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Running iteration 0 | |
Running iteration 1 | |
Running iteration 2 | |
Running iteration 3 | |
Running iteration 4 | |
Running iteration 5 | |
Running iteration 6 | |
Running iteration 7 | |
Running iteration 8 | |
Running iteration 9 |
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mski1743:Submission zamparol$ conda info | |
Current conda install: | |
platform : osx-64 | |
conda version : 3.19.0 | |
conda-build version : 1.11.0 | |
python version : 2.7.11.final.0 | |
requests version : 2.9.0 | |
root environment : /Users/zamparol/anaconda (writable) | |
default environment : /Users/zamparol/anaconda |
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import numpy as np | |
cimport numpy as np | |
cimport cython | |
include "random.pyx" | |
@cython.boundscheck(False) | |
def example(n): |
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> band_class_pvals | |
test_name upper Pvalue region | |
1: unannotated to CTCF 10000 13.0077750 1 | |
2: unannotated to CTCF 20000 0.0000000 1 | |
3: unannotated to CTCF 30000 0.9957614 1 | |
4: unannotated to CTCF 40000 0.2821918 1 | |
5: unannotated to CTCF 50000 0.3926610 1 | |
--- | |
1996: DNase to DNase 1960000 0.0000000 20 | |
1997: DNase to DNase 1970000 0.0000000 20 |
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root@dfad87219936:~/torch# luarocks install cutorch | |
Installing https://raw.githubusercontent.com/torch/rocks/master/cutorch-scm-1.rockspec... | |
Using https://raw.githubusercontent.com/torch/rocks/master/cutorch-scm-1.rockspec... switching to 'build' mode | |
Cloning into 'cutorch'... | |
remote: Counting objects: 70, done. | |
remote: Compressing objects: 100% (64/64), done. | |
remote: Total 70 (delta 8), reused 22 (delta 4), pack-reused 0 | |
Receiving objects: 100% (70/70), 94.12 KiB | 0 bytes/s, done. | |
Resolving deltas: 100% (8/8), done. | |
Checking connectivity... done. |
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# here's what the data looks like: | |
> all_chrs_dt | |
lower upper signif_label signif_unlabel not_signif_label not_signif_unlabel test_name | |
1: 0 100000 1293 1121 1235366 224096 unnannotated to unnannotated | |
2: 100000 200000 465 1335 1244847 227812 unnannotated to unnannotated | |
3: 200000 300000 1296 2358 1244090 225916 unnannotated to unnannotated | |
4: 300000 400000 1245 1840 1242731 226852 unnannotated to unnannotated | |
5: 400000 500000 627 995 1241226 227550 unnannotated to unnannotated | |
--- | |
5056: 1500000 1600000 0 76 0 895216 DNase to DNase |
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Script started on Tue May 5 20:36:43 2015 | |
-- The C compiler identification is AppleClang 6.1.0.6020049 | |
-- The CXX compiler identification is AppleClang 6.1.0.6020049 | |
-- Check for working C compiler: /usr/bin/cc | |
-- Check for working C compiler: /usr/bin/cc -- works | |
-- Detecting C compiler ABI info | |
-- Detecting C compiler ABI info - done | |
-- Check for working CXX compiler: /usr/bin/c++ | |
-- Check for working CXX compiler: /usr/bin/c++ -- works | |
-- Detecting CXX compiler ABI info |
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from numpy import bincount, log, log2, seterr, unique, zeros | |
from scipy.special import gammaln | |
from math_utils import log_sample, vi | |
def iteration(V, D, N_DV, N_D, alpha, beta, z_D, inv_z_T, active_topics, inactive_topics, N_TV, N_T, D_T): | |
""" | |
Performs a single iteration of Radford Neal's Algorithm 3. | |
""" |
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""" | |
A deep neural network with or w/o dropout in one file. | |
License: Do What The Fuck You Want to Public License http://www.wtfpl.net/ | |
""" | |
import numpy, theano, sys, math | |
from theano import tensor as T | |
from theano import shared | |
from theano.tensor.shared_randomstreams import RandomStreams |
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import numpy as np | |
import theano.tensor as T | |
from theano import shared, config | |
from theano.tensor.shared_randomstreams import RandomStreams | |
class AutoEncoder(object): | |
def __init__(self, numpy_rng=None, theano_rng=None, input=None, n_visible=784, n_hidden=500, | |
W=None, bhid=None, bvis=None, W_name=None, bvis_name=None, bhid_name=None, sparse_init=-1): |
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