File size: 25,910 Bytes
b233cf7
 
 
bd9df8b
b233cf7
 
 
 
 
 
 
 
a2d3e6a
b233cf7
cbadf3b
e15f88d
b233cf7
 
 
fcf5411
4cb605e
 
 
 
 
 
df9e052
c9282b0
b233cf7
 
 
 
 
 
 
 
 
 
 
 
 
 
b8be6fc
 
 
36ec872
 
 
 
 
 
 
 
b8be6fc
b233cf7
 
 
 
 
 
 
 
 
 
 
 
 
f4f9dd3
bf57e19
 
8377646
 
f4f9dd3
bf57e19
b233cf7
8377646
b233cf7
 
a2d3e6a
4cb605e
 
a2d3e6a
b233cf7
 
 
 
 
 
 
4cb605e
b233cf7
a2d3e6a
 
 
4cb605e
 
a2d3e6a
b233cf7
ab0e6ff
 
 
 
b8be6fc
 
 
 
36ec872
b8be6fc
36ec872
 
 
 
 
 
 
 
 
b8be6fc
b233cf7
 
 
 
 
 
 
 
4cb605e
 
a2d3e6a
b233cf7
 
 
 
 
 
 
 
254d9db
df9e052
900e4c0
b233cf7
31604c9
 
 
 
 
b233cf7
31604c9
2742c36
 
 
b233cf7
a2d3e6a
 
b233cf7
254d9db
4cb605e
 
 
 
 
 
254d9db
 
31604c9
 
254d9db
 
 
 
 
 
 
4cb605e
254d9db
 
b233cf7
900e4c0
b233cf7
 
 
 
4cb605e
254d9db
b233cf7
 
900e4c0
b233cf7
 
 
 
 
 
 
 
df9e052
b233cf7
 
 
 
 
4cb605e
b233cf7
 
 
 
 
 
 
 
 
 
 
 
 
4cb605e
 
b233cf7
 
 
ad424e4
 
900e4c0
a2d3e6a
254d9db
a2d3e6a
b233cf7
 
 
 
 
 
 
 
4cb605e
b233cf7
4cb605e
 
 
b233cf7
 
 
 
 
 
 
 
 
 
 
df9e052
b233cf7
 
 
 
4cb605e
b233cf7
 
 
 
 
 
 
 
 
 
 
4cb605e
 
b233cf7
 
ad424e4
900e4c0
a2d3e6a
254d9db
a2d3e6a
b233cf7
 
 
 
 
 
 
 
 
 
a440fe9
 
4cb605e
 
a440fe9
b233cf7
 
 
 
 
 
aa54b95
b233cf7
 
 
c9282b0
 
fcf5411
b233cf7
bf57e19
376e3b9
b8be6fc
36ec872
b233cf7
 
36ec872
b8be6fc
36ec872
 
 
b8be6fc
b233cf7
 
 
 
 
 
 
 
 
 
 
 
 
 
f4f9dd3
5ebd8b6
fcf5411
 
 
 
 
 
8377646
 
 
 
f4f9dd3
b233cf7
 
 
 
 
 
 
 
7cc735d
b233cf7
 
 
2671b56
2cefd29
 
 
 
 
 
 
 
 
bd9df8b
 
 
 
 
 
 
376e3b9
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
2671b56
 
376e3b9
2671b56
78283bd
a1355e6
bd9df8b
 
a1355e6
a2d3e6a
 
 
d3bb757
e15f88d
bd9df8b
e15f88d
8377646
e15f88d
8377646
bf57e19
e15f88d
 
bd9df8b
d3bb757
8377646
d3bb757
8377646
bf57e19
b233cf7
e15f88d
b233cf7
e15f88d
b233cf7
 
e15f88d
b233cf7
 
bf57e19
b233cf7
f4f9dd3
bf57e19
b233cf7
 
 
 
8377646
b233cf7
 
 
 
 
31604c9
 
4cb605e
9ddcf86
4cb605e
9ddcf86
b233cf7
 
 
 
 
 
 
 
254d9db
 
b233cf7
 
 
 
 
 
 
4cb605e
b233cf7
4cb605e
b233cf7
 
 
 
 
 
 
 
 
 
 
 
 
254d9db
b233cf7
4cb605e
 
b233cf7
 
 
 
 
 
 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
from __future__ import annotations

import argparse
import json
import logging
import random
from pathlib import Path
from typing import Any

import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from datasets import DatasetDict
from torch.utils.data import DataLoader
from torch.utils.tensorboard import SummaryWriter

from pino.heads import PIMTHeads
from pino.embeddings import COMBINED_DIM_REAL_POM, MORGAN2048_TOKEN_DIM
from pino.pimt_model import (
    DEFAULT_EMBEDDING_DIM,
    FragranceTrajectoryDataset,
    PhysicsInformedMixtureTransformer,
    objective_targets_to_pyramid,
)
from pino.thermo.losses import AdaptiveLossBalancer
from pino.upload_data import DEFAULT_TRAIN_RATIO, create_molecule_disjoint_split_from_records

logger = logging.getLogger("pino.train")

SMOKE_TEST_CONFIG = {
    "hidden_dim": 64,
    "num_layers": 2,
    "num_heads": 2,
    "batch_size": 4,
    "max_batches_per_epoch": 20,
    "lr": 1e-3,
    "weight_decay": 1e-2,
    "checkpoint_name": "pimt_smoke_test.pt",
}

# Idea3 physics-off ablation: when True, pad_trajectory_collate zeroes the
# physics tensor for every batch (train + val). Set from --physics-off-train.
_PHYSICS_OFF_TRAIN = False
# Factorial physics-channel ablation (idea-3 follow-up): which channel carries
# the drydown gain? Channels are [x_liquid, log10 OAV, log10 gamma_prop].
#   full           : all channels live (default; physics_gamma arm)
#   off            : all zeroed (physics_off arm; legacy --physics-off-train)
#   gamma_only     : keep channel 2 (log gamma), zero 0-1 -- isolates the
#                    non-redundant blend-interaction channel
#   headspace_only : keep channels 0-1, zero channel 2 -- the E2-redundant part
_PHYSICS_MODE = "full"

def pad_trajectory_collate(batch: list[dict[str, Any]]) -> dict[str, Any]:
    """
    Collate variable-length formulations into a single padded batch.

    Because recipes contain a variable number of ingredients (K), this function
    finds K_max in the batch and pads shorter token/physics tensors with zeros.
    It also emits a `src_key_padding_mask` of shape (B, K_max) where True marks
    padding positions and False marks valid chemical tokens.
    """
    max_molecules = max(item["tokens"].size(0) for item in batch)
    max_timesteps = max(item["physics"].size(0) for item in batch)
    bsz = len(batch)

    emb_dim = batch[0]["tokens"].size(1)
    # physics channel count from the batch (2 = x_liq/logOAV, 3 = + gamma interaction)
    phys_dim = batch[0]["physics"].size(-1)
    # objective target width from the batch itself (138 for pyramid, 575 for all-tags)
    obj_dim = batch[0]["target_obj"].size(-1)
    tokens = torch.zeros(bsz, max_molecules, emb_dim, dtype=torch.float32)
    physics = torch.zeros(bsz, max_timesteps, max_molecules, phys_dim, dtype=torch.float32)
    src_key_padding_mask = torch.ones(bsz, max_molecules, dtype=torch.bool)
    target_obj = torch.zeros(bsz, 3, obj_dim, dtype=torch.float32)
    target_sub_seasonality = torch.zeros(bsz, 4, dtype=torch.float32)
    target_sub_gender = torch.zeros(bsz, dtype=torch.float32)
    target_sub_wearability = torch.zeros(bsz, 2, dtype=torch.float32)
    target_substantivity = torch.zeros(bsz, dtype=torch.float32)
    target_substantivity_mask = torch.zeros(bsz, dtype=torch.float32)
    genre_labels = torch.zeros(bsz, dtype=torch.int64)

