BigMLer - A command-line tool for BigML’s API

BigMLer makes BigML even easier.

BigMLer wraps BigML’s API Python bindings to offer a high-level command-line script to easily create and publish datasets and models, create ensembles, make local predictions from multiple models, clusters and simplify many other machine learning tasks.

BigMLer is open sourced under the Apache License, Version 2.0.

BigMLer subcommands

In addition to the BigMLer simple command, that covers the main functionality, there are some additional subcommands:

bigmler analyze:

Used for feature analysis, node threshold analysis and k-fold cross-validation. See Analyze subcommand.

bigmler cluster:

Used to generate clusters and centroids’ predictions See Cluster subcommand.

bigmler anomaly:

Used to generate anomaly detectors and anomaly scores. See Anomaly subcommand.

bigmler delete:

Used to delete the remotely created resources. See Delete subcommand.

Quick Start

Let’s see some basic usage examples. Check the installation and authentication sections below if you are not familiar with BigML.

Basics

You can create a new model just with

bigmler --train data/iris.csv

If you check your dashboard at BigML, you will see a new source, dataset, and model. Isn’t it magic?

You can generate predictions for a test set using

bigmler --train data/iris.csv --test data/test_iris.csv

You can also specify a file name to save the newly created predictions

bigmler --train data/iris.csv --test data/test_iris.csv --output predictions

If you do not specify the path to an output file, BigMLer will auto-generate one for you under a new directory named after the current date and time (e.g., MonNov1212_174715/predictions.csv). With --prediction-info flag set to brief only the prediction result will be stored (default is normal and includes confidence information). You can also set it to full if you prefer the result to be presented as a row with your test input data followed by the corresponding prediction. To include a headers row in the prediction file you can set --prediction-header. For both the --prediction-info full and --prediction-info brief options, if you want to include a subset of the fields in your test file you can select them by setting --prediction-fields to a comma-separated list of them. Then

bigmler --train data/iris.csv --test data/test_iris.csv \
        --prediction-info full --prediction-header \
        --prediction-fields 'petal length','petal width'

will include in the generated predictions file a headers row

petal length,petal width,species,confidence

and only the values of petal length and petal width will be shown before the objective field prediction species.

A different objective field (the field that you want to predict) can be selected using

bigmler --train data/iris.csv --test data/test_iris.csv \
        --objective 'sepal length'

If you do not explicitly specify an objective field, BigML will default to the last column in your dataset. You can also use as selector the field column number instead of the name (when –no-train-header is used, for instance).

Also, if your test file uses a particular field separator for its data, you can tell BigMLer using --test-separator. For example, if your test file uses the tab character as field separator the call should be like

bigmler --train data/iris.csv --test data/test_iris.tsv \
        --test-separator '\t'

The model’s predictions in BigMLer are based on the mean of the distribution of training values in the predicted node. In case you would like to use the median instead, you could just add the --median flag to your command

bigmler --train data/grades.csv --test data/test_grades.csv \
        --median

Note that this flag can only be applied to regression models.

If you don’t provide a file name for your training source, BigMLer will try to read it from the standard input

cat data/iris.csv | bigmler --train

or you can also read the test info from there

cat data/test_iris.csv | bigmler --train data/iris.csv --test

BigMLer will try to use the locale of the model both to create a new source (if the --train flag is used) and to interpret test data. In case it fails, it will try en_US.UTF-8 or English_United States.1252 and a warning message will be printed. If you want to change this behaviour you can specify your preferred locale

bigmler --train data/iris.csv --test data/test_iris.csv \
        --locale "English_United States.1252"

If you check your working directory you will see that BigMLer creates a file with the model ids that have been generated (e.g., FriNov0912_223645/models). This file is handy if then you want to use those model ids to generate local predictions. BigMLer also creates a file with the dataset id that has been generated (e.g., TueNov1312_003451/dataset) and another one summarizing the steps taken in the session progress: bigmler_sessions. You can also store a copy of every created or retrieved resource in your output directory (e.g., TueNov1312_003451/model_50c23e5e035d07305a00004f) by setting the flag --store.

Remote Predictions

All the predictions we saw in the previous section are computed locally in your computer. BigMLer allows you to ask for a remote computation by adding the --remote flag. Remote computations are treated as batch computations. This means that your test data will be loaded in BigML as a regular source and the corresponding dataset will be created and fed as input data to your model to generate a remote batch prediction object. BigMLer will download the predictions file created as a result of this batch prediction and save it to local storage just as it did for local predictions

bigmler --train data/iris.csv --test data/test_iris.csv \
        --remote --output my_dir/remote_predictions.csv

This command will create a source, dataset and model for your training data, a source and dataset for your test data and a batch prediction using the model and the test dataset. The results will be stored in the my_dir/remote_predictions.csv file. If you prefer the result not to be dowloaded but to be stored as a new dataset remotely, add --no-csv and to-dataset to the command line. This can be specially helpful when dealing with a high number of scores or when adding to the final result the original dataset fields with --prediction-info full, that may result in a large CSV to be created as output.

In case you prefer BigMLer to issue one-by-one remote prediction calls, you can use the --no-batch flag

bigmler --train data/iris.csv --test data/test_iris.csv \
        --remote --no-batch

Remote Sources

You can create models using remote sources as well. You just need a valid URL that points to your data. BigML recognizes a growing list of schemas (http, https, s3, azure, odata, etc). For example

bigmler --train https://test:test@static.bigml.com/csv/iris.csv

bigmler --train "s3://bigml-public/csv/iris.csv?access-key=[your-access-key]&secret-key=[your-secret-key]"

bigmler --train azure://csv/diabetes.csv?AccountName=bigmlpublic

bigmler --train odata://api.datamarket.azure.com/www.bcn.cat/BCNOFFERING0005/v1/CARRegistration?$top=100

Can you imagine how powerful this feature is? You can create predictive models for huge amounts of data without using you local CPU, memory, disk or bandwidth. Welcome to the cloud!!!

Ensembles

You can also easily create ensembles. For example, using bagging is as easy as

bigmler --train data/iris.csv --test data/test_iris.csv \
        --number-of-models 10 --sample-rate 0.75 --replacement \
        --tag my_ensemble

To create a random decision forest just use the –randomize option

bigmler --train data/iris.csv --test data/test_iris.csv \
        --number-of-models 10 --sample-rate 0.75 --replacement \
        --tag my_ensemble --randomize

The fields to choose from will be randomized at each split creating a random decision forest that when used together will increase the prediction performance of the individual models.

Once you have an existing ensemble, you can use it to predict. You can do so with the command

bigmler --ensemble ensemble/51901f4337203f3a9a000215 \
        --test data/test_iris.csv

Or if you want to evaluate it

bigmler --ensemble ensemble/51901f4337203f3a9a000215 \
        --test data/iris.csv --evaluate

There are some more advanced options that can help you build local predictions with your ensembles. When the number of local models becomes quite large holding all the models in memory may exhaust your resources. To avoid this problem you can use the --max_batch_models flag which controls how many local models are held in memory at the same time

bigmler --train data/iris.csv --test data/test_iris.csv \
        --number-of-models 10 --sample-rate 0.75 --max-batch-models 5

The predictions generated when using this option will be stored in a file per model and named after the models’ id (e.g. model_50c23e5e035d07305a00004f__predictions.csv”). Each line contains the prediction, its confidence, the node’s distribution and the node’s total number of instances. The default value for ``max-batch-models` is 10.

When using ensembles, model’s predictions are combined to issue a final prediction. There are several different methods to build the combination. You can choose plurality, confidence weighted, probability weighted or threshold using the --method flag

bigmler --train data/iris.csv --test data/test_iris.csv \
        --number-of-models 10 --sample-rate 0.75 \
        --method "confidence weighted"

For classification ensembles, the combination is made by majority vote: plurality weights each model’s prediction as one vote, confidence weighted uses confidences as weight for the prediction, probability weighted uses the probability of the class in the distribution of classes in the node as weight, and threshold uses an integer number as threshold and a class name to issue the prediction: if the votes for the chosen class reach the threshold value, then the class is predicted and plurality for the rest of predictions is used otherwise

bigmler --train data/iris.csv --test data/test_iris.csv \
        --number-of-models 10 --sample-rate 0.75 \
        --method threshold --threshold 4 --class 'Iris-setosa'

For regression ensembles, the predicted values are averaged: plurality again weights each predicted value as one, confidence weighted weights each prediction according to the associated error and probability weighted gives the same results as plurality.

As in the model’s case, you can base your prediction on the median of the predicted node’s distribution by adding --median to your BigMLer command.

It is also possible to enlarge the number of models that build your prediction gradually. You can build more than one ensemble for the same test data and combine the votes of all of them by using the flag combine_votes followed by the comma separated list of directories where predictions are stored. For instance

bigmler --train data/iris.csv --test data/test_iris.csv \
        --number-of-models 20 --sample-rate 0.75 \
        --output ./dir1/predictions.csv
bigmler --dataset dataset/50c23e5e035d07305a000056 \
        --test data/test_iris.csv  --number-of-models 20 \
        --sample-rate 0.75 --output ./dir2/predictions.csv
bigmler --combine-votes ./dir1,./dir2

would generate a set of 20 prediction files, one for each model, in ./dir1, a similar set in ./dir2 and combine all of them to generate the final prediction.

