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train/config.yaml

@@ -0,0 +1,18 @@
+DATA_PATH: "./data/test_smi.csv"
+OUTPUT_DIR: "./chmbedv2-warmup"
+LOSS_TYPE: "barlow"  
+
+
+BATCH_SIZE: 16
+EFFECTIVE_BATCH: 64
+EPOCHS: 5
+MAX_LENGTH: 512
+LR: 1e-4           # Higher LR for random init
+WEIGHT_DECAY: 0.01
+SEED: 42
+
+EVAL_EVERY_N_PERCENT: 25
+BEST_BY_HEALTH: true
+
+# Loss-specific params (optional)
+BARLOW_LAMBDA: 5.0

train/initmodel/config.json

@@ -0,0 +1,26 @@
+{
+  "architectures": [
+    "RobertaModel"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "bos_token_id": 0,
+  "classifier_dropout": null,
+  "dtype": "float32",
+  "eos_token_id": 2,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 320,
+  "initializer_range": 0.02,
+  "intermediate_size": 1280,
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 514,
+  "model_type": "roberta",
+  "num_attention_heads": 4,
+  "num_hidden_layers": 6,
+  "pad_token_id": 1,
+  "position_embedding_type": "absolute",
+  "transformers_version": "4.56.2",
+  "type_vocab_size": 1,
+  "use_cache": true,
+  "vocab_size": 767
+}

train/initmodel/merges.txt

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train/initmodel/model.safetensors

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train/initmodel/special_tokens_map.json

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train/initmodel/tokenizer.json

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+        "CCCNc"
+      ],
+      [
+        "Br",
+        "CC"
+      ],
+      [
+        "Br",
+        "CCC"
+      ],
+      [
+        "12",
+        "3"
+      ],
+      [
+        "CCCCC",
+        "OC"
+      ],
+      [
+        "CCCCC",
+        "Oc"
+      ],
+      [
+        "CCCCC",
+        "Sc"
+      ],
+      [
+        "CCOCC",
+        "Sc"
+      ],
+      [
+        "CCS",
+        "CCOc"
+      ],
+      [
+        "NN",
+        "N"
+      ],
+      [
+        "NCCC",
+        "SC"
+      ],
+      [
+        "CCCCN",
+        "S"
+      ],
+      [
+        "COCCN",
+        "Cc"
+      ],
+      [
+        "OCCC",
+        "Nc"
+      ],
+      [
+        "OCCC",
+        "SC"
+      ],
+      [
+        "NO",
+        "CCc"
+      ],
+      [
+        "COCCO",
+        "CCN"
+      ],
+      [
+        "NCCO",
+        "CCO"
+      ],
+      [
+        "CCOCCO",
+        "CCOCC"
+      ],
+      [
+        "OCCOCCOCCO",
+        "CCO"
+      ]
+    ]
+  }
+}

train/initmodel/tokenizer_config.json

@@ -0,0 +1,59 @@
+{
+  "add_prefix_space": false,
+  "added_tokens_decoder": {
+    "0": {
+      "content": "<s>",
+      "lstrip": false,
+      "normalized": true,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "1": {
+      "content": "<pad>",
+      "lstrip": false,
+      "normalized": true,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "2": {
+      "content": "</s>",
+      "lstrip": false,
+      "normalized": true,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "3": {
+      "content": "<unk>",
+      "lstrip": false,
+      "normalized": true,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "4": {
+      "content": "<mask>",
+      "lstrip": true,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    }
+  },
+  "bos_token": "<s>",
+  "clean_up_tokenization_spaces": false,
+  "cls_token": "<s>",
+  "eos_token": "</s>",
+  "errors": "replace",
+  "extra_special_tokens": {},
+  "mask_token": "<mask>",
+  "max_len": 512,
+  "model_max_length": 512,
+  "pad_token": "<pad>",
+  "sep_token": "</s>",
+  "tokenizer_class": "RobertaTokenizer",
+  "trim_offsets": true,
+  "unk_token": "<unk>"
+}

