MLAir - Machine Learning on Air Data

MLAir (Machine Learning on Air data) is an environment that simplifies and accelerates the creation of new machine learning (ML) models for the analysis and forecasting of meteorological and air quality time series. You can find the docs here.

• MLAir - Machine Learning on Air Data
• Installation
• How to start with MLAir
  • Example 1
  • Example 2
  • Example 3
• Default Workflow
• Customised Run Module and Workflow
• Custom Model
  • How to create a customised model?
  • How to plug in the customised model into the workflow?
  • Specials for Branched Models
  • How to access my customised model?
• Data Handlers
• Special Remarks
  • Special instructions for installation on Jülich HPC systems
  • Security using JOIN

Installation

MLAir is based on several python frameworks. To work properly, you have to install all packages from the requirements.txt file. Additionally to support the geographical plotting part it is required to install geo packages built for your operating system. Name names of these package may differ for different systems, we refer here to the opensuse / leap OS. The geo plot can be removed from the plot_list, in this case there is no need to install the geo packages. For special instructions to install MLAir on the Juelich HPC systems, see here.

• (geo) Install proj on your machine using the console. E.g. for opensuse / leap zypper install proj
• (geo) A c++ compiler is required for the installation of the program cartopy
• Install all requirements from requirements.txt preferably in a virtual environment
• (tf) Currently, TensorFlow-1.13 is mentioned in the requirements. We already tested the TensorFlow-1.15 version and couldn't find any compatibility errors. Please note, that tf-1.13 and 1.15 have two distinct branches each, the default branch for CPU support, and the "-gpu" branch for GPU support. If the GPU version is installed, MLAir will make use of the GPU device.
• Installation of MLAir:
  • Either clone MLAir from the gitlab repository and use it without installation (beside the requirements)
  • or download the distribution file (current version) and install it via pip install <dist_file>.whl. In this case, you can simply import MLAir in any python script inside your virtual environment using import mlair.

How to start with MLAir

In this section, we show three examples how to work with MLAir. Note, that for these examples MLAir was installed using the distribution file. In case you are using the git clone it is required to adjust the import path if not directly executed inside the source directory of MLAir.

Example 1

We start MLAir in a dry run without any modification. Just import mlair and run it.

import mlair

# just give it a dry run without any modification 
mlair.run()

The logging output will show you many informations. Additional information (including debug messages) are collected inside the experiment path in the logging folder.

INFO: DefaultWorkflow started
INFO: ExperimentSetup started
INFO: Experiment path is: /home/<usr>/mlair/testrun_network 
...
INFO: load data for DEBW107 from JOIN
INFO: load data for DEBY081 from JOIN
INFO: load data for DEBW013 from JOIN
INFO: load data for DEBW076 from JOIN
INFO: load data for DEBW087 from JOIN
...
INFO: Training started
...
INFO: DefaultWorkflow finished after 0:03:04 (hh:mm:ss)

Example 2

Now we update the stations and customise the window history size parameter.

import mlair

# our new stations to use
stations = ['DEBW030', 'DEBW037', 'DEBW031', 'DEBW015', 'DEBW107']

# expanded temporal context to 14 (days, because of default sampling="daily")
window_history_size = 14

# restart the experiment with little customisation
mlair.run(stations=stations, 
          window_history_size=window_history_size)

The output looks similar, but we can see, that the new stations are loaded.

INFO: DefaultWorkflow started
INFO: ExperimentSetup started
...
INFO: load data for DEBW030 from JOIN 
INFO: load data for DEBW037 from JOIN 
INFO: load data for DEBW031 from JOIN 
INFO: load data for DEBW015 from JOIN 
...
INFO: Training started
...
INFO: DefaultWorkflow finished after 00:02:03 (hh:mm:ss)

Example 3

Let's just apply our trained model to new data. Therefore we keep the window history size parameter but change the stations. In the run method, we need to disable the trainable and create new model parameters. MLAir will use the model we have trained before. Note, this only works if the experiment path has not changed or a suitable trained model is placed inside the experiment path.

import mlair

# our new stations to use
stations = ['DEBY002', 'DEBY079']

# same setting for window_history_size
window_history_size = 14

# run experiment without training
mlair.run(stations=stations, 
          window_history_size=window_history_size, 
          create_new_model=False, 
          train_model=False)

We can see from the terminal that no training was performed. Analysis is now made on the new stations.

