Spaces:
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manpreet88 commited on
Commit ·
4700e18
1
Parent(s): 70ec142
Create Polymer_Generation.py
Browse files
Downstream Tasks/Polymer_Generation.py
ADDED
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|
| 1 |
+
# G2.py — PolyBART-style inverse design (single-task, fivefold per property, G1-style I/O)
|
| 2 |
+
|
| 3 |
+
import os
|
| 4 |
+
import re
|
| 5 |
+
import sys
|
| 6 |
+
import csv
|
| 7 |
+
import json
|
| 8 |
+
import math
|
| 9 |
+
import time
|
| 10 |
+
import copy
|
| 11 |
+
import random
|
| 12 |
+
import shutil
|
| 13 |
+
import warnings
|
| 14 |
+
from dataclasses import dataclass
|
| 15 |
+
from pathlib import Path
|
| 16 |
+
from typing import List, Dict, Optional, Tuple, Any
|
| 17 |
+
|
| 18 |
+
import numpy as np
|
| 19 |
+
import pandas as pd
|
| 20 |
+
|
| 21 |
+
from sklearn.model_selection import train_test_split, KFold
|
| 22 |
+
from sklearn.preprocessing import StandardScaler
|
| 23 |
+
from sklearn.decomposition import PCA
|
| 24 |
+
from sklearn.gaussian_process import GaussianProcessRegressor
|
| 25 |
+
from sklearn.gaussian_process.kernels import RBF, ConstantKernel as C, WhiteKernel
|
| 26 |
+
|
| 27 |
+
import torch
|
| 28 |
+
import torch.nn as nn
|
| 29 |
+
import torch.nn.functional as F
|
| 30 |
+
from torch.utils.data import Dataset, DataLoader
|
| 31 |
+
|
| 32 |
+
# Increase csv field size limit safely
|
| 33 |
+
try:
|
| 34 |
+
csv.field_size_limit(sys.maxsize)
|
| 35 |
+
except OverflowError:
|
| 36 |
+
csv.field_size_limit(2**31 - 1)
|
| 37 |
+
|
| 38 |
+
# HF Transformers
|
| 39 |
+
from transformers import DebertaV2ForMaskedLM, DebertaV2Tokenizer
|
| 40 |
+
from transformers import AutoTokenizer, AutoModelForSeq2SeqLM
|
| 41 |
+
from transformers.modeling_outputs import BaseModelOutput
|
| 42 |
+
|
| 43 |
+
# Optional: RDKit + selfies (required for this pipeline)
|
| 44 |
+
RDKit_AVAILABLE = False
|
| 45 |
+
SELFIES_AVAILABLE = False
|
| 46 |
+
try:
|
| 47 |
+
from rdkit import Chem
|
| 48 |
+
from rdkit.Chem import AllChem, DataStructs
|
| 49 |
+
RDKit_AVAILABLE = True
|
| 50 |
+
except Exception:
|
| 51 |
+
RDKit_AVAILABLE = False
|
| 52 |
+
|
| 53 |
+
try:
|
| 54 |
+
import selfies as sf
|
| 55 |
+
SELFIES_AVAILABLE = True
|
| 56 |
+
except Exception:
|
| 57 |
+
SELFIES_AVAILABLE = False
|
| 58 |
+
|
| 59 |
+
# PyG (optional)
|
| 60 |
+
try:
|
| 61 |
+
from torch_geometric.nn import GINEConv
|
| 62 |
+
from torch_geometric.nn.models import SchNet as PyGSchNet
|
| 63 |
+
from torch_geometric.nn import radius_graph
|
| 64 |
+
except Exception:
|
| 65 |
+
GINEConv = None
|
| 66 |
+
PyGSchNet = None
|
| 67 |
+
radius_graph = None
|
| 68 |
+
|
| 69 |
+
# =============================================================================
|
| 70 |
+
# Configuration
|
| 71 |
+
# =============================================================================
|
| 72 |
+
|
| 73 |
+
BASE_DIR = "Polymer_Foundational_Model"
|
| 74 |
+
POLYINFO_PATH = os.path.join(BASE_DIR, "polyinfo_with_modalities.csv")
|
| 75 |
+
|
| 76 |
+
# Pretrained model directories (your paths)
|
| 77 |
+
PRETRAINED_MULTIMODAL_DIR = "multimodal_output_5M/best"
|
| 78 |
+
BEST_GINE_DIR = "gin_output_5M/best"
|
| 79 |
+
BEST_SCHNET_DIR = "schnet_output_5M/best"
|
| 80 |
+
BEST_FP_DIR = "fingerprint_mlm_output_5M/best"
|
| 81 |
+
BEST_PSMILES_DIR = "polybert_output_5M/best"
|
| 82 |
+
|
| 83 |
+
# Output
|
| 84 |
+
OUTPUT_DIR = "multimodal_inverse_design_output_5M_polybart_style"
|
| 85 |
+
OUTPUT_RESULTS = os.path.join(OUTPUT_DIR, "inverse_design_results.txt")
|
| 86 |
+
OUTPUT_MODELS_DIR = os.path.join(OUTPUT_DIR, "best_models")
|
| 87 |
+
OUTPUT_GENERATIONS_DIR = os.path.join(OUTPUT_DIR, "best_fold_generations")
|
| 88 |
+
|
| 89 |
+
# Properties (order preserved)
|
| 90 |
+
REQUESTED_PROPERTIES = [
|
| 91 |
+
"density",
|
| 92 |
+
"glass transition",
|
| 93 |
+
"melting",
|
| 94 |
+
"specific volume",
|
| 95 |
+
"thermal decomposition"
|
| 96 |
+
]
|
| 97 |
+
|
| 98 |
+
# -------------------------------------------------------------------------
|
| 99 |
+
# Model sizes / dims (match your CL encoder)
|
| 100 |
+
# -------------------------------------------------------------------------
|
| 101 |
+
|
| 102 |
+
CL_EMB_DIM = 600
|
| 103 |
+
|
| 104 |
+
# Model hyperparameters (matching your multimodal training)
|
| 105 |
+
MAX_ATOMIC_Z = 85
|
| 106 |
+
MASK_ATOM_ID = MAX_ATOMIC_Z + 1
|
| 107 |
+
|
| 108 |
+
# GINE params
|
| 109 |
+
NODE_EMB_DIM = 300
|
| 110 |
+
EDGE_EMB_DIM = 300
|
| 111 |
+
NUM_GNN_LAYERS = 5
|
| 112 |
+
|
| 113 |
+
# SchNet params
|
| 114 |
+
SCHNET_NUM_GAUSSIANS = 50
|
| 115 |
+
SCHNET_NUM_INTERACTIONS = 6
|
| 116 |
+
SCHNET_CUTOFF = 10.0
|
| 117 |
+
SCHNET_MAX_NEIGHBORS = 64
|
| 118 |
+
SCHNET_HIDDEN = 600
|
| 119 |
+
|
| 120 |
+
# Fingerprint params
|
| 121 |
+
FP_LENGTH = 2048
|
| 122 |
+
MASK_TOKEN_ID_FP = 2
|
| 123 |
+
VOCAB_SIZE_FP = 3
|
| 124 |
+
|
| 125 |
+
# DeBERTa params
|
| 126 |
+
DEBERTA_HIDDEN = 600
|
| 127 |
+
PSMILES_MAX_LEN = 128
|
| 128 |
+
|
| 129 |
+
# SELFIES-TED generation
|
| 130 |
+
GEN_MAX_LEN = 256
|
| 131 |
+
GEN_MIN_LEN = 10
|
| 132 |
+
|
| 133 |
+
# -------------------------------------------------------------------------
|
| 134 |
+
# Decoder fine-tuning params (single head; match G1-style simple schedule)
|
| 135 |
+
# -------------------------------------------------------------------------
|
| 136 |
+
BATCH_SIZE = 32
|
| 137 |
+
NUM_EPOCHS = 100
|
| 138 |
+
PATIENCE = 10
|
| 139 |
+
WEIGHT_DECAY = 0.0
|
| 140 |
+
LEARNING_RATE = 1e-4
|
| 141 |
+
COSINE_ETA_MIN = 1e-6
|
| 142 |
+
|
| 143 |
+
# PolyBART-style noise injection (latent space)
|
| 144 |
+
LATENT_NOISE_STD_TRAIN = 0.10 # training-time denoising std
|
| 145 |
+
LATENT_NOISE_STD_GEN = 0.15 # generation-time exploration std
|
| 146 |
+
N_FOLD_NOISE_SAMPLING = 16 # n-fold sampling around each seed embedding
|
| 147 |
+
|
| 148 |
+
# Sampling config (decoder)
|
| 149 |
+
GEN_TOP_P = 0.92
|
| 150 |
+
GEN_TEMPERATURE = 1.0
|
| 151 |
+
GEN_REPETITION_PENALTY = 1.05
|
| 152 |
+
|
| 153 |
+
# CV
|
| 154 |
+
NUM_FOLDS = 5
|
| 155 |
+
|
| 156 |
+
# Property guidance tolerance (scaled and optionally absolute)
|
| 157 |
+
PROP_TOL_SCALED = 0.5
|
| 158 |
+
PROP_TOL_UNSCALED_ABS = None
|
| 159 |
+
|
| 160 |
+
# GPR settings (PSMILES latent)
|
| 161 |
+
USE_PCA_BEFORE_GPR = True
|
| 162 |
+
PCA_DIM = 64
|
| 163 |
+
GPR_ALPHA = 1e-6
|
| 164 |
+
|
| 165 |
+
# Verification (optional auxiliary predictor)
|
| 166 |
+
VERIFY_GENERATED_PROPERTIES = True
|
| 167 |
+
PROP_PRED_EPOCHS = 20
|
| 168 |
+
PROP_PRED_PATIENCE = 5
|
| 169 |
+
PROP_PRED_BATCH_SIZE = 32
|
| 170 |
+
PROP_PRED_LR = 3e-4
|
| 171 |
+
PROP_PRED_WEIGHT_DECAY = 0.0
|
| 172 |
+
|
| 173 |
+
DEVICE = "cuda" if torch.cuda.is_available() else "cpu"
|
| 174 |
+
USE_AMP = bool(torch.cuda.is_available())
|
| 175 |
+
AMP_DTYPE = torch.float16
|
| 176 |
+
|
| 177 |
+
NUM_WORKERS = 0 if os.name == "nt" else 1
|
| 178 |
+
|
| 179 |
+
os.makedirs(OUTPUT_DIR, exist_ok=True)
|
| 180 |
+
os.makedirs(OUTPUT_MODELS_DIR, exist_ok=True)
|
| 181 |
+
os.makedirs(OUTPUT_GENERATIONS_DIR, exist_ok=True)
|
| 182 |
+
|
| 183 |
+
warnings.filterwarnings("ignore", category=UserWarning)
|
| 184 |
+
|
| 185 |
+
# =============================================================================
|
| 186 |
+
# Utilities
|
| 187 |
+
# =============================================================================
|
| 188 |
+
def _safe_json_load(x):
|
| 189 |
+
if x is None:
|
| 190 |
+
return None
|
| 191 |
+
if isinstance(x, (dict, list)):
|
| 192 |
+
return x
|
| 193 |
+
s = str(x).strip()
|
| 194 |
+
if not s:
|
| 195 |
+
return None
|
| 196 |
+
try:
|
| 197 |
+
return json.loads(s)
|
| 198 |
+
except Exception:
|
| 199 |
+
try:
|
| 200 |
+
return json.loads(s.replace("'", '"'))
|
| 201 |
+
except Exception:
|
| 202 |
+
return None
|
| 203 |
+
|
| 204 |
+
def set_seed(seed: int):
|
| 205 |
+
random.seed(seed)
|
| 206 |
+
np.random.seed(seed)
|
| 207 |
+
torch.manual_seed(seed)
|
| 208 |
+
if torch.cuda.is_available():
|
| 209 |
+
torch.cuda.manual_seed_all(seed)
|
| 210 |
+
try:
|
| 211 |
+
torch.backends.cudnn.benchmark = True
|
| 212 |
+
except Exception:
|
| 213 |
+
pass
|
| 214 |
+
|
| 215 |
+
def make_json_serializable(obj):
|
| 216 |
+
if isinstance(obj, dict):
|
| 217 |
+
return {make_json_serializable(k): make_json_serializable(v) for k, v in obj.items()}
|
| 218 |
+
if isinstance(obj, (list, tuple, set)):
|
| 219 |
+
return [make_json_serializable(x) for x in obj]
|
| 220 |
+
if isinstance(obj, np.ndarray):
|
| 221 |
+
return obj.tolist()
|
| 222 |
+
if isinstance(obj, np.generic):
|
| 223 |
+
try:
|
| 224 |
+
return obj.item()
|
| 225 |
+
except Exception:
|
| 226 |
+
return float(obj)
|
| 227 |
+
if isinstance(obj, torch.Tensor):
|
| 228 |
+
try:
|
| 229 |
+
return obj.detach().cpu().tolist()
|
| 230 |
+
except Exception:
|
| 231 |
+
return None
|
| 232 |
+
if isinstance(obj, (pd.Timestamp, pd.Timedelta)):
|
| 233 |
+
return str(obj)
|
| 234 |
+
try:
|
| 235 |
+
if isinstance(obj, (float, int, str, bool, type(None))):
|
| 236 |
+
return obj
|
| 237 |
+
except Exception:
|
| 238 |
+
pass
|
| 239 |
+
return str(obj)
|
| 240 |
+
|
| 241 |
+
def safe_get(d: dict, key: str, default=None):
|
| 242 |
+
return d[key] if (isinstance(d, dict) and key in d) else default
|
| 243 |
+
|
| 244 |
+
def find_property_columns(columns):
|
| 245 |
+
lowered = {c.lower(): c for c in columns}
|
| 246 |
+
found = {}
|
| 247 |
+
for req in REQUESTED_PROPERTIES:
|
| 248 |
+
req_low = req.lower().strip()
|
| 249 |
+
exact = None
|
| 250 |
+
for c_low, c_orig in lowered.items():
|
| 251 |
+
tokens = set(c_low.replace('_', ' ').split())
|
| 252 |
+
if req_low in tokens or c_low == req_low:
|
| 253 |
+
if req_low == "density" and ("cohesive" in c_low or "cohesive energy" in c_low):
|
| 254 |
+
continue
|
| 255 |
+
exact = c_orig
|
| 256 |
+
break
|
| 257 |
+
if exact is not None:
|
| 258 |
+
found[req] = exact
|
| 259 |
+
continue
|
| 260 |
+
candidates = [c_orig for c_low, c_orig in lowered.items() if req_low in c_low]
|
| 261 |
+
if req_low == "density":
|
| 262 |
+
candidates = [c for c in candidates if "cohesive" not in c.lower() and "cohesive energy" not in c.lower()]
|
| 263 |
+
chosen = candidates[0] if candidates else None
|
| 264 |
+
found[req] = chosen
|
| 265 |
+
if chosen is None:
|
| 266 |
+
print(f"[WARN] No candidates found for '{req}'.")
