manpreet88 commited on
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Delete CL.py

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  1. CL.py +0 -1803
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- import os
2
- import sys
3
- import csv
4
- import json
5
- import time
6
- import math
7
- import random
8
- import shutil
9
- from pathlib import Path
10
- from typing import List, Optional, Tuple, Dict
11
-
12
- # Increase csv field size limit safely
13
- try:
14
- csv.field_size_limit(sys.maxsize)
15
- except OverflowError:
16
- csv.field_size_limit(2**31 - 1)
17
-
18
- import numpy as np
19
- import pandas as pd
20
- import torch
21
- import torch.nn as nn
22
- import torch.nn.functional as F
23
- from torch.utils.data import Dataset, DataLoader
24
-
25
- # PyG building blocks
26
- try:
27
- from torch_geometric.nn import GINEConv
28
- from torch_geometric.nn.models import SchNet as PyGSchNet
29
- from torch_geometric.nn import radius_graph
30
- except Exception as e:
31
- # we keep imports guarded — if these fail, user will get a clear error later
32
- GINEConv = None
33
- PyGSchNet = None
34
- radius_graph = None
35
-
36
- # HF Trainer & Transformers
37
- from transformers import TrainingArguments, Trainer, DebertaV2ForMaskedLM, DebertaV2Tokenizer
38
- from transformers import DataCollatorForLanguageModeling
39
- from transformers.trainer_callback import TrainerCallback
40
-
41
- from sklearn.model_selection import train_test_split
42
- from sklearn.metrics import accuracy_score, f1_score, mean_squared_error, mean_absolute_error
43
-
44
- # ---------------------------
45
- # Config / Hyperparams (kept same as in your scripts)
46
- # ---------------------------
47
- P_MASK = 0.15
48
- MAX_ATOMIC_Z = 85
49
- MASK_ATOM_ID = MAX_ATOMIC_Z + 1
50
-
51
- # GINE params
52
- NODE_EMB_DIM = 300
53
- EDGE_EMB_DIM = 300
54
- NUM_GNN_LAYERS = 5
55
-
56
- # SchNet params (from your file)
57
- SCHNET_NUM_GAUSSIANS = 50
58
- SCHNET_NUM_INTERACTIONS = 6
59
- SCHNET_CUTOFF = 10.0
60
- SCHNET_MAX_NEIGHBORS = 64
61
- SCHNET_HIDDEN = 600
62
-
63
- # Fingerprint (MLM) params
64
- FP_LENGTH = 2048
65
- MASK_TOKEN_ID_FP = 2 # consistent with your fingerprint file
66
- VOCAB_SIZE_FP = 3
67
-
68
- # PSMILES/Deberta params (from your file)
69
- DEBERTA_HIDDEN = 600
70
- PSMILES_MAX_LEN = 128
71
-
72
- # Contrastive params
73
- TEMPERATURE = 0.07
74
-
75
- # Reconstruction loss weight (balance between contrastive and reconstruction objectives)
76
- REC_LOSS_WEIGHT = 1.0 # you can tune this (e.g., 0.5, 1.0)
77
-
78
- # Training args (same across files)
79
- OUTPUT_DIR = "./multimodal_output"
80
- os.makedirs(OUTPUT_DIR, exist_ok=True)
81
- BEST_GINE_DIR = "./gin_output/best"
82
- BEST_SCHNET_DIR = "./schnet_output/best"
83
- BEST_FP_DIR = "./fingerprint_mlm_output/best"
84
- BEST_PSMILES_DIR = "./polybert_output/best"
85
-
86
- training_args = TrainingArguments(
87
- output_dir=OUTPUT_DIR,
88
- overwrite_output_dir=True,
89
- num_train_epochs=25,
90
- per_device_train_batch_size=16,
91
- per_device_eval_batch_size=8,
92
- gradient_accumulation_steps=4,
93
- eval_strategy="epoch",
94
- logging_steps=100,
95
- learning_rate=1e-4,
96
- weight_decay=0.01,
97
- eval_accumulation_steps=1000,
98
- fp16=torch.cuda.is_available(),
99
- save_strategy="epoch",
100
- save_steps=500,
101
- disable_tqdm=False,
102
- logging_first_step=True,
103
- report_to=[],
104
- dataloader_num_workers=0,
105
- load_best_model_at_end=True,
106
- metric_for_best_model="eval_loss",
107
- greater_is_better=False,
108
- )
109
-
110
- # ======== robust device selection =========
111
- USE_CUDA = torch.cuda.is_available()
112
- if USE_CUDA:
113
- device = torch.device("cuda") # respects CUDA_VISIBLE_DEVICES
114
- else:
115
- device = torch.device("cpu")
116
- print("Device:", device)
117
-
118
- # ======== deterministic seeds =========
119
- SEED = 42
120
- random.seed(SEED)
121
- np.random.seed(SEED)
122
- torch.manual_seed(SEED)
123
- if USE_CUDA:
124
- torch.cuda.manual_seed_all(SEED)
125
-
126
- # ---------------------------
127
- # Utility / small helpers
128
- # ---------------------------
129
-
130
- def safe_get(d: dict, key: str, default=None):
131
- return d[key] if (isinstance(d, dict) and key in d) else default
132
-
133
-
134
- def match_edge_attr_to_index(edge_index: torch.Tensor, edge_attr: torch.Tensor, target_dim: int = 3):
135
- # determine device to allocate zero tensors on
136
- dev = None
137
- if edge_attr is not None and hasattr(edge_attr, "device"):
138
- dev = edge_attr.device
139
- elif edge_index is not None and hasattr(edge_index, "device"):
140
- dev = edge_index.device
141
- else:
142
- dev = torch.device("cpu")
143
-
144
- if edge_index is None or edge_index.numel() == 0:
145
- return torch.zeros((0, target_dim), dtype=torch.float, device=dev)
146
- E_idx = edge_index.size(1)
147
- if edge_attr is None or edge_attr.numel() == 0:
148
- return torch.zeros((E_idx, target_dim), dtype=torch.float, device=dev)
149
- E_attr = edge_attr.size(0)
150
- if E_attr == E_idx:
151
- if edge_attr.size(1) != target_dim:
152
- D = edge_attr.size(1)
153
- if D < target_dim:
154
- pad = torch.zeros((E_attr, target_dim - D), dtype=torch.float, device=edge_attr.device)
155
- return torch.cat([edge_attr, pad], dim=1)
156
- else:
157
- return edge_attr[:, :target_dim]
158
- return edge_attr
159
- if E_attr * 2 == E_idx:
160
- try:
161
- return torch.cat([edge_attr, edge_attr], dim=0)
162
- except Exception:
163
- pass
164
- reps = (E_idx + E_attr - 1) // E_attr
165
- edge_rep = edge_attr.repeat(reps, 1)[:E_idx]
166
- if edge_rep.size(1) != target_dim:
167
- D = edge_rep.size(1)
168
- if D < target_dim:
169
- pad = torch.zeros((E_idx, target_dim - D), dtype=torch.float, device=edge_rep.device)
170
- edge_rep = torch.cat([edge_rep, pad], dim=1)
171
- else:
172
- edge_rep = edge_rep[:, :target_dim]
173
- return edge_rep
174
-
175
- # Optimized BFS to compute distances to visible anchors (used if needed)
176
- def bfs_distances_to_visible(edge_index: torch.Tensor, num_nodes: int, masked_idx: np.ndarray, visible_idx: np.ndarray, k_anchors: int):
177
- INF = num_nodes + 1
178
- selected_dists = np.zeros((num_nodes, k_anchors), dtype=np.float32)
179
- selected_mask = np.zeros((num_nodes, k_anchors), dtype=np.bool_)
180
- if edge_index is None or edge_index.numel() == 0:
181
- return selected_dists, selected_mask
182
- src = edge_index[0].tolist()
183
- dst = edge_index[1].tolist()
184
- adj = [[] for _ in range(num_nodes)]
185
- for u, v in zip(src, dst):
186
- if 0 <= u < num_nodes and 0 <= v < num_nodes:
187
- adj[u].append(v)
188
- visible_set = set(visible_idx.tolist()) if isinstance(visible_idx, (np.ndarray, list)) else set(visible_idx.cpu().tolist())
189
- for a in np.atleast_1d(masked_idx).tolist():
190
- if a < 0 or a >= num_nodes:
191
- continue
192
- q = [a]
193
- visited = [-1] * num_nodes
194
- visited[a] = 0
195
- head = 0
196
- found = []
197
- while head < len(q) and len(found) < k_anchors:
198
- u = q[head]; head += 1
199
- for v in adj[u]:
200
- if visited[v] == -1:
201
- visited[v] = visited[u] + 1
202
- q.append(v)
203
- if v in visible_set:
204
- found.append((visited[v], v))
205
- if len(found) >= k_anchors:
206
- break
207
- if len(found) > 0:
208
- found.sort(key=lambda x: x[0])
209
- k = min(k_anchors, len(found))
210
- for i in range(k):
211
- selected_dists[a, i] = float(found[i][0])
212
- selected_mask[a, i] = True
213
- return selected_dists, selected_mask
214
-
215
- # ---------------------------
216
- # Data loading / preprocessing (streaming to disk to avoid memory spike)
217
- # ---------------------------
218
- CSV_PATH = "Polymer_Foundational_Model/polymer_structures_unified_processed.csv"
219
- TARGET_ROWS = 2000000
220
- CHUNKSIZE = 50000
221
-
222
- PREPROC_DIR = "preprocessed_samples"
223
- os.makedirs(PREPROC_DIR, exist_ok=True)
224
-
225
- # The per-sample file format: torch.save(sample_dict, sample_path)
226
- # sample_dict keys: 'gine', 'schnet', 'fp', 'psmiles_raw'
227
- # 'gine' -> dict with: node_atomic (list/int tensor), chirality (list/float tensor), formal_charge (list/float tensor), edge_index (2xE list), edge_attr (E x 3 list)
228
- # 'schnet' -> dict with: atomic (list), coords (list of [x,y,z])
229
- # 'fp' -> list of length FP_LENGTH (0/1 ints)
230
- # 'psmiles_raw' -> raw psmiles string
231
-
232
- def prepare_or_load_data_streaming():
233
- # If PREPROC_DIR already contains per-sample files, reuse them
234
- existing = sorted([p for p in Path(PREPROC_DIR).glob("sample_*.pt")])
235
- if len(existing) > 0:
236
- print(f"Found {len(existing)} preprocessed sample files in {PREPROC_DIR}; reusing those (no reparse).")
237
- return [str(p) for p in existing]
238
-
239
- print("No existing per-sample preprocessed folder found. Parsing CSV chunked and writing per-sample files (streaming).")