INFO: DefaultWorkflow started
...
INFO: No training has started, because train_model parameter was false. 
...
INFO: DefaultWorkflow finished after 0:01:27 (hh:mm:ss)

Default Workflow

MLAir is constituted of so-called run_modules which are executed in a distinct order called workflow. MLAir provides a default_workflow. This workflow runs the run modules ExperimentSetup, PreProcessing, ModelSetup, Training, and PostProcessing one by one.

import mlair

# create your custom MLAir workflow
DefaultWorkflow = mlair.DefaultWorkflow()
# execute default workflow
DefaultWorkflow.run()

The output of running this default workflow will be structured like the following.

INFO: DefaultWorkflow started
INFO: ExperimentSetup started
...
INFO: ExperimentSetup finished after 00:00:01 (hh:mm:ss)
INFO: PreProcessing started
...
INFO: PreProcessing finished after 00:00:11 (hh:mm:ss)
INFO: ModelSetup started
...
INFO: ModelSetup finished after 00:00:01 (hh:mm:ss)
INFO: Training started
...
INFO: Training finished after 00:02:15 (hh:mm:ss)
INFO: PostProcessing started
...
INFO: PostProcessing finished after 00:01:37 (hh:mm:ss)
INFO: DefaultWorkflow finished after 00:04:05 (hh:mm:ss)

Customised Run Module and Workflow

It is possible to create new custom run modules. A custom run module is required to inherit from the base class RunEnvironment and to hold the constructor method __init__(). This method has to execute the module on call. In the following example, this is done by using the _run() method that is called by the initialiser. It is possible to parse arguments to the custom run module as shown.

import mlair
import logging

class CustomStage(mlair.RunEnvironment):
    """A custom MLAir stage for demonstration."""

    def __init__(self, test_string):
        super().__init__()  # always call super init method
        self._run(test_string)  # call a class method

    def _run(self, test_string):
        logging.info("Just running a custom stage.")
        logging.info("test_string = " + test_string)
        epochs = self.data_store.get("epochs")
        logging.info("epochs = " + str(epochs))

If a custom run module is defined, it is required to adjust the workflow. For this, you need to load the empty Workflow class and add each run module that is required. The order of adding modules defines the order of execution if running the workflow.

# create your custom MLAir workflow
CustomWorkflow = mlair.Workflow()
# provide stages without initialisation
CustomWorkflow.add(mlair.ExperimentSetup, epochs=128)
# add also keyword arguments for a specific stage
CustomWorkflow.add(CustomStage, test_string="Hello World")
# finally execute custom workflow in order of adding
CustomWorkflow.run()

The output will look like:

INFO: Workflow started
...
INFO: ExperimentSetup finished after 00:00:12 (hh:mm:ss)
INFO: CustomStage started
INFO: Just running a custom stage.
INFO: test_string = Hello World
INFO: epochs = 128
INFO: CustomStage finished after 00:00:01 (hh:mm:ss)
INFO: Workflow finished after 00:00:13 (hh:mm:ss)

Custom Model

Create your own model to run your personal experiment. To guarantee a proper integration in the MLAir workflow, models are restricted to inherit from the AbstractModelClass. This will ensure a smooth training and evaluation behaviour.

How to create a customised model?