Making your Dataset and Model public or share it privately

Creating a model and making it public in BigML’s gallery is as easy as

bigmler --train data/iris.csv --white-box

If you just want to share it as a black-box model just use

bigmler --train data/iris.csv --black-box

If you also want to make public your dataset

bigmler --train data/iris.csv --public-dataset

You can also share your datasets, models and evaluations privately with whomever you choose by generating a private link. The --shared flag will create such a link

bigmler --dataset dataset/534487ef37203f0d6b000894 --shared --no-model

and the link will be listed in the output of the command

bigmler --dataset dataset/534487ef37203f0d6b000894 --shared --no-model
[2014-04-18 09:29:27] Retrieving dataset. https://bigml.com/dashboard/dataset/534487ef37203f0d6b000894
[2014-04-18 09:29:30] Updating dataset. https://bigml.com/dashboard/dataset/534487ef37203f0d6b000894
[2014-04-18 09:29:30] Shared dataset link. https://bigml.com/shared/dataset/8VPwG7Ny39g1mXBRD1sKQLuHrqE

or can also be found in the information pannel for the resource through the web interface.

Content

Before making your model public, probably you want to add a name, a category, a description, and tags to your resources. This is easy too. For example

bigmler --train data/iris.csv --name "My model" --category 6 \
        --description data/description.txt --tag iris --tag my_tag

Please note:

  • You can get a full list of BigML category codes here.
  • Descriptions are provided in a text file that can also include markdown.
  • Many tags can be added to the same resource.
  • Use --no_tag if you do not want default BigMLer tags to be added.
  • BigMLer will add the name, category, description, and tags to all the newly created resources in each request.

Projects

Each resource created in BigML can be associated to a project. Projects are intended for organizational purposes, and BigMLer can create projects each time a source is created using a --project option. For instance

bigmler --train data/iris.csv --project "my new project"

will first check for the existence of a project by that name. If it exists, will associate the source, dataset and model resources to this project. If it doesn’t, a new project is created and then associated.

You can also associate resources to an existing project by specifying the option --project-id followed by its id

bigmler --train data/iris.csv --project-id project/524487ef37203f0d6b000894

Note: Once a source has been associated to a project, all the resources derived from this source will be automatically associated to the same project.

Using previous Sources, Datasets, and Models

You don’t need to create a model from scratch every time that you use BigMLer. You can generate predictions for a test set using a previously generated model

bigmler --model model/50a1f43deabcb404d3000079 --test data/test_iris.csv

You can also use a number of models providing a file with a model/id per line

bigmler --models TueDec0412_174148/models --test data/test_iris.csv

Or all the models that were tagged with a specific tag

bigmler --model-tag my_tag --test data/test_iris.csv

You can also use a previously generated dataset to create a new model

bigmler --dataset dataset/50a1f441035d0706d9000371

You can also input the dataset from a file

bigmler --datasets iris_dataset

A previously generated source can also be used to generate a new dataset and model

bigmler --source source/50a1e520eabcb404cd0000d1

And test sources and datasets can also be referenced by id in new BigMLer requests for remote predictions

bigmler --model model/52af53a437203f1cfe0001f0 --remote \
        --test-source source/52b0cbe637203f1d3e0015db

bigmler --model model/52af53a437203f1cfe0001f0 --remote \
        --test-dataset dataset/52b0fb5637203f5c4f000018

Evaluations

BigMLer can also help you to measure the performance of your models. The simplest way to build a model and evaluate it all at once is

bigmler --train data/iris.csv --evaluate

which will build the source, dataset and model objects for you using 80% of the data in your training file chosen at random. After that, the remaining 20% of the data will be run through the model to obtain the corresponding evaluation. You can use the same procedure with a previously existing source or dataset

bigmler --source source/50a1e520eabcb404cd0000d1 --evaluate
bigmler --dataset dataset/50a1f441035d0706d9000371 --evaluate

The results of an evaluation are stored both in txt and json files. Its contents will follow the description given in the Developers guide, evaluation section and vary depending on the model being a classification or regression one.

Finally, you can also evaluate a preexisting model using a separate set of data stored in a file or a previous dataset

bigmler --model model/50a1f43deabcb404d3000079 --test data/iris.csv \
        --evaluate
bigmler --model model/50a1f43deabcb404d3000079 \
        --test-dataset dataset/50a1f441035d0706d9000371 --evaluate

As for predictions, you can specify a particular file name to store the evaluation in

bigmler --train data/iris.csv --evaluate --output my_dir/evaluation

Cross-validation

If you need cross-validation techniques to ponder which parameters (like the ones related to different kinds of pruning) can improve the quality of your models, you can use the --cross-validation-rate flag to settle the part of your training data that will be separated for cross validation. BigMLer will use a Monte-Carlo cross-validation variant, building 2*n different models, each of which is constructed by a subset of the training data, holding out randomly n% of the instances. The held-out data will then be used to evaluate the corresponding model. For instance, both

bigmler --train data/iris.csv --cross-validation-rate 0.02
bigmler --dataset dataset/519029ae37203f3a9a0002bf \
        --cross-validation-rate 0.02

will hold out 2% of the training data to evaluate a model built upon the remaining 98%. The evaluations will be averaged and the result saved in json and human-readable formats in cross-validation.json and cross-validation.txt respectively. Of course, in this kind of cross-validation you can choose the number of evaluations yourself by setting the --number-of-evaluations flag. You should just keep in mind that it must be high enough to ensure low variance, for instance

bigmler --train data/iris.csv --cross-validation-rate 0.1 \
        --number-of-evaluations 20

The --max-parallel-evaluations flag will help you limit the number of parallel evaluation creation calls.

bigmler --train data/iris.csv --cross-validation-rate 0.1 \
        --number-of-evaluations 20 --max-parallel-evaluations 2

Configuring Datasets and Models

What if your raw data isn’t necessarily in the format that BigML expects? So we have good news: you can use a number of options to configure your sources, datasets, and models.

Imagine that you want to alter BigML’s default field names or the ones provided by the training set header and capitalize them, even to add a label or a description to each field. You can use a text file with a change per line as follows

bigmler --train data/iris.csv --field-attributes fields.csv

where fields.csv would be

0,'SEPAL LENGTH','label for SEPAL LENGTH','description for SEPAL LENGTH'
1,'SEPAL WIDTH','label for SEPAL WIDTH','description for SEPAL WIDTH'
2,'PETAL LENGTH','label for PETAL LENGTH','description for PETAL LENGTH'
3,'PETAL WIDTH','label for PETAL WIDTH','description for PETAL WIDTH'
4,'SPECIES','label for SPECIES','description for SPECIES'

The number on the left in each line is the column number of the field in your source and is followed by the new field’s name, label and description.

Similarly you can also alter the auto-detect type behavior from BigML assigning specific types to specific fields

bigmler --train data/iris.csv --types types.txt

where types.txt would be

0, 'numeric'
1, 'numeric'
2, 'numeric'
3, 'numeric'
4, 'categorical'

You can specify the fields that you want to include in the dataset by naming them explicitly

bigmler --train data/iris.csv \
        --dataset-fields 'sepal length','sepal width','species'

or the fields that you want to include as predictors in the model

bigmler --train data/iris.csv --model-fields 'sepal length','sepal width'

You can also specify the chosen fields by adding or removing the ones you choose to the list of preferred fields of the previous resource. Just prefix their names with + or - respectively. For example, you could create a model from an existing dataset using all their fields but the sepal length by saying

bigmler --dataset dataset/50a1f441035d0706d9000371 \
        --model-fields -'sepal length'

When evaluating, you can map the fields of the evaluated model to those of the test dataset by writing in a file the field column of the model and the field column of the dataset separated by a comma and using –fields-map flag to specify the name of the file

bigmler --dataset dataset/50a1f441035d0706d9000371 \
        --model model/50a1f43deabcb404d3000079 --evaluate \
        --fields-map fields_map.txt

where fields_map.txt would contain

0, 1
1, 0
2, 2
3, 3
4, 4

if the first two fields had been reversed.

