import gradio as gr from fuse.data.tokenizers.modular_tokenizer.op import ModularTokenizerOp from mammal.examples.protein_solubility.task import ProteinSolubilityTask from mammal.keys import ( CLS_PRED, ENCODER_INPUTS_STR, SCORES, ) from mammal.model import Mammal from mammal_demo.demo_framework import MammalObjectBroker, MammalTask class PsTask(MammalTask): def __init__(self, model_dict): super().__init__(name="Protein Solubility", model_dict=model_dict) self.description = "Protein Solubility (PS)" self.examples = { "protein_seq": "LLQTGIHVRVSQPSL", } self.markup_text = """ # Mammal based protein solubility estimation Given the protein sequance, estimate if it's soluble or insoluble. """ 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_inputs) # shallow copy sample_dict = ProteinSolubilityTask.data_preprocessing( sample_dict=sample_dict, protein_sequence_key="protein_seq", tokenizer_op=model_holder.tokenizer_op, device=model_holder.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 def decode_output(self, batch_dict, tokenizer_op: ModularTokenizerOp) -> list: """ Extract predicted class and scores """ ans_dict = ProteinSolubilityTask.process_model_output( tokenizer_op=tokenizer_op, decoder_output=batch_dict[CLS_PRED][0], decoder_output_scores=batch_dict[SCORES][0], ) ans = [ tokenizer_op._tokenizer.decode(batch_dict[CLS_PRED][0]), ans_dict["pred"], ans_dict["not_normalized_scores"].item(), ans_dict["normalized_scores"].item(), ] return ans def create_and_run_prompt(self, model_name, protein_seq): model_holder = self.model_dict[model_name] inputs = { "protein_seq": protein_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(): protein_textbox = gr.Textbox( label="Protein sequance", # info="standard", interactive=True, lines=3, value=self.examples["protein_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") with gr.Column(): non_norm_score = gr.Number(label="Non normelized score") norm_score = gr.Number(label="Normelized score") run_mammal.click( fn=self.create_and_run_prompt, inputs=[model_name_widget, protein_textbox], outputs=[ prompt_box, decoded, predicted_class, non_norm_score, norm_score, ], ) demo.visible = False return demo