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import argparse
import json
import random
import re
from collections import Counter
from pathlib import Path
from typing import Any
import numpy as np
import torch
import yaml
from sklearn.utils.class_weight import compute_class_weight
from torch.utils.data import Dataset, WeightedRandomSampler
from transformers import EarlyStoppingCallback, Trainer, TrainingArguments, set_seed
from src.data.io_utils import read_csv_dicts, read_jsonl, write_csv, write_json, write_jsonl
from src.eval.calibration import expected_calibration_error
from src.eval.confusion_matrix import confusion_matrix_rows
from src.models.encoder_verifier import load_sequence_classifier, load_tokenizer, sanitize_model_name
from src.utils.metrics import classification_metrics, softmax
class VerifierDataset(Dataset):
def __init__(self, rows: list[dict[str, Any]], tokenizer: Any, label2id: dict[str, int], max_length: int):
self.rows = rows
self.encodings = tokenizer(
[row["input_text"] for row in rows],
padding=True,
truncation=True,
max_length=max_length,
)
self.labels = [label2id[row["label"]] for row in rows]
def __len__(self) -> int:
return len(self.rows)
def __getitem__(self, idx: int) -> dict[str, torch.Tensor]:
item = {key: torch.tensor(value[idx]) for key, value in self.encodings.items()}
item["labels"] = torch.tensor(self.labels[idx], dtype=torch.long)
return item
class WeightedTrainer(Trainer):
def __init__(
self,
class_weights: torch.Tensor | None = None,
train_sampler: WeightedRandomSampler | None = None,
loss_type: str = "cross_entropy",
focal_gamma: float = 2.0,
**kwargs: Any,
):
super().__init__(**kwargs)
self.class_weights = class_weights
self.train_sampler = train_sampler
self.loss_type = loss_type
self.focal_gamma = focal_gamma
def _get_train_sampler(self, train_dataset: Dataset | None = None) -> torch.utils.data.Sampler | None:
if self.train_sampler is not None:
return self.train_sampler
return super()._get_train_sampler(train_dataset)
def compute_loss(
self,
model: torch.nn.Module,
inputs: dict[str, torch.Tensor | Any],
return_outputs: bool = False,
num_items_in_batch: torch.Tensor | int | None = None,
) -> torch.Tensor | tuple[torch.Tensor, Any]:
labels = inputs.pop("labels")
outputs = model(**inputs)
logits = outputs.logits
weights = self.class_weights.to(logits.device) if self.class_weights is not None else None
logits = logits.view(-1, logits.shape[-1])
labels = labels.view(-1)
if self.loss_type == "focal_loss":
log_probs = torch.nn.functional.log_softmax(logits, dim=-1)
log_pt = log_probs.gather(1, labels.unsqueeze(1)).squeeze(1)
pt = log_pt.exp()
ce_loss = torch.nn.functional.nll_loss(log_probs, labels, weight=weights, reduction="none")
loss = ((1 - pt) ** self.focal_gamma * ce_loss).mean()
else:
loss = torch.nn.functional.cross_entropy(logits, labels, weight=weights)
return (loss, outputs) if return_outputs else loss
def effective_max_length(tokenizer: Any, requested: int) -> int:
tokenizer_max = getattr(tokenizer, "model_max_length", None)
if isinstance(tokenizer_max, int) and 0 < tokenizer_max < 100_000:
return min(requested, tokenizer_max)
return requested
def token_length_stats(rows: list[dict[str, Any]], tokenizer: Any, max_length: int) -> dict[str, Any]:
lengths: list[int] = []
for row in rows:
ids = tokenizer(row["input_text"], truncation=False, add_special_tokens=True)["input_ids"]
lengths.append(len(ids))
if not lengths:
return {"avg_tokens": 0.0, "max_tokens": 0, "pct_over_max_length": 0.0}
over = sum(1 for length in lengths if length > max_length)
