app.py

import logging
import pathlib
from typing import List

import gradio as gr
import pandas as pd
from gt4sd.algorithms.controlled_sampling.paccmann_gp import (
    PaccMannGPGenerator,
    PaccMannGP,
)
from gt4sd.algorithms.controlled_sampling.paccmann_gp.implementation import (
    MINIMIZATION_FUNCTIONS,
)

from gt4sd.algorithms.registry import ApplicationsRegistry

from utils import draw_grid_generate

logger = logging.getLogger(__name__)
logger.addHandler(logging.NullHandler())


MINIMIZATION_FUNCTIONS.pop("callable", None)
MINIMIZATION_FUNCTIONS.pop("molwt", None)


def run_inference(
    algorithm_version: str,
    targets: List[str],
    protein_target: str,
    temperature: float,
    length: float,
    number_of_samples: int,
    limit: int,
    number_of_steps: int,
    number_of_initial_points: int,
    number_of_optimization_rounds: int,
    sampling_variance: float,
    samples_for_evaluation: int,
    maximum_number_of_sampling_steps: int,
    seed: int,
):

    config = PaccMannGPGenerator(
        algorithm_version=algorithm_version.split("_")[-1],
        batch_size=32,
        temperature=temperature,
        generated_length=length,
        limit=limit,
        acquisition_function="EI",
        number_of_steps=number_of_steps,
        number_of_initial_points=number_of_initial_points,
        initial_point_generator="random",
        number_of_optimization_rounds=number_of_optimization_rounds,
        sampling_variance=sampling_variance,
        samples_for_evaluation=samples_for_evaluation,
        maximum_number_of_sampling_steps=maximum_number_of_sampling_steps,
        seed=seed,
    )
    target = {i: {} for i in targets}
    if "affinity" in targets:
        if protein_target == "" or not isinstance(protein_target, str):
            raise ValueError(
                f"Protein target must be specified for affinity prediction, not ={protein_target}"
            )
        target["affinity"]["protein"] = protein_target
    else:
        protein_target = ""

    model = PaccMannGP(config, target=target)
    samples = list(model.sample(number_of_samples))

    return draw_grid_generate(
        samples=samples,
        n_cols=5,
        properties=set(target.keys()),
        protein_target=protein_target,
    )


if __name__ == "__main__":

    # Preparation (retrieve all available algorithms)
    all_algos = ApplicationsRegistry.list_available()
    algos = [
        x["algorithm_version"]
        for x in list(filter(lambda x: "PaccMannGP" in x["algorithm_name"], all_algos))
    ]

    # Load metadata
    metadata_root = pathlib.Path(__file__).parent.joinpath("model_cards")

    examples = pd.read_csv(
        metadata_root.joinpath("examples.csv"), header=None, sep="|"
    ).fillna("")
    examples[1] = examples[1].apply(eval)

    with open(metadata_root.joinpath("article.md"), "r") as f:
        article = f.read()
    with open(metadata_root.joinpath("description.md"), "r") as f:
        description = f.read()

    demo = gr.Interface(
        fn=run_inference,
        title="PaccMannGP",
        inputs=[
            gr.Dropdown(algos, label="Algorithm version", value="v0"),
            gr.CheckboxGroup(
                choices=list(MINIMIZATION_FUNCTIONS.keys()),
                value=["qed"],
                multiselect=True,
                label="Property goals",
            ),
            gr.Textbox(
                label="Protein target",
                placeholder="MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTT",
                lines=1,
            ),
            gr.Slider(minimum=0.5, maximum=2, value=1, label="Decoding temperature"),
            gr.Slider(
                minimum=5,
                maximum=400,
                value=100,
                label="Maximal sequence length",
                step=1,
            ),
            gr.Slider(
                minimum=1, maximum=50, value=10, label="Number of samples", step=1
            ),
            gr.Slider(minimum=1, maximum=8, value=4.0, label="Limit"),
            gr.Slider(minimum=1, maximum=32, value=8, label="Number of steps", step=1),
            gr.Slider(
                minimum=1, maximum=32, value=4, label="Number of initial points", step=1
            ),
            gr.Slider(
                minimum=1,
                maximum=4,
                value=1,
                label="Number of optimization rounds",
                step=1,
            ),
            gr.Slider(minimum=0.01, maximum=1, value=0.1, label="Sampling variance"),
            gr.Slider(
                minimum=1,
                maximum=10,
                value=1,
                label="Samples used for evaluation",
                step=1,
            ),
            gr.Slider(
                minimum=1,
                maximum=64,
                value=4,
                label="Maximum number of sampling steps",
                step=1,
            ),
            gr.Number(value=42, label="Seed", precision=0),
        ],
        outputs=gr.HTML(label="Output"),
        article=article,
        description=description,
        examples=examples.values.tolist(),
    )
    demo.launch(debug=True, show_error=True)