Finally, you can also tell BigML whether your training and test set come with a header row or not. For example, if both come without header

bigmler --train data/iris_nh.csv --test data/test_iris_nh.csv \
        --no-train-header --no-test-header

Splitting Datasets

When following the usual proceedings to evaluate your models you’ll need to separate the available data in two sets: the training set and the test set. With BigMLer you won’t need to create two separate physical files. Instead, you can set a --test-split flag that will set the percentage of data used to build the test set and leave the rest for training. For instance

bigmler --train data/iris.csv --test-split 0.2 --name iris --evaluate

will build a source with your entire file contents, create the corresponding dataset and split it in two: a test dataset with 20% of instances and a training dataset with the remaining 80%. Then, a model will be created based on the training set data and evaluated using the test set. By default, split is deterministic, so that every time you issue the same command will get the same split datasets. If you want to generate different splits from a unique dataset you can set the --seed option to a different string in every call

bigmler --train data/iris.csv --test-split 0.2 --name iris \
        --seed my_random_string_382734627364 --evaluate

Advanced Dataset management

As you can find in the BigML’s API documentation on datasets besides the basic name, label and description that we discussed in previous sections, there are many more configurable options in a dataset resource. In order to set or update dataset options, you can use the --dataset-attributes option pointing to a file path that contains the configuration settings in JSON format

bigmler --dataset dataset/52b8a12037203f48bc00000a \
        --dataset-attributes my_dir/attributes.json

Let’s say this dataset has a text field with id 000001. The attributes.json to change its text parsing mode to full field contents would read

{"fields": {"000001": {"term_analysis": {"token_mode": "full_terms_only"}}}}

There are other kinds of updatable options in the dataset besides controlling its fields features. As an example, to publish a dataset in the gallery and set its price you could use

{"private": false, "price": 120.4}

Similarly, you might want to add fields to your existing dataset by combining some of its fields or simply tagging their rows. Using BigMLer, you can set the --new-fields option to a file path that contains a JSON structure that describes the fields you want to select or exclude from the original dataset, or the ones you want to combine and the Flatline expression to combine them. This structure must follow the rules of a specific languange described in the Transformations item of the developers section

bigmler --dataset dataset/52b8a12037203f48bc00000a \
        --new-fields my_dir/generators.json

To see a simple example, should you want to include all the fields but the one with id 000001 and add a new one with a label depending on whether the value of the field sepal length is smaller than 1, you would write in generators.json

{"all_but": ["000001"], "new_fields": [{"name": "new_field", "field": "(if (< (f \"sepal length\") 1) \"small\" \"big\")"}]}

Or, as another example, to tag the outliers of the same field one coud use

{"new_fields": [{"name": "outlier?", "field": "(if (within-percentiles? \"sepal length\" 0.5 0.95) \"normal\" \"outlier\")"}]}

You can also export the contents of a generated dataset by using the --to-csv option. Thus,

bigmler --dataset dataset/52b8a12037203f48bc00000a \
        --to-csv my_dataset.csv --no-model

will create a CSV file named my_dataset.csv in the default directory created by BigMLer to place the command output files. If no file name is given, the file will be named after the dataset id.

A dataset can also be generated as the union of several datasets using the flag --multi-dataset. The datasets will be read from a file specified in the --datasets option and the file must contain one dataset id per line.

bigmler --datasets my_datasets --multi-dataset --no-model

This syntax is used when all the datasets in the my_datasets file share a common field structre, so the correspondence of the fields of all the datasets is straight forward. In the general case, the multi-dataset will inherit the field structure of the first component dataset. If you want to build a multi-dataset with datasets whose fields share not the same column disposition, you can specify which fields are correlated to the ones of the first dataset by mapping the fields of the rest of datasets to them. The option --multi-dataset-attributes can point to a JSON file that contains such a map. The command line syntax would then be

bigmler --datasets my_datasets --multi-dataset \
        --multi-dataset-attributes my_fields_map.json \
        --no-model

and for a simple case where the second dataset had flipped the first and second fields with respect to the first one, the file would read

where dataset/53330bce37203f222e00004b would be the id of the second dataset in the multi-dataset.

Model Weights

To deal with imbalanced datasets, BigMLer offers three options: --balance, --weight-field and --objective-weights.

For classification models, the --balance flag will cause all the classes in the dataset to contribute evenly. A weight will be assigned automatically to each instance. This weight is inversely proportional to the number of instances in the class it belongs to, in order to ensure even distribution for the classes.

You can also use a field in the dataset that contains the weight you would like to use for each instance. Using the --weight-field option followed by the field name or column number will cause BigMLer to use its data as instance weight. This is valid for both regression and classification models.

The --objective-weights option is used in classification models to transmit to BigMLer what weight is assigned to each class. The option accepts a path to a CSV file that should contain the class,``weight`` values one per row

bigmler --dataset dataset/52b8a12037203f48bc00000a \
        --objective-weights my_weights.csv

where the my_weights.csv file could read

Iris-setosa,5
Iris-versicolor,3

so that BigMLer would associate a weight of 5 to the Iris-setosa class and 3 to the Iris-versicolor class. For additional classes in the model, like Iris-virginica in the previous example, weight 1 is used as default. All specified weights must be non-negative numbers (with either integer or real values) and at least one of them must be non-zero.

Predictions’ missing strategy

Sometimes the available data lacks some of the features our models use to predict. In these occasions, BigML offers two different ways of handling input data with missing values, that is to say, the missing strategy. When the path to the prediction reaches a split point that checks the value of a field which is missing in your input data, using the last prediction strategy the final prediction will be the prediction for the last node in the path before that point, and using the proportional strategy it will be a weighted average of all the predictions for the final nodes reached considering that both branches of the split are possible.

BigMLer adds the --missing-strategy option, that can be set either to last or proportional to choose the behavior in such cases. Last prediction is the one used when this option is not used.

bigmler --model model/52b8a12037203f48bc00001a \
        --missing-strategy proportional --test my_test.csv

Models with missing splits

Another configuration argument that can change models when the training data has instances with missing values in some of its features is --missing-splits. By setting this flag, the model building algorithm will be able to include the instances that have missing values for the field used to split the data in each node in one of the stemming branches. This will, obviously, affect also the predictions given by the model for input data with missing values. Here’s an example to build a model using missing-splits and predict with it.

bigmler --dataset dataset/52b8a12037203f48bc00023b \
        --missing-splits --test my_test.csv

Fitering Sources

Imagine that you have create a new source and that you want to create a specific dataset filtering the rows of the source that only meet certain criteria. You can do that using a JSON expresion as follows

bigmler --source source/50a2bb64035d0706db0006cc --json-filter filter.json

where filter.json is a file containg a expression like this

["<", 7.00, ["field", "000000"]]

or a LISP expression as follows

bigmler --source source/50a2bb64035d0706db0006cc --lisp-filter filter.lisp

where filter.lisp is a file containing a expression like this

(< 7.00 (field "sepal length"))

For more details, see the BigML’s API documentation on filtering rows.

Multi-labeled categories in training data

Sometimes the information you want to predict is not a single category but a set of complementary categories. In this case, training data is usually presented as a row of features and an objective field that contains the associated set of categories joined by some kind of delimiter. BigMLer can also handle this scenario.

Let’s say you have a simple file

color,year,sex,class
red,2000,male,"Student,Teenager"
green,1990,female,"Student,Adult"
red,1995,female,"Teenager,Adult"

with information about a group of people and we want to predict the class another person will fall into. As you can see, each record has more than one class per person (for example, the first person is labeled as being both a Student and a Teenager) and they are all stored in the class field by concatenating all the applicable labels using , as separator. Each of these labels is, ‘per se’, an objective to be predicted, and that’s what we can rely on BigMLer to do.

The simplest multi-label command in BigMLer is

bigmler --multi-label --train data/tiny_multilabel.csv

First, it will analyze the training file to extract all the labels stored in the objective field. Then, a new extended file will be generated from it by adding a new field per label. Each generated field will contain a boolean set to True if the associated label is in the objective field and False otherwise

color,year,sex,class - Adult,class - Student,class - Teenager
red,2000,male,False,True,True
green,1990,female,True,True,False
red,1995,female,True,False,True

This new file will be fed to BigML to build a source, a dataset and a set of models using four input fields: the first three fields as input features and one of the label fields as objective. Thus, each of the classes that label the training set can be predicted independently using one of the models.

But, naturally, when predicting a multi-labeled field you expect to obtain all the labels that qualify the input features at once, as you provide them in the training data records. That’s also what BigMLer does. The syntax to predict using multi-labeled training data sets is similar to the single labeled case

bigmler --multi-label --train data/tiny_multilabel.csv \
        --test data/tiny_test_multilabel.csv

the main difference being that the ouput file predictions.csv will have the following structure

"Adult,Student","0.34237,0.20654"
"Adult,Teenager","0.34237,0.34237"

where the first column contains the class prediction and the second one the confidences for each label prediction. If the models predict True for more than one label, the prediction is presented as a sequence of labels (and their corresponding confidences) delimited by ,.

As you may have noted, BigMLer uses , both as default training data fields separator and as label separator. You can change this behaviour by using the --training-separator, --label-separator and --test-separator flags to use different one-character separators

bigmler --multi-label --train data/multilabel.tsv \
        --test data/test_multilabel.tsv --training-separator '\t' \
        --test-separator '\t' --label-separator ':'

This command would use the tab character as train and test data field delimiter and : as label delimiter (the examples in the tests set use , as field delimiter and ‘:’ as label separator).

You can also choose to restrict the prediction to a subset of labels using the --labels flag. The flag should be set to a comma-separated list of labels. Setting this flag can also reduce the processing time for the training file, because BigMLer will rely on them to produce the extended version of the training file. Be careful, though, to avoid typos in the labels in this case, or no objective fields will be created. Following the previous example

bigmler --multi-label --train data/multilabel.csv \
        --test data/test_multilabel.csv --label-separator ':' \
        --labels Adult,Student

will limit the predictions to the Adult and Student classes, leaving out the Teenager classification.