train/initmodel/vocab.json

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train/trainbarlow.py

@@ -0,0 +1,349 @@
+#!/usr/bin/env python3
+"""
+Self-Supervised Training for Molecular Representations (SMILES)
+
+Usage:
+    python trainbarlow.py --config config.yaml
+"""
+print("Initializing ...")
+import os
+import json
+import argparse
+import random
+from pathlib import Path
+from typing import Dict, Any, Tuple, List
+
+import numpy as np
+import pandas as pd
+import torch
+import torch.nn as nn
+from torch.utils.data import DataLoader
+from tqdm.auto import tqdm
+from sklearn.metrics.pairwise import cosine_similarity
+from sklearn.preprocessing import normalize
+
+# Suppress RDKit warnings
+from rdkit import RDLogger
+RDLogger.DisableLog('rdApp.*')
+
+try:
+    from rdkit.Chem import MolFromSmiles, MolToSmiles, AllChem
+    from rdkit import DataStructs
+except ImportError:
+    raise ImportError("RDKit is required. Install with: conda install -c conda-forge rdkit")
+
+try:
+    from sentence_transformers import SentenceTransformer, InputExample
+except ImportError:
+    raise ImportError("Install sentence-transformers: pip install sentence-transformers")
+
+
+# ======================
+# Projector
+# ======================
+
+class BarlowTwinsProjector(nn.Module):
+    """Projector with BatchNorm (for Barlow Twins)."""
+    def __init__(self, in_dim: int, hidden_dim: int = 2048, out_dim: int = 2048):
+        super().__init__()
+        self.layers = nn.Sequential(
+            nn.Linear(in_dim, hidden_dim, bias=False),
+            nn.BatchNorm1d(hidden_dim),
+            nn.ReLU(),
+            nn.Linear(hidden_dim, hidden_dim, bias=False),
+            nn.BatchNorm1d(hidden_dim),
+            nn.ReLU(),
+            nn.Linear(hidden_dim, out_dim, bias=False),
+            nn.BatchNorm1d(out_dim, affine=False)
+        )
+
+    def forward(self, x):
+        return self.layers(x)
+
+# ======================
+# Loss Function
+# ======================
+
+class BarlowTwinsLoss(nn.Module):
+    def __init__(self, λ: float = 0.005):
+        super().__init__()
+        self.λ = λ
+
+    def forward(self, z1: torch.Tensor, z2: torch.Tensor) -> Tuple[torch.Tensor, Dict[str, float]]:
+        B, d = z1.shape
+        # Shared standardization
+        z = torch.cat([z1, z2], dim=0)
+        z = (z - z.mean(dim=0)) / (z.std(dim=0) + 1e-8)
+        z1, z2 = z[:B], z[B:]
+        c = (z1.T @ z2) / B
+        on_diag = (1 - torch.diagonal(c)).pow(2).sum()
+        off_diag = (c ** 2).sum() - torch.diagonal(c).pow(2).sum()
+        off_diag = off_diag / d
+        total_loss = on_diag + self.λ * off_diag
+        with torch.no_grad():
+            diag_mean = torch.diagonal(c).mean().item()
+            off_diag_mask = ~torch.eye(d, dtype=torch.bool, device=c.device)
+            off_diag_mean = c[off_diag_mask].abs().mean().item()
+        return total_loss, {
+            'od': on_diag.item(),
+            'ofsc': (self.λ * off_diag).item(),
+            'ofrw': off_diag.item(),
+            'cr_onm': diag_mean,
+            'cr_offm': off_diag_mean
+        }
+
+
+# ======================
+# Utilities
+# ======================
+
+def load_config(config_path: str) -> Dict[str, Any]:
+    config_path = Path(config_path)
+    if config_path.suffix in {'.yaml', '.yml'}:
+        import yaml
+        with open(config_path) as f:
+            return yaml.safe_load(f)
+    elif config_path.suffix == '.json':
+        with open(config_path) as f:
+            return json.load(f)
+    else:
+        raise ValueError(f"Unsupported config format: {config_path.suffix}")
+
+def sanitize_config(config: Dict[str, Any]) -> Dict[str, Any]:
+    float_keys = {
+        "LR", "WEIGHT_DECAY", "BARLOW_LAMBDA", "VICREG_LAMBDA",
+        "VICREG_MU", "VICREG_NU", "CORINFOMAX_ALPHA"
+    }
+    int_keys = {
+        "BATCH_SIZE", "EFFECTIVE_BATCH", "EPOCHS", "MAX_LENGTH",
+        "SEED", "EVAL_EVERY_N_PERCENT"
+    }
+    bool_keys = {"BEST_BY_HEALTH"}
+    for key in float_keys:
+        if key in config:
+            config[key] = float(config[key])
+    for key in int_keys:
+        if key in config:
+            config[key] = int(config[key])
+    for key in bool_keys:
+        if key in config:
+            val = config[key]
