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annotate doc/v2_planning/plugin_JB.py @ 1200:acfd5e747a75

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v2planning - a few changes to plugin proposals
author James Bergstra <bergstrj@iro.umontreal.ca>
date Mon, 20 Sep 2010 11:28:23 -0400
parents 98954d8cb92d
children 865936d8221b
rev   line source
1200
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1 """plugin_JB - draft of potential library architecture using iterators
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2
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3 This strategy makes use of a simple imperative language whose statements are python function
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4 calls to create learning algorithms that can be manipulated and executed in several desirable
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5 ways.
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6
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7 The training procedure for a PCA module is easy to express:
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8
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9 # allocate the relevant modules
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10 dataset = Dataset(numpy.random.RandomState(123).randn(13,1))
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11 pca = PCA_Analysis()
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12 pca_batchsize=1000
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13
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14 # define the control-flow of the algorithm
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15 train_pca = SEQ([
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16 BUFFER_REPEAT(pca_batchsize, CALL(dataset.next)),
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17 FILT(pca.analyze)])
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18
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19 # run the program
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20 VirtualMachine(train_pca).run()
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21
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22 The CALL, SEQ, FILT, and BUFFER_REPEAT are control-flow elements. The control-flow elements I
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23 defined so far are:
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24
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25 - CALL - a basic statement, just calls a python function
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26 - FILT - like call, but passes the return value of the last CALL or FILT to the python function
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27 - SEQ - a sequence of elements to run in order
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28 - REPEAT - do something N times (and return None or maybe the last CALL?)
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29 - BUFFER_REPEAT - do something N times and accumulate the return value from each iter
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30 - LOOP - do something an infinite number of times
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31 - CHOOSE - like a switch statement (should rename to SWITCH)
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32 - WEAVE - interleave execution of multiple control-flow elements
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33
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34
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35 We don't have many requirements per-se for the architecture, but I think this design respects
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36 and realizes all of them.
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37 The advantages of this approach are:
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38
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39 - algorithms (including partially run ones) are COPYABLE, and SERIALIZABLE
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40
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41 - algorithms can be executed without seizing control of the python process (the VM is an
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42 iterator) so your main loop (aka alternate VM implementation) can be checking for network
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43 or filesystem events related to job management
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44
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45 - the library can provide learning algorithms via control-flow templates, and the user can
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46 edit them (with search/replace calls) to include HOOKS, and DIAGNOSTIC plug-in
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47 functionality
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48
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49 e.g. prog.find(CALL(cd1_update, layer=layer1)).replace_with(
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50 SEQ([CALL(cd1_update, layer=layer1), CALL(my_debugfn)]))
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51
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52 - user can print the 'program code' of an algorithm built from library pieces
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53
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54 - program can be optimized automatically.
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55
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56 - e.g. BUFFER(N, CALL(dataset.next)) could be replaced if dataset.next implements the
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57 right attribute/protocol for 'bufferable' or something.
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58
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59 - e.g. SEQ([a,b,c,d]) could be compiled to a single CALL to a Theano-compiled function
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60 if a, b, c, and d are calls to callable objects that export something like a
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61 'theano_SEQ' interface
1198
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62
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63
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64 """
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65
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66 __license__ = 'TODO'
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67 __copyright__ = 'TODO'
1198
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68
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69 import copy, sys, cPickle
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70 import numpy
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71
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72 ###################################################
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73 # Virtual Machine for executing programs
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74
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75 class VirtualMachine(object):
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76 def __init__(self, prog):
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77 self.prog = prog
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78 self.started = False
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79 self.finished=False
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80 def __iter__(self):
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81 assert not self.started
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82 self.prog.start(None)
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83 self.started = True
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84 return self
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85 def next(self):
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86 if self.finished:
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87 raise StopIteration()
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88 r = self.prog.step()
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89 if r is INCOMPLETE:
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90 return r
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91 else:
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92 self.finished=True
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93 return r
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94 def run(self,n_steps=float('inf')):
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95 i = 0
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96 for r in self:
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97 i += 1
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98 if i > n_steps:
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99 break
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100 return r
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101
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102
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103 ####################################################
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104 # CONTROL-FLOW CONSTRUCTS
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105
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106 class INCOMPLETE:
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107 """Return value for Element.step"""
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108
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109 class ELEMENT(object):
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110 """
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111 every execution block has a driver
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112
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113 the driver calls start when entering a new control element
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114 - this would be called once per e.g. outer loop iteration
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115
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116 the driver calls step to advance the control element
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117 - which returns INCOMPLETE
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118 - which returns any other object to indicate completion
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119 """
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120
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121 def start(self, arg):
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122 pass
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123 def step(self):
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124 pass
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125
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126 class BUFFER_REPEAT(ELEMENT):
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127 """
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128 Accumulate a number of return values into one list / array.