|
| 267 |
+
else:
|
| 268 |
+
print(f"[INFO] Requested property '{req}' -> chosen column: {chosen}")
|
| 269 |
+
return found
|
| 270 |
+
|
| 271 |
+
# =============================================================================
|
| 272 |
+
# Graph / geometry / FP parsing for multimodal CL
|
| 273 |
+
# =============================================================================
|
| 274 |
+
def _parse_graph_for_gine(graph_field):
|
| 275 |
+
gf = _safe_json_load(graph_field)
|
| 276 |
+
if not isinstance(gf, dict):
|
| 277 |
+
return None
|
| 278 |
+
node_features = gf.get("node_features", None)
|
| 279 |
+
if not node_features or not isinstance(node_features, list):
|
| 280 |
+
return None
|
| 281 |
+
atomic_nums, chirality_vals, formal_charges = [], [], []
|
| 282 |
+
for nf in node_features:
|
| 283 |
+
if not isinstance(nf, dict):
|
| 284 |
+
continue
|
| 285 |
+
an = nf.get("atomic_num", nf.get("atomic_number", 0))
|
| 286 |
+
ch = nf.get("chirality", 0)
|
| 287 |
+
fc = nf.get("formal_charge", 0)
|
| 288 |
+
try: atomic_nums.append(int(an))
|
| 289 |
+
except Exception: atomic_nums.append(0)
|
| 290 |
+
try: chirality_vals.append(float(ch))
|
| 291 |
+
except Exception: chirality_vals.append(0.0)
|
| 292 |
+
try: formal_charges.append(float(fc))
|
| 293 |
+
except Exception: formal_charges.append(0.0)
|
| 294 |
+
if len(atomic_nums) == 0:
|
| 295 |
+
return None
|
| 296 |
+
edge_indices_raw = gf.get("edge_indices", None)
|
| 297 |
+
edge_features_raw = gf.get("edge_features", None)
|
| 298 |
+
srcs, dsts = [], []
|
| 299 |
+
if edge_indices_raw is None:
|
| 300 |
+
adj = gf.get("adjacency_matrix", None)
|
| 301 |
+
if isinstance(adj, list):
|
| 302 |
+
for i_r, row_adj in enumerate(adj):
|
| 303 |
+
if not isinstance(row_adj, list):
|
| 304 |
+
continue
|
| 305 |
+
for j, val in enumerate(row_adj):
|
| 306 |
+
if val:
|
| 307 |
+
srcs.append(i_r); dsts.append(j)
|
| 308 |
+
else:
|
| 309 |
+
try:
|
| 310 |
+
if isinstance(edge_indices_raw, list) and len(edge_indices_raw) > 0:
|
| 311 |
+
if isinstance(edge_indices_raw[0], list) and len(edge_indices_raw[0]) == 2:
|
| 312 |
+
srcs = [int(p[0]) for p in edge_indices_raw]
|
| 313 |
+
dsts = [int(p[1]) for p in edge_indices_raw]
|
| 314 |
+
elif len(edge_indices_raw) == 2:
|
| 315 |
+
srcs = [int(x) for x in edge_indices_raw[0]]
|
| 316 |
+
dsts = [int(x) for x in edge_indices_raw[1]]
|
| 317 |
+
except Exception:
|
| 318 |
+
srcs, dsts = [], []
|
| 319 |
+
if len(srcs) == 0:
|
| 320 |
+
edge_index = torch.empty((2, 0), dtype=torch.long)
|
| 321 |
+
edge_attr = torch.zeros((0, 3), dtype=torch.float)
|
| 322 |
+
return {
|
| 323 |
+
"z": torch.tensor(atomic_nums, dtype=torch.long),
|
| 324 |
+
"chirality": torch.tensor(chirality_vals, dtype=torch.float),
|
| 325 |
+
"formal_charge": torch.tensor(formal_charges, dtype=torch.float),
|
| 326 |
+
"edge_index": edge_index,
|
| 327 |
+
"edge_attr": edge_attr,
|
| 328 |
+
}
|
| 329 |
+
edge_index = torch.tensor([srcs, dsts], dtype=torch.long)
|
| 330 |
+
edge_attr = None
|
| 331 |
+
if isinstance(edge_features_raw, list) and len(edge_features_raw) == len(srcs):
|
| 332 |
+
bt, st, ic = [], [], []
|
| 333 |
+
for ef in edge_features_raw:
|
| 334 |
+
if isinstance(ef, dict):
|
| 335 |
+
bt.append(float(ef.get("bond_type", 0)))
|
| 336 |
+
st.append(float(ef.get("stereo", 0)))
|
| 337 |
+
ic.append(float(1.0 if ef.get("is_conjugated", False) else 0.0))
|
| 338 |
+
else:
|
| 339 |
+
bt.append(0.0); st.append(0.0); ic.append(0.0)
|
| 340 |
+
edge_attr = torch.tensor(list(zip(bt, st, ic)), dtype=torch.float)
|
| 341 |
+
else:
|
| 342 |
+
edge_attr = torch.zeros((len(srcs), 3), dtype=torch.float)
|
| 343 |
+
return {
|
| 344 |
+
"z": torch.tensor(atomic_nums, dtype=torch.long),
|
| 345 |
+
"chirality": torch.tensor(chirality_vals, dtype=torch.float),
|
| 346 |
+
"formal_charge": torch.tensor(formal_charges, dtype=torch.float),
|
| 347 |
+
"edge_index": edge_index,
|
| 348 |
+
"edge_attr": edge_attr,
|
| 349 |
+
}
|
| 350 |
+
|
| 351 |
+
def _parse_geometry_for_schnet(geom_field):
|
| 352 |
+
gf = _safe_json_load(geom_field)
|
| 353 |
+
if not isinstance(gf, dict):
|
| 354 |
+
return None
|
| 355 |
+
conf = gf.get("best_conformer", None)
|
| 356 |
+
if not isinstance(conf, dict):
|
| 357 |
+
return None
|
| 358 |
+
atomic = conf.get("atomic_numbers", [])
|
| 359 |
+
coords = conf.get("coordinates", [])
|
| 360 |
+
if not (isinstance(atomic, list) and isinstance(coords, list)):
|
| 361 |
+
return None
|
| 362 |
+
if len(atomic) == 0 or len(atomic) != len(coords):
|
| 363 |
+
return None
|
| 364 |
+
return {"z": torch.tensor(atomic, dtype=torch.long), "pos": torch.tensor(coords, dtype=torch.float)}
|
| 365 |
+
|
| 366 |
+
def _parse_fingerprints(fp_field, fp_len: int = 2048):
|
| 367 |
+
fp = _safe_json_load(fp_field)
|
| 368 |
+
bits = None
|
| 369 |
+
if isinstance(fp, dict):
|
| 370 |
+
bits = fp.get("morgan_r3_bits", None)
|
| 371 |
+
elif isinstance(fp, list):
|
| 372 |
+
bits = fp
|
| 373 |
+
elif fp is None:
|
| 374 |
+
bits = None
|
| 375 |
+
if bits is None:
|
| 376 |
+
bits = [0] * fp_len
|
| 377 |
+
else:
|
| 378 |
+
norm = []
|
| 379 |
+
for b in bits[:fp_len]:
|
| 380 |
+
if isinstance(b, str):
|
| 381 |
+
bc = b.strip().strip('"').strip("'")
|
| 382 |
+
norm.append(1 if bc in ("1", "True", "true") else 0)
|
| 383 |
+
elif isinstance(b, (int, np.integer, float, np.floating)):
|
| 384 |
+
norm.append(1 if int(b) != 0 else 0)
|
| 385 |
+
else:
|
| 386 |
+
norm.append(0)
|
| 387 |
+
if len(norm) < fp_len:
|
| 388 |
+
norm.extend([0] * (fp_len - len(norm)))
|
| 389 |
+
bits = norm
|
| 390 |
+
return {
|
| 391 |
+
"input_ids": torch.tensor(bits, dtype=torch.long),
|
| 392 |
+
"attention_mask": torch.ones(fp_len, dtype=torch.bool),
|
| 393 |
+
}
|
| 394 |
+
|
| 395 |
+
# =============================================================================
|
| 396 |
+
# PSELFIES utilities
|
| 397 |
+
# =============================================================================
|
| 398 |
+
|
| 399 |
+
_SELFIES_TOKEN_RE = re.compile(r"\[[^\[\]]+\]")
|
| 400 |
+
|
| 401 |
+
def _split_selfies_tokens(selfies_str: str) -> List[str]:
|
| 402 |
+
if not isinstance(selfies_str, str) or len(selfies_str) == 0:
|
| 403 |
+
return []
|
| 404 |
+
if SELFIES_AVAILABLE:
|
| 405 |
+
try:
|
| 406 |
+
toks = list(sf.split_selfies(selfies_str.replace(" ", "")))
|
| 407 |
+
return [t for t in toks if isinstance(t, str) and t]
|
| 408 |
+
except Exception:
|
| 409 |
+
pass
|
| 410 |
+
return _SELFIES_TOKEN_RE.findall(selfies_str)
|
| 411 |
+
|
| 412 |
+
def _selfies_for_tokenizer(selfies_str: str) -> str:
|
| 413 |
+
s = str(selfies_str).strip()
|
| 414 |
+
if not s:
|
| 415 |
+
return ""
|
| 416 |
+
s = s.replace(" ", "")
|
| 417 |
+
s = s.replace("][", "] [")
|
| 418 |
+
return s
|
| 419 |
+
|
| 420 |
+
def _selfies_compact(selfies_str: str) -> str:
|
| 421 |
+
return str(selfies_str).replace(" ", "").strip()
|
| 422 |
+
|
| 423 |
+
def _ensure_two_at_endpoints(selfies_str: str) -> str:
|
| 424 |
+
s = _selfies_compact(selfies_str)
|
| 425 |
+
toks = _split_selfies_tokens(s)
|
| 426 |
+
if not toks:
|
| 427 |
+
return s
|
| 428 |
+
at = "[At]"
|
| 429 |
+
at_pos = [i for i, t in enumerate(toks) if t == at]
|
| 430 |
+
if len(at_pos) == 0:
|
| 431 |
+
toks = [at] + toks + [at]
|
| 432 |
+
elif len(at_pos) == 1:
|
| 433 |
+
toks = toks + [at]
|
| 434 |
+
elif len(at_pos) > 2:
|
| 435 |
+
first = at_pos[0]; last = at_pos[-1]
|
| 436 |
+
new = []
|
| 437 |
+
for i, t in enumerate(toks):
|
| 438 |
+
if t == at and i not in (first, last):
|
| 439 |
+
continue
|
| 440 |
+
new.append(t)
|
| 441 |
+
toks = new
|
| 442 |
+
return "".join(toks)
|
| 443 |
+
|
| 444 |
+
def psmiles_to_at_smiles(psmiles: str, root_at: bool = True) -> Optional[str]:
|
| 445 |
+
if not RDKit_AVAILABLE:
|
| 446 |
+
return None
|
| 447 |
+
try:
|
| 448 |
+
mol = Chem.MolFromSmiles(psmiles)
|
| 449 |
+
if mol is None:
|
| 450 |
+
return None
|
| 451 |
+
mol = Chem.RWMol(mol)
|
| 452 |
+
at_indices = []
|
| 453 |
+
for atom in mol.GetAtoms():
|
| 454 |
+
if atom.GetAtomicNum() == 0:
|
| 455 |
+
atom.SetAtomicNum(85)
|
| 456 |
+
try: atom.SetNoImplicit(True)
|
| 457 |
+
except Exception: pass
|
| 458 |
+
try: atom.SetNumExplicitHs(0)
|
| 459 |
+
except Exception: pass
|
| 460 |
+
try: atom.SetFormalCharge(0)
|
| 461 |
+
except Exception: pass
|
| 462 |
+
at_indices.append(int(atom.GetIdx()))
|
| 463 |
+
mol = mol.GetMol()
|
| 464 |
+
try:
|
| 465 |
+
Chem.SanitizeMol(mol, catchErrors=True)
|
| 466 |
+
except Exception:
|
| 467 |
+
return None
|
| 468 |
+
if root_at and len(at_indices) > 0:
|
| 469 |
+
try:
|
| 470 |
+
can = Chem.MolToSmiles(mol, canonical=True, rootedAtAtom=at_indices[0])
|
| 471 |
+
except Exception:
|
| 472 |
+
can = Chem.MolToSmiles(mol, canonical=True)
|
| 473 |
+
else:
|
| 474 |
+
can = Chem.MolToSmiles(mol, canonical=True)
|
| 475 |
+
return can
|
| 476 |
+
except Exception:
|
| 477 |
+
return None
|
| 478 |
+
|
| 479 |
+
def at_smiles_to_psmiles(at_smiles: str) -> Optional[str]:
|
| 480 |
+
if not RDKit_AVAILABLE:
|
| 481 |
+
return None
|
| 482 |
+
try:
|
| 483 |
+
mol = Chem.MolFromSmiles(at_smiles)
|
| 484 |
+
if mol is None:
|
| 485 |
+
return None
|
| 486 |
+
rw = Chem.RWMol(mol)
|
| 487 |
+
for atom in rw.GetAtoms():
|
| 488 |
+
if atom.GetAtomicNum() == 85:
|
| 489 |
+
atom.SetAtomicNum(0)
|
| 490 |
+
try: atom.SetNoImplicit(True)
|
| 491 |
+
except Exception: pass
|
| 492 |
+
try: atom.SetNumExplicitHs(0)
|
| 493 |
+
except Exception: pass
|
| 494 |
+
try: atom.SetFormalCharge(0)
|
| 495 |
+
except Exception: pass
|
| 496 |
+
mol2 = rw.GetMol()
|
| 497 |
+
try:
|
| 498 |
+
Chem.SanitizeMol(mol2, catchErrors=True)
|
| 499 |
+
except Exception:
|
| 500 |
+
return None
|
| 501 |
+
can = Chem.MolToSmiles(mol2, canonical=True)
|
| 502 |
+
can = can.replace("[*]", "*")
|
| 503 |
+
return can
|
| 504 |
+
except Exception:
|
| 505 |
+
return None
|
| 506 |
+
|
| 507 |
+
def smiles_to_pselfies(smiles: str) -> Optional[str]:
|
| 508 |
+
if not (RDKit_AVAILABLE and SELFIES_AVAILABLE):
|
| 509 |
+
return None
|
| 510 |
+
try:
|
| 511 |
+
mol = Chem.MolFromSmiles(smiles)
|
| 512 |
+
if mol is None:
|
| 513 |
+
return None
|
| 514 |
+
can = Chem.MolToSmiles(mol, canonical=True)
|
| 515 |
+
s = sf.encoder(can)
|
| 516 |
+
if not isinstance(s, str) or len(s) == 0:
|
| 517 |
+
return None
|
| 518 |
+
return s
|
| 519 |
+
except Exception:
|
| 520 |
+
return None
|
| 521 |
+
|
| 522 |
+
def psmiles_to_pselfies(psmiles: str) -> Optional[str]:
|
| 523 |
+
if not (RDKit_AVAILABLE and SELFIES_AVAILABLE):
|
| 524 |
+
return None
|
| 525 |
+
at_smiles = psmiles_to_at_smiles(psmiles, root_at=True)
|
| 526 |
+
if at_smiles is None:
|
| 527 |
+
return None
|
| 528 |
+
s = smiles_to_pselfies(at_smiles)
|
| 529 |
+
if s is None:
|
| 530 |
+
return None
|
| 531 |
+
return _ensure_two_at_endpoints(s)
|
| 532 |
+
|
| 533 |
+
def selfies_to_smiles(selfies_str: str) -> Optional[str]:
|
| 534 |
+
if not (RDKit_AVAILABLE and SELFIES_AVAILABLE):
|
| 535 |
+
return None
|
| 536 |
+
try:
|
| 537 |
+
s = _selfies_compact(selfies_str)
|
| 538 |
+
smi = sf.decoder(s)
|
| 539 |
+
if not isinstance(smi, str) or len(smi) == 0:
|
| 540 |
+
return None
|
| 541 |
+
mol = Chem.MolFromSmiles(smi)
|
| 542 |
+
if mol is None:
|
| 543 |
+
return None
|
| 544 |
+
try:
|
| 545 |
+
Chem.SanitizeMol(mol, catchErrors=True)
|
| 546 |
+
except Exception:
|
| 547 |
+
return None
|
| 548 |
+
can = Chem.MolToSmiles(mol, canonical=True)
|
| 549 |
+
return can
|
| 550 |
+
except Exception:
|
| 551 |
+
return None
|
| 552 |
+
|
| 553 |
+
def pselfies_to_psmiles(selfies_str: str) -> Optional[str]:
|
| 554 |
+
if not (RDKit_AVAILABLE and SELFIES_AVAILABLE):
|
| 555 |
+
return None
|
| 556 |
+
at_smiles = selfies_to_smiles(selfies_str)
|
| 557 |
+
if at_smiles is None:
|
| 558 |
+
return None
|
| 559 |
+
return at_smiles_to_psmiles(at_smiles)
|
| 560 |
+
|
| 561 |
+
def canonicalize_psmiles(psmiles: str) -> Optional[str]:
|
| 562 |
+
psmiles = str(psmiles).strip()
|
| 563 |
+
if not psmiles:
|
| 564 |
+
return None
|
| 565 |
+
if not RDKit_AVAILABLE:
|
| 566 |
+
return psmiles
|
| 567 |
+
try:
|
| 568 |
+
mol = Chem.MolFromSmiles(psmiles)
|
| 569 |
+
if mol is None:
|
| 570 |
+
return None
|
| 571 |
+
try:
|
| 572 |
+
Chem.SanitizeMol(mol, catchErrors=True)
|
| 573 |
+
except Exception:
|
| 574 |
+
return None
|
| 575 |
+
can = Chem.MolToSmiles(mol, canonical=True)
|
| 576 |
+
can = can.replace("[*]", "*")
|
| 577 |
+
return can
|
| 578 |
+
except Exception:
|
| 579 |
+
return None
|
| 580 |
+
|
| 581 |
+
def chem_validity_psmiles(psmiles: str) -> bool:
|
| 582 |
+
if not RDKit_AVAILABLE:
|
| 583 |
+
return False
|
| 584 |
+
try:
|
| 585 |
+
s = str(psmiles).strip()
|
| 586 |
+
if not s:
|
| 587 |
+
return False
|
| 588 |
+
mol = Chem.MolFromSmiles(s)
|
| 589 |
+
if mol is None:
|
| 590 |
+
return False
|
| 591 |
+
try:
|
| 592 |
+
Chem.SanitizeMol(mol, catchErrors=True)
|
| 593 |
+
except Exception:
|
| 594 |
+
return False
|
| 595 |
+
return True
|
| 596 |
+
except Exception:
|
| 597 |
+
return False
|
| 598 |
+
|
| 599 |
+
def polymer_validity_psmiles_strict(psmiles: str) -> bool:
|
| 600 |
+
if not RDKit_AVAILABLE:
|
| 601 |
+
return False
|
| 602 |
+
try:
|
| 603 |
+
s = str(psmiles).strip()
|
| 604 |
+
if not s:
|
| 605 |
+
return False
|
| 606 |
+
mol = Chem.MolFromSmiles(s)
|
| 607 |
+
if mol is None:
|
| 608 |
+
return False
|
| 609 |
+
try:
|
| 610 |
+
Chem.SanitizeMol(mol, catchErrors=True)
|
| 611 |
+
except Exception:
|
| 612 |
+
return False
|
| 613 |
+
stars = [a for a in mol.GetAtoms() if a.GetAtomicNum() == 0]
|
| 614 |
+
if len(stars) != 2:
|
| 615 |
+
return False
|
| 616 |
+
for a in stars:
|
| 617 |
+
if a.GetTotalDegree() != 1:
|
| 618 |
+
return False
|
| 619 |
+
return True
|
| 620 |
+
except Exception:
|
| 621 |
+
return False
|
| 622 |
+
|
| 623 |
+
# =============================================================================
|
| 624 |
+
# CL encoder (multimodal) + fusion pooling (same heads/dims as CL pretraining)
|
| 625 |
+
# =============================================================================
|
| 626 |
+
|
| 627 |
+
def resolve_cl_checkpoint_path(cl_weights_dir: str) -> Optional[str]:
|
| 628 |
+
if cl_weights_dir is None:
|
| 629 |
+
return None
|
| 630 |
+
if os.path.isfile(cl_weights_dir):
|
| 631 |
+
return cl_weights_dir
|
| 632 |
+
if not os.path.isdir(cl_weights_dir):
|
| 633 |
+
return None
|
| 634 |
+
candidates = [
|
| 635 |
+
os.path.join(cl_weights_dir, "pytorch_model.bin"),
|
| 636 |
+
os.path.join(cl_weights_dir, "model.pt"),
|
| 637 |
+
os.path.join(cl_weights_dir, "best.pt"),
|
| 638 |
+
os.path.join(cl_weights_dir, "state_dict.pt"),
|
| 639 |
+
]
|
| 640 |
+
for p in candidates:
|
| 641 |
+
if os.path.isfile(p):
|
| 642 |
+
return p
|
| 643 |
+
for ext in ("*.bin", "*.pt"):
|
| 644 |
+
files = sorted(Path(cl_weights_dir).glob(ext))
|
| 645 |
+
if files:
|
| 646 |
+
return str(files[0])
|
| 647 |
+
return None
|
| 648 |
+
|
| 649 |
+
def load_state_dict_any(ckpt_path: str) -> Dict[str, torch.Tensor]:
|
| 650 |
+
obj = torch.load(ckpt_path, map_location="cpu")
|
| 651 |
+
if isinstance(obj, dict):
|
| 652 |
+
if "state_dict" in obj and isinstance(obj["state_dict"], dict):
|
| 653 |
+
return obj["state_dict"]
|
| 654 |
+
if "model_state_dict" in obj and isinstance(obj["model_state_dict"], dict):
|
| 655 |
+
return obj["model_state_dict"]
|
| 656 |
+
if not isinstance(obj, dict):
|
| 657 |
+
raise RuntimeError(f"Checkpoint at {ckpt_path} did not contain a state_dict-like dict.")