return {
"avg_tokens": round(float(np.mean(lengths)), 4),
"max_tokens": int(max(lengths)),
"pct_over_max_length": round(over / len(lengths), 6),
}
def normalized_class_weights(counts: list[int], mode: str) -> np.ndarray:
total = sum(counts)
safe_counts = np.array([max(1, count) for count in counts], dtype=np.float64)
if mode == "inverse_frequency":
weights = total / safe_counts
elif mode == "inverse_sqrt_frequency":
weights = np.sqrt(total / safe_counts)
else:
raise ValueError(f"Unsupported class weight mode: {mode}")
return weights / weights.mean()
def class_weights_for(rows: list[dict[str, Any]], label_set: list[str], label2id: dict[str, int], mode: str | None) -> torch.Tensor | None:
if mode in (None, "", "none", "None"):
return None
mode = str(mode)
labels = np.array([label2id[row["label"]] for row in rows])
classes = np.arange(len(label_set))
if mode == "balanced":
weights = compute_class_weight(class_weight="balanced", classes=classes, y=labels)
elif mode in {"inverse_frequency", "inverse_sqrt_frequency"}:
counts_by_id = Counter(int(label_id) for label_id in labels)
counts = [counts_by_id.get(class_id, 0) for class_id in classes]
weights = normalized_class_weights(counts, mode)
else:
raise ValueError(f"Unsupported class weight mode: {mode}")
return torch.tensor(weights, dtype=torch.float)
def sampler_for(rows: list[dict[str, Any]], label2id: dict[str, int], cfg: dict[str, Any] | None) -> WeightedRandomSampler | None:
if not cfg or cfg.get("type") != "weighted_random_sampler":
return None
mode = str(cfg.get("weight_mode", "inverse_frequency"))
cap = float(cfg.get("minority_sampling_cap", cfg.get("cap", 3.0)))
labels = [label2id[row["label"]] for row in rows]
counts_by_id = Counter(labels)
counts = [counts_by_id.get(class_id, 0) for class_id in range(len(label2id))]
class_weights = normalized_class_weights(counts, mode)
if cap > 0:
min_weight = float(class_weights.min())
class_weights = np.minimum(class_weights, min_weight * cap)
sample_weights = torch.tensor([float(class_weights[label_id]) for label_id in labels], dtype=torch.double)
return WeightedRandomSampler(sample_weights, num_samples=len(sample_weights), replacement=True)
def write_predictions(
path: Path,
rows: list[dict[str, Any]],
probs: np.ndarray,
pred_ids: np.ndarray,
id2label: dict[int, str],
model_name: str,
seed: int,
) -> None:
out_rows: list[dict[str, Any]] = []
for row, prob, pred_id in zip(rows, probs, pred_ids, strict=False):
evidence = row.get("evidence", [])
out_rows.append(
{
"id": row.get("id"),
"dataset": row.get("dataset"),
"split": row.get("split"),
"gold": row.get("label"),
"prediction": id2label[int(pred_id)],
"confidence": round(float(prob.max()), 6),
"probabilities": {id2label[idx]: round(float(value), 6) for idx, value in enumerate(prob)},
"model_name": model_name,
"seed": seed,
"claim": row.get("claim"),
"evidence_ids": [item.get("candidate_id") for item in evidence],
}
)
write_jsonl(path, out_rows)
def evaluate_split(
trainer: Trainer,
rows: list[dict[str, Any]],
dataset: VerifierDataset,
split_key: str,
output_dir: Path,
label_set: list[str],
id2label: dict[int, str],
model_name: str,
seed: int,
) -> dict[str, Any]:
pred = trainer.predict(dataset)
logits = np.asarray(pred.predictions)
probs = softmax(logits)
pred_ids = probs.argmax(axis=1)
true_ids = np.asarray([label_set.index(row["label"]) for row in rows])
y_true = [row["label"] for row in rows]
y_pred = [id2label[int(idx)] for idx in pred_ids]
metrics = classification_metrics(label_set, y_true, y_pred)
metrics["ece"] = expected_calibration_error(probs, true_ids)