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129
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130 The source of return values `src` is a control element that will be restarted repeatedly in
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131 order to fulfil the requiement of gathering N samples.
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132
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133 TODO: support accumulating of tuples of arrays
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134 """
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135 def __init__(self, N, src, storage=None):
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136 """
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137 TODO: use preallocated `storage`
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138 """
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139 self.N = N
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140 self.n = 0
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141 self.src = src
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142 self.storage = storage
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143 self.src.start(None)
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parents:
diff changeset
144 if self.storage != None:
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parents:
diff changeset
145 raise NotImplementedError()
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parents:
diff changeset
146 def start(self, arg):
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147 self.buf = [None] * self.N
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parents:
diff changeset
148 self.n = 0
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
149 self.finished = False
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
150 def step(self):
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parents:
diff changeset
151 assert not self.finished
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parents:
diff changeset
152 r = self.src.step()
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
153 if r is INCOMPLETE:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
154 return r
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
155 self.src.start(None) # restart our stream
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
156 self.buf[self.n] = r
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
157 self.n += 1
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
158 if self.n == self.N:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
159 self.finished = True
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
160 return self.buf
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
161 else:
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parents:
diff changeset
162 return INCOMPLETE
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
163 assert 0
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parents:
diff changeset
164
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James Bergstra <bergstrj@iro.umontreal.ca>
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165 class CALL(ELEMENT):
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parents:
diff changeset
166 """
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
167 Control flow terminal - call a python function or method.
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parents:
diff changeset
168
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169 Returns the return value of the call.
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
170 """
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
171 def __init__(self, fn, *args, **kwargs):
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parents:
diff changeset
172 self.fn = fn
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
173 self.args = args
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
174 self.kwargs=kwargs
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
175 self.use_start_arg = kwargs.pop('use_start_arg', False)
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parents:
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176 def start(self, arg):
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177 self.start_arg = arg
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
178 self.finished = False
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
179 return self
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
180 def step(self):
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parents:
diff changeset
181 assert not self.finished
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
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182 self.finished = True
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
183 if self.use_start_arg:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
184 if self.args:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
185 raise TypeError('cant get positional args both ways')
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
186 return self.fn(self.start_arg, **self.kwargs)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
187 else:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
188 return self.fn(*self.args, **self.kwargs)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
189 def __getstate__(self):
1199
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parents: 1198
diff changeset
190 rval = dict(self.__dict__)
1198
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
191 if type(self.fn) is type(self.step): #instancemethod
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
192 fn = rval.pop('fn')
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
193 rval['i fn'] = fn.im_func, fn.im_self, fn.im_class
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
194 return rval
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
195 def __setstate__(self, dct):
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parents:
diff changeset
196 if 'i fn' in dct:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
197 dct['fn'] = type(self.step)(*dct.pop('i fn'))
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
198 self.__dict__.update(dct)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
199
1199
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
200 def FILT(fn, **kwargs):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
201 """
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
202 Return a CALL object that uses the return value from the previous CALL as the first and
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
203 only positional argument.
