MNIST notebook run

%% Cell type:code id: tags:

``` python

from tensorflow.examples.tutorials.mnist import input_data

```

%% Cell type:code id: tags:

``` python

mnist = input_data.read_data_sets("MNIST_data/", one_hot=True)

```

%% Output

    Extracting MNIST_data/train-images-idx3-ubyte.gz

    Extracting MNIST_data/train-labels-idx1-ubyte.gz

    Extracting MNIST_data/t10k-images-idx3-ubyte.gz

    Extracting MNIST_data/t10k-labels-idx1-ubyte.gz

%% Cell type:code id: tags:

``` python

import deepchem as dc

import tensorflow as tf

from deepchem.models.tensorgraph.layers import Layer, Input, Reshape, Flatten, Conv2D, Label, Feature

from deepchem.models.tensorgraph.layers import Dense, SoftMaxCrossEntropy, ReduceMean, SoftMax

```

%% Output

    /home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/sklearn/cross_validation.py:44: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.

    /home/kleswing/miniconda3/envs/j3udBScCYSIoPrpc/lib/python2.7/site-packages/sklearn/cross_validation.py:44: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.

      "This module will be removed in 0.20.", DeprecationWarning)

%% Cell type:code id: tags:

``` python

train = dc.data.NumpyDataset(mnist.train.images, mnist.train.labels)

valid = dc.data.NumpyDataset(mnist.validation.images, mnist.validation.labels)

```

%% Cell type:code id: tags:

``` python

tg = dc.models.TensorGraph(tensorboard=True, model_dir='/tmp/mnist')

feature = Feature(shape=(None, 784))

# Images are square 28x28 (batch, height, width, channel)

make_image = Reshape(shape=(-1, 28, 28, 1), in_layers=[feature])

conv2d_1 = Conv2D(num_outputs=32, in_layers=[make_image])

conv2d_2 = Conv2D(num_outputs=64, in_layers=[conv2d_1])

flatten = Flatten(in_layers=[conv2d_2])

dense1 = Dense(out_channels=1024, activation_fn=tf.nn.relu, in_layers=[flatten])

dense2 = Dense(out_channels=10, in_layers=[dense1])

label = Label(shape=(None, 10))

smce = SoftMaxCrossEntropy(in_layers=[label, dense2])

loss = ReduceMean(in_layers=[smce])

tg.set_loss(loss)

output = SoftMax(in_layers=[dense2])

tg.add_output(output)

```

%% Cell type:code id: tags:

``` python

tg.fit(train, nb_epoch=10)

tg.save()

```

%% Output

    Exception in thread Thread-5:

    Traceback (most recent call last):

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/threading.py", line 801, in __bootstrap_inner

        self.run()

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/threading.py", line 754, in run

        self.__target(*self.__args, **self.__kwargs)

      File "/home/leswing/Documents/deepchem/deepchem/models/tensorgraph/tensor_graph.py", line 635, in _enqueue_batch

        sess.run(tg.input_queue.out_tensor, feed_dict=enq)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/tensorflow/python/client/session.py", line 767, in run

        run_metadata_ptr)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/tensorflow/python/client/session.py", line 965, in _run

        feed_dict_string, options, run_metadata)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/tensorflow/python/client/session.py", line 1015, in _do_run

        target_list, options, run_metadata)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/tensorflow/python/client/session.py", line 1035, in _do_call

        raise type(e)(node_def, op, message)

    CancelledError: Enqueue operation was cancelled

    	 [[Node: InputFifoQueue_12/fifo_queue_enqueue = QueueEnqueueV2[Tcomponents=[DT_FLOAT, DT_FLOAT], timeout_ms=-1, _device="/job:localhost/replica:0/task:0/cpu:0"](InputFifoQueue_12/fifo_queue, _recv_Feature_10_pre_q/Placeholder_0, _recv_Label_3_pre_q/Placeholder_0)]]

    Caused by op u'InputFifoQueue_12/fifo_queue_enqueue', defined at:

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/runpy.py", line 174, in _run_module_as_main

        "__main__", fname, loader, pkg_name)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/runpy.py", line 72, in _run_code

        exec code in run_globals

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/ipykernel_launcher.py", line 16, in <module>

        app.launch_new_instance()

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/traitlets/config/application.py", line 658, in launch_instance

        app.start()

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/ipykernel/kernelapp.py", line 477, in start

        ioloop.IOLoop.instance().start()

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/zmq/eventloop/ioloop.py", line 177, in start

        super(ZMQIOLoop, self).start()

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/tornado/ioloop.py", line 888, in start

        handler_func(fd_obj, events)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper

        return fn(*args, **kwargs)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 440, in _handle_events

        self._handle_recv()

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 472, in _handle_recv

        self._run_callback(callback, msg)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 414, in _run_callback

        callback(*args, **kwargs)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper

        return fn(*args, **kwargs)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher

        return self.dispatch_shell(stream, msg)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 235, in dispatch_shell

        handler(stream, idents, msg)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 399, in execute_request

        user_expressions, allow_stdin)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/ipykernel/ipkernel.py", line 196, in do_execute

        res = shell.run_cell(code, store_history=store_history, silent=silent)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/ipykernel/zmqshell.py", line 533, in run_cell

        return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2717, in run_cell

        interactivity=interactivity, compiler=compiler, result=result)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2821, in run_ast_nodes

        if self.run_code(code, result):

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2881, in run_code

        exec(code_obj, self.user_global_ns, self.user_ns)

      File "<ipython-input-6-fa9f01cb3d14>", line 1, in <module>

        tg.fit(train, nb_epoch=1)

      File "/home/leswing/Documents/deepchem/deepchem/models/tensorgraph/tensor_graph.py", line 127, in fit

        max_checkpoints_to_keep, checkpoint_interval)

      File "/home/leswing/Documents/deepchem/deepchem/models/tensorgraph/tensor_graph.py", line 144, in fit_generator

        self.build()

      File "/home/leswing/Documents/deepchem/deepchem/models/tensorgraph/tensor_graph.py", line 374, in build

        node_layer.create_tensor(training=self._training_placeholder)

      File "/home/leswing/Documents/deepchem/deepchem/models/tensorgraph/layers.py", line 910, in create_tensor

        self.out_tensor = self.queue.enqueue(feed_dict)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/tensorflow/python/ops/data_flow_ops.py", line 322, in enqueue

        self._queue_ref, vals, name=scope)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/tensorflow/python/ops/gen_data_flow_ops.py", line 1569, in _queue_enqueue_v2

        name=name)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/tensorflow/python/framework/op_def_library.py", line 763, in apply_op

        op_def=op_def)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/tensorflow/python/framework/ops.py", line 2327, in create_op

        original_op=self._default_original_op, op_def=op_def)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/tensorflow/python/framework/ops.py", line 1226, in __init__

        self._traceback = _extract_stack()

    CancelledError (see above for traceback): Enqueue operation was cancelled

    	 [[Node: InputFifoQueue_12/fifo_queue_enqueue = QueueEnqueueV2[Tcomponents=[DT_FLOAT, DT_FLOAT], timeout_ms=-1, _device="/job:localhost/replica:0/task:0/cpu:0"](InputFifoQueue_12/fifo_queue, _recv_Feature_10_pre_q/Placeholder_0, _recv_Label_3_pre_q/Placeholder_0)]]

    ERROR:root:Internal Python error in the inspect module.

    Below is the traceback from this internal error.

