is Q = 0.00552197 After 16 runs, maximum modularity is Q = 0.00552206 Louvain completed 36 runs in 13.90524697303772 seconds Similarity is 0.8198563; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.7074315547943115 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00411288 After 3 runs, maximum modularity is Q = 0.00413864 After 5 runs, maximum modularity is Q = 0.00414135 After 6 runs, maximum modularity is Q = 0.00452861 Louvain completed 26 runs in 9.242239713668823 seconds Similarity is 0.8779705; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.4563925266265869 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00396207 Louvain completed 21 runs in 6.902742624282837 seconds Similarity is 0.91017836; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.41028285026550293 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00478221 After 2 runs, maximum modularity is Q = 0.00478263 Louvain completed 22 runs in 7.319305181503296 seconds Similarity is 0.8287699; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.38095951080322266 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00542467 Louvain completed 21 runs in 6.6480872631073 seconds Similarity is 0.95550156; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.28071141242980957 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.0045395 Louvain completed 21 runs in 6.43311882019043 seconds Similarity is 0.95848453; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.16794228553771973 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00455859 After 14 runs, maximum modularity is Q = 0.00455919 Louvain completed 34 runs in 10.197011947631836 seconds Similarity is 0.8101196; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.17093992233276367 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00487057 After 2 runs, maximum modularity is Q = 0.00487147 After 8 runs, maximum modularity is Q = 0.00487257 Louvain completed 28 runs in 8.762409210205078 seconds Similarity is 0.85416365; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.12067031860351562 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00466681 After 3 runs, maximum modularity is Q = 0.00466773 After 11 runs, maximum modularity is Q = 0.00467478 Louvain completed 31 runs in 9.442825555801392 seconds Similarity is 0.82785136; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.1267070770263672 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00439833 After 4 runs, maximum modularity is Q = 0.0047683 Louvain completed 24 runs in 7.80460262298584 seconds Similarity is 0.8733609; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.09595561027526855 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00526389 After 2 runs, maximum modularity is Q = 0.00540827 Louvain completed 22 runs in 6.913608074188232 seconds Similarity is 0.775664; is_dissimilar is True Inspecting for spurious merging Wrote graph to binary file in 0.026412487030029297 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00366981 After 2 runs, maximum modularity is Q = 0.00371541 Louvain completed 22 runs in 6.490928411483765 seconds Similarity is 0.9330266; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.024262428283691406 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00724151 After 5 runs, maximum modularity is Q = 0.00724152 Louvain completed 25 runs in 7.257654905319214 seconds Similarity is 0.76841575; is_dissimilar is True Inspecting for spurious merging Wrote graph to binary file in 0.007512331008911133 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00523494 After 8 runs, maximum modularity is Q = 0.00567467 Louvain completed 28 runs in 8.279329538345337 seconds Similarity is 0.6330159; is_dissimilar is True Got 4 subclusters Inspecting for spurious merging Wrote graph to binary file in 0.09163475036621094 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00779223 Louvain completed 21 runs in 6.418339252471924 seconds Similarity is 0.85547394; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.08720588684082031 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = -0.000392897 After 2 runs, maximum modularity is Q = -0.000367387 After 3 runs, maximum modularity is Q = 0.00388567 Louvain completed 23 runs in 7.315288782119751 seconds Similarity is 0.82440853; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.09656405448913574 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00735352 After 2 runs, maximum modularity is Q = 0.0075461 After 9 runs, maximum modularity is Q = 0.00755681 Louvain completed 29 runs in 8.982174158096313 seconds Similarity is 0.7522481; is_dissimilar is True Inspecting for spurious merging Wrote graph to binary file in 0.02894115447998047 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.0036922 Louvain completed 21 runs in 6.463350772857666 seconds Similarity is 0.8692113; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.021619081497192383 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.0116146 Louvain completed 21 runs in 6.318153381347656 seconds Similarity is 0.60243195; is_dissimilar is True Inspecting for spurious merging Wrote graph to binary file in 0.0074808597564697266 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00813871 Louvain completed 21 runs in 6.138269662857056 seconds Similarity is 0.3966871; is_dissimilar is True Got 4 subclusters Inspecting for spurious merging Wrote graph to binary file in 0.026814699172973633 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00801927 After 2 runs, maximum modularity is Q = 0.0093038 Louvain completed 22 runs in 6.3336615562438965 seconds Similarity is 0.80851513; is_dissimilar is False Inspecting for spurious merging Wrote graph to binary file in 0.018332719802856445 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00871946 After 4 runs, maximum modularity is Q = 0.0087199 Louvain completed 24 runs in 7.220625638961792 seconds Similarity is 0.5963003; is_dissimilar is True Got 2 subclusters Inspecting for spurious merging Wrote graph to binary file in 0.015324592590332031 seconds Running Louvain modularity optimization After 1 runs, maximum modularity is Q = 0.00535572 After 7 runs, maximum modularity is Q = 0.00535573 Louvain completed 27 runs in 7.9639997482299805 seconds Similarity is 0.8100425; is_dissimilar is False Merging on 33 clusters MEMORY 7.286857728 On merging iteration 1 Numbers for each pattern pre-subsample: [913, 643, 513, 489, 470, 405, 311, 316, 263, 268, 120, 34, 55, 26, 230, 220, 125, 30, 48, 30, 121, 57, 41, 90, 50, 42, 27, 24, 19, 9, 3, 1, 1] Numbers after subsampling: [300, 300, 300, 300, 300, 300, 300, 300, 263, 268, 120, 34, 55, 26, 230, 220, 125, 30, 48, 30, 121, 57, 41, 90, 50, 42, 27, 24, 19, 9, 3, 1, 1] Computing sim between patterns 0 and 1 Time taken: 5.455727815628052 Computing sim between patterns 0 and 2 Time taken: 0.6849052906036377 Computing sim between patterns 0 and 3 Time taken: 0.5459725856781006 Computing sim between patterns 0 and 4 Time taken: 0.5553059577941895 Computing sim between patterns 0 and 5 Time taken: 0.5877456665039062 Computing sim between patterns 0 and 6 Time taken: 0.5868134498596191 Computing sim between patterns 0 and 7 Time taken: 0.5657408237457275 Computing sim between patterns 0 and 8 Time taken: 0.5549657344818115 Computing sim between patterns 0 and 9 Time taken: 0.5845654010772705 Computing sim between patterns 0 and 10 Time taken: 0.5407874584197998 Computing sim between patterns 0 and 11 Time taken: 0.474102258682251 Computing sim between patterns 0 and 12 Time taken: 0.46868014335632324 Computing sim between patterns 0 and 13 Time taken: 0.45297741889953613 Computing sim between patterns 0 and 14 Time taken: 0.505328893661499 Computing sim between patterns 0 and 15 Time taken: 0.4982876777648926 Computing sim between patterns 0 and 16 Time taken: 0.48192930221557617 Computing sim between patterns 0 and 17 Time taken: 0.43721914291381836 Computing sim between patterns 0 and 18 Time taken: 0.4433736801147461 Computing sim between patterns 0 and 19 Time taken: 0.473888635635376 Computing sim between patterns 0 and 20 Time taken: 0.47051429748535156 Computing sim between patterns 0 and 21 Time taken: 0.44431114196777344 Computing sim between patterns 0 and 22 Time taken: 0.4615769386291504 Computing sim between patterns 0 and 23 Time taken: 0.4957578182220459 Computing sim between patterns 0 and 24 Time taken: 0.4406883716583252 Computing sim between patterns 0 and 25 Time taken: 0.4500110149383545 Computing sim between patterns 0 and 26 Time taken: 0.5096147060394287 Computing sim between patterns 0 and 27 Time taken: 0.4699430465698242 Computing sim between patterns 0 and 28 Time taken: 0.46210551261901855 Computing sim between patterns 0 and 29 Time taken: 0.47966933250427246 Computing sim between patterns 0 and 30 Time taken: 0.4443492889404297 Computing sim between patterns 0 and 31 Time taken: 0.4597470760345459 Computing sim between patterns 0 and 32 Time taken: 0.459209680557251 Computing sim between patterns 1 and 0 Time taken: 0.5556416511535645 Computing sim between patterns 1 and 2 Time taken: 0.5455365180969238 Computing sim between patterns 1 and 3 Time taken: 0.5534210205078125 Computing sim between patterns 1 and 4 Time taken: 0.5520434379577637 Computing sim between patterns 1 and 5 Time taken: 0.5522515773773193 Computing sim between patterns 1 and 6 Time taken: 0.6243774890899658 Computing sim between patterns 1 and 7 Time taken: 0.5423836708068848 Computing sim between patterns 1 and 8 Time taken: 0.5330257415771484 Computing sim between patterns 1 and 9 Time taken: 0.5739240646362305 Computing sim between patterns 1 and 10 Time taken: 0.484363317489624 Computing sim between patterns 1 and 11 Time taken: 0.4592781066894531 Computing sim between patterns 1 and 12 Time taken: 0.46018195152282715 Computing sim between patterns 1 and 13 Time taken: 0.46375370025634766 Computing sim between patterns 1 and 14 Time taken: 0.538825511932373 Computing sim between patterns 1 and 15 Time taken: 0.519355058670044 Computing sim between patterns 1 and 16 Time taken: 0.482774019241333 Computing sim between patterns 1 and 17 Time taken: 0.45851635932922363 Computing sim between patterns 1 and 18 Time taken: 0.516089916229248 Computing sim between patterns 1 and 19 Time taken: 0.45224642753601074 Computing sim between patterns 1 and 20 Time taken: 0.5473887920379639 Computing sim between patterns 1 and 21 Time taken: 0.4660828113555908 Computing sim between patterns 1 and 22 Time taken: 0.4810492992401123 Computing sim between patterns 1 and 23 Time taken: 0.5154416561126709 Computing sim between patterns 1 and 24 Time taken: 0.4877450466156006 Computing sim between patterns 1 and 25 Time taken: 0.5047845840454102 Computing sim between patterns 1 and 26 Time taken: 0.45813536643981934 Computing sim between patterns 1 and 27 Time taken: 0.48764753341674805 Computing sim between patterns 1 and 28 Time taken: 0.4843754768371582 Computing sim between patterns 1 and 29 Time taken: 0.4379398822784424 Computing sim between patterns 1 and 30 Time taken: 0.4875643253326416 Computing sim between patterns 1 and 31 Time taken: 0.4712197780609131 Computing sim between patterns 1 and 32 Time taken: 0.44930505752563477 Computing sim between patterns 2 and 0 Time taken: 0.5767800807952881 Computing sim between patterns 2 and 1 Time taken: 0.6106915473937988 Computing sim between patterns 2 and 3 Time taken: 0.5595803260803223 Computing sim between patterns 2 and 4 Time taken: 0.6033375263214111 Computing sim between patterns 2 and 5 Time taken: 0.5653624534606934 Computing sim between patterns 2 and 6 Time taken: 0.5600550174713135 Computing sim between patterns 2 and 7 Time taken: 0.5879695415496826 Computing sim between patterns 2 and 8 Time taken: 0.5406956672668457 Computing sim between patterns 2 and 9 Time taken: 0.5618619918823242 Computing sim between patterns 2 and 10 Time taken: 0.5002591609954834 Computing sim between patterns 2 and 11 Time taken: 0.5060577392578125 Computing sim between patterns 2 and 12 Time taken: 0.6222951412200928 Computing sim between patterns 2 and 13 Time taken: 0.4862639904022217 Computing sim between patterns 2 and 14 Time taken: 0.5167922973632812 Computing sim between patterns 2 and 15 Time taken: 0.5187587738037109 Computing sim between patterns 2 and 16 Time taken: 0.48281264305114746 Computing sim between patterns 2 and 17 Time taken: 0.8979694843292236 Computing sim between patterns 2 and 18 Time taken: 0.47479701042175293 Computing sim between patterns 2 and 19 Time taken: 0.4448106288909912 Computing sim between patterns 2 and 20 Time taken: 0.4806065559387207 Computing sim between patterns 2 and 21 Time taken: 0.4518616199493408 Computing sim between patterns 2 and 22 Time taken: 0.46547722816467285 Computing sim between patterns 2 and 23 Time taken: 0.48954176902770996 Computing sim between patterns 2 and 24 Time taken: 0.46669745445251465 Computing sim between patterns 2 and 25 Time taken: 0.4986855983734131 Computing sim between patterns 2 and 26 Time taken: 0.4542884826660156 Computing sim between patterns 2 and 27 Time taken: 0.4400308132171631 Computing sim between patterns 2 and 28 Time taken: 0.4676856994628906 Computing sim between patterns 2 and 29 Time taken: 0.4460868835449219 Computing sim between patterns 2 and 30 Time taken: 0.45402050018310547 Computing sim between patterns 2 and 31 Time taken: 0.44857239723205566 Computing sim between patterns 2 and 32 Time taken: 0.47265100479125977 Computing sim between patterns 3 and 0 Time taken: 0.547832727432251 Computing sim between patterns 3 and 1 Time taken: 0.5278480052947998 Computing sim between patterns 3 and 2 Time taken: 0.5865809917449951 Computing sim between patterns 3 and 4 Time taken: 0.57244873046875 Computing sim between patterns 3 and 5 Time taken: 0.5622093677520752 Computing sim between patterns 3 and 6 Time taken: 0.5756502151489258 Computing sim between patterns 3 and 7 Time taken: 0.5699493885040283 Computing sim between patterns 3 and 8 Time taken: 0.585259199142456 Computing sim between patterns 3 and 9 Time taken: 0.5244419574737549 Computing sim between patterns 3 and 10 Time taken: 0.483079195022583 Computing sim between patterns 3 and 11 Time taken: 0.5239114761352539 Computing sim between patterns 3 and 12 Time taken: 0.511652946472168 Computing sim between patterns 3 and 13 Time taken: 0.44462037086486816 Computing sim between patterns 3 and 14 Time taken: 0.5408172607421875 Computing sim between patterns 3 and 15 Time taken: 0.5140151977539062 Computing sim between patterns 3 and 16 Time taken: 0.4749283790588379 Computing sim between patterns 3 and 17 Time taken: 0.4801638126373291 Computing sim between patterns 3 and 18 Time taken: 0.5024993419647217 Computing sim between patterns 3 and 19 Time taken: 0.44225454330444336 Computing sim between patterns 3 and 20 Time taken: 0.4970998764038086 Computing sim between patterns 3 and 21 Time taken: 0.487135648727417 Computing sim between patterns 3 and 22 Time taken: 0.48138880729675293 Computing sim between patterns 3 and 