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
204 """
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
205 return CALL(fn, use_start_arg=True, **kwargs)
1198
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
206
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
207 def CHOOSE(which, options):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
208 """
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
209 Execute one out of a number of optional control flow paths
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
210 """
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
211 raise NotImplementedError()
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
212
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
213 def LOOP(elements):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
214 #TODO: implement a true infinite loop
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
215 try:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
216 iter(elements)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
217 return REPEAT(sys.maxint, elements)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
218 except TypeError:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
219 return REPEAT(sys.maxint, [elements])
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
220
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
221 class REPEAT(ELEMENT):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
222 def __init__(self, N, elements, pass_rvals=False):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
223 self.N = N
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
224 self.elements = elements
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
225 self.pass_rvals = pass_rvals
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
226 #TODO: check for N being callable
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
227 def start(self, arg):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
228 self.n = 0 #loop iteration
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
229 self.idx = 0 #element idx
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
230 self.finished = False
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
231 self.elements[0].start(arg)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
232 def step(self):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
233 assert not self.finished
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
234 r = self.elements[self.idx].step()
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
235 if r is INCOMPLETE:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
236 return INCOMPLETE
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
237 self.idx += 1
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
238 if self.idx < len(self.elements):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
239 self.elements[self.idx].start(r)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
240 return INCOMPLETE
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
241 self.n += 1
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
242 if self.n < self.N:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
243 self.idx = 0
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
244 self.elements[self.idx].start(r)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
245 return INCOMPLETE
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
246 else:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
247 self.finished = True
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
248 return r
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
249
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
250 def SEQ(elements):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
251 return REPEAT(1, elements)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
252
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
253 class WEAVE(ELEMENT):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
254 """
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
255 Interleave execution of a number of elements.
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
256
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
257 TODO: allow a schedule (at least relative frequency) of elements from each program
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
258 """
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
259 def __init__(self, elements):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
260 self.elements = elements
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
261 def start(self, arg):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
262 for el in self.elements:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
263 el.start(arg)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
264 self.idx = 0
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
265 self.any_is_finished = False
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
266 self.finished= False
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
267 def step(self):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
268 assert not self.finished # if this is triggered, we have a broken driver
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
269 self.idx = self.idx % len(self.elements)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
270 r = self.elements[self.idx].step()
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
271 if r is not INCOMPLETE:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
272 self.any_is_finished = True
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
273 self.idx += 1
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
274 if self.idx == len(self.elements) and self.any_is_finished:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
275 self.finished = True
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
276 return None # dummy completion value
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
277 else:
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
278 return INCOMPLETE
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
279
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
280
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
281 ####################################################
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
282 # [Dummy] Components involved in learning algorithms
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
283
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
284 class Dataset(object):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
285 def __init__(self, data):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
286 self.pos = 0
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
287 self.data = data
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
288 def next(self):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
289 rval = self.data[self.pos]
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
290 self.pos += 1
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
291 if self.pos == len(self.data):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
292 self.pos = 0
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
293 return rval
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
294 def seek(self, pos):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
295 self.pos = pos
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
296
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
297 class KFold(object):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
298 def __init__(self, data, K):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
299 self.data = data
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
300 self.k = -1
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
301 self.scores = [None]*K
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
302 self.K = K
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
303 def next_fold(self):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
304 self.k += 1
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
305 self.data.seek(0) # restart the stream
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
306 def next(self):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
307 #TODO: skip the examples that are ommitted in this split
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
308 return self.data.next()
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
309 def init_test(self):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
310 pass
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
311 def next_test(self):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
312 return self.data.next()
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
313 def test_size(self):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
314 return 5
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
315 def store_scores(self, scores):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
316 self.scores[self.k] = scores
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
317
1199
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318 def prog(self, clear, train, test):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
319 return REPEAT(self.K, [
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
320 CALL(self.next_fold),
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
321 clear,
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
322 train,
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
323 CALL(self.init_test),
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
324 BUFFER_REPEAT(self.test_size(),
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
325 SEQ([ CALL(self.next_test), test])),
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
326 FILT(self.store_scores) ])
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
327
1198
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
328 class PCA_Analysis(object):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
329 def __init__(self):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
330 self.clear()
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
331
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
332 def clear(self):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
333 self.mean = 0
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
334 self.eigvecs=0
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
335 self.eigvals=0
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
336 def analyze(self, X):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
337 self.mean = numpy.mean(X, axis=0)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
338 self.eigvecs=1
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
339 self.eigvals=1
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
340 def filt(self, X):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
341 return (X - self.mean) * self.eigvecs #TODO: divide by root eigvals?