|
| 658 |
+
return obj
|
| 659 |
+
|
| 660 |
+
def safe_load_into_module(module: nn.Module, sd: Dict[str, torch.Tensor], strict: bool = False) -> Tuple[int, int]:
|
| 661 |
+
incompatible = module.load_state_dict(sd, strict=strict)
|
| 662 |
+
missing = getattr(incompatible, "missing_keys", [])
|
| 663 |
+
unexpected = getattr(incompatible, "unexpected_keys", [])
|
| 664 |
+
return len(missing), len(unexpected)
|
| 665 |
+
|
| 666 |
+
class GineBlock(nn.Module):
|
| 667 |
+
def __init__(self, node_dim):
|
| 668 |
+
super().__init__()
|
| 669 |
+
self.mlp = nn.Sequential(nn.Linear(node_dim, node_dim), nn.ReLU(), nn.Linear(node_dim, node_dim))
|
| 670 |
+
if GINEConv is None:
|
| 671 |
+
raise RuntimeError("GINEConv is not available. Install torch_geometric with compatible versions.")
|
| 672 |
+
self.conv = GINEConv(self.mlp)
|
| 673 |
+
self.bn = nn.BatchNorm1d(node_dim)
|
| 674 |
+
self.act = nn.ReLU()
|
| 675 |
+
def forward(self, x, edge_index, edge_attr):
|
| 676 |
+
x = self.conv(x, edge_index, edge_attr)
|
| 677 |
+
x = self.bn(x)
|
| 678 |
+
x = self.act(x)
|
| 679 |
+
return x
|
| 680 |
+
|
| 681 |
+
class GineEncoder(nn.Module):
|
| 682 |
+
def __init__(self, node_emb_dim=NODE_EMB_DIM, edge_emb_dim=EDGE_EMB_DIM, num_layers=NUM_GNN_LAYERS, max_atomic_z=MAX_ATOMIC_Z):
|
| 683 |
+
super().__init__()
|
| 684 |
+
self.atom_emb = nn.Embedding(num_embeddings=MASK_ATOM_ID+1, embedding_dim=node_emb_dim, padding_idx=None)
|
| 685 |
+
self.node_attr_proj = nn.Sequential(nn.Linear(2, node_emb_dim), nn.ReLU(), nn.Linear(node_emb_dim, node_emb_dim))
|
| 686 |
+
self.edge_encoder = nn.Sequential(nn.Linear(3, edge_emb_dim), nn.ReLU(), nn.Linear(edge_emb_dim, edge_emb_dim))
|
| 687 |
+
self._edge_to_node_proj = nn.Linear(edge_emb_dim, node_emb_dim) if edge_emb_dim != node_emb_dim else None
|
| 688 |
+
self.gnn_layers = nn.ModuleList([GineBlock(node_emb_dim) for _ in range(num_layers)])
|
| 689 |
+
self.pool_proj = nn.Linear(node_emb_dim, node_emb_dim)
|
| 690 |
+
self.node_classifier = nn.Linear(node_emb_dim, MASK_ATOM_ID+1)
|
| 691 |
+
def _compute_node_reps(self, z, chirality, formal_charge, edge_index, edge_attr):
|
| 692 |
+
device = next(self.parameters()).device
|
| 693 |
+
atom_embedding = self.atom_emb(z.to(device))
|
| 694 |
+
if chirality is None or formal_charge is None:
|
| 695 |
+
node_attr = torch.zeros((z.size(0), 2), device=device)
|
| 696 |
+
else:
|
| 697 |
+
node_attr = torch.stack([chirality, formal_charge], dim=1).to(atom_embedding.device)
|
| 698 |
+
node_attr_emb = self.node_attr_proj(node_attr)
|
| 699 |
+
x = atom_embedding + node_attr_emb
|
| 700 |
+
if edge_attr is None or edge_attr.numel() == 0:
|
| 701 |
+
edge_emb = torch.zeros((0, EDGE_EMB_DIM), dtype=torch.float, device=x.device)
|
| 702 |
+
else:
|
| 703 |
+
edge_emb = self.edge_encoder(edge_attr.to(x.device))
|
| 704 |
+
edge_for_conv = self._edge_to_node_proj(edge_emb) if (self._edge_to_node_proj is not None and edge_emb.numel() > 0) else edge_emb
|
| 705 |
+
h = x
|
| 706 |
+
for layer in self.gnn_layers:
|
| 707 |
+
h = layer(h, edge_index.to(h.device), edge_for_conv)
|
| 708 |
+
return h
|
| 709 |
+
def forward(self, z, chirality, formal_charge, edge_index, edge_attr, batch=None):
|
| 710 |
+
h = self._compute_node_reps(z, chirality, formal_charge, edge_index, edge_attr)
|
| 711 |
+
if batch is None:
|
| 712 |
+
pooled = torch.mean(h, dim=0, keepdim=True)
|
| 713 |
+
else:
|
| 714 |
+
bsize = int(batch.max().item() + 1) if batch.numel() > 0 else 1
|
| 715 |
+
pooled = torch.zeros((bsize, h.size(1)), device=h.device)
|
| 716 |
+
for i in range(bsize):
|
| 717 |
+
mask = batch == i
|
| 718 |
+
if mask.sum() == 0:
|
| 719 |
+
continue
|
| 720 |
+
pooled[i] = h[mask].mean(dim=0)
|
| 721 |
+
return self.pool_proj(pooled)
|
| 722 |
+
|
| 723 |
+
class NodeSchNetWrapper(nn.Module):
|
| 724 |
+
def __init__(self, hidden_channels=SCHNET_HIDDEN, num_interactions=SCHNET_NUM_INTERACTIONS,
|
| 725 |
+
num_gaussians=SCHNET_NUM_GAUSSIANS, cutoff=SCHNET_CUTOFF, max_num_neighbors=SCHNET_MAX_NEIGHBORS):
|
| 726 |
+
super().__init__()
|
| 727 |
+
if PyGSchNet is None:
|
| 728 |
+
raise RuntimeError("PyG SchNet is not available. Install torch_geometric with compatible extras.")
|
| 729 |
+
self.schnet = PyGSchNet(hidden_channels=hidden_channels, num_filters=hidden_channels,
|
| 730 |
+
num_interactions=num_interactions, num_gaussians=SCHNET_NUM_GAUSSIANS,
|
| 731 |
+
cutoff=cutoff, max_num_neighbors=max_num_neighbors)
|
| 732 |
+
self.pool_proj = nn.Linear(hidden_channels, hidden_channels)
|
| 733 |
+
self.cutoff = cutoff
|
| 734 |
+
self.max_num_neighbors = max_num_neighbors
|
| 735 |
+
self.node_classifier = nn.Linear(hidden_channels, MASK_ATOM_ID+1)
|
| 736 |
+
def forward(self, z, pos, batch=None):
|
| 737 |
+
device = next(self.parameters()).device
|
| 738 |
+
z = z.to(device); pos = pos.to(device)
|
| 739 |
+
if batch is None:
|
| 740 |
+
batch = torch.zeros(z.size(0), dtype=torch.long, device=z.device)
|
| 741 |
+
try:
|
| 742 |
+
edge_index = radius_graph(pos, r=self.cutoff, batch=batch, max_num_neighbors=self.max_num_neighbors)
|
| 743 |
+
except Exception:
|
| 744 |
+
edge_index = None
|
| 745 |
+
node_h = None
|
| 746 |
+
try:
|
| 747 |
+
node_h = self.schnet.embedding(z)
|
| 748 |
+
except Exception:
|
| 749 |
+
node_h = None
|
| 750 |
+
if node_h is not None and edge_index is not None and edge_index.numel() > 0:
|
| 751 |
+
row, col = edge_index
|
| 752 |
+
edge_weight = (pos[row] - pos[col]).norm(dim=-1)
|
| 753 |
+
edge_attr = None
|
| 754 |
+
if hasattr(self.schnet, "distance_expansion"):
|
| 755 |
+
try: edge_attr = self.schnet.distance_expansion(edge_weight)
|
| 756 |
+
except Exception: edge_attr = None
|
| 757 |
+
if edge_attr is None and hasattr(self.schnet, "gaussian_smearing"):
|
| 758 |
+
try: edge_attr = self.schnet.gaussian_smearing(edge_weight)
|
| 759 |
+
except Exception: edge_attr = None
|
| 760 |
+
if hasattr(self.schnet, "interactions") and getattr(self.schnet, "interactions") is not None:
|
| 761 |
+
for interaction in self.schnet.interactions:
|
| 762 |
+
try:
|
| 763 |
+
node_h = node_h + interaction(node_h, edge_index, edge_weight, edge_attr)
|
| 764 |
+
except TypeError:
|
| 765 |
+
node_h = node_h + interaction(node_h, edge_index, edge_weight)
|
| 766 |
+
if node_h is None:
|
| 767 |
+
try:
|
| 768 |
+
out = self.schnet(z=z, pos=pos, batch=batch)
|
| 769 |
+
if isinstance(out, torch.Tensor) and out.dim() == 2 and out.size(0) == z.size(0):
|
| 770 |
+
node_h = out
|
| 771 |
+
elif hasattr(out, "last_hidden_state"):
|
| 772 |
+
node_h = out.last_hidden_state
|
| 773 |
+
elif isinstance(out, (tuple, list)) and len(out) > 0 and isinstance(out[0], torch.Tensor):
|
| 774 |
+
cand = out[0]
|
| 775 |
+
if cand.dim() == 2 and cand.size(0) == z.size(0):
|
| 776 |
+
node_h = cand
|
| 777 |
+
except Exception as e:
|
| 778 |
+
raise RuntimeError("Failed to obtain node-level embeddings from PyG SchNet.") from e
|
| 779 |
+
bsize = int(batch.max().item()) + 1 if z.numel() > 0 else 1
|
| 780 |
+
pooled = torch.zeros((bsize, node_h.size(1)), device=node_h.device)
|
| 781 |
+
for i in range(bsize):
|
| 782 |
+
mask = batch == i
|
| 783 |
+
if mask.sum() == 0:
|
| 784 |
+
continue
|
| 785 |
+
pooled[i] = node_h[mask].mean(dim=0)
|
| 786 |
+
return self.pool_proj(pooled)
|
| 787 |
+
|
| 788 |
+
class FingerprintEncoder(nn.Module):
|
| 789 |
+
def __init__(self, vocab_size=VOCAB_SIZE_FP, hidden_dim=256, seq_len=FP_LENGTH,
|
| 790 |
+
num_layers=4, nhead=8, dim_feedforward=1024, dropout=0.1):
|
| 791 |
+
super().__init__()
|
| 792 |
+
self.token_emb = nn.Embedding(vocab_size, hidden_dim)
|
| 793 |
+
self.pos_emb = nn.Embedding(seq_len, hidden_dim)
|
| 794 |
+
encoder_layer = nn.TransformerEncoderLayer(d_model=hidden_dim, nhead=nhead,
|
| 795 |
+
dim_feedforward=dim_feedforward, dropout=dropout, batch_first=True)
|
| 796 |
+
self.transformer = nn.TransformerEncoder(encoder_layer, num_layers=num_layers)
|
| 797 |
+
self.pool_proj = nn.Linear(hidden_dim, hidden_dim)
|
| 798 |
+
self.seq_len = seq_len
|
| 799 |
+
self.token_proj = nn.Linear(hidden_dim, vocab_size)
|
| 800 |
+
def forward(self, input_ids, attention_mask=None):
|
| 801 |
+
device = next(self.parameters()).device
|
| 802 |
+
input_ids = input_ids.to(device)
|
| 803 |
+
B, L = input_ids.shape
|
| 804 |
+
x = self.token_emb(input_ids)
|
| 805 |
+
pos_ids = torch.arange(L, device=input_ids.device).unsqueeze(0).expand(B, -1)
|
| 806 |
+
x = x + self.pos_emb(pos_ids)
|
| 807 |
+
key_padding_mask = (~attention_mask.to(input_ids.device)) if attention_mask is not None else None
|
| 808 |
+
out = self.transformer(x, src_key_padding_mask=key_padding_mask)
|
| 809 |
+
if attention_mask is None:
|
| 810 |
+
pooled = out.mean(dim=1)
|
| 811 |
+
else:
|
| 812 |
+
am = attention_mask.to(out.device).float().unsqueeze(-1)
|
| 813 |
+
pooled = (out * am).sum(dim=1) / (am.sum(dim=1).clamp(min=1.0))
|
| 814 |
+
return self.pool_proj(pooled)
|
| 815 |
+
|
| 816 |
+
class PSMILESDebertaEncoder(nn.Module):
|
| 817 |
+
def __init__(self, model_dir_or_name: Optional[str] = None, vocab_size: Optional[int] = None):
|
| 818 |
+
super().__init__()
|
| 819 |
+
try:
|
| 820 |
+
if model_dir_or_name is not None and os.path.isdir(model_dir_or_name):
|
| 821 |
+
self.model = DebertaV2ForMaskedLM.from_pretrained(model_dir_or_name)
|
| 822 |
+
else:
|
| 823 |
+
self.model = DebertaV2ForMaskedLM.from_pretrained(model_dir_or_name or "microsoft/deberta-v2-xlarge")
|
| 824 |
+
except Exception:
|
| 825 |
+
from transformers import DebertaV2Config
|
| 826 |
+
cfg = DebertaV2Config(
|
| 827 |
+
vocab_size=int(vocab_size) if vocab_size is not None else 300,
|
| 828 |
+
hidden_size=DEBERTA_HIDDEN,
|
| 829 |
+
num_attention_heads=12,
|
| 830 |
+
num_hidden_layers=12,
|
| 831 |
+
intermediate_size=4 * DEBERTA_HIDDEN,
|
| 832 |
+
)
|
| 833 |
+
self.model = DebertaV2ForMaskedLM(cfg)
|
| 834 |
+
self.pool_proj = nn.Linear(self.model.config.hidden_size, self.model.config.hidden_size)
|
| 835 |
+
@property
|
| 836 |
+
def out_dim(self) -> int:
|
| 837 |
+
return int(self.model.config.hidden_size)
|
| 838 |
+
def forward(self, input_ids, attention_mask=None):
|
| 839 |
+
device = next(self.parameters()).device
|
| 840 |
+
input_ids = input_ids.to(device)
|
| 841 |
+
if attention_mask is not None:
|
| 842 |
+
attention_mask = attention_mask.to(device)
|
| 843 |
+
outputs = self.model.base_model(input_ids=input_ids, attention_mask=attention_mask, return_dict=True)
|
| 844 |
+
last_hidden = outputs.last_hidden_state
|
| 845 |
+
if attention_mask is None:
|
| 846 |
+
pooled = last_hidden.mean(dim=1)
|
| 847 |
+
else:
|
| 848 |
+
am = attention_mask.unsqueeze(-1).to(last_hidden.device).float()
|
| 849 |
+
pooled = (last_hidden * am).sum(dim=1) / (am.sum(dim=1).clamp(min=1.0))
|
| 850 |
+
return self.pool_proj(pooled)
|
| 851 |
+
|
| 852 |
+
class UniPolyFusionModule(nn.Module):
|
| 853 |
+
def __init__(self, d_model: int, nhead: int = 8, ffn_mult: int = 4, dropout: float = 0.1):
|
| 854 |
+
super().__init__()
|
| 855 |
+
self.ln1 = nn.LayerNorm(d_model)
|
| 856 |
+
self.attn = nn.MultiheadAttention(d_model, nhead, dropout=dropout, batch_first=True)
|
| 857 |
+
self.ln2 = nn.LayerNorm(d_model)
|
| 858 |
+
self.ffn = nn.Sequential(
|
| 859 |
+
nn.Linear(d_model, ffn_mult * d_model), nn.GELU(), nn.Dropout(dropout),
|
| 860 |
+
nn.Linear(ffn_mult * d_model, d_model), nn.Dropout(dropout),
|
| 861 |
+
)
|
| 862 |
+
self.pool_ln = nn.LayerNorm(d_model)
|
| 863 |
+
self.pool_q = nn.Parameter(torch.randn(d_model))
|
| 864 |
+
def forward(self, x: torch.Tensor, mask: torch.Tensor) -> torch.Tensor:
|
| 865 |
+
key_padding = ~mask
|
| 866 |
+
h = self.ln1(x)
|
| 867 |
+
attn_out, _ = self.attn(h, h, h, key_padding_mask=key_padding)
|
| 868 |
+
x = x + attn_out
|
| 869 |
+
x = x + self.ffn(self.ln2(x))
|
| 870 |
+
x = self.pool_ln(x)
|
| 871 |
+
q = self.pool_q.unsqueeze(0).unsqueeze(-1)
|
| 872 |
+
scores = torch.matmul(x, q).squeeze(-1)
|
| 873 |
+
scores = scores.masked_fill(~mask, -1e9)
|
| 874 |
+
w = torch.softmax(scores, dim=-1).unsqueeze(-1)
|
| 875 |
+
pooled = (x * w).sum(dim=1)
|
| 876 |
+
return pooled
|
| 877 |
+
|
| 878 |
+
class MultiModalCLPolymerEncoder(nn.Module):
|
| 879 |
+
def __init__(self, psmiles_tokenizer, emb_dim: int = CL_EMB_DIM,
|
| 880 |
+
cl_weights_dir: Optional[str] = PRETRAINED_MULTIMODAL_DIR,
|
| 881 |
+
use_gine: bool = True, use_schnet: bool = True, use_fp: bool = True, use_psmiles: bool = True):
|
| 882 |
+
super().__init__()
|
| 883 |
+
self.psm_tok = psmiles_tokenizer
|
| 884 |
+
self.emb_dim = int(emb_dim)
|
| 885 |
+
self.gine = None; self.schnet = None; self.fp = None; self.psmiles = None
|
| 886 |
+
if use_gine:
|
| 887 |
+
try:
|
| 888 |
+
self.gine = GineEncoder(NODE_EMB_DIM, EDGE_EMB_DIM, NUM_GNN_LAYERS, MAX_ATOMIC_Z)
|
| 889 |
+
except Exception as e:
|
| 890 |
+
print(f"[CL] GINE disabled: {e}"); self.gine = None
|
| 891 |
+
if use_schnet:
|
| 892 |
+
try:
|
| 893 |
+
self.schnet = NodeSchNetWrapper(SCHNET_HIDDEN, SCHNET_NUM_INTERACTIONS,
|
| 894 |
+
SCHNET_NUM_GAUSSIANS, SCHNET_CUTOFF, SCHNET_MAX_NEIGHBORS)
|
| 895 |
+
except Exception as e:
|
| 896 |
+
print(f"[CL] SchNet disabled: {e}"); self.schnet = None
|
| 897 |
+
if use_fp:
|
| 898 |
+
try:
|
| 899 |
+
self.fp = FingerprintEncoder(VOCAB_SIZE_FP, 256, FP_LENGTH, 4, 8, 1024, 0.1)
|
| 900 |
+
except Exception as e:
|
| 901 |
+
print(f"[CL] FP encoder disabled: {e}"); self.fp = None
|
| 902 |
+
if use_psmiles:
|
| 903 |
+
enc_src = BEST_PSMILES_DIR if (BEST_PSMILES_DIR and os.path.isdir(BEST_PSMILES_DIR)) else None
|
| 904 |
+
self.psmiles = PSMILESDebertaEncoder(model_dir_or_name=enc_src, vocab_size=getattr(psmiles_tokenizer, "vocab_size", None))
|
| 905 |
+
self.proj_gine = nn.Linear(NODE_EMB_DIM, self.emb_dim) if self.gine is not None else None
|
| 906 |
+
self.proj_schnet = nn.Linear(SCHNET_HIDDEN, self.emb_dim) if self.schnet is not None else None
|
| 907 |
+
self.proj_fp = nn.Linear(256, self.emb_dim) if self.fp is not None else None
|
| 908 |
+
self.proj_psmiles = nn.Linear(DEBERTA_HIDDEN, self.emb_dim) if self.psmiles is not None else None
|
| 909 |
+
self.dropout = nn.Dropout(0.1)
|
| 910 |
+
self.out_dim = self.emb_dim
|
| 911 |
+
self.fusion = UniPolyFusionModule(d_model=self.emb_dim, nhead=8, ffn_mult=4, dropout=0.1)
|
| 912 |
+
self._load_multimodal_cl_checkpoint(cl_weights_dir)
|
| 913 |
+
def _load_multimodal_cl_checkpoint(self, cl_weights_dir: Optional[str]):
|
| 914 |
+
ckpt_path = resolve_cl_checkpoint_path(cl_weights_dir) if cl_weights_dir else None
|
| 915 |
+
if ckpt_path is None:
|
| 916 |
+
print(f"[CL] No multimodal CL checkpoint found at: {cl_weights_dir}. Using initialized encoders/projections.")