23 Time taken: 0.5116736888885498 Computing sim between patterns 3 and 24 Time taken: 0.48902463912963867 Computing sim between patterns 3 and 25 Time taken: 0.44394469261169434 Computing sim between patterns 3 and 26 Time taken: 0.4447367191314697 Computing sim between patterns 3 and 27 Time taken: 0.4629478454589844 Computing sim between patterns 3 and 28 Time taken: 0.4714539051055908 Computing sim between patterns 3 and 29 Time taken: 0.46468067169189453 Computing sim between patterns 3 and 30 Time taken: 0.4619777202606201 Computing sim between patterns 3 and 31 Time taken: 0.49353933334350586 Computing sim between patterns 3 and 32 Time taken: 0.5289499759674072 Computing sim between patterns 4 and 0 Time taken: 0.6019320487976074 Computing sim between patterns 4 and 1 Time taken: 0.5631821155548096 Computing sim between patterns 4 and 2 Time taken: 0.5250058174133301 Computing sim between patterns 4 and 3 Time taken: 0.5957019329071045 Computing sim between patterns 4 and 5 Time taken: 0.5549020767211914 Computing sim between patterns 4 and 6 Time taken: 0.6103620529174805 Computing sim between patterns 4 and 7 Time taken: 0.5488927364349365 Computing sim between patterns 4 and 8 Time taken: 0.5265154838562012 Computing sim between patterns 4 and 9 Time taken: 0.5535409450531006 Computing sim between patterns 4 and 10 Time taken: 0.4878346920013428 Computing sim between patterns 4 and 11 Time taken: 0.46501660346984863 Computing sim between patterns 4 and 12 Time taken: 0.48875975608825684 Computing sim between patterns 4 and 13 Time taken: 0.4637300968170166 Computing sim between patterns 4 and 14 Time taken: 0.5122060775756836 Computing sim between patterns 4 and 15 Time taken: 0.5229012966156006 Computing sim between patterns 4 and 16 Time taken: 0.47882509231567383 Computing sim between patterns 4 and 17 Time taken: 0.443331241607666 Computing sim between patterns 4 and 18 Time taken: 0.48633480072021484 Computing sim between patterns 4 and 19 Time taken: 0.45314550399780273 Computing sim between patterns 4 and 20 Time taken: 0.4841423034667969 Computing sim between patterns 4 and 21 Time taken: 0.44539690017700195 Computing sim between patterns 4 and 22 Time taken: 0.49315857887268066 Computing sim between patterns 4 and 23 Time taken: 0.475231409072876 Computing sim between patterns 4 and 24 Time taken: 0.45552706718444824 Computing sim between patterns 4 and 25 Time taken: 0.5527455806732178 Computing sim between patterns 4 and 26 Time taken: 0.45336174964904785 Computing sim between patterns 4 and 27 Time taken: 0.4477236270904541 Computing sim between patterns 4 and 28 Time taken: 0.44989800453186035 Computing sim between patterns 4 and 29 Time taken: 0.48605871200561523 Computing sim between patterns 4 and 30 Time taken: 0.46524715423583984 Computing sim between patterns 4 and 31 Time taken: 0.48218655586242676 Computing sim between patterns 4 and 32 Time taken: 0.45865750312805176 Computing sim between patterns 5 and 0 Time taken: 0.5579891204833984 Computing sim between patterns 5 and 1 Time taken: 0.5353798866271973 Computing sim between patterns 5 and 2 Time taken: 0.6112115383148193 Computing sim between patterns 5 and 3 Time taken: 0.5502462387084961 Computing sim between patterns 5 and 4 Time taken: 0.5739641189575195 Computing sim between patterns 5 and 6 Time taken: 0.5599420070648193 Computing sim between patterns 5 and 7 Time taken: 0.5534586906433105 Computing sim between patterns 5 and 8 Time taken: 0.5817887783050537 Computing sim between patterns 5 and 9 Time taken: 0.9871478080749512 Computing sim between patterns 5 and 10 Time taken: 0.5042471885681152 Computing sim between patterns 5 and 11 Time taken: 0.45281338691711426 Computing sim between patterns 5 and 12 Time taken: 0.4458444118499756 Computing sim between patterns 5 and 13 Time taken: 0.44104623794555664 Computing sim between patterns 5 and 14 Time taken: 0.5586414337158203 Computing sim between patterns 5 and 15 Time taken: 0.49494314193725586 Computing sim between patterns 5 and 16 Time taken: 0.48517870903015137 Computing sim between patterns 5 and 17 Time taken: 0.6039023399353027 Computing sim between patterns 5 and 18 Time taken: 0.4964118003845215 Computing sim between patterns 5 and 19 Time taken: 0.46128010749816895 Computing sim between patterns 5 and 20 Time taken: 0.5218393802642822 Computing sim between patterns 5 and 21 Time taken: 0.46262216567993164 Computing sim between patterns 5 and 22 Time taken: 0.4736368656158447 Computing sim between patterns 5 and 23 Time taken: 0.48993897438049316 Computing sim between patterns 5 and 24 Time taken: 0.4539213180541992 Computing sim between patterns 5 and 25 Time taken: 0.45131945610046387 Computing sim between patterns 5 and 26 Time taken: 0.48613595962524414 Computing sim between patterns 5 and 27 Time taken: 0.4802248477935791 Computing sim between patterns 5 and 28 Time taken: 0.472736120223999 Computing sim between patterns 5 and 29 Time taken: 0.4640319347381592 Computing sim between patterns 5 and 30 Time taken: 0.49123477935791016 Computing sim between patterns 5 and 31 Time taken: 0.4327254295349121 Computing sim between patterns 5 and 32 Time taken: 0.43706250190734863 Computing sim between patterns 6 and 0 Time taken: 0.5737202167510986 Computing sim between patterns 6 and 1 Time taken: 0.5899324417114258 Computing sim between patterns 6 and 2 Time taken: 0.5773296356201172 Computing sim between patterns 6 and 3 Time taken: 0.5878748893737793 Computing sim between patterns 6 and 4 Time taken: 0.5561678409576416 Computing sim between patterns 6 and 5 Time taken: 0.5674448013305664 Computing sim between patterns 6 and 7 Time taken: 0.5695843696594238 Computing sim between patterns 6 and 8 Time taken: 0.5201334953308105 Computing sim between patterns 6 and 9 Time taken: 0.5810089111328125 Computing sim between patterns 6 and 10 Time taken: 0.6318256855010986 Computing sim between patterns 6 and 11 Time taken: 0.44913458824157715 Computing sim between patterns 6 and 12 Time taken: 0.4663820266723633 Computing sim between patterns 6 and 13 Time taken: 0.4631154537200928 Computing sim between patterns 6 and 14 Time taken: 0.5147466659545898 Computing sim between patterns 6 and 15 Time taken: 0.5375697612762451 Computing sim between patterns 6 and 16 Time taken: 0.4665381908416748 Computing sim between patterns 6 and 17 Time taken: 0.44019198417663574 Computing sim between patterns 6 and 18 Time taken: 0.46738481521606445 Computing sim between patterns 6 and 19 Time taken: 0.448012113571167 Computing sim between patterns 6 and 20 Time taken: 0.4830770492553711 Computing sim between patterns 6 and 21 Time taken: 0.48612403869628906 Computing sim between patterns 6 and 22 Time taken: 0.4727783203125 Computing sim between patterns 6 and 23 Time taken: 0.47852659225463867 Computing sim between patterns 6 and 24 Time taken: 0.4758622646331787 Computing sim between patterns 6 and 25 Time taken: 0.4926273822784424 Computing sim between patterns 6 and 26 Time taken: 0.45550537109375 Computing sim between patterns 6 and 27 Time taken: 0.4520223140716553 Computing sim between patterns 6 and 28 Time taken: 0.4769463539123535 Computing sim between patterns 6 and 29 Time taken: 0.5155091285705566 Computing sim between patterns 6 and 30 Time taken: 0.47185301780700684 Computing sim between patterns 6 and 31 Time taken: 0.4607253074645996 Computing sim between patterns 6 and 32 Time taken: 0.4672117233276367 Computing sim between patterns 7 and 0 Time taken: 0.5608687400817871 Computing sim between patterns 7 and 1 Time taken: 0.5434908866882324 Computing sim between patterns 7 and 2 Time taken: 0.5500850677490234 Computing sim between patterns 7 and 3 Time taken: 0.6291732788085938 Computing sim between patterns 7 and 4 Time taken: 0.574347972869873 Computing sim between patterns 7 and 5 Time taken: 0.5229241847991943 Computing sim between patterns 7 and 6 Time taken: 0.5524797439575195 Computing sim between patterns 7 and 8 Time taken: 0.5304443836212158 Computing sim between patterns 7 and 9 Time taken: 0.5450448989868164 Computing sim between patterns 7 and 10 Time taken: 0.4971139430999756 Computing sim between patterns 7 and 11 Time taken: 0.4563775062561035 Computing sim between patterns 7 and 12 Time taken: 0.4672725200653076 Computing sim between patterns 7 and 13 Time taken: 0.4664595127105713 Computing sim between patterns 7 and 14 Time taken: 0.5074424743652344 Computing sim between patterns 7 and 15 Time taken: 0.5386831760406494 Computing sim between patterns 7 and 16 Time taken: 0.46661829948425293 Computing sim between patterns 7 and 17 Time taken: 0.47472476959228516 Computing sim between patterns 7 and 18 Time taken: 0.5383896827697754 Computing sim between patterns 7 and 19 Time taken: 0.46166157722473145 Computing sim between patterns 7 and 20 Time taken: 0.49146437644958496 Computing sim between patterns 7 and 21 Time taken: 0.4574894905090332 Computing sim between patterns 7 and 22 Time taken: 0.4584224224090576 Computing sim between patterns 7 and 23 Time taken: 0.4889543056488037 Computing sim between patterns 7 and 24 Time taken: 0.4984133243560791 Computing sim between patterns 7 and 25 Time taken: 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0.6570401191711426 Computing sim between patterns 8 and 7 Time taken: 0.5932722091674805 Computing sim between patterns 8 and 9 Time taken: 0.570929765701294 Computing sim between patterns 8 and 10 Time taken: 0.5383384227752686 Computing sim between patterns 8 and 11 Time taken: 0.5633420944213867 Computing sim between patterns 8 and 12 Time taken: 0.5160634517669678 Computing sim between patterns 8 and 13 Time taken: 0.5649714469909668 Computing sim between patterns 8 and 14 Time taken: 0.5458080768585205 Computing sim between patterns 8 and 15 Time taken: 0.5419003963470459 Computing sim between patterns 8 and 16 Time taken: 0.5190179347991943 Computing sim between patterns 8 and 17 Time taken: 0.5352039337158203 Computing sim between patterns 8 and 18 Time taken: 0.49914026260375977 Computing sim between patterns 8 and 19 Time taken: 0.49529266357421875 Computing sim between patterns 8 and 20 Time taken: 0.5386981964111328 Computing sim between patterns 8 and 21 Time taken: 0.5667669773101807 Computing sim between patterns 8 and 22 Time taken: 0.5525975227355957 Computing sim between patterns 8 and 23 Time taken: 0.5338840484619141 Computing sim between patterns 8 and 24 Time taken: 0.5282163619995117 Computing sim between patterns 8 and 25 Time taken: 0.5553035736083984 Computing sim between patterns 8 and 26 Time taken: 0.5441303253173828 Computing sim between patterns 8 and 27 Time taken: 0.49922871589660645 Computing sim between patterns 8 and 28 Time taken: 0.5402884483337402 Computing sim between patterns 8 and 29 Time taken: 0.5681314468383789 Computing sim between patterns 8 and 30 Time taken: 0.4927394390106201 Computing sim between patterns 8 and 31 Time taken: 0.5149235725402832 Computing sim between patterns 8 and 32 Time taken: 0.505702018737793 Computing sim between patterns 9 and 0 Time taken: 0.6504290103912354 Computing sim between patterns 9 and 1 Time taken: 0.6621532440185547 Computing sim between patterns 9 and 2 Time taken: 0.620368480682373 Computing sim between patterns 9 and 3 Time taken: 0.6351699829101562 Computing sim between patterns 9 and 4 Time taken: 0.6664485931396484 Computing sim between patterns 9 and 5 Time taken: 0.61464524269104 Computing sim between patterns 9 and 6 Time taken: 0.626312255859375 Computing sim between patterns 9 and 7 Time taken: 0.6503355503082275 Computing sim between patterns 9 and 8 Time taken: 0.652947187423706 Computing sim between patterns 9 and 10 Time taken: 0.6247594356536865 Computing sim between patterns 9 and 11 Time taken: 0.5155844688415527 Computing sim between patterns 9 and 12 Time taken: 0.5342602729797363 Computing sim between patterns 9 and 13 Time taken: 0.6802637577056885 Computing sim between patterns 9 and 14 Time taken: 0.6075053215026855 Computing sim between patterns 9 and 15 Time taken: 0.641524076461792 Computing sim between patterns 9 and 16 Time taken: 0.5676395893096924 Computing sim between patterns 9 and 17 Time taken: 0.5497829914093018 Computing sim between patterns 9 and 18 Time taken: 0.5348489284515381 Computing sim between patterns 9 and 19 Time taken: 0.540414571762085 Computing sim between patterns 9 and 20 Time taken: 0.5422043800354004 Computing sim between patterns 9 and 21 Time taken: 0.5473968982696533 Computing sim between patterns 9 and 22 Time taken: 0.5611011981964111 Computing sim between patterns 9 and 23 Time taken: 0.5901844501495361 Computing sim between patterns 9 and 24 Time taken: 0.547196626663208 Computing sim between patterns 9 and 25 Time taken: 0.5298705101013184 Computing sim between patterns 9 and 26 Time taken: 0.5648467540740967 Computing sim between patterns 9 and 27 Time taken: 0.566901683807373 Computing sim between patterns 9 and 28 Time taken: 0.5388708114624023 Computing sim between patterns 9 and 29 Time taken: 0.5283327102661133 Computing sim between patterns 9 and 30 Time taken: 0.5544545650482178 Computing sim between patterns 9 and 31 Time taken: 0.522862434387207 Computing sim between patterns 9 and 32 Time taken: 0.5259897708892822 Computing sim between patterns 10 and 0 Time taken: 0.3208801746368408 Computing sim between patterns 10 and 1 Time taken: 0.3454580307006836 Computing sim between patterns 10 and 2 Time taken: 0.31954002380371094 Computing sim between patterns 10 and 3 Time taken: 0.34113287925720215 Computing sim between patterns 10 and 4 Time taken: 0.3364524841308594 Computing sim between patterns 10 and 5 Time taken: 0.33609676361083984 Computing sim between patterns 10 and 6 Time taken: 0.3581583499908447 Computing sim between patterns 10 and 7 Time taken: 0.32643604278564453 Computing sim between patterns 10 and 8 Time taken: 0.45102572441101074 Computing sim between patterns 10 and 9 Time taken: 0.30877113342285156 Computing sim between patterns 10 and 11 Time taken: 0.3011751174926758 Computing sim between patterns 10 and 12 Time taken: 0.29967665672302246 Computing sim between patterns 10 and 13 Time taken: 0.2888026237487793 Computing sim between patterns 10 and 14 Time taken: 0.3160862922668457 Computing sim between patterns 10 and 15 Time taken: 0.3060338497161865 Computing sim between patterns 10 and 16 Time taken: 0.3046724796295166 Computing sim between patterns 10 and 17 Time taken: 0.2892138957977295 Computing sim between patterns 10 and 18 Time taken: 0.2899436950683594 Computing sim between patterns 10 and 19 Time taken: 0.2998642921447754 Computing sim between patterns 10 and 20 Time taken: 0.32016587257385254 Computing sim between patterns 10 and 21 Time taken: 0.3034238815307617 Computing sim between patterns 10 and 22 Time taken: 0.29686737060546875 Computing sim between patterns 10 and 23 Time taken: 0.2847611904144287 Computing sim between patterns 10 and 24 Time taken: 0.3129689693450928 Computing sim between patterns 10 and 25 Time taken: 