240
- rows_read = 0
241
- sample_idx = 0
242
-
243
- # We'll parse CSV in chunks and for each row, if it contains all modalities, write sample to disk
244
- for chunk in pd.read_csv(CSV_PATH, engine="python", chunksize=CHUNKSIZE):
245
- # Pre-extract columns presence
246
- has_graph = "graph" in chunk.columns
247
- has_geometry = "geometry" in chunk.columns
248
- has_fp = "fingerprints" in chunk.columns
249
- has_psmiles = "psmiles" in chunk.columns
250
-
251
- for i_row in range(len(chunk)):
252
- if rows_read >= TARGET_ROWS:
253
- break
254
- row = chunk.iloc[i_row]
255
-
256
- # Prepare placeholders
257
- gine_sample = None
258
- schnet_sample = None
259
- fp_sample = None
260
- psmiles_raw = None
261
-
262
- # Parse graph
263
- if has_graph:
264
- val = row.get("graph", "")
265
- try:
266
- graph_field = json.loads(val) if isinstance(val, str) and val.strip() != "" else (val if not isinstance(val, str) else None)
267
- except Exception:
268
- graph_field = None
269
- if graph_field:
270
- node_features = safe_get(graph_field, "node_features", None)
271
- if node_features:
272
- atomic_nums = []
273
- chirality_vals = []
274
- formal_charges = []
275
- for nf in node_features:
276
- an = safe_get(nf, "atomic_num", None)
277
- if an is None:
278
- an = safe_get(nf, "atomic_number", 0)
279
- ch = safe_get(nf, "chirality", 0)
280
- fc = safe_get(nf, "formal_charge", 0)
281
- try:
282
- atomic_nums.append(int(an))
283
- except Exception:
284
- atomic_nums.append(0)
285
- chirality_vals.append(float(ch))
286
- formal_charges.append(float(fc))
287
- n_nodes = len(atomic_nums)
288
- edge_indices_raw = safe_get(graph_field, "edge_indices", None)
289
- edge_features_raw = safe_get(graph_field, "edge_features", None)
290
- edge_index = None
291
- edge_attr = None
292
- if edge_indices_raw is None:
293
- adj_mat = safe_get(graph_field, "adjacency_matrix", None)
294
- if adj_mat:
295
- srcs = []
296
- dsts = []
297
- for i_r, row_adj in enumerate(adj_mat):
298
- for j, val2 in enumerate(row_adj):
299
- if val2:
300
- srcs.append(i_r); dsts.append(j)
301
- if len(srcs) > 0:
302
- edge_index = [srcs, dsts]
303
- E = len(srcs)
304
- edge_attr = [[0.0, 0.0, 0.0] for _ in range(E)]
305
- else:
306
- srcs, dsts = [], []
307
- # handle multiple formats
308
- if isinstance(edge_indices_raw, list) and len(edge_indices_raw) > 0 and isinstance(edge_indices_raw[0], list):
309
- # either list of pairs or two lists
310
- first = edge_indices_raw[0]
311
- if len(first) == 2 and isinstance(first[0], int):
312
- # maybe list of pairs
313
- try:
314
- srcs = [int(p[0]) for p in edge_indices_raw]
315
- dsts = [int(p[1]) for p in edge_indices_raw]
316
- except Exception:
317
- srcs, dsts = [], []
318
- else:
319
- # maybe [[srcs],[dsts]]
320
- try:
321
- srcs = [int(x) for x in edge_indices_raw[0]]
322
- dsts = [int(x) for x in edge_indices_raw[1]]
323
- except Exception:
324
- srcs, dsts = [], []
325
- if len(srcs) == 0 and isinstance(edge_indices_raw, list) and all(isinstance(p, (list, tuple)) and len(p) == 2 for p in edge_indices_raw):
326
- srcs = [int(p[0]) for p in edge_indices_raw]
327
- dsts = [int(p[1]) for p in edge_indices_raw]
328
- if len(srcs) > 0:
329
- edge_index = [srcs, dsts]
330
- if edge_features_raw and isinstance(edge_features_raw, list):
331
- bond_types = []
332
- stereos = []
333
- is_conjs = []
334
- for ef in edge_features_raw:
335
- bt = safe_get(ef, "bond_type", 0)
336
- st = safe_get(ef, "stereo", 0)
337
- ic = safe_get(ef, "is_conjugated", False)
338
- bond_types.append(float(bt)); stereos.append(float(st)); is_conjs.append(float(1.0 if ic else 0.0))
339
- edge_attr = list(zip(bond_types, stereos, is_conjs))
340
- else:
341
- E = len(srcs)
342
- edge_attr = [[0.0, 0.0, 0.0] for _ in range(E)]
343
-
344
- if edge_index is not None:
345
- gine_sample = {
346
- "node_atomic": atomic_nums,
347
- "node_chirality": chirality_vals,
348
- "node_charge": formal_charges,
349
- "edge_index": edge_index,
350
- "edge_attr": edge_attr,
351
- }
352
-
353
- # Parse geometry for SchNet
354
- if has_geometry and schnet_sample is None:
355
- val = row.get("geometry", "")
356
- try:
357
- geom = json.loads(val) if isinstance(val, str) and val.strip() != "" else (val if not isinstance(val, str) else None)
358
- conf = geom.get("best_conformer") if isinstance(geom, dict) else None
359
- if conf:
360
- atomic = conf.get("atomic_numbers", [])
361
- coords = conf.get("coordinates", [])
362
- if len(atomic) == len(coords) and len(atomic) > 0:
363
- schnet_sample = {"atomic": atomic, "coords": coords}
364
- except Exception:
365
- schnet_sample = None
366
-
367
- # Parse fingerprints
368
- if has_fp:
369
- fpval = row.get("fingerprints", "")
370
- if fpval is None or (isinstance(fpval, str) and fpval.strip() == ""):
371
- fp_sample = [0] * FP_LENGTH
372
- else:
373
- try:
374
- fp_json = json.loads(fpval) if isinstance(fpval, str) else fpval
375
- except Exception:
376
- try:
377
- fp_json = json.loads(str(fpval).replace("'", '"'))
378
- except Exception:
379
- parts = [p.strip().strip('"').strip("'") for p in str(fpval).split(",")]
380
- bits = [1 if p in ("1", "True", "true") else 0 for p in parts[:FP_LENGTH]]
381
- if len(bits) < FP_LENGTH:
382
- bits += [0] * (FP_LENGTH - len(bits))
383
- fp_sample = bits
384
- if fp_sample is None:
385
- bits = safe_get(fp_json, "morgan_r3_bits", None) if isinstance(fp_json, dict) else (fp_json if isinstance(fp_json, list) else None)
386
- if bits is None:
387
- fp_sample = [0] * FP_LENGTH
388
- else:
389
- normalized = []
390
- for b in bits:
391
- if isinstance(b, str):
392
- b_clean = b.strip().strip('"').strip("'")
393
- normalized.append(1 if b_clean in ("1", "True", "true") else 0)
394
- elif isinstance(b, (int, np.integer)):
395
- normalized.append(1 if int(b) != 0 else 0)
396
- else:
397
- normalized.append(0)
398
- if len(normalized) >= FP_LENGTH:
399
- break
400
- if len(normalized) < FP_LENGTH:
401
- normalized.extend([0] * (FP_LENGTH - len(normalized)))
402
- fp_sample = normalized[:FP_LENGTH]
403
-
404
- # Parse psmiles
405
- if has_psmiles:
406
- s = row.get("psmiles", "")
407
- if s is None:
408
- psmiles_raw = ""
409
- else:
410
- psmiles_raw = str(s)
411
-
412
- # If we have at least two modalities (prefer all four), write the sample
413
- # For safety, we require psmiles and fp at minimum OR graph+psmiles etc.
414
- modalities_present = sum([1 if x is not None else 0 for x in [gine_sample, schnet_sample, fp_sample, psmiles_raw]])
415
- if modalities_present >= 2:
416
- sample = {
417
- "gine": gine_sample,
418
- "schnet": schnet_sample,
419
- "fp": fp_sample,
420
- "psmiles_raw": psmiles_raw
421
- }
422
- sample_path = os.path.join(PREPROC_DIR, f"sample_{sample_idx:08d}.pt")
423
- try:
424
- torch.save(sample, sample_path)
425
- except Exception as save_e:
426
- print("Warning: failed to torch.save sample:", save_e)
427
- # fallback to json write small dict (safe)
428
- try:
429
- with open(sample_path + ".json", "w") as fjson:
430
- json.dump(sample, fjson)
431
- # indicate via filename with .json
432
- sample_path = sample_path + ".json"
433
- except Exception:
434
- pass
435
-
436
- sample_idx += 1
437
- rows_read += 1
438
-
439
- # continue to next row
440
- if rows_read >= TARGET_ROWS:
441
- break
442
-
443
- print(f"Wrote {sample_idx} sample files to {PREPROC_DIR}.")
444
- return [str(p) for p in sorted(Path(PREPROC_DIR).glob("sample_*.pt"))]
445
-
446
- sample_files = prepare_or_load_data_streaming()
447
-
448
- # ---------------------------
449
- # Prepare tokenizer for psmiles (deferred, but we still attempt HF tokenizer; fallback created)
450
- # ---------------------------
451
- try:
452
- SPM_MODEL = "spm.model"
453
- if Path(SPM_MODEL).exists():
454
- tokenizer = DebertaV2Tokenizer(vocab_file=SPM_MODEL, do_lower_case=False)
455
- tokenizer.add_special_tokens({"pad_token": "<pad>", "mask_token": "<mask>"})
456
- tokenizer.pad_token = "<pad>"
457
- tokenizer.mask_token = "<mask>"
458
- else:
459
- tokenizer = DebertaV2Tokenizer.from_pretrained("microsoft/deberta-v2-xlarge", use_fast=False)
460
- tokenizer.add_special_tokens({"pad_token": "<pad>", "mask_token": "<mask>"})
461
- tokenizer.pad_token = "<pad>"
462
- tokenizer.mask_token = "<mask>"
463
- except Exception as e:
464
- print("Warning: Deberta tokenizer creation failed:", e)
465
- # create a simple fallback tokenizer (char-level)
466
- class SimplePSMILESTokenizer:
467
- def __init__(self, max_len=PSMILES_MAX_LEN):
468
- chars = list("ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789-=#()[]@+/\\.")
