app.py

import subprocess
subprocess.run('pip install flash-attn --no-build-isolation', env={'FLASH_ATTENTION_SKIP_CUDA_BUILD': "TRUE"}, shell=True)
subprocess.run('pip install -U timm', shell=True)
import spaces
import os
import torch
import argparse
import warnings
from rdkit import Chem
from rdkit.Chem import CanonSmiles
from rdkit.Chem import MolFromSmiles, MolToSmiles
from data_provider.pretrain_dm import PretrainDM
from data_provider.tune_dm import *
from model.opt_flash_attention import replace_opt_attn_with_flash_attn
from model.blip2_model import Blip2Model
from data_provider.data_utils import json_read, json_write
from data_provider.data_utils import smiles2data, reformat_smiles
import gradio as gr
from datetime import datetime

## disable online tokenizers parallelism to avoid deadlocks
os.environ["TOKENIZERS_PARALLELISM"] = "false"
## for pyg bug
warnings.filterwarnings('ignore', category=UserWarning, message='TypedStorage is deprecated')
## for A5000 gpus
torch.set_float32_matmul_precision('medium') # can be medium (bfloat16), high (tensorfloat32), highest (float32)

def smiles_split(string, separator='.'):
    string = str(string)
    mols = []
    for smi in string.split(separator):
        mol = MolFromSmiles(smi)
        if mol is None:
            continue  # Skip invalid SMILES strings
        mols.append(mol)

    parts = []
    current_part = []
    charge_count = 0

    for mol in mols:
        charge = Chem.GetFormalCharge(mol)
        if charge==0:
            if current_part:
                smiles = '.'.join([MolToSmiles(m) for m in current_part])
                smiles = CanonSmiles(smiles)
                parts.append(smiles)
                current_part = []
                charge_count = 0
            parts.append(MolToSmiles(mol))
        else:
            charge_count += charge
            current_part.append(mol)
            if charge_count == 0:
                smiles = '.'.join([MolToSmiles(m) for m in current_part])
                smiles = CanonSmiles(smiles)
                parts.append(smiles)
                current_part = []
                charge_count = 0
    if current_part:
        smiles = '.'.join([MolToSmiles(m) for m in current_part])
        smiles = CanonSmiles(smiles)
        parts.append(smiles)

    return parts

def get_args():
    parser = argparse.ArgumentParser()
    parser.add_argument('--filename', type=str, default="main")
    parser.add_argument('--seed', type=int, default=42, help='random seed')
    # MM settings
    parser.add_argument('--mode', type=str, default='pretrain', choices=['pretrain', 'ft', 'eval', 'pretrain_eval'])
    parser.add_argument('--strategy_name', type=str, default='mydeepspeed')
    parser.add_argument('--iupac_prediction', action='store_true', default=False)
    parser.add_argument('--ckpt_path', type=str, default=None)
    # parser = Trainer.add_argparse_args(parser)
    parser = Blip2Model.add_model_specific_args(parser)  # add model args
    parser = PretrainDM.add_model_specific_args(parser)
    parser.add_argument('--accelerator', type=str, default='gpu')
    parser.add_argument('--devices', type=str, default='0,1,2,3')
    parser.add_argument('--precision', type=str, default='bf16-mixed')
    parser.add_argument('--downstream_task', type=str, default='action', choices=['action', 'synthesis', 'caption', 'chebi'])
    parser.add_argument('--max_epochs', type=int, default=10)
    parser.add_argument('--enable_flash', action='store_true', default=False)
    parser.add_argument('--disable_graph_cache', action='store_true', default=False)
    parser.add_argument('--generate_restrict_tokens', action='store_true', default=False)
    parser.add_argument('--train_restrict_tokens', action='store_true', default=False)
    parser.add_argument('--smiles_type', type=str, default='default', choices=['default', 'canonical', 'restricted', 'unrestricted', 'r_smiles'])
    parser.add_argument('--accumulate_grad_batches', type=int, default=1)
    parser.add_argument('--tqdm_interval', type=int, default=50)
    parser.add_argument('--check_val_every_n_epoch', type=int, default=1)
    args = parser.parse_args()

    if args.enable_flash:
        replace_opt_attn_with_flash_attn()
    return args

app_config = {
    "init_checkpoint": "all_checkpoints/ckpt_tune_hybridFeb11_May31/last_converted.ckpt",
    "filename": "app",
    "opt_model": "facebook/galactica-1.3b",
    "num_workers": 4,
    "rxn_max_len": 512,
    "text_max_len": 512,
    "precision": "bf16-mixed",
    "max_inference_len": 512,
}