0.2922687530517578 Computing sim between patterns 10 and 26 Time taken: 0.2817261219024658 Computing sim between patterns 10 and 27 Time taken: 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taken: 0.14172053337097168 Computing sim between patterns 11 and 9 Time taken: 0.14276456832885742 Computing sim between patterns 11 and 10 Time taken: 0.12247633934020996 Computing sim between patterns 11 and 12 Time taken: 0.11976408958435059 Computing sim between patterns 11 and 13 Time taken: 0.11969304084777832 Computing sim between patterns 11 and 14 Time taken: 0.14375066757202148 Computing sim between patterns 11 and 15 Time taken: 0.13706707954406738 Computing sim between patterns 11 and 16 Time taken: 0.12301135063171387 Computing sim between patterns 11 and 17 Time taken: 0.11819720268249512 Computing sim between patterns 11 and 18 Time taken: 0.11752033233642578 Computing sim between patterns 11 and 19 Time taken: 0.11678767204284668 Computing sim between patterns 11 and 20 Time taken: 0.12621545791625977 Computing sim between patterns 11 and 21 Time taken: 0.11672854423522949 Computing sim between patterns 11 and 22 Time taken: 0.11436963081359863 Computing sim between patterns 11 and 23 Time taken: 0.1172628402709961 Computing sim between patterns 11 and 24 Time taken: 0.11361980438232422 Computing sim between patterns 11 and 25 Time taken: 0.11643695831298828 Computing sim between patterns 11 and 26 Time taken: 0.1181180477142334 Computing sim between patterns 11 and 27 Time taken: 0.11722421646118164 Computing sim between patterns 11 and 28 Time taken: 0.11717987060546875 Computing sim between patterns 11 and 29 Time taken: 0.11465740203857422 Computing sim between patterns 11 and 30 Time taken: 0.11482715606689453 Computing sim between patterns 11 and 31 Time taken: 0.1147925853729248 Computing sim between patterns 11 and 32 Time taken: 0.11493158340454102 Computing sim between patterns 12 and 0 Time taken: 0.21902060508728027 Computing sim between patterns 12 and 1 Time taken: 0.2121260166168213 Computing sim between patterns 12 and 2 Time taken: 0.21198463439941406 Computing sim between patterns 12 and 3 Time taken: 0.20984625816345215 Computing sim between patterns 12 and 4 Time taken: 0.2135615348815918 Computing sim between patterns 12 and 5 Time taken: 0.19636130332946777 Computing sim between patterns 12 and 6 Time taken: 0.1979377269744873 Computing sim between patterns 12 and 7 Time taken: 0.1988997459411621 Computing sim between patterns 12 and 8 Time taken: 0.19402670860290527 Computing sim between patterns 12 and 9 Time taken: 0.1836097240447998 Computing sim between patterns 12 and 10 Time taken: 0.16177940368652344 Computing sim between patterns 12 and 11 Time taken: 0.15551519393920898 Computing sim between patterns 12 and 13 Time taken: 0.19157004356384277 Computing sim between patterns 12 and 14 Time taken: 0.22270417213439941 Computing sim between patterns 12 and 15 Time taken: 0.1913313865661621 Computing sim between patterns 12 and 16 Time taken: 0.17864537239074707 Computing sim between patterns 12 and 17 Time taken: 0.16604828834533691 Computing sim between patterns 12 and 18 Time taken: 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and 32 Time taken: 0.16303420066833496 Computing sim between patterns 13 and 0 Time taken: 0.11977338790893555 Computing sim between patterns 13 and 1 Time taken: 0.1193079948425293 Computing sim between patterns 13 and 2 Time taken: 0.12520623207092285 Computing sim between patterns 13 and 3 Time taken: 0.11722946166992188 Computing sim between patterns 13 and 4 Time taken: 0.11855792999267578 Computing sim between patterns 13 and 5 Time taken: 0.11960935592651367 Computing sim between patterns 13 and 6 Time taken: 0.11876583099365234 Computing sim between patterns 13 and 7 Time taken: 0.11916089057922363 Computing sim between patterns 13 and 8 Time taken: 0.11945796012878418 Computing sim between patterns 13 and 9 Time taken: 0.11581206321716309 Computing sim between patterns 13 and 10 Time taken: 0.0991215705871582 Computing sim between patterns 13 and 11 Time taken: 0.08951568603515625 Computing sim between patterns 13 and 12 Time taken: 0.09302783012390137 Computing sim between patterns 13 and 14 Time taken: 0.11029911041259766 Computing sim between patterns 13 and 15 Time taken: 0.11020755767822266 Computing sim between patterns 13 and 16 Time taken: 0.10106110572814941 Computing sim between patterns 13 and 17 Time taken: 0.09357452392578125 Computing sim between patterns 13 and 18 Time taken: 0.0988004207611084 Computing sim between patterns 13 and 19 Time taken: 0.09108138084411621 Computing sim between patterns 13 and 20 Time taken: 0.09646964073181152 Computing sim between patterns 13 and 21 Time taken: 0.09971427917480469 Computing sim between patterns 13 and 22 Time taken: 0.0913095474243164 Computing sim between patterns 13 and 23 Time taken: 0.09535002708435059 Computing sim between patterns 13 and 24 Time taken: 0.09195160865783691 Computing sim between patterns 13 and 25 Time taken: 0.09228038787841797 Computing sim between patterns 13 and 26 Time taken: 0.09310722351074219 Computing sim between patterns 13 and 27 Time taken: 0.10348391532897949 Computing sim between patterns 13 and 28 Time taken: 0.0909719467163086 Computing sim between patterns 13 and 29 Time taken: 0.08871221542358398 Computing sim between patterns 13 and 30 Time taken: 0.09624576568603516 Computing sim between patterns 13 and 31 Time taken: 0.08842802047729492 Computing sim between patterns 13 and 32 Time taken: 0.08864307403564453 Computing sim between patterns 14 and 0 Time taken: 0.48514556884765625 Computing sim between patterns 14 and 1 Time taken: 0.4907341003417969 Computing sim between patterns 14 and 2 Time taken: 0.4566333293914795 Computing sim between patterns 14 and 3 Time taken: 0.46616268157958984 Computing sim between patterns 14 and 4 Time taken: 0.46815991401672363 Computing sim between patterns 14 and 5 Time taken: 0.47081756591796875 Computing sim between patterns 14 and 6 Time taken: 0.43981480598449707 Computing sim between patterns 14 and 7 Time taken: 0.44132304191589355 Computing sim between patterns 14 and 8 Time taken: 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Time taken: 0.38602566719055176 Computing sim between patterns 14 and 24 Time taken: 0.3792400360107422 Computing sim between patterns 14 and 25 Time taken: 0.38295650482177734 Computing sim between patterns 14 and 26 Time taken: 0.38866567611694336 Computing sim between patterns 14 and 27 Time taken: 0.3847506046295166 Computing sim between patterns 14 and 28 Time taken: 0.36080026626586914 Computing sim between patterns 14 and 29 Time taken: 0.38398313522338867 Computing sim between patterns 14 and 30 Time taken: 0.37660741806030273 Computing sim between patterns 14 and 31 Time taken: 0.39810824394226074 Computing sim between patterns 14 and 32 Time taken: 0.3841373920440674 Computing sim between patterns 15 and 0 Time taken: 0.43550682067871094 Computing sim between patterns 15 and 1 Time taken: 0.4646120071411133 Computing sim between patterns 15 and 2 Time taken: 0.43555450439453125 Computing sim between patterns 15 and 3 Time taken: 0.46312856674194336 Computing sim between patterns 15 and 4 Time taken: 0.5044770240783691 Computing sim between patterns 15 and 5 Time taken: 0.47779083251953125 Computing sim between patterns 15 and 6 Time taken: 0.44104504585266113 Computing sim between patterns 15 and 7 Time taken: 0.43892765045166016 Computing sim between patterns 15 and 8 Time taken: 0.4356412887573242 Computing sim between patterns 15 and 9 Time taken: 0.4285142421722412 Computing sim between patterns 15 and 10 Time taken: 0.4035506248474121 Computing sim between patterns 15 and 11 Time taken: 0.36038732528686523 Computing sim between patterns 15 and 12 Time taken: 0.3527102470397949 Computing sim between patterns 15 and 13 Time taken: 0.3785684108734131 Computing sim between patterns 15 and 14 Time taken: 0.4448277950286865 Computing sim between patterns 15 and 16 Time taken: 0.6903884410858154 Computing sim between patterns 15 and 17 Time taken: 0.3713870048522949 Computing sim between patterns 15 and 18 Time taken: 0.36255645751953125 Computing sim between patterns 15 and 19 Time taken: 0.3848123550415039 Computing sim between patterns 15 and 20 Time taken: 0.38313865661621094 Computing sim between patterns 15 and 21 Time taken: 0.36231446266174316 Computing sim between patterns 15 and 22 Time taken: 0.36027026176452637 Computing sim between patterns 15 and 23 Time taken: 0.7421913146972656 Computing sim between patterns 15 and 24 Time taken: 0.3528118133544922 Computing sim between patterns 15 and 25 Time taken: 0.3594167232513428 Computing sim between patterns 15 and 26 Time taken: 0.35307979583740234 Computing sim between patterns 15 and 27 Time taken: 0.3549964427947998 Computing sim between patterns 15 and 28 Time taken: 0.3821132183074951 Computing sim between patterns 15 and 29 Time taken: 0.38413190841674805 Computing sim between patterns 15 and 30 Time taken: 0.37490367889404297 Computing sim between patterns 15 and 31 Time taken: 0.3509542942047119 Computing sim between patterns 15 and 32 Time taken: 0.3524661064147949 Computing sim between patterns 16 and 0 Time taken: 0.359236478805542 Computing sim between patterns 16 and 1 Time taken: 0.3445315361022949 Computing sim between patterns 16 and 2 Time taken: 0.33220601081848145 Computing sim between patterns 16 and 3 Time taken: 0.3441047668457031 Computing sim between patterns 16 and 4 Time taken: 0.3737974166870117 Computing sim between patterns 16 and 5 Time taken: 0.3697824478149414 Computing sim between patterns 16 and 6 Time taken: 0.3841521739959717 Computing sim between patterns 16 and 7 Time taken: 0.37570905685424805 Computing sim between patterns 16 and 8 Time taken: 0.3593599796295166 Computing sim between patterns 16 and 9 Time taken: 0.31627655029296875 Computing sim between patterns 16 and 10 Time taken: 0.2949950695037842 Computing sim between patterns 16 and 11 Time taken: 0.311809778213501 Computing sim between patterns 16 and 12 Time taken: 0.3123905658721924 Computing sim between patterns 16 and 13 Time taken: 0.30492258071899414 Computing sim between patterns 16 and 14 Time taken: 0.361370325088501 Computing sim between patterns 16 and 15 Time taken: 0.345534086227417 Computing sim between patterns 16 and 17 Time taken: 0.2906346321105957 Computing sim between patterns 16 and 18 Time taken: 0.29081249237060547 Computing sim between patterns 16 and 19 Time taken: 0.2982492446899414 Computing sim between patterns 16 and 20 Time taken: 0.32355809211730957 Computing sim between patterns 16 and 21 Time taken: 0.32044339179992676 Computing sim between patterns 16 and 22 Time taken: 0.35620594024658203 Computing sim between patterns 16 and 23 Time taken: 0.3477785587310791 Computing sim between patterns 16 and 24 Time taken: 0.38668060302734375 Computing sim between patterns 16 and 25 Time taken: 0.3672301769256592 Computing sim between patterns 16 and 26 Time taken: 0.34164881706237793 Computing sim between patterns 16 and 27 Time taken: 0.2879140377044678 Computing sim between patterns 16 and 28 Time taken: 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taken: 0.13550519943237305 Computing sim between patterns 17 and 10 Time taken: 0.11232924461364746 Computing sim between patterns 17 and 11 Time taken: 0.1089317798614502 Computing sim between patterns 17 and 12 Time taken: 0.10876750946044922 Computing sim between patterns 17 and 13 Time taken: 0.10483288764953613 Computing sim between patterns 17 and 14 Time taken: 0.12839508056640625 Computing sim between patterns 17 and 15 Time taken: 0.1308298110961914 Computing sim between patterns 17 and 16 Time taken: 0.12569594383239746 Computing sim between patterns 17 and 18 Time taken: 0.12616348266601562 Computing sim between patterns 17 and 19 Time taken: 0.10199713706970215 Computing sim between patterns 17 and 20 Time taken: 0.10482478141784668 Computing sim between patterns 17 and 21 Time taken: 0.11467361450195312 Computing sim between patterns 17 and 22 Time taken: 0.11145138740539551 Computing sim between patterns 17 and 23 Time taken: 0.1034841537475586 Computing sim between patterns 17 and 24 Time taken: 0.10869383811950684 Computing sim between patterns 17 and 25 Time taken: 0.10530972480773926 Computing sim between patterns 17 and 26 Time taken: 0.1017305850982666 Computing sim between patterns 17 and 27 Time taken: 0.09703278541564941 Computing sim between patterns 17 and 28 Time taken: 0.09611392021179199 Computing sim between patterns 17 and 29 Time taken: 0.09465980529785156 Computing sim between patterns 17 and 30 Time taken: 0.09410810470581055 Computing sim between patterns 17 and 31 Time taken: 0.09555220603942871 Computing sim between patterns 17 and 32 Time taken: 0.09838509559631348 Computing sim between patterns 18 and 0 Time taken: 0.17241120338439941 Computing sim between patterns 18 and 1 Time taken: 0.16609597206115723 Computing sim between patterns 18 and 2 Time taken: 0.16766595840454102 Computing sim between patterns 18 and 3 Time taken: 0.17030882835388184 Computing sim between patterns 18 and 4 Time taken: 0.1763911247253418 Computing sim between patterns 18 and 5 Time taken: 0.18065667152404785 Computing sim between patterns 18 and 6 Time taken: 0.17859959602355957 Computing sim between patterns 18 and 7 Time taken: 0.16882109642028809 Computing sim between patterns 18 and 8 Time taken: 0.16740965843200684 Computing sim between patterns 18 and 9 Time taken: 0.16013860702514648 Computing sim between patterns 18 and 10 Time taken: 0.13768815994262695 Computing sim between patterns 18 and 11 Time taken: 0.13071250915527344 Computing sim between patterns 18 and 12 Time taken: 0.13484930992126465 Computing sim between patterns 18 and 13 Time taken: 0.13538908958435059 Computing sim between patterns 18 and 14 Time taken: 0.16882038116455078 Computing sim between patterns 18 and 15 Time taken: 0.15265321731567383 Computing sim between patterns 18 and 16 Time taken: 0.1387932300567627 Computing sim between patterns 18 and 17 Time taken: 0.1345062255859375 Computing sim between patterns 18 and 19 Time taken: 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and 0 Time taken: 0.12876272201538086 Computing sim between patterns 19 and 1 Time taken: 0.1376488208770752 Computing sim between patterns 19 and 2 Time taken: 0.13001346588134766 Computing sim between patterns 19 and 3 Time taken: 0.15222406387329102 Computing sim between patterns 19 and 4 Time taken: 0.12720322608947754 Computing sim between patterns 19 and 5 Time taken: 0.12468934059143066 Computing sim between patterns 19 and 6 Time taken: 0.12740588188171387 Computing sim between patterns 19 and 7 Time taken: 0.1301107406616211 Computing sim between patterns 19 and 8 Time taken: 0.12012767791748047 Computing sim between patterns 19 and 9 Time taken: 0.12205624580383301 Computing sim between patterns 19 and 10 Time taken: 0.10643124580383301 Computing sim