generate_condition.py

import pandas as pd
import argparse
from utils import set_seed
import numpy as np
import wandb
import os
import torch
import torch.nn as nn
from torch.utils.data import DataLoader
from torch.nn import functional as F
from torch.nn.utils.rnn import pad_sequence
from torch.cuda.amp import GradScaler
from transformers import AutoTokenizer
from model import GPT, GPTConfig
# from trainer import Trainer, TrainerConfig
from dataset import Mol3DDataset, SimpleTokenizer, SubChTokenizer
import math
import re
import json
import random
from collections import Counter
from tqdm import tqdm


def load_model(model_path, config):
    model = GPT(config)
    model.load_state_dict(torch.load(model_path, map_location='cpu'), strict=True)
    model.eval()
    return model


def load_tokenizer(tokenizer_path,max_length,tokenizer_type='simple'):
    tokenizer = SimpleTokenizer(max_length)
    if tokenizer_type == 'subch':
        tokenizer = SubChTokenizer(max_length)
    tokenizer.load_vocab(tokenizer_path)
    return tokenizer


def get_first_token_distribution(train_data_path):
    with open(train_data_path, 'r') as file:
        data = file.readlines()
    first_tokens = [line.strip().split()[0] for line in data if len(line.strip())]
    token_counts = Counter(first_tokens)
    total = sum(token_counts.values())
    token_probs = {token: count / total for token, count in token_counts.items()}
    return token_probs


def sample_first_token(token_probs):
    tokens, probs = zip(*token_probs.items())
    first_token = random.choices(tokens, weights=probs)[0]
    return first_token

def top_k_logits(logits, k):
    values, _ = torch.topk(logits, k)
    min_values = values[:, -1].unsqueeze(1).expand_as(logits)
    return torch.where(logits < min_values, torch.full_like(logits, float('-inf')), logits)

def sample_from_logits(logits, top_k, temp=1.0):
    logits = top_k_logits(logits, top_k)
    probabilities = F.softmax(logits / temp, dim=-1)
    next_token = torch.multinomial(probabilities, 1, replacement=True)
    return next_token

def generate_sample(model, tokenizer, first_tokens, max_length, top_k=100, temp=1.0, beam_size=None):
    model.eval()
    first_token_ids = [tokenizer.generation_encode(token) for token in first_tokens]
    input_ids = pad_sequence([torch.tensor(ids, dtype=torch.long) for ids in first_token_ids], batch_first=True, padding_value=tokenizer.vocab["<pad>"]).cuda()
    init_len = input_ids.size(1)
    with torch.no_grad():
        for _ in range(max_length - init_len):
            output = model(input_ids)
            next_token_logits = output[0][:, -1, :]
            next_token = sample_from_logits(next_token_logits, top_k, temp=temp)
            input_ids = torch.cat([input_ids, next_token], dim=1)

            # Check if all sequences in the batch have reached the end token or pad token
            if all(token.item() in [tokenizer.vocab["</s>"], tokenizer.vocab["<pad>"]] for token in next_token):
                break

    return [tokenizer.decode(ids) for ids in input_ids]


if __name__ == '__main__':
    parser = argparse.ArgumentParser()

