code/scripts/evaluate_molt5.py

#!/usr/bin/env python
"""
Comprehensive evaluation script for MolT5 RAG model.
Computes multiple metrics including Tanimoto similarity, validity, exact match, etc.
"""
from __future__ import annotations

import argparse
import json
import sys
from pathlib import Path
from typing import Dict, List, Tuple

import numpy as np
import torch
from tqdm import tqdm

ROOT = Path(__file__).resolve().parents[1]
if str(ROOT) not in sys.path:
    sys.path.insert(0, str(ROOT))

from transformers import AutoModelForSeq2SeqLM, AutoTokenizer

from spec_rag.io import load_embeddings
from spec_rag.molt5_with_embeddings import MolT5WithEmbeddings


def load_jsonl(path: Path) -> List[dict]:
    """Load JSONL file."""
    data = []
    with open(path, "r") as f:
        for line in f:
            line = line.strip()
            if line:
                data.append(json.loads(line))
    return data


def compute_molecular_metrics(
    predictions: List[str], 
    ground_truths: List[str]
) -> Dict[str, float]:
    """
    Compute comprehensive molecular generation metrics.
    
    Returns:
        Dictionary with metrics:
        - exact_match: Raw string exact match
        - canonical_exact_match: After canonicalization
        - validity_rate: Percentage of valid SMILES
        - tanimoto_similarity: Mean Tanimoto similarity
        - tanimoto_similarity_valid: Mean Tanimoto (only valid predictions)
        - top1_tanimoto: Mean max Tanimoto in top-1
        - top10_tanimoto: Mean max Tanimoto in top-10 (if multiple predictions)
    """
    try:
        from rdkit import Chem
        from rdkit.Chem import AllChem, DataStructs
        from rdkit import rdBase
        rdBase.DisableLog("rdApp.*")
    except ImportError:
        raise ImportError("RDKit is required for molecular metrics. Install with: conda install -c conda-forge rdkit")
    
    if len(predictions) != len(ground_truths):
        raise ValueError(f"Mismatch: {len(predictions)} predictions vs {len(ground_truths)} ground truths")
    
    exact_matches = 0
    canonical_matches = 0
    valid_count = 0
    tanimoto_sum = 0.0
    tanimoto_valid_sum = 0.0
    valid_predictions = []
    valid_ground_truths = []
    
    # For detailed analysis
    tanimoto_scores = []
    validity_flags = []
    
    for pred, gt in zip(predictions, ground_truths):
        pred = pred.strip()
        gt = gt.strip()
        
        # Exact match (raw string)
        if pred == gt:
            exact_matches += 1
        
        # Try to parse as molecules
        try:
            mol_pred = Chem.MolFromSmiles(pred)
            mol_gt = Chem.MolFromSmiles(gt)
            
            if mol_pred is not None:
                valid_count += 1
                validity_flags.append(1)
                pred_canon = Chem.MolToSmiles(mol_pred, canonical=True)
                valid_predictions.append(mol_pred)
            else:
                validity_flags.append(0)
                pred_canon = None
            
            if mol_gt is not None:
                gt_canon = Chem.MolToSmiles(mol_gt, canonical=True)
                valid_ground_truths.append(mol_gt)
            else:
                gt_canon = None
            
            # Canonical exact match
            if pred_canon and gt_canon and pred_canon == gt_canon:
                canonical_matches += 1
            
            # Tanimoto similarity
            if mol_pred is not None and mol_gt is not None:
                fp_pred = AllChem.GetMorganFingerprintAsBitVect(mol_pred, radius=2, nBits=2048)
                fp_gt = AllChem.GetMorganFingerprintAsBitVect(mol_gt, radius=2, nBits=2048)
                tanimoto = DataStructs.TanimotoSimilarity(fp_pred, fp_gt)
                tanimoto_sum += tanimoto
                tanimoto_scores.append(tanimoto)
                if mol_pred is not None:
                    tanimoto_valid_sum += tanimoto
            else:
                tanimoto_scores.append(0.0)
                
        except Exception as e:
            # Invalid SMILES or parsing error
            validity_flags.append(0)
            tanimoto_scores.append(0.0)
            continue
    
    n = len(predictions)
    metrics = {
        "exact_match": exact_matches / n if n > 0 else 0.0,
        "canonical_exact_match": canonical_matches / n if n > 0 else 0.0,
        "validity_rate": valid_count / n if n > 0 else 0.0,
        "tanimoto_similarity": tanimoto_sum / n if n > 0 else 0.0,
        "tanimoto_similarity_valid": tanimoto_valid_sum / valid_count if valid_count > 0 else 0.0,
        "n_total": n,
        "n_valid": valid_count,
    }
    
    # Additional statistics
    if tanimoto_scores:
        metrics["tanimoto_mean"] = np.mean(tanimoto_scores)
        metrics["tanimoto_std"] = np.std(tanimoto_scores)
        metrics["tanimoto_median"] = np.median(tanimoto_scores)
        metrics["tanimoto_min"] = np.min(tanimoto_scores)
        metrics["tanimoto_max"] = np.max(tanimoto_scores)
        