between patterns 19 and 11 Time taken: 0.0976572036743164 Computing sim between patterns 19 and 12 Time taken: 0.10361099243164062 Computing sim between patterns 19 and 13 Time taken: 0.1006772518157959 Computing sim between patterns 19 and 14 Time taken: 0.1187136173248291 Computing sim between patterns 19 and 15 Time taken: 0.1602795124053955 Computing sim between patterns 19 and 16 Time taken: 0.1553354263305664 Computing sim between patterns 19 and 17 Time taken: 0.11604976654052734 Computing sim between patterns 19 and 18 Time taken: 0.11221742630004883 Computing sim between patterns 19 and 20 Time taken: 0.11788558959960938 Computing sim between patterns 19 and 21 Time taken: 0.11425924301147461 Computing sim between patterns 19 and 22 Time taken: 0.11133146286010742 Computing sim between patterns 19 and 23 Time taken: 0.10765647888183594 Computing sim between patterns 19 and 24 Time taken: 0.10512471199035645 Computing sim between patterns 19 and 25 Time taken: 0.1060173511505127 Computing sim between patterns 19 and 26 Time taken: 0.10591292381286621 Computing sim between patterns 19 and 27 Time taken: 0.10486721992492676 Computing sim between patterns 19 and 28 Time taken: 0.10619997978210449 Computing sim between patterns 19 and 29 Time taken: 0.10599040985107422 Computing sim between patterns 19 and 30 Time taken: 0.10875296592712402 Computing sim between patterns 19 and 31 Time taken: 0.10080623626708984 Computing sim between patterns 19 and 32 Time taken: 0.10225629806518555 Computing sim between patterns 20 and 0 Time taken: 0.3580131530761719 Computing sim between patterns 20 and 1 Time taken: 0.3558506965637207 Computing sim between patterns 20 and 2 Time taken: 0.35120248794555664 Computing sim between patterns 20 and 3 Time taken: 0.3281862735748291 Computing sim between patterns 20 and 4 Time taken: 0.360837459564209 Computing sim between patterns 20 and 5 Time taken: 0.7084066867828369 Computing sim between patterns 20 and 6 Time taken: 0.32340312004089355 Computing sim between patterns 20 and 7 Time taken: 0.3477437496185303 Computing sim between patterns 20 and 8 Time taken: 0.32631349563598633 Computing sim between patterns 20 and 9 Time taken: 0.3133585453033447 Computing sim between patterns 20 and 10 Time taken: 0.27950382232666016 Computing sim between patterns 20 and 11 Time taken: 0.27464914321899414 Computing sim between patterns 20 and 12 Time taken: 0.29613399505615234 Computing sim between patterns 20 and 13 Time taken: 0.30448079109191895 Computing sim between patterns 20 and 14 Time taken: 0.3464341163635254 Computing sim between patterns 20 and 15 Time taken: 0.3366689682006836 Computing sim between patterns 20 and 16 Time taken: 0.301377534866333 Computing sim between patterns 20 and 17 Time taken: 0.2712843418121338 Computing sim between patterns 20 and 18 Time taken: 0.2973482608795166 Computing sim between patterns 20 and 19 Time taken: 0.288555383682251 Computing sim between patterns 20 and 21 Time taken: 0.28528451919555664 Computing sim between patterns 20 and 22 Time taken: 0.2937803268432617 Computing sim between patterns 20 and 23 Time taken: 0.29532432556152344 Computing sim between patterns 20 and 24 Time taken: 0.28117847442626953 Computing sim between patterns 20 and 25 Time taken: 0.28863000869750977 Computing sim between patterns 20 and 26 Time taken: 0.2891092300415039 Computing sim between patterns 20 and 27 Time taken: 0.2917301654815674 Computing sim between patterns 20 and 28 Time taken: 0.28428006172180176 Computing sim between patterns 20 and 29 Time taken: 0.27749037742614746 Computing sim between patterns 20 and 30 Time taken: 0.28373050689697266 Computing sim between patterns 20 and 31 Time taken: 0.2836642265319824 Computing sim between patterns 20 and 32 Time taken: 0.2996227741241455 Computing sim between patterns 21 and 0 Time taken: 0.22323036193847656 Computing sim between patterns 21 and 1 Time taken: 0.22325348854064941 Computing sim between patterns 21 and 2 Time taken: 0.2250368595123291 Computing sim between patterns 21 and 3 Time taken: 0.20986080169677734 Computing sim between patterns 21 and 4 Time taken: 0.21381711959838867 Computing sim between patterns 21 and 5 Time taken: 0.22162532806396484 Computing sim between patterns 21 and 6 Time taken: 0.2173755168914795 Computing sim between patterns 21 and 7 Time taken: 0.20525336265563965 Computing sim between patterns 21 and 8 Time taken: 0.1948380470275879 Computing sim between patterns 21 and 9 Time taken: 0.2536804676055908 Computing sim between patterns 21 and 10 Time taken: 0.2138376235961914 Computing sim between patterns 21 and 11 Time taken: 0.19010710716247559 Computing sim between patterns 21 and 12 Time taken: 0.17904281616210938 Computing sim between patterns 21 and 13 Time taken: 0.1747756004333496 Computing sim between patterns 21 and 14 Time taken: 0.19894099235534668 Computing sim between patterns 21 and 15 Time taken: 0.20510530471801758 Computing sim between patterns 21 and 16 Time taken: 0.18845033645629883 Computing sim between patterns 21 and 17 Time taken: 0.1793522834777832 Computing sim between patterns 21 and 18 Time taken: 0.181793212890625 Computing sim 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taken: 0.13038897514343262 Computing sim between patterns 22 and 15 Time taken: 0.12454628944396973 Computing sim between patterns 22 and 16 Time taken: 0.1196293830871582 Computing sim between patterns 22 and 17 Time taken: 0.10803461074829102 Computing sim between patterns 22 and 18 Time taken: 0.11053943634033203 Computing sim between patterns 22 and 19 Time taken: 0.11185526847839355 Computing sim between patterns 22 and 20 Time taken: 0.1229252815246582 Computing sim between patterns 22 and 21 Time taken: 0.1138758659362793 Computing sim between patterns 22 and 23 Time taken: 0.11600446701049805 Computing sim between patterns 22 and 24 Time taken: 0.10867452621459961 Computing sim between patterns 22 and 25 Time taken: 0.10978245735168457 Computing sim between patterns 22 and 26 Time taken: 0.10706782341003418 Computing sim between patterns 22 and 27 Time taken: 0.10907363891601562 Computing sim between patterns 22 and 28 Time taken: 0.10759353637695312 Computing sim between patterns 22 and 29 Time taken: 0.11711478233337402 Computing sim between patterns 22 and 30 Time taken: 0.11312556266784668 Computing sim between patterns 22 and 31 Time taken: 0.10306000709533691 Computing sim between patterns 22 and 32 Time taken: 0.12027621269226074 Computing sim between patterns 23 and 0 Time taken: 0.3106701374053955 Computing sim between patterns 23 and 1 Time taken: 0.34083104133605957 Computing sim between patterns 23 and 2 Time taken: 0.33994579315185547 Computing sim between patterns 23 and 3 Time taken: 0.3408544063568115 Computing sim between patterns 23 and 4 Time taken: 0.3246471881866455 Computing sim between patterns 23 and 5 Time taken: 0.3260993957519531 Computing sim between patterns 23 and 6 Time taken: 0.3313608169555664 Computing sim between patterns 23 and 7 Time taken: 0.32665324211120605 Computing sim between patterns 23 and 8 Time taken: 0.31534552574157715 Computing sim between patterns 23 and 9 Time taken: 0.33220624923706055 Computing sim between patterns 23 and 10 Time taken: 0.29099273681640625 Computing sim between patterns 23 and 11 Time taken: 0.2737743854522705 Computing sim between patterns 23 and 12 Time taken: 0.275524377822876 Computing sim between patterns 23 and 13 Time taken: 0.2676088809967041 Computing sim between patterns 23 and 14 Time taken: 0.3170144557952881 Computing sim between patterns 23 and 15 Time taken: 0.31761765480041504 Computing sim between patterns 23 and 16 Time taken: 0.29026079177856445 Computing sim between patterns 23 and 17 Time taken: 0.2724735736846924 Computing sim between patterns 23 and 18 Time taken: 0.25896573066711426 Computing sim between patterns 23 and 19 Time taken: 0.303011417388916 Computing sim between patterns 23 and 20 Time taken: 0.33894872665405273 Computing sim between patterns 23 and 21 Time taken: 0.262620210647583 Computing sim between patterns 23 and 22 Time taken: 0.27434301376342773 Computing sim between patterns 23 and 24 Time taken: 0.25987768173217773 Computing sim between patterns 23 and 25 Time taken: 0.2759408950805664 Computing sim between patterns 23 and 26 Time taken: 0.26800060272216797 Computing sim between patterns 23 and 27 Time taken: 0.26746129989624023 Computing sim between patterns 23 and 28 Time taken: 0.2719554901123047 Computing sim between patterns 23 and 29 Time taken: 0.25726890563964844 Computing sim between patterns 23 and 30 Time taken: 0.25070714950561523 Computing sim between patterns 23 and 31 Time taken: 0.2487163543701172 Computing sim between patterns 23 and 32 Time taken: 0.27207040786743164 Computing sim between patterns 24 and 0 Time taken: 0.18204903602600098 Computing sim between patterns 24 and 1 Time taken: 0.17726659774780273 Computing sim between patterns 24 and 2 Time taken: 0.17677879333496094 Computing sim between patterns 24 and 3 Time taken: 0.180649995803833 Computing sim between patterns 24 and 4 Time taken: 0.17421936988830566 Computing sim between patterns 24 and 5 Time taken: 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taken: 0.14992117881774902 Computing sim between patterns 24 and 20 Time taken: 0.15333199501037598 Computing sim between patterns 24 and 21 Time taken: 0.15697264671325684 Computing sim between patterns 24 and 22 Time taken: 0.15816903114318848 Computing sim between patterns 24 and 23 Time taken: 0.16245245933532715 Computing sim between patterns 24 and 25 Time taken: 0.1537609100341797 Computing sim between patterns 24 and 26 Time taken: 0.1513690948486328 Computing sim between patterns 24 and 27 Time taken: 0.14702296257019043 Computing sim between patterns 24 and 28 Time taken: 0.13862919807434082 Computing sim between patterns 24 and 29 Time taken: 0.13915038108825684 Computing sim between patterns 24 and 30 Time taken: 0.1416001319885254 Computing sim between patterns 24 and 31 Time taken: 0.14746928215026855 Computing sim between patterns 24 and 32 Time taken: 0.1449878215789795 Computing sim between patterns 25 and 0 Time taken: 0.1484513282775879 Computing sim between patterns 25 and 1 Time taken: 0.14187121391296387 Computing sim between patterns 25 and 2 Time taken: 0.1423335075378418 Computing sim between patterns 25 and 3 Time taken: 0.14022397994995117 Computing sim between patterns 25 and 4 Time taken: 0.14334774017333984 Computing sim between patterns 25 and 5 Time taken: 0.15445756912231445 Computing sim between patterns 25 and 6 Time taken: 0.1387472152709961 Computing sim between patterns 25 and 7 Time taken: 0.14091038703918457 Computing sim between patterns 25 and 8 Time taken: 0.14975857734680176 Computing sim between patterns 25 and 9 Time taken: 0.1482686996459961 Computing sim between patterns 25 and 10 Time taken: 0.12624025344848633 Computing sim between patterns 25 and 11 Time taken: 0.12426233291625977 Computing sim between patterns 25 and 12 Time taken: 0.1263720989227295 Computing sim between patterns 25 and 13 Time taken: 0.11952400207519531 Computing sim between patterns 25 and 14 Time taken: 0.14199233055114746 Computing sim between patterns 25 and 15 Time taken: 0.14467310905456543 Computing sim between patterns 25 and 16 Time taken: 0.13829898834228516 Computing sim between patterns 25 and 17 Time taken: 0.12061762809753418 Computing sim between patterns 25 and 18 Time taken: 0.12111091613769531 Computing sim between patterns 25 and 19 Time taken: 0.11610937118530273 Computing sim between patterns 25 and 20 Time taken: 0.12609100341796875 Computing sim between patterns 25 and 21 Time taken: 0.12435197830200195 Computing sim between patterns 25 and 22 Time taken: 0.11819720268249512 Computing sim between patterns 25 and 23 Time taken: 0.11766862869262695 Computing sim between patterns 25 and 24 Time taken: 0.11699819564819336 Computing sim between patterns 25 and 26 Time taken: 0.11626696586608887 Computing sim between patterns 25 and 27 Time taken: 0.11262726783752441 Computing sim between patterns 25 and 28 Time taken: 0.11087584495544434 Computing sim between patterns 25 and 29 Time taken: 0.10897135734558105 Computing sim between patterns 25 and 30 Time taken: 0.10859131813049316 Computing sim between patterns 25 and 31 Time taken: 0.10908746719360352 Computing sim between patterns 25 and 32 Time taken: 0.10640835762023926 Computing sim between patterns 26 and 0 Time taken: 0.11969780921936035 Computing sim between patterns 26 and 1 Time taken: 0.11968636512756348 Computing sim between patterns 26 and 2 Time taken: 0.1155552864074707 Computing sim between patterns 26 and 3 Time taken: 0.1157233715057373 Computing sim between patterns 26 and 4 Time taken: 0.11579394340515137 Computing sim between patterns 26 and 5 Time taken: 0.11592793464660645 Computing sim between patterns 26 and 6 Time taken: 0.12218856811523438 Computing sim between patterns 26 and 7 Time taken: 0.11841511726379395 Computing sim between patterns 26 and 8 Time taken: 0.1677570343017578 Computing sim between patterns 26 and 9 Time taken: 0.16023778915405273 Computing sim between patterns 26 and 10 Time taken: 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and 24 Time taken: 0.09550690650939941 Computing sim between patterns 26 and 25 Time taken: 0.09415650367736816 Computing sim between patterns 26 and 27 Time taken: 0.09403729438781738 Computing sim between patterns 26 and 28 Time taken: 0.09015250205993652 Computing sim between patterns 26 and 29 Time taken: 0.09112071990966797 Computing sim between patterns 26 and 30 Time taken: 0.09652185440063477 Computing sim between patterns 26 and 31 Time taken: 0.09029483795166016 Computing sim between patterns 26 and 32 Time taken: 0.08846783638000488 Computing sim between patterns 27 and 0 Time taken: 0.11199283599853516 Computing sim between patterns 27 and 1 Time taken: 0.1126244068145752 Computing sim between patterns 27 and 2 Time taken: 0.11276054382324219 Computing sim between patterns 27 and 3 Time taken: 0.11587691307067871 Computing sim between patterns 27 and 4 Time taken: 0.11178016662597656 Computing sim between patterns 27 and 5 Time taken: 0.10255670547485352 Computing sim 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Time taken: 0.08247494697570801 Computing sim between patterns 28 and 2 Time taken: 0.08176636695861816 Computing sim between patterns 28 and 3 Time taken: 0.08418893814086914 Computing sim between patterns 28 and 4 Time taken: 0.08478736877441406 Computing sim between patterns 28 and 5 Time taken: 0.08609843254089355 Computing sim between patterns 28 and 6 Time taken: 0.08511972427368164 Computing sim between patterns 28 and 7 Time taken: 0.09210968017578125 Computing sim between patterns 28 and 8 Time taken: 0.08509063720703125 Computing sim between patterns 28 and 9 Time taken: 0.10631442070007324 Computing sim between patterns 28 and 10 Time taken: 0.07008004188537598 Computing sim between patterns 28 and 11 Time taken: 