    parser.add_argument('--run_name', type=str,
                        help="name for wandb run", required=False)
    parser.add_argument('--debug', action='store_true',
                        default=False, help='debug')
    # in moses dataset, on average, there are only 5 molecules per scaffold
    parser.add_argument('--scaffold', action='store_true',
                        default=False, help='condition on scaffold')
    parser.add_argument('--lstm', action='store_true',
                        default=False, help='use lstm for transforming scaffold')
    parser.add_argument('--data_name', type=str, default='moses2',
                        help="name of the dataset to train on", required=False)
    # parser.add_argument('--property', type=str, default = 'qed', help="which property to use for condition", required=False)
    parser.add_argument('--props', nargs="+", default=['qed'],
                        help="properties to be used for condition", required=False)
    parser.add_argument('--num_props', type=int, default = 0, help="number of properties to use for condition", required=False)
    # parser.add_argument('--prop1_unique', type=int, default = 0, help="unique values in that property", required=False)
    parser.add_argument('--n_layer', type=int, default=8,
                        help="number of layers", required=False)
    parser.add_argument('--n_head', type=int, default=8,
                        help="number of heads", required=False)
    parser.add_argument('--n_embd', type=int, default=768,
                        help="embedding dimension", required=False)
    parser.add_argument('--max_epochs', type=int, default=30,
                        help="total epochs", required=False)
    parser.add_argument('--batch_size', type=int, default=80,
                        help="batch size", required=False)
    parser.add_argument('--sample_repeats', type=int, default=12000,
                        help="number of generate samples", required=False)
    parser.add_argument('--top_k', type=int, default=100,
                        help="top_k for sampling", required=False)
    parser.add_argument('--temp', type=float, default=1.0,
                        help="sampling temperature", required=False)
    parser.add_argument('--tokenizer', type=str, default='simple',
                        help="name of the tokenizer", required=False)
    parser.add_argument('--num_workers', type=int, default=8,
                        help="number of workers for data loaders", required=False)
    parser.add_argument('--learning_rate', type=float,
                        default=1e-4, help="learning rate", required=False)
    parser.add_argument('--lstm_layers', type=int, default=0,
                        help="number of layers in lstm", required=False)
    parser.add_argument('--max_len', type=int, default=512,
                        help="max_len", required=False)
    parser.add_argument('--epoch', type=int, default=0,
                        help="saved model epoch", required=False)
    parser.add_argument('--root_path', default='QM9_seq/spherical_seq',
                        help="Path to the root data directory", required=False)
    parser.add_argument('--output_tokenizer_dir', default='spherical_seq/tokenizer',
                        help="Path to the saved tokenizer directory", required=False)
    parser.add_argument('--conditions_path', default=None,
                        help="Path to the generation condition", required=False)
    parser.add_argument('--save_path', default='gpt_p1',
                        help="Path to the generation file dir", required=False)

    args = parser.parse_args()

    set_seed(56)

    os.environ["WANDB_MODE"] = "dryrun"

    max_len = args.max_len
    tokenizer_path = args.output_tokenizer_dir + "/vocab.json"
    print(tokenizer_path)
    print("tokenizer:")
    tokenizer = load_tokenizer(tokenizer_path, max_len, args.tokenizer)
    print(tokenizer.get_vocab())  # Print vocabulary
    vocab_size = tokenizer.get_vocab_size()

    if args.conditions_path is not None:
        isconditional = True
    else:
        isconditional = False

    mconf = GPTConfig(vocab_size, max_len, num_props=args.num_props,  # args.num_props,
                          n_layer=args.n_layer, n_head=args.n_head, n_embd=args.n_embd, scaffold=args.scaffold,
                          scaffold_maxlen=max_len, lstm=args.lstm, lstm_layers=args.lstm_layers,
                          isconditional=isconditional)
    print("loading model")
    # model = GPT(mconf)
    if args.epoch == 0:
        model_path = f'cond_gpt/weights/{args.run_name}.pt'
        gen_name = f'{args.run_name}'
    else:
        model_path = f'cond_gpt/weights/{args.run_name}_ep{args.epoch}.pt'
        gen_name = f'{args.run_name}_ep{args.epoch}_top{args.top_k}_temp{args.temp}'
    train_data_path = args.root_path + '.txt'

    # Load model and tokenizer
    model = load_model(model_path, mconf).cuda()
    print("loaded model")
    print('total params:', sum(p.numel() for p in model.parameters()))

    if args.conditions_path is not None:
        print("loading conditions")
        with open(args.conditions_path, 'r') as file:
            data = file.readlines()
        first_tokens = [line.strip() for line in data]
        print('loaded conditions')
    else:
        print("missing conditions")

    num_samples = args.sample_repeats  # Number of samples to generate for each first token

    os.makedirs(args.save_path, exist_ok=True)
    print(f'Saving samples to: {args.save_path}')
    # Generate samples for each first token and write to separate files
    for idx, first_token in enumerate(first_tokens):
        batch_first_tokens = [first_token for _ in range(num_samples)]
        samples = generate_sample(model, tokenizer, batch_first_tokens, max_len, top_k=args.top_k, temp=args.temp, beam_size=None)
        print(f'Completed {idx} with {len(samples)} samples')
        print(samples[0])
        with open(f'{args.save_path}/gen_mol_{idx}.txt', 'w') as f:
            for sample in samples:
                if sample.startswith(first_token):
                    gen_sample = sample[len(first_token):]
                    f.write(gen_sample + '\n')
                else:
                    print(f"{sample} does not start with {first_token}")