train_eval_utils.py

# train_eval_utils.py
# Helpers for training and benchmarking
# Feel free to adjust these setup acc. to your use case
# - gbyuvd

import os
import math
import torch
from torch.utils.data import DataLoader, IterableDataset
from tqdm import tqdm
import json
import random
import pandas as pd
from sklearn.model_selection import train_test_split
from ranger21 import Ranger21
from datasets import load_dataset

# ----------------------------
# CSV Logger
# ----------------------------
import csv

class CSVLogger:
    def __init__(self, filename, fieldnames):
        self.filename = filename
        self.fieldnames = fieldnames
        self._initialized = False

    def log(self, row_dict):
        if not self._initialized:
            self._init_file()
        with open(self.filename, 'a', newline='', encoding='utf-8') as f:
            writer = csv.DictWriter(f, fieldnames=self.fieldnames)
            writer.writerow(row_dict)

    def _init_file(self):
        with open(self.filename, 'w', newline='', encoding='utf-8') as f:
            writer = csv.DictWriter(f, fieldnames=self.fieldnames)
            writer.writeheader()
        self._initialized = True

# ----------------------------
# Streaming dataset
# ----------------------------
class SelfiesStreamingDataset(IterableDataset):
    def __init__(self, csv_file, tokenizer, max_seq_len=512, mask_prob=0.15, global_token_ids=None):
        self.tokenizer = tokenizer
        self.max_seq_len = max_seq_len
        self.mask_prob = mask_prob
        self.global_token_ids = global_token_ids or []

        dataset = load_dataset("csv", data_files=csv_file, split="train", streaming=True)
        dataset = dataset.shuffle(seed=42, buffer_size=10000)
        self.dataset_iter = iter(dataset)

        self.mask_id = tokenizer.mask_token_id
        self.pad_id = tokenizer.pad_token_id

    def __iter__(self):
        for example in self.dataset_iter:
            smiles = example["SMILES"]
            enc = self.tokenizer(smiles, truncation=True, max_length=self.max_seq_len, return_tensors=None)

            input_ids = enc["input_ids"]
            attention_mask = enc["attention_mask"]
            labels = input_ids.copy()

            vocab_size = len(self.tokenizer)
            for i in range(len(input_ids)):
                if input_ids[i] in self.global_token_ids:
                    continue
                if random.random() < self.mask_prob:
                    rand = random.random()
                    if rand < 0.8:
                        input_ids[i] = self.mask_id
                    elif rand < 0.9:
                        input_ids[i] = random.randint(0, vocab_size - 1)
                        while input_ids[i] in self.global_token_ids:
                            input_ids[i] = random.randint(0, vocab_size - 1)
                    else:
                        pass

            global_positions = [idx for idx, tid in enumerate(input_ids) if tid in self.global_token_ids]

            yield (
                torch.tensor(input_ids, dtype=torch.long),
                torch.tensor(attention_mask, dtype=torch.long),
                torch.tensor(labels, dtype=torch.long),
                global_positions,
            )


def collate_fn(batch):
    input_ids_list, attention_mask_list, labels_list, global_positions_list = zip(*batch)
    input_ids = torch.nn.utils.rnn.pad_sequence(input_ids_list, batch_first=True, padding_value=0)
    attention_mask = torch.nn.utils.rnn.pad_sequence(attention_mask_list, batch_first=True, padding_value=0)
    labels = torch.nn.utils.rnn.pad_sequence(labels_list, batch_first=True, padding_value=-100)
    return input_ids, attention_mask, labels, global_positions_list


def get_dataloader(csv_file, tokenizer, batch_size=16, max_seq_len=512, mask_prob=0.15, global_token_ids=None):
    dataset = SelfiesStreamingDataset(csv_file, tokenizer, max_seq_len, mask_prob, global_token_ids)
    return DataLoader(dataset, batch_size=batch_size, collate_fn=collate_fn)


# ----------------------------
# Dataset splitting
# ----------------------------
def prepare_train_val_test_split(full_csv, train_csv, val_csv, test_csv,

                                 val_test_size=0.3, test_size_ratio=0.5, random_state=42):
    if all(os.path.exists(f) for f in [train_csv, val_csv, test_csv]):
        print(f"  Train/val/test splits already exist. Skipping split.")
        train_count = sum(1 for _ in open(train_csv, encoding='utf-8')) - 1
        val_count = sum(1 for _ in open(val_csv, encoding='utf-8')) - 1
        test_count = sum(1 for _ in open(test_csv, encoding='utf-8')) - 1
        return train_count, val_count, test_count

    df = pd.read_csv(full_csv)
    train_df, val_test_df = train_test_split(df, test_size=val_test_size, random_state=random_state)
    val_df, test_df = train_test_split(val_test_df, test_size=test_size_ratio, random_state=random_state)

    train_df.to_csv(train_csv, index=False)
    val_df.to_csv(val_csv, index=False)
    test_df.to_csv(test_csv, index=False)

    return len(train_df), len(val_df), len(test_df)