469
- self.vocab = {c: i + 5 for i, c in enumerate(chars)}
470
- self.vocab["<pad>"] = 0
471
- self.vocab["<mask>"] = 1
472
- self.vocab["<unk>"] = 2
473
- self.vocab["<cls>"] = 3
474
- self.vocab["<sep>"] = 4
475
- self.mask_token = "<mask>"
476
- self.mask_token_id = self.vocab[self.mask_token]
477
- self.vocab_size = len(self.vocab)
478
- self.max_len = max_len
479
-
480
- def __call__(self, s, truncation=True, padding="max_length", max_length=None):
481
- max_len = max_length or self.max_len
482
- toks = [self.vocab.get(ch, self.vocab["<unk>"]) for ch in list(s)][:max_len]
483
- attn = [1] * len(toks)
484
- if len(toks) < max_len:
485
- pad = [self.vocab["<pad>"]] * (max_len - len(toks))
486
- toks = toks + pad
487
- attn = attn + [0] * (max_len - len(attn))
488
- return {"input_ids": toks, "attention_mask": attn}
489
-
490
- tokenizer = SimplePSMILESTokenizer()
491
-
492
- # ---------------------------
493
- # Lazy dataset: loads per-sample file on demand and tokenizes psmiles on-the-fly
494
- # ---------------------------
495
- class LazyMultimodalDataset(Dataset):
496
- def __init__(self, sample_file_list: List[str], tokenizer, fp_length=FP_LENGTH, psmiles_max_len=PSMILES_MAX_LEN):
497
- self.files = sample_file_list
498
- self.tokenizer = tokenizer
499
- self.fp_length = fp_length
500
- self.psmiles_max_len = psmiles_max_len
501
-
502
- def __len__(self):
503
- return len(self.files)
504
-
505
- def __getitem__(self, idx):
506
- sample_path = self.files[idx]
507
- # prefer torch.load if .pt, else try json
508
- if sample_path.endswith(".pt"):
509
- sample = torch.load(sample_path, map_location="cpu")
510
- else:
511
- # fallback json load
512
- with open(sample_path, "r") as f:
513
- sample = json.load(f)
514
-
515
- # GINE: convert lists to tensors (still on CPU)
516
- gine_raw = sample.get("gine", None)
517
- gine_item = None
518
- if gine_raw:
519
- node_atomic = torch.tensor(gine_raw.get("node_atomic", []), dtype=torch.long)
520
- node_chirality = torch.tensor(gine_raw.get("node_chirality", []), dtype=torch.float)
521
- node_charge = torch.tensor(gine_raw.get("node_charge", []), dtype=torch.float)
522
- if gine_raw.get("edge_index", None) is not None:
523
- ei = gine_raw["edge_index"]
524
- edge_index = torch.tensor(ei, dtype=torch.long)
525
- else:
526
- edge_index = torch.tensor([[], []], dtype=torch.long)
527
- ea_raw = gine_raw.get("edge_attr", None)
528
- if ea_raw:
529
- edge_attr = torch.tensor(ea_raw, dtype=torch.float)
530
- else:
531
- edge_attr = torch.zeros((edge_index.size(1), 3), dtype=torch.float)
532
- gine_item = {"z": node_atomic, "chirality": node_chirality, "formal_charge": node_charge, "edge_index": edge_index, "edge_attr": edge_attr}
533
- else:
534
- gine_item = {"z": torch.tensor([], dtype=torch.long), "chirality": torch.tensor([], dtype=torch.float), "formal_charge": torch.tensor([], dtype=torch.float), "edge_index": torch.tensor([[], []], dtype=torch.long), "edge_attr": torch.zeros((0, 3), dtype=torch.float)}
535
-
536
- # SchNet
537
- schnet_raw = sample.get("schnet", None)
538
- if schnet_raw:
539
- s_z = torch.tensor(schnet_raw.get("atomic", []), dtype=torch.long)
540
- s_pos = torch.tensor(schnet_raw.get("coords", []), dtype=torch.float)
541
- schnet_item = {"z": s_z, "pos": s_pos}
542
- else:
543
- schnet_item = {"z": torch.tensor([], dtype=torch.long), "pos": torch.tensor([], dtype=torch.float)}
544
-
545
- # Fingerprint — stored as list of ints; convert to tensor here
546
- fp_raw = sample.get("fp", None)
547
- if fp_raw is None:
548
- fp_vec = torch.zeros((self.fp_length,), dtype=torch.long)
549
- else:
550
- # if fp_raw is already tensor-like, handle it
551
- if isinstance(fp_raw, (list, tuple)):
552
- arr = list(fp_raw)[:self.fp_length]
553
- if len(arr) < self.fp_length:
554
- arr = arr + [0] * (self.fp_length - len(arr))
555
- fp_vec = torch.tensor(arr, dtype=torch.long)
556
- elif isinstance(fp_raw, torch.Tensor):
557
- fp_vec = fp_raw.clone().to(torch.long)
558
- else:
559
- # fallback
560
- fp_vec = torch.zeros((self.fp_length,), dtype=torch.long)
561
-
562
- # PSMILES: raw string, tokenize now
563
- psm_raw = sample.get("psmiles_raw", "")
564
- if psm_raw is None:
565
- psm_raw = ""
566
- enc = self.tokenizer(psm_raw, truncation=True, padding="max_length", max_length=self.psmiles_max_len)
567
- p_input_ids = torch.tensor(enc["input_ids"], dtype=torch.long)
568
- p_attn = torch.tensor(enc["attention_mask"], dtype=torch.bool)
569
-
570
- return {
571
- "gine": {"z": gine_item["z"], "chirality": gine_item["chirality"], "formal_charge": gine_item["formal_charge"], "edge_index": gine_item["edge_index"], "edge_attr": gine_item["edge_attr"], "num_nodes": int(gine_item["z"].size(0)) if gine_item["z"].numel() > 0 else 0},
572
- "schnet": {"z": schnet_item["z"], "pos": schnet_item["pos"]},
573
- "fp": {"input_ids": fp_vec},
574
- "psmiles": {"input_ids": p_input_ids, "attention_mask": p_attn}
575
- }
576
-
577
- # instantiate dataset lazily
578
- dataset = LazyMultimodalDataset(sample_files, tokenizer, fp_length=FP_LENGTH, psmiles_max_len=PSMILES_MAX_LEN)
579
-
580
- # train/val split
581
- train_idx, val_idx = train_test_split(list(range(len(dataset))), test_size=0.2, random_state=42)
582
- train_subset = torch.utils.data.Subset(dataset, train_idx)
583
- val_subset = torch.utils.data.Subset(dataset, val_idx)
584
-
585
- # For manual evaluation (used by evaluate_multimodal), create a DataLoader with num_workers=0
586
- def multimodal_collate(batch_list):
587
- """
588
- Given a list of items as returned by MultimodalDataset.__getitem__, build a batched mini-batch
589
- that the encoders accept.
590
- """
591
- B = len(batch_list)
592
- # GINE batching
593
- all_z = []
594
- all_ch = []
595
- all_fc = []
596
- all_edge_index = []
597
- all_edge_attr = []
598
- batch_mapping = []
599
- node_offset = 0
600
- for i, item in enumerate(batch_list):
601
- g = item["gine"]
602
- z = g["z"]
603
- n = z.size(0)
604
- all_z.append(z)
605
- all_ch.append(g["chirality"])
606
- all_fc.append(g["formal_charge"])
607
- batch_mapping.append(torch.full((n,), i, dtype=torch.long))
608
- if g["edge_index"] is not None and g["edge_index"].numel() > 0:
609
- ei_offset = g["edge_index"] + node_offset
610
- all_edge_index.append(ei_offset)
611
- ea = match_edge_attr_to_index(g["edge_index"], g["edge_attr"], target_dim=3)
612
- all_edge_attr.append(ea)
613
- node_offset += n
614
- if len(all_z) == 0:
615
- # create zero-length placeholders for empty batch
616
- z_batch = torch.tensor([], dtype=torch.long)
617
- ch_batch = torch.tensor([], dtype=torch.float)
618
- fc_batch = torch.tensor([], dtype=torch.float)
619
- batch_batch = torch.tensor([], dtype=torch.long)
620
- edge_index_batched = torch.empty((2,0), dtype=torch.long)
621
- edge_attr_batched = torch.zeros((0,3), dtype=torch.float)
622
- else:
623
- z_batch = torch.cat(all_z, dim=0)
624
- ch_batch = torch.cat(all_ch, dim=0)
625
- fc_batch = torch.cat(all_fc, dim=0)
626
- batch_batch = torch.cat(batch_mapping, dim=0)
627
- if len(all_edge_index) > 0:
628
- edge_index_batched = torch.cat(all_edge_index, dim=1)
629
- edge_attr_batched = torch.cat(all_edge_attr, dim=0)
630
- else:
631
- edge_index_batched = torch.empty((2,0), dtype=torch.long)
632
- edge_attr_batched = torch.zeros((0,3), dtype=torch.float)
633
-
634
- # SchNet batching: concat nodes and create batch indices
635
- all_sz = []
636
- all_pos = []
637
- schnet_batch = []
638
- for i, item in enumerate(batch_list):
639
- s = item["schnet"]
640
- s_z = s["z"]
641
- s_pos = s["pos"]
642
- if s_z.numel() == 0:
643
- continue
644
- all_sz.append(s_z)
645
- all_pos.append(s_pos)
646
- schnet_batch.append(torch.full((s_z.size(0),), i, dtype=torch.long))
647
- if len(all_sz) == 0:
648
- s_z_batch = torch.tensor([], dtype=torch.long)
649
- s_pos_batch = torch.tensor([], dtype=torch.float)
650
- s_batch_batch = torch.tensor([], dtype=torch.long)
651
- else:
652
- s_z_batch = torch.cat(all_sz, dim=0)
653
- s_pos_batch = torch.cat(all_pos, dim=0)
654
- s_batch_batch = torch.cat(schnet_batch, dim=0)
655
-
656
- # FP batching: each fp is vector [L] (long 0/1). We make attention_mask all ones.
657
- fp_ids = torch.stack([item["fp"]["input_ids"] if isinstance(item["fp"]["input_ids"], torch.Tensor) else torch.tensor(item["fp"]["input_ids"], dtype=torch.long) for item in batch_list], dim=0)
658
- fp_attn = torch.ones_like(fp_ids, dtype=torch.bool)
659
-
660
- # PSMILES
661
- p_ids = torch.stack([item["psmiles"]["input_ids"] for item in batch_list], dim=0)
662
- p_attn = torch.stack([item["psmiles"]["attention_mask"] for item in batch_list], dim=0)
663
-
664
- return {
665
- "gine": {"z": z_batch, "chirality": ch_batch, "formal_charge": fc_batch, "edge_index": edge_index_batched, "edge_attr": edge_attr_batched, "batch": batch_batch},
666
- "schnet": {"z": s_z_batch, "pos": s_pos_batch, "batch": s_batch_batch},
667
- "fp": {"input_ids": fp_ids, "attention_mask": fp_attn},
668
- "psmiles": {"input_ids": p_ids, "attention_mask": p_attn}
669
- }
670
-
671
- train_loader = DataLoader(train_subset, batch_size=training_args.per_device_train_batch_size, shuffle=True, collate_fn=multimodal_collate, num_workers=0, drop_last=False)
672
- val_loader = DataLoader(val_subset, batch_size=training_args.per_device_eval_batch_size, shuffle=False, collate_fn=multimodal_collate, num_workers=0, drop_last=False)
673
-
674
- # ---------------------------
675
- # Encoder definitions (kept same as original with minimal device-safe guards)
676
- # ---------------------------
677
-
678
- class GineBlock(nn.Module):
679
- def __init__(self, node_dim):
680
- super().__init__()
681
- self.mlp = nn.Sequential(
682
- nn.Linear(node_dim, node_dim),
683
- nn.ReLU(),
684
- nn.Linear(node_dim, node_dim)
685
- )
686
- # If GINEConv is not available, we still construct placeholder to fail later with message
687
- if GINEConv is None:
688
- raise RuntimeError("GINEConv is not available. Install torch_geometric with compatible versions.")
689
- self.conv = GINEConv(self.mlp)
690
- self.bn = nn.BatchNorm1d(node_dim)
691
- self.act = nn.ReLU()
692
-
693
- def forward(self, x, edge_index, edge_attr):
694
- x = self.conv(x, edge_index, edge_attr)
695
- x = self.bn(x)
696
- x = self.act(x)
697
- return x
698
-
699
- class GineEncoder(nn.Module):
700
- 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):
701
- super().__init__()
702
- self.atom_emb = nn.Embedding(num_embeddings=MASK_ATOM_ID+1, embedding_dim=node_emb_dim, padding_idx=None)
703
- self.node_attr_proj = nn.Sequential(
704
- nn.Linear(2, node_emb_dim),
705
- nn.ReLU(),
706
- nn.Linear(node_emb_dim, node_emb_dim)
707
- )
708
- self.edge_encoder = nn.Sequential(
709
- nn.Linear(3, edge_emb_dim),
710
- nn.ReLU(),
711
- nn.Linear(edge_emb_dim, edge_emb_dim)
712
- )
713
- if edge_emb_dim != node_emb_dim:
714
- self._edge_to_node_proj = nn.Linear(edge_emb_dim, node_emb_dim)
715
- else:
716
- self._edge_to_node_proj = None
717
- self.gnn_layers = nn.ModuleList([GineBlock(node_emb_dim) for _ in range(num_layers)])
718
- # global pooling projection
719
- self.pool_proj = nn.Linear(node_emb_dim, node_emb_dim)
720
-
721
- # node-level classifier head for reconstructing atomic ids if needed
722
- self.node_classifier = nn.Linear(node_emb_dim, MASK_ATOM_ID+1)
723
-
724
- def _compute_node_reps(self, z, chirality, formal_charge, edge_index, edge_attr):
725
- device = next(self.parameters()).device
726
- atom_embedding = self.atom_emb(z.to(device))
727
- if chirality is None or formal_charge is None:
728
- node_attr = torch.zeros((z.size(0), 2), device=device)
729
- else:
730
- node_attr = torch.stack([chirality, formal_charge], dim=1).to(atom_embedding.device)
731
- node_attr_emb = self.node_attr_proj(node_attr)
732
- x = atom_embedding + node_attr_emb
733
- if edge_attr is None or edge_attr.numel() == 0:
734
- edge_emb = torch.zeros((0, EDGE_EMB_DIM), dtype=torch.float, device=x.device)
735
- else:
736
- edge_emb = self.edge_encoder(edge_attr.to(x.device))
737
- if self._edge_to_node_proj is not None and edge_emb.numel() > 0:
738
- edge_for_conv = self._edge_to_node_proj(edge_emb)
739
- else:
740
- edge_for_conv = edge_emb
741
-
742
- h = x
743
- for layer in self.gnn_layers:
744
- h = layer(h, edge_index.to(h.device), edge_for_conv)
745
- return h
746
-
747
- def forward(self, z, chirality, formal_charge, edge_index, edge_attr, batch=None):
748
- h = self._compute_node_reps(z, chirality, formal_charge, edge_index, edge_attr)
749
- if batch is None:
750
- pooled = torch.mean(h, dim=0, keepdim=True)
751
- else:
752
- bsize = int(batch.max().item() + 1) if batch.numel() > 0 else 1
753
- pooled = torch.zeros((bsize, h.size(1)), device=h.device)
754
- for i in range(bsize):
755
- mask = batch == i
756
- if mask.sum() == 0:
757
- continue
758
- pooled[i] = h[mask].mean(dim=0)
759
- return self.pool_proj(pooled)
760
-
761
- def node_logits(self, z, chirality, formal_charge, edge_index, edge_attr):
762
- h = self._compute_node_reps(z, chirality, formal_charge, edge_index, edge_attr)
763
- logits = self.node_classifier(h)
764
- return logits
765
-
766
- class NodeSchNetWrapper(nn.Module):
767
- def __init__(self, hidden_channels=SCHNET_HIDDEN, num_interactions=SCHNET_NUM_INTERACTIONS, num_gaussians=SCHNET_NUM_GAUSSIANS, cutoff=SCHNET_CUTOFF, max_num_neighbors=SCHNET_MAX_NEIGHBORS):
768
- super().__init__()
769
- if PyGSchNet is None:
770
- raise RuntimeError("PyG SchNet is not available. Install torch_geometric with compatible extras.")
