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From Joseph Bradley <jos...@databricks.com>
Subject Re: Some questions after playing a little with the new ml.Pipeline.
Date Tue, 03 Mar 2015 21:04:13 GMT
I see.  I think your best bet is to create the cnnModel on the master and
then serialize it to send to the workers.  If it's big (1M or so), then you
can broadcast it and use the broadcast variable in the UDF.  There is not a
great way to do something equivalent to mapPartitions with UDFs right now.

On Tue, Mar 3, 2015 at 4:36 AM, Jaonary Rabarisoa <jaonary@gmail.com> wrote:

> Here is my current implementation with current master version of spark
>
>
>
>
> *class DeepCNNFeature extends Transformer with HasInputCol with
> HasOutputCol ... {   override def transformSchema(...) { ... }*
> *    override def transform(dataSet: DataFrame, paramMap: ParamMap):
> DataFrame = {*
>
> *                  transformSchema(dataSet.schema, paramMap, logging = true)*
>
>
>
> *                  val map = this.paramMap ++ paramMap                  val deepCNNFeature
= udf((v: Vector)=> {*
>
> *                              val cnnModel = new CaffeModel *
>
> *                              cnnModel.transform(v)*
>
>
>
>
> *                  } : Vector )                  dataSet.withColumn(map(outputCol), deepCNNFeature(col(map(inputCol))))*
>
>
> *     }*
> *}*
>
> where CaffeModel is a java api to Caffe C++ model.
>
> The problem here is that for every row it will create a new instance of
> CaffeModel which is inefficient since creating a new model
> means loading a large model file. And it will transform only a single row
> at a time. Or a Caffe network can process a batch of rows efficiently. In
> other words, is it possible to create an UDF that can operatats on a
> partition in order to minimize the creation of a CaffeModel and
> to take advantage of the Caffe network batch processing ?
>
>
>
> On Tue, Mar 3, 2015 at 7:26 AM, Joseph Bradley <joseph@databricks.com>
> wrote:
>
>> I see, thanks for clarifying!
>>
>> I'd recommend following existing implementations in spark.ml
>> transformers.  You'll need to define a UDF which operates on a single Row
>> to compute the value for the new column.  You can then use the DataFrame
>> DSL to create the new column; the DSL provides a nice syntax for what would
>> otherwise be a SQL statement like "select ... from ...".  I'm recommending
>> looking at the existing implementation (rather than stating it here)
>> because it changes between Spark 1.2 and 1.3.  In 1.3, the DSL is much
>> improved and makes it easier to create a new column.
>>
>> Joseph
>>
>> On Sun, Mar 1, 2015 at 1:26 AM, Jaonary Rabarisoa <jaonary@gmail.com>
>> wrote:
>>
>>> class DeepCNNFeature extends Transformer ... {
>>>
>>>     override def transform(data: DataFrame, paramMap: ParamMap):
>>> DataFrame = {
>>>
>>>
>>>                  // How can I do a map partition on the underlying RDD
>>> and then add the column ?
>>>
>>>      }
>>> }
>>>
>>> On Sun, Mar 1, 2015 at 10:23 AM, Jaonary Rabarisoa <jaonary@gmail.com>
>>> wrote:
>>>
>>>> Hi Joseph,
>>>>
>>>> Thank your for the tips. I understand what should I do when my data are
>>>> represented as a RDD. The thing that I can't figure out is how to do the
>>>> same thing when the data is view as a DataFrame and I need to add the
>>>> result of my pretrained model as a new column in the DataFrame. Preciselly,
>>>> I want to implement the following transformer :
>>>>
>>>> class DeepCNNFeature extends Transformer ... {
>>>>
>>>> }
>>>>
>>>> On Sun, Mar 1, 2015 at 1:32 AM, Joseph Bradley <joseph@databricks.com>
>>>> wrote:
>>>>
>>>>> Hi Jao,
>>>>>
>>>>> You can use external tools and libraries if they can be called from
>>>>> your Spark program or script (with appropriate conversion of data types,
>>>>> etc.).  The best way to apply a pre-trained model to a dataset would
be to
>>>>> call the model from within a closure, e.g.:
>>>>>
>>>>> myRDD.map { myDatum => preTrainedModel.predict(myDatum) }
>>>>>
>>>>> If your data is distributed in an RDD (myRDD), then the above call
>>>>> will distribute the computation of prediction using the pre-trained model.
>>>>> It will require that all of your Spark workers be able to run the
>>>>> preTrainedModel; that may mean installing Caffe and dependencies on all
>>>>> nodes in the compute cluster.
>>>>>
>>>>> For the second question, I would modify the above call as follows:
>>>>>
>>>>> myRDD.mapPartitions { myDataOnPartition =>
>>>>>   val myModel = // instantiate neural network on this partition
>>>>>   myDataOnPartition.map { myDatum => myModel.predict(myDatum) }
>>>>> }
>>>>>
>>>>> I hope this helps!
>>>>> Joseph
>>>>>
>>>>> On Fri, Feb 27, 2015 at 10:27 PM, Jaonary Rabarisoa <jaonary@gmail.com
>>>>> > wrote:
>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>>
>>>>>> We mainly do large scale computer vision task (image classification,
>>>>>> retrieval, ...). The pipeline is really great stuff for that. We're
trying
>>>>>> to reproduce the tutorial given on that topic during the latest spark
>>>>>> summit (
>>>>>> http://ampcamp.berkeley.edu/5/exercises/image-classification-with-pipelines.html
)
>>>>>> using the master version of spark pipeline and dataframe. The tutorial
>>>>>> shows different examples of feature extraction stages before running
>>>>>> machine learning algorithms. Even the tutorial is straightforward
to
>>>>>> reproduce with this new API, we still have some questions :
>>>>>>
>>>>>>    - Can one use external tools (e.g via pipe) as a pipeline stage
?
>>>>>>    An example of use case is to extract feature learned with convolutional
>>>>>>    neural network. In our case, this corresponds to a pre-trained
neural
>>>>>>    network with Caffe library (http://caffe.berkeleyvision.org/)
.
>>>>>>
>>>>>>
>>>>>>    - The second question is about the performance of the pipeline.
>>>>>>    Library such as Caffe processes the data in batch and instancing
one Caffe
>>>>>>    network can be time consuming when this network is very deep.
So, we can
>>>>>>    gain performance if we minimize the number of Caffe network creation
and
>>>>>>    give data in batch to the network. In the pipeline, this corresponds
to run
>>>>>>    transformers that work on a partition basis and give the whole
partition to
>>>>>>    a single caffe network. How can we create such a transformer ?
>>>>>>
>>>>>>
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Jao
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>

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