Multi-labeled predictions can also be computed using ensembles, one for each label. To create an ensemble prediction, use the --number-of-models option that will set the number of models in each ensemble

bigmler --multi-label --train data/multilabel.csv \
        --number-of-models 20 --label-separator ':' \
        --test data/test_multilabel.csv

The ids of the ensembles will be stored in an ensembles file in the output directory, and can be used in other predictions by setting the --ensembles option

bigmler --multi-label --ensembles multilabel/ensembles \
        --test data/test_multilabel.csv

or you can retrieve all previously tagged ensembles with --ensemble-tag

bigmler --multi-label --ensemble-tag multilabel \
        --test data/test_multilabel.csv

Multi-labeled resources

The resources generated from a multi-labeled training data file can also be recovered and used to generate more multi-labeled predictions. As in the single-labeled case

bigmler --multi-label --source source/522521bf37203f412f000100 \
        --test data/test_multilabel.csv

would generate a dataset and the corresponding set of models needed to create a predictions.csv file that contains the multi-labeled predictions.

Similarly, starting from a previously created multi-labeled dataset

bigmler --multi-label --dataset source/522521bf37203f412fac0135 \
        --test data/test_multilabel.csv --output multilabel/predictions.csv

creates a bunch of models, one per label, and predicts storing the results of each operation in the multilabel directory, and finally

bigmler --multi-label --models multilabel/models \
        --test data/test_multilabel.csv

will retrieve the set of models created in the last example and use them in new predictions. In addition, for these three cases you can restrict the labels to predict to a subset of the complete list available in the original objective field. The --labels option can be set to a comma-separated list of the selected labels in order to do so.

The --model-tag can be used as well to retrieve multi-labeled models and predict with them

bigmler --multi-label --model-tag my_multilabel \
        --test data/test_multilabel.csv

Finally, BigMLer is also able to handle training files with more than one multi-labeled field. Using the --multi-label-fields option you can settle the fields that will be expanded as containing multiple labels in the generated source and dataset.

bigmler --multi-label --multi-label-fields class,type \
        --train data/multilabel_multi.csv --objective class

This command creates a source (and its corresponding dataset) where both the class and type fields have been analysed to create a new field per label. Then the --objective option sets class to be the objective field and only the models needed to predict this field are created. You could also create a new multi-label prediction for another multi-label field, type in this case, by issuing a new BigMLer command that uses the previously generated dataset as starting point

bigmler --multi-label --dataset dataset/52cafddb035d07269000075b \
        --objective type

This would generate the models needed to predict type. It’s important to remark that the models used to predict class in the first example will use the rest of fields (including type as well as the ones generated by expanding it) to build the prediction tree. If you don’t want this fields to be used in the model construction, you can set the --model-fields option to exclude them. For instance, if type has two labels, label1 and label2, then excluding them from the models that predict class could be achieved using

bigmler --multi-label --dataset dataset/52cafddb035d07269000075b \
        --objective class
        --model-fields=' -type,-type - label1,-type - label2'

You can also generate new fields applying aggregation functions such as count, first or last on the labels of the multi label fields. The option --label-aggregates can be set to a comma-separated list of these functions and a new column per multi label field and aggregation function will be added to your source

bigmler --multi-label --train data/multilabel.csv \
        --label-separator ':' --label-aggregates count,last \
        --objective class

will generate class - count and class - last in addition to the set of per label fields.

Multi-label evaluations

Multi-label predictions are computed using a set of binary models (or ensembles), one for each label to predict. Each model can be evaluated to check its performance. In order to do so, you can mimic the commands explained in the evaluations section for the single-label models and ensembles. Starting from a local CSV file

bigmler --multi-label --train data/multilabel.csv \
        --label-separator ":" --evaluate

will build the source, dataset and model objects for you using a random 80% portion of data in your training file. After that, the remaining 20% of the data will be run through each of the models to obtain an evaluation of the corresponding model. BigMLer retrieves all evaluations and saves them locally in json and txt format. They are named using the objective field name and the value of the label that they refer to. Finally, it averages the results obtained in all the evaluations to generate a mean evaluation stored in the evaluation.txt and evaluation.json files. As an example, if your objective field name is class and the labels it contains are Adult,Student, the generated files will be

Generated files:

MonNov0413_201326
  • evaluations
  • extended_multilabel.csv
  • source
  • evaluation_class_student.txt
  • models
  • evaluation_class_adult.json
  • dataset
  • evaluation.json
  • evaluation.txt
  • evaluation_class_student.json
  • bigmler_sessions
  • evaluation_class_adult.txt

You can use the same procedure with a previously existing multi-label source or dataset

bigmler --multi-label --source source/50a1e520eabcb404cd0000d1 \
        --evaluate
bigmler --multi-label --dataset dataset/50a1f441035d0706d9000371 \
        --evaluate

Finally, you can also evaluate a preexisting set of models or ensembles using a separate set of data stored in a file or a previous dataset

bigmler --multi-label --models MonNov0413_201326/models \
        --test data/test_multilabel.csv --evaluate
bigmler --multi-label --ensembles MonNov0413_201328/ensembles \
        --dataset dataset/50a1f441035d0706d9000371 --evaluate

High number of Categories

In BigML there’s a limit in the number of categories of a categorical objective field. This limit is set to ensure the quality of the resulting models. This may become a restriction when dealing with categorical objective fields with a high number of categories. To cope with these cases, BigMLer offers the –max-categories option. Setting to a number lower than the mentioned limit, the existing categories will be organized in subsets of that size. Then the original dataset will be copied many times, one per subset, and its objective field will only keep the categories belonging to each subset plus a generic ***** other ***** category that will summarize the rest of categories. Then a model will be created from each dataset and the test data will be run through them to generate partial predictions. The final prediction will be extracted by choosing the class with highest confidence from the distributions obtained for each model’s prediction ignoring the ***** other ****** generic category. For instance, to use the same iris.csv example, you could do

bigmler --train data/iris.csv --max-categories 1 \
        --test data/test_iris.csv --objective species

This command would generate a source and dataset object, as usual, but then, as the total number of categories is three and –max-categories is set to 1, three more datasets will be created, one per each category. After generating the corresponding models, the test data will be run through them and their predictions combined to obtain the final predictions file. The same procedure would be applied if starting from a preexisting source or dataset using the --source or --dataset options. Please note that the --objective flag is mandatory in this case to ensure that the right categorical field is selected as objective field.

--method option accepts a new combine value to use such kind of combination. You can use it if you need to create a new group of predictions based on the same models produced in the first example. Filling the path to the model ids file

bigmler --models my_dir/models --method combine \
        --test data/new_test.csv

the new predictions will be created. Also, you could use the set of datasets created in the first case as starting point. Their ids are stored in a dataset_parts file that can be found in the output location

bigmler --dataset my_dir/dataset_parts --method combine \
        --test data/test.csv

This command would cause a new set of models, one per dataset, to be generated and their predictions would be combined in a final predictions file.

Advanced subcommands in BigMLer

Analyze subcommand

In addition to the main BigMLer capabilities explained so far, there’s a subcommand bigmler analyze with more options to evaluate the performance of your models. For instance

bigmler analyze --dataset dataset/5357eb2637203f1668000004 \
                --cross-validation --k-folds 5

will create a k-fold cross-validation by dividing the data in your dataset in the number of parts given in --k-folds. Then evaluations are created by selecting one of the parts to be the test set and using the rest of data to build the model for testing. The generated evaluations are placed in your output directory and its average is stored in evaluation.txt and evaluation.json.

Similarly, you’ll be able to create an evaluation for ensembles. Using the same command above and adding the options to define the ensembles’ properties, such as --number-of-models, --sample-rate, --randomize or --replacement

bigmler analyze --dataset dataset/5357eb2637203f1668000004 \
                --cross-validation --k-folds 5 --number-of-models 20
                --sample-rate 0.8 --replacement

More insights can be drawn from the bigmler analyze --features command. In this case, the aim of the command is to analyze the complete set of features in your dataset to single out the ones that produce models with better evaluation scores. In this case, we focus on accuracy for categorical objective fields and r-squared for regressions.

bigmler analyze --dataset dataset/5357eb2637203f1668000004 \
                --features

This command uses an algorithm for smart feature selection as described in this blog post that evaluates models built by using subsets of features. It starts by building one model per feature, chooses the subset of features used in the model that scores best and, from there on, repeats the procedure by adding another of the available features in the dataset to the chosen subset. The iteration stops when no improvement in score is found for a number of repetitions that can be controlled using the --staleness option (default is 5). There’s also a --penalty option (default is 0.1%) that sets the amount that is substracted from the score per feature added to the subset. This penalty is intended to mitigate overfitting, but it also favors models which are quicker to build and evaluate. The evaluations for the scores are k-fold cross-validations. The --k-folds value is set to 5 by default, but you can change it to whatever suits your needs using the --k-folds option.

bigmler analyze --dataset dataset/5357eb2637203f1668000004 \
                --features --k-folds 10 --staleness 3 --penalty 0.002

Would select the best subset of features using 10-fold cross-validation and a 0.2% penalty per feature, stopping after 3 non-improving iterations.