+            config[key] = val.lower() in {"true", "1", "yes", "on"} if isinstance(val, str) else bool(val)
+    return config
+
+def set_seed(seed: int):
+    torch.manual_seed(seed)
+    np.random.seed(seed)
+    random.seed(seed)
+    if torch.cuda.is_available():
+        torch.cuda.manual_seed_all(seed)
+
+def enum_smiles(smi: str, k: int = 2) -> List[str]:
+    from rdkit.Chem import MolFromSmiles, MolToSmiles
+    mol = MolFromSmiles(smi)
+    if mol is None:
+        return [smi] * k
+    variants = set()
+    attempts = 0
+    while len(variants) < k and attempts < 100:
+        variants.add(MolToSmiles(mol, doRandom=True, canonical=False))
+        attempts += 1
+    return list(variants)[:k]
+
+def tanimoto(s1: str, s2: str) -> float:
+    m1, m2 = MolFromSmiles(s1), MolFromSmiles(s2)
+    if not m1 or not m2:
+        return 0.0
+    fp1 = AllChem.GetMorganFingerprintAsBitVect(m1, radius=2, nBits=2048)
+    fp2 = AllChem.GetMorganFingerprintAsBitVect(m2, radius=2, nBits=2048)
+    return DataStructs.TanimotoSimilarity(fp1, fp2)
+
+def uniformity_metrics(emb: np.ndarray) -> Dict[str, float]:
+    emb = normalize(emb)
+    sim = cosine_similarity(emb)
+    mask = ~np.eye(len(sim), dtype=bool)
+    pairwise = sim[mask]
+    mean_sim, std_sim = pairwise.mean(), pairwise.std()
+    distances = 1 - sim
+    uniformity = np.log(np.exp(-2 * distances[mask]).mean())
+    return {
+        'mean': float(mean_sim),
+        'std': float(std_sim),
+        'uniformity': float(uniformity),
+        'health_old': float(1 - mean_sim),
+        'collapsed': mean_sim > 0.7 or std_sim < 0.05
+    }
+
+def forward_pooled(model: SentenceTransformer, text_list: List[str], device: torch.device) -> torch.Tensor:
+    tok = model.tokenize(text_list)
+    tok = {k: v.to(device) for k, v in tok.items()}
+    hf_output = model(tok)
+    return hf_output['token_embeddings'][:, 0, :]
+
+def evaluate(model, eval_smiles: List[str], device: torch.device, step: int) -> Dict[str, Any]:
+    model.eval()
+    with torch.no_grad():
+        emb = model.encode(eval_smiles, convert_to_numpy=True, show_progress_bar=False, batch_size=32)
+    um = uniformity_metrics(emb)
+    same_view = [enum_smiles(s, 1)[0] for s in eval_smiles]
+    with torch.no_grad():
+        emb2 = model.encode(same_view, convert_to_numpy=True, show_progress_bar=False, batch_size=32)
+    same_cos = np.diag(cosine_similarity(emb, emb2))
+    alignment = 1 - same_cos.mean()
+    barlow_health = same_cos.mean() - um['mean']
+    print(f"\n📊 Step {step} | Alignment={alignment:.3f} | Uniformity={um['uniformity']:.3f}")
+    print(f"   Same-mol cos: {same_cos.mean():.3f}±{same_cos.std():.3f} | Pairwise: {um['mean']:.3f}±{um['std']:.3f}")
+    print(f"   Barlow Health: {barlow_health:.3f} (higher = better)")
+    model.train()
+    um['health'] = barlow_health
+    um['alignment'] = alignment
+    um['same_cos_mean'] = same_cos.mean()
+    um['same_cos_std'] = same_cos.std()
+    return um
+
+
+# ======================
+# Main
+# ======================
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--config", type=str, required=True)
+    parser.add_argument("--epochs", type=int)
+    parser.add_argument("--lr", type=float)
+    parser.add_argument("--batch_size", type=int)
+    parser.add_argument("--loss_type", type=str, choices=["barlow", "vicreg", "corinfomax"])
+    args = parser.parse_args()
+
+    config = load_config(args.config)
+    for key, value in vars(args).items():
+        if value is not None and key != "config":
+            config[key] = value
+    config = sanitize_config(config)
+
+    set_seed(config.get("SEED", 42))
+    device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+    output_dir = Path(config["OUTPUT_DIR"])
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    df = pd.read_csv(config["DATA_PATH"])
+    smiles_list = df["SMILES"].dropna().tolist()
+    print(f"📂 Loaded {len(smiles_list)} SMILES")
+
+    train_examples = []
+    for smi in tqdm(smiles_list, desc="Enumerating SMILES"):
+        variants = enum_smiles(smi, 2)
+        if len(variants) < 2:
+            variants = [smi, smi]
+        train_examples.append(InputExample(texts=[variants[0], variants[1]]))
+    print(f"   Created {len(train_examples)} pairs")