|
| 917 |
+
return
|
| 918 |
+
sd = load_state_dict_any(ckpt_path); model_sd = self.state_dict()
|
| 919 |
+
filtered = {}
|
| 920 |
+
for k, v in sd.items():
|
| 921 |
+
if k not in model_sd:
|
| 922 |
+
continue
|
| 923 |
+
if hasattr(v, "shape") and hasattr(model_sd[k], "shape") and tuple(v.shape) != tuple(model_sd[k].shape):
|
| 924 |
+
continue
|
| 925 |
+
filtered[k] = v
|
| 926 |
+
missing, unexpected = safe_load_into_module(self, filtered, strict=False)
|
| 927 |
+
print(f"[CL] Loaded multimodal CL from {ckpt_path}. loaded={len(filtered)} missing={missing} unexpected={unexpected}")
|
| 928 |
+
def freeze_cl_encoders(self):
|
| 929 |
+
for encoder_name, encoder in [("gine", self.gine), ("schnet", self.schnet), ("fp", self.fp), ("psmiles", self.psmiles)]:
|
| 930 |
+
if encoder is not None:
|
| 931 |
+
encoder.eval()
|
| 932 |
+
for p in encoder.parameters(): p.requires_grad = False
|
| 933 |
+
print(f"[CL] Froze {encoder_name} encoder")
|
| 934 |
+
self.fusion.eval()
|
| 935 |
+
for p in self.fusion.parameters(): p.requires_grad = False
|
| 936 |
+
def forward_multimodal(self, batch_mods: dict) -> torch.Tensor:
|
| 937 |
+
device = next(self.parameters()).device
|
| 938 |
+
B = None
|
| 939 |
+
if batch_mods.get("fp", None) is not None and isinstance(batch_mods["fp"].get("input_ids", None), torch.Tensor):
|
| 940 |
+
B = int(batch_mods["fp"]["input_ids"].size(0))
|
| 941 |
+
elif batch_mods.get("psmiles", None) is not None and isinstance(batch_mods["psmiles"].get("input_ids", None), torch.Tensor):
|
| 942 |
+
B = int(batch_mods["psmiles"]["input_ids"].size(0))
|
| 943 |
+
else:
|
| 944 |
+
if batch_mods.get("gine", None) is not None and isinstance(batch_mods["gine"].get("batch", None), torch.Tensor):
|
| 945 |
+
B = int(batch_mods["gine"]["batch"].max().item() + 1) if batch_mods["gine"]["batch"].numel() > 0 else 1
|
| 946 |
+
elif batch_mods.get("schnet", None) is not None and isinstance(batch_mods["schnet"].get("batch", None), torch.Tensor):
|
| 947 |
+
B = int(batch_mods["schnet"]["batch"].max().item() + 1) if batch_mods["schnet"]["batch"].numel() > 0 else 1
|
| 948 |
+
else:
|
| 949 |
+
B = 1
|
| 950 |
+
tokens = []; masks = []
|
| 951 |
+
def _append_token(z_token: torch.Tensor):
|
| 952 |
+
tokens.append(z_token); masks.append(torch.ones((z_token.size(0),), dtype=torch.bool, device=device))
|
| 953 |
+
if self.gine is not None and batch_mods.get("gine", None) is not None:
|
| 954 |
+
g = batch_mods["gine"]
|
| 955 |
+
if isinstance(g.get("z", None), torch.Tensor) and g["z"].numel() > 0:
|
| 956 |
+
emb_g = self.gine(
|
| 957 |
+
g["z"].to(device),
|
| 958 |
+
g.get("chirality", torch.zeros_like(g["z"], dtype=torch.float)).to(device) if isinstance(g.get("chirality", None), torch.Tensor) else None,
|
| 959 |
+
g.get("formal_charge", torch.zeros_like(g["z"], dtype=torch.float)).to(device) if isinstance(g.get("formal_charge", None), torch.Tensor) else None,
|
| 960 |
+
g.get("edge_index", torch.empty((2,0), dtype=torch.long)).to(device),
|
| 961 |
+
g.get("edge_attr", torch.zeros((0,3), dtype=torch.float)).to(device),
|
| 962 |
+
g.get("batch", None).to(device) if isinstance(g.get("batch", None), torch.Tensor) else None
|
| 963 |
+
)
|
| 964 |
+
zg = self.proj_gine(emb_g); zg = self.dropout(zg); _append_token(zg)
|
| 965 |
+
if self.schnet is not None and batch_mods.get("schnet", None) is not None:
|
| 966 |
+
s = batch_mods["schnet"]
|
| 967 |
+
if isinstance(s.get("z", None), torch.Tensor) and s["z"].numel() > 0:
|
| 968 |
+
emb_s = self.schnet(s["z"].to(device), s["pos"].to(device), s.get("batch", None).to(device) if isinstance(s.get("batch", None), torch.Tensor) else None)
|
| 969 |
+
zs = self.proj_schnet(emb_s); zs = self.dropout(zs); _append_token(zs)
|
| 970 |
+
if self.fp is not None and batch_mods.get("fp", None) is not None:
|
| 971 |
+
f = batch_mods["fp"]
|
| 972 |
+
if isinstance(f.get("input_ids", None), torch.Tensor) and f["input_ids"].numel() > 0:
|
| 973 |
+
emb_f = self.fp(f["input_ids"].to(device), f.get("attention_mask", None).to(device) if isinstance(f.get("attention_mask", None), torch.Tensor) else None)
|
| 974 |
+
zf = self.proj_fp(emb_f); zf = self.dropout(zf); _append_token(zf)
|
| 975 |
+
if self.psmiles is not None and batch_mods.get("psmiles", None) is not None:
|
| 976 |
+
p = batch_mods["psmiles"]
|
| 977 |
+
if isinstance(p.get("input_ids", None), torch.Tensor) and p["input_ids"].numel() > 0:
|
| 978 |
+
emb_p = self.psmiles(p["input_ids"].to(device), p.get("attention_mask", None).to(device) if isinstance(p.get("attention_mask", None), torch.Tensor) else None)
|
| 979 |
+
zp = self.proj_psmiles(emb_p); zp = self.dropout(zp); _append_token(zp)
|
| 980 |
+
if not tokens:
|
| 981 |
+
z = torch.zeros((B, self.emb_dim), device=device)
|
| 982 |
+
return F.normalize(z, dim=-1)
|
| 983 |
+
X = torch.stack(tokens, dim=1)
|
| 984 |
+
mask = torch.ones((B, X.size(1)), dtype=torch.bool, device=device)
|
| 985 |
+
pooled = self.fusion(X, mask)
|
| 986 |
+
pooled = F.normalize(pooled, dim=-1)
|
| 987 |
+
return pooled
|
| 988 |
+
@torch.no_grad()
|
| 989 |
+
def encode_psmiles(self, psmiles_list: List[str], max_len: int = PSMILES_MAX_LEN, batch_size: int = 64, device: str = DEVICE) -> np.ndarray:
|
| 990 |
+
self.eval()
|
| 991 |
+
if self.psm_tok is None or self.psmiles is None or self.proj_psmiles is None:
|
| 992 |
+
raise RuntimeError("PSMILES tokenizer/encoder/projection not available.")
|
| 993 |
+
dev = torch.device(device)
|
| 994 |
+
self.to(dev)
|
| 995 |
+
outs = []
|
| 996 |
+
for i in range(0, len(psmiles_list), batch_size):
|
| 997 |
+
chunk = [str(x) for x in psmiles_list[i:i + batch_size]]
|
| 998 |
+
enc = self.psm_tok(chunk, truncation=True, padding="max_length", max_length=max_len, return_tensors="pt")
|
| 999 |
+
input_ids = enc["input_ids"].to(dev)
|
| 1000 |
+
attn = enc["attention_mask"].to(dev).bool()
|
| 1001 |
+
emb_p = self.psmiles(input_ids, attn)
|
| 1002 |
+
z = self.proj_psmiles(emb_p)
|
| 1003 |
+
z = F.normalize(z, dim=-1)
|
| 1004 |
+
outs.append(z.detach().cpu().numpy())
|
| 1005 |
+
return np.concatenate(outs, axis=0) if outs else np.zeros((0, self.emb_dim), dtype=np.float32)
|
| 1006 |
+
@torch.no_grad()
|
| 1007 |
+
def encode_multimodal(self, records: List[dict], batch_size: int = 32, device: str = DEVICE) -> np.ndarray:
|
| 1008 |
+
self.eval(); dev = torch.device(device); self.to(dev)
|
| 1009 |
+
outs = []
|
| 1010 |
+
for i in range(0, len(records), batch_size):
|
| 1011 |
+
chunk = records[i:i + batch_size]
|
| 1012 |
+
psmiles_texts = [str(r.get("psmiles", "")) for r in chunk]
|
| 1013 |
+
p_enc = None
|
| 1014 |
+
if self.psm_tok is not None:
|
| 1015 |
+
p_enc = self.psm_tok(psmiles_texts, truncation=True, padding="max_length",
|
| 1016 |
+
max_length=PSMILES_MAX_LEN, return_tensors="pt")
|
| 1017 |
+
fp_ids, fp_attn = [], []
|
| 1018 |
+
for r in chunk:
|
| 1019 |
+
f = _parse_fingerprints(r.get("fingerprints", None), fp_len=FP_LENGTH)
|
| 1020 |
+
fp_ids.append(f["input_ids"]); fp_attn.append(f["attention_mask"])
|
| 1021 |
+
fp_ids = torch.stack(fp_ids, dim=0); fp_attn = torch.stack(fp_attn, dim=0)
|
| 1022 |
+
gine_all = {"z": [], "chirality": [], "formal_charge": [], "edge_index": [], "edge_attr": [], "batch": []}
|
| 1023 |
+
node_offset = 0
|
| 1024 |
+
for bi, r in enumerate(chunk):
|
| 1025 |
+
g = _parse_graph_for_gine(r.get("graph", None))
|
| 1026 |
+
if g is None or g["z"].numel() == 0: continue
|
| 1027 |
+
n = g["z"].size(0)
|
| 1028 |
+
gine_all["z"].append(g["z"]); gine_all["chirality"].append(g["chirality"]); gine_all["formal_charge"].append(g["formal_charge"])
|
| 1029 |
+
gine_all["batch"].append(torch.full((n,), bi, dtype=torch.long))
|
| 1030 |
+
ei = g["edge_index"]; ea = g["edge_attr"]
|
| 1031 |
+
if ei is not None and ei.numel() > 0:
|
| 1032 |
+
gine_all["edge_index"].append(ei + node_offset); gine_all["edge_attr"].append(ea)
|
| 1033 |
+
node_offset += n
|
| 1034 |
+
gine_batch = None
|
| 1035 |
+
if len(gine_all["z"]) > 0:
|
| 1036 |
+
z_b = torch.cat(gine_all["z"], dim=0)
|
| 1037 |
+
ch_b = torch.cat(gine_all["chirality"], dim=0)
|
| 1038 |
+
fc_b = torch.cat(gine_all["formal_charge"], dim=0)
|
| 1039 |
+
b_b = torch.cat(gine_all["batch"], dim=0)
|
| 1040 |
+
if len(gine_all["edge_index"]) > 0:
|
| 1041 |
+
ei_b = torch.cat(gine_all["edge_index"], dim=1)
|
| 1042 |
+
ea_b = torch.cat(gine_all["edge_attr"], dim=0)
|
| 1043 |
+
else:
|
| 1044 |
+
ei_b = torch.empty((2, 0), dtype=torch.long); ea_b = torch.zeros((0, 3), dtype=torch.float)
|
| 1045 |
+
gine_batch = {"z": z_b, "chirality": ch_b, "formal_charge": fc_b, "edge_index": ei_b, "edge_attr": ea_b, "batch": b_b}
|
| 1046 |
+
sch_all_z, sch_all_pos, sch_all_batch = [], [], []
|
| 1047 |
+
for bi, r in enumerate(chunk):
|
| 1048 |
+
s = _parse_geometry_for_schnet(r.get("geometry", None))
|
| 1049 |
+
if s is None or s["z"].numel() == 0: continue
|
| 1050 |
+
n = s["z"].size(0)
|
| 1051 |
+
sch_all_z.append(s["z"]); sch_all_pos.append(s["pos"]); sch_all_batch.append(torch.full((n,), bi, dtype=torch.long))
|
| 1052 |
+
schnet_batch = None
|
| 1053 |
+
if len(sch_all_z) > 0:
|
| 1054 |
+
schnet_batch = {"z": torch.cat(sch_all_z, dim=0), "pos": torch.cat(sch_all_pos, dim=0), "batch": torch.cat(sch_all_batch, dim=0)}
|
| 1055 |
+
batch_mods = {
|
| 1056 |
+
"gine": gine_batch,
|
| 1057 |
+
"schnet": schnet_batch,
|
| 1058 |
+
"fp": {"input_ids": fp_ids, "attention_mask": fp_attn},
|
| 1059 |
+
"psmiles": {"input_ids": p_enc["input_ids"], "attention_mask": p_enc["attention_mask"]} if p_enc is not None else None
|
| 1060 |
+
}
|
| 1061 |
+
z = self.forward_multimodal(batch_mods)
|
| 1062 |
+
outs.append(z.detach().cpu().numpy())
|
| 1063 |
+
return np.concatenate(outs, axis=0) if outs else np.zeros((0, self.emb_dim), dtype=np.float32)
|
| 1064 |
+
|
| 1065 |
+
# =============================================================================
|
| 1066 |
+
# SELFIES-TED decoder conditioned on CL embeddings
|
| 1067 |
+
# =============================================================================
|
| 1068 |
+
|
| 1069 |
+
SELFIES_TED_MODEL_NAME = os.environ.get("SELFIES_TED_MODEL_NAME", "ibm-research/materials.selfies-ted")
|
| 1070 |
+
HF_TOKEN = os.environ.get("HF_TOKEN", None)
|
| 1071 |
+
|
| 1072 |
+
def _hf_load_with_retries(load_fn, max_tries: int = 5, base_sleep: float = 2.0):
|
| 1073 |
+
last_err = None
|
| 1074 |
+
for t in range(max_tries):
|
| 1075 |
+
try:
|
| 1076 |
+
return load_fn()
|
| 1077 |
+
except Exception as e:
|
| 1078 |
+
last_err = e
|
| 1079 |
+
sleep_s = base_sleep * (1.6 ** t) + random.random()
|
| 1080 |
+
print(f"[WARN] HF load attempt {t+1}/{max_tries} failed: {e}. Sleeping {sleep_s:.1f}s then retry.")
