mammal_demo/tcr_task.py

import gradio as gr
import torch
from fuse.data.tokenizers.modular_tokenizer.op import ModularTokenizerOp
from mammal.keys import (
    CLS_PRED,
    ENCODER_INPUTS_ATTENTION_MASK,
    ENCODER_INPUTS_STR,
    ENCODER_INPUTS_TOKENS,
    SCORES,
)
from mammal.model import Mammal

from mammal_demo.demo_framework import MammalObjectBroker, MammalTask


class TcrTask(MammalTask):
    def __init__(self, model_dict):
        super().__init__(
            name="Mammal based TCRbeta-epitope binding affinity", model_dict=model_dict
        )
        self.description = "Mammal based TCRbeta-epitope binding affinity (TCR)"
        self.examples = {
            "tcr_beta_seq": "NAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYSWDRVLEQYFGPGTRLTVT",
            "epitope_seq": "LLQTGIHVRVSQPSL",
        }
        self.markup_text = """
# Mammal based Mammal based TCRbeta-epitope binding affinity demonstration

Given a TCR beta chain and epitope amino acid sequences, estimate the binding affinity score.
"""

    def create_prompt(self, tcr_beta_seq, epitope_seq):
        prompt = (
            "<@TOKENIZER-TYPE=AA><BINDING_AFFINITY_CLASS><SENTINEL_ID_0>"
            + f"<@TOKENIZER-TYPE=AA><MOLECULAR_ENTITY><MOLECULAR_ENTITY_TCR_BETA_VDJ><SEQUENCE_NATURAL_START>{tcr_beta_seq}<SEQUENCE_NATURAL_END>"
            + f"<@TOKENIZER-TYPE=AA><MOLECULAR_ENTITY><MOLECULAR_ENTITY_EPITOPE><SEQUENCE_NATURAL_START>{epitope_seq}<SEQUENCE_NATURAL_END><EOS>"
        )

        return prompt

    def crate_sample_dict(self, sample_inputs: dict, model_holder: MammalObjectBroker):
        """convert sample_inputs to sample_dict including creating a proper prompt

        Args:
            sample_inputs (dict): dictionary containing the inputs to the model
            model_holder (MammalObjectBroker): model holder
        Returns:
           dict: sample_dict for feeding into model
        """
        sample_dict = dict()
        sample_dict[ENCODER_INPUTS_STR] = self.create_prompt(**sample_inputs)
        tokenizer_op = model_holder.tokenizer_op
        model = model_holder.model
        tokenizer_op(
            sample_dict=sample_dict,
            key_in=ENCODER_INPUTS_STR,
            key_out_tokens_ids=ENCODER_INPUTS_TOKENS,
            key_out_attention_mask=ENCODER_INPUTS_ATTENTION_MASK,
        )
        sample_dict[ENCODER_INPUTS_TOKENS] = torch.tensor(
            sample_dict[ENCODER_INPUTS_TOKENS], device=model.device
        )
        sample_dict[ENCODER_INPUTS_ATTENTION_MASK] = torch.tensor(
            sample_dict[ENCODER_INPUTS_ATTENTION_MASK], device=model.device
        )

        return sample_dict

    def run_model(self, sample_dict, model: Mammal):
        # Generate Prediction
        batch_dict = model.generate(
            [sample_dict],
            output_scores=True,
            return_dict_in_generate=True,
            max_new_tokens=5,
        )
        return batch_dict

    @staticmethod
    def positive_token_id(tokenizer_op: ModularTokenizerOp):
        """token for positive binding

        Args:
            model (MammalTrainedModel): model holding tokenizer

        Returns:
            int: id of positive binding token
        """
        return tokenizer_op.get_token_id("<1>")

    @staticmethod
    def negative_token_id(tokenizer_op: ModularTokenizerOp):
        """token for negative binding

        Args:
            model (MammalTrainedModel): model holding tokenizer

        Returns:
            int: id of negative binding token
        """
        return tokenizer_op.get_token_id("<0>")

    def decode_output(self, batch_dict, tokenizer_op: ModularTokenizerOp) -> list:
        """
        Extract predicted class and scores
        """

        # positive_token_id = self.positive_token_id(tokenizer_op)
        # negative_token_id = self.negative_token_id(tokenizer_op)

        negative_token_id = tokenizer_op.get_token_id("<0>")
        positive_token_id = tokenizer_op.get_token_id("<1>")

        label_id_to_int = {
            negative_token_id: 0,
            positive_token_id: 1,
        }
        classification_position = 1

        decoder_output = batch_dict[CLS_PRED][0]
        decoder_output_scores = batch_dict[SCORES][0]

        if decoder_output_scores is not None:
            scores = decoder_output_scores[classification_position, positive_token_id]
        else:
            scores = [None]

        ans = [
            tokenizer_op._tokenizer.decode(batch_dict[CLS_PRED][0]),
            label_id_to_int.get(int(decoder_output[classification_position]), -1),
            scores.item(),
        ]
        return ans

    def create_and_run_prompt(self, model_name, tcr_beta_seq, epitope_seq):
        model_holder = self.model_dict[model_name]
        inputs = {
            "tcr_beta_seq": tcr_beta_seq,
            "epitope_seq": epitope_seq,
        }
        sample_dict = self.crate_sample_dict(
            sample_inputs=inputs, model_holder=model_holder
        )
        prompt = sample_dict[ENCODER_INPUTS_STR]
        batch_dict = self.run_model(sample_dict=sample_dict, model=model_holder.model)
        res = prompt, *self.decode_output(
            batch_dict, tokenizer_op=model_holder.tokenizer_op
        )
        return res

    def create_demo(self, model_name_widget):

        with gr.Group() as demo:
            gr.Markdown(self.markup_text)
            with gr.Row():
                tcr_textbox = gr.Textbox(
                    label="T-cell receptor beta sequence",
                    # info="standard",
                    interactive=True,
                    lines=3,
                    value=self.examples["tcr_beta_seq"],
                )
                epitope_textbox = gr.Textbox(
                    label="Epitope sequence",
                    # info="standard",
                    interactive=True,
                    lines=3,
                    value=self.examples["epitope_seq"],
                )
            with gr.Row():
                run_mammal = gr.Button(
                    "Run Mammal prompt for TCL-Epitope Interaction",
                    variant="primary",
                )
            with gr.Row():
                prompt_box = gr.Textbox(label="Mammal prompt", lines=5)

            with gr.Row():
                decoded = gr.Textbox(label="Mammal output")
                predicted_class = gr.Textbox(label="Mammal prediction")
                binding_score = gr.Number(label="Binding score")
                run_mammal.click(
                    fn=self.create_and_run_prompt,
                    inputs=[model_name_widget, tcr_textbox, epitope_textbox],
                    outputs=[prompt_box, decoded, predicted_class, binding_score],
                )
            demo.visible = False
            return demo