import gradio as gr from mammal.examples.dti_bindingdb_kd.task import DtiBindingdbKdTask from mammal.keys import * from mammal.model import Mammal from mammal_demo.demo_framework import MammalObjectBroker, MammalTask class DtiTask(MammalTask): def __init__(self, model_dict): super().__init__(name="Drug-Target Binding Affinity", model_dict=model_dict) self.description = "Drug-Target Binding Affinity (tdi)" self.examples = { "target_seq": "NLMKRCTRGFRKLGKCTTLEEEKCKTLYPRGQCTCSDSKMNTHSCDCKSC", "drug_seq": "CC(=O)NCCC1=CNc2c1cc(OC)cc2", } self.markup_text = """ # Mammal based Target-Drug binding affinity demonstration Given a protein sequence and a drug (in SMILES), estimate the binding affinity. """ 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) sample_dict = DtiBindingdbKdTask.data_preprocessing( sample_dict=sample_dict, tokenizer_op=model_holder.tokenizer_op, target_sequence_key="target_seq", drug_sequence_key="drug_seq", norm_y_mean=None, norm_y_std=None, device=model_holder.model.device, ) return sample_dict def run_model(self, sample_dict, model: Mammal): # Generate Prediction batch_dict = model.forward_encoder_only([sample_dict]) return batch_dict def decode_output(self, batch_dict, model_holder): # Get output batch_dict = DtiBindingdbKdTask.process_model_output( batch_dict, scalars_preds_processed_key="model.out.dti_bindingdb_kd", norm_y_mean=5.79384684128215, norm_y_std=1.33808027428196, ) ans = ( "model.out.dti_bindingdb_kd", float(batch_dict["model.out.dti_bindingdb_kd"][0]), ) return ans def create_and_run_prompt(self, model_name, target_seq, drug_seq): model_holder = self.model_dict[model_name] inputs = { "target_seq": target_seq, "drug_seq": drug_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, model_holder=model_holder) return res def create_demo(self, model_name_widget): # """ # ### Using the model from # ```{model} ``` # """ with gr.Group() as demo: gr.Markdown(self.markup_text) with gr.Row(): target_textbox = gr.Textbox( label="target sequence", # info="standard", interactive=True, lines=3, value=self.examples["target_seq"], ) drug_textbox = gr.Textbox( label="Drug sequance (in SMILES)", # info="standard", interactive=True, lines=3, value=self.examples["drug_seq"], ) with gr.Row(): run_mammal = gr.Button( "Run Mammal prompt for Protein-Protein Interaction", variant="primary", ) with gr.Row(): prompt_box = gr.Textbox(label="Mammal prompt", lines=5) with gr.Row(): decoded = gr.Textbox(label="Mammal output key") run_mammal.click( fn=self.create_and_run_prompt, inputs=[model_name_widget, target_textbox, drug_textbox], outputs=[prompt_box, decoded, gr.Number(label="binding affinity")], ) demo.visible = False return demo