|
| 1081 |
+
time.sleep(sleep_s)
|
| 1082 |
+
raise RuntimeError(f"Failed to load model from HF. Last error: {last_err}")
|
| 1083 |
+
|
| 1084 |
+
def load_selfies_ted_and_tokenizer(model_name: str = SELFIES_TED_MODEL_NAME):
|
| 1085 |
+
def _load_tok():
|
| 1086 |
+
return AutoTokenizer.from_pretrained(model_name, token=HF_TOKEN, use_fast=True)
|
| 1087 |
+
def _load_model():
|
| 1088 |
+
return AutoModelForSeq2SeqLM.from_pretrained(model_name, token=HF_TOKEN)
|
| 1089 |
+
tok = _hf_load_with_retries(_load_tok, max_tries=5)
|
| 1090 |
+
model = _hf_load_with_retries(_load_model, max_tries=5)
|
| 1091 |
+
return tok, model
|
| 1092 |
+
|
| 1093 |
+
class CLConditionedSelfiesTEDGenerator(nn.Module):
|
| 1094 |
+
def __init__(self, tok, seq2seq_model, cl_emb_dim: int = CL_EMB_DIM, mem_len: int = 4):
|
| 1095 |
+
super().__init__()
|
| 1096 |
+
self.tok = tok
|
| 1097 |
+
self.model = seq2seq_model
|
| 1098 |
+
self.mem_len = int(mem_len)
|
| 1099 |
+
d_model = int(getattr(self.model.config, "d_model", 1024))
|
| 1100 |
+
self.cl_to_d = nn.Sequential(nn.Linear(cl_emb_dim, d_model), nn.Tanh(), nn.Dropout(0.1), nn.Linear(d_model, d_model))
|
| 1101 |
+
self.mem_pos = nn.Embedding(self.mem_len, d_model)
|
| 1102 |
+
def build_encoder_outputs(self, z: torch.Tensor) -> Tuple[BaseModelOutput, torch.Tensor]:
|
| 1103 |
+
device = z.device
|
| 1104 |
+
B = z.size(0)
|
| 1105 |
+
d = self.cl_to_d(z)
|
| 1106 |
+
d = d.unsqueeze(1).expand(B, self.mem_len, d.size(-1)).contiguous()
|
| 1107 |
+
pos = torch.arange(self.mem_len, device=device).unsqueeze(0).expand(B, -1)
|
| 1108 |
+
d = d + self.mem_pos(pos)
|
| 1109 |
+
attn = torch.ones((B, self.mem_len), dtype=torch.long, device=device)
|
| 1110 |
+
return BaseModelOutput(last_hidden_state=d), attn
|
| 1111 |
+
def forward_train(self, z: torch.Tensor, labels: torch.Tensor) -> Dict[str, torch.Tensor]:
|
| 1112 |
+
enc_out, attn = self.build_encoder_outputs(z)
|
| 1113 |
+
out = self.model(encoder_outputs=enc_out, attention_mask=attn, labels=labels)
|
| 1114 |
+
loss = out.loss
|
| 1115 |
+
return {"loss": loss, "ce": loss.detach()}
|
| 1116 |
+
@torch.no_grad()
|
| 1117 |
+
def generate(self, z: torch.Tensor, num_return_sequences: int = 1, max_len: int = GEN_MAX_LEN,
|
| 1118 |
+
top_p: float = GEN_TOP_P, temperature: float = GEN_TEMPERATURE, repetition_penalty: float = GEN_REPETITION_PENALTY) -> List[str]:
|
| 1119 |
+
self.eval()
|
| 1120 |
+
z = z.to(next(self.parameters()).device)
|
| 1121 |
+
enc_out, attn = self.build_encoder_outputs(z)
|
| 1122 |
+
gen = self.model.generate(
|
| 1123 |
+
encoder_outputs=enc_out,
|
| 1124 |
+
attention_mask=attn,
|
| 1125 |
+
do_sample=True,
|
| 1126 |
+
top_p=float(top_p),
|
| 1127 |
+
temperature=float(temperature),
|
| 1128 |
+
repetition_penalty=float(repetition_penalty),
|
| 1129 |
+
num_return_sequences=int(num_return_sequences),
|
| 1130 |
+
max_length=int(max_len),
|
| 1131 |
+
min_length=int(GEN_MIN_LEN),
|
| 1132 |
+
pad_token_id=int(self.tok.pad_token_id) if self.tok.pad_token_id is not None else None,
|
| 1133 |
+
eos_token_id=int(self.tok.eos_token_id) if self.tok.eos_token_id is not None else None,
|
| 1134 |
+
)
|
| 1135 |
+
outs = self.tok.batch_decode(gen, skip_special_tokens=True, clean_up_tokenization_spaces=True)
|
| 1136 |
+
outs = [_ensure_two_at_endpoints(_selfies_compact(o)) for o in outs]
|
| 1137 |
+
return outs
|
| 1138 |
+
|
| 1139 |
+
def create_optimizer_and_scheduler_decoder(model: CLConditionedSelfiesTEDGenerator):
|
| 1140 |
+
for p in model.parameters():
|
| 1141 |
+
p.requires_grad = True
|
| 1142 |
+
opt = torch.optim.AdamW(model.parameters(), lr=LEARNING_RATE, weight_decay=WEIGHT_DECAY)
|
| 1143 |
+
sch = torch.optim.lr_scheduler.CosineAnnealingLR(opt, T_max=NUM_EPOCHS, eta_min=COSINE_ETA_MIN)
|
| 1144 |
+
return opt, sch
|
| 1145 |
+
|
| 1146 |
+
# =============================================================================
|
| 1147 |
+
# Datasets for latent-to-SELFIES training
|
| 1148 |
+
# =============================================================================
|
| 1149 |
+
|
| 1150 |
+
class LatentToPSELFIESDataset(Dataset):
|
| 1151 |
+
def __init__(self, records: List[dict], cl_encoder: MultiModalCLPolymerEncoder, selfies_tok,
|
| 1152 |
+
max_len: int = GEN_MAX_LEN, latent_noise_std: float = 0.0,
|
| 1153 |
+
cache_embeddings: bool = True, renormalize_after_noise: bool = True, use_multimodal: bool = True):
|
| 1154 |
+
self.records = records
|
| 1155 |
+
self.cl_encoder = cl_encoder
|
| 1156 |
+
self.tok = selfies_tok
|
| 1157 |
+
self.max_len = int(max_len)
|
| 1158 |
+
self.latent_noise_std = float(latent_noise_std)
|
| 1159 |
+
self.renorm = bool(renormalize_after_noise)
|
| 1160 |
+
self.use_multimodal = bool(use_multimodal)
|
| 1161 |
+
self.pad_id = int(self.tok.pad_token_id) if getattr(self.tok, "pad_token_id", None) is not None else 1
|
| 1162 |
+
self._cache = None
|
| 1163 |
+
if cache_embeddings:
|
| 1164 |
+
if self.use_multimodal:
|
| 1165 |
+
emb = self.cl_encoder.encode_multimodal(self.records, batch_size=32, device=DEVICE)
|
| 1166 |
+
else:
|
| 1167 |
+
psm = [str(r.get("psmiles", "")) for r in self.records]
|
| 1168 |
+
emb = self.cl_encoder.encode_psmiles(psm, max_len=PSMILES_MAX_LEN, batch_size=64, device=DEVICE)
|
| 1169 |
+
self._cache = emb.astype(np.float32)
|
| 1170 |
+
def __len__(self):
|
| 1171 |
+
return len(self.records)
|
| 1172 |
+
def __getitem__(self, idx):
|
| 1173 |
+
r = self.records[idx]
|
| 1174 |
+
tgt = str(r["pselfies"]).strip()
|
| 1175 |
+
tgt = _selfies_for_tokenizer(tgt)
|
| 1176 |
+
if self._cache is not None:
|
| 1177 |
+
z = torch.tensor(self._cache[idx], dtype=torch.float32)
|
| 1178 |
+
else:
|
| 1179 |
+
if self.use_multimodal:
|
| 1180 |
+
z_np = self.cl_encoder.encode_multimodal([r], batch_size=1, device=DEVICE)
|
| 1181 |
+
z = torch.tensor(z_np[0], dtype=torch.float32)
|
| 1182 |
+
else:
|
| 1183 |
+
psm = str(r.get("psmiles", "")).strip()
|
| 1184 |
+
z_np = self.cl_encoder.encode_psmiles([psm], max_len=PSMILES_MAX_LEN, batch_size=1, device=DEVICE)
|
| 1185 |
+
z = torch.tensor(z_np[0], dtype=torch.float32)
|
| 1186 |
+
if self.latent_noise_std > 0:
|
| 1187 |
+
z = z + torch.randn_like(z) * self.latent_noise_std
|
| 1188 |
+
if self.renorm:
|
| 1189 |
+
z = F.normalize(z, dim=-1)
|
| 1190 |
+
enc = self.tok(tgt, truncation=True, padding="max_length", max_length=self.max_len, return_tensors=None)
|
| 1191 |
+
labels = torch.tensor(enc["input_ids"], dtype=torch.long)
|
| 1192 |
+
labels = labels.masked_fill(labels == self.pad_id, -100)
|
| 1193 |
+
return {"z": z, "labels": labels, "psmiles": str(r.get("psmiles", "")).strip(), "pselfies_raw": _selfies_compact(r["pselfies"])}
|
| 1194 |
+
|
| 1195 |
+
def latent_collate(batch: List[dict]) -> dict:
|
| 1196 |
+
z = torch.stack([b["z"] for b in batch], dim=0)
|
| 1197 |
+
labels = torch.stack([b["labels"] for b in batch], dim=0)
|
| 1198 |
+
return {"z": z, "labels": labels, "psmiles": [b["psmiles"] for b in batch], "pselfies_raw": [b["pselfies_raw"] for b in batch]}
|
| 1199 |
+
|
| 1200 |
+
def move_latent_batch_to_device(batch: dict, device: str):
|
| 1201 |
+
batch["z"] = batch["z"].to(device)
|
| 1202 |
+
batch["labels"] = batch["labels"].to(device)
|
| 1203 |
+
|
| 1204 |
+
# =============================================================================
|
| 1205 |
+
# Aux PSMILES property oracle (optional)
|
| 1206 |
+
# =============================================================================
|
| 1207 |
+
|
| 1208 |
+
class PSMILESPropertyDataset(Dataset):
|
| 1209 |
+
def __init__(self, samples: List[dict], psmiles_tokenizer, max_len: int = PSMILES_MAX_LEN):
|
| 1210 |
+
self.samples = samples
|
| 1211 |
+
self.tok = psmiles_tokenizer
|
| 1212 |
+
self.max_len = max_len
|
| 1213 |
+
def __len__(self):
|
| 1214 |
+
return len(self.samples)
|
| 1215 |
+
def __getitem__(self, idx):
|
| 1216 |
+
s = str(self.samples[idx].get("psmiles", "")).strip()
|
| 1217 |
+
y = float(self.samples[idx].get("target_scaled", self.samples[idx].get("target", 0.0)))
|
| 1218 |
+
enc = self.tok(s, truncation=True, padding="max_length", max_length=self.max_len)
|
| 1219 |
+
return {"input_ids": torch.tensor(enc["input_ids"], dtype=torch.long),
|
| 1220 |
+
"attention_mask": torch.tensor(enc["attention_mask"], dtype=torch.bool),
|
| 1221 |
+
"y": torch.tensor([y], dtype=torch.float32)}
|
| 1222 |
+
|
| 1223 |
+
def psmiles_prop_collate_fn(batch: List[dict]):
|
| 1224 |
+
input_ids = torch.stack([b["input_ids"] for b in batch], dim=0)
|
| 1225 |
+
attn = torch.stack([b["attention_mask"] for b in batch], dim=0)
|
| 1226 |
+
y = torch.stack([b["y"] for b in batch], dim=0)
|
| 1227 |
+
return {"input_ids": input_ids, "attention_mask": attn, "y": y}
|
| 1228 |
+
|
| 1229 |
+
class TextPropertyOracle(nn.Module):
|
| 1230 |
+
def __init__(self, encoder_dir: Optional[str], vocab_size: Optional[int] = None, y_dim: int = 1):
|
| 1231 |
+
super().__init__()
|
| 1232 |
+
enc_src = None
|
| 1233 |
+
if encoder_dir is not None and os.path.isdir(encoder_dir):
|
| 1234 |
+
enc_src = encoder_dir
|
| 1235 |
+
elif os.path.isdir(BEST_PSMILES_DIR):
|
| 1236 |
+
enc_src = BEST_PSMILES_DIR
|
| 1237 |
+
else:
|
| 1238 |
+
enc_src = "microsoft/deberta-v2-xlarge"
|
| 1239 |
+
self.encoder = PSMILESDebertaEncoder(model_dir_or_name=enc_src, vocab_size=vocab_size)
|
| 1240 |
+
h = getattr(self.encoder, "out_dim", DEBERTA_HIDDEN)
|
| 1241 |
+
self.head = nn.Sequential(nn.Linear(h, 256), nn.ReLU(), nn.Dropout(0.1), nn.Linear(256, y_dim))
|
| 1242 |
+
def forward(self, input_ids: torch.Tensor, attention_mask: Optional[torch.Tensor] = None) -> torch.Tensor:
|
| 1243 |
+
h = self.encoder(input_ids=input_ids, attention_mask=attention_mask)
|
| 1244 |
+
return self.head(h)
|
| 1245 |
+
|
| 1246 |
+
def move_prop_batch_to_device(batch: dict, device: str):
|
| 1247 |
+
batch["input_ids"] = batch["input_ids"].to(device)
|
| 1248 |
+
batch["attention_mask"] = batch["attention_mask"].to(device)
|
| 1249 |
+
batch["y"] = batch["y"].to(device)
|
| 1250 |
+
|
| 1251 |
+
def train_prop_oracle_one_epoch(model: TextPropertyOracle, dl: DataLoader, opt, scaler_amp, device: str):
|
| 1252 |
+
model.train()
|
| 1253 |
+
total = 0.0; n = 0
|
| 1254 |
+
for batch in dl:
|
| 1255 |
+
move_prop_batch_to_device(batch, device)
|
| 1256 |
+
y = batch["y"]
|
| 1257 |
+
opt.zero_grad(set_to_none=True)
|
| 1258 |
+
with torch.cuda.amp.autocast(enabled=USE_AMP, dtype=AMP_DTYPE):
|
| 1259 |
+
y_hat = model(batch["input_ids"], batch["attention_mask"])
|
| 1260 |
+
loss = F.smooth_l1_loss(y_hat, y, beta=1.0)
|
| 1261 |
+
if USE_AMP:
|
| 1262 |
+
scaler_amp.scale(loss).backward()
|
| 1263 |
+
scaler_amp.unscale_(opt)
|
| 1264 |
+
torch.nn.utils.clip_grad_norm_(model.parameters(), 1.0)
|
| 1265 |
+
scaler_amp.step(opt)
|
| 1266 |
+
scaler_amp.update()
|
| 1267 |
+
else:
|
| 1268 |
+
loss.backward()
|
| 1269 |
+
torch.nn.utils.clip_grad_norm_(model.parameters(), 1.0)
|
| 1270 |
+
opt.step()
|
| 1271 |
+
bs = y.size(0)
|
| 1272 |
+
total += float(loss.item()) * bs; n += bs
|
| 1273 |
+
return total / max(1, n)
|
| 1274 |
+
|
| 1275 |
+
@torch.no_grad()
|
| 1276 |
+
def eval_prop_oracle(model: TextPropertyOracle, dl: DataLoader, device: str):
|
| 1277 |
+
model.eval()
|
| 1278 |
+
total = 0.0; n = 0
|
| 1279 |
+
for batch in dl:
|
| 1280 |
+
move_prop_batch_to_device(batch, device)
|
| 1281 |
+
y = batch["y"]
|
| 1282 |
+
with torch.cuda.amp.autocast(enabled=USE_AMP, dtype=AMP_DTYPE):
|
| 1283 |
+
y_hat = model(batch["input_ids"], batch["attention_mask"])
|
| 1284 |
+
loss = F.smooth_l1_loss(y_hat, y, beta=1.0)
|
| 1285 |
+
bs = y.size(0); total += float(loss.item()) * bs; n += bs
|
| 1286 |
+
return total / max(1, n)
|
| 1287 |
+
|
| 1288 |
+
def train_property_oracle_per_fold(train_samples: List[dict], val_samples: List[dict], psmiles_tokenizer, device: str, max_len: int = PSMILES_MAX_LEN) -> Optional[TextPropertyOracle]:
|
| 1289 |
+
if psmiles_tokenizer is None:
|
| 1290 |
+
return None
|
| 1291 |
+
try:
|
| 1292 |
+
model = TextPropertyOracle(
|
| 1293 |
+
encoder_dir=BEST_PSMILES_DIR if os.path.isdir(BEST_PSMILES_DIR) else None,
|
| 1294 |
+
vocab_size=getattr(psmiles_tokenizer, "vocab_size", None),
|
| 1295 |
+
y_dim=1
|
| 1296 |
+
).to(device)
|
| 1297 |
+
except Exception as e:
|
| 1298 |
+
print(f"[WARN] Could not initialize auxiliary property predictor: {e}")
|
| 1299 |
+
return None
|
| 1300 |
+
for p in model.encoder.parameters(): p.requires_grad = False
|
| 1301 |
+
for p in model.head.parameters(): p.requires_grad = True
|
| 1302 |
+
ds_tr = PSMILESPropertyDataset(train_samples, psmiles_tokenizer, max_len=max_len)
|
| 1303 |
+
ds_va = PSMILESPropertyDataset(val_samples, psmiles_tokenizer, max_len=max_len)
|
| 1304 |
+
dl_tr = DataLoader(ds_tr, batch_size=PROP_PRED_BATCH_SIZE, shuffle=True, num_workers=NUM_WORKERS, pin_memory=True, collate_fn=psmiles_prop_collate_fn)
|
| 1305 |
+
dl_va = DataLoader(ds_va, batch_size=PROP_PRED_BATCH_SIZE, shuffle=False, num_workers=NUM_WORKERS, pin_memory=True, collate_fn=psmiles_prop_collate_fn)
|
| 1306 |
+
opt = torch.optim.AdamW([p for p in model.parameters() if p.requires_grad], lr=PROP_PRED_LR, weight_decay=PROP_PRED_WEIGHT_DECAY)
|
| 1307 |
+
scaler_amp = torch.cuda.amp.GradScaler(enabled=USE_AMP)
|
| 1308 |
+
best_val = float("inf"); best_state = None; no_imp = 0
|
| 1309 |
+
for epoch in range(1, PROP_PRED_EPOCHS + 1):
|
| 1310 |
+
tr = train_prop_oracle_one_epoch(model, dl_tr, opt, scaler_amp, device)
|
| 1311 |
+
va = eval_prop_oracle(model, dl_va, device)
|
| 1312 |
+
if va < best_val - 1e-8:
|
| 1313 |
+
best_val = va; no_imp = 0
|
| 1314 |
+
best_state = {k: v.detach().cpu().clone() for k, v in model.state_dict().items()}
|
| 1315 |
+
else:
|
| 1316 |
+
no_imp += 1
|
| 1317 |
+
if no_imp >= PROP_PRED_PATIENCE:
|
| 1318 |
+
break
|
| 1319 |
+
if best_state is not None:
|
| 1320 |
+
model.load_state_dict({k: v.to(device) for k, v in best_state.items()}, strict=False)
|
| 1321 |
+
try: model.aux_val_loss = float(best_val)
|
| 1322 |
+
except Exception: pass
|
| 1323 |
+
return model
|