        # Distribution analysis
        metrics["tanimoto_ge_0.9"] = sum(1 for t in tanimoto_scores if t >= 0.9) / n
        metrics["tanimoto_ge_0.8"] = sum(1 for t in tanimoto_scores if t >= 0.8) / n
        metrics["tanimoto_ge_0.7"] = sum(1 for t in tanimoto_scores if t >= 0.7) / n
        metrics["tanimoto_ge_0.5"] = sum(1 for t in tanimoto_scores if t >= 0.5) / n
        metrics["tanimoto_ge_0.3"] = sum(1 for t in tanimoto_scores if t >= 0.3) / n
    
    return metrics


def generate_predictions(
    model,
    tokenizer,
    inputs: List[str],
    spectrum_embeddings: torch.Tensor | None = None,
    max_length: int = 512,
    num_beams: int = 1,
    batch_size: int = 8,
) -> List[str]:
    """Generate predictions in batches with spectrum embeddings."""
    predictions = []
    
    for i in tqdm(range(0, len(inputs), batch_size), desc="Generating predictions"):
        batch = inputs[i:i + batch_size]
        batch_embeddings = None
        if spectrum_embeddings is not None:
            batch_embeddings = spectrum_embeddings[i:i + batch_size].to(model.device)
        
        # Tokenize inputs
        encoded = tokenizer(
            batch,
            return_tensors="pt",
            padding=True,
            truncation=True,
            max_length=max_length,
        ).to(model.device)
        
        # Generate
        with torch.no_grad():
            if batch_embeddings is not None:
                # Use model's generate with embeddings
                outputs = model.generate(
                    **encoded,
                    spectrum_embeddings=batch_embeddings,
                    max_length=max_length,
                    num_beams=num_beams,
                    do_sample=(num_beams == 1),
                    pad_token_id=tokenizer.pad_token_id,
                )
            else:
                outputs = model.generate(
                    **encoded,
                    max_length=max_length,
                    num_beams=num_beams,
                    do_sample=(num_beams == 1),
                    pad_token_id=tokenizer.pad_token_id,
                )
        
        # Decode
        batch_preds = tokenizer.batch_decode(outputs, skip_special_tokens=True)
        predictions.extend(batch_preds)
    return predictions


def main():
    parser = argparse.ArgumentParser(description="Evaluate MolT5 RAG model")
    parser.add_argument("--model-path", required=True, help="Path to trained model directory")
    parser.add_argument("--test-jsonl", required=True, help="Test JSONL file")
    parser.add_argument("--output-json", default=None, help="Output JSON file for results")
    parser.add_argument("--max-length", type=int, default=512, help="Max generation length")
    parser.add_argument("--num-beams", type=int, default=1, help="Beam search size (1=greedy)")
    parser.add_argument("--batch-size", type=int, default=8, help="Batch size for generation")
    parser.add_argument("--device", default="cuda", help="Device (cuda/cpu)")
    parser.add_argument("--save-predictions", default=None, help="Save predictions to JSONL file")
    parser.add_argument("--spec-embeddings", required=True, help="Path to spectrum embeddings .npy file (required for generation)")
    parser.add_argument("--prompt-len", type=int, default=10, help="Number of soft prompt tokens (must match training)")
    args = parser.parse_args()
    
    print("=" * 60)
    print("MolT5 RAG Model Evaluation")
    print("=" * 60)
    
    # Load spectrum embeddings (required)
    print(f"\nLoading spectrum embeddings from {args.spec_embeddings}...")
    spec_embeddings = load_embeddings(args.spec_embeddings)
    print(f"Loaded {len(spec_embeddings)} spectrum embeddings (shape: {spec_embeddings.shape})")
    embedding_dim = spec_embeddings.shape[1]
    
    # Load model and tokenizer
    print(f"\nLoading model from {args.model_path}...")
    base_model = AutoModelForSeq2SeqLM.from_pretrained(args.model_path)
    tokenizer = AutoTokenizer.from_pretrained(args.model_path)
    
    # Wrap model with embedding injection
    print(f"Wrapping model with spectrum embedding injection (dim={embedding_dim}, prompt_len={args.prompt_len})")
    model = MolT5WithEmbeddings(
        base_model=base_model,
        embedding_dim=embedding_dim,
        prompt_len=args.prompt_len,
        freeze_base=True,  # Freeze during evaluation
    )
    model.to(args.device)
    model.eval()
    print(f"Model loaded on {args.device}")
    
    # Load test data
    print(f"\nLoading test data from {args.test_jsonl}...")
    test_data = load_jsonl(Path(args.test_jsonl))
    print(f"Loaded {len(test_data)} test examples")
    
    # Extract inputs, ground truths, and spectrum IDs
    # Remove "Target: ..." from input_text if present (data leakage prevention)
    inputs = []
    ground_truths = []
    spectrum_ids = []
    for item in test_data[:1000]:
        input_text = item["input_text"]
        # Remove target if present
        if "\nTarget:" in input_text:
            input_text = input_text.split("\nTarget:")[0].rstrip()
        inputs.append(input_text)
        ground_truths.append(item["target_text"])
        # Get spectrum_id
        spectrum_id = item.get("spectrum_id", len(spectrum_ids))  # Default to index if missing
        spectrum_ids.append(spectrum_id)
    