• Create a new model class inheriting from AbstractModelClass

from mlair import AbstractModelClass

class MyCustomisedModel(AbstractModelClass):

    def __init__(self, input_shape: list, output_shape: list):

        # set attributes shape_inputs and shape_outputs
        super().__init__(input_shape[0], output_shape[0])

        # apply to model
        self.set_model()
        self.set_compile_options()
        self.set_custom_objects(loss=self.compile_options['loss'])

• Make sure to add the super().__init__() and at least set_model() and set_compile_options() to your custom init method.
• The shown model expects a single input and output branch provided in a list. Therefore shapes of input and output are extracted and then provided to the super class initialiser.
• Some general settings like the dropout rate are set in the init method additionally.
• If you have custom objects in your model, that are not part of the keras or tensorflow frameworks, you need to add them to custom objects. To do this, call set_custom_objects with arbitrarily kwargs. In the shown example, the loss has been added for demonstration only, because we use a build-in loss function. Nonetheless, we always encourage you to add the loss as custom object, to prevent potential errors when loading an already created model instead of training a new one.
• Now build your model inside set_model() by using the instance attributes self._input_shape and self._output_shape and storing the model as self.model.

import keras
from keras.layers import PReLU, Input, Conv2D, Flatten, Dropout, Dense

class MyCustomisedModel(AbstractModelClass):

    def set_model(self):
        x_input = Input(shape=self._input_shape)
        x_in = Conv2D(4, (1, 1))(x_input)
        x_in = PReLU()(x_in)
        x_in = Flatten()(x_in)
        x_in = Dropout(0.1)(x_in)
        x_in = Dense(16)(x_in)
        x_in = PReLU()(x_in)
        x_in = Dense(self._output_shape)(x_in)
        out = PReLU()(x_in)
        self.model = keras.Model(inputs=x_input, outputs=[out])

• Your are free how to design your model. Just make sure to save it in the class attribute model.
• Additionally, set your custom compile options including the loss definition.

from keras.losses import mean_squared_error as mse

class MyCustomisedModel(AbstractModelClass):

    def set_compile_options(self):
        self.initial_lr = 1e-2
        self.optimizer = keras.optimizers.SGD(lr=self.initial_lr, momentum=0.9)
        self.loss = mse
        self.compile_options = {"metrics": ["mse", "mae"]}

• The allocation of the instance parameters initial_lr, optimizer, and lr_decay could be also part of the model class' initialiser. The same applies to self.loss and compile_options, but we recommend to use the set_compile_options method for the definition of parameters, that are related to the compile options.

• More important is that the compile options are actually saved. There are three ways to achieve this.

  • (1): Set all compile options by parsing a dictionary with all options to self.compile_options.

  • (2): Set all compile options as instance attributes. MLAir will search for these attributes and store them.

  • (3): Define your compile options partly as dictionary and instance attributes (as shown in this example).

  • If using (3) and defining the same compile option with different values, MLAir will raise an error.

    Incorrect: (Will raise an error because of a mismatch for the optimizer parameter.)

    def set_compile_options(self):
        self.optimizer = keras.optimizers.SGD()
        self.loss = keras.losses.mean_squared_error
        self.compile_options = {"optimizer" = keras.optimizers.Adam()}

How to plug in the customised model into the workflow?

• Make use of the model argument and pass MyCustomisedModel when instantiating a workflow.

from mlair.workflows import DefaultWorkflow

workflow = DefaultWorkflow(model=MyCustomisedModel)
workflow.run()

Specials for Branched Models

• If you have a branched model with multiple outputs, you need either set only a single loss for all branch outputs or provide the same number of loss functions considering the right order.

class MyCustomisedModel(AbstractModelClass):

    def set_model(self):
        ...
        self.model = keras.Model(inputs=x_input, outputs=[out_minor_1, out_minor_2, out_main])

    def set_compile_options(self):
        self.loss = [keras.losses.mean_absolute_error] +  # for out_minor_1
                    [keras.losses.mean_squared_error] +   # for out_minor_2
                    [keras.losses.mean_squared_error]     # for out_main

How to access my customised model?

If the customised model is created, you can easily access the model with

>>> MyCustomisedModel().model
<your custom model>

The loss is accessible via

>>> MyCustomisedModel().loss
<your custom loss>

You can treat the instance of your model as instance but also as the model itself. If you call a method, that refers to the model instead of the model instance, you can directly apply the command on the instance instead of adding the model parameter call.