    Traceback (most recent call last):

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/IPython/core/ultratb.py", line 1132, in get_records

        return _fixed_getinnerframes(etb, number_of_lines_of_context, tb_offset)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/IPython/core/ultratb.py", line 313, in wrapped

        return f(*args, **kwargs)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/IPython/core/ultratb.py", line 358, in _fixed_getinnerframes

        records = fix_frame_records_filenames(inspect.getinnerframes(etb, context))

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/inspect.py", line 1048, in getinnerframes

        framelist.append((tb.tb_frame,) + getframeinfo(tb, context))

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/inspect.py", line 1008, in getframeinfo

        filename = getsourcefile(frame) or getfile(frame)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/inspect.py", line 453, in getsourcefile

        if hasattr(getmodule(object, filename), '__loader__'):

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/inspect.py", line 499, in getmodule

        os.path.realpath(f)] = module.__name__

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/posixpath.py", line 376, in realpath

        return abspath(path)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/posixpath.py", line 366, in abspath

        return normpath(path)

      File "/home/leswing/anaconda3/envs/deepchem27/lib/python2.7/posixpath.py", line 348, in normpath

        new_comps.append(comp)

    KeyboardInterrupt

    ---------------------------------------------------------------------------

    IndexError                                Traceback (most recent call last)

    /home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in run_code(self, code_obj, result)

       2896             if result is not None:

       2897                 result.error_in_exec = sys.exc_info()[1]

    -> 2898             self.showtraceback()

       2899         else:

       2900             outflag = 0

    /home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in showtraceback(self, exc_tuple, filename, tb_offset, exception_only)

       1822                     except Exception:

       1823                         stb = self.InteractiveTB.structured_traceback(etype,

    -> 1824                                             value, tb, tb_offset=tb_offset)

       1825

       1826                     self._showtraceback(etype, value, stb)

    /home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/IPython/core/ultratb.pyc in structured_traceback(self, etype, value, tb, tb_offset, number_of_lines_of_context)

       1410         self.tb = tb

       1411         return FormattedTB.structured_traceback(

    -> 1412             self, etype, value, tb, tb_offset, number_of_lines_of_context)

       1413

       1414

    /home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/IPython/core/ultratb.pyc in structured_traceback(self, etype, value, tb, tb_offset, number_of_lines_of_context)

       1318             # Verbose modes need a full traceback

       1319             return VerboseTB.structured_traceback(

    -> 1320                 self, etype, value, tb, tb_offset, number_of_lines_of_context

       1321             )

       1322         else:

    /home/leswing/anaconda3/envs/deepchem27/lib/python2.7/site-packages/IPython/core/ultratb.pyc in structured_traceback(self, etype, evalue, etb, tb_offset, number_of_lines_of_context)

       1202                 structured_traceback_parts += formatted_exception

       1203         else:

    -> 1204             structured_traceback_parts += formatted_exception[0]

       1205

       1206         return structured_traceback_parts

    IndexError: string index out of range

    Ending global_step 999: Average loss 0.0826627

    Ending global_step 1999: Average loss 0.0179067

    Ending global_step 2999: Average loss 0.0104273

    Ending global_step 3999: Average loss 0.00756823

    Ending global_step 4999: Average loss 0.00675081

    Ending global_step 5446: Average loss 0.00677046

    TIMING: model fitting took 91.544 s

%% Cell type:code id: tags:

``` python

from sklearn.metrics import roc_curve, auc

import numpy as np

print("Validation")

prediction = np.squeeze(tg.predict_on_batch(valid.X))

fpr = dict()

tpr = dict()

roc_auc = dict()

for i in range(10):

    fpr[i], tpr[i], thresh = roc_curve(valid.y[:, i], prediction[:, i])

    roc_auc[i] = auc(fpr[i], tpr[i])

    print("class %s:auc=%s" % (i, roc_auc[i]))

```

%% Output

    Validation

    class 0:auc=0.99998060547

    class 1:auc=0.999953963742

    class 2:auc=0.999864659633

    class 3:auc=0.99996714599

    class 4:auc=0.999773524087

    class 5:auc=0.999956097059

    class 6:auc=0.999952972472

    class 7:auc=0.99973442288

    class 8:auc=0.999880756822

    class 9:auc=0.999752015157

%% Cell type:code id: tags:

``` python

```

%% Cell type:code id: tags:

``` python

```