| 1324 |
+
|
| 1325 |
+
@torch.no_grad()
|
| 1326 |
+
def oracle_predict_scaled(oracle: Optional[TextPropertyOracle], psmiles_tokenizer, psmiles_list: List[str], device: str, max_len: int = PSMILES_MAX_LEN) -> Optional[np.ndarray]:
|
| 1327 |
+
if oracle is None or psmiles_tokenizer is None:
|
| 1328 |
+
return None
|
| 1329 |
+
if not psmiles_list:
|
| 1330 |
+
return np.array([], dtype=np.float32)
|
| 1331 |
+
oracle.eval()
|
| 1332 |
+
ys = []; bs = 32
|
| 1333 |
+
for i in range(0, len(psmiles_list), bs):
|
| 1334 |
+
chunk = psmiles_list[i:i+bs]
|
| 1335 |
+
enc = psmiles_tokenizer(chunk, truncation=True, padding="max_length", max_length=max_len, return_tensors="pt")
|
| 1336 |
+
input_ids = enc["input_ids"].to(device)
|
| 1337 |
+
attn = enc["attention_mask"].to(device).bool()
|
| 1338 |
+
with torch.cuda.amp.autocast(enabled=USE_AMP, dtype=AMP_DTYPE):
|
| 1339 |
+
y_hat = oracle(input_ids, attn)
|
| 1340 |
+
ys.append(y_hat.detach().cpu().numpy().reshape(-1))
|
| 1341 |
+
return np.concatenate(ys, axis=0) if ys else np.array([], dtype=np.float32)
|
| 1342 |
+
|
| 1343 |
+
# =============================================================================
|
| 1344 |
+
# PolyBART-style latent property model (per property)
|
| 1345 |
+
# =============================================================================
|
| 1346 |
+
|
| 1347 |
+
@dataclass
|
| 1348 |
+
class LatentPropertyModel:
|
| 1349 |
+
y_scaler: StandardScaler
|
| 1350 |
+
pca: Optional[PCA]
|
| 1351 |
+
gpr: GaussianProcessRegressor
|
| 1352 |
+
|
| 1353 |
+
def fit_latent_property_model(z_train: np.ndarray, y_train: np.ndarray, y_scaler: StandardScaler) -> LatentPropertyModel:
|
| 1354 |
+
y_train = np.array(y_train, dtype=np.float32).reshape(-1, 1)
|
| 1355 |
+
y_s = y_scaler.transform(y_train).reshape(-1).astype(np.float32)
|
| 1356 |
+
z_use = z_train.astype(np.float32)
|
| 1357 |
+
pca = None
|
| 1358 |
+
if USE_PCA_BEFORE_GPR:
|
| 1359 |
+
ncomp = int(min(PCA_DIM, z_use.shape[0] - 1, z_use.shape[1]))
|
| 1360 |
+
ncomp = max(2, ncomp)
|
| 1361 |
+
pca = PCA(n_components=ncomp, random_state=0)
|
| 1362 |
+
z_use = pca.fit_transform(z_use)
|
| 1363 |
+
kernel = C(1.0, (1e-3, 1e3)) * RBF(length_scale=1.0, length_scale_bounds=(1e-2, 1e2)) + WhiteKernel(noise_level=1e-3, noise_level_bounds=(1e-6, 1e-1))
|
| 1364 |
+
gpr = GaussianProcessRegressor(kernel=kernel, alpha=GPR_ALPHA, normalize_y=True, random_state=0, n_restarts_optimizer=2)
|
| 1365 |
+
gpr.fit(z_use, y_s)
|
| 1366 |
+
return LatentPropertyModel(y_scaler=y_scaler, pca=pca, gpr=gpr)
|
| 1367 |
+
|
| 1368 |
+
def predict_latent_property(model: LatentPropertyModel, z: np.ndarray) -> Tuple[np.ndarray, np.ndarray]:
|
| 1369 |
+
z_use = z.astype(np.float32)
|
| 1370 |
+
if model.pca is not None:
|
| 1371 |
+
z_use = model.pca.transform(z_use)
|
| 1372 |
+
y_s = model.gpr.predict(z_use, return_std=False)
|
| 1373 |
+
y_s = np.array(y_s, dtype=np.float32).reshape(-1)
|
| 1374 |
+
y_u = model.y_scaler.inverse_transform(y_s.reshape(-1, 1)).reshape(-1)
|
| 1375 |
+
return y_s, y_u
|
| 1376 |
+
|
| 1377 |
+
# =============================================================================
|
| 1378 |
+
# Train / eval loops (decoder)
|
| 1379 |
+
# =============================================================================
|
| 1380 |
+
|
| 1381 |
+
def train_one_epoch_decoder(model: CLConditionedSelfiesTEDGenerator, dl: DataLoader, optimizer, scaler_amp, device: str):
|
| 1382 |
+
model.train()
|
| 1383 |
+
total = 0.0; n = 0; ce_sum = 0.0
|
| 1384 |
+
for batch in dl:
|
| 1385 |
+
move_latent_batch_to_device(batch, device)
|
| 1386 |
+
z = batch["z"]; labels = batch["labels"]
|
| 1387 |
+
optimizer.zero_grad(set_to_none=True)
|
| 1388 |
+
with torch.cuda.amp.autocast(enabled=USE_AMP, dtype=AMP_DTYPE):
|
| 1389 |
+
out = model.forward_train(z, labels)
|
| 1390 |
+
loss = out["loss"]
|
| 1391 |
+
if USE_AMP:
|
| 1392 |
+
scaler_amp.scale(loss).backward()
|
| 1393 |
+
scaler_amp.unscale_(optimizer)
|
| 1394 |
+
torch.nn.utils.clip_grad_norm_(model.parameters(), 1.0)
|
| 1395 |
+
scaler_amp.step(optimizer)
|
| 1396 |
+
scaler_amp.update()
|
| 1397 |
+
else:
|
| 1398 |
+
loss.backward()
|
| 1399 |
+
torch.nn.utils.clip_grad_norm_(model.parameters(), 1.0)
|
| 1400 |
+
optimizer.step()
|
| 1401 |
+
bs = z.size(0)
|
| 1402 |
+
total += float(loss.item()) * bs; ce_sum += float(out["ce"].item()) * bs; n += bs
|
| 1403 |
+
return {"loss": total / max(1, n), "ce": ce_sum / max(1, n)}
|
| 1404 |
+
|
| 1405 |
+
@torch.no_grad()
|
| 1406 |
+
def evaluate_decoder(model: CLConditionedSelfiesTEDGenerator, dl: DataLoader, device: str):
|
| 1407 |
+
model.eval()
|
| 1408 |
+
total = 0.0; n = 0; ce_sum = 0.0
|
| 1409 |
+
for batch in dl:
|
| 1410 |
+
move_latent_batch_to_device(batch, device)
|
| 1411 |
+
z = batch["z"]; labels = batch["labels"]
|
| 1412 |
+
with torch.cuda.amp.autocast(enabled=USE_AMP, dtype=AMP_DTYPE):
|
| 1413 |
+
out = model.forward_train(z, labels)
|
| 1414 |
+
loss = out["loss"]
|
| 1415 |
+
bs = z.size(0)
|
| 1416 |
+
total += float(loss.item()) * bs; ce_sum += float(out["ce"].item()) * bs; n += bs
|
| 1417 |
+
return {"loss": total / max(1, n), "ce": ce_sum / max(1, n)}
|
| 1418 |
+
|
| 1419 |
+
# =============================================================================
|
| 1420 |
+
# Generation / filtering (per target value, per property)
|
| 1421 |
+
# =============================================================================
|
| 1422 |
+
|
| 1423 |
+
def compute_diversity_morgan(smiles_list: List[str], radius: int = 2, nbits: int = 2048, p: float = 1.0) -> Optional[float]:
|
| 1424 |
+
if not RDKit_AVAILABLE:
|
| 1425 |
+
return None
|
| 1426 |
+
try:
|
| 1427 |
+
p = float(p)
|
| 1428 |
+
if not np.isfinite(p) or p <= 0:
|
| 1429 |
+
p = 1.0
|
| 1430 |
+
except Exception:
|
| 1431 |
+
p = 1.0
|
| 1432 |
+
uniq = []
|
| 1433 |
+
seen = set()
|
| 1434 |
+
for smi in smiles_list:
|
| 1435 |
+
smi = str(smi).strip()
|
| 1436 |
+
if not smi or smi in seen:
|
| 1437 |
+
continue
|
| 1438 |
+
seen.add(smi)
|
| 1439 |
+
uniq.append(smi)
|
| 1440 |
+
fps = []
|
| 1441 |
+
for smi in uniq:
|
| 1442 |
+
try:
|
| 1443 |
+
mol = Chem.MolFromSmiles(smi)
|
| 1444 |
+
if mol is None:
|
| 1445 |
+
continue
|
| 1446 |
+
try:
|
| 1447 |
+
Chem.SanitizeMol(mol, catchErrors=True)
|
| 1448 |
+
except Exception:
|
| 1449 |
+
continue
|
| 1450 |
+
fp = AllChem.GetMorganFingerprintAsBitVect(mol, radius, nBits=nbits)
|
| 1451 |
+
fps.append(fp)
|
| 1452 |
+
except Exception:
|
| 1453 |
+
continue
|
| 1454 |
+
if len(fps) < 2:
|
| 1455 |
+
return 0.0 if len(fps) == 1 else None
|
| 1456 |
+
sims_p = []
|
| 1457 |
+
for i in range(len(fps)):
|
| 1458 |
+
for j in range(i + 1, len(fps)):
|
| 1459 |
+
try:
|
| 1460 |
+
s = float(DataStructs.TanimotoSimilarity(fps[i], fps[j]))
|
| 1461 |
+
sims_p.append(s ** p)
|
| 1462 |
+
except Exception:
|
| 1463 |
+
continue
|
| 1464 |
+
if not sims_p:
|
| 1465 |
+
return None
|
| 1466 |
+
mean_sim_p = float(np.mean(sims_p))
|
| 1467 |
+
try:
|
| 1468 |
+
mean_sim = mean_sim_p ** (1.0 / p)
|
| 1469 |
+
except Exception:
|
| 1470 |
+
mean_sim = float(np.mean([float(DataStructs.TanimotoSimilarity(fps[i], fps[j])) for i in range(len(fps)) for j in range(i + 1, len(fps))]))
|
| 1471 |
+
return float(1.0 - mean_sim)
|
| 1472 |
+
|
| 1473 |
+
@torch.no_grad()
|
| 1474 |
+
def decode_from_latents(generator: CLConditionedSelfiesTEDGenerator, z: torch.Tensor, n_samples: int = 1) -> List[str]:
|
| 1475 |
+
outs = generator.generate(z=z, num_return_sequences=int(n_samples), max_len=GEN_MAX_LEN,
|
| 1476 |
+
top_p=GEN_TOP_P, temperature=GEN_TEMPERATURE, repetition_penalty=GEN_REPETITION_PENALTY)
|
| 1477 |
+
return outs
|
| 1478 |
+
|
| 1479 |
+
def polybart_style_generate_for_target(
|
| 1480 |
+
target_y_scaled: float,
|
| 1481 |
+
prop_model: LatentPropertyModel,
|
| 1482 |
+
cl_encoder: MultiModalCLPolymerEncoder,
|
| 1483 |
+
generator: CLConditionedSelfiesTEDGenerator,
|
| 1484 |
+
train_seed_pool: List[dict],
|
| 1485 |
+
train_targets_set: set,
|
| 1486 |
+
n_seeds: int = 8,
|
| 1487 |
+
n_noise: int = N_FOLD_NOISE_SAMPLING,
|
| 1488 |
+
noise_std: float = LATENT_NOISE_STD_GEN,
|
| 1489 |
+
prop_tol_scaled: float = PROP_TOL_SCALED,
|
| 1490 |
+
oracle: Optional[TextPropertyOracle] = None,
|
| 1491 |
+
psmiles_tokenizer=None,
|
| 1492 |
+
) -> Dict[str, Any]:
|
| 1493 |
+
|
| 1494 |
+
def _l2_normalize_np(x: np.ndarray, eps: float = 1e-12) -> np.ndarray:
|
| 1495 |
+
n = np.linalg.norm(x, axis=-1, keepdims=True)
|
| 1496 |
+
return x / np.clip(n, eps, None)
|
| 1497 |
+
|
| 1498 |
+
ys = np.array([float(d["y_scaled"]) for d in train_seed_pool], dtype=np.float32)
|
| 1499 |
+
diffs = np.abs(ys - float(target_y_scaled))
|
| 1500 |
+
order = np.argsort(diffs)
|
| 1501 |
+
chosen = [train_seed_pool[i] for i in order[:max(1, int(n_seeds))]]
|
| 1502 |
+
|
| 1503 |
+
z_seed = cl_encoder.encode_multimodal(chosen, batch_size=32, device=DEVICE)
|
| 1504 |
+
if z_seed.shape[0] == 0:
|
| 1505 |
+
return {"generated": [], "metrics": {}}
|
| 1506 |
+
|
| 1507 |
+
z_list = []
|
| 1508 |
+
for i in range(z_seed.shape[0]):
|
| 1509 |
+
z0 = z_seed[i].astype(np.float32)
|
| 1510 |
+
for _ in range(int(n_noise)):
|
| 1511 |
+
z = z0 + np.random.randn(z0.shape[0]).astype(np.float32) * float(noise_std)
|
| 1512 |
+
z = _l2_normalize_np(z.reshape(1, -1)).reshape(-1)
|
| 1513 |
+
z_list.append(z)
|
| 1514 |
+
|
| 1515 |
+
z_all = np.stack(z_list, axis=0).astype(np.float32)
|
| 1516 |
+
z_t = torch.tensor(z_all, dtype=torch.float32, device=DEVICE)
|
| 1517 |
+
|
| 1518 |
+
pselfies = decode_from_latents(generator, z_t, n_samples=1)
|
| 1519 |
+
|
| 1520 |
+
valid_psmiles = []
|
| 1521 |
+
valid_flags, poly_flags = [], []
|
| 1522 |
+
|
| 1523 |
+
for s in pselfies:
|
| 1524 |
+
s = _ensure_two_at_endpoints(_selfies_compact(s))
|
| 1525 |
+
psm = pselfies_to_psmiles(s) if (RDKit_AVAILABLE and SELFIES_AVAILABLE) else None
|
| 1526 |
+
if psm is None:
|
| 1527 |
+
valid_flags.append(False); poly_flags.append(False)
|
| 1528 |
+
continue
|
| 1529 |
+
psm_can = canonicalize_psmiles(psm)
|
| 1530 |
+
ok = chem_validity_psmiles(psm_can) if psm_can else False
|
| 1531 |
+
poly_ok = polymer_validity_psmiles_strict(psm_can) if psm_can else False
|
| 1532 |
+
valid_flags.append(bool(ok)); poly_flags.append(bool(poly_ok))
|
| 1533 |
+
if ok and poly_ok and psm_can:
|
| 1534 |
+
valid_psmiles.append(psm_can)
|
| 1535 |
+
|
| 1536 |
+
uniq_valid = sorted(set(valid_psmiles))
|
| 1537 |
+
novelty_valid = [1.0 if s not in train_targets_set else 0.0 for s in uniq_valid] if uniq_valid else []
|
| 1538 |
+
|
| 1539 |
+
n_valid_poly = int(len(valid_psmiles))
|
| 1540 |
+
uniqueness_valid_unique = float(len(uniq_valid)) / float(max(1, n_valid_poly)) if n_valid_poly > 0 else 0.0
|
| 1541 |
+
|
| 1542 |
+
if uniq_valid:
|
| 1543 |
+
z_cand = cl_encoder.encode_psmiles(uniq_valid, max_len=PSMILES_MAX_LEN, batch_size=64, device=DEVICE)
|
| 1544 |
+
else:
|
| 1545 |
+
z_cand = np.zeros((0, cl_encoder.out_dim), dtype=np.float32)
|
| 1546 |
+
|
| 1547 |
+
yhat_s, yhat_u = (np.array([], dtype=np.float32), np.array([], dtype=np.float32))
|
| 1548 |
+
if z_cand.shape[0] > 0:
|
| 1549 |
+
yhat_s, yhat_u = predict_latent_property(prop_model, z_cand)
|
| 1550 |
+
|
| 1551 |
+
keep, keep_pred_scaled, keep_pred_unscaled = [], [], []
|
| 1552 |
+
for i, psm in enumerate(uniq_valid):
|
| 1553 |
+
if abs(float(yhat_s[i]) - float(target_y_scaled)) <= float(prop_tol_scaled):
|
| 1554 |
+
keep.append(psm)
|
| 1555 |
+
keep_pred_scaled.append(float(yhat_s[i]))
|
| 1556 |
+
keep_pred_unscaled.append(float(yhat_u[i]))
|
| 1557 |
+
|
| 1558 |
+
novelty_keep = [1.0 if s not in train_targets_set else 0.0 for s in keep] if keep else []
|
| 1559 |
+
|
| 1560 |
+
aux_pred_scaled = None
|
| 1561 |
+
if VERIFY_GENERATED_PROPERTIES and oracle is not None and psmiles_tokenizer is not None and keep:
|
| 1562 |
+
aux = oracle_predict_scaled(oracle, psmiles_tokenizer, keep, DEVICE, PSMILES_MAX_LEN)
|
| 1563 |
+
aux_pred_scaled = aux.tolist() if aux is not None else None
|
| 1564 |
+
|
| 1565 |
+
at_smiles = []
|
| 1566 |
+
if RDKit_AVAILABLE and keep:
|
| 1567 |
+
for psm in keep:
|
| 1568 |
+
at_smi = psmiles_to_at_smiles(psm, root_at=False)
|
| 1569 |
+
if at_smi is not None:
|
| 1570 |
+
at_smiles.append(at_smi)
|
| 1571 |
+
div = compute_diversity_morgan(at_smiles) if at_smiles else None
|
| 1572 |
+
|
| 1573 |
+
metrics = {
|
| 1574 |
+
"n_total": int(len(pselfies)),
|
| 1575 |
+
"validity": float(np.mean(valid_flags)) if valid_flags else 0.0,
|
| 1576 |
+
"polymer_validity": float(np.mean(poly_flags)) if poly_flags else 0.0,
|
| 1577 |
+
"n_valid_unique": int(len(uniq_valid)),
|
| 1578 |
+
"novelty_valid_unique": float(np.mean(novelty_valid)) if novelty_valid else 0.0,
|
| 1579 |
+
"uniqueness_valid_unique": float(uniqueness_valid_unique),
|
| 1580 |
+
"n_kept_property_filtered": int(len(keep)),
|
| 1581 |
+
"novelty_kept": float(np.mean(novelty_keep)) if novelty_keep else 0.0,
|
| 1582 |
+
"diversity": float(div) if div is not None else 0.0,
|
| 1583 |
+
}
|
| 1584 |
+
|
| 1585 |
+
return {
|
| 1586 |
+
"generated": keep,
|
| 1587 |
+
"pred_scaled_kept": keep_pred_scaled,
|
| 1588 |
+
"pred_unscaled_kept": keep_pred_unscaled,
|
| 1589 |
+
"aux_pred_scaled": aux_pred_scaled,
|
| 1590 |
+
"metrics": metrics,
|
| 1591 |
+
}
|
| 1592 |
+
|
| 1593 |
+
# =============================================================================
|
| 1594 |
+
# Data assembly (per property)
|
| 1595 |
+
# =============================================================================
|
| 1596 |
+
|
| 1597 |
+
def build_polymer_records(df: pd.DataFrame, prop_col: str) -> List[dict]:
|
| 1598 |
+
"""
|
| 1599 |
+
Build records for a single property:
|
| 1600 |
+
- require valid polymer psmiles (chem + polymer validity)
|
| 1601 |
+
- carry pselfies, modalities, and the *single* target value
|
| 1602 |
+
"""
|
| 1603 |
+
if not (RDKit_AVAILABLE and SELFIES_AVAILABLE):
|
| 1604 |
+
raise RuntimeError("RDKit + selfies are required for this PolyBART-style pipeline.")