    for i, item in enumerate(batch):
        n_mol = item["tokens"].size(0)
        t_steps = item["physics"].size(0)
        tokens[i, :n_mol] = item["tokens"]
        physics[i, :t_steps, :n_mol] = item["physics"]
        src_key_padding_mask[i, :n_mol] = False
        target_obj[i] = objective_targets_to_pyramid(item["target_obj"]).float()
        sub = item["target_sub"]
        target_sub_seasonality[i] = sub[[0,1,2,3]]
        target_sub_gender[i] = sub[4]
        target_sub_wearability[i] = sub[[5,6]]
        target_substantivity[i] = item.get("target_substantivity", torch.tensor(0.0))
        target_substantivity_mask[i] = item.get("target_substantivity_mask", torch.tensor(0.0))
        genre_labels[i] = item.get("genre_label", 0)

    # Force padding positions to a neutral log10_OAV sentinel so the Synergistic
    # Objective Head treats them as zero-contribution even without the mask.
    physics[..., 1] = physics[..., 1].masked_fill(src_key_padding_mask.unsqueeze(1), -6.0)

    # Idea3 physics-off ablation arm: zero the entire physics state so the FiLM
    # block and physics-informed heads receive no physics signal during BOTH
    # training and validation. This is a fair trained baseline (not an
    # inference-time shock), isolating the physics channel's contribution.
    if _PHYSICS_OFF_TRAIN or _PHYSICS_MODE == "off":
        physics = torch.zeros_like(physics)
    elif _PHYSICS_MODE == "gamma_only":
        # Keep only channel 2 (log gamma); zero x_liquid and log10 OAV.
        physics = physics.clone()
        physics[..., 0] = 0.0
        physics[..., 1] = 0.0
    elif _PHYSICS_MODE == "headspace_only":
        # Keep channels 0-1 (x_liquid, log10 OAV); zero the gamma channel.
        physics = physics.clone()
        physics[..., 2] = 0.0

    return {
        "tokens": tokens,
        "physics": physics,
        "src_key_padding_mask": src_key_padding_mask,
        "target_obj": target_obj,
        "target_sub_seasonality": target_sub_seasonality,
        "target_sub_gender": target_sub_gender,
        "target_sub_wearability": target_sub_wearability,
        "target_substantivity": target_substantivity,
        "target_substantivity_mask": target_substantivity_mask,
        "genre_label": genre_labels,
    }


def multitask_loss(
    pred_obj: torch.Tensor,
    target_obj: torch.Tensor,
    pred_sub: dict[str, torch.Tensor],
    target_sub: dict[str, torch.Tensor],
    pred_alignment: torch.Tensor,
    loss_balancer: AdaptiveLossBalancer,
) -> tuple[torch.Tensor, dict[str, float]]:
    """
    Multi-task loss for pyramid targets.

    The objective task is now binary multi-label classification over three static
    tiers (top, middle, base notes).  Sigmoid BCE replaces MSE on the 49-step
    trajectory, while subjective and alignment tasks remain unchanged.
    """
    # Pyramid objective: binary multi-label classification (B, 3, 138).
    # Clamp targets into [0,1]: some all-tags labels carry a float32 rounding
    # artifact (1.00000012) that trips the CUDA BCE device-side assert on GPU.
    obj_loss = nn.functional.binary_cross_entropy(pred_obj, target_obj.clamp(0.0, 1.0), reduction="mean")

    season_loss = nn.functional.cross_entropy(pred_sub["seasonality"], target_sub["seasonality"].argmax(dim=-1))
    gender_loss = nn.functional.mse_loss(pred_sub["gender_profile"].squeeze(-1), target_sub["gender_profile"])
    wear_loss = nn.functional.binary_cross_entropy_with_logits(pred_sub["wearability"], target_sub["wearability"])
    wear_loss = wear_loss + gender_loss
    sub_mask = target_sub.get("substantivity_mask")
    if sub_mask is not None and float(sub_mask.sum().detach().cpu()) > 0:
        sub_pred = pred_sub["substantivity"].squeeze(-1)
        sub_loss = ((sub_pred - target_sub["substantivity"]) ** 2 * sub_mask).sum() / sub_mask.sum().clamp_min(1.0)
    else:
        sub_loss = pred_obj.new_tensor(0.0)

    # Continuous cosine alignment between predicted 138-D descriptor profile and
    # the mean of the true pyramid tiers over the three tiers.  This keeps the
    # overall descriptor profile aligned even as the pyramid specialises.
    true_profile = target_obj.mean(dim=1)  # (B, 138)
    alignment_loss = 1.0 - nn.functional.cosine_similarity(pred_alignment, true_profile, dim=-1).mean()

    loss_payload = {
        "obj": obj_loss,
        "season": season_loss,
        "wear": wear_loss,
        "substantivity": sub_loss,
        "alignment": alignment_loss,
    }

    total = loss_balancer(loss_payload)
    components = {
        "obj": obj_loss.item(),
        "season": season_loss.item(),
        "wear": wear_loss.item(),
        "substantivity": sub_loss.item(),
        "alignment": alignment_loss.item(),
        "total": total.item(),
    }
    return total, components


def train_epoch(
    model: nn.Module,
    heads: nn.Module,
    loader: DataLoader,
    optimizer: optim.Optimizer,
    device: torch.device,
    loss_balancer: AdaptiveLossBalancer,
    max_batches: int | None = None,
) -> dict[str, float]:
    model.train()
    heads.train()
    total_loss = 0.0
    totals = {"obj": 0.0, "season": 0.0, "wear": 0.0, "substantivity": 0.0, "alignment": 0.0}
    count = 0

    for batch_idx, batch in enumerate(loader, start=1):
        if max_batches is not None and batch_idx > max_batches:
            break
        tokens = batch["tokens"].to(device)
        physics = batch["physics"].to(device)
        src_key_padding_mask = batch["src_key_padding_mask"].to(device)
        target_obj = batch["target_obj"].to(device)
        target_sub = {
            "seasonality": batch["target_sub_seasonality"].to(device),
            "gender_profile": batch["target_sub_gender"].to(device),
            "wearability": batch["target_sub_wearability"].to(device),
            "substantivity": batch["target_substantivity"].to(device),
            "substantivity_mask": batch["target_substantivity_mask"].to(device),
        }
        optimizer.zero_grad()
        latent = model(tokens, physics, src_key_padding_mask)  # (B, T, S, H)
        # Compute pyramid objective predictions with physics-informed routing.
        pred = heads(latent, physics, src_key_padding_mask)
        loss, comps = multitask_loss(
            pred["objective"], target_obj, pred["subjective"], target_sub,
            pred["alignment"], loss_balancer,
        )
        loss.backward()
        torch.nn.utils.clip_grad_norm_(list(model.parameters()) + list(heads.parameters()), 1.0)
        optimizer.step()

        total_loss += comps["total"]
        for k in totals:
            totals[k] += comps[k]
        count += 1
        weights = getattr(loss_balancer, "last_weights", [0.35, 0.12, 0.12, 0.16, 0.25])
        logger.info(
            "Batch %d | total=%.4f | obj=%.4f | season=%.4f | wear=%.4f | substantivity=%.4f | alignment=%.4f | weights=%s",
            batch_idx, comps["total"], comps["obj"], comps["season"], comps["wear"], comps["substantivity"], comps["alignment"],
            [round(float(w), 3) for w in weights],
        )

    return {k: v / max(count, 1) for k, v in {**totals, "total": total_loss}.items()}


@torch.no_grad()
def validate(
    model: nn.Module,
    heads: nn.Module,
    loader: DataLoader,
    device: torch.device,
    loss_balancer: AdaptiveLossBalancer,
) -> dict[str, float]:
    model.eval()
    heads.eval()
    total_loss = 0.0
    totals = {"obj": 0.0, "season": 0.0, "wear": 0.0, "substantivity": 0.0, "alignment": 0.0}
    count = 0

    for batch in loader:
        tokens = batch["tokens"].to(device)
        physics = batch["physics"].to(device)
        src_key_padding_mask = batch["src_key_padding_mask"].to(device)
        target_obj = batch["target_obj"].to(device)
        target_sub = {
            "seasonality": batch["target_sub_seasonality"].to(device),
            "gender_profile": batch["target_sub_gender"].to(device),
            "wearability": batch["target_sub_wearability"].to(device),
            "substantivity": batch["target_substantivity"].to(device),
            "substantivity_mask": batch["target_substantivity_mask"].to(device),
        }
        latent = model(tokens, physics, src_key_padding_mask)
        pred = heads(latent, physics, src_key_padding_mask)
        loss, comps = multitask_loss(
            pred["objective"], target_obj, pred["subjective"], target_sub,
            pred["alignment"], loss_balancer,
        )
        total_loss += comps["total"]
        for k in totals:
            totals[k] += comps[k]
        count += 1

    return {k: v / max(count, 1) for k, v in {**totals, "total": total_loss}.items()}


def main():
    parser = argparse.ArgumentParser(description="Train the PINO Physics-Informed Mixture Transformer")
    parser.add_argument(
        "--data",
        default="data/empirical_dataset_v9_plus_wisemoor.jsonl",
        help="Path to the empirical dataset JSONL (default: v9 plus resolved WiseMoor formulas).",
    )
    parser.add_argument("--epochs", type=int, default=5)
    parser.add_argument("--batch-size", type=int, default=4)
    parser.add_argument("--lr", type=float, default=1e-3)
    parser.add_argument("--hidden-dim", type=int, default=256)
    parser.add_argument("--num-layers", type=int, default=4)
    parser.add_argument("--num-heads", type=int, default=4)
    parser.add_argument("--workers", type=int, default=0, help="DataLoader workers; 0 for local CPU check cycles")
    parser.add_argument("--seed", type=int, default=2026)
    parser.add_argument("--output-dir", default="models")
    parser.add_argument("--log-dir", default="runs")
    parser.add_argument("--checkpoint-name", default="pimt_v9.pt", help="Filename for the best checkpoint")
    parser.add_argument("--train-ratio", type=float, default=DEFAULT_TRAIN_RATIO, help="Molecule-disjoint train molecule ratio; default keeps a 15% molecule holdout")
    parser.add_argument("--structural-source", choices=["morgan", "morgan_2048_rp", "morgan_2048_direct", "openpom_256", "pom_alltags", "disjoint_256"], default="morgan", help="Structural embedding block + objective target: 'morgan' (138-dim Morgan, input 151, 138-dim pyramid) | 'morgan_2048_rp' (2048-bit Morgan token randomly projected to 269 for input-parameter parity with the OpenPOM arm, 138-dim pyramid) | 'morgan_2048_direct' (2048-bit Morgan token fed directly to a learned projection, input 2071 β€” round-10 control for the RP subspace constraint) | 'openpom_256' (genuine 256-dim OpenPOM, input 269, 138-dim pyramid) | 'disjoint_256' (256-dim MPNN encoder retrained on the benchmark-disjoint corpus, input 269, 138-dim pyramid β€” leakage-free OpenPOM-style arm) | 'pom_alltags' (genuine 256-dim OpenPOM, input 269, 575-dim molequles all-tags objective)")
    parser.add_argument("--smoke-test", action="store_true", help="Run lightweight CPU smoke test")
    parser.add_argument("--use-gamma", action="store_true", help="Add the UNIFAC blend-interaction (gamma) 3rd physics channel; requires a gamma-augmented dataset (physics_gamma field)")
    parser.add_argument("--split-strategy", choices=["molecule", "formula"], default="molecule", help="molecule = strict molecule-disjoint holdout (default, used for frozen-task headline results); formula = random formula-level holdout (E1 physics-gamma substantivity experiment; discloses molecule leakage for measured-Poucher eval power)")
    parser.add_argument("--physics-off-train", action="store_true", help="Idea3 ablation: zero the physics tensor for every batch (train+val) so the model is a fair no-physics baseline")
    parser.add_argument("--physics-mode", choices=["full", "off", "gamma_only", "headspace_only"], default="full", help="Factorial channel ablation: full = all channels; off = all zeroed; gamma_only = keep only log-gamma channel (zero x_liquid/OAV); headspace_only = keep x_liquid/OAV (zero gamma). Applied during BOTH train and val so each arm is a fair trained baseline.")
    args = parser.parse_args()

    global _PHYSICS_OFF_TRAIN, _PHYSICS_MODE
    _PHYSICS_OFF_TRAIN = bool(getattr(args, "physics_off_train", False))
    _PHYSICS_MODE = getattr(args, "physics_mode", "full")
    if _PHYSICS_OFF_TRAIN:
        _PHYSICS_MODE = "off"

    logging.basicConfig(
        level=logging.INFO,
        format="%(asctime)s %(levelname)s %(name)s: %(message)s",
    )
    logger.info("Training PIMT with fallback embeddings (use_fallback=True)")
    logger.info("Embedding backend: deterministic 128-bit Morgan + 10 physicochemical descriptors")

    torch.manual_seed(args.seed)
    np.random.seed(args.seed)
    random.seed(args.seed)

    device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
    logger.info("Device: %s", device)

    logger.info("Structural source: %s", args.structural_source)
    use_pom = args.structural_source in ("openpom_256", "pom_alltags", "disjoint_256")
    if use_pom or args.structural_source == "morgan_2048_rp":
        embedding_dim = COMBINED_DIM_REAL_POM
    elif args.structural_source == "morgan_2048_direct":
        embedding_dim = MORGAN2048_TOKEN_DIM
    else:
        embedding_dim = DEFAULT_EMBEDDING_DIM
    objective_dim = 575 if args.structural_source == "pom_alltags" else 138
    # engine only knows the two structural blocks; the tag target is selected in the dataset via objective_dim
    engine_source = "openpom_256" if args.structural_source == "pom_alltags" else args.structural_source
    logger.info("Embedding input dim: %d | objective target dim: %d", embedding_dim, objective_dim)

    cfg = SMOKE_TEST_CONFIG if args.smoke_test else {
        "hidden_dim": args.hidden_dim,
        "num_layers": args.num_layers,
        "num_heads": args.num_heads,
        "batch_size": args.batch_size,
        "max_batches_per_epoch": None,
        "lr": args.lr,
        "weight_decay": 1e-2,
        "checkpoint_name": args.checkpoint_name,
    }
    logger.info("Configuration: %s", cfg)

    # Ingest and split the dataset with strict active-molecule isolation.
    # NOTE (leakage review): a connected-components split over the formula-molecule
    # co-occurrence graph was evaluated and REJECTED for this corpus. The graph is
    # dominated by a single giant component (5,592/5,707 records; shared carriers +
    # genre ingredient pools link nearly all molecules), so a strict component split
    # is mathematically impossible, and the hub-excluded variant yields a validation
    # set of only singleton/duplicate formulas (degenerate, unrepresentative).
    # Molecule-disjoint splitting is therefore the correct instrument here: it gives
    # a representative held-out set with a strict zero-active-molecule guarantee.
    # See scripts/split_leakage_analysis.py for the full evidence + assertion.
    print("⏳ Splicing empirical bootstrap data streams...")
    with open(args.data, "r") as f:
        all_records = [json.loads(line) for line in f]

    control_records = [r for r in all_records if r.get("is_control", False)]
    print(f"πŸ“Š Extracted {len(control_records)} pure single-molecule anchors.")

    if getattr(args, "split_strategy", "molecule") == "formula":
        # Formula-level random holdout. Used by the E1 physics-gamma substantivity
        # experiment, where strict molecule-disjointness starves the measured-
        # Poucher eval (n~10) because Poucher molecules are ubiquitous. Trades a
        # weaker generalization claim (molecules may leak) for eval power; the
        # leakage is disclosed in the run summary. The frozen-task headline
        # results in the paper still use the molecule-disjoint path below.
        rng = np.random.default_rng(args.seed)
        n_total = len(all_records)
        n_val = max(1, int(round(n_total * (1.0 - args.train_ratio))))
        perm = rng.permutation(n_total)
        val_idx = set(perm[:n_val].tolist())
        train_records = [all_records[i] for i in range(n_total) if i not in val_idx]
        val_records = [all_records[i] for i in sorted(val_idx)]
        print(f"πŸ“Š Formula-level split (E1; leakage disclosed): train={len(train_records)} val={len(val_records)}")
    else:
        split = create_molecule_disjoint_split_from_records(
            all_records,
            train_ratio=args.train_ratio,
            seed=args.seed,
        )
        train_records = split["train"]
        val_records = split["validation"]

    if getattr(args, "split_strategy", "molecule") == "molecule":
        train_cas = set(split["train_compounds"])
        val_cas = set(split["validation_compounds"])
        overlap = train_cas & val_cas
        print(f"πŸ”’ Molecule isolation check: {len(overlap)} active CAS shared between splits.")
        print(f"🚫 Excluded mixed-boundary records: {len(split['excluded_indices'])}")
        assert len(overlap) == 0, f"Molecule leakage detected: {sorted(overlap)}"
        # Persist the zero-intersection assertion for the paper's reproducibility ledger.
        try:
            leakage_report = {
                "split_strategy": "molecule_disjoint",
                "seed": args.seed,
                "train_ratio": args.train_ratio,
                "n_train_records": len(train_records),
                "n_validation_records": len(val_records),
                "n_excluded_records": len(split["excluded_indices"]),
                "n_train_molecules": len(train_cas),
                "n_validation_molecules": len(val_cas),
                "shared_molecule_count": len(overlap),
                "zero_intersection_assertion": "PASSED" if not overlap else "FAILED",
            }
            Path(args.output_dir).mkdir(parents=True, exist_ok=True)
            report_name = f"split_leakage_report_seed{args.seed}.json"
            with open(Path(args.output_dir) / report_name, "w") as rf:
                json.dump(leakage_report, rf, indent=2)
            print(f"πŸ“ Split leakage report: {report_name} (zero-intersection: {leakage_report['zero_intersection_assertion']})")
        except Exception as e:  # noqa: BLE001
            logger.warning("Could not write split leakage report: %s", e)
    if not train_records or not val_records:
        raise RuntimeError(
            "Split produced an empty train or validation set. "
            "Adjust --train-ratio or --seed."
        )

    total_rows = len(train_records) + len(val_records)
    print(f"πŸ“Š Dataset fully loaded. Total rows: {total_rows} | Training samples: {len(train_records)} | Validation samples: {len(val_records)}")