Depending on the machine learning problem you intend to tackle, you might want to optimize other evaluation metric, such as precision or recall. The --optimize option will allow you to set the evaluation metric you’d like to optimize.

bigmler analyze --dataset dataset/5357eb2637203f1668000004 \
                --features --optimize recall

For categorical models, the evaluation values are obtained by counting the positive and negative matches for all the instances in the test set, but sometimes it can be more useful to optimize the performance of the model for a single category. This can be specially important in highly non-balanced datasets or when the cost function is mainly associated to one of the existing classes in the objective field. Using ``–optimize-category” you can set the category whose evaluation metrics you’d like to optimize

bigmler analyze --dataset dataset/5357eb2637203f1668000004 \
                --features --optimize recall \
                --optimize-category Iris-setosa

You should be aware that the smart feature selection command still generates a high number of BigML resources. Using k as the k-folds number and n as the number of explored feature sets, it will be generating k datasets (1/k``th of the instances each), and ``k * n models and evaluations. Setting the --max-parallel-models and --max-parallel-evaluations to higher values (up to k) can help you speed up partially the creation process because resources will be created in parallel. You must keep in mind, though, that this parallelization is limited by the task limit associated to your subscription or account type.

As another optimization method, the bigmler analyze --nodes subcommand will find for you the best performing model by changing the number of nodes in its tree. You provide the --min-nodes and --max-nodes that define the range and --nodes-step controls the increment in each step. The command runs a k-fold evaluation (see --k-folds option) on a model built with each node threshold in you range and tries to optimize the evaluation metric you chose (again, default is accuracy). If improvement stops (see the –staleness option) or the node threshold reaches the --max-nodes limit, the process ends and shows the node threshold that lead to the best score.

Cluster subcommand

Just as the simple bigmler command can generate all the resources leading to finding models and predictions for a supervised learning problem, the bigmler cluster subcommand will follow the steps to generate clusters and predict the centroids associated to your test data. To mimic what we saw in the bigmler command section, the simplest call is

bigmler cluster --train data/diabetes.csv

This command will upload the data in the data/diabetes.csv file and generate the corresponding source, dataset and cluster objects in BigML. You can use any of the generated objects to produce new clusters. For instance, you could set a subgroup of the fields of the generated dataset to produce a different cluster by using

bigmler cluster --dataset dataset/53b1f71437203f5ac30004ed \
                --cluster-fields="-blood pressure"

that would exclude the field blood pressure from the cluster creation input fields.

Similarly to the models and datasets, the generated clusters can be shared using the --shared option, e.g.

bigmler cluster --source source/53b1f71437203f5ac30004e0 \
                --shared

will generate a secret link for both the created dataset and cluster that can be used to share the resource selectively.

As models were used to generate predictions (class names in classification problems and an estimated number for regressions), clusters can be used to predict the subgroup of data that our input data is more similar to. Each subgroup is represented by its centroid, and the centroid is labelled by a centroid name. Thus, a cluster would classify our test data by assigning to each input an associated centroid name. The command

bigmler cluster --cluster cluster/53b1f71437203f5ac30004f0 \
                --test data/my_test.csv

would produce a file centroids.csv with the centroid name associated to each input. When the command is executed, the cluster information is downloaded to your local computer and the centroid predictions are computed locally, with no more latencies involved. Just in case you prefer to use BigML to compute the centroid predictions remotely, you can do so too

bigmler cluster --cluster cluster/53b1f71437203f5ac30004f0 \
                --test data/my_test.csv --remote

would create a remote source and dataset from the test file data, generate a batch centroid also remotely and finally download the result to your computer. If you prefer the result not to be dowloaded but to be stored as a new dataset remotely, add --no-csv and to-dataset to the command line. This can be specially helpful when dealing with a high number of scores or when adding to the final result the original dataset fields with --prediction-info full, that may result in a large CSV to be created as output.

The k-means algorithm used in clustering can only use training data that has no missing values in their numeric fields. Any data that does not comply with that is discarded in cluster construction, so you should ensure that enough number of rows in your training data file has non-missing values in their numeric fields for the cluster to be built and relevant. Similarly, the cluster cannot issue a centroid prediction for input data that has missing values in its numeric fields, so centroid predictions will give a “-” string as output in this case.

You can change the number of centroids used to group the data in the clustering procedure

bigmler cluster --dataset dataset/53b1f71437203f5ac30004ed \
                --k 3

And also generate the datasets associated to each centroid of a cluster. Using the --cluster-datasets option

bigmler cluster –cluster cluster/53b1f71437203f5ac30004f0
–cluster-datasets “Cluster 1,Cluster 2”

you can generate the datasets associated to a comma-separated list of centroid names. If no centroid name is provided, all datasets are generated.

Similarly, you can generate the models to predict if one instance is associated to each centroid of a cluster. Using the --cluster-models option

bigmler cluster –cluster cluster/53b1f71437203f5ac30004f0
–cluster-models “Cluster 1,Cluster 2”

you can generate the models associated to a comma-separated list of centroid names. If no centroid name is provided, all models are generated. Models can be useful to see which features are important to determine whether a certain instance belongs to a concrete cluster.

Anomaly subcommand

The bigmler anomaly subcommand generates all the resources needed to buid an anomaly detection model and/or predict the anomaly scores associated to your test data. As usual, the simplest call

bigmler anomaly --train data/tiny_kdd.csv

uploads the data in the data/tiny_kdd.csv file and generates the corresponding source, dataset and anomaly objects in BigML. You can use any of the generated objects to produce new anomaly detectors. For instance, you could set a subgroup of the fields of the generated dataset to produce a different anomaly detector by using

bigmler anomaly --dataset dataset/53b1f71437203f5ac30004ed \
                --anomaly-fields="-urgent"

that would exclude the field urgent from the anomaly detector creation input fields. You can also change the number of top anomalies enclosed in the anomaly detector list and the number of trees that the anomaly detector iforest uses. The default values are 10 top anomalies and 128 trees per iforest:

bigmler anomaly --dataset dataset/53b1f71437203f5ac30004ed \
                --top-n 15 --forest-size 50

with this code, the anomaly detector is built using an iforest of 50 trees and will produce a list of the 15 top anomalies.

Similarly to the models and datasets, the generated anomaly detectors can be shared using the --shared option, e.g.

bigmler anomaly --source source/53b1f71437203f5ac30004e0 \
                --shared

will generate a secret link for both the created dataset and anomaly detector that can be used to share the resource selectively.

The anomaly detector can be used to assign an anomaly score to each new input data set. The anomaly score is a number between 0 (not anomalous) and 1 (highest anomaly). The command

bigmler anomaly --anomaly anomaly/53b1f71437203f5ac30005c0 \
                --test data/test_kdd.csv

would produce a file anomaly_scores.csv with the anomaly score associated to each input. When the command is executed, the anomaly detector information is downloaded to your local computer and the anomaly score predictions are computed locally, with no more latencies involved. Just in case you prefer to use BigML to compute the anomaly score predictions remotely, you can do so too

bigmler anomaly --anomaly anomaly/53b1f71437203f5ac30005c0 \
                --test data/my_test.csv --remote

would create a remote source and dataset from the test file data, generate a batch anomaly score also remotely and finally download the result to your computer. If you prefer the result not to be dowloaded but to be stored as a new dataset remotely, add --no-csv and to-dataset to the command line. This can be specially helpful when dealing with a high number of scores or when adding to the final result the original dataset fields with --prediction-info full, that may result in a large CSV to be created as output.

Similarly, you can split your data in train/test datasets to build the anomaly detector and create batch anomaly scores with the test portion of data

bigmler anomaly --train data/tiny_kdd.csv --test-split 0.2 --remote

or if you want to apply the anomaly detector on the same training data set to create a batch anomaly score, use:

bigmler anomaly --train data/tiny_kdd.csv --score --remote

To extract the top anomalies as a new dataset, or to exclude from the training dataset the top anomalies in the anomaly detector, set the

--anomalies-dataset to ìn or out respectively:
bigmler anomaly --dataset dataset/53b1f71437203f5ac30004ed \
                --anomalies-dataset out

will create a new dataset excluding the top anomalous instances according to the anomaly detector.

Sample subcommand

You can extract samples from your datasets in BigML using the bigmler sample subcommand. When a new sample is requested, a copy of the dataset is stored in a special format in an in-memory cache. This sample can then be used, before its expiration time, to extract data from the related dataset by setting some options like the number of rows or the fields to be retrieved. You can either begin from scratch uploading your data to BigML, creating the corresponding source and dataset and extracting your sample from it

bigmler sample --train data/iris.csv --rows 10 --row-offset 20

This command will create a source, a dataset, a sample object, whose id will be stored in the samples file in the output directory, and extract 10 rows of data starting from the 21st that will be stored in the sample.csv file.

You can reuse an existing sample by using its id in the command.

bigmler sample --sample sample/53b1f71437203f5ac303d5c0 \
               --sample-header --row-order-by="-petal length" \
               --row-fields "petal length,petal width" --mode linear

will create a new sample.csv file with a headers row where only the petal length and petal width are retrieved. The --mode linear option will cause the first available rows to be returned and the --row-order-by="-petal length" option returns these rows sorted in descending order according to the contents of petal length.

You can also add to the sample rows some statistical information by using the --stat-field or --stat-fields options. Adding them to the command will generate a stat-info.json file where the Pearson’s and Spearman’s correlations, and linear regression terms will be stored in a JSON format.