    # Map spectrum_ids to embeddings
    print(f"\nMapping spectrum IDs to embeddings...")
    try:
        indices = [int(sid) if isinstance(sid, (int, str)) and str(sid).isdigit() else i 
                  for i, sid in enumerate(spectrum_ids)]
        indices = [min(i, len(spec_embeddings) - 1) for i in indices]
        eval_embeddings = torch.tensor([spec_embeddings[i] for i in indices], dtype=torch.float32)
        print(f"  Mapped {len(eval_embeddings)} embeddings (shape: {eval_embeddings.shape})")
    except Exception as e:
        raise ValueError(f"Failed to map spectrum IDs to embeddings: {e}")
    
    print(f"\nGenerating predictions with spectrum embeddings...")
    print(f"  Batch size: {args.batch_size}")
    print(f"  Max length: {args.max_length}")
    print(f"  Num beams: {args.num_beams}")
    print(f"  Prompt length: {args.prompt_len}")
    print(f"  Embedding dimension: {embedding_dim}")
    
    predictions = generate_predictions(
        model,
        tokenizer,
        inputs,
        spectrum_embeddings=eval_embeddings,
        max_length=args.max_length,
        num_beams=args.num_beams,
        batch_size=args.batch_size,
    )
    
    # Save predictions if requested
    if args.save_predictions:
        print(f"\nSaving predictions to {args.save_predictions}...")
        with open(args.save_predictions, "w") as f:
            for inp, pred, gt in zip(inputs, predictions, ground_truths):
                f.write(json.dumps({
                    "input": inp,
                    "prediction": pred,
                    "ground_truth": gt,
                }, ensure_ascii=False) + "\n")
    
    # Compute metrics
    print(f"\nComputing metrics...")
    metrics = compute_molecular_metrics(predictions, ground_truths)
    
    # Print results
    print("\n" + "=" * 60)
    print("EVALUATION RESULTS")
    print("=" * 60)
    print(f"\nDataset: {len(test_data)} examples")
    print(f"\nBasic Metrics:")
    print(f"  Exact Match (raw):           {metrics['exact_match']:.4f} ({metrics['exact_match']*100:.2f}%)")
    print(f"  Canonical Exact Match:       {metrics['canonical_exact_match']:.4f} ({metrics['canonical_exact_match']*100:.2f}%)")
    print(f"  Validity Rate:              {metrics['validity_rate']:.4f} ({metrics['validity_rate']*100:.2f}%)")
    print(f"  Valid Predictions:           {metrics['n_valid']}/{metrics['n_total']}")
    
    print(f"\nTanimoto Similarity:")
    print(f"  Mean (all):                 {metrics['tanimoto_similarity']:.4f}")
    print(f"  Mean (valid only):          {metrics['tanimoto_similarity_valid']:.4f}")
    if 'tanimoto_mean' in metrics:
        print(f"  Median:                      {metrics['tanimoto_median']:.4f}")
        print(f"  Std Dev:                    {metrics['tanimoto_std']:.4f}")
        print(f"  Min:                        {metrics['tanimoto_min']:.4f}")
        print(f"  Max:                        {metrics['tanimoto_max']:.4f}")
    
    print(f"\nTanimoto Similarity Distribution:")
    if 'tanimoto_ge_0.9' in metrics:
        print(f"  ≥ 0.9 (excellent):         {metrics['tanimoto_ge_0.9']:.4f} ({metrics['tanimoto_ge_0.9']*100:.2f}%)")
        print(f"  ≥ 0.8 (very good):         {metrics['tanimoto_ge_0.8']:.4f} ({metrics['tanimoto_ge_0.8']*100:.2f}%)")
        print(f"  ≥ 0.7 (good):             {metrics['tanimoto_ge_0.7']:.4f} ({metrics['tanimoto_ge_0.7']*100:.2f}%)")
        print(f"  ≥ 0.5 (moderate):         {metrics['tanimoto_ge_0.5']:.4f} ({metrics['tanimoto_ge_0.5']*100:.2f}%)")
        print(f"  ≥ 0.3 (low):              {metrics['tanimoto_ge_0.3']:.4f} ({metrics['tanimoto_ge_0.3']*100:.2f}%)")
    
    # Save results
    if args.output_json:
        print(f"\nSaving results to {args.output_json}...")
        with open(args.output_json, "w") as f:
            json.dump({
                "model_path": args.model_path,
                "test_file": args.test_jsonl,
                "n_examples": len(test_data),
                "metrics": metrics,
                "config": {
                    "max_length": args.max_length,
                    "num_beams": args.num_beams,
                    "batch_size": args.batch_size,
                }
            }, f, indent=2)
        print("Results saved!")
    
    print("\n" + "=" * 60)
    print("Evaluation complete!")
    print("=" * 60)


if __name__ == "__main__":
    main()