    # Use the genre column for both stratification and the contrastive loss.
    all_genres = ["citrus_cologne", "fougere", "floral_woody", "amber_oriental", "wildcard"]
    genre_map = {genre: idx for idx, genre in enumerate(all_genres)}

    train_dataset = FragranceTrajectoryDataset(
        records=train_records,
        use_embedding_fallback=True,
        structural_source=engine_source,
        genre_map=genre_map,
        objective_dim=objective_dim,
        use_gamma=args.use_gamma,
    )
    val_dataset = FragranceTrajectoryDataset(
        records=val_records,
        use_embedding_fallback=True,
        structural_source=engine_source,
        genre_map=genre_map,
        objective_dim=objective_dim,
        use_gamma=args.use_gamma,
    )

    train_loader = DataLoader(
        train_dataset, batch_size=cfg["batch_size"], shuffle=True, num_workers=args.workers, collate_fn=pad_trajectory_collate
    )
    val_loader = DataLoader(
        val_dataset, batch_size=cfg["batch_size"], shuffle=False, num_workers=args.workers, collate_fn=pad_trajectory_collate
    )

    state_dim = 3 if args.use_gamma else 2
    model = PhysicsInformedMixtureTransformer(
        embedding_dim=embedding_dim,
        state_dim=state_dim,
        hidden_dim=cfg["hidden_dim"],
        num_heads=cfg["num_heads"],
        num_layers=cfg["num_layers"],
    ).to(device)
    heads = PIMTHeads(hidden_dim=cfg["hidden_dim"], objective_dim=objective_dim).to(device)

    params = list(model.parameters()) + list(heads.parameters())
    optimizer = optim.AdamW(params, lr=cfg["lr"], weight_decay=cfg["weight_decay"])
    scheduler = optim.lr_scheduler.CosineAnnealingLR(optimizer, T_max=args.epochs)

    # Multi-task loss balancer.  Fix objective high so the pyramid head is not
    # starved by the easier subjective tasks.
    loss_weights = torch.tensor([0.35, 0.12, 0.12, 0.16, 0.25])
    loss_balancer = AdaptiveLossBalancer(
        num_tasks=5, fixed_weights=loss_weights
    ).to(device)

    writer = SummaryWriter(log_dir=args.log_dir)
    output_dir = Path(args.output_dir)
    output_dir.mkdir(parents=True, exist_ok=True)
    checkpoint_path = output_dir / cfg["checkpoint_name"]

    best_val = float("inf")
    for epoch in range(1, args.epochs + 1):
        train_metrics = train_epoch(model, heads, train_loader, optimizer, device, loss_balancer, max_batches=cfg.get("max_batches_per_epoch"))
        val_metrics = validate(model, heads, val_loader, device, loss_balancer)
        scheduler.step()

        for split, metrics in [("train", train_metrics), ("val", val_metrics)]:
            for k, v in metrics.items():
                writer.add_scalar(f"{split}/{k}", v, epoch)

        logger.info(
            "Epoch %d/%d | train_total=%.4f | val_total=%.4f | obj=%.4f | season=%.4f | wear=%.4f | substantivity=%.4f | alignment=%.4f",
            epoch, args.epochs, train_metrics["total"], val_metrics["total"],
            val_metrics["obj"], val_metrics["season"], val_metrics["wear"], val_metrics["substantivity"], val_metrics["alignment"],
        )

        if val_metrics["total"] < best_val:
            best_val = val_metrics["total"]
            torch.save({
                "epoch": epoch,
                "model_state_dict": model.state_dict(),
                "heads_state_dict": heads.state_dict(),
                "optimizer_state_dict": optimizer.state_dict(),
                "val_loss": best_val,
            }, checkpoint_path)
            logger.info("Saved best checkpoint to %s", checkpoint_path)

    val_final_metrics = validate(model, heads, val_loader, device, loss_balancer)
    logger.info(
        "Final Val | total=%.4f | obj=%.4f | season=%.4f | wear=%.4f | substantivity=%.4f | alignment=%.4f",
        val_final_metrics["total"], val_final_metrics["obj"], val_final_metrics["season"], val_final_metrics["wear"], val_final_metrics["substantivity"], val_final_metrics["alignment"],
    )
    writer.close()
    return checkpoint_path


if __name__ == "__main__":
    main()