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
342 def pseudo_inverse(self, Y):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
343 return Y
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
344
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
345 class Layer(object):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
346 def __init__(self, w):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
347 self.w = w
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
348 def filt(self, x):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
349 return self.w*x
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
350 def clear(self):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
351 self.w =0
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
352
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
353 def print_obj(obj):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
354 print obj
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
355 def print_obj_attr(obj, attr):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
356 print getattr(obj, attr)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
357 def no_op(*args, **kwargs):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
358 pass
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
359
1199
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
360 def cd1_update(X, layer, lr):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
361 # update self.layer from observation X
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
362 layer.w += X.mean() * lr #TODO: not exactly correct math!
1198
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
363
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
364 def simple_main():
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
365
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
366 l = [0]
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
367 def f(a):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
368 print l
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
369 l[0] += a
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
370 return l[0]
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
371
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
372 print VirtualMachine(WEAVE([
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
373 BUFFER_REPEAT(3,CALL(f,1)),
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
374 BUFFER_REPEAT(5,CALL(f,1)),
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
375 ])).run()
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
376
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
377 def main():
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
378 # create components
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
379 dataset = Dataset(numpy.random.RandomState(123).randn(13,1))
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
380 pca = PCA_Analysis()
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
381 layer1 = Layer(w=4)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
382 layer2 = Layer(w=3)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
383 kf = KFold(dataset, K=10)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
384
1199
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
385 pca_batchsize=1000
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
386 cd_batchsize = 5
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
387 n_cd_updates_layer1 = 10
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
388 n_cd_updates_layer2 = 10
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
389
1198
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
390 # create algorithm
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
391
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
392 train_pca = SEQ([
1199
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
393 BUFFER_REPEAT(pca_batchsize, CALL(kf.next)),
1198
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
394 FILT(pca.analyze)])
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
395
1199
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
396 train_layer1 = REPEAT(n_cd_updates_layer1, [
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
397 BUFFER_REPEAT(cd_batchsize, CALL(kf.next)),
1198
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
398 FILT(pca.filt),
1199
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
399 FILT(cd1_update, layer=layer1, lr=.01)])
1198
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
400
1199
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
401 train_layer2 = REPEAT(n_cd_updates_layer2, [
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
402 BUFFER_REPEAT(cd_batchsize, CALL(kf.next)),
1198
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
403 FILT(pca.filt),
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
404 FILT(layer1.filt),
1199
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
405 FILT(cd1_update, layer=layer2, lr=.01)])
1198
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
406
1199
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
407 kfold_prog = kf.prog(
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
408 clear = SEQ([ # FRAGMENT 1: this bit is the reset/clear stage
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
409 CALL(pca.clear),
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
410 CALL(layer1.clear),
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
411 CALL(layer2.clear),
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
412 ]),
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
413 train = SEQ([
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
414 train_pca,
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
415 WEAVE([ # Silly example of how to do debugging / loggin with WEAVE
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
416 train_layer1,
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
417 LOOP(CALL(print_obj_attr, layer1, 'w'))]),
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
418 train_layer2,
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
419 ]),
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
420 test=SEQ([
1198
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
421 FILT(pca.filt), # may want to allow this SEQ to be
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
422 FILT(layer1.filt), # optimized into a shorter one that
1199
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
423 FILT(layer2.filt), # compiles these calls together with
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
424 FILT(numpy.mean)])) # Theano
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
425
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
426 pkg1 = dict(prog=kfold_prog, kf=kf)
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
427 pkg2 = copy.deepcopy(pkg1) # programs can be copied
1198
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
428
1199
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
429 try:
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
430 pkg3 = cPickle.loads(cPickle.dumps(pkg1))
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
431 except:
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
432 print >> sys.stderr, "pickling doesnt work, but it can be fixed I think"
1198
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
433
1199
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
434 pkg = pkg2
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
435
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
436 # running a program updates the variables in its package, but not the other package
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
437 VirtualMachine(pkg['prog']).run()
98954d8cb92d v2planning - modifs to plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 1198
diff changeset
438 print pkg['kf'].scores
1198
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
439
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
440
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
441 if __name__ == '__main__':
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
442 sys.exit(main())
1387771296a8 v2planning adding plugin_JB
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
443