771
- self.schnet = PyGSchNet(hidden_channels=hidden_channels, num_filters=hidden_channels, num_interactions=num_interactions, num_gaussians=num_gaussians, cutoff=cutoff, max_num_neighbors=max_num_neighbors)
772
- self.pool_proj = nn.Linear(hidden_channels, hidden_channels)
773
- self.cutoff = cutoff
774
- self.max_num_neighbors = max_num_neighbors
775
- self.node_classifier = nn.Linear(hidden_channels, MASK_ATOM_ID+1)
776
-
777
- def forward(self, z, pos, batch=None):
778
- device = next(self.parameters()).device
779
- z = z.to(device)
780
- pos = pos.to(device)
781
- if batch is None:
782
- batch = torch.zeros(z.size(0), dtype=torch.long, device=z.device)
783
- try:
784
- edge_index = radius_graph(pos, r=self.cutoff, batch=batch, max_num_neighbors=self.max_num_neighbors)
785
- except Exception:
786
- edge_index = None
787
-
788
- node_h = None
789
- try:
790
- if hasattr(self.schnet, "embedding"):
791
- node_h = self.schnet.embedding(z)
792
- else:
793
- node_h = self.schnet.embedding(z)
794
- except Exception:
795
- node_h = None
796
-
797
- if node_h is not None and edge_index is not None and edge_index.numel() > 0:
798
- row, col = edge_index
799
- edge_weight = (pos[row] - pos[col]).norm(dim=-1)
800
- edge_attr = None
801
- if hasattr(self.schnet, "distance_expansion"):
802
- try:
803
- edge_attr = self.schnet.distance_expansion(edge_weight)
804
- except Exception:
805
- edge_attr = None
806
- if edge_attr is None and hasattr(self.schnet, "gaussian_smearing"):
807
- try:
808
- edge_attr = self.schnet.gaussian_smearing(edge_weight)
809
- except Exception:
810
- edge_attr = None
811
- if hasattr(self.schnet, "interactions") and getattr(self.schnet, "interactions") is not None:
812
- for interaction in self.schnet.interactions:
813
- try:
814
- node_h = node_h + interaction(node_h, edge_index, edge_weight, edge_attr)
815
- except TypeError:
816
- node_h = node_h + interaction(node_h, edge_index, edge_weight)
817
- if node_h is None:
818
- try:
819
- out = self.schnet(z=z, pos=pos, batch=batch)
820
- if isinstance(out, torch.Tensor) and out.dim() == 2 and out.size(0) == z.size(0):
821
- node_h = out
822
- elif hasattr(out, "last_hidden_state"):
823
- node_h = out.last_hidden_state
824
- elif isinstance(out, (tuple, list)) and len(out) > 0 and isinstance(out[0], torch.Tensor):
825
- cand = out[0]
826
- if cand.dim() == 2 and cand.size(0) == z.size(0):
827
- node_h = cand
828
- except Exception as e:
829
- raise RuntimeError("Failed to obtain node-level embeddings from PyG SchNet.") from e
830
-
831
- bsize = int(batch.max().item()) + 1 if z.numel() > 0 else 1
832
- pooled = torch.zeros((bsize, node_h.size(1)), device=node_h.device)
833
- for i in range(bsize):
834
- mask = batch == i
835
- if mask.sum() == 0:
836
- continue
837
- pooled[i] = node_h[mask].mean(dim=0)
838
- return self.pool_proj(pooled)
839
-
840
- def node_logits(self, z, pos, batch=None):
841
- device = next(self.parameters()).device
842
- z = z.to(device)
843
- pos = pos.to(device)
844
- if batch is None:
845
- batch = torch.zeros(z.size(0), dtype=torch.long, device=z.device)
846
- try:
847
- edge_index = radius_graph(pos, r=self.cutoff, batch=batch, max_num_neighbors=self.max_num_neighbors)
848
- except Exception:
849
- edge_index = None
850
-
851
- node_h = None
852
- try:
853
- if hasattr(self.schnet, "embedding"):
854
- node_h = self.schnet.embedding(z)
855
- except Exception:
856
- node_h = None
857
-
858
- if node_h is not None and edge_index is not None and edge_index.numel() > 0:
859
- row, col = edge_index
860
- edge_weight = (pos[row] - pos[col]).norm(dim=-1)
861
- edge_attr = None
862
- if hasattr(self.schnet, "distance_expansion"):
863
- try:
864
- edge_attr = self.schnet.distance_expansion(edge_weight)
865
- except Exception:
866
- edge_attr = None
867
- if edge_attr is None and hasattr(self.schnet, "gaussian_smearing"):
868
- try:
869
- edge_attr = self.schnet.gaussian_smearing(edge_weight)
870
- except Exception:
871
- edge_attr = None
872
- if hasattr(self.schnet, "interactions") and getattr(self.schnet, "interactions") is not None:
873
- for interaction in self.schnet.interactions:
874
- try:
875
- node_h = node_h + interaction(node_h, edge_index, edge_weight, edge_attr)
876
- except TypeError:
877
- node_h = node_h + interaction(node_h, edge_index, edge_weight)
878
-
879
- if node_h is None:
880
- out = self.schnet(z=z, pos=pos, batch=batch)
881
- if isinstance(out, torch.Tensor):
882
- node_h = out
883
- elif hasattr(out, "last_hidden_state"):
884
- node_h = out.last_hidden_state
885
- elif isinstance(out, (tuple, list)) and len(out) > 0 and isinstance(out[0], torch.Tensor):
886
- node_h = out[0]
887
- else:
888
- raise RuntimeError("Unable to obtain node embeddings for SchNet node_logits")
889
-
890
- logits = self.node_classifier(node_h)
891
- return logits
892
-
893
- class FingerprintEncoder(nn.Module):
894
- def __init__(self, vocab_size=VOCAB_SIZE_FP, hidden_dim=256, seq_len=FP_LENGTH, num_layers=4, nhead=8, dim_feedforward=1024, dropout=0.1):
895
- super().__init__()
896
- self.token_emb = nn.Embedding(vocab_size, hidden_dim)
897
- self.pos_emb = nn.Embedding(seq_len, hidden_dim)
898
- encoder_layer = nn.TransformerEncoderLayer(d_model=hidden_dim, nhead=nhead, dim_feedforward=dim_feedforward, dropout=dropout, batch_first=True)
899
- self.transformer = nn.TransformerEncoder(encoder_layer, num_layers=num_layers)
900
- self.pool_proj = nn.Linear(hidden_dim, hidden_dim)
901
- self.seq_len = seq_len
902
- self.token_proj = nn.Linear(hidden_dim, vocab_size)
903
-
904
- def forward(self, input_ids, attention_mask=None):
905
- device = next(self.parameters()).device
906
- input_ids = input_ids.to(device)
907
- B, L = input_ids.shape
908
- x = self.token_emb(input_ids)
909
- pos_ids = torch.arange(L, device=input_ids.device).unsqueeze(0).expand(B, -1)
910
- x = x + self.pos_emb(pos_ids)
911
- if attention_mask is not None:
912
- key_padding_mask = ~attention_mask.to(input_ids.device)
913
- else:
914
- key_padding_mask = None
915
- out = self.transformer(x, src_key_padding_mask=key_padding_mask)
916
- if attention_mask is None:
917
- pooled = out.mean(dim=1)
918
- else:
919
- am = attention_mask.to(out.device).float().unsqueeze(-1)
920
- pooled = (out * am).sum(dim=1) / (am.sum(dim=1).clamp(min=1.0))
921
- return self.pool_proj(pooled)
922
-
923
- def token_logits(self, input_ids, attention_mask=None):
924
- device = next(self.parameters()).device
925
- input_ids = input_ids.to(device)
926
- B, L = input_ids.shape
927
- x = self.token_emb(input_ids)
928
- pos_ids = torch.arange(L, device=input_ids.device).unsqueeze(0).expand(B, -1)
929
- x = x + self.pos_emb(pos_ids)
930
- if attention_mask is not None:
931
- key_padding_mask = ~attention_mask.to(input_ids.device)
932
- else:
933
- key_padding_mask = None
934
- out = self.transformer(x, src_key_padding_mask=key_padding_mask)
935
- logits = self.token_proj(out)
936
- return logits
937
-
938
- class PSMILESDebertaEncoder(nn.Module):
939
- def __init__(self, model_dir_or_name: Optional[str] = None):
940
- super().__init__()
941
- try:
942
- if model_dir_or_name is not None and os.path.isdir(model_dir_or_name):
943
- self.model = DebertaV2ForMaskedLM.from_pretrained(model_dir_or_name)
944
- else:
945
- self.model = DebertaV2ForMaskedLM.from_pretrained("microsoft/deberta-v2-xlarge")
946
- except Exception as e:
947
- print("Warning: couldn't load DebertaV2 pretrained weights; initializing randomly.", e)
948
- from transformers import DebertaV2Config
949
- cfg = DebertaV2Config(vocab_size=getattr(tokenizer, "vocab_size", 300), hidden_size=DEBERTA_HIDDEN, num_attention_heads=12, num_hidden_layers=12, intermediate_size=512)
950
- self.model = DebertaV2ForMaskedLM(cfg)
951
- self.pool_proj = nn.Linear(self.model.config.hidden_size, self.model.config.hidden_size)
952
-
953
- def forward(self, input_ids, attention_mask=None):
954
- device = next(self.parameters()).device
955
- input_ids = input_ids.to(device)
956
- if attention_mask is not None:
957
- attention_mask = attention_mask.to(device)
958
- outputs = self.model.base_model(input_ids=input_ids, attention_mask=attention_mask, return_dict=True)
959
- last_hidden = outputs.last_hidden_state
960
- if attention_mask is None:
961
- pooled = last_hidden.mean(dim=1)
962
- else:
963
- am = attention_mask.unsqueeze(-1).to(last_hidden.device).float()
964
- pooled = (last_hidden * am).sum(dim=1) / (am.sum(dim=1).clamp(min=1.0))
965
- return self.pool_proj(pooled)
966
-
967
- def token_logits(self, input_ids, attention_mask=None, labels=None):
968
- device = next(self.parameters()).device
969
- input_ids = input_ids.to(device)
970
- if attention_mask is not None:
971
- attention_mask = attention_mask.to(device)
972
- if labels is not None:
973
- labels = labels.to(device)
974
- outputs = self.model(input_ids=input_ids, attention_mask=attention_mask, labels=labels, return_dict=True)
975
- return outputs.loss
976
- else:
977
- outputs = self.model(input_ids=input_ids, attention_mask=attention_mask, return_dict=True)
978
- return outputs.logits
979
-
980
- # ---------------------------
981
- # Multimodal wrapper & loss (kept same)
982
- # ---------------------------
983
- class MultimodalContrastiveModel(nn.Module):
984
- def __init__(self,
985
- gine_encoder: Optional[GineEncoder],
986
- schnet_encoder: Optional[NodeSchNetWrapper],
987
- fp_encoder: Optional[FingerprintEncoder],
988
- psmiles_encoder: Optional[PSMILESDebertaEncoder],
989
- emb_dim: int = 600):
990
- super().__init__()
991
- self.gine = gine_encoder
992
- self.schnet = schnet_encoder
993
- self.fp = fp_encoder
994
- self.psmiles = psmiles_encoder
995
- self.proj_gine = nn.Linear(getattr(self.gine, "pool_proj").out_features if self.gine is not None else emb_dim, emb_dim) if self.gine is not None else None
996
- self.proj_schnet = nn.Linear(getattr(self.schnet, "pool_proj").out_features if self.schnet is not None else emb_dim, emb_dim) if self.schnet is not None else None
997
- self.proj_fp = nn.Linear(getattr(self.fp, "pool_proj").out_features if self.fp is not None else emb_dim, emb_dim) if self.fp is not None else None
998
- self.proj_psmiles = nn.Linear(getattr(self.psmiles, "pool_proj").out_features if self.psmiles is not None else emb_dim, emb_dim) if self.psmiles is not None else None
999
- self.temperature = TEMPERATURE
1000
- self.ce_loss = nn.CrossEntropyLoss(ignore_index=-100, reduction='mean')
1001
-
1002
- def encode(self, batch_mods: Dict[str, torch.Tensor]) -> Dict[str, torch.Tensor]:
1003
- device = next(self.parameters()).device
1004
- embs = {}
1005
- B = None
1006
- if 'gine' in batch_mods and self.gine is not None:
1007
- g = batch_mods['gine']
1008
- emb_g = self.gine(g['z'], g['chirality'], g['formal_charge'], g['edge_index'], g['edge_attr'], g.get('batch', None))
1009
- embs['gine'] = F.normalize(self.proj_gine(emb_g), dim=-1)
1010
- B = embs['gine'].size(0) if B is None else B
1011
- if 'schnet' in batch_mods and self.schnet is not None:
1012
- s = batch_mods['schnet']
1013
- emb_s = self.schnet(s['z'], s['pos'], s.get('batch', None))
1014
- embs['schnet'] = F.normalize(self.proj_schnet(emb_s), dim=-1)
1015
- B = embs['schnet'].size(0) if B is None else B
1016
- if 'fp' in batch_mods and self.fp is not None:
1017
- f = batch_mods['fp']
1018
- emb_f = self.fp(f['input_ids'], f.get('attention_mask', None))
1019
- embs['fp'] = F.normalize(self.proj_fp(emb_f), dim=-1)
1020
- B = embs['fp'].size(0) if B is None else B
1021
- if 'psmiles' in batch_mods and self.psmiles is not None:
1022
- p = batch_mods['psmiles']
1023
- emb_p = self.psmiles(p['input_ids'], p.get('attention_mask', None))
1024
- embs['psmiles'] = F.normalize(self.proj_psmiles(emb_p), dim=-1)
1025
- B = embs['psmiles'].size(0) if B is None else B
1026
- return embs
1027
-
1028
- def forward(self, batch_mods: Dict[str, torch.Tensor], mask_target: str):
1029
- device = next(self.parameters()).device
1030
- embs = self.encode(batch_mods)
1031
- info = {}
1032
- if mask_target not in embs:
1033
- return torch.tensor(0.0, device=device), {"batch_size": 0}
1034
- target = embs[mask_target]
1035
- other_keys = [k for k in embs.keys() if k != mask_target]
1036
- if len(other_keys) == 0:
1037
- return torch.tensor(0.0, device=device), {"batch_size": target.size(0)}
1038
- anchor = torch.stack([embs[k] for k in other_keys], dim=0).mean(dim=0)
1039
- logits = torch.matmul(anchor, target.T) / self.temperature
1040
- B = logits.size(0)
1041
- labels = torch.arange(B, device=logits.device)
1042
- info_nce_loss = F.cross_entropy(logits, labels)
1043
- info['info_nce_loss'] = float(info_nce_loss.detach().cpu().item())
1044
-
1045
- rec_losses = []
1046
- rec_details = {}
1047
-
1048
- try:
1049
- if 'gine' in batch_mods and self.gine is not None:
1050
- gm = batch_mods['gine']
1051
- labels_nodes = gm.get('labels', None)
1052
- if labels_nodes is not None:
1053
- node_logits = self.gine.node_logits(gm['z'], gm['chirality'], gm['formal_charge'], gm['edge_index'], gm['edge_attr'])
1054
- if labels_nodes.dim() == 1 and node_logits.size(0) == labels_nodes.size(0):
1055
- loss_gine = self.ce_loss(node_logits, labels_nodes.to(node_logits.device))
1056
- rec_losses.append(loss_gine)
1057
- rec_details['gine_rec_loss'] = float(loss_gine.detach().cpu().item())
1058
- except Exception as e:
1059
- print("Warning: GINE reconstruction loss computation failed:", e)
1060
-
1061
- try:
1062
- if 'schnet' in batch_mods and self.schnet is not None:
1063
- sm = batch_mods['schnet']
1064
- labels_nodes = sm.get('labels', None)
1065
- if labels_nodes is not None:
1066
- node_logits = self.schnet.node_logits(sm['z'], sm['pos'], sm.get('batch', None))
1067
- if labels_nodes.dim() == 1 and node_logits.size(0) == labels_nodes.size(0):
1068
- loss_schnet = self.ce_loss(node_logits, labels_nodes.to(node_logits.device))
1069
- rec_losses.append(loss_schnet)
1070
- rec_details['schnet_rec_loss'] = float(loss_schnet.detach().cpu().item())
1071
- except Exception as e:
1072
- print("Warning: SchNet reconstruction loss computation failed:", e)
1073
-
1074
- try:
1075
- if 'fp' in batch_mods and self.fp is not None:
1076
- fm = batch_mods['fp']
1077
- labels_fp = fm.get('labels', None)
1078
- if labels_fp is not None:
1079
- token_logits = self.fp.token_logits(fm['input_ids'], fm.get('attention_mask', None))
1080
- Bf, Lf, V = token_logits.shape
1081
- logits2 = token_logits.view(-1, V)
1082
- labels2 = labels_fp.view(-1).to(logits2.device)
1083
- loss_fp = self.ce_loss(logits2, labels2)
1084
- rec_losses.append(loss_fp)
1085
- rec_details['fp_rec_loss'] = float(loss_fp.detach().cpu().item())
1086
- except Exception as e:
1087
- print("Warning: FP reconstruction loss computation failed:", e)
1088
-
1089
- try:
1090
- if 'psmiles' in batch_mods and self.psmiles is not None:
1091
- pm = batch_mods['psmiles']
1092
- labels_ps = pm.get('labels', None)
1093
- if labels_ps is not None and tokenizer is not None:
1094
- loss_ps = self.psmiles.token_logits(pm['input_ids'], pm.get('attention_mask', None), labels=labels_ps)
1095
- if isinstance(loss_ps, torch.Tensor):
1096
- rec_losses.append(loss_ps)
1097
- rec_details['psmiles_mlm_loss'] = float(loss_ps.detach().cpu().item())
1098
- except Exception as e:
1099
- print("Warning: PSMILES MLM loss computation failed:", e)
1100
-
1101
- if len(rec_losses) > 0:
1102
- rec_loss_total = sum(rec_losses) / len(rec_losses)
1103
- info['reconstruction_loss'] = float(rec_loss_total.detach().cpu().item())
1104
- total_loss = info_nce_loss + REC_LOSS_WEIGHT * rec_loss_total
1105
- info['total_loss'] = float(total_loss.detach().cpu().item())
1106
- info.update(rec_details)
1107
- else:
1108
- total_loss = info_nce_loss
1109
- info['reconstruction_loss'] = 0.0
1110
- info['total_loss'] = float(total_loss.detach().cpu().item())
1111
-
1112
- return total_loss, info
1113
-
1114
- # ---------------------------
1115
- # Instantiate encoders (load weights if available) and move to device with .to(device)
1116
- gine_encoder = GineEncoder(node_emb_dim=NODE_EMB_DIM, edge_emb_dim=EDGE_EMB_DIM, num_layers=NUM_GNN_LAYERS, max_atomic_z=MAX_ATOMIC_Z)
1117
- if os.path.exists(os.path.join(BEST_GINE_DIR, "pytorch_model.bin")):
1118
- try:
1119
- gine_encoder.load_state_dict(torch.load(os.path.join(BEST_GINE_DIR, "pytorch_model.bin"), map_location="cpu"), strict=False)
1120
- print("Loaded GINE best weights from", BEST_GINE_DIR)
1121
- except Exception as e:
1122
- print("Could not load GINE best weights:", e)
1123
- gine_encoder.to(device)
1124
-
1125
- schnet_encoder = NodeSchNetWrapper(hidden_channels=SCHNET_HIDDEN, num_interactions=SCHNET_NUM_INTERACTIONS, num_gaussians=SCHNET_NUM_GAUSSIANS, cutoff=SCHNET_CUTOFF, max_num_neighbors=SCHNET_MAX_NEIGHBORS)
1126
- if os.path.exists(os.path.join(BEST_SCHNET_DIR, "pytorch_model.bin")):
1127
- try:
1128
- schnet_encoder.load_state_dict(torch.load(os.path.join(BEST_SCHNET_DIR, "pytorch_model.bin"), map_location="cpu"), strict=False)
1129
- print("Loaded SchNet best weights from", BEST_SCHNET_DIR)
1130
- except Exception as e:
1131
- print("Could not load SchNet best weights:", e)
1132
- schnet_encoder.to(device)
1133
-
1134
- fp_encoder = FingerprintEncoder(vocab_size=VOCAB_SIZE_FP, hidden_dim=256, seq_len=FP_LENGTH, num_layers=4, nhead=8, dim_feedforward=1024, dropout=0.1)
1135
- if os.path.exists(os.path.join(BEST_FP_DIR, "pytorch_model.bin")):
1136
- try:
1137
- fp_encoder.load_state_dict(torch.load(os.path.join(BEST_FP_DIR, "pytorch_model.bin"), map_location="cpu"), strict=False)
1138
- print("Loaded fingerprint encoder best weights from", BEST_FP_DIR)
1139
- except Exception as e:
1140
- print("Could not load fingerprint best weights:", e)
1141
- fp_encoder.to(device)
1142
-
1143
- psmiles_encoder = None
1144
- if os.path.isdir(BEST_PSMILES_DIR):
1145
- try:
1146
- psmiles_encoder = PSMILESDebertaEncoder(model_dir_or_name=BEST_PSMILES_DIR)
1147
- print("Loaded Deberta (PSMILES) from", BEST_PSMILES_DIR)
1148
- except Exception as e:
1149
- print("Failed to load Deberta from saved directory:", e)
1150
- if psmiles_encoder is None:
1151
- try:
1152
- psmiles_encoder = PSMILESDebertaEncoder(model_dir_or_name=None)
1153
- except Exception as e:
1154
- print("Failed to instantiate Deberta encoder:", e)
1155
- psmiles_encoder.to(device)
1156
-
1157
- multimodal_model = MultimodalContrastiveModel(gine_encoder, schnet_encoder, fp_encoder, psmiles_encoder, emb_dim=600)
1158
- multimodal_model.to(device)
1159
-
1160
- # ---------------------------
1161
- # Helper to sample masked variant for modalities: (kept same, device-safe)
1162
- def mask_batch_for_modality(batch: dict, modality: str, p_mask: float = P_MASK):
1163
- b = {}
1164
- # GINE:
1165
- if 'gine' in batch:
1166
- z = batch['gine']['z'].clone()
1167
- chir = batch['gine']['chirality'].clone()
1168
- fc = batch['gine']['formal_charge'].clone()
1169
- edge_index = batch['gine']['edge_index']
1170
- edge_attr = batch['gine']['edge_attr']
1171
- batch_map = batch['gine'].get('batch', None)
1172
- n_nodes = z.size(0)
1173
- dev = z.device
1174
- is_selected = torch.rand(n_nodes, device=dev) < p_mask
1175
- if is_selected.numel() > 0 and is_selected.all():
1176
- is_selected[torch.randint(0, n_nodes, (1,), device=dev)] = False
1177
- labels_z = torch.full_like(z, fill_value=-100)
1178
- if is_selected.any():
1179
- sel_idx = torch.nonzero(is_selected).squeeze(-1)
1180
- if sel_idx.dim() == 0:
1181
- sel_idx = sel_idx.unsqueeze(0)
1182
- labels_z[is_selected] = z[is_selected]
1183
- rand_atomic = torch.randint(1, MAX_ATOMIC_Z+1, (sel_idx.size(0),), dtype=torch.long, device=dev)
1184
- probs = torch.rand(sel_idx.size(0), device=dev)
1185
- mask_choice = probs < 0.8
1186
- rand_choice = (probs >= 0.8) & (probs < 0.9)
1187
- if mask_choice.any():
1188
- z[sel_idx[mask_choice]] = MASK_ATOM_ID
1189
- if rand_choice.any():
1190
- z[sel_idx[rand_choice]] = rand_atomic[rand_choice]
1191
- b['gine'] = {"z": z, "chirality": chir, "formal_charge": fc, "edge_index": edge_index, "edge_attr": edge_attr, "batch": batch_map, "labels": labels_z}
1192
-
1193
- # SchNet:
1194
- if 'schnet' in batch:
1195
- z = batch['schnet']['z'].clone()
1196
- pos = batch['schnet']['pos'].clone()
1197
- batch_map = batch['schnet'].get('batch', None)
1198
- n_nodes = z.size(0)
1199
- dev = z.device
1200
- is_selected = torch.rand(n_nodes, device=dev) < p_mask
1201
- if is_selected.numel() > 0 and is_selected.all():
1202
- is_selected[torch.randint(0, n_nodes, (1,), device=dev)] = False
1203
- labels_z = torch.full((n_nodes,), -100, dtype=torch.long, device=dev)
1204
- if is_selected.any():
1205
- sel_idx = torch.nonzero(is_selected).squeeze(-1)
1206
- if sel_idx.dim() == 0:
1207
- sel_idx = sel_idx.unsqueeze(0)
1208
- labels_z[is_selected] = z[is_selected]
1209
- probs_c = torch.rand(sel_idx.size(0), device=dev)
1210
- noisy_choice = probs_c < 0.8
1211
- randpos_choice = (probs_c >= 0.8) & (probs_c < 0.9)
1212
- if noisy_choice.any():
1213
- idx = sel_idx[noisy_choice]
1214
- noise = torch.randn((idx.size(0), 3), device=pos.device) * 0.5
1215
- pos[idx] = pos[idx] + noise
1216
- if randpos_choice.any():
1217
- idx = sel_idx[randpos_choice]
1218
- mins = pos.min(dim=0).values
1219
- maxs = pos.max(dim=0).values
1220
- randpos = (torch.rand((idx.size(0), 3), device=pos.device) * (maxs - mins)) + mins
1221
- pos[idx] = randpos
1222
- b['schnet'] = {"z": z, "pos": pos, "batch": batch_map, "labels": labels_z}
1223
-
1224
- # FP:
1225
- if 'fp' in batch:
1226
- input_ids = batch['fp']['input_ids'].clone()
1227
- attn = batch['fp'].get('attention_mask', torch.ones_like(input_ids, dtype=torch.bool))
1228
- B, L = input_ids.shape
1229
- dev = input_ids.device
1230
- labels_z = torch.full_like(input_ids, -100)
1231
- for i in range(B):
1232
- sel = torch.rand(L, device=dev) < p_mask
1233
- if sel.numel() > 0 and sel.all():
1234
- sel[torch.randint(0, L, (1,), device=dev)] = False
1235
- sel_idx = torch.nonzero(sel).squeeze(-1)
1236
- if sel_idx.numel() > 0:
1237
- if sel_idx.dim() == 0:
1238
- sel_idx = sel_idx.unsqueeze(0)
1239
- labels_z[i, sel_idx] = input_ids[i, sel_idx]
1240
- probs = torch.rand(sel_idx.size(0), device=dev)
1241
- mask_choice = probs < 0.8
1242
- rand_choice = (probs >= 0.8) & (probs < 0.9)
1243
- if mask_choice.any():
1244
- input_ids[i, sel_idx[mask_choice]] = MASK_TOKEN_ID_FP
1245
- if rand_choice.any():
1246
- rand_bits = torch.randint(0, 2, (rand_choice.sum().item(),), dtype=torch.long, device=dev)
1247
- input_ids[i, sel_idx[rand_choice]] = rand_bits
1248
- b['fp'] = {"input_ids": input_ids, "attention_mask": attn, "labels": labels_z}
1249
-
1250
- # PSMILES:
1251
- if 'psmiles' in batch:
1252
- input_ids = batch['psmiles']['input_ids'].clone()
1253
- attn = batch['psmiles']['attention_mask'].clone()
1254
- B, L = input_ids.shape
1255
- dev = input_ids.device
1256
- labels_z = torch.full_like(input_ids, -100)
1257
- if tokenizer is None:
1258
- b['psmiles'] = {"input_ids": input_ids, "attention_mask": attn, "labels": labels_z}
1259
- else:
1260
- mask_token_id = tokenizer.mask_token_id if getattr(tokenizer, "mask_token_id", None) is not None else getattr(tokenizer, "vocab", {}).get("<mask>", 1)
1261
- for i in range(B):
1262
- sel = torch.rand(L, device=dev) < p_mask
1263
- if sel.numel() > 0 and sel.all():
1264
- sel[torch.randint(0, L, (1,), device=dev)] = False
1265
- sel_idx = torch.nonzero(sel).squeeze(-1)
1266
- if sel_idx.numel() > 0:
1267
- if sel_idx.dim() == 0:
1268
- sel_idx = sel_idx.unsqueeze(0)
1269
- labels_z[i, sel_idx] = input_ids[i, sel_idx]
1270
- probs = torch.rand(sel_idx.size(0), device=dev)
1271
- mask_choice = probs < 0.8
1272
- rand_choice = (probs >= 0.8) & (probs < 0.9)
1273
- if mask_choice.any():
1274
- input_ids[i, sel_idx[mask_choice]] = mask_token_id
1275
- if rand_choice.any():
1276
- rand_ids = torch.randint(0, getattr(tokenizer, "vocab_size", 300), (rand_choice.sum().item(),), dtype=torch.long, device=dev)
1277
- input_ids[i, sel_idx[rand_choice]] = rand_ids
1278
- b['psmiles'] = {"input_ids": input_ids, "attention_mask": attn, "labels": labels_z}
1279
-
1280
- return b
1281
-
1282
- def mm_batch_to_model_input(masked_batch):
1283
- mm = {}
1284
- if 'gine' in masked_batch:
1285
- gm = masked_batch['gine']
1286
- mm['gine'] = {"z": gm['z'], "chirality": gm['chirality'], "formal_charge": gm['formal_charge'], "edge_index": gm['edge_index'], "edge_attr": gm['edge_attr'], "batch": gm.get('batch', None), "labels": gm.get('labels', None)}
1287
- if 'schnet' in masked_batch:
1288
- sm = masked_batch['schnet']
1289
- mm['schnet'] = {"z": sm['z'], "pos": sm['pos'], "batch": sm.get('batch', None), "labels": sm.get('labels', None)}
1290
- if 'fp' in masked_batch:
1291
- fm = masked_batch['fp']
1292
- mm['fp'] = {"input_ids": fm['input_ids'], "attention_mask": fm.get('attention_mask', None), "labels": fm.get('labels', None)}
1293
- if 'psmiles' in masked_batch:
1294
- pm = masked_batch['psmiles']
1295
- mm['psmiles'] = {"input_ids": pm['input_ids'], "attention_mask": pm.get('attention_mask', None), "labels": pm.get('labels', None)}
1296
- return mm
1297
-
1298
- # ---------------------------
1299
- # Evaluation function (keeps same semantics)
1300
- def evaluate_multimodal(model: MultimodalContrastiveModel, val_loader, device, mask_target="fp"):
1301
- model.eval()
1302
- total_loss = 0.0
1303
- total_examples = 0
1304
- acc_sum = 0.0
1305
- top5_sum = 0.0
1306
- mrr_sum = 0.0
1307
- mean_pos_logit_sum = 0.0
1308
- mean_neg_logit_sum = 0.0
1309
- f1_sum = 0.0
1310
-
1311
- with torch.no_grad():
1312
- for batch in val_loader:
1313
- masked_batch = mask_batch_for_modality(batch, mask_target, p_mask=P_MASK)
1314
- # move to device
1315
- for k in masked_batch:
1316
- for subk in masked_batch[k]:
1317
- if isinstance(masked_batch[k][subk], torch.Tensor):
1318
- masked_batch[k][subk] = masked_batch[k][subk].to(device)
1319
- mm_in = mm_batch_to_model_input(masked_batch)
1320
- embs = model.encode(mm_in)
1321
- if mask_target not in embs:
1322
- continue
1323
- target = embs[mask_target]
1324
- other_keys = [k for k in embs.keys() if k != mask_target]
1325
- if len(other_keys) == 0:
1326
- continue
1327
- anchor = torch.stack([embs[k] for k in other_keys], dim=0).mean(dim=0)
1328
- logits = torch.matmul(anchor, target.T) / model.temperature
1329
- B = logits.size(0)
1330
- labels = torch.arange(B, device=logits.device)
1331
- loss = F.cross_entropy(logits, labels)
1332
- total_loss += loss.item() * B
1333
- total_examples += B
1334
-
1335
- preds = logits.argmax(dim=1)
1336
- acc = (preds == labels).float().mean().item()
1337
- acc_sum += acc * B
1338
-
1339
- if B >= 5:
1340
- topk = min(5, B)
1341
- topk_indices = torch.topk(logits, k=topk, dim=1).indices
1342
- hits_topk = (topk_indices == labels.unsqueeze(1)).any(dim=1).float().mean().item()
1343
- top5_sum += hits_topk * B
1344
- else:
1345
- top5_sum += acc * B
1346
-
1347
- sorted_desc = torch.argsort(logits, dim=1, descending=True)
1348
- positions = (sorted_desc == labels.unsqueeze(1)).nonzero(as_tuple=False)
1349
- ranks = torch.zeros(B, device=logits.device).float()
1350
- if positions.numel() > 0:
1351
- for p in positions:
1352
- i, pos = int(p[0].item()), int(p[1].item())
1353
- ranks[i] = pos + 1.0
1354
- ranks_nonzero = ranks.clone()
1355
- ranks_nonzero[ranks_nonzero == 0] = float('inf')
1356
- mrr = (1.0 / ranks_nonzero).mean().item()
1357
- mrr_sum += mrr * B
1358
-
1359
- pos_logits = logits[torch.arange(B), labels]
1360
- neg_logits = logits.clone()
1361
- neg_logits[torch.arange(B), labels] = float('-inf')
1362
- neg_mask = neg_logits != float('-inf')
1363
- if neg_mask.any():
1364
- row_counts = neg_mask.sum(dim=1).clamp(min=1).float()
1365
- sum_neg_per_row = neg_logits.masked_fill(~neg_mask, 0.0).sum(dim=1)
1366
- mean_neg = (sum_neg_per_row / row_counts).mean().item()
1367
- else:
1368
- mean_neg = 0.0
1369
- mean_pos_logit_sum += pos_logits.mean().item() * B
1370
- mean_neg_logit_sum += mean_neg * B
1371
-
1372
- try:
1373
- labels_np = labels.cpu().numpy()
1374
- preds_np = preds.cpu().numpy()
1375
- if len(np.unique(labels_np)) < 2:
1376
- batch_f1 = float(acc)
1377
- else:
1378
- batch_f1 = f1_score(labels_np, preds_np, average='weighted')
1379
- except Exception:
1380
- batch_f1 = float(acc)
1381
- f1_sum += batch_f1 * B
1382
-
1383
- if total_examples == 0:
1384
- return {"eval_loss": float("nan"), "eval_accuracy": 0.0, "eval_f1_weighted": 0.0}
1385
-
1386
- avg_loss = total_loss / total_examples
1387
- accuracy = acc_sum / total_examples
1388
- f1_weighted = f1_sum / total_examples
1389
-
1390
- return {"eval_loss": avg_loss, "eval_accuracy": accuracy, "eval_f1_weighted": f1_weighted}
1391
-
1392
- # ---------------------------
1393
- # HF wrapper / Trainer integration (kept same as your part 2, uses lazy loaders)
1394
- class HFMultimodalModule(nn.Module):
1395
- def __init__(self, mm_model: MultimodalContrastiveModel):
1396
- super().__init__()
1397
- self.mm = mm_model
1398
-
1399
- def forward(self, **kwargs):
1400
- if "batch" in kwargs:
1401
- batch = kwargs["batch"]
1402
- mask_target = kwargs.get("mask_target", "fp")
1403
- else:
1404
- modality_keys = ["gine", "schnet", "fp", "psmiles"]
1405
- found = {k: v for k, v in kwargs.items() if k in modality_keys}
1406
- if len(found) > 0:
1407
- batch = {k: found[k] for k in found}
1408
- mask_target = kwargs.get("mask_target", "fp")
1409
- else:
1410
- raise ValueError("HFMultimodalModule.forward could not find 'batch' nor modality keys in inputs. Inputs keys: {}".format(list(kwargs.keys())))
1411
- masked_batch = mask_batch_for_modality(batch, mask_target, p_mask=P_MASK)
1412
- device = next(self.parameters()).device
1413
- for k in masked_batch:
1414
- for subk in list(masked_batch[k].keys()):
1415
- val = masked_batch[k][subk]
1416
- if isinstance(val, torch.Tensor):
1417
- masked_batch[k][subk] = val.to(device)
1418
- mm_in = mm_batch_to_model_input(masked_batch)
1419
- loss, info = self.mm(mm_in, mask_target)
1420
- logits = None
1421
- labels = None
1422
- try:
1423
- with torch.no_grad():
1424
- embs = self.mm.encode(mm_in)
1425
- if mask_target in embs:
1426
- target = embs[mask_target]
1427
- other_keys = [k for k in embs.keys() if k != mask_target]
1428
- if len(other_keys) > 0:
1429
- anchor = torch.stack([embs[k] for k in other_keys], dim=0).mean(dim=0)
1430
- logits = torch.matmul(anchor, target.T) / self.mm.temperature
1431
- B = logits.size(0)
1432
- labels = torch.arange(B, device=logits.device)
1433
- except Exception as e:
1434
- print("Warning: failed to compute logits/labels inside HFMultimodalModule.forward:", e)
1435
- logits = None
1436
- labels = None
1437
- eval_loss = loss.detach() if isinstance(loss, torch.Tensor) else torch.tensor(float(loss), device=device)
1438
- out = {"loss": loss, "eval_loss": eval_loss}
1439
- if logits is not None:
1440
- out["logits"] = logits
1441
- if labels is not None:
1442
- out["labels"] = labels
1443
- out["mm_info"] = info
1444
- return out
1445
-
1446
- hf_model = HFMultimodalModule(multimodal_model)
1447
- hf_model.to(device)
1448
-
1449
- class ContrastiveDataCollator:
1450
- def __init__(self, mask_prob=P_MASK, modalities: Optional[List[str]] = None):
1451
- self.mask_prob = mask_prob
1452
- self.modalities = modalities if modalities is not None else ["gine", "schnet", "fp", "psmiles"]
1453
-
1454
- def __call__(self, features):
1455
- if isinstance(features, dict):
1456
- collated = features
1457
- mask_target = random.choice([m for m in self.modalities if m in collated])
1458
- return {"batch": collated, "mask_target": mask_target}
1459
- if isinstance(features, (list, tuple)) and len(features) > 0:
1460
- first = features[0]
1461
- if isinstance(first, dict) and 'gine' in first:
1462
- collated = multimodal_collate(list(features))
1463
- mask_target = random.choice([m for m in self.modalities if m in collated])
1464
- return {"batch": collated, "mask_target": mask_target}
1465
- if isinstance(first, dict) and 'batch' in first:
1466
- collated = first['batch']
1467
- mask_target = first.get("mask_target", random.choice([m for m in self.modalities if m in collated]))
1468
- return {"batch": collated, "mask_target": mask_target}
1469
- print("ContrastiveDataCollator received unexpected 'features' shape/type.")
1470
- raise ValueError("ContrastiveDataCollator could not collate input. Expected list[dict] with 'gine' key or already-collated dict.")
1471
-
1472
- data_collator = ContrastiveDataCollator(mask_prob=P_MASK)
1473
-
1474
- class VerboseTrainingCallback(TrainerCallback):
1475
- def __init__(self, patience: int = 10):
1476
- self.start_time = time.time()
1477
- self.epoch_start_time = time.time()
1478
- self._last_train_loss = None
1479
- self.best_val_loss = float("inf")
1480
- self.best_epoch = 0
1481
- self.epochs_no_improve = 0
1482
- self.patience = patience
1483
- self.trainer_ref = None
1484
-
1485
- def save_best_model(self, output_dir_suffix: str = "best"):
1486
- if self.trainer_ref is None:
1487
- return
1488
- try:
1489
- ckpt_dir = os.path.join(OUTPUT_DIR, output_dir_suffix)
1490
- os.makedirs(ckpt_dir, exist_ok=True)
1491
- self.trainer_ref._save(ckpt_dir)
1492
- print(f"Saved best model checkpoint to {ckpt_dir}")
1493
- except Exception as e:
1494
- try:
1495
- self.trainer_ref.save_model(os.path.join(OUTPUT_DIR, output_dir_suffix))
1496
- print(f"Saved best model (fallback) to {os.path.join(OUTPUT_DIR, output_dir_suffix)}")
1497
- except Exception as e2:
1498
- print("Warning: failed to save best model:", e, e2)
1499
-
1500
- def on_train_begin(self, args, state, control, **kwargs):
1501
- self.start_time = time.time()
1502
- print("" + "="*80)
1503
- print("🚀 STARTING MULTIMODAL CONTRASTIVE LEARNING TRAINING")
1504
- print("="*80)
1505
- model = kwargs.get('model')
1506
- if model is not None:
1507
- total_params = sum(p.numel() for p in model.parameters())
1508
- trainable_params = sum(p.numel() for p in model.parameters() if p.requires_grad)
1509
- non_trainable_params = total_params - trainable_params
1510
- print(f"📊 MODEL PARAMETERS:")
1511
- print(f" Total Parameters: {total_params:,}")
1512
- print(f" Trainable Parameters: {trainable_params:,}")
1513
- print(f" Non-trainable Parameters: {non_trainable_params:,}")
1514
- print(f" Training Progress: 0/{args.num_train_epochs} epochs")
1515
- print("="*80)
1516
-
1517
- def on_epoch_begin(self, args, state, control, **kwargs):
1518
- self.epoch_start_time = time.time()
1519
- current_epoch = state.epoch if state is not None else 0.0
1520
- print(f"📈 Epoch {current_epoch + 1:.1f}/{args.num_train_epochs} Starting...")
1521
-
1522
- def on_epoch_end(self, args, state, control, **kwargs):
1523
- train_loss = None
1524
- for log in reversed(state.log_history):
1525
- if isinstance(log, dict) and 'loss' in log and float(log.get('loss', 0)) != 0.0:
1526
- train_loss = log['loss']
1527
- break
1528
- self._last_train_loss = train_loss
1529
-
1530
- def on_log(self, args, state, control, logs=None, **kwargs):
1531
- if logs is not None and 'loss' in logs:
1532
- current_step = state.global_step
1533
- current_epoch = state.epoch
1534
- try:
1535
- steps_per_epoch = max(1, len(train_loader) // args.gradient_accumulation_steps)
1536
- except Exception:
1537
- steps_per_epoch = 1
1538
- if current_step % max(1, steps_per_epoch // 10) == 0:
1539
- progress = current_epoch + (current_step % steps_per_epoch) / steps_per_epoch
1540
- print(f" Step {current_step:4d} | Epoch {progress:.1f} | Train Loss: {logs['loss']:.6f}")
1541
-
1542
- def on_evaluate(self, args, state, control, metrics=None, **kwargs):
1543
- current_epoch = state.epoch if state is not None else 0.0
1544
- epoch_time = time.time() - self.epoch_start_time
1545
- hf_metrics = metrics if metrics is not None else kwargs.get('metrics', None)
1546
- hf_eval_loss = None
1547
- hf_train_loss = self._last_train_loss
1548
- if hf_metrics is not None:
1549
- hf_eval_loss = hf_metrics.get('eval_loss', hf_metrics.get('loss', None))
1550
- if hf_train_loss is None:
1551
- hf_train_loss = hf_metrics.get('train_loss', hf_train_loss)
1552
- cl_metrics = {}
1553
- try:
1554
- model = kwargs.get('model', None)
1555
- if model is not None:
1556
- cl_model = model.mm if hasattr(model, "mm") else model
1557
- cl_metrics = evaluate_multimodal(cl_model, val_loader, device, mask_target="fp")
1558
- else:
1559
- cl_metrics = evaluate_multimodal(multimodal_model, val_loader, device, mask_target="fp")
1560
- except Exception as e:
1561
- print("Warning: evaluate_multimodal inside callback failed:", e)
1562
- if hf_eval_loss is None:
1563
- hf_eval_loss = cl_metrics.get('eval_loss', None)
1564
- val_acc = cl_metrics.get('eval_accuracy', 'N/A')
1565
- val_f1 = cl_metrics.get('eval_f1_weighted', 'N/A')
1566
- print(f"🔍 EPOCH {current_epoch + 1:.1f} RESULTS:")
1567
- if hf_train_loss is not None:
1568
- try:
1569
- print(f" Train Loss (HF reported): {hf_train_loss:.6f}")
1570
- except Exception:
1571
- print(f" Train Loss (HF reported): {hf_train_loss}")
1572
- else:
1573
- print(f" Train Loss (HF reported): N/A")
1574
- if hf_eval_loss is not None:
1575
- try:
1576
- print(f" Eval Loss (HF reported): {hf_eval_loss:.6f}")
1577
- except Exception:
1578
- print(f" Eval Loss (HF reported): {hf_eval_loss}")
1579
- else:
1580
- print(f" Eval Loss (HF reported): N/A")
1581
- if isinstance(val_acc, float):
1582
- print(f" Eval Acc (CL evaluator): {val_acc:.6f}")
1583
- else:
1584
- print(f" Eval Acc (CL evaluator): {val_acc}")
1585
- if isinstance(val_f1, float):
1586
- print(f" Eval F1 Weighted (CL evaluator): {val_f1:.6f}")
1587
- else:
1588
- print(f" Eval F1 Weighted (CL evaluator): {val_f1}")
1589
- current_val = hf_eval_loss if hf_eval_loss is not None else float('inf')
1590
- improved = False
1591
- if current_val < self.best_val_loss - 1e-6:
1592
- improved = True
1593
- self.best_val_loss = current_val
1594
- self.best_epoch = current_epoch
1595
- self.epochs_no_improve = 0
1596
- try:
1597
- self.save_best_model("best")
1598
- except Exception as e:
1599
- print("Warning: saving best model failed:", e)
1600
- else:
1601
- self.epochs_no_improve += 1
1602
- if self.epochs_no_improve >= self.patience:
1603
- print(f"Early stopping: no improvement in val_loss for {self.patience} epochs.")
1604
- control.should_training_stop = True
1605
- print(f" Epoch Training Time: {epoch_time:.2f}s")
1606
- print(f" Best Val Loss so far: {self.best_val_loss}")
1607
- print(f" Epochs since improvement: {self.epochs_no_improve}/{self.patience}")
1608
- print("-" * 50)
1609
-
1610
- def on_train_end(self, args, state, control, **kwargs):
1611
- total_time = time.time() - self.start_time
1612
- print("" + "="*80)
1613
- print("🏁 TRAINING COMPLETED")
1614
- print("="*80)
1615
- print(f" Total Training Time: {total_time:.2f}s")
1616
- if state is not None:
1617
- try:
1618
- print(f" Total Epochs Completed: {state.epoch + 1:.1f}")
1619
- except Exception:
1620
- pass
1621
- print("="*80)
1622
-
1623
- from transformers import Trainer as HfTrainer
1624
-
1625
- class CLTrainer(HfTrainer):
1626
- def evaluate(self, eval_dataset=None, ignore_keys=None, metric_key_prefix="eval"):
1627
- try:
1628
- metrics = super().evaluate(eval_dataset=eval_dataset, ignore_keys=ignore_keys, metric_key_prefix=metric_key_prefix) or {}
1629
- except Exception as e:
1630
- print("Warning: super().evaluate() raised an exception. Falling back to CL-only evaluator.")
1631
- import traceback
1632
- traceback.print_exc()
1633
- try:
1634
- cl_model = self.model.mm if hasattr(self.model, "mm") else self.model
1635
- cl_metrics = evaluate_multimodal(cl_model, val_loader, device, mask_target="fp")
1636
- metrics = {k: float(v) if isinstance(v, (float, int, np.floating, np.integer)) else v for k, v in cl_metrics.items()}
1637
- metrics["epoch"] = float(self.state.epoch) if getattr(self.state, "epoch", None) is not None else metrics.get("epoch", 0.0)
1638
- except Exception as e2:
1639
- print("Fallback evaluate_multimodal failed as well:", e2)
1640
- traceback.print_exc()
1641
- metrics = {"eval_loss": float("nan"), "epoch": float(self.state.epoch) if getattr(self.state, "epoch", None) is not None else 0.0}
1642
- return metrics
1643
- try:
1644
- cl_model = self.model.mm if hasattr(self.model, "mm") else self.model
1645
- cl_metrics = evaluate_multimodal(cl_model, val_loader, device, mask_target="fp")
1646
- except Exception as e:
1647
- print("Warning: evaluate_multimodal failed inside CLTrainer.evaluate():", e)
1648
- cl_metrics = {}
1649
- for k, v in cl_metrics.items():
1650
- try:
1651
- metrics[k] = float(v)
1652
- except Exception:
1653
- metrics[k] = v
1654
- if 'eval_loss' not in metrics and 'eval_loss' in cl_metrics:
1655
- try:
1656
- metrics['eval_loss'] = float(cl_metrics['eval_loss'])
1657
- except Exception:
1658
- metrics['eval_loss'] = cl_metrics['eval_loss']
1659
- if "epoch" not in metrics:
1660
- metrics["epoch"] = float(self.state.epoch) if getattr(self.state, "epoch", None) is not None else metrics.get("epoch", 0.0)
1661
- return metrics
1662
-
1663
- def _save(self, output_dir: str):
1664
- os.makedirs(output_dir, exist_ok=True)
1665
- try:
1666
- self.state.save_to_json(os.path.join(output_dir, "trainer_state.json"))
1667
- except Exception:
1668
- pass
1669
- try:
1670
- model_to_save = self.model.mm if hasattr(self.model, "mm") else self.model
1671
- torch.save(model_to_save.state_dict(), os.path.join(output_dir, "pytorch_model.bin"))
1672
- except Exception as e:
1673
- try:
1674
- if hasattr(self.model, "save_pretrained"):
1675
- self.model.save_pretrained(output_dir)
1676
- else:
1677
- raise e
1678
- except Exception as e2:
1679
- print("Warning: failed to save model state_dict:", e2)
1680
- try:
1681
- torch.save(self.optimizer.state_dict(), os.path.join(output_dir, "optimizer.pt"))
1682
- except Exception:
1683
- pass
1684
- try:
1685
- torch.save(self.lr_scheduler.state_dict(), os.path.join(output_dir, "scheduler.pt"))
1686
- except Exception:
1687
- pass
1688
-
1689
- def _load_best_model(self):
1690
- best_ckpt = self.state.best_model_checkpoint
1691
- if not best_ckpt:
1692
- return
1693
- candidate = os.path.join(best_ckpt, "pytorch_model.bin")
1694
- if not os.path.exists(candidate):
1695
- candidate = os.path.join(best_ckpt, "model.bin")
1696
- if not os.path.exists(candidate):
1697
- candidate = None
1698
- if candidate is None:
1699
- print(f"CLTrainer._load_best_model(): no compatible pytorch_model.bin found in {best_ckpt}; skipping load.")
1700
- return
1701
- try:
1702
- state_dict = torch.load(candidate, map_location=self.args.device)
1703
- model_to_load = self.model.mm if hasattr(self.model, "mm") else self.model
1704
- model_to_load.load_state_dict(state_dict, strict=False)
1705
- print(f"CLTrainer: loaded best model state_dict from {candidate}")
1706
- except Exception as e:
1707
- print("CLTrainer._load_best_model: failed to load state_dict using torch.load:", e)
1708
- return
1709
-
1710
- callback = VerboseTrainingCallback(patience=10)
1711
-
1712
- trainer = CLTrainer(
1713
- model=hf_model,
1714
- args=training_args,
1715
- train_dataset=train_subset,
1716
- eval_dataset=val_subset,
1717
- data_collator=data_collator,
1718
- callbacks=[callback],
1719
- )
1720
-
1721
- callback.trainer_ref = trainer
1722
-
1723
- # Force HF Trainer to use our prebuilt PyTorch DataLoaders
1724
- trainer.get_train_dataloader = lambda dataset=None: train_loader
1725
- trainer.get_eval_dataloader = lambda eval_dataset=None: val_loader
1726
-
1727
- training_args.metric_for_best_model = "eval_loss"
1728
- training_args.greater_is_better = False
1729
-
1730
- optimizer = torch.optim.AdamW(multimodal_model.parameters(), lr=training_args.learning_rate, weight_decay=training_args.weight_decay)
1731
-
1732
- total_params = sum(p.numel() for p in multimodal_model.parameters())
1733
- trainable_params = sum(p.numel() for p in multimodal_model.parameters() if p.requires_grad)
1734
- non_trainable_params = total_params - trainable_params
1735
-
1736
- print(f"\n📊 MODEL PARAMETERS:")
1737
- print(f" Total Parameters: {total_params:,}")
1738
- print(f" Trainable Parameters: {trainable_params:,}")
1739
- print(f" Non-trainable Parameters: {non_trainable_params:,}")
1740
-
1741
- def compute_metrics_wrapper(eval_pred):
1742
- return evaluate_multimodal(multimodal_model, val_loader, device, mask_target="fp")
1743
-
1744
- # ---------------------------
1745
- # Clear any cached GPU memory before starting (helpful)
1746
- if USE_CUDA:
1747
- try:
1748
- torch.cuda.empty_cache()
1749
- except Exception:
1750
- pass
1751
-
1752
- # ---------------------------
1753
- # Start training
1754
- training_start_time = time.time()
1755
- trainer.train()
1756
- training_end_time = time.time()
1757
-
1758
- # Save best
1759
- BEST_MULTIMODAL_DIR = os.path.join(OUTPUT_DIR, "best")
1760
- os.makedirs(BEST_MULTIMODAL_DIR, exist_ok=True)
1761
-
1762
- try:
1763
- best_ckpt = trainer.state.best_model_checkpoint
1764
- if best_ckpt:
1765
- multimodal_model.load_state_dict(torch.load(os.path.join(best_ckpt, "pytorch_model.bin"), map_location=device), strict=False)
1766
- print(f"Loaded best checkpoint from {best_ckpt} into multimodal_model for final evaluation.")
1767
- torch.save(multimodal_model.state_dict(), os.path.join(BEST_MULTIMODAL_DIR, "pytorch_model.bin"))
1768
- print(f"✅ Saved best multimodal model to {os.path.join(BEST_MULTIMODAL_DIR, 'pytorch_model.bin')}")
1769
- except Exception as e:
1770
- print("Warning: failed to load/save best model from Trainer:", e)
1771
-
1772
- # Final evaluation
1773
- final_metrics = {}
1774
- try:
1775
- if trainer.state.best_model_checkpoint:
1776
- trainer._load_best_model()
1777
- final_metrics = trainer.evaluate(eval_dataset=val_subset)
1778
- else:
1779
- final_metrics = evaluate_multimodal(multimodal_model, val_loader, device, mask_target="fp")
1780
- except Exception as e:
1781
- print("Warning: final evaluation via trainer.evaluate failed, falling back to direct evaluate_multimodal:", e)
1782
- final_metrics = evaluate_multimodal(multimodal_model, val_loader, device, mask_target="fp")
1783
-
1784
- print("\n" + "="*80)
1785
- print("🏁 FINAL TRAINING RESULTS")
1786
- print("="*80)
1787
- training_time = training_end_time - training_start_time
1788
- print(f"Total Training Time: {training_time:.2f}s")
1789
- best_ckpt = trainer.state.best_model_checkpoint if hasattr(trainer.state, 'best_model_checkpoint') else None
1790
- if best_ckpt:
1791
- print(f"Best Checkpoint: {best_ckpt}")
1792
- else:
1793
- print("Best Checkpoint: (none saved)")
1794
-
1795
- hf_eval_loss = final_metrics.get('eval_loss', float('nan'))
1796
- hf_eval_acc = final_metrics.get('eval_accuracy', 0.0)
1797
- hf_eval_f1 = final_metrics.get('eval_f1_weighted', 0.0)
1798
- print(f"Val Loss (HF reported / trainer.evaluate): {hf_eval_loss:.4f}")
1799
- print(f"Val Acc (CL evaluator): {hf_eval_acc:.4f}")
1800
- print(f"Val F1 Weighted (CL evaluator): {hf_eval_f1:.4f}")
1801
- print(f"Total Trainable Params: {trainable_params:,}")
1802
- print(f"Total Non-trainable Params: {non_trainable_params:,}")
1803
- print("="*80)