>>> MyCustomisedModel().model.compile(**kwargs) == MyCustomisedModel().compile(**kwargs)
True

Data Handlers

Data handlers are responsible for all tasks related to data like data acquisition, preparation and provision. A data handler must inherit from the abstract base class AbstractDataHandler and requires the implementation of the __init__() method and the accessors get_X() and get_Y(). In the following, we show an example how a custom data handler could look like.

import datetime as dt
import numpy as np
import pandas as pd
import xarray as xr

from mlair.data_handler import AbstractDataHandler

class DummyDataHandler(AbstractDataHandler):

    def __init__(self, name, number_of_samples=None):
        """This data handler takes a name argument and the number of samples to generate. If not provided, a random 
        number between 100 and 150 is set."""
        super().__init__()
        self.name = name
        self.number_of_samples = number_of_samples if number_of_samples is not None else np.random.randint(100, 150)
        self._X = self.create_X()
        self._Y = self.create_Y()

    def create_X(self):
        """Inputs are random numbers between 0 and 10 with shape (no_samples, window=14, variables=5)."""
        X = np.random.randint(0, 10, size=(self.number_of_samples, 14, 5))  # samples, window, variables
        datelist = pd.date_range(dt.datetime.today().date(), periods=self.number_of_samples, freq="H").tolist()
        return xr.DataArray(X, dims=['datetime', 'window', 'variables'], coords={"datetime": datelist,
                                                                                 "window": range(14),
                                                                                 "variables": range(5)})
    
    def create_Y(self):
        """Targets are normal distributed random numbers with shape (no_samples, window=5, variables=1)."""
        Y = np.round(0.5 * np.random.randn(self.number_of_samples, 5, 1), 1)  # samples, window, variables
        datelist = pd.date_range(dt.datetime.today().date(), periods=self.number_of_samples, freq="H").tolist()
        return xr.DataArray(Y, dims=['datetime', 'window', 'variables'], coords={"datetime": datelist,
                                                                                 "window": range(5),
                                                                                 "variables": range(1)})

    def get_X(self, upsampling=False, as_numpy=False):
        """Upsampling parameter is not used for X."""
        return np.copy(self._X) if as_numpy is True else self._X

    def get_Y(self, upsampling=False, as_numpy=False):
        """Upsampling parameter is not used for Y."""
        return np.copy(self._Y) if as_numpy is True else self._Y

    def __str__(self):
        return self.name

Special Remarks

Special instructions for installation on Jülich HPC systems

Please note, that the HPC setup is customised for JUWELS and HDFML. When using another HPC system, you can use the HPC setup files as a skeleton and customise it to your needs.

The following instruction guide you through the installation on JUWELS and HDFML.

• Clone the repo to HPC system (we recommend to place it in /p/projects/<project name>).
• Setup venv by executing source setupHPC.sh. This script loads all pre-installed modules and creates a venv for all other packages. Furthermore, it creates slurm/batch scripts to execute code on compute nodes.
  You have to enter the HPC project's budget name (--account flag).
• The default external data path on JUWELS and HDFML is set to /p/project/deepacf/intelliaq/<user>/DATA/toar_<sampling>.
  To choose a different location open run.py and add the following keyword argument to ExperimentSetup: data_path=<your>/<custom>/<path>.
• Execute python run.py on a login node to download example data. The program will throw an OSerror after downloading.
• Execute either sbatch run_juwels_develgpus.bash or sbatch run_hdfml_batch.bash to verify that the setup went well.
• Currently cartopy is not working on our HPC system, therefore PlotStations does not create any output.

Note: The method PartitionCheck currently only checks if the hostname starts with ju or hdfmll. Therefore, it might be necessary to adopt the if statement in PartitionCheck._run.

Security using JOIN

• To use hourly data from ToarDB via JOIN interface, a private token is required. Request your personal access token and add it to src/join_settings.py in the hourly data section. Replace the TOAR_SERVICE_URL and the Authorization value. To make sure, that this sensitive data is not uploaded to the remote server, use the following command to prevent git from tracking this file: git update-index --assume-unchanged src/join_settings.py