# ----------------------------
# Model call helper
# ----------------------------
import inspect

def call_model(model, input_ids, attention_mask, labels, global_positions):
    # Prepare base args
    model_kwargs = {
        "input_ids": input_ids,
        "attention_mask": attention_mask,
        "labels": labels,
        "output_attentions": False,
    }

    # Check if model's forward method accepts 'global_positions'
    sig = inspect.signature(model.forward)
    if "global_positions" in sig.parameters:
        # Convert global_positions to tensor if needed (for RougeBERT)
        if isinstance(global_positions, (tuple, list)):
            if len(global_positions) == 0:
                global_positions = None
            else:
                max_len = max(len(g) for g in global_positions)
                padded = [
                    list(g) + [-1] * (max_len - len(g)) if isinstance(g, (list, tuple)) else [g] + [-1] * (max_len - 1)
                    for g in global_positions
                ]
                global_positions = torch.tensor(padded, dtype=torch.long, device=input_ids.device)
        elif isinstance(global_positions, torch.Tensor):
            pass  # already good
        elif global_positions is None:
            pass
        else:
            raise TypeError(f"Unsupported type for global_positions: {type(global_positions)}")

        model_kwargs["global_positions"] = global_positions

    # Call model
    return model(**model_kwargs)


# ----------------------------
# Metrics
# ----------------------------
def compute_metrics(logits, labels):
    """Compute MLM loss sum, correct preds, total tokens."""
    loss_fn = torch.nn.CrossEntropyLoss(ignore_index=-100, reduction="sum")

    vocab_size = logits.size(-1)
    logits_flat = logits.view(-1, vocab_size)
    labels_flat = labels.view(-1)

    loss = loss_fn(logits_flat, labels_flat)
    count = (labels_flat != -100).sum().item()

    preds = torch.argmax(logits_flat, dim=-1)
    correct = ((preds == labels_flat) & (labels_flat != -100)).sum().item()

    return loss.item(), correct, count


def evaluate_model(model, dataloader, device):
    model.eval()
    total_loss, total_correct, total_count = 0.0, 0, 0

    with torch.no_grad():
        for input_ids, attention_mask, labels, global_positions in dataloader:
            input_ids, attention_mask, labels = (
                input_ids.to(device),
                attention_mask.to(device),
                labels.to(device),
            )
            outputs = call_model(model, input_ids, attention_mask, labels, global_positions)
            logits = outputs.logits
            loss, correct, count = compute_metrics(logits, labels)
            total_loss += loss
            total_correct += correct
            total_count += count

    avg_loss = total_loss / total_count if total_count > 0 else float("inf")
    perplexity = math.exp(avg_loss) if avg_loss < 20 else float("inf")
    accuracy = total_correct / total_count if total_count > 0 else 0.0

    return avg_loss, perplexity, accuracy


# ----------------------------
# Training + Evaluation loop
# ----------------------------
def train_and_eval(

    model,

    tokenizer,

    train_csv,

    val_csv,

    test_csv,

    config,

    run_name="experiment",

    batch_size=16,

    grad_accum=4,

    num_epochs=1,

    learning_rate=3e-6,

    mask_prob=0.15,

    max_seq_len=None,

    patience=10,

    save_dir="./checkpoints",

):
    # pick max seq length
    if max_seq_len is None:
        if hasattr(config, "max_seq"):
            max_seq_len = config.max_seq
        elif hasattr(config, "max_position_embeddings"):
            max_seq_len = config.max_position_embeddings
        else:
            max_seq_len = 512

    device = "cuda" if torch.cuda.is_available() else "cpu"
    model.to(device)

    global_token_ids = [tokenizer.bos_token_id, tokenizer.eos_token_id, tokenizer.mask_token_id]

    # Dataset counts
    train_count = sum(1 for _ in open(train_csv, encoding="utf-8")) - 1
    val_count = sum(1 for _ in open(val_csv, encoding="utf-8")) - 1
    test_count = sum(1 for _ in open(test_csv, encoding="utf-8")) - 1

    train_steps_per_epoch = max(1, train_count // batch_size)
    optimizer_steps_per_epoch = max(1, train_steps_per_epoch // grad_accum)
    val_steps_total = max(1, val_count // batch_size)
    test_steps_total = max(1, test_count // batch_size)

    print(f"  Train steps/epoch: {train_steps_per_epoch}")
    print(f"  Optimizer steps/epoch: {optimizer_steps_per_epoch}")
    print(f"  Val steps total: {val_steps_total}")
    print(f"  Test steps total: {test_steps_total}")