You can also apply a filter to select the sample rows by the values in their fields using the --fields-filter option. This must be set to a string containing the conditions that must be met using field ids and values.

bigmler sample --sample sample/53b1f71437203f5ac303d5c0 \
               --fields-filter "000001=&!000004=Iris-setosa"

With this command, only rows where field id 000001 is missing and field id 000004 is not Iris-setosa will be retrieved. You can check the available operators and syntax in the samples’ developers doc . More available options can be found in the Samples subcommand Options section.

Delete subcommand

You have seen that BigMLer is an agile tool that empowers you to create a great number of resources easily. This is a tremedous help, but it also can lead to a garbage-prone environment. To keep a control of each new created remote resource use the flag –resources-log followed by the name of the log file you choose.

bigmler --train data/iris.csv --resources-log my_log.log

Each new resource created by that command will cause its id to be appended as a new line of the log file.

BigMLer can help you as well in deleting these resources. Using the delete subcommand there are many options available. For instance, deleting a comma-separated list of ids

bigmler delete \
        --ids source/50a2bb64035d0706db0006cc,dataset/50a1f441035d0706d9000371

deleting resources listed in a file

bigmler delete --from-file to_delete.log

where to_delete.log contains a resource id per line.

As we’ve previously seen, each BigMLer command execution generates a bunch of remote resources whose ids are stored in files located in a directory that can be set using the --output-dir option. The bigmler delete subcommand can retrieve the ids stored in such files by using the --from-dir option.

bigmler --train data/iris.csv --output my_BigMLer_output_dir
bigmler delete --from-dir my_BigMLer_output_dir

The last command will delete all the remote resources previously generated by the fist command by retrieving their ids from the files in my_BigMLer_output_dir directory.

You can also delete resources based on the tags they are associated to

bigmler delete --all-tag my_tag

or restricting the operation to a specific type

bigmler delete --source-tag my_tag
bigmler delete --dataset-tag my_tag
bigmler delete --model-tag my_tag
bigmler delete --prediction-tag my_tag
bigmler delete --evaluation-tag my_tag
bigmler delete --ensemble-tag my_tag
bigmler delete --batch-prediction-tag my_tag
bigmler delete --cluster-tag my_tag
bigmler delete --centroid-tag my_tag
bigmler delete --batch-centroid-tag my_tag
bigmler delete --anomaly-tag my_tag
bigmler delete --anomaly-score-tag my_tag
bigmler delete --batch-anomaly-score-tag my_tag

You can also delete resources by date. The options --newer-than and --older-than let you specify a reference date. Resources created after and before that date respectively, will be deleted. Both options can be combined to set a range of dates. The allowed values are:

  • dates in a YYYY-MM-DD format
  • integers, that will be interpreted as number of days before now
  • resource id, the creation datetime of the resource will be used

Thus,

bigmler delete --newer-than 2

will delete all resources created less than two days ago (now being 2014-03-23 14:00:00.00000, its creation time will be greater than 2014-03-21 14:00:00.00000).

bigmler delete --older-than 2014-03-20 --newer-than 2014-03-19

will delete all resources created during 2014, March the 19th (creation time between 2014-03-19 00:00:00 and 2014-03-20 00:00:00) and

bigmler delete --newer-than source/532db2b637203f3f1a000104

will delete all resources created after the source/532db2b637203f3f1a000104 was created.

You can also combine both types of options, to delete sources tagged as my_tag starting from a certain date on

bigmler delete --newer-than 2 --source-tag my_tag

And finally, you can filter the type of resource to be deleted using the --resource-types option to specify a comma-separated list of resource types to be deleted

bigmler delete --older-than 2 --resource-types source,model

will delete the sources and models created more than two days ago.

You can simulate the a delete subcommand using the --dry-run flag

bigmler delete --newer-than source/532db2b637203f3f1a000104 \
               --source-tag my_source --dry-run

The output for the command will be a list of resources that would be deleted if the --dry-run flag was removed. In this case, they will be sources that contain the tag my_source and were created after the one given as --newer-than value. The first 15 resources will be logged to console, and the complete list can be found in the bigmler_sessions file.

Additional Features

Using local models to predict

Most of the previously described commands need the remote resources to be downloaded to work. For instance, when you want to create a new model from an existing dataset, BigMLer is going to download the dataset JSON structure to extract the fields and objective field information, and only then ask for the model creation. As mentioned, the --store flag forces BigMLer to store the downloaded JSON structures in local files inside your output directory. If you use that flag when building a model with BigMLer, then the model is stored in your computer. This model file contains all the information you need in order to make new predictions, so you can use the --model-file option to set the path to this file and predict the value of your objective field for new input data with no reference at all to your remote resources. You could even delete the original remote model and work exclusively with the locally downloaded file

bigmler --model-file my_dir/model_532db2b637203f3f1a000136 \
        --test data/test_iris.csv

The same is available for clusters

bigmler cluster --cluster-file my_dir/cluster_532db2b637203f3f1a000348 \
                --test data/test_diabetes.csv

or anomaly detectors

bigmler anomaly --anomaly-file my_dir/anomaly_532db2b637203f3f1a00053a \
                --test data/test_kdd.csv

Even for ensembles

bigmler --ensemble-file my_dir/ensemble_532db2b637203f3f1a00053b \
        --test data/test_iris.csv --store

where we added the --store flag to ensure that also the downloaded models that set up the ensemble are stored and used from the local repository.

Resuming Previous Commands

Network connections failures or other external causes can break the BigMLer command process. To resume a command ended by an unexpected event you can issue

bigmler --resume

BigMLer keeps track of each command you issue in a .bigmler file and of the output directory in .bigmler_dir_stack of your working directory. Then --resume will recover the last issued command and try to continue work from the point it was stopped. There’s also a --stack-level flag

bigmler --resume --stack-level 1

to allow resuming a previous command in the stack. In the example, the one before the last.

Building reports

The resources generated in the execution of a BigMLer command are listed in the standard output by default, but they can be summarized as well in a Gazibit format. Gazibit is a platform where you can create interactive presentations in a flexible and dynamic way. Using BigMLer’s --reports gazibit option you’ll be able to generate a Gazibit summary report of your newly created resources. In case you use also the --shared flag, a second template will be generated where the links for the shared resources will be used. Both reports will be stored in the reports subdirectory of your output directory, where all of the files generated by the BigMLer command are. Thus,

bigmler --train data/iris.csv --reports gazibit --shared \
        --output-dir my_dir

will generate two files: gazibit.json and gazibit_shared.json in a reports subdirectory of your my_dir directory. In case you provide your Gazibit token in the GAZIBIT_TOKEN environment variable, they will also be uploaded to your account in Gazibit. Upload can be avoided, by using the --no-upload flag.

User Chosen Defaults

BigMLer will look for bigmler.ini file in the working directory where users can personalize the default values they like for the most relevant flags. The options should be written in a config style, e.g.

[BigMLer]
dev = true
resources_log = ./my_log.log

as you can see, under a [BigMLer] section the file should contain one line per option. Dashes in flags are transformed to undescores in options. The example would keep development mode on and would log all created resources to my_log.log for any new bigmler command issued under the same working directory if none of the related flags are set.

Naturally, the default value options given in this file will be overriden by the corresponding flag value in the present command. To follow the previous example, if you use

bigmler --train data/iris.csv --resources-log ./another_log.log

in the same working directory, the value of the flag will be preeminent and resources will be logged in another_log.log. For boolean-valued flags, such as --dev itself, you’ll need to use the associated negative flags to overide the default behaviour. Than is, following the former example if you want to override the dev mode used by default you should use

bigmler --train data/iris.csv --no-dev

The set of negative flags is:

--no-debug as opposed to --debug
--no-dev as opposed to --dev
--no-train-header as opposed to --train-header
--no-test-header as opposed to --test-header
--local as opposed to --remote
--no-replacement as opposed to --replacement
--no-randomize as opposed to --randomize
--no-no-tag as opposed to --no-tag
--no-public-dataset as opposed to --public-dataset
--no-black-box as opposed to --black-box
--no-white-box as opposed to --white-box
--no-progress-bar as opposed to --progress-bar
--no-no-dataset as opposed to --no-dataset
--no-no-model as opposed to --no-model
--no-clear-logs as opposed to --clear-logs
--no-store as opposed to --store
--no-multi-label as opposed to --multi-label
--no-prediction-header as opposed to --prediction-header
--batch as opposed to --no-batch
--no-balance as opposed to --balance
--no-multi-dataset as opposed to --multi-dataset
--unshared as opposed to --shared
--upload as opposed to --no-upload
--fast as opposed to --no-fast
--no-no-csv as opposed to --no-csv
--no-median as opposed to --median
--no-score as opposed to --score

Support

Please report problems and bugs to our BigML.io issue tracker.

Discussions about the different bindings take place in the general BigML mailing list. Or join us in our Campfire chatroom.

Requirements

Python 2.7 and 3 are currently supported by BigMLer.

BigMLer requires bigml 4.1.5 or higher. Using proportional missing strategy will additionally request the use of the numpy and scipy libraries. They are not automatically installed as a dependency, as they are quite heavy and exclusively required in this case. Therefore, they have been left for the user to install them if required.

Note that using proportional missing strategy for local predictions can also require numpy and scipy libraries. They are not installed by default. Check the bindings documentation for more info.