class InferenceRunner:
    def __init__(self, model, tokenizer, rxn_max_len, smi_max_len,
                 smiles_type='default', device='cuda', args=None):
        self.model = model
        self.rxn_max_len = rxn_max_len
        self.smi_max_len = smi_max_len
        self.tokenizer = tokenizer
        self.collater = Collater([], [])
        self.mol_ph = '<mol>' * args.num_query_token
        self.mol_token_id = tokenizer.mol_token_id
        self.is_gal = args.opt_model.find('galactica') >= 0
        self.collater = Collater([], [])
        self.device = device
        self.smiles_type = smiles_type
        self.args = args
        time_stamp = datetime.now().strftime("%Y.%m.%d-%H:%M")
        self.cache_dir = f'results/{self.args.filename}/{time_stamp}'
        os.makedirs(self.cache_dir, exist_ok=True)
    
    def make_query_dict(self, rxn_string):
        try:
            reactant, solvent, product = rxn_string.split('>')
            reactant = smiles_split(reactant)
            product = smiles_split(product)
            solvent = smiles_split(solvent) if solvent else []
            assert reactant and product
        except:
            raise gr.Error('Please input a valid reaction string')

        extracted_molecules = {product[0]: "$-1$"}
        for mol in reactant+solvent:
            extracted_molecules[mol] = f"${len(extracted_molecules)}$"

        result_dict = {}
        result_dict['time_stamp'] = datetime.now().strftime("%Y.%m.%d %H:%M:%S.%f")[:-3]
        result_dict['reaction_string'] = rxn_string
        result_dict['REACTANT'] = reactant
        result_dict['SOLVENT'] = solvent
        result_dict['CATALYST'] = []
        result_dict['PRODUCT'] = product
        result_dict['extracted_molecules'] = extracted_molecules
        return result_dict
    
    def save_prediction(self, result_dict):
        os.makedirs(self.cache_dir, exist_ok=True)
        result_id = result_dict['time_stamp']
        result_path = os.path.join(self.cache_dir, f'{result_id}.json')
        json_write(result_path, result_dict)

    def make_prompt(self, param_dict, smi_max_len=128):
        smiles_list = []
        prompt = ''
        prompt += 'Reactants: '
        smiles_wrapper = lambda x: reformat_smiles(x, smiles_type=self.smiles_type)[:smi_max_len]
        for smi in param_dict['REACTANT']:
            prompt += f'{param_dict["extracted_molecules"][smi]}: [START_SMILES]{smiles_wrapper(smi)}[END_SMILES] '
            smiles_list.append(smi)
            
        prompt += 'Product: '
        for smi in param_dict['PRODUCT']:
            prompt += f'{param_dict["extracted_molecules"][smi]}: [START_SMILES]{smiles_wrapper(smi)}[END_SMILES] '
            smiles_list.append(smi)

        if param_dict['CATALYST']:
            prompt += 'Catalysts: '
            for smi in param_dict['CATALYST']:
                if smi in param_dict["extracted_molecules"]:
                    prompt += f'{param_dict["extracted_molecules"][smi]}: [START_SMILES]{smiles_wrapper(smi)}[END_SMILES] '
                else:
                    prompt += f'[START_SMILES]{smiles_wrapper(smi)}[END_SMILES] '
                smiles_list.append(smi)

        if param_dict['SOLVENT']:
            prompt += 'Solvents: '
            for smi in param_dict['SOLVENT']:
                if smi in param_dict["extracted_molecules"]:
                    prompt += f'{param_dict["extracted_molecules"][smi]}: [START_SMILES]{smiles_wrapper(smi)}[END_SMILES] '
                else:
                    prompt += f'[START_SMILES]{smiles_wrapper(smi)}[END_SMILES] '
                smiles_list.append(smi)

        prompt += 'Action Squence: '
        return prompt, smiles_list

    def get_action_elements(self, rxn_dict):
        input_text, smiles_list = self.make_prompt(rxn_dict, self.smi_max_len)

        graph_list = []
        for smiles in smiles_list:
            graph_item = smiles2data(smiles)
            graph_list.append(graph_item)
        return graph_list, input_text