    # Optimizer
    optimizer = Ranger21(
        model.parameters(),
        lr=learning_rate,
        weight_decay=0.01,
        use_adabelief=True,
        use_warmup=True,
        use_madgrad=True,
        num_epochs=num_epochs,
        warmdown_active=False,
        num_batches_per_epoch=optimizer_steps_per_epoch,
    )

    os.makedirs(save_dir, exist_ok=True)
    with open(os.path.join(save_dir, f"{run_name}_config.json"), "w") as f:
        if hasattr(config, "to_dict"):
            json.dump(config.to_dict(), f, indent=2)
        else:
            json.dump(config.__dict__, f, indent=2)

    best_val_loss = float("inf")
    patience_counter = 0
    final_val_loss, final_val_perplexity, final_val_acc = None, None, None

    #   Initialize unified CSV logger
    metrics_log_path = os.path.join(save_dir, f"{run_name}_metrics.csv")
    metrics_logger = CSVLogger(metrics_log_path, ["epoch", "step", "train_loss", "val_loss", "ppl", "mlm_acc"])

    for epoch in range(num_epochs):
        model.train()
        train_loader = get_dataloader(train_csv, tokenizer, batch_size, max_seq_len, mask_prob, global_token_ids)

        running_loss = 0.0
        optimizer.zero_grad()

        pbar = tqdm(enumerate(train_loader), desc=f"{run_name} | Epoch {epoch+1}/{num_epochs}", total=train_steps_per_epoch)
        for step, (input_ids, attention_mask, labels, global_positions) in pbar:
            input_ids, attention_mask, labels = input_ids.to(device), attention_mask.to(device), labels.to(device)

            outputs = call_model(model, input_ids, attention_mask, labels, global_positions)
            loss = outputs.loss / grad_accum
            loss.backward()
            running_loss += loss.item()

            if (step + 1) % grad_accum == 0:
                optimizer.step()
                optimizer.zero_grad()

            #   Log every 10 steps
            if (step + 1) % 10 == 0:
                avg_loss = running_loss / 10
                running_loss = 0.0

                #   Validation every 10 steps
                val_loader = get_dataloader(val_csv, tokenizer, batch_size, max_seq_len, mask_prob, global_token_ids)
                val_loss, val_perplexity, val_acc = evaluate_model(model, val_loader, device)

                #   Log unified metrics
                metrics_logger.log({
                    "epoch": epoch + 1,
                    "step": step + 1,
                    "train_loss": avg_loss,
                    "val_loss": val_loss,
                    "ppl": val_perplexity,
                    "mlm_acc": val_acc
                })

                #   Print to console
                print(f"\n[Step {step+1}] Train Loss: {avg_loss:.4f} | "
                      f"Val Loss: {val_loss:.4f} | Perplexity: {val_perplexity:.4f} | MLM Acc: {val_acc:.2%}")

                #   Save best model
                if val_loss < best_val_loss:
                    best_val_loss = val_loss
                    patience_counter = 0
                    model.save_pretrained(os.path.join(save_dir, f"{run_name}_best"))
                    tokenizer.save_pretrained(save_dir)
                else:
                    patience_counter += 1
                    if patience_counter >= patience:
                        print(" Early stopping triggered")
                        break

                model.train()  # back to train mode after val

        if patience_counter >= patience:
            break

    # Final test evaluation
    test_loader = get_dataloader(test_csv, tokenizer, batch_size, max_seq_len, mask_prob, global_token_ids)
    test_loss, test_perplexity, test_acc = evaluate_model(model, test_loader, device)

    print(f"\n  Final Test | Loss: {test_loss:.4f} | "
          f"Perplexity: {test_perplexity:.4f} | MLM Acc: {test_acc:.2%}")

    model.save_pretrained(os.path.join(save_dir, f"{run_name}_final"))
    tokenizer.save_pretrained(save_dir)

    return {
        "best_val_loss": best_val_loss,
        "final_val_loss": final_val_loss,
        "final_val_perplexity": final_val_perplexity,
        "final_val_acc": final_val_acc,
        "test_loss": test_loss,
        "test_perplexity": test_perplexity,
        "test_acc": test_acc,

    }