BigMLer Installation

To install the latest stable release with pip

$ pip install bigmler

You can also install the development version of bigmler directly from the Git repository

$ pip install -e git://github.com/bigmlcom/bigmler.git#egg=bigmler

For a detailed description of install instructions on Windows see the BigMLer on Windows section.

BigML Authentication

All the requests to BigML.io must be authenticated using your username and API key and are always transmitted over HTTPS.

BigML module will look for your username and API key in the environment variables BIGML_USERNAME and BIGML_API_KEY respectively. You can add the following lines to your .bashrc or .bash_profile to set those variables automatically when you log in

export BIGML_USERNAME=myusername
export BIGML_API_KEY=ae579e7e53fb9abd646a6ff8aa99d4afe83ac291

Otherwise, you can initialize directly when running the BigMLer script as follows

bigmler --train data/iris.csv --username myusername --api_key ae579e7e53fb9abd646a6ff8aa99d4afe83ac291

For a detailed description of authentication instructions on Windows see the BigMLer on Windows section.

BigMLer on Windows

To install BigMLer on Windows environments, you’ll need Python for Windows (v.2.7.x) installed.

In addition to that, you’ll need the pip tool to install BigMLer. To install pip, first you need to open your command line window (write cmd in the input field that appears when you click on Start and hit enter), download this python file and execute it

c:\Python27\python.exe ez_setup.py

After that, you’ll be able to install pip by typing the following command

c:\Python27\Scripts\easy_install.exe pip

And finally, to install BigMLer, just type

c:\Python27\Scripts\pip.exe install bigmler

and BigMLer should be installed in your computer. Then issuing

bigmler --version

should show BigMLer version information.

Finally, to start using BigMLer to handle your BigML resources, you need to set your credentials in BigML for authentication. If you want them to be permanently stored in your system, use

setx BIGML_USERNAME myusername
setx BIGML_API_KEY ae579e7e53fb9abd646a6ff8aa99d4afe83ac291

BigML Development Mode

Also, you can instruct BigMLer to work in BigML’s Sandbox environment by using the parameter --dev

bigmler --train data/iris.csv --dev

Using the development flag you can run tasks under 1 MB without spending any of your BigML credits.

Using BigMLer

To run BigMLer you can use the console script directly. The --help option will describe all the available options

bigmler --help

Alternatively you can just call bigmler as follows

python bigmler.py --help

This will display the full list of optional arguments. You can read a brief explanation for each option below.

Optional Arguments

General configuration

--username BigML’s username. If left unspecified, it will default to the values of the BIGML_USERNAME environment variable
--api-key BigML’s api_key. If left unspecified, it will default to the values of the BIGML_API_KEY environment variable
--dev Uses FREE development environment. Sizes must be under 16MB though
--debug Activates debug level and shows log info for each https request

Basic Functionality

--train TRAINING_SET Full path to a training set. It can be a remote URL to a (gzipped or compressed) CSV file. The protocol schemes can be http, https, s3, azure, odata
--test TEST_SET Full path to a test set. A file containing the data that you want to input to generate predictions
--objective OBJECTIVE_FIELD The column number of the Objective Field (the field that you want to predict) or its name
--output PREDICTIONS Full path to a file to save predictions. If unspecified, it will default to an auto-generated file created by BigMLer. It overrides --output-dir
--output-dir DIRECTORY Directory where all the session files will be stored. It is overriden by --output
--method METHOD Prediction method used: plurality, "confidence weighted", "probability weighted", threshold or combined
--pruning PRUNING_TYPE The pruning applied in building the model. It’s allowed values are smart, statistical and no-pruning The default value is smart
--missing-strategy STRATEGY The strategy applied predicting when a missing value is found in a model split. It’s allowed values are last or proportional. The default value is last
--missing-splits Turns on the missing_splits flag in model creation. The model splits can include in one of its branches the data with missing values
--evaluate Turns on evaluation mode
--resume Retries command execution
--stack-level LEVEL Level of the retried command in the stack
--cross-validation-rate RATE Fraction of the training data held out for Monte-Carlo cross-validation
--number-of-evaluations NUMBER_OF_EVALUATIONS Number of runs that will be used in cross-validation
--max-parallel-evaluations MAX_PARALLEL_EVALUATIONS Maximum number of evaluations to create in parallel
--project PROJECT_NAME Project name for the project to be associated to newly created sources
--project-id PROJECT_ID Project id for the project to be associated to newly created sources
--no-csv Causes the output of a batch prediction, batch centroid or batch anomaly score not to be downloaded as a CSV file
--to-dataset Causes the output of a batch prediction, batch centroid or batch anomaly score to be stored remotely as a new dataset
--median Predictions for single models are returned based on the median of the distribution in the predicted node

Content

--name NAME Name for the resources in BigML.
--category CATEGORY Category code. See full list.
--description DESCRIPTION Path to a file with a description in plain text or markdown
--tag TAG Tag to later retrieve new resources
--no-tag Puts BigMLer default tag if no other tag is given

Data Configuration

--no-train-header The train set file hasn’t a header
--no-test-header The test set file hasn’t a header
--field-attributes PATH Path to a file describing field attributes One definition per line (e.g., 0,’Last Name’)
--types PATH Path to a file describing field types. One definition per line (e.g., 0, ‘numeric’)
--test-field-attributes PATH Path to a file describing test field attributes. One definition per line (e.g., 0,’Last Name’)
--test-types PATH Path to a file describing test field types. One definition per line (e.g., 0, ‘numeric’)
--dataset-fields DATASET_FIELDS Comma-separated list of field column numbers to include in the dataset
--model-fields MODEL_FIELDS Comma-separated list of input fields (predictors) to create the model
--source-attributes PATH Path to a file containing a JSON expression with attributes to be used as arguments in create source calls
--dataset-attributes PATH Path to a file containing a JSON expression with attributes to be used as arguments in create dataset calls
--model-attributes PATH Path to a file containing a JSON expression with attributes to be used as arguments in create model calls
--ensemble-attributes PATH Path to a file containing a JSON expression with attributes to be used as arguments in create ensemble calls
--evaluation-attributes PATH Path to a file containing a JSON expression with attributes to be used as arguments in create evaluation calls
--batch_prediction-attributes PATH Path to a file containing a JSON expression with attributes to be used as arguments in create batch prediction calls
--json-filter PATH Path to a file containing a JSON expression to filter the source
--lisp-filter PATH Path to a file containing a LISP expression to filter the source
--locale LOCALE Locale code string
--fields-map PATH Path to a file containing the dataset to model fields map for evaluation
--test-separator SEPARATOR Character used as test data field separator
--prediction-header Include a headers row in the prediction file
--prediction-fields TEST_FIELDS Comma-separated list of fields of the test file to be included in the prediction file
--max-categories CATEGORIES_NUMBER Sets the maximum number of categories that will be used in a dataset. When more categories are found, new datasets are generated to analize the remaining categories
--new-fields PATH Path to a file containing a JSON expression used to generate a new dataset with new fields created via Flatline <https://github.com/bigmlcom/flatline> by combining or setting their values
--node-threshold Maximum number or nodes to grow the tree with
--balance Automatically balance data to treat all classes evenly
--weight-field FIELD Field name or column number that contains the weights to be used for each instance
--shared Creates a secret link for every dataset, model or evaluation used in the command
--reports Report formats: “gazibit”
--no-upload Disables reports upload
--dataset-off Sets the evaluation mode that uses the list of test datasets and extracts one each time to test the model built with the rest of them (k-fold cross-validation)
--args-separator Character used as separator in multi-valued arguments (default is comma)
--no-missing-splits Turns off the missing_splits flag in model creation.

Remote Resources

--source SOURCE BigML source Id
--dataset DATASET BigML dataset Id
--datasets PATH Path to a file containing a dataset Id
--model MODEL BigML model Id
--models PATH Path to a file containing model/ids. One model per line (e.g., model/4f824203ce80053)
--ensemble ENSEMBLE BigML ensemble Id
--ensembles PATH Path to a file containing ensembles Ids
--test-source SOURCE BigML test source Id (only for remote predictions)
--test-dataset DATASET BigML test dataset Id (only for remote predictions)
--test-datasets PATH Path to the file that contains datasets ids used in evaluations, one id per line.
--source SOURCE BigML source Id
--dataset DATASET BigML dataset Id
--remote Computes predictions remotely (in batch mode by default)
--no-batch Remote predictions are computed individually
--no-fast Ensemble’s local predictions are computed storing the predictions of each model in a separate local file before combining them (the default is –fast, that keeps in memory each model’s prediction)
--model-tag MODEL_TAG Retrieve models that were tagged with tag
--ensemble-tag ENSEMBLE_TAG Retrieve ensembles that were tagged with tag

Ensembles

--number-of-models NUMBER_OF_MODELS Number of models to create
--sample-rate SAMPLE_RATE Sample rate to use (a float between 0.01 and 1)
--replacement Use replacement when sampling
--max-parallel-models MAX_PARALLEL_MODELS Max number of models to create in parallel
--max-batch-models MAX_BATCH_MODELS Max number of local models to be predicted from in parallel. For ensembles with a number of models over it, predictions are stored in files as they are computed and retrived and combined eventually
--randomize Use a random set of fields to split on
--combine-votes LIST_OF_DIRS Combines the votes of models generated in a list of directories
--tlp LEVEL Task-level parallelization

If you are not choosing to create an ensemble, make sure that you tag your models conveniently so that you can then retrieve them later to generate predictions.