0.06475377082824707 Computing sim between patterns 28 and 12 Time taken: 0.06877756118774414 Computing sim between patterns 28 and 13 Time taken: 0.06454730033874512 Computing sim between patterns 28 and 14 Time taken: 0.08373522758483887 Computing sim between patterns 28 and 15 Time taken: 0.08313369750976562 Computing sim between patterns 28 and 16 Time taken: 0.07773089408874512 Computing sim between patterns 28 and 17 Time taken: 0.06913137435913086 Computing sim between patterns 28 and 18 Time taken: 0.06819891929626465 Computing sim between patterns 28 and 19 Time taken: 0.0664212703704834 Computing sim between patterns 28 and 20 Time taken: 0.0758819580078125 Computing sim between patterns 28 and 21 Time taken: 0.06893181800842285 Computing sim between patterns 28 and 22 Time taken: 0.06871438026428223 Computing sim between patterns 28 and 23 Time taken: 0.07207417488098145 Computing sim between patterns 28 and 24 Time taken: 0.0693979263305664 Computing sim between patterns 28 and 25 Time taken: 0.06929159164428711 Computing sim between patterns 28 and 26 Time taken: 0.06780600547790527 Computing sim between patterns 28 and 27 Time taken: 0.06859111785888672 Computing sim between patterns 28 and 29 Time taken: 0.06956982612609863 Computing sim between patterns 28 and 30 Time taken: 0.06756854057312012 Computing sim between patterns 28 and 31 Time taken: 0.06453752517700195 Computing sim between patterns 28 and 32 Time taken: 0.06163763999938965 Computing sim between patterns 29 and 0 Time taken: 0.04814743995666504 Computing sim between patterns 29 and 1 Time taken: 0.04674792289733887 Computing sim between patterns 29 and 2 Time taken: 0.04797482490539551 Computing sim between patterns 29 and 3 Time taken: 0.04947328567504883 Computing sim between patterns 29 and 4 Time taken: 0.04735827445983887 Computing sim between patterns 29 and 5 Time taken: 0.049048662185668945 Computing sim between patterns 29 and 6 Time taken: 0.04846620559692383 Computing sim between patterns 29 and 7 Time taken: 0.04757070541381836 Computing sim between patterns 29 and 8 Time taken: 0.055770158767700195 Computing sim between patterns 29 and 9 Time taken: 0.04645562171936035 Computing sim between patterns 29 and 10 Time taken: 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0.014966011047363281 Computing sim between patterns 31 and 1 Time taken: 0.015205621719360352 Computing sim between patterns 31 and 2 Time taken: 0.01696324348449707 Computing sim between patterns 31 and 3 Time taken: 0.016400575637817383 Computing sim between patterns 31 and 4 Time taken: 0.01693868637084961 Computing sim between patterns 31 and 5 Time taken: 0.01738762855529785 Computing sim between patterns 31 and 6 Time taken: 0.015398263931274414 Computing sim between patterns 31 and 7 Time taken: 0.015287637710571289 Computing sim between patterns 31 and 8 Time taken: 0.014271736145019531 Computing sim between patterns 31 and 9 Time taken: 0.014494895935058594 Computing sim between patterns 31 and 10 Time taken: 0.011500835418701172 Computing sim between patterns 31 and 11 Time taken: 0.010524749755859375 Computing sim between patterns 31 and 12 Time taken: 0.012282133102416992 Computing sim between patterns 31 and 13 Time taken: 0.010499954223632812 Computing sim between patterns 31 and 14 Time taken: 0.014096736907958984 Computing sim between patterns 31 and 15 Time taken: 0.013363838195800781 Computing sim between patterns 31 and 16 Time taken: 0.012160062789916992 Computing sim between patterns 31 and 17 Time taken: 0.010251045227050781 Computing sim between patterns 31 and 18 Time taken: 0.01085209846496582 Computing sim between patterns 31 and 19 Time taken: 0.010416030883789062 Computing sim between patterns 31 and 20 Time taken: 0.011617183685302734 Computing sim between patterns 31 and 21 Time taken: 0.011049270629882812 Computing sim between patterns 31 and 22 Time taken: 0.010058164596557617 Computing sim between patterns 31 and 23 Time taken: 0.011275768280029297 Computing sim between patterns 31 and 24 Time taken: 0.01037907600402832 Computing sim between patterns 31 and 25 Time taken: 0.010180950164794922 Computing sim between patterns 31 and 26 Time taken: 0.01033473014831543 Computing sim between patterns 31 and 27 Time taken: 0.009715795516967773 Computing sim between patterns 31 and 28 Time taken: 0.010001420974731445 Computing sim between patterns 31 and 29 Time taken: 0.009230613708496094 Computing sim between patterns 31 and 30 Time taken: 0.010219335556030273 Computing sim between patterns 31 and 32 Time taken: 0.00951695442199707 Computing sim between patterns 32 and 0 Time taken: 0.014792919158935547 Computing sim between patterns 32 and 1 Time taken: 0.016381263732910156 Computing sim between patterns 32 and 2 Time taken: 0.016295433044433594 Computing sim between patterns 32 and 3 Time taken: 0.018749713897705078 Computing sim between patterns 32 and 4 Time taken: 0.019533395767211914 Computing sim between patterns 32 and 5 Time taken: 0.015961647033691406 Computing sim between patterns 32 and 6 Time taken: 0.016710996627807617 Computing sim between patterns 32 and 7 Time taken: 0.016696929931640625 Computing sim between patterns 32 and 8 Time taken: 0.014932870864868164 Computing sim between patterns 32 and 9 Time taken: 0.015967607498168945 Computing sim between patterns 32 and 10 Time taken: 0.012213706970214844 Computing sim between patterns 32 and 11 Time taken: 0.012139320373535156 Computing sim between patterns 32 and 12 Time taken: 0.011929988861083984 Computing sim between patterns 32 and 13 Time taken: 0.010341644287109375 Computing sim between patterns 32 and 14 Time taken: 0.014101028442382812 Computing sim between patterns 32 and 15 Time taken: 0.013516664505004883 Computing sim between patterns 32 and 16 Time taken: 0.011692285537719727 Computing sim between patterns 32 and 17 Time taken: 0.00991058349609375 Computing sim between patterns 32 and 18 Time taken: 0.010225534439086914 Computing sim between patterns 32 and 19 Time taken: 0.010219335556030273 Computing sim between patterns 32 and 20 Time taken: 0.012387752532958984 Computing sim between patterns 32 and 21 Time taken: 0.01314997673034668 Computing sim between patterns 32 and 22 Time taken: 0.011207103729248047 Computing sim between patterns 32 and 23 Time taken: 0.011330366134643555 Computing sim between patterns 32 and 24 Time taken: 0.010223150253295898 Computing sim between patterns 32 and 25 Time taken: 0.009977340698242188 Computing sim between patterns 32 and 26 Time taken: 0.009890317916870117 Computing sim between patterns 32 and 27 Time taken: 0.009689807891845703 Computing sim between patterns 32 and 28 Time taken: 0.009737253189086914 Computing sim between patterns 32 and 29 Time taken: 0.009617090225219727 Computing sim between patterns 32 and 30 Time taken: 0.00917196273803711 Computing sim between patterns 32 and 31 Time taken: 0.009829521179199219 Cluster sizes [913 643 513 489 470 405 311 316 263 268 120 34 55 26 230 220 125 30 48 30 121 57 41 90 50 42 27 24 19 9 3 1 1] Cross-contamination matrix: [[1. 0.57 0.11 ... 0.25 0.09 0.2 ] [0.63 1. 0.19 ... 0.22 0.12 0.26] [0.32 0.45 1. ... 0.27 0.2 0.73] ... [0. 0. 0. ... 1. 0. 0. ] [0. 0. 0. ... 0. 1. 0. ] [0. 0. 0. ... 0. 0. 1. ]] Pattern-to-pattern sim matrix: [[1. 0.78 0.42 ... 0.37 0.22 0.39] [0.78 1. 0.55 ... 0.38 0.27 0.44] [0.42 0.55 1. ... 0.35 0.38 0.4 ] ... [0.37 0.38 0.35 ... 1. 0.19 0.26] [0.23 0.27 0.39 ... 0.19 1. 0.27] [0.4 0.44 0.43 ... 0.25 0.25 1. ]] Collapsing 0 & 24 with crosscontam 0.9455851733333334 and sim 0.9617805329671375 Collapsing 1 & 9 with crosscontam 0.908540953220011 and sim 0.9614295753090576 Collapsing 2 & 21 with crosscontam 0.8393274069160281 and sim 0.9087645875025883 Collapsing 3 & 21 with crosscontam 0.9058860460555564 and sim 0.9075665764126676 Collapsing 20 & 21 with crosscontam 0.8517217441192576 and sim 0.9059949685941837 Collapsing 14 & 25 with crosscontam 0.7786248022328325 and sim 0.9038139577022374 Collapsing 2 & 3 with crosscontam 0.8369448448148148 and sim 0.8829563163823642 Collapsing 12 & 17 with crosscontam 0.6777296268469821 and sim 0.8753826495444164 Collapsing 1 & 8 with crosscontam 0.7861692394260316 and sim 0.8524169806117968 Collapsing 10 & 17 with crosscontam 0.8035373167438271 and sim 0.8486012834298768 Collapsing 3 & 7 with crosscontam 0.8324044701234568 and sim 0.8448689575718417 Collapsing 8 & 9 with crosscontam 0.8116995430920837 and sim 0.8326304023617115 Collapsing 3 & 20 with crosscontam 0.8228698427518317 and sim 0.8324697760035703 Collapsing 2 & 6 with crosscontam 0.8033418211728395 and sim 0.8319248564393509 Collapsing 6 & 20 with crosscontam 0.828467783010054 and sim 0.8217024655006696 Collapsing 7 & 21 with crosscontam 0.8149394935391727 and sim 0.8112319013755912 Trimming eliminated 0 seqlets out of 963 Removed 35 duplicate seqlets Trimming eliminated 0 seqlets out of 911 Removed 45 duplicate seqlets Removed 1 duplicate seqlets Trimming eliminated 0 seqlets out of 570 Removed 1 duplicate seqlets Trimming eliminated 2 seqlets out of 1058 Skipped 1 seqlets Removed 18 duplicate seqlets Trimming eliminated 0 seqlets out of 1158 Removed 5 duplicate seqlets Trimming eliminated 0 seqlets out of 272 Removed 30 duplicate seqlets Trimming eliminated 0 seqlets out of 79 Trimming eliminated 0 seqlets out of 1116 Skipped 2 seqlets Removed 8 duplicate seqlets Removed 2 duplicate seqlets Trimming eliminated 0 seqlets out of 199 Removed 6 duplicate seqlets Trimming eliminated 0 seqlets out of 1468 Removed 23 duplicate seqlets Trimming eliminated 0 seqlets out of 1746 Removed 13 duplicate seqlets Unmerged patterns remapping: OrderedDict([(4, 3), (5, 4), (11, 12), (13, 15), (15, 6), (16, 8), (18, 10), (19, 13), (22, 11), (23, 9), (26, 14), (27, 16), (28, 17), (29, 18), (30, 19), (31, 20), (32, 21)]) On merging iteration 2 Numbers for each pattern pre-subsample: [1733, 1104, 928, 470, 405, 242, 220, 193, 125, 90, 48, 41, 34, 30, 27, 26, 24, 19, 9, 3, 1, 1] Numbers after subsampling: [300, 300, 300, 300, 300, 242, 220, 193, 125, 90, 48, 41, 34, 30, 27, 26, 24, 19, 9, 3, 1, 1] Computing sim between patterns 0 and 1 Time taken: 0.5403766632080078 Computing sim between patterns 0 and 2 Time taken: 0.663794994354248 Computing sim between patterns 0 and 3 Time taken: 0.6262791156768799 Computing sim between patterns 0 and 4 Time taken: 0.5638370513916016 Computing sim between patterns 0 and 5 Time taken: 0.5507712364196777 Computing sim between patterns 0 and 6 Time taken: 0.5828371047973633 Computing sim between patterns 0 and 7 Time taken: 0.5380058288574219 Computing sim between patterns 0 and 8 Time taken: 0.5014514923095703 Computing sim between patterns 0 and 9 Time taken: 0.49830007553100586 Computing sim between patterns 0 and 10 Time taken: 0.5243964195251465 Computing sim between patterns 0 and 11 Time taken: 0.5120987892150879 Computing sim between patterns 0 and 12 Time taken: 0.5045580863952637 Computing sim between patterns 0 and 13 Time taken: 0.47039008140563965 Computing sim between patterns 0 and 14 Time taken: 0.496265172958374 Computing sim between patterns 0 and 15 Time taken: 0.46080732345581055 Computing sim between patterns 0 and 16 Time taken: 0.46564149856567383 Computing sim between patterns 0 and 17 Time taken: 0.4514169692993164 Computing sim between patterns 0 and 18 Time taken: 0.48444533348083496 Computing sim between patterns 0 and 19 Time taken: 0.4592325687408447 Computing sim between patterns 0 and 20 Time taken: 0.4963569641113281 Computing sim between patterns 0 and 21 Time taken: 0.49368715286254883 Computing sim between patterns 1 and 0 Time taken: 0.5880653858184814 Computing sim between patterns 1 and 2 Time taken: 0.5676326751708984 Computing sim between patterns 1 and 3 Time taken: 0.5925049781799316 Computing sim between patterns 1 and 4 Time taken: 0.6114165782928467 Computing sim between patterns 1 and 5 Time taken: 0.5442409515380859 Computing sim between patterns 1 and 6 Time taken: 0.6059122085571289 Computing sim between patterns 1 and 7 Time taken: 0.5593912601470947 Computing sim between patterns 1 and 8 Time taken: 0.5101971626281738 Computing sim between patterns 1 and 9 Time taken: 0.48301100730895996 Computing sim between patterns 1 and 10 Time taken: 0.4670548439025879 Computing sim between patterns 1 and 11 Time taken: 0.4666719436645508 Computing sim between patterns 1 and 12 Time taken: 0.45863819122314453 Computing sim between patterns 1 and 13 Time taken: 0.45033812522888184 Computing sim between patterns 1 and 14 Time taken: 0.4657444953918457 Computing sim between patterns 1 and 15 Time taken: 0.45674681663513184 Computing sim between patterns 1 and 16 Time taken: 0.4703187942504883 Computing sim between patterns 1 and 17 Time taken: 0.4562830924987793 Computing sim between patterns 1 and 18 Time taken: 0.4706406593322754 Computing sim between patterns 1 and 19 Time taken: 0.4570302963256836 Computing sim between patterns 1 and 20 Time taken: 0.4408564567565918 Computing sim between patterns 1 and 21 Time taken: 0.4335908889770508 Computing sim between patterns 2 and 0 Time taken: 0.5292880535125732 Computing sim between patterns 2 and 1 Time taken: 0.538684606552124 Computing sim between patterns 2 and 3 Time taken: 0.5574753284454346 Computing sim between patterns 2 and 4 Time taken: 0.5458989143371582 Computing sim between patterns 2 and 5 Time taken: 0.5071275234222412 Computing sim between patterns 2 and 6 Time taken: 0.5281417369842529 Computing sim between patterns 2 and 7 Time taken: 0.47968196868896484 Computing sim between patterns 2 and 8 Time taken: 0.5076594352722168 Computing sim between patterns 2 and 9 Time taken: 0.47812795639038086 Computing sim between patterns 2 and 10 Time taken: 0.4856679439544678 Computing sim between patterns 2 and 11 Time taken: 0.490020751953125 Computing sim between patterns 2 and 12 Time taken: 0.461625337600708 Computing sim between patterns 2 and 13 Time taken: 0.4790835380554199 Computing sim between patterns 2 and 14 Time taken: 0.48574066162109375 Computing sim between patterns 2 and 15 Time taken: 0.4412045478820801 Computing sim between patterns 2 and 16 Time taken: 0.4846510887145996 Computing sim between patterns 2 and 17 Time taken: 0.47170329093933105 Computing sim between patterns 2 and 18 Time taken: 0.47057461738586426 Computing sim between patterns 2 and 19 Time taken: 0.4963057041168213 Computing sim between patterns 2 and 20 Time taken: 0.4792919158935547 Computing sim between patterns 2 and 21 Time taken: 0.5027635097503662 Computing sim between patterns 3 and 0 Time taken: 0.5737028121948242 Computing sim between patterns 3 and 1 Time taken: 0.6190853118896484 Computing sim between patterns 3 and 2 Time taken: 0.5242767333984375 Skipping prepopulated (3, 4) Computing sim between patterns 3 and 5 Time taken: 0.5264739990234375 Skipping prepopulated (3, 6) Computing sim between patterns 3 and 7 Time taken: 0.5158889293670654 Skipping prepopulated (3, 8) Skipping prepopulated (3, 9) Skipping prepopulated (3, 10) Skipping prepopulated (3, 11) Skipping prepopulated (3, 12) Skipping prepopulated (3, 13) Skipping prepopulated (3, 14) Skipping prepopulated (3, 15) Skipping prepopulated (3, 16) Skipping prepopulated (3, 17) Skipping prepopulated (3, 18) Skipping prepopulated (3, 19) Skipping prepopulated (3, 20) Skipping prepopulated (3, 21) Computing sim between patterns 4 and 0 Time taken: 0.550915002822876 Computing sim between patterns 4 and 1 Time taken: 0.5341091156005859 Computing sim between patterns 4 and 2 Time taken: 0.6014506816864014 Skipping prepopulated (4, 3) Computing sim between patterns 4 and 5 Time taken: 0.534949541091919 Skipping prepopulated (4, 6) Computing sim between patterns 4 and 7 Time taken: 0.5329160690307617 Skipping prepopulated (4, 8) Skipping prepopulated (4, 9) Skipping prepopulated (4, 10) Skipping prepopulated (4, 11) Skipping prepopulated (4, 12) Skipping prepopulated (4, 13) Skipping prepopulated (4, 14) Skipping prepopulated (4, 15) Skipping prepopulated (4, 16) Skipping prepopulated (4, 17) Skipping prepopulated (4, 18) Skipping prepopulated (4, 19) Skipping prepopulated (4, 20) Skipping prepopulated (4, 21) Computing sim between patterns 5 and 0 Time taken: 0.4817318916320801 Computing sim between patterns 5 and 1 Time taken: 0.500108003616333 Computing sim between patterns 5 and 2 Time taken: 0.473618745803833 Computing sim between patterns 5 and 3 Time taken: 0.6205875873565674 Computing sim between patterns 5 and 4 Time taken: 0.6086366176605225 Computing sim between patterns 5 and 6 Time taken: 0.4576554298400879 Computing sim between patterns 5 and 7 Time taken: 0.47888684272766113 Computing sim between patterns 5 and 8 Time taken: 0.4524362087249756 Computing sim between patterns 5 and 9 Time taken: 0.4755887985229492 Computing sim between patterns 5 and 10 Time taken: 0.43183231353759766 Computing sim between patterns 5 and 11 Time taken: 0.4380338191986084 Computing sim between patterns 5 and 12 Time taken: 0.42954421043395996 Computing sim between patterns 5 and 13 Time taken: 0.4409306049346924 Computing sim between patterns 5 and 14 Time taken: 0.4632716178894043 Computing sim between patterns 5 and 15 Time taken: 0.478792667388916 Computing sim between patterns 5 and 16 Time taken: 0.5001430511474609 Computing sim between patterns 5 and 17 Time taken: 0.4406619071960449 Computing sim between patterns 5 and 18 Time taken: 0.4651334285736084 Computing sim between patterns 5 and 19 Time taken: 0.9251174926757812 Computing sim between patterns 5 and 20 Time taken: 0.4685220718383789 Computing sim between patterns 5 and 21 Time taken: 0.42160534858703613 Computing sim between patterns 6 and 0 Time taken: 0.4600069522857666 Computing sim between patterns 6 and 1 Time taken: 0.4511702060699463 Computing sim between patterns 6 and 2 Time taken: 0.4583451747894287 Skipping prepopulated (6, 3) Skipping prepopulated (6, 4) Computing sim between patterns 6 and 5 Time taken: 0.4527285099029541 Computing sim between patterns 6 and 7 Time taken: 0.3937215805053711 Skipping prepopulated (6, 8) Skipping prepopulated (6, 9) Skipping prepopulated (6, 10) Skipping prepopulated (6, 11) Skipping prepopulated (6, 12) Skipping prepopulated (6, 13) Skipping prepopulated (6, 14) Skipping prepopulated (6, 15) Skipping prepopulated (6, 16) Skipping prepopulated (6, 17) Skipping prepopulated (6, 18) Skipping prepopulated (6, 19) Skipping prepopulated (6, 20) Skipping prepopulated (6, 21) Computing sim between patterns 7 and 0 Time taken: 0.561903715133667 Computing sim between patterns 7 and 1 Time taken: 0.5578231811523438 Computing sim between patterns 7 and 2 Time taken: 0.5208656787872314 Computing sim between patterns 7 and 3 Time taken: 0.554527997970581 Computing sim between patterns 7 and 4 Time taken: 0.5957777500152588 Computing sim between patterns 7 and 5 Time taken: 0.5633425712585449 Computing sim between patterns 7 and 6 Time taken: 0.5432620048522949 Computing sim between patterns 7 and 8 Time taken: 0.4797194004058838 Computing sim between patterns 7 and 9 Time taken: 0.45446252822875977 Computing sim between patterns 7 and 10 Time taken: 0.4676327705383301 Computing sim between patterns 7 and 11 Time taken: 0.5058543682098389 Computing sim between patterns 7 and 12 Time taken: 0.5005941390991211 Computing sim between patterns 7 and 13 Time taken: 0.46341395378112793 Computing sim between patterns 7 and 14 Time taken: 0.4627234935760498 Computing sim between patterns 7 and 15 Time taken: 0.4461398124694824 Computing sim between patterns 7 and 16 Time taken: 0.501957893371582 Computing sim between patterns 7 and 17 Time taken: 0.4961214065551758 Computing sim between patterns 7 and 18 Time taken: 0.45775341987609863 Computing sim between patterns 7 and 19 Time taken: 0.43915271759033203 Computing sim between patterns 7 and 20 Time taken: 0.46971607208251953 Computing sim between patterns 7 and 21 Time taken: 0.4396936893463135 Computing sim between patterns 8 and 0 Time taken: 0.3391580581665039 Computing sim between patterns 8 and 1 Time taken: 0.3305199146270752 Computing sim between patterns 8 and 2 Time taken: 0.3500707149505615 Skipping prepopulated (8, 3) Skipping prepopulated (8, 4) Computing sim between patterns 8 and 5 Time taken: 0.32143449783325195 Skipping prepopulated (8, 6) Computing sim between patterns 8 and 7 Time taken: 0.3199341297149658 Skipping prepopulated (8, 9) Skipping prepopulated (8, 10) Skipping prepopulated (8, 11) Skipping prepopulated (8, 12) Skipping prepopulated (8, 13) Skipping prepopulated (8, 14) Skipping prepopulated (8, 15) Skipping prepopulated (8, 16) Skipping prepopulated (8, 17) Skipping prepopulated (8, 18) Skipping prepopulated (8, 19) Skipping prepopulated (8, 20) Skipping prepopulated (8, 21) Computing sim between patterns 9 and 0 Time taken: 0.29339122772216797 Computing sim between patterns 9 and 1 Time taken: 0.305971622467041 Computing sim between patterns 9 and 2 Time taken: 0.32041358947753906 Skipping prepopulated (9, 3) Skipping prepopulated (9, 4) Computing sim between patterns 9 and 5 Time taken: 0.280869722366333 Skipping prepopulated (9, 6) Computing sim between patterns 9 and 7 Time taken: 0.26889634132385254 Skipping prepopulated (9, 8) Skipping prepopulated (9, 10) Skipping prepopulated (9, 11) Skipping prepopulated (9, 12) Skipping prepopulated (9, 13) Skipping prepopulated (9, 14) Skipping prepopulated (9, 15) Skipping prepopulated (9, 16) Skipping prepopulated (9, 17) Skipping prepopulated (9, 18) Skipping prepopulated (9, 19) Skipping prepopulated (9, 20) Skipping prepopulated (9, 21) Computing sim between patterns 10 and 0 Time taken: 0.18592309951782227 Computing sim between patterns 10 and 1 Time taken: 0.18970251083374023 Computing sim between patterns 10 and 2 Time taken: 0.18037033081054688 Skipping prepopulated (10, 3) Skipping prepopulated (10, 4) Computing sim between patterns 10 and 5 Time taken: 0.17192959785461426 Skipping prepopulated (10, 6) Computing sim between patterns 10 and 7 Time taken: 0.16991400718688965 Skipping prepopulated (10, 8) Skipping prepopulated (10, 9) Skipping prepopulated (10, 11) Skipping prepopulated (10, 12) Skipping prepopulated (10, 13) Skipping prepopulated (10, 14) Skipping prepopulated (10, 15) Skipping prepopulated (10, 16) Skipping prepopulated (10, 17) Skipping prepopulated (10, 18) Skipping prepopulated (10, 19) Skipping prepopulated (10, 20) Skipping prepopulated (10, 21) Computing sim between patterns 11 and 0 Time taken: 0.14003634452819824 Computing sim between patterns 11 and 1 Time taken: 0.13977742195129395 Computing sim between patterns 11 and 2 Time taken: 0.1496737003326416 Skipping prepopulated (11, 3) Skipping prepopulated (11, 4) Computing sim between patterns 11 and 5 Time taken: 0.1464531421661377 Skipping prepopulated (11, 6) Computing sim between patterns 11 and 7 Time taken: 0.13246822357177734 Skipping prepopulated (11, 8) Skipping prepopulated (11, 9) Skipping prepopulated (11, 10) Skipping prepopulated (11, 12) Skipping prepopulated (11, 13) Skipping prepopulated (11, 14) Skipping prepopulated (11, 15) Skipping prepopulated (11, 16) Skipping prepopulated (11, 17) Skipping prepopulated (11, 18) Skipping prepopulated (11, 19) Skipping prepopulated (11, 20) Skipping prepopulated (11, 21) Computing sim between patterns 12 and 0 Time taken: 0.1436917781829834 Computing sim between patterns 12 and 1 Time taken: 0.1405189037322998 Computing sim between patterns 12 and 2 Time taken: 0.14273834228515625 Skipping prepopulated (12, 3) Skipping prepopulated (12, 4) Computing sim between patterns 12 and 5 Time taken: 0.13074874877929688 Skipping prepopulated (12, 6) Computing sim between patterns 12 and 7 Time taken: 0.12470388412475586 Skipping prepopulated (12, 8) Skipping prepopulated (12, 9) Skipping prepopulated (12, 10) Skipping prepopulated (12, 11) Skipping prepopulated (12, 13) Skipping prepopulated (12, 14) Skipping prepopulated (12, 15) Skipping prepopulated (12, 16) Skipping prepopulated (12, 17) Skipping prepopulated (12, 18) Skipping prepopulated (12, 19) Skipping prepopulated (12, 20) Skipping prepopulated (12, 21) Computing sim between patterns 13 and 0 Time taken: 0.13526582717895508 Computing sim between patterns 13 and 1 Time taken: 0.1362011432647705 Computing sim between patterns 13 and 2 Time taken: 0.1428840160369873 Skipping prepopulated (13, 3) Skipping prepopulated (13, 4) Computing sim between patterns 13 and 5 Time taken: 0.1524066925048828 Skipping prepopulated (13, 6) Computing sim between patterns 13 and 7 Time taken: 0.18394064903259277 Skipping prepopulated (13, 8) Skipping prepopulated (13, 9) Skipping prepopulated (13, 10) Skipping prepopulated (13, 11) Skipping prepopulated (13, 12) Skipping prepopulated (13, 14) Skipping prepopulated (13, 15) Skipping prepopulated (13, 16) Skipping prepopulated (13, 17) Skipping prepopulated (13, 18) Skipping prepopulated (13, 19) Skipping prepopulated (13, 20) Skipping prepopulated (13, 21) Computing sim between patterns 14 and 0 Time taken: 0.13010764122009277 Computing sim between patterns 14 and 1 Time taken: 0.11502885818481445 Computing sim between patterns 14 and 2 Time taken: 0.11967277526855469 Skipping prepopulated (14, 3) Skipping prepopulated (14, 4) Computing sim between patterns 14 and 5 Time taken: 0.10851263999938965 Skipping prepopulated (14, 6) Computing sim between patterns 14 and 7 Time taken: 0.10374259948730469 Skipping prepopulated (14, 8) Skipping prepopulated (14, 9) Skipping prepopulated (14, 10) Skipping prepopulated (14, 11) Skipping prepopulated (14, 12) Skipping prepopulated (14, 13) Skipping prepopulated (14, 15) Skipping prepopulated (14, 16) Skipping prepopulated (14, 17) Skipping prepopulated (14, 18) Skipping prepopulated (14, 19) Skipping prepopulated (14, 20) Skipping prepopulated (14, 21) Computing sim between patterns 15 and 0 Time taken: 0.11328005790710449 Computing sim between patterns 15 and 1 Time taken: 0.12183117866516113 Computing sim between patterns 15 and 2 Time taken: 0.12124967575073242 Skipping prepopulated (15, 3) Skipping prepopulated (15, 4) Computing sim between patterns 15 and 5 Time taken: 0.11363601684570312 Skipping prepopulated (15, 6) Computing sim between patterns 15 and 7 Time taken: 0.1086585521697998 Skipping prepopulated (15, 8) Skipping prepopulated (15, 9) Skipping prepopulated (15, 10) Skipping prepopulated (15, 11) Skipping prepopulated (15, 12) Skipping prepopulated (15, 13) Skipping prepopulated (15, 14) Skipping prepopulated (15, 16) Skipping prepopulated (15, 17) Skipping prepopulated (15, 18) Skipping prepopulated (15, 19) Skipping prepopulated (15, 20) Skipping prepopulated (15, 21) Computing sim between patterns 16 and 0 Time taken: 0.11379289627075195 Computing sim between patterns 16 and 1 Time taken: 0.11942267417907715 Computing sim between patterns 16 and 2 Time taken: 0.1141805648803711 Skipping prepopulated (16, 3) Skipping prepopulated (16, 4) Computing sim between patterns 16 and 5 Time taken: 0.10104870796203613 Skipping prepopulated (16, 6) Computing sim between patterns 16 and 7 Time taken: 0.09491419792175293 Skipping prepopulated (16, 8) Skipping prepopulated (16, 9) Skipping prepopulated (16, 10) Skipping prepopulated (16, 11) Skipping prepopulated (16, 12) Skipping prepopulated (16, 13) Skipping prepopulated (16, 14) Skipping prepopulated (16, 15) Skipping prepopulated (16, 17) Skipping prepopulated (16, 18) Skipping prepopulated (16, 19) Skipping prepopulated (16, 20) Skipping prepopulated (16, 21) Computing sim between patterns 17 and 0 Time taken: 0.08710193634033203 Computing sim between patterns 17 and 1 Time taken: 0.08787322044372559 Computing sim between patterns 17 and 2 Time taken: 0.08777475357055664 Skipping prepopulated (17, 3) Skipping prepopulated (17, 4) Computing sim between patterns 17 and 5 Time taken: 0.08111238479614258 Skipping prepopulated (17, 6) Computing sim between patterns 17 and 7 Time taken: 0.08121585845947266 Skipping prepopulated (17, 8) Skipping prepopulated (17, 9) Skipping prepopulated (17, 10) Skipping prepopulated (17, 11) Skipping prepopulated (17, 12) Skipping prepopulated (17, 13) Skipping prepopulated (17, 14) Skipping prepopulated (17, 15) Skipping prepopulated (17, 16) Skipping prepopulated (17, 18) Skipping prepopulated (17, 19) Skipping prepopulated (17, 20) Skipping prepopulated (17, 21) Computing sim between patterns 18 and 0 Time taken: 0.05016207695007324 Computing sim between patterns 18 and 1 Time taken: 0.048543691635131836 Computing sim between patterns 18 and 2 Time taken: 0.04689431190490723 Skipping prepopulated (18, 3) Skipping prepopulated (18, 4) Computing sim between patterns 18 and 5 Time taken: 0.046835899353027344 Skipping prepopulated (18, 6) Computing sim between patterns 18 and 7 Time taken: 0.0423893928527832 Skipping prepopulated (18, 8) Skipping prepopulated (18, 9) Skipping prepopulated (18, 10) Skipping prepopulated (18, 11) Skipping prepopulated (18, 12) Skipping prepopulated (18, 13) Skipping prepopulated (18, 14) Skipping prepopulated (18, 15) Skipping prepopulated (18, 16) Skipping prepopulated (18, 17) Skipping prepopulated (18, 19) Skipping prepopulated (18, 20) Skipping prepopulated (18, 21) Computing sim between patterns 19 and 0 Time taken: 0.022393465042114258 Computing sim between patterns 19 and 1 Time taken: 0.021877050399780273 Computing sim between patterns 19 and 2 Time taken: 0.021082639694213867 Skipping prepopulated (19, 3) Skipping prepopulated (19, 4) Computing sim between patterns 19 and 5 Time taken: 0.021903514862060547 Skipping prepopulated (19, 6) Computing sim between patterns 19 and 7 Time taken: 0.019354820251464844 Skipping prepopulated (19, 8) Skipping prepopulated (19, 9) Skipping prepopulated (19, 10) Skipping prepopulated (19, 11) Skipping prepopulated (19, 12) Skipping prepopulated (19, 13) Skipping prepopulated (19, 14) Skipping prepopulated (19, 15) Skipping prepopulated (19, 16) Skipping prepopulated (19, 17) Skipping prepopulated (19, 18) Skipping prepopulated (19, 20) Skipping prepopulated (19, 21) Computing sim between patterns 20 and 0 Time taken: 0.016215085983276367 Computing sim between patterns 20 and 1 Time taken: 0.015387535095214844 Computing sim between patterns 20 and 2 Time taken: 0.016743183135986328 Skipping prepopulated (20, 3) Skipping prepopulated (20, 4) Computing sim between patterns 20 and 5 Time taken: 0.015308141708374023 Skipping prepopulated (20, 6) Computing sim between patterns 20 and 7 Time taken: 0.015384197235107422 Skipping prepopulated (20, 8) Skipping prepopulated (20, 9) Skipping prepopulated (20, 10) Skipping prepopulated (20, 11) Skipping prepopulated (20, 12) Skipping prepopulated (20, 13) Skipping prepopulated (20, 14) Skipping prepopulated (20, 15) Skipping prepopulated (20, 16) Skipping prepopulated (20, 17) Skipping prepopulated (20, 18) Skipping prepopulated (20, 19) Skipping prepopulated (20, 21) Computing sim between patterns 21 and 0 Time taken: 0.01719069480895996 Computing sim between patterns 21 and 1 Time taken: 0.01660776138305664 Computing sim between patterns 21 and 2 Time taken: 0.016944408416748047 Skipping prepopulated (21, 3) Skipping prepopulated (21, 4) Computing sim between patterns 21 and 5 Time taken: 0.014694929122924805 Skipping prepopulated (21, 6) Computing sim between patterns 21 and 7 Time taken: 0.015585184097290039 Skipping prepopulated (21, 8) Skipping prepopulated (21, 9) Skipping prepopulated (21, 10) Skipping prepopulated (21, 11) Skipping prepopulated (21, 12) Skipping prepopulated (21, 13) Skipping prepopulated (21, 14) Skipping prepopulated (21, 15) Skipping prepopulated (21, 16) Skipping prepopulated (21, 17) Skipping prepopulated (21, 18) Skipping prepopulated (21, 19) Skipping prepopulated (21, 20) Cluster sizes [1733 1104 928 470 405 242 220 193 125 90 48 41 34 30 27 26 24 19 9 3 1 1] Cross-contamination matrix: [[1. 