    @spaces.GPU
    @torch.no_grad()
    def predict(self, rxn_dict, temperature=1):
        graphs, prompt_tokens = self.tokenize(rxn_dict)
        self.model.blip2opt = self.model.blip2opt.to('cuda')
        result_dict = rxn_dict
        samples = {'graphs': graphs, 'prompt_tokens': prompt_tokens}
        prediction = self.model.blip2opt.generate(
            samples,
            do_sample=self.args.do_sample,
            num_beams=self.args.num_beams,
            max_length=self.args.max_inference_len,
            min_length=self.args.min_inference_len,
            num_captions=self.args.num_generate_captions,
            temperature=temperature,
            use_graph=True
        )[0]
        for k, v in result_dict['extracted_molecules'].items():
            prediction = prediction.replace(v, k)
        result_dict['prediction'] = prediction
        return result_dict
    
    def tokenize(self, rxn_dict):
        graph_list, input_text = self.get_action_elements(rxn_dict)
        if graph_list:
            graphs = self.collater(graph_list).to(self.device)
        input_prompt = smiles_handler(input_text, self.mol_ph, self.is_gal)[0]

        ## deal with prompt
        self.tokenizer.padding_side = 'left'
        input_prompt_tokens = self.tokenizer(input_prompt, 
                                              truncation=True, 
                                              padding='max_length', 
                                              add_special_tokens=True,
                                              max_length=self.rxn_max_len, 
                                              return_tensors='pt', 
                                              return_attention_mask=True).to(self.device)
        is_mol_token = input_prompt_tokens.input_ids == self.mol_token_id
        input_prompt_tokens['is_mol_token'] = is_mol_token
        return graphs, input_prompt_tokens

def main(args):
    device = torch.device('cuda')
    # model
    if args.init_checkpoint:
        model = Blip2Model(args).to(device)
        ckpt = torch.load(args.init_checkpoint, map_location='cpu')
        model.load_state_dict(ckpt['state_dict'], strict=False)
        print(f"loaded model from {args.init_checkpoint}")
    else:
        model = Blip2Model(args).to(device)
    model.eval()

    print('total params:', sum(p.numel() for p in model.parameters()))

    if args.opt_model.find('galactica') >= 0 or args.opt_model.find('t5') >= 0:
        tokenizer = model.blip2opt.opt_tokenizer
    elif args.opt_model.find('llama') >= 0 or args.opt_model.find('vicuna') >= 0:
        tokenizer = model.blip2opt.llm_tokenizer
    else:
        raise NotImplementedError

    infer_runner = InferenceRunner(
        model=model,
        tokenizer=tokenizer,
        rxn_max_len=args.rxn_max_len,
        smi_max_len=args.smi_max_len,
        device=device,
        args=args
    )
    example_inputs = json_read('demo.json')
    example_inputs = [[e] for e in example_inputs]

    def online_chat(reaction_string, temperature=1):
        data_item = infer_runner.make_query_dict(reaction_string)
        result = infer_runner.predict(data_item, temperature=temperature)
        infer_runner.save_prediction(result)
        prediction = result['prediction'].replace(' ; ', ' ;\n')
        return prediction
    
    with gr.Blocks(css="""
            .center { display: flex; justify-content: center; }
        """) as demo:
        gr.HTML(
        """
        <center><h1><b>ReactXT</b></h1></center>
        <p style="font-size:20px; font-weight:bold;">This is the demo page of our ACL 2024 paper 
        <i>ReactXT: Understanding Molecular “Reaction-ship” via Reaction-Contextualized Molecule-Text Pretraining.</i></p>
        <center><img src="/file=./figures/frameworks.jpg" alt="Framework" style="width:1000px;"></center>
        <p style="font-size:16px;"> Please input one chemical reaction below, and we will generate the predicted experimental procedure.</p>
        <p style="font-size:16px;"> The reaction should be in form of <b>Reactants>Reagents>Product</b>.</p>
        """)

        reaction_string = gr.Textbox(placeholder="Input one reaction", label='Input Reaction')
        gr.Examples(example_inputs, [reaction_string,], fn=online_chat, label='Example Reactions')
        with gr.Row():
            btn = gr.Button("Submit")
            clear_btn = gr.Button("Clear")
        temperature = gr.Slider(0.1, 1, value=1, label='Temperature')
        with gr.Row():
            out = gr.Textbox(label="ReactXT's Output", placeholder="Predicted experimental procedure")
        btn.click(fn=online_chat, inputs=[reaction_string, temperature], outputs=[out])
        clear_btn.click(fn=lambda:("", ""), inputs=[], outputs=[reaction_string, out])

    demo.launch(allowed_paths=['/home/user/app/figures/'])



if __name__ == '__main__':
    args = get_args()
    vars(args).update(app_config)
    main(args)