GT4SD inference examples

Note

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Contents

• GT4SD inference examples

  • Overview

  • Running algorithms explicitly

  • Running algorithms via the registry

Overview

This notebook show the basic usage of the GT4SD algorithms.

• running an algorithm explicitly calling the implementation

• use the ApplicationsRegistry to instantiate and call the algorithms

A note on the setup

In the following we assume that the toolkit has been setup using your preferred environment file (conda*.yml):

# create and activate environment
conda env create -f conda_cpu_mac.yml # or conda_cpu_linux.yml or conda_gpu.yml
conda activate gt4sd
# install the toolkit
pip install .

Running algorithms explicitly

To run algorithms explicitly we only need to instantiate a GeneratorAlgorithm and the companion AlgorithmConfiguration. Then based on the actual algorithm type we might need to pass a target for generation.

Next we see an example of PaccMannRL, a conditional_generation algorithm:

from gt4sd.algorithms.conditional_generation.paccmann_rl.core import (
    PaccMannRLProteinBasedGenerator, PaccMannRL
)
target = 'MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTT'
configuration = PaccMannRLProteinBasedGenerator()
algorithm = PaccMannRL(configuration=configuration, target=target)
items = list(algorithm.sample(10))
print(items)

For vanilla generation algorithms (generation), like PolymerBlocks, the usage is analogous, but no target is required:

from gt4sd.algorithms.generation.polymer_blocks.core import (
    PolymerBlocksGenerator, PolymerBlocksGenerator
)
configuration = PolymerBlocksGenerator()
algorithm = PolymerBlocksGenerator(configuration=configuration)
items = list(algorithm.sample(10))
print(items)

Running algorithms via the registry

Here we show how the toolkit algorithms can be instantiated and run using the ApplicationsRegistry.

Next we see an example of PaccMannRL, a conditional_generation algorithm:

from gt4sd.algorithms.registry import ApplicationsRegistry
target = 'MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTT'
algorithm = ApplicationsRegistry.get_application_instance(
    target=target,
    algorithm_type='conditional_generation',
    domain='materials',
    algorithm_name='PaccMannRL',
    algorithm_application='PaccMannRLProteinBasedGenerator',
    generated_length=5,
)
items = list(algorithm.sample(10))
print(items)

Similarly we can use the registry to run PolymerBlocks:

from gt4sd.algorithms.registry import ApplicationsRegistry
algorithm = ApplicationsRegistry.get_application_instance(
    algorithm_type='generation',
    domain='materials',
    algorithm_name='PolymerBlocks',
    algorithm_application='PolymerBlocksGenerator',
    generated_length=10,
)
items = list(algorithm.sample(10))
print(items)