0.69 0.65 0.35 0.37 0.86 0.68 0.56 0.55 0.96 0.71 0.88 0.89 0.45 0.78 0.57 0.65 0.71 0.96 0.57 0.49 0.93] [0.55 1. 0.91 0.39 0.28 0.85 0.9 0.44 0.51 0.88 0.69 0.59 0.64 0.49 0.84 0.41 0.54 0.43 0.62 0.51 0.66 0.66] [0.12 0.49 1. 0.06 0.03 0.4 0.39 0.11 0.1 0.35 0.24 0.56 0.39 0.14 0.51 0.06 0.14 0.22 0.61 0.24 0.07 0.17] [0.08 0.12 0.1 1. 0.19 0.1 0.07 0.18 0.15 0.1 0.07 0.09 0.07 0.07 0.11 0.07 0.07 0.09 0.1 0.13 0.13 0.08] [0.13 0.11 0.11 0.42 1. 0.12 0.09 0.27 0.22 0.09 0.16 0.13 0.19 0.12 0.11 0.12 0.07 0.11 0.11 0.53 0.11 0.06] [0.52 0.69 0.68 0.18 0.13 1. 0.65 0.38 0.29 0.56 0.43 0.4 0.42 0.31 0.56 0.29 0.35 0.2 0.69 0.27 0.39 0.62] [0.38 0.78 0.71 0.13 0.09 0.68 1. 0.19 0.36 0.65 0.45 0.65 0.38 0.28 0.33 0.23 0.39 0.54 0.42 0.3 0.29 0.37] [0.27 0.25 0.3 0.29 0.28 0.35 0.2 1. 0.23 0.23 0.26 0.35 0.78 0.2 0.33 0.31 0.3 0.27 0.29 0.28 0.26 0.24] [0.03 0.03 0.03 0.02 0.02 0.03 0.04 0.02 1. 0.09 0.58 0.01 0.03 0.1 0.02 0.01 0.03 0.04 0.03 0.04 0.01 0.02] [0.46 0.6 0.52 0.11 0.05 0.47 0.54 0.18 0.35 1. 0.59 0.3 0.24 0.24 0.38 0.15 0.31 0.36 0.38 0.27 0.28 0.49] [0.1 0.22 0.24 0.02 0.04 0.16 0.15 0.05 0.7 0.38 1. 0.07 0.08 0.26 0.16 0.02 0.11 0.07 0.08 0.11 0.24 0.13] [0.48 0.39 0.78 0.12 0.12 0.37 0.6 0.32 0.18 0.36 0.26 1. 0.66 0.23 0.63 0.25 0.34 0.19 0.46 0.44 0.22 0.77] [0.27 0.22 0.43 0.02 0.05 0.18 0.16 0.63 0.05 0.18 0.08 0.48 1. 0.06 0.33 0.19 0.27 0.21 0.15 0.08 0.11 0.27] [0.67 0.84 0.9 0.42 0.43 0.83 0.84 0.65 1. 0.89 1. 0.73 0.75 1. 0.82 0.54 0.76 0.7 0.91 0.94 0.91 0.59] [0.37 0.56 0.68 0.14 0.08 0.44 0.26 0.26 0.16 0.36 0.3 0.56 0.45 0.19 1. 0.28 0.23 0.33 0.33 0.37 0.09 0.4 ] [0.85 0.77 0.8 0.61 0.57 0.94 0.88 1. 0.73 0.75 0.71 0.82 1. 0.74 1. 1. 0.71 0.8 0.81 0.88 0.75 0.93] [0.69 0.69 0.71 0.31 0.21 0.65 0.69 0.6 0.52 0.64 0.64 0.8 0.85 0.53 0.68 0.42 1. 0.44 0.68 0.9 0.57 0.68] [0.02 0.01 0.03 0. 0. 0.01 0.03 0.01 0.01 0.03 0.01 0.04 0.03 0.01 0.03 0.01 0.01 1. 0. 0.07 0. 0.01] [0.18 0.11 0.31 0.01 0. 0.22 0.09 0.05 0.02 0.07 0.01 0.13 0.09 0.09 0.05 0.06 0.09 0.12 1. 0.08 0. 0. ] [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. ] [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. ] [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. ]] Pattern-to-pattern sim matrix: [[1. 0.61 0.48 0.13 0.16 0.68 0.61 0.48 0.38 0.72 0.54 0.66 0.69 0.47 0.57 0.4 0.58 0.34 0.54 0.37 0.38 0.5 ] [0.61 1. 0.81 0.21 0.15 0.73 0.8 0.39 0.48 0.73 0.59 0.61 0.63 0.55 0.74 0.35 0.63 0.37 0.44 0.38 0.51 0.45] [0.48 0.81 1. 0.12 0.06 0.62 0.66 0.37 0.36 0.59 0.52 0.7 0.7 0.46 0.74 0.37 0.51 0.41 0.41 0.37 0.22 0.39] [0.13 0.21 0.12 1. 0.46 0.14 0.11 0.34 0.29 0.19 0.14 0.1 0.13 0.08 0.16 0.15 0.14 0.15 0.13 0.17 0.3 0.09] [0.16 0.15 0.06 0.47 1. 0.08 0.05 0.36 0.28 0.12 0.17 0.08 0.21 0.13 0.11 0.06 0.07 0.15 0.09 0.32 0.18 0.06] [0.68 0.73 0.62 0.14 0.08 1. 0.58 0.48 0.34 0.53 0.44 0.47 0.51 0.41 0.55 0.34 0.49 0.27 0.47 0.28 0.36 0.5 ] [0.61 0.81 0.68 0.11 0.05 0.58 1. 0.32 0.42 0.61 0.45 0.64 0.52 0.48 0.43 0.44 0.58 0.34 0.39 0.34 0.38 0.42] [0.47 0.39 0.37 0.34 0.36 0.48 0.32 1. 0.33 0.3 0.34 0.44 0.75 0.3 0.42 0.44 0.49 0.29 0.32 0.21 0.31 0.27] [0.38 0.48 0.36 0.29 0.28 0.34 0.42 0.33 1. 0.55 0.8 0.25 0.31 0.54 0.29 0.15 0.35 0.26 0.21 0.35 0.37 0.26] [0.72 0.73 0.59 0.19 0.12 0.53 0.61 0.3 0.55 1. 0.72 0.39 0.43 0.56 0.49 0.28 0.52 0.44 0.36 0.39 0.44 0.44] [0.54 0.59 0.53 0.14 0.18 0.44 0.46 0.34 0.8 0.72 1. 0.34 0.35 0.69 0.4 0.21 0.47 0.32 0.23 0.4 0.44 0.39] [0.66 0.61 0.71 0.1 0.09 0.47 0.66 0.44 0.26 0.39 0.34 1. 0.74 0.35 0.59 0.47 0.58 0.3 0.42 0.34 0.18 0.5 ] [0.69 0.63 0.7 0.13 0.21 0.51 0.53 0.75 0.31 0.43 0.35 0.73 1. 0.36 0.65 0.42 0.66 0.35 0.42 0.22 0.36 0.42] [0.47 0.55 0.48 0.09 0.15 0.42 0.5 0.3 0.54 0.56 0.69 0.37 0.37 1. 0.37 0.28 0.47 0.29 0.39 0.37 0.42 0.37] [0.57 0.74 0.74 0.16 0.11 0.55 0.41 0.42 0.29 0.49 0.4 0.59 0.65 0.34 1. 0.38 0.49 0.29 0.32 0.3 0.27 0.41] [0.42 0.36 0.39 0.15 0.06 0.36 0.46 0.44 0.16 0.3 0.22 0.47 0.42 0.28 0.39 1. 0.37 0.27 0.36 0.27 0.23 0.37] [0.58 0.63 0.53 0.14 0.07 0.49 0.59 0.49 0.36 0.52 0.47 0.6 0.67 0.47 0.54 0.36 1. 0.32 0.38 0.42 0.41 0.47] [0.35 0.37 0.48 0.16 0.15 0.28 0.4 0.3 0.31 0.45 0.34 0.35 0.36 0.29 0.34 0.27 0.32 1. 0.28 0.37 0.28 0.29] [0.55 0.43 0.48 0.14 0.11 0.48 0.38 0.32 0.25 0.36 0.23 0.41 0.42 0.38 0.33 0.35 0.38 0.26 1. 0.25 0.23 0.3 ] [0.38 0.39 0.37 0.19 0.38 0.28 0.33 0.21 0.36 0.4 0.41 0.34 0.22 0.35 0.31 0.32 0.39 0.37 0.21 1. 0.19 0.26] [0.39 0.53 0.23 0.3 0.18 0.37 0.38 0.32 0.38 0.45 0.44 0.19 0.37 0.42 0.27 0.25 0.41 0.28 0.23 0.19 1. 0.27] [0.53 0.48 0.4 0.09 0.07 0.54 0.43 0.29 0.28 0.47 0.42 0.5 0.45 0.36 0.41 0.37 0.47 0.3 0.3 0.25 0.25 1. ]] Collapsing 1 & 6 with crosscontam 0.8395440718465649 and sim 0.8006393361887985 Trimming eliminated 0 seqlets out of 1322 Skipped 1 seqlets Removed 22 duplicate seqlets Unmerged patterns remapping: OrderedDict([(0, 0), (2, 2), (3, 3), (4, 4), (5, 5), (7, 6), (8, 7), (9, 8), (10, 9), (11, 10), (12, 11), (13, 12), (14, 13), (15, 14), (16, 15), (17, 16), (18, 17), (19, 18), (20, 19), (21, 20)]) On merging iteration 3 Numbers for each pattern pre-subsample: [1733, 1299, 928, 470, 405, 242, 193, 125, 90, 48, 41, 34, 30, 27, 26, 24, 19, 9, 3, 1, 1] Numbers after subsampling: [300, 300, 300, 300, 300, 242, 193, 125, 90, 48, 41, 34, 30, 27, 26, 24, 19, 9, 3, 1, 1] Computing sim between patterns 0 and 1 Time taken: 0.6171858310699463 Skipping prepopulated (0, 2) Skipping prepopulated (0, 3) Skipping prepopulated (0, 4) Skipping prepopulated (0, 5) Skipping prepopulated (0, 6) Skipping prepopulated (0, 7) Skipping prepopulated (0, 8) Skipping prepopulated (0, 9) Skipping prepopulated (0, 10) Skipping prepopulated (0, 11) Skipping prepopulated (0, 12) Skipping prepopulated (0, 13) Skipping prepopulated (0, 14) Skipping prepopulated (0, 15) Skipping prepopulated (0, 16) Skipping prepopulated (0, 17) Skipping prepopulated (0, 18) Skipping prepopulated (0, 19) Skipping prepopulated (0, 20) Computing sim between patterns 1 and 0 Time taken: 0.577923059463501 Computing sim between patterns 1 and 2 Time taken: 0.5991907119750977 Computing sim between patterns 1 and 3 Time taken: 0.6095030307769775 Computing sim between patterns 1 and 4 Time taken: 0.5852200984954834 Computing sim between patterns 1 and 5 Time taken: 0.6132569313049316 Computing sim between patterns 1 and 6 Time taken: 0.5781476497650146 Computing sim between patterns 1 and 7 Time taken: 0.49297499656677246 Computing sim between patterns 1 and 8 Time taken: 0.5156605243682861 Computing sim between patterns 1 and 9 Time taken: 0.5236177444458008 Computing sim between patterns 1 and 10 Time taken: 0.47346925735473633 Computing sim between patterns 1 and 11 Time taken: 0.48538732528686523 Computing sim between patterns 1 and 12 Time taken: 0.4955456256866455 Computing sim between patterns 1 and 13 Time taken: 0.5966613292694092 Computing sim between patterns 1 and 14 Time taken: 0.4672987461090088 Computing sim between patterns 1 and 15 Time taken: 0.4626138210296631 Computing sim between patterns 1 and 16 Time taken: 0.5187652111053467 Computing sim between patterns 1 and 17 Time taken: 0.4577057361602783 Computing sim between patterns 1 and 18 Time taken: 0.46962451934814453 Computing sim between patterns 1 and 19 Time taken: 0.4798281192779541 Computing sim between patterns 1 and 20 Time taken: 0.4541926383972168 Skipping prepopulated (2, 0) Computing sim between patterns 2 and 1 Time taken: 0.6029207706451416 Skipping prepopulated (2, 3) Skipping prepopulated (2, 4) Skipping prepopulated (2, 5) Skipping prepopulated (2, 6) Skipping prepopulated (2, 7) Skipping prepopulated (2, 8) Skipping prepopulated (2, 9) Skipping prepopulated (2, 10) Skipping prepopulated (2, 11) Skipping prepopulated (2, 12) Skipping prepopulated (2, 13) Skipping prepopulated (2, 14) Skipping prepopulated (2, 15) Skipping prepopulated (2, 16) Skipping prepopulated (2, 17) Skipping prepopulated (2, 18) Skipping prepopulated (2, 19) Skipping prepopulated (2, 20) Skipping prepopulated (3, 0) Computing sim between patterns 3 and 1 Time taken: 0.6099538803100586 Skipping prepopulated (3, 2) Skipping prepopulated (3, 4) Skipping prepopulated (3, 5) Skipping prepopulated (3, 6) Skipping prepopulated (3, 7) Skipping prepopulated (3, 8) Skipping prepopulated (3, 9) Skipping prepopulated (3, 10) Skipping prepopulated (3, 11) Skipping prepopulated (3, 12) Skipping prepopulated (3, 13) Skipping prepopulated (3, 14) Skipping prepopulated (3, 15) Skipping prepopulated (3, 16) Skipping prepopulated (3, 17) Skipping prepopulated (3, 18) Skipping prepopulated (3, 19) Skipping prepopulated (3, 20) Skipping prepopulated (4, 0) Computing sim between patterns 4 and 1 Time taken: 0.5692770481109619 Skipping prepopulated (4, 2) Skipping prepopulated (4, 3) Skipping prepopulated (4, 5) Skipping prepopulated (4, 6) Skipping prepopulated (4, 7) Skipping prepopulated (4, 8) Skipping prepopulated (4, 9) Skipping prepopulated (4, 10) Skipping prepopulated (4, 11) Skipping prepopulated (4, 12) Skipping prepopulated (4, 13) Skipping prepopulated (4, 14) Skipping prepopulated (4, 15) Skipping prepopulated (4, 16) Skipping prepopulated (4, 17) Skipping prepopulated (4, 18) Skipping prepopulated (4, 19) Skipping prepopulated (4, 20) Skipping prepopulated (5, 0) Computing sim between patterns 5 and 1 Time taken: 0.5306763648986816 Skipping prepopulated (5, 2) Skipping prepopulated (5, 3) Skipping prepopulated (5, 4) Skipping prepopulated (5, 6) Skipping prepopulated (5, 7) Skipping prepopulated (5, 8) Skipping prepopulated (5, 9) Skipping prepopulated (5, 10) Skipping prepopulated (5, 11) Skipping prepopulated (5, 12) Skipping prepopulated (5, 13) Skipping prepopulated (5, 14) Skipping prepopulated (5, 15) Skipping prepopulated (5, 16) Skipping prepopulated (5, 17) Skipping prepopulated (5, 18) Skipping prepopulated (5, 19) Skipping prepopulated (5, 20) Skipping prepopulated (6, 0) Computing sim between patterns 6 and 1 Time taken: 0.5968654155731201 Skipping prepopulated (6, 2) Skipping prepopulated (6, 3) Skipping prepopulated (6, 4) Skipping prepopulated (6, 5) Skipping prepopulated (6, 7) Skipping prepopulated (6, 8) Skipping prepopulated (6, 9) Skipping prepopulated (6, 10) Skipping prepopulated (6, 11) Skipping prepopulated (6, 12) Skipping prepopulated (6, 13) Skipping prepopulated (6, 14) Skipping prepopulated (6, 15) Skipping prepopulated (6, 16) Skipping prepopulated (6, 17) Skipping prepopulated (6, 18) Skipping prepopulated (6, 19) Skipping prepopulated (6, 20) Skipping prepopulated (7, 0) Computing sim between patterns 7 and 1 Time taken: 0.37833333015441895 Skipping prepopulated (7, 2) Skipping prepopulated (7, 3) Skipping prepopulated (7, 4) Skipping prepopulated (7, 5) Skipping prepopulated (7, 6) Skipping prepopulated (7, 8) Skipping prepopulated (7, 9) Skipping prepopulated (7, 10) Skipping prepopulated (7, 11) Skipping prepopulated (7, 12) Skipping prepopulated (7, 13) Skipping prepopulated (7, 14) Skipping prepopulated (7, 15) Skipping prepopulated (7, 16) Skipping prepopulated (7, 17) Skipping prepopulated (7, 18) Skipping prepopulated (7, 19) Skipping prepopulated (7, 20) Skipping prepopulated (8, 0) Computing sim between patterns 8 and 1 Time taken: 0.33173465728759766 Skipping prepopulated (8, 2) Skipping prepopulated (8, 3) Skipping prepopulated (8, 4) Skipping prepopulated (8, 5) Skipping prepopulated (8, 6) Skipping prepopulated (8, 7) Skipping prepopulated (8, 9) Skipping prepopulated (8, 10) Skipping prepopulated (8, 11) Skipping prepopulated (8, 12) Skipping prepopulated (8, 13) Skipping prepopulated (8, 14) Skipping prepopulated (8, 15) Skipping prepopulated (8, 16) Skipping prepopulated (8, 17) Skipping prepopulated (8, 18) Skipping prepopulated (8, 19) Skipping prepopulated (8, 20) Skipping prepopulated (9, 0) Computing sim between patterns 9 and 1 Time taken: 0.18640804290771484 Skipping prepopulated (9, 2) Skipping prepopulated (9, 3) Skipping prepopulated (9, 4) Skipping prepopulated (9, 5) Skipping prepopulated (9, 6) Skipping prepopulated (9, 7) Skipping prepopulated (9, 8) Skipping prepopulated (9, 10) Skipping prepopulated (9, 11) Skipping prepopulated (9, 12) Skipping prepopulated (9, 13) Skipping prepopulated (9, 14) Skipping prepopulated (9, 15) Skipping prepopulated (9, 16) Skipping prepopulated (9, 17) Skipping prepopulated (9, 18) Skipping prepopulated (9, 19) Skipping prepopulated (9, 20) Skipping prepopulated (10, 0) Computing sim between patterns 10 and 1 Time taken: 0.16111040115356445 Skipping prepopulated (10, 2) Skipping prepopulated (10, 3) Skipping prepopulated (10, 4) Skipping prepopulated (10, 5) Skipping prepopulated (10, 6) Skipping prepopulated (10, 7) Skipping prepopulated (10, 8) Skipping prepopulated (10, 9) Skipping prepopulated (10, 11) Skipping prepopulated (10, 12) Skipping prepopulated (10, 13) Skipping prepopulated (10, 14) Skipping prepopulated (10, 15) Skipping prepopulated (10, 16) Skipping prepopulated (10, 17) Skipping prepopulated (10, 18) Skipping prepopulated (10, 19) Skipping prepopulated (10, 20) Skipping prepopulated (11, 0) Computing sim between patterns 11 and 1 Time taken: 0.1531975269317627 Skipping prepopulated (11, 2) Skipping prepopulated (11, 3) Skipping prepopulated (11, 4) Skipping prepopulated (11, 5) Skipping prepopulated (11, 