text_generation.py

import numpy as np
import torch
from transformers import AutoTokenizer, Pipeline


class TextGenerationPipeline(Pipeline):
    def __init__(self, model, **kwargs):  # type: ignore
        super().__init__(model=model, **kwargs)
        # Load tokenizers
        model_name = "InstaDeepAI/ChatNT"
        self.english_tokenizer = AutoTokenizer.from_pretrained(
            model_name, subfolder="english_tokenizer"
        )
        self.bio_tokenizer = AutoTokenizer.from_pretrained(
            model_name, subfolder="bio_tokenizer"
        )

    def _sanitize_parameters(self, **kwargs: dict) -> tuple[dict, dict, dict]:
        preprocess_kwargs = {}
        forward_kwargs = {}
        postprocess_kwargs = {}  # type: ignore

        if "max_num_tokens_to_decode" in kwargs:
            forward_kwargs["max_num_tokens_to_decode"] = kwargs[
                "max_num_tokens_to_decode"
            ]
        if "english_tokens_max_length" in kwargs:
            preprocess_kwargs["english_tokens_max_length"] = kwargs[
                "english_tokens_max_length"
            ]
        if "bio_tokens_max_length" in kwargs:
            preprocess_kwargs["bio_tokens_max_length"] = kwargs["bio_tokens_max_length"]

        return preprocess_kwargs, forward_kwargs, postprocess_kwargs

    def preprocess(
        self,
        inputs: dict,
        english_tokens_max_length: int = 512,
        bio_tokens_max_length: int = 512,
    ) -> dict:
        english_sequence = inputs["english_sequence"]
        dna_sequences = inputs["dna_sequences"]

        context = "A chat between a curious user and an artificial intelligence assistant that can handle bio sequences. The assistant gives helpful, detailed, and polite answers to the user's questions. USER: "  # noqa
        space = " "
        if english_sequence[-1] == " ":
            space = ""
        english_sequence = context + english_sequence + space + "ASSISTANT:"

        english_tokens = self.english_tokenizer(
            english_sequence,
            return_tensors="pt",
            padding="max_length",
            truncation=True,
            max_length=english_tokens_max_length,
        ).input_ids
        bio_tokens = self.bio_tokenizer(
            dna_sequences,
            return_tensors="pt",
            padding="max_length",
            max_length=bio_tokens_max_length,
            truncation=True,
        ).input_ids.unsqueeze(0)

        return {"english_tokens": english_tokens, "bio_tokens": bio_tokens}

    def _forward(self, model_inputs: dict, max_num_tokens_to_decode: int = 50) -> dict:
        english_tokens = model_inputs["english_tokens"].clone()
        bio_tokens = model_inputs["bio_tokens"].clone()
        projected_bio_embeddings = None

        actual_num_steps = 0
        with torch.no_grad():
            for _ in range(max_num_tokens_to_decode):
                # Check if no more pad token id
                if (
                    self.english_tokenizer.pad_token_id
                    not in english_tokens[0].cpu().numpy()
                ):
                    break

                # Predictions
                outs = self.model(
                    multi_omics_tokens_ids=(english_tokens, bio_tokens),
                    projection_english_tokens_ids=english_tokens,
                    projected_bio_embeddings=projected_bio_embeddings,
                )
                projected_bio_embeddings = outs["projected_bio_embeddings"]
                logits = outs["logits"].detach().cpu().numpy()

                # Get predicted token
                first_idx_pad_token = np.where(
                    english_tokens[0].cpu() == self.english_tokenizer.pad_token_id
                )[0][0]
                predicted_token = np.argmax(logits[0, first_idx_pad_token - 1])

                # If it's <eos> then stop, else add the predicted token
                if predicted_token == self.english_tokenizer.eos_token_id:
                    break
                else:
                    english_tokens[0, first_idx_pad_token] = predicted_token
                    actual_num_steps += 1

            # Get the position where generation started
            idx_begin_generation = np.where(
                model_inputs["english_tokens"][0].cpu()
                == self.english_tokenizer.pad_token_id
            )[0][0]

            # Get generated tokens
            generated_tokens = english_tokens[
                0, idx_begin_generation : idx_begin_generation + actual_num_steps
            ]

        return {
            "generated_tokens": generated_tokens,
        }

    def postprocess(self, model_outputs: dict) -> str:
        generated_tokens = model_outputs["generated_tokens"]
        generated_sequence: str = self.english_tokenizer.decode(generated_tokens)
        return generated_sequence