|
| 1605 |
+
|
| 1606 |
+
recs = []
|
| 1607 |
+
for _, row in df.iterrows():
|
| 1608 |
+
psmiles_raw = str(row.get("psmiles", "")).strip()
|
| 1609 |
+
if not psmiles_raw:
|
| 1610 |
+
continue
|
| 1611 |
+
psm_can = canonicalize_psmiles(psmiles_raw)
|
| 1612 |
+
if not psm_can:
|
| 1613 |
+
continue
|
| 1614 |
+
if not chem_validity_psmiles(psm_can):
|
| 1615 |
+
continue
|
| 1616 |
+
if not polymer_validity_psmiles_strict(psm_can):
|
| 1617 |
+
continue
|
| 1618 |
+
|
| 1619 |
+
val = row.get(prop_col, None)
|
| 1620 |
+
if val is None:
|
| 1621 |
+
continue
|
| 1622 |
+
try:
|
| 1623 |
+
y = float(val)
|
| 1624 |
+
if not np.isfinite(y):
|
| 1625 |
+
continue
|
| 1626 |
+
except Exception:
|
| 1627 |
+
continue
|
| 1628 |
+
|
| 1629 |
+
pself = psmiles_to_pselfies(psm_can)
|
| 1630 |
+
if pself is None:
|
| 1631 |
+
continue
|
| 1632 |
+
|
| 1633 |
+
recs.append({
|
| 1634 |
+
"psmiles": psm_can,
|
| 1635 |
+
"pselfies": pself,
|
| 1636 |
+
"y": y,
|
| 1637 |
+
"graph": row.get("graph", None),
|
| 1638 |
+
"geometry": row.get("geometry", None),
|
| 1639 |
+
"fingerprints": row.get("fingerprints", None),
|
| 1640 |
+
})
|
| 1641 |
+
return recs
|
| 1642 |
+
|
| 1643 |
+
# =============================================================================
|
| 1644 |
+
# Best-fold artifact saving (per property, G1-style)
|
| 1645 |
+
# =============================================================================
|
| 1646 |
+
|
| 1647 |
+
def save_best_fold_artifacts_for_property(
|
| 1648 |
+
property_name: str,
|
| 1649 |
+
fold_idx: int,
|
| 1650 |
+
decoder_state: Dict[str, torch.Tensor],
|
| 1651 |
+
prop_model: Optional[LatentPropertyModel],
|
| 1652 |
+
scaler: Optional[StandardScaler],
|
| 1653 |
+
best_val_loss: float,
|
| 1654 |
+
generations_payload: List[dict],
|
| 1655 |
+
):
|
| 1656 |
+
safe_prop = property_name.replace(" ", "_")
|
| 1657 |
+
prop_dir = os.path.join(OUTPUT_MODELS_DIR, safe_prop)
|
| 1658 |
+
os.makedirs(prop_dir, exist_ok=True)
|
| 1659 |
+
|
| 1660 |
+
# Decoder weights (state dict only; like G1 best_state)
|
| 1661 |
+
decoder_path = os.path.join(prop_dir, f"decoder_best_fold{fold_idx+1}.pt")
|
| 1662 |
+
torch.save(decoder_state, decoder_path)
|
| 1663 |
+
|
| 1664 |
+
# Scaler + GPR
|
| 1665 |
+
try:
|
| 1666 |
+
import joblib
|
| 1667 |
+
except Exception:
|
| 1668 |
+
joblib = None
|
| 1669 |
+
if joblib is not None:
|
| 1670 |
+
if scaler is not None:
|
| 1671 |
+
joblib.dump(scaler, os.path.join(prop_dir, f"standardscaler_{safe_prop}.joblib"))
|
| 1672 |
+
if prop_model is not None:
|
| 1673 |
+
joblib.dump(prop_model, os.path.join(prop_dir, f"gpr_psmiles_{safe_prop}.joblib"))
|
| 1674 |
+
|
| 1675 |
+
# Meta (mirror G1 spirit)
|
| 1676 |
+
meta = {
|
| 1677 |
+
"property": property_name,
|
| 1678 |
+
"best_fold": int(fold_idx + 1),
|
| 1679 |
+
"best_val_loss": float(best_val_loss),
|
| 1680 |
+
"selfies_ted_model": str(SELFIES_TED_MODEL_NAME),
|
| 1681 |
+
"cl_emb_dim": int(CL_EMB_DIM),
|
| 1682 |
+
"mem_len": 4,
|
| 1683 |
+
"tol_scaled": float(PROP_TOL_SCALED),
|
| 1684 |
+
"tol_unscaled_abs": float(PROP_TOL_UNSCALED_ABS) if PROP_TOL_UNSCALED_ABS is not None else None,
|
| 1685 |
+
"optimizer": "AdamW",
|
| 1686 |
+
"lr": float(LEARNING_RATE),
|
| 1687 |
+
"weight_decay": float(WEIGHT_DECAY),
|
| 1688 |
+
"lr_scheduler": "CosineAnnealingLR",
|
| 1689 |
+
"epochs": int(NUM_EPOCHS),
|
| 1690 |
+
"batch_size": int(BATCH_SIZE),
|
| 1691 |
+
"patience": int(PATIENCE),
|
| 1692 |
+
}
|
| 1693 |
+
try:
|
| 1694 |
+
with open(os.path.join(prop_dir, "meta.json"), "w", encoding="utf-8") as f:
|
| 1695 |
+
json.dump(meta, f, indent=2)
|
| 1696 |
+
except Exception:
|
| 1697 |
+
pass
|
| 1698 |
+
|
| 1699 |
+
# Save generations (jsonl) for this best fold
|
| 1700 |
+
out_path = os.path.join(OUTPUT_GENERATIONS_DIR, f"{safe_prop}_best_fold{fold_idx+1}_generated_psmiles.jsonl")
|
| 1701 |
+
try:
|
| 1702 |
+
with open(out_path, "w", encoding="utf-8") as fh:
|
| 1703 |
+
for r in generations_payload:
|
| 1704 |
+
fh.write(json.dumps(make_json_serializable({"property": property_name, "best_fold": fold_idx+1, **r})) + "\n")
|
| 1705 |
+
except Exception as e:
|
| 1706 |
+
print(f"[WARN] Could not write generations for '{property_name}': {e}")
|
| 1707 |
+
|
| 1708 |
+
# =============================================================================
|
| 1709 |
+
# Main per-property CV loop (single-task; mirrors G1)
|
| 1710 |
+
# =============================================================================
|
| 1711 |
+
|
| 1712 |
+
def run_inverse_design_single_property(
|
| 1713 |
+
df: pd.DataFrame,
|
| 1714 |
+
property_name: str,
|
| 1715 |
+
prop_col: str,
|
| 1716 |
+
cl_encoder: MultiModalCLPolymerEncoder,
|
| 1717 |
+
selfies_tok,
|
| 1718 |
+
selfies_model
|
| 1719 |
+
) -> Dict[str, Any]:
|
| 1720 |
+
|
| 1721 |
+
# Build all valid polymers for this property
|
| 1722 |
+
polymers = build_polymer_records(df, prop_col)
|
| 1723 |
+
if len(polymers) < 200:
|
| 1724 |
+
print(f"[WARN] Too few samples for '{property_name}': {len(polymers)}. Results may be unstable.")
|
| 1725 |
+
if len(polymers) < 50:
|
| 1726 |
+
print(f"[WARN] Skipping '{property_name}' due to insufficient samples.")
|
| 1727 |
+
return {"property": property_name, "runs": [], "agg": None, "n_samples": len(polymers)}
|
| 1728 |
+
|
| 1729 |
+
indices = np.arange(len(polymers))
|
| 1730 |
+
kf = KFold(n_splits=NUM_FOLDS, shuffle=True, random_state=42)
|
| 1731 |
+
|
| 1732 |
+
runs = []
|
| 1733 |
+
best_overall_val = float("inf")
|
| 1734 |
+
best_bundle = None
|
| 1735 |
+
|
| 1736 |
+
# For novelty computation
|
| 1737 |
+
all_targets_set = set(p["psmiles"] for p in polymers)
|
| 1738 |
+
|
| 1739 |
+
for fold_idx, (trainval_idx, test_idx) in enumerate(kf.split(indices)):
|
| 1740 |
+
seed = 42 + fold_idx
|
| 1741 |
+
set_seed(seed)
|
| 1742 |
+
print(f"\n=== {property_name} | fold {fold_idx+1}/{NUM_FOLDS} ===")
|
| 1743 |
+
|
| 1744 |
+
trainval_polys = [polymers[i] for i in trainval_idx]
|
| 1745 |
+
test_polys = [polymers[i] for i in test_idx]
|
| 1746 |
+
|
| 1747 |
+
# Train/val split within trainval (same spirit as G1: separate val)
|
| 1748 |
+
tr_idx, va_idx = train_test_split(np.arange(len(trainval_polys)), test_size=0.10, random_state=seed, shuffle=True)
|
| 1749 |
+
train_polys = [copy.deepcopy(trainval_polys[i]) for i in tr_idx]
|
| 1750 |
+
val_polys = [copy.deepcopy(trainval_polys[i]) for i in va_idx]
|
| 1751 |
+
|
| 1752 |
+
# Scaler fit on TRAIN targets only (G1-style)
|
| 1753 |
+
sc = StandardScaler()
|
| 1754 |
+
sc.fit(np.array([p["y"] for p in train_polys], dtype=np.float32).reshape(-1, 1))
|
| 1755 |
+
|
| 1756 |
+
# Train datasets (latent-to-SELFIES) use multimodal encoding for seeds
|
| 1757 |
+
def _to_rec(p):
|
| 1758 |
+
return {
|
| 1759 |
+
"psmiles": p["psmiles"],
|
| 1760 |
+
"pselfies": p["pselfies"],
|
| 1761 |
+
"graph": p.get("graph", None),
|
| 1762 |
+
"geometry": p.get("geometry", None),
|
| 1763 |
+
"fingerprints": p.get("fingerprints", None),
|
| 1764 |
+
}
|
| 1765 |
+
|
| 1766 |
+
ds_train = LatentToPSELFIESDataset([_to_rec(p) for p in train_polys], cl_encoder, selfies_tok,
|
| 1767 |
+
max_len=GEN_MAX_LEN, latent_noise_std=LATENT_NOISE_STD_TRAIN,
|
| 1768 |
+
cache_embeddings=True, use_multimodal=True)
|
| 1769 |
+
ds_val = LatentToPSELFIESDataset([_to_rec(p) for p in val_polys], cl_encoder, selfies_tok,
|
| 1770 |
+
max_len=GEN_MAX_LEN, latent_noise_std=0.0,
|
| 1771 |
+
cache_embeddings=True, use_multimodal=True)
|
| 1772 |
+
|
| 1773 |
+
dl_train = DataLoader(ds_train, batch_size=BATCH_SIZE, shuffle=True, num_workers=NUM_WORKERS, pin_memory=True, collate_fn=latent_collate)
|
| 1774 |
+
dl_val = DataLoader(ds_val, batch_size=BATCH_SIZE, shuffle=False, num_workers=NUM_WORKERS, pin_memory=True, collate_fn=latent_collate)
|
| 1775 |
+
|
| 1776 |
+
# Fit GPR on PSMILES latent for THIS property fold (train only)
|
| 1777 |
+
y_tr = [float(p["y"]) for p in train_polys]
|
| 1778 |
+
psm_tr = [p["psmiles"] for p in train_polys]
|
| 1779 |
+
z_tr = cl_encoder.encode_psmiles(psm_tr, max_len=PSMILES_MAX_LEN, batch_size=64, device=DEVICE)
|
| 1780 |
+
prop_model = fit_latent_property_model(z_tr, np.array(y_tr, dtype=np.float32), y_scaler=sc)
|
| 1781 |
+
print(f"[INFO] Fit PSMILES-latent GPR for '{property_name}' fold {fold_idx+1} (n={len(y_tr)}).")
|
| 1782 |
+
|
| 1783 |
+
# Optional aux oracle (scaled target)
|
| 1784 |
+
oracle = None
|
| 1785 |
+
if VERIFY_GENERATED_PROPERTIES and len(train_polys) >= 200 and len(val_polys) >= 50:
|
| 1786 |
+
tr_s, va_s = [], []
|
| 1787 |
+
for p in train_polys:
|
| 1788 |
+
y_s = float(sc.transform(np.array([[p["y"]]], dtype=np.float32))[0, 0])
|
| 1789 |
+
tr_s.append({"psmiles": p["psmiles"], "target": p["y"], "target_scaled": y_s})
|
| 1790 |
+
for p in val_polys:
|
| 1791 |
+
y_s = float(sc.transform(np.array([[p["y"]]], dtype=np.float32))[0, 0])
|
| 1792 |
+
va_s.append({"psmiles": p["psmiles"], "target": p["y"], "target_scaled": y_s})
|
| 1793 |
+
try:
|
| 1794 |
+
oracle = train_property_oracle_per_fold(tr_s, va_s, cl_encoder.psm_tok, DEVICE, PSMILES_MAX_LEN)
|
| 1795 |
+
print(f"[INFO] Trained aux verification predictor for '{property_name}' fold {fold_idx+1}.")
|
| 1796 |
+
except Exception as e:
|
| 1797 |
+
print(f"[WARN] Oracle training failed for '{property_name}': {e}")
|
| 1798 |
+
oracle = None
|
| 1799 |
+
|
| 1800 |
+
# Fresh decoder per fold (single-task) + optimizer (single head)
|
| 1801 |
+
selfies_tok_f, selfies_model_f = load_selfies_ted_and_tokenizer(SELFIES_TED_MODEL_NAME)
|
| 1802 |
+
decoder = CLConditionedSelfiesTEDGenerator(selfies_tok_f, selfies_model_f, cl_emb_dim=CL_EMB_DIM, mem_len=4).to(DEVICE)
|
| 1803 |
+
optimizer, scheduler = create_optimizer_and_scheduler_decoder(decoder)
|
| 1804 |
+
scaler_amp = torch.cuda.amp.GradScaler(enabled=USE_AMP)
|
| 1805 |
+
|
| 1806 |
+
best_val = float("inf")
|
| 1807 |
+
best_state = None
|
| 1808 |
+
no_improve = 0
|
| 1809 |
+
|
| 1810 |
+
for epoch in range(1, NUM_EPOCHS + 1):
|
| 1811 |
+
tr = train_one_epoch_decoder(decoder, dl_train, optimizer, scaler_amp, DEVICE)
|
| 1812 |
+
va = evaluate_decoder(decoder, dl_val, DEVICE)
|
| 1813 |
+
try: scheduler.step()
|
| 1814 |
+
except Exception: pass
|
| 1815 |
+
try:
|
| 1816 |
+
lr = float(optimizer.param_groups[0]["lr"])
|
| 1817 |
+
print(f"[{property_name}] fold {fold_idx+1}/{NUM_FOLDS} epoch {epoch:03d} | lr={lr:.2e} | train={tr['loss']:.6f} | val={va['loss']:.6f}")
|
| 1818 |
+
except Exception:
|
| 1819 |
+
print(f"[{property_name}] fold {fold_idx+1}/{NUM_FOLDS} epoch {epoch:03d} | train={tr['loss']:.6f} | val={va['loss']:.6f}")
|
| 1820 |
+
|
| 1821 |
+
if va["loss"] < best_val - 1e-8:
|
| 1822 |
+
best_val = va["loss"]; no_improve = 0
|
| 1823 |
+
best_state = {k: v.detach().cpu().clone() for k, v in decoder.state_dict().items()}
|
| 1824 |
+
else:
|
| 1825 |
+
no_improve += 1
|
| 1826 |
+
if no_improve >= PATIENCE:
|
| 1827 |
+
print(f"[{property_name}] Early stopping at epoch {epoch} (patience={PATIENCE}).")
|
| 1828 |
+
break
|
| 1829 |
+
|
| 1830 |
+
if best_state is None:
|
| 1831 |
+
print(f"[WARN] No best state saved for {property_name} fold {fold_idx+1}; skipping fold.")