6) Skipping prepopulated (11, 7) Skipping prepopulated (11, 8) Skipping prepopulated (11, 9) Skipping prepopulated (11, 10) Skipping prepopulated (11, 12) Skipping prepopulated (11, 13) Skipping prepopulated (11, 14) Skipping prepopulated (11, 15) Skipping prepopulated (11, 16) Skipping prepopulated (11, 17) Skipping prepopulated (11, 18) Skipping prepopulated (11, 19) Skipping prepopulated (11, 20) Skipping prepopulated (12, 0) Computing sim between patterns 12 and 1 Time taken: 0.13790464401245117 Skipping prepopulated (12, 2) Skipping prepopulated (12, 3) Skipping prepopulated (12, 4) Skipping prepopulated (12, 5) Skipping prepopulated (12, 6) Skipping prepopulated (12, 7) Skipping prepopulated (12, 8) Skipping prepopulated (12, 9) Skipping prepopulated (12, 10) Skipping prepopulated (12, 11) Skipping prepopulated (12, 13) Skipping prepopulated (12, 14) Skipping prepopulated (12, 15) Skipping prepopulated (12, 16) Skipping prepopulated (12, 17) Skipping prepopulated (12, 18) Skipping prepopulated (12, 19) Skipping prepopulated (12, 20) Skipping prepopulated (13, 0) Computing sim between patterns 13 and 1 Time taken: 0.12338852882385254 Skipping prepopulated (13, 2) Skipping prepopulated (13, 3) Skipping prepopulated (13, 4) Skipping prepopulated (13, 5) Skipping prepopulated (13, 6) Skipping prepopulated (13, 7) Skipping prepopulated (13, 8) Skipping prepopulated (13, 9) Skipping prepopulated (13, 10) Skipping prepopulated (13, 11) Skipping prepopulated (13, 12) Skipping prepopulated (13, 14) Skipping prepopulated (13, 15) Skipping prepopulated (13, 16) Skipping prepopulated (13, 17) Skipping prepopulated (13, 18) Skipping prepopulated (13, 19) Skipping prepopulated (13, 20) Skipping prepopulated (14, 0) Computing sim between patterns 14 and 1 Time taken: 0.12043070793151855 Skipping prepopulated (14, 2) Skipping prepopulated (14, 3) Skipping prepopulated (14, 4) Skipping prepopulated (14, 5) Skipping prepopulated (14, 6) Skipping prepopulated (14, 7) Skipping prepopulated (14, 8) Skipping prepopulated (14, 9) Skipping prepopulated (14, 10) Skipping prepopulated (14, 11) Skipping prepopulated (14, 12) Skipping prepopulated (14, 13) Skipping prepopulated (14, 15) Skipping prepopulated (14, 16) Skipping prepopulated (14, 17) Skipping prepopulated (14, 18) Skipping prepopulated (14, 19) Skipping prepopulated (14, 20) Skipping prepopulated (15, 0) Computing sim between patterns 15 and 1 Time taken: 0.11427187919616699 Skipping prepopulated (15, 2) Skipping prepopulated (15, 3) Skipping prepopulated (15, 4) Skipping prepopulated (15, 5) Skipping prepopulated (15, 6) Skipping prepopulated (15, 7) Skipping prepopulated (15, 8) Skipping prepopulated (15, 9) Skipping prepopulated (15, 10) Skipping prepopulated (15, 11) Skipping prepopulated (15, 12) Skipping prepopulated (15, 13) Skipping prepopulated (15, 14) Skipping prepopulated (15, 16) Skipping prepopulated (15, 17) Skipping prepopulated (15, 18) Skipping prepopulated (15, 19) Skipping prepopulated (15, 20) Skipping prepopulated (16, 0) Computing sim between patterns 16 and 1 Time taken: 0.09570670127868652 Skipping prepopulated (16, 2) Skipping prepopulated (16, 3) Skipping prepopulated (16, 4) Skipping prepopulated (16, 5) Skipping prepopulated (16, 6) Skipping prepopulated (16, 7) Skipping prepopulated (16, 8) Skipping prepopulated (16, 9) Skipping prepopulated (16, 10) Skipping prepopulated (16, 11) Skipping prepopulated (16, 12) Skipping prepopulated (16, 13) Skipping prepopulated (16, 14) Skipping prepopulated (16, 15) Skipping prepopulated (16, 17) Skipping prepopulated (16, 18) Skipping prepopulated (16, 19) Skipping prepopulated (16, 20) Skipping prepopulated (17, 0) Computing sim between patterns 17 and 1 Time taken: 0.0507662296295166 Skipping prepopulated (17, 2) Skipping prepopulated (17, 3) Skipping prepopulated (17, 4) Skipping prepopulated (17, 5) Skipping prepopulated (17, 6) Skipping prepopulated (17, 7) Skipping prepopulated (17, 8) Skipping prepopulated (17, 9) Skipping prepopulated (17, 10) Skipping prepopulated (17, 11) Skipping prepopulated (17, 12) Skipping prepopulated (17, 13) Skipping prepopulated (17, 14) Skipping prepopulated (17, 15) Skipping prepopulated (17, 16) Skipping prepopulated (17, 18) Skipping prepopulated (17, 19) Skipping prepopulated (17, 20) Skipping prepopulated (18, 0) Computing sim between patterns 18 and 1 Time taken: 0.02234363555908203 Skipping prepopulated (18, 2) Skipping prepopulated (18, 3) Skipping prepopulated (18, 4) Skipping prepopulated (18, 5) Skipping prepopulated (18, 6) Skipping prepopulated (18, 7) Skipping prepopulated (18, 8) Skipping prepopulated (18, 9) Skipping prepopulated (18, 10) Skipping prepopulated (18, 11) Skipping prepopulated (18, 12) Skipping prepopulated (18, 13) Skipping prepopulated (18, 14) Skipping prepopulated (18, 15) Skipping prepopulated (18, 16) Skipping prepopulated (18, 17) Skipping prepopulated (18, 19) Skipping prepopulated (18, 20) Skipping prepopulated (19, 0) Computing sim between patterns 19 and 1 Time taken: 0.015065431594848633 Skipping prepopulated (19, 2) Skipping prepopulated (19, 3) Skipping prepopulated (19, 4) Skipping prepopulated (19, 5) Skipping prepopulated (19, 6) Skipping prepopulated (19, 7) Skipping prepopulated (19, 8) Skipping prepopulated (19, 9) Skipping prepopulated (19, 10) Skipping prepopulated (19, 11) Skipping prepopulated (19, 12) Skipping prepopulated (19, 13) Skipping prepopulated (19, 14) Skipping prepopulated (19, 15) Skipping prepopulated (19, 16) Skipping prepopulated (19, 17) Skipping prepopulated (19, 18) Skipping prepopulated (19, 20) Skipping prepopulated (20, 0) Computing sim between patterns 20 and 1 Time taken: 0.0167386531829834 Skipping prepopulated (20, 2) Skipping prepopulated (20, 3) Skipping prepopulated (20, 4) Skipping prepopulated (20, 5) Skipping prepopulated (20, 6) Skipping prepopulated (20, 7) Skipping prepopulated (20, 8) Skipping prepopulated (20, 9) Skipping prepopulated (20, 10) Skipping prepopulated (20, 11) Skipping prepopulated (20, 12) Skipping prepopulated (20, 13) Skipping prepopulated (20, 14) Skipping prepopulated (20, 15) Skipping prepopulated (20, 16) Skipping prepopulated (20, 17) Skipping prepopulated (20, 18) Skipping prepopulated (20, 19) Cluster sizes [1733 1299 928 470 405 242 193 125 90 48 41 34 30 27 26 24 19 9 3 1 1] Cross-contamination matrix: [[1. 0.69 0.65 0.35 0.37 0.86 0.56 0.55 0.96 0.71 0.88 0.89 0.45 0.78 0.57 0.65 0.71 0.96 0.57 0.49 0.93] [0.54 1. 0.93 0.4 0.31 0.85 0.44 0.52 0.86 0.69 0.59 0.62 0.5 0.83 0.42 0.55 0.45 0.59 0.53 0.67 0.62] [0.12 0.51 1. 0.06 0.03 0.4 0.11 0.1 0.35 0.24 0.56 0.39 0.14 0.51 0.06 0.14 0.22 0.61 0.24 0.07 0.17] [0.08 0.12 0.1 1. 0.19 0.1 0.18 0.15 0.1 0.07 0.09 0.07 0.07 0.11 0.07 0.07 0.09 0.1 0.13 0.13 0.08] [0.13 0.11 0.11 0.42 1. 0.12 0.27 0.22 0.09 0.16 0.13 0.19 0.12 0.11 0.12 0.07 0.11 0.11 0.53 0.11 0.06] [0.52 0.71 0.68 0.18 0.13 1. 0.38 0.29 0.56 0.43 0.4 0.42 0.31 0.56 0.29 0.35 0.2 0.69 0.27 0.39 0.62] [0.27 0.24 0.3 0.29 0.28 0.35 1. 0.23 0.23 0.26 0.35 0.78 0.2 0.33 0.31 0.3 0.27 0.29 0.28 0.26 0.24] [0.03 0.04 0.03 0.02 0.02 0.03 0.02 1. 0.09 0.58 0.01 0.03 0.1 0.02 0.01 0.03 0.04 0.03 0.04 0.01 0.02] [0.46 0.61 0.52 0.11 0.05 0.47 0.18 0.35 1. 0.59 0.3 0.24 0.24 0.38 0.15 0.31 0.36 0.38 0.27 0.28 0.49] [0.1 0.24 0.24 0.02 0.04 0.16 0.05 0.7 0.38 1. 0.07 0.08 0.26 0.16 0.02 0.11 0.07 0.08 0.11 0.24 0.13] [0.48 0.39 0.78 0.12 0.12 0.37 0.32 0.18 0.36 0.26 1. 0.66 0.23 0.63 0.25 0.34 0.19 0.46 0.44 0.22 0.77] [0.27 0.21 0.43 0.02 0.05 0.18 0.63 0.05 0.18 0.08 0.48 1. 0.06 0.33 0.19 0.27 0.21 0.15 0.08 0.11 0.27] [0.67 0.85 0.9 0.42 0.43 0.83 0.65 1. 0.89 1. 0.73 0.75 1. 0.82 0.54 0.76 0.7 0.91 0.94 0.91 0.59] [0.37 0.56 0.68 0.14 0.08 0.44 0.26 0.16 0.36 0.3 0.56 0.45 0.19 1. 0.28 0.23 0.33 0.33 0.37 0.09 0.4 ] [0.85 0.83 0.8 0.61 0.57 0.94 1. 0.73 0.75 0.71 0.82 1. 0.74 1. 1. 0.71 0.8 0.81 0.88 0.75 0.93] [0.69 0.69 0.71 0.31 0.21 0.65 0.6 0.52 0.64 0.64 0.8 0.85 0.53 0.68 0.42 1. 0.44 0.68 0.9 0.57 0.68] [0.02 0.01 0.03 0. 0. 0.01 0.01 0.01 0.03 0.01 0.04 0.03 0.01 0.03 0.01 0.01 1. 0. 0.07 0. 0.01] [0.18 0.11 0.31 0.01 0. 0.22 0.05 0.02 0.07 0.01 0.13 0.09 0.09 0.05 0.06 0.09 0.12 1. 0.08 0. 0. ] [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. ] [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. ] [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. ]] Pattern-to-pattern sim matrix: [[1. 0.62 0.48 0.13 0.16 0.68 0.48 0.38 0.72 0.54 0.66 0.69 0.47 0.57 0.4 0.58 0.34 0.54 0.37 0.38 0.5 ] [0.62 1. 0.81 0.2 0.14 0.73 0.39 0.48 0.73 0.58 0.62 0.64 0.55 0.74 0.36 0.64 0.36 0.43 0.39 0.5 0.45] [0.48 0.81 1. 0.12 0.06 0.62 0.37 0.36 0.59 0.52 0.7 0.7 0.46 0.74 0.37 0.51 0.41 0.41 0.37 0.22 0.39] [0.13 0.2 0.12 1. 0.46 0.14 0.34 0.29 0.19 0.14 0.1 0.13 0.08 0.16 0.15 0.14 0.15 0.13 0.17 0.3 0.09] [0.16 0.14 0.06 0.47 1. 0.08 0.36 0.28 0.12 0.17 0.08 0.21 0.13 0.11 0.06 0.07 0.15 0.09 0.32 0.18 0.06] [0.68 0.73 0.62 0.14 0.08 1. 0.48 0.34 0.53 0.44 0.47 0.51 0.41 0.55 0.34 0.49 0.27 0.47 0.28 0.36 0.5 ] [0.47 0.39 0.37 0.34 0.36 0.48 1. 0.33 0.3 0.34 0.44 0.75 0.3 0.42 0.44 0.49 0.29 0.32 0.21 0.31 0.27] [0.38 0.48 0.36 0.29 0.28 0.34 0.33 1. 0.55 0.8 0.25 0.31 0.54 0.29 0.15 0.35 0.26 0.21 0.35 0.37 0.26] [0.72 0.73 0.59 0.19 0.12 0.53 0.3 0.55 1. 0.72 0.39 0.43 0.56 0.49 0.28 0.52 0.44 0.36 0.39 0.44 0.44] [0.54 0.58 0.53 0.14 0.18 0.44 0.34 0.8 0.72 1. 0.34 0.35 0.69 0.4 0.21 0.47 0.32 0.23 0.4 0.44 0.39] [0.66 0.62 0.71 0.1 0.09 0.47 0.44 0.26 0.39 0.34 1. 0.74 0.35 0.59 0.47 0.58 0.3 0.42 0.34 0.18 0.5 ] [0.69 0.64 0.7 0.13 0.21 0.51 0.75 0.31 0.43 0.35 0.73 1. 0.36 0.65 0.42 0.66 0.35 0.42 0.22 0.36 0.42] [0.47 0.55 0.48 0.09 0.15 0.42 0.3 0.54 0.56 0.69 0.37 0.37 1. 0.37 0.28 0.47 0.29 0.39 0.37 0.42 0.37] [0.57 0.74 0.74 0.16 0.11 0.55 0.42 0.29 0.49 0.4 0.59 0.65 0.34 1. 0.38 0.49 0.29 0.32 0.3 0.27 0.41] [0.42 0.36 0.39 0.15 0.06 0.36 0.44 0.16 0.3 0.22 0.47 0.42 0.28 0.39 1. 0.37 0.27 0.36 0.27 0.23 0.37] [0.58 0.64 0.53 0.14 0.07 0.49 0.49 0.36 0.52 0.47 0.6 0.67 0.47 0.54 0.36 1. 0.32 0.38 0.42 0.41 0.47] [0.35 0.37 0.48 0.16 0.15 0.28 0.3 0.31 0.45 0.34 0.35 0.36 0.29 0.34 0.27 0.32 1. 0.28 0.37 0.28 0.29] [0.55 0.43 0.48 0.14 0.11 0.48 0.32 0.25 0.36 0.23 0.41 0.42 0.38 0.33 0.35 0.38 0.26 1. 0.25 0.23 0.3 ] [0.38 0.4 0.37 0.19 0.38 0.28 0.21 0.36 0.4 0.41 0.34 0.22 0.35 0.31 0.32 0.39 0.37 0.21 1. 0.19 0.26] [0.39 0.52 0.23 0.3 0.18 0.37 0.32 0.38 0.45 0.44 0.19 0.37 0.42 0.27 0.25 0.41 0.28 0.23 0.19 1. 0.27] [0.53 0.49 0.4 0.09 0.07 0.54 0.29 0.28 0.47 0.42 0.5 0.45 0.36 0.41 0.37 0.47 0.3 0.3 0.25 0.25 1. ]] Got 21 patterns after merging MEMORY 7.288692736 Performing seqlet reassignment MEMORY 7.288692736 Cross contin jaccard time taken: 0.12 s Cross contin jaccard time taken: 0.11 s Discarded 46 seqlets Skipped 1 seqlets Removed 2 duplicate seqlets Removed 5 duplicate seqlets Removed 9 duplicate seqlets Removed 1 duplicate seqlets Removed 3 duplicate seqlets Got 9 patterns after reassignment MEMORY 7.288692736 Total time taken is 2945.09s MEMORY 7.288692736
In [8]:
from modisco.visualization import viz_sequence
for idx,node in enumerate(results.metacluster_idx_to_submetacluster_results[0]
.seqlets_to_patterns_result.pattern_merge_hierarchy.root_nodes):
print("patternidx",idx)
pattern = node.pattern
print("num seqlets",len(pattern.seqlets))
viz_sequence.plot_weights(pattern["Nanog_profile_wn_contrib_scores"].fwd)
viz_sequence.plot_weights(pattern["sequence"].fwd)
viz_sequence.plot_weights(pattern["sequence"].rev)
patternidx 0 num seqlets 1733
patternidx 1 num seqlets 1299
patternidx 2 num seqlets 928
patternidx 3 num seqlets 470
patternidx 4 num seqlets 405
patternidx 5 num seqlets 242
patternidx 6 num seqlets 193
patternidx 7 num seqlets 125
patternidx 8 num seqlets 90
patternidx 9 num seqlets 48
patternidx 10 num seqlets 41
patternidx 11 num seqlets 34
patternidx 12 num seqlets 30
patternidx 13 num seqlets 27
patternidx 14 num seqlets 26
patternidx 15 num seqlets 24
patternidx 16 num seqlets 19
patternidx 17 num seqlets 9
patternidx 18 num seqlets 3
patternidx 19 num seqlets 1
patternidx 20 num seqlets 1
In [ ]:
import h5py
import modisco.util
reload(modisco.util)
import os
file_path = "agkmfewerseqles_newclustermerging.h5"
if (os.path.exists(file_path)):
os.remove(file_path)
grp = h5py.File(file_path, "w")
results.save_hdf5(grp)
grp.close()
In [ ]:
from modisco.visualization import viz_sequence
%matplotlib inline
hdf5_results = h5py.File(file_path,"r")
metacluster_names = [
x.decode("utf-8") for x in
list(hdf5_results["metaclustering_results"]
["all_metacluster_names"][:])]
all_patterns = []
background = np.array([0.27, 0.23, 0.23, 0.27])
for metacluster_name in metacluster_names:
print(metacluster_name)
metacluster_grp = (hdf5_results["metacluster_idx_to_submetacluster_results"]
[metacluster_name])
print("activity pattern:",metacluster_grp["activity_pattern"][:])
all_pattern_names = [x.decode("utf-8") for x in
list(metacluster_grp["seqlets_to_patterns_result"]
["patterns"]["all_pattern_names"][:])]
print(len(all_pattern_names))
if (len(all_pattern_names)==0):
print("No motifs found for this activity pattern")
for pattern_name in all_pattern_names:
print(metacluster_name, pattern_name)
all_patterns.append((metacluster_name, pattern_name))
pattern = metacluster_grp["seqlets_to_patterns_result"]["patterns"][pattern_name]
print("total seqlets:",len(pattern["seqlets_and_alnmts"]["seqlets"]))
print("Task 0 hypothetical scores:")
viz_sequence.plot_weights(pattern["Nanog_profile_wn_hypothetical_contribs"]["fwd"])
print("Task 0 actual importance scores:")
viz_sequence.plot_weights(pattern["Nanog_profile_wn_contrib_scores"]["fwd"])
print("onehot, fwd and rev:")
viz_sequence.plot_weights(np.array(pattern["sequence"]["fwd"]))
viz_sequence.plot_weights(np.array(pattern["sequence"]["rev"]))
hdf5_results.close()
In [ ]:
track_set = modisco.tfmodisco_workflow.workflow.prep_track_set(
task_names=["Nanog_profile_wn"],
contrib_scores=contrib_scores,
hypothetical_contribs=hypothetical_contribs,
one_hot=one_hot)
grp = h5py.File("results.hdf5","r")
loaded_tfmodisco_results =\
workflow.TfModiscoResults.from_hdf5(grp, track_set=track_set)
grp.close()
In [ ]:
def recursive_plot_hierarchy_motifs(nodes, path):
for i in range(len(nodes)):
nodepath = path+"/"+str(i)
print("Path to node:",nodepath)
print("Number of seqlets",len(nodes[i].pattern.seqlets))
if (nodes[i].indices_merged is not None):
print("indices merged:",nodes[i].indices_merged)
print("submat crosscontam:\n",nodes[i].submat_crosscontam)
print("submat alignersim:\n",nodes[i].submat_alignersim)
viz_sequence.plot_weights(nodes[i].pattern["sequence"].fwd)
viz_sequence.plot_weights(nodes[i].pattern["task0_contrib_scores"].fwd)
viz_sequence.plot_weights(nodes[i].pattern["task0_hypothetical_contribs"].fwd)
recursive_plot_hierarchy_motifs(nodes[i].child_nodes, path=nodepath)
pattern_merge_hierarchy = recursive_plot_hierarchy_motifs(loaded_tfmodisco_results
.metacluster_idx_to_submetacluster_results["metacluster_0"]
.seqlets_to_patterns_result.pattern_merge_hierarchy.root_nodes,
path="root")
In [ ]: