lzamparo

Running iteration  0
Running iteration  1
Running iteration  2
Running iteration  3
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Running iteration  5
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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

lzamparo

import numpy as np
cimport numpy as np

cimport cython

include "random.pyx"

@cython.boundscheck(False)
def example(n):

lzamparo

> 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

lzamparo

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

lzamparo

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

lzamparo

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

lzamparo

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):