+
+    eval_size = min(200, len(smiles_list))
+    eval_smiles = np.random.choice(smiles_list, eval_size, replace=False).tolist()
+
+    # Model
+    model = SentenceTransformer('./chmbedv2-warmup-l5/final')
+    model.max_seq_length = config.get("MAX_LENGTH", 512)
+    embed_dim = model.get_sentence_embedding_dimension()
+
+    # Projector & Loss
+    loss_type = config.get("LOSS_TYPE", "barlow")
+    if loss_type == "barlow":
+        projector = BarlowTwinsProjector(
+            embed_dim,
+            hidden_dim=2048,
+            out_dim=2048
+        ).to(device)
+        train_loss = BarlowTwinsLoss(
+            λ=config.get("BARLOW_LAMBDA", 0.005)
+        ).to(device)
+    else:
+        raise ValueError(f"Unknown loss_type: {loss_type}")
+
+    model.to(device)
+
+    # Optimizer (include projector!)
+    from ranger21 import Ranger21
+
+    no_decay = ["bias", "LayerNorm.bias", "LayerNorm.weight"]
+    model_params = [
+        {"params": [p for n, p in model.named_parameters() if not any(nd in n for nd in no_decay)],
+        "weight_decay": config.get("WEIGHT_DECAY", 0.01)},
+        {"params": [p for n, p in model.named_parameters() if any(nd in n for nd in no_decay)],
+        "weight_decay": 0.0}
+    ]
+
+    # Calculate training parameters for Ranger21 scheduling
+    batch_size = config.get("BATCH_SIZE", 8)
+    effective_batch = config.get("EFFECTIVE_BATCH", 32)
+    grad_acc = effective_batch // batch_size
+    epochs = config.get("EPOCHS", 1)
+    total_steps = (len(train_examples) // effective_batch) * epochs
+    train_loader = DataLoader(train_examples, batch_size=batch_size, shuffle=True, collate_fn=lambda x: x)
+    num_batches_per_epoch = len(train_examples) // effective_batch
+
+    no_decay = ["bias", "LayerNorm.bias", "LayerNorm.weight"]
+    model_params = [
+        {"params": [p for n, p in model.named_parameters() if not any(nd in n for nd in no_decay)],
+        "weight_decay": config.get("WEIGHT_DECAY", 0.01)},
+        {"params": [p for n, p in model.named_parameters() if any(nd in n for nd in no_decay)],
+        "weight_decay": 0.0}
+    ]
+
+    optimizer = Ranger21(
+        model_params + [{"params": projector.parameters(), "weight_decay": config.get("WEIGHT_DECAY", 0.01)}],
+        lr=config.get("LR", 1e-5),
+        num_epochs=epochs,
+        num_batches_per_epoch=num_batches_per_epoch,
+        weight_decay=0.0,  # Handle weight decay manually in param groups
+    )
+
+    # Training loop setup
+    scheduler = torch.optim.lr_scheduler.LinearLR(
+        optimizer, start_factor=1.0, end_factor=0.0, total_iters=total_steps
+    )
+
+
+    # Train
+    model.train()
+    step = 0
+    best_health = 0.0
+    best_step = 0
+    log_interval = max(1, int(total_steps * config.get("EVAL_EVERY_N_PERCENT", 25) / 100))
+
+    for epoch in range(epochs):
+        pbar = tqdm(train_loader, desc=f"Epoch {epoch + 1}/{epochs}")
+        for batch_idx, batch in enumerate(pbar):
+            texts = [[ex.texts[i] for ex in batch] for i in range(2)]
+            z1 = forward_pooled(model, texts[0], device)
+            z2 = forward_pooled(model, texts[1], device)
+            p1 = projector(z1)
+            p2 = projector(z2)
+            loss, extras = train_loss(p1, p2)
+
+            loss = loss / grad_acc
+            loss.backward()
+
+            if (batch_idx + 1) % grad_acc == 0:
+                optimizer.step()
+                scheduler.step()
+                optimizer.zero_grad()
+                step += 1
+
+                postfix = {"step": step, "lr": scheduler.get_last_lr()[0]}
+                for k, v in extras.items():
+                    postfix[k] = f"{v:.3f}"
+                pbar.set_postfix(postfix)
+
+                if step % log_interval == 0 or step == total_steps:
+                    um = evaluate(model, eval_smiles, device, step)
+                    if config.get("BEST_BY_HEALTH", True) and um["health"] > best_health:
+                        best_health, best_step = um["health"], step
+                        model.save(str(output_dir / "best"))
+
+    model.save(str(output_dir / "final"))
+    print(f"\n✅ Training complete! Best health: {best_health:.3f} at step {best_step}")
+
+
+if __name__ == "__main__":
+    main()