|
| 1832 |
+
continue
|
| 1833 |
+
|
| 1834 |
+
decoder.load_state_dict({k: v.to(DEVICE) for k, v in best_state.items()}, strict=False)
|
| 1835 |
+
|
| 1836 |
+
# Prepare seed pool in scaled space
|
| 1837 |
+
seed_pool = []
|
| 1838 |
+
for p in train_polys:
|
| 1839 |
+
y_s = float(sc.transform(np.array([[p["y"]]], dtype=np.float32))[0, 0])
|
| 1840 |
+
seed_pool.append({
|
| 1841 |
+
"psmiles": p["psmiles"],
|
| 1842 |
+
"y_scaled": y_s,
|
| 1843 |
+
"graph": p.get("graph", None),
|
| 1844 |
+
"geometry": p.get("geometry", None),
|
| 1845 |
+
"fingerprints": p.get("fingerprints", None),
|
| 1846 |
+
})
|
| 1847 |
+
|
| 1848 |
+
# Train target set (novelty)
|
| 1849 |
+
train_targets_set = set(ps["psmiles"] for ps in train_polys)
|
| 1850 |
+
|
| 1851 |
+
# Compose test targets (scaled) — sample up to 64 to keep compute modest
|
| 1852 |
+
ys_test_scaled = []
|
| 1853 |
+
for p in test_polys:
|
| 1854 |
+
ys_test_scaled.append(float(sc.transform(np.array([[p["y"]]], dtype=np.float32))[0, 0]))
|
| 1855 |
+
ys_test_scaled = np.array(ys_test_scaled, dtype=np.float32)
|
| 1856 |
+
if len(ys_test_scaled) > 64:
|
| 1857 |
+
ys_test_scaled = np.random.choice(ys_test_scaled, size=64, replace=False)
|
| 1858 |
+
|
| 1859 |
+
# Generate per target; collect metrics and candidate payload
|
| 1860 |
+
all_valid, all_poly, all_kept, success_scaled, mae_best, diversity_vals = [], [], [], [], [], []
|
| 1861 |
+
novelty_vals, uniqueness_vals = [], []
|
| 1862 |
+
per_target_records = []
|
| 1863 |
+
|
| 1864 |
+
for y_t in ys_test_scaled:
|
| 1865 |
+
out = polybart_style_generate_for_target(
|
| 1866 |
+
target_y_scaled=float(y_t),
|
| 1867 |
+
prop_model=prop_model,
|
| 1868 |
+
cl_encoder=cl_encoder,
|
| 1869 |
+
generator=decoder,
|
| 1870 |
+
train_seed_pool=seed_pool,
|
| 1871 |
+
train_targets_set=train_targets_set,
|
| 1872 |
+
n_seeds=8,
|
| 1873 |
+
n_noise=min(N_FOLD_NOISE_SAMPLING, 16),
|
| 1874 |
+
noise_std=LATENT_NOISE_STD_GEN,
|
| 1875 |
+
prop_tol_scaled=PROP_TOL_SCALED,
|
| 1876 |
+
oracle=oracle,
|
| 1877 |
+
psmiles_tokenizer=cl_encoder.psm_tok,
|
| 1878 |
+
)
|
| 1879 |
+
m = out["metrics"]
|
| 1880 |
+
all_valid.append(float(m.get("validity", 0.0)))
|
| 1881 |
+
all_poly.append(float(m.get("polymer_validity", 0.0)))
|
| 1882 |
+
all_kept.append(int(m.get("n_kept_property_filtered", 0)))
|
| 1883 |
+
diversity_vals.append(float(m.get("diversity", 0.0)))
|
| 1884 |
+
success_scaled.append(1.0 if int(m.get("n_kept_property_filtered", 0)) > 0 else 0.0)
|
| 1885 |
+
novelty_vals.append(float(m.get("novelty_kept", 0.0)))
|
| 1886 |
+
uniqueness_vals.append(float(m.get("uniqueness_valid_unique", 0.0)))
|
| 1887 |
+
|
| 1888 |
+
if out["generated"]:
|
| 1889 |
+
z_keep = cl_encoder.encode_psmiles(out["generated"], max_len=PSMILES_MAX_LEN, batch_size=64, device=DEVICE)
|
| 1890 |
+
y_pred_s, _ = predict_latent_property(prop_model, z_keep)
|
| 1891 |
+
if len(y_pred_s):
|
| 1892 |
+
err = np.abs(y_pred_s - float(y_t))
|
| 1893 |
+
mae_best.append(float(np.min(err)))
|
| 1894 |
+
else:
|
| 1895 |
+
mae_best.append(float("inf"))
|
| 1896 |
+
else:
|
| 1897 |
+
mae_best.append(float("inf"))
|
| 1898 |
+
|
| 1899 |
+
target_y_unscaled = float(sc.inverse_transform(np.array([[float(y_t)]], dtype=np.float32))[0, 0])
|
| 1900 |
+
aux_list = out.get("aux_pred_scaled", None)
|
| 1901 |
+
if aux_list is not None and not isinstance(aux_list, list):
|
| 1902 |
+
aux_list = None
|
| 1903 |
+
|
| 1904 |
+
candidates = []
|
| 1905 |
+
gen_list = out.get("generated", []) or []
|
| 1906 |
+
pred_s_list = out.get("pred_scaled_kept", []) or []
|
| 1907 |
+
pred_u_list = out.get("pred_unscaled_kept", []) or []
|
| 1908 |
+
for i_c, psm in enumerate(gen_list):
|
| 1909 |
+
cand = {
|
| 1910 |
+
"psmiles": str(psm),
|
| 1911 |
+
"pred_scaled": float(pred_s_list[i_c]) if i_c < len(pred_s_list) else None,
|
| 1912 |
+
"pred_unscaled": float(pred_u_list[i_c]) if i_c < len(pred_u_list) else None,
|
| 1913 |
+
"aux_pred_scaled": float(aux_list[i_c]) if (aux_list is not None and i_c < len(aux_list)) else None,
|
| 1914 |
+
}
|
| 1915 |
+
candidates.append(cand)
|
| 1916 |
+
|
| 1917 |
+
scaler_meta = {
|
| 1918 |
+
"scaler_type": "StandardScaler",
|
| 1919 |
+
"mean_": getattr(sc, "mean_", None),
|
| 1920 |
+
"scale_": getattr(sc, "scale_", None),
|
| 1921 |
+
"with_mean": bool(getattr(sc, "with_mean", True)),
|
| 1922 |
+
"with_std": bool(getattr(sc, "with_std", True)),
|
| 1923 |
+
}
|
| 1924 |
+
|
| 1925 |
+
per_target_records.append({
|
| 1926 |
+
"target_y_scaled": float(y_t),
|
| 1927 |
+
"target_y_unscaled": float(target_y_unscaled),
|
| 1928 |
+
"tol_scaled": float(PROP_TOL_SCALED),
|
| 1929 |
+
"tol_unscaled_abs": float(PROP_TOL_UNSCALED_ABS) if PROP_TOL_UNSCALED_ABS is not None else None,
|
| 1930 |
+
"scaler_meta": scaler_meta,
|
| 1931 |
+
"candidates": candidates,
|
| 1932 |
+
"metrics": m
|
| 1933 |
+
})
|
| 1934 |
+
|
| 1935 |
+
def _finite(xs):
|
| 1936 |
+
return [x for x in xs if np.isfinite(x)]
|
| 1937 |
+
|
| 1938 |
+
metrics_fold = {
|
| 1939 |
+
"validity_mean": float(np.mean(all_valid)) if all_valid else 0.0,
|
| 1940 |
+
"polymer_validity_mean": float(np.mean(all_poly)) if all_poly else 0.0,
|
| 1941 |
+
"avg_n_kept": float(np.mean(all_kept)) if all_kept else 0.0,
|
| 1942 |
+
"success_at_k_scaled": float(np.mean(success_scaled)) if success_scaled else 0.0,
|
| 1943 |
+
"mae_best_scaled": float(np.mean(_finite(mae_best))) if _finite(mae_best) else 0.0,
|
| 1944 |
+
"diversity_mean": float(np.mean(diversity_vals)) if diversity_vals else 0.0,
|
| 1945 |
+
"novelty_mean": float(np.mean(novelty_vals)) if novelty_vals else 0.0,
|
| 1946 |
+
"uniqueness_mean": float(np.mean(uniqueness_vals)) if uniqueness_vals else 0.0,
|
| 1947 |
+
"tol_scaled": float(PROP_TOL_SCALED),
|
| 1948 |
+
"tol_unscaled_abs": float(PROP_TOL_UNSCALED_ABS) if PROP_TOL_UNSCALED_ABS is not None else None,
|
| 1949 |
+
}
|
| 1950 |
+
|
| 1951 |
+
run_record = {
|
| 1952 |
+
"property": property_name,
|
| 1953 |
+
"fold": int(fold_idx + 1),
|
| 1954 |
+
"seed": int(seed),
|
| 1955 |
+
"n_train": int(len(train_polys)),
|
| 1956 |
+
"n_val": int(len(val_polys)),
|
| 1957 |
+
"n_test": int(len(test_polys)),
|
| 1958 |
+
"best_val_loss": float(best_val),
|
| 1959 |
+
"gen_metrics": metrics_fold
|
| 1960 |
+
}
|
| 1961 |
+
runs.append(run_record)
|
| 1962 |
+
|
| 1963 |
+
with open(OUTPUT_RESULTS, "a", encoding="utf-8") as fh:
|
| 1964 |
+
fh.write(json.dumps(make_json_serializable(run_record)) + "\n")
|
| 1965 |
+
|
| 1966 |
+
# Track best fold (by lowest val loss) and save G1-style artifacts
|
| 1967 |
+
if best_val < best_overall_val - 1e-8:
|
| 1968 |
+
best_overall_val = best_val
|
| 1969 |
+
best_bundle = {
|
| 1970 |
+
"fold": int(fold_idx + 1),
|
| 1971 |
+
"decoder_state": best_state,
|
| 1972 |
+
"prop_model": prop_model,
|
| 1973 |
+
"scaler": sc,
|
| 1974 |
+
"best_val_loss": float(best_val),
|
| 1975 |
+
"generations": per_target_records
|
| 1976 |
+
}
|
| 1977 |
+
save_best_fold_artifacts_for_property(
|
| 1978 |
+
property_name=property_name,
|
| 1979 |
+
fold_idx=fold_idx,
|
| 1980 |
+
decoder_state=best_state,
|
| 1981 |
+
prop_model=prop_model,
|
| 1982 |
+
scaler=sc,
|
| 1983 |
+
best_val_loss=best_val,
|
| 1984 |
+
generations_payload=per_target_records
|
| 1985 |
+
)
|
| 1986 |
+
print(f"[INFO] Saved best-fold artifacts for '{property_name}' (fold {fold_idx+1})")
|
| 1987 |
+
|
| 1988 |
+
# Aggregate across folds (G1-style)
|
| 1989 |
+
if not runs:
|
| 1990 |
+
return {"property": property_name, "runs": [], "agg": None, "n_samples": len(polymers)}
|
| 1991 |
+
|
| 1992 |
+
def _collect(key):
|
| 1993 |
+
xs = [float(r["gen_metrics"].get(key, 0.0)) for r in runs if r.get("gen_metrics", None) is not None]
|
| 1994 |
+
return (float(np.mean(xs)) if xs else 0.0, float(np.std(xs)) if xs else 0.0)
|
| 1995 |
+
|
| 1996 |
+
agg = {}
|
| 1997 |
+
for k in ["validity_mean", "polymer_validity_mean", "avg_n_kept", "success_at_k_scaled",
|
| 1998 |
+
"mae_best_scaled", "diversity_mean", "novelty_mean", "uniqueness_mean"]:
|
| 1999 |
+
m, s = _collect(k)
|
| 2000 |
+
agg[k] = {"mean": m, "std": s}
|
| 2001 |
+
agg["tol_scaled"] = float(PROP_TOL_SCALED)
|
| 2002 |
+
agg["tol_unscaled_abs"] = float(PROP_TOL_UNSCALED_ABS) if PROP_TOL_UNSCALED_ABS is not None else None
|
| 2003 |
+
|
| 2004 |
+
# Write AGG line for this property (like G1)
|
| 2005 |
+
with open(OUTPUT_RESULTS, "a", encoding="utf-8") as fh:
|
| 2006 |
+
fh.write("AGG_PROPERTY: " + json.dumps(make_json_serializable({property_name: agg})) + "\n")
|
| 2007 |
+
|
| 2008 |
+
return {"property": property_name, "runs": runs, "agg": agg, "n_samples": len(polymers)}
|
| 2009 |
+
|
| 2010 |
+
# =============================================================================
|
| 2011 |
+
# Tokenizer for PSMILES (matching your preference)
|
| 2012 |
+
# =============================================================================
|
| 2013 |
+
|
| 2014 |
+
def build_psmiles_tokenizer():
|
| 2015 |
+
try:
|
| 2016 |
+
spm_path = "spm_5M.model"
|
| 2017 |
+
if Path(spm_path).exists():
|
| 2018 |
+
print(f"[Tokenizer] Using SentencePiece model: {spm_path}")
|
| 2019 |
+
tok = DebertaV2Tokenizer(vocab_file=spm_path, do_lower_case=False)
|
| 2020 |
+
if tok.pad_token is None:
|
| 2021 |
+
tok.add_special_tokens({"pad_token": "<pad>"})
|
| 2022 |
+
if tok.mask_token is None:
|
| 2023 |
+
tok.add_special_tokens({"mask_token": "<mask>"})
|
| 2024 |
+
tok.pad_token = tok.pad_token if tok.pad_token is not None else "<pad>"
|
| 2025 |
+
tok.mask_token = tok.mask_token if tok.mask_token is not None else "<mask>"
|
| 2026 |
+
return tok
|
| 2027 |
+
except Exception as e:
|
| 2028 |
+
print("Warning: Deberta tokenizer creation failed:", e)
|
| 2029 |
+
return None
|
| 2030 |
+
|
| 2031 |
+
# =============================================================================
|
| 2032 |
+
# Entrypoint (single-task per property; G1-style logging and summary)
|
| 2033 |
+
# =============================================================================
|
| 2034 |
+
|
| 2035 |
+
def main():
|
| 2036 |
+
if not (RDKit_AVAILABLE and SELFIES_AVAILABLE):
|
| 2037 |
+
raise RuntimeError("This script requires RDKit and selfies. Install them before running.")
|
| 2038 |
+
|
| 2039 |
+
if os.path.exists(OUTPUT_RESULTS):
|
| 2040 |
+
backup = OUTPUT_RESULTS + ".bak"
|
| 2041 |
+
shutil.copy(OUTPUT_RESULTS, backup)
|
| 2042 |
+
print(f"[INFO] Existing {OUTPUT_RESULTS} backed up to {backup}")
|
| 2043 |
+
open(OUTPUT_RESULTS, "w", encoding="utf-8").close()
|
| 2044 |
+
|
| 2045 |
+
if not os.path.isfile(POLYINFO_PATH):
|
| 2046 |
+
raise FileNotFoundError(f"PolyInfo file not found at {POLYINFO_PATH}")
|
| 2047 |
+
|
| 2048 |
+
df = pd.read_csv(POLYINFO_PATH, engine="python")
|
| 2049 |
+
found = find_property_columns(df.columns)
|
| 2050 |
+
prop_map = {req: found.get(req) for req in REQUESTED_PROPERTIES}
|
| 2051 |
+
print(f"[INFO] Property-to-column map: {prop_map}")
|
| 2052 |
+
print(f"[INFO] RDKit_AVAILABLE={RDKit_AVAILABLE}, SELFIES_AVAILABLE={SELFIES_AVAILABLE}")
|
| 2053 |
+
print(f"[INFO] VERIFY_GENERATED_PROPERTIES={VERIFY_GENERATED_PROPERTIES} (tol_scaled={PROP_TOL_SCALED}, tol_unscaled_abs={PROP_TOL_UNSCALED_ABS})")
|
| 2054 |
+
print(f"[INFO] USE_AMP={USE_AMP}, DEVICE={DEVICE}, NUM_WORKERS={NUM_WORKERS}")
|
| 2055 |
+
print(f"[INFO] SELFIES_TED_MODEL_NAME={SELFIES_TED_MODEL_NAME}")
|
| 2056 |
+
print(f"[INFO] CL encoder dir: {PRETRAINED_MULTIMODAL_DIR}")
|
| 2057 |
+
print(f"[INFO] Decoder FT params: batch_size={BATCH_SIZE}, epochs={NUM_EPOCHS}, patience={PATIENCE}, "
|
| 2058 |
+
f"optimizer=AdamW, lr={LEARNING_RATE}, weight_decay={WEIGHT_DECAY}, scheduler=CosineAnnealingLR, eta_min={COSINE_ETA_MIN}")
|
| 2059 |
+
|
| 2060 |
+
# Build PSMILES tokenizer for CL text encoder
|
| 2061 |
+
psmiles_tok = build_psmiles_tokenizer()
|
| 2062 |
+
if psmiles_tok is None:
|
| 2063 |
+
raise RuntimeError("Failed to build PSMILES tokenizer.")
|
| 2064 |
+
|
| 2065 |
+
# Multimodal CL encoder (frozen for seeds; same as your prior script)
|
| 2066 |
+
cl_encoder = MultiModalCLPolymerEncoder(
|
| 2067 |
+
psmiles_tokenizer=psmiles_tok,
|
| 2068 |
+
emb_dim=CL_EMB_DIM,
|
| 2069 |
+
cl_weights_dir=PRETRAINED_MULTIMODAL_DIR,
|
| 2070 |
+
use_gine=True, use_schnet=True, use_fp=True, use_psmiles=True
|
| 2071 |
+
).to(DEVICE)
|
| 2072 |
+
cl_encoder.freeze_cl_encoders()
|
| 2073 |
+
|
| 2074 |
+
# Load SELFIES-TED backbone once (weights re-used when instantiating decoders per fold)
|
| 2075 |
+
selfies_tok, selfies_model = load_selfies_ted_and_tokenizer(SELFIES_TED_MODEL_NAME)
|
| 2076 |
+
print(f"[INFO] Loaded SELFIES-TED backbone: {SELFIES_TED_MODEL_NAME}")
|
| 2077 |
+
|
| 2078 |
+
overall = {"per_property": {}}
|
| 2079 |
+
|
| 2080 |
+
# Single-task loop per property (G1-style)
|
| 2081 |
+
for pname in REQUESTED_PROPERTIES:
|
| 2082 |
+
pcol = prop_map.get(pname, None)
|
| 2083 |
+
if pcol is None:
|
| 2084 |
+
print(f"[WARN] Could not find a column for requested property '{pname}'. Skipping.")
|
| 2085 |
+
continue
|
| 2086 |
+
print(f"\n=== Running PolyBART-style inverse design (single-task) for property: {pname} (col='{pcol}') ===")
|
| 2087 |
+
res = run_inverse_design_single_property(df, pname, pcol, cl_encoder, selfies_tok, selfies_model)
|
| 2088 |
+
overall["per_property"][pname] = res
|
| 2089 |
+
|
| 2090 |
+
# Final summary (aggregated per property)
|
| 2091 |
+
final_agg = {}
|
| 2092 |
+
for pname, info in overall["per_property"].items():
|
| 2093 |
+
final_agg[pname] = info.get("agg", None)
|
| 2094 |
+
|
| 2095 |
+
with open(OUTPUT_RESULTS, "a", encoding="utf-8") as fh:
|
| 2096 |
+
fh.write("\nFINAL_SUMMARY\n")
|
| 2097 |
+
fh.write(json.dumps(make_json_serializable(final_agg), indent=2))
|
| 2098 |
+
fh.write("\n")
|
| 2099 |
+
|
| 2100 |
+
print(f"\n[DONE] Results written to: {OUTPUT_RESULTS}")
|
| 2101 |
+
print(f"[DONE] Best models in: {OUTPUT_MODELS_DIR}")
|
| 2102 |
+
print(f"[DONE] Best-fold generations in: {OUTPUT_GENERATIONS_DIR}")
|
| 2103 |
+
|
| 2104 |
+
if __name__ == "__main__":
|
| 2105 |
+
main()
|