Multi-labels

--multi-label Use multiple labels in the objective field
--labels Comma-separated list of labels used
--training-separator SEPARATOR Character used as field separator in train data field
--label-separator SEPARATOR Character used as label separator in the multi-labeled objective field

Public Resources

--public-dataset Makes newly created dataset public
--black-box Makes newly created model a public black-box
--white-box Makes newly created model a public white-box
--model-price Sets the price for a public model
--dataset-price Sets the price for a public dataset
--cpp Sets the credits consumed by prediction

Notice that datasets and models will be made public without assigning any price to them.

Local Resources

--model-file PATH Path to a JSON file containing the model info
--ensemble-file PATH Path to a JSON file containing the ensemble info

Fancy Options

--progress-bar Shows an update on the bytes uploaded when creating a new source. This option might run into issues depending on the locale settings of your OS
--no-dataset Does not create a model. BigMLer will only create a source
--no-model Does not create a model. BigMLer will only create a dataset
--resources-log LOG_FILE Keeps a log of the resources generated in each command
--version Shows the version number
--verbosity LEVEL Turns on (1) or off (0) the verbosity.
--clear-logs Clears the .bigmler, .bigmler_dir_stack, .bigmler_dirs and user log file given in --resources-log (if any)
--store Stores every created or retrieved resource in your output directory

Analyze subcommand Options

--cross-validation Sets the k-fold cross-validation mode
--k-folds Number of folds used in k-fold cross-validation (default is 5)
--features Sets the smart selection features mode
--staleness INTEGER Number of iterations with no improvement that is considered the limit for the analysis to stop (default is 5)
--penalty FLOAT Coefficient used to penalyze models with many features in the smart selection features mode (default is 0.001). Also used in node threshold selection (default is 0)
--optimize METRIC Metric that is being optimized in the smart selection features mode or the node threshold search mode (default is accuracy)
--optimize-category CATEGORY Category whoese metric is being optimized in the smart selection features mode or the node threshold search mode (only for categorical models)
--nodes Sets the node threshold search mode
--min-nodes INTEGER Minimum number of nodes to start the node threshold search mode (default 3)
--max-nodes INTEGER Maximum number of nodes to end the node threshold search mode (default 2000)
--nodes-step INTEGER Step in the node threshold search iteration (default 50)
--exclude-features Comma-separated list of features in the dataset to be excluded from the features analysis
--score Causes the training set to be run through the anomaly detector generating a batch anomaly score. Only used with the --remote flag.

Cluster Specific Subcommand Options

--cluster CLUSTER BigML cluster Id
--clusters PATH Path to a file containing cluster/ids. One cluster per line (e.g., cluster/4f824203ce80051)
--k NUMBER_OF_CENTROIDS Number of final centroids in the clustering
--no-cluster No cluster will be generated
--cluster-fields Comma-separated list of fields that will be used in the cluster construction
--cluster-attributes PATH Path to a JSON file containing attributes to be used in the cluster creation call
--cluster-datasets CENTROID_NAMES Comma-separated list of centroid names to generate the related datasets from a cluster. If no CENTROID_NAMES argument is provided all datasets are generated
--cluster-file PATH Path to a JSON file containing the cluster info
--cluster-seed SEED Seed to generate deterministic clusters
--centroid-attributes PATH Path to a JSON file containing attributes to be used in the centroid creation call
--batch-centroid-attributes PATH Path to a JSON file containing attributes to be used in the batch centroid creation call
--cluster-models CENTROID_NAMES Comma-separated list of centroid names to generate the related models from a cluster. If no CENTROID_NAMES argument is provided all models are generated

Anomaly Specific Subcommand Options

--anomaly ANOMALY BigML anomaly Id
--anomalies PATH Path to a file containing anomaly/ids. One anomaly per line (e.g., anomaly/4f824203ce80051)
--no-anomaly No anomaly detector will be generated
--anomaly-fields Comma-separated list of fields that will be used in the anomaly detector construction
--top-n Number of listed top anomalies
--forest-size Number of models in the anomaly detector iforest
--anomaly-attributes PATH Path to a JSON file containing attributes to be used in the anomaly creation call
--anomaly-file PATH Path to a JSON file containing the anomaly info
--anomaly-seed SEED Seed to generate deterministic anomalies
--anomaly-score-attributes PATH Path to a JSON file containing attributes to be used in the anomaly score creation call
--batch-anomaly-score-attributes PATH Path to a JSON file containing attributes to be used in the batch anomaly score creation call
--anomalies-datasets [in |out] Separates from the training dataset the top anomalous instances enclosed in the top anomalies list and generates a new dataset including them (in option) or excluding them (out option).

.._sample_options:

Samples Subcommand Options

--sample SAMPLE BigML sample Id
--samples PATH Path to a file containing sample/ids. One sample per line (e.g., sample/4f824203ce80051)
--no-sample No sample will be generated
--sample-fields FIELD_NAMES Comma-separated list of fields that will be used in the sample detector construction
--sample-attributes PATH Path to a JSON file containing attributes to be used in the sample creation call
--fields-filter QUERY Query string that will be used as filter before selecting the sample rows. The query string can be built using the field ids, their values and the usual operators. You can see some examples in the developers section
--sample-header Adds a headers row to the sample.csv output
--row-index Prepends acolumn to the sample rows with the absolute row number
--occurrence Prepends a column to the sample rows with the number of occurences of each row. When used with –row-index, the occurrence column will be placed after the index column
--precision Decimal numbers precision
--rows SIZE Number of rows returned
--row-offset OFFSET Skip the given number of rows
--row-order-by FIELD_NAME Field name whose values will be used to sort the returned rows
--row-fields FIELD_NAMES Comma-separated list of fields that will be returned in the sample
--stat-fields FIELD_NAME,FIELD_NAME Two comma-separated numeric field names that will be used to compute their Pearson’s and Spearman’s correlations and linear regression terms
--stat-field FIELD_NAME Numeric field that will be used to compute Pearson’s and Spearman’s correlations and linear regression terms against the rest of numeric fields in the sample
--unique Repeated rows are removed from the sample

Delete Subcommand Options

--ids LIST_OF_IDS Comma separated list of ids to be deleted
--from-file FILE_OF_IDS Path to a file containing the resources’ ids to be deleted
--from-dir Path to a directory where BigMLer has stored its session data and created resources
--all-tag TAG Retrieves resources that were tagged with tag to delete them
--source-tag TAG Retrieves sources that were tagged with tag to delete them
--dataset-tag TAG Retrieves datasets that were tagged with tag to delete them
--model-tag TAG Retrieves models that were tagged with tag to delete them
--prediction-tag TAG Retrieves predictions that were tagged with tag to delete them
--evaluation-tag TAG Retrieves evaluations that were tagged with tag to delete them
--ensemble-tag TAG Retrieves ensembles that were tagged with tag to delete them
--batch-prediction-tag TAG Retrieves batch predictions that were tagged with tag to delete them
--cluster-tag TAG Retrieves clusters that were tagged with tag to delete them
--centroid-tag TAG Retrieves centroids that were tagged with tag to delete them
--batch-centroid-tag TAG Retrieves batch centroids that were tagged with tag to delete them
--anomaly-tag TAG Retrieves anomalies that were tagged with tag to delete them
--anomaly-score-tag TAG Retrieves anomaly scores that were tagged with tag to delete them
--batch-anomlay-score-tag TAG Retrieves batch anomaly scores that were tagged with tag to delete them
--older-than DATE Retrieves resources created before the specified date. Date can be any YYYY-MM-DD string, an integer meaning the number of days before the current datetime or a resource id, meaning the creation datetime of the resource
--newer-than DATE Retrieves resources created after the specified date. Date can be any YYYY-MM-DD string, an integer meaning the number of days before the current datetime or a resource id, meaning the creation datetime of the resource
--resource-types Comma-separated list of types of resources to be deleted. Allowed values are source, dataset, model, ensemble, prediction, batch_prediction, cluster, centroid, batch_centroid
--dry-run Delete simulation. No removal.

Prior Versions Compatibility Issues

BigMLer will accept flags written with underscore as word separator like --clear_logs for compatibility with prior versions. Also --field-names is accepted, although the more complete --field-attributes flag is preferred. --stat_pruning and --no_stat_pruning are discontinued and their effects can be achived by setting the actual --pruning flag to statistical or no-pruning values respectively.

Running the Tests

To run the tests you will need to install lettuce

$ pip install lettuce

and set up your authentication via environment variables, as explained above. With that in place, you can run the test suite simply by

$ cd tests
$ lettuce

Building the Documentation

Install the tools required to build the documentation

$ pip install sphinx

To build the HTML version of the documentation

$ cd docs/
$ make html

Then launch docs/_build/html/index.html in your browser.

Additional Information

For additional information, see the full documentation for the Python bindings on Read the Docs. For more information about BigML’s API, see the BigML developer’s documentation.

How to Contribute

Please follow the next steps:

  1. Fork the project on github.
  2. Create a new branch.
  3. Commit changes to the new branch.
  4. Send a pull request.

For details on the underlying API, see the BigML API documentation.