metrics["split"] = split_key
metrics["eval_size"] = len(rows)
write_predictions(output_dir / f"predictions_{split_key}.jsonl", rows, probs, pred_ids, id2label, model_name, seed)
write_csv(output_dir / f"confusion_matrix_{split_key}.csv", confusion_matrix_rows(label_set, y_true, y_pred))
return metrics
def update_csv_by_key(path: Path, new_rows: list[dict[str, Any]], key_fields: list[str]) -> None:
existing = read_csv_dicts(path) if path.exists() else []
new_keys = {tuple(str(row.get(field, "")) for field in key_fields) for row in new_rows}
kept = [row for row in existing if tuple(str(row.get(field, "")) for field in key_fields) not in new_keys]
write_csv(path, kept + new_rows)
def aggregate_seed_metrics(seed_metrics: list[dict[str, Any]], key: str) -> tuple[float, float]:
values = [float(row[key]) for row in seed_metrics]
return round(float(np.mean(values)), 6), round(float(np.std(values, ddof=0)), 6)
def load_available_seed_results(base_dir: Path, in_memory_results: list[dict[str, Any]]) -> list[dict[str, Any]]:
results_by_seed = {int(row["seed"]): row for row in in_memory_results}
for metrics_path in base_dir.glob("seed_*/metrics.json"):
try:
metrics = json.loads(metrics_path.read_text(encoding="utf-8"))
except (OSError, json.JSONDecodeError):
continue
if "seed" in metrics and "test" in metrics:
results_by_seed[int(metrics["seed"])] = metrics
return [results_by_seed[seed] for seed in sorted(results_by_seed)]
def loss_name(cfg: dict[str, Any]) -> str:
loss_cfg = cfg.get("loss") or {}
loss_type = str(loss_cfg.get("type", "cross_entropy"))
class_weight_mode = loss_cfg.get("class_weight_mode")
if class_weight_mode is None:
class_weight_mode = (cfg.get("training") or {}).get("class_weight")
if loss_type == "focal_loss":
gamma = float(loss_cfg.get("gamma", 2.0))
suffix = f":{class_weight_mode}" if class_weight_mode else ""
return f"focal_loss:gamma={gamma:g}{suffix}"
if class_weight_mode:
return f"weighted_cross_entropy:{class_weight_mode}"
return loss_type
def input_metadata(cfg: dict[str, Any]) -> dict[str, str]:
train_path = Path(cfg["input"]["train"])
top_match = re.search(r"_top(\d+)", train_path.stem)
top_k = top_match.group(1) if top_match else ""
input_format = str((cfg.get("input") or {}).get("format") or cfg.get("input_format") or "flat")
if train_path.stem.endswith("_qa"):
input_format = "qa"
return {"top_k": top_k, "input_format": input_format}
def method_metadata(
dataset: str,
model_name: str,
top_k: str,
loss: str,
sampler: dict[str, Any] | None,
input_format: str,
) -> dict[str, str]:
if dataset == "healthver":
return {
"Protocol": "P6",
"Method": "PubMedBERT baseline",
"Evidence source": "paired evidence + augmentation",
"Notes": "pair-level anchored protocol",
}
if dataset == "vifactcheck":
return {
"Protocol": "P1",
"Method": "XLM-R baseline",
"Evidence source": "context chunks",
"Notes": "gold Evidence excluded from main input",
}
model_family = "DeBERTa-v3-large" if "deberta" in model_name.lower() else "ModernBERT"
sampler_suffix = " sampler" if sampler and sampler.get("type") == "weighted_random_sampler" else ""
qa_suffix = " QA" if input_format == "qa" else ""
if "deberta" in model_name.lower():
loss_suffix = " focal" if loss.startswith("focal_loss") else ""
return {
"Protocol": "P4",
"Method": f"{model_family} top{top_k}{qa_suffix}{loss_suffix} weighted{sampler_suffix} rescue",
"Evidence source": "retrieved evidence",
"Notes": "AVeriTeC rescue candidate; official dev used as local_test; hidden test excluded",
}
if sampler and sampler.get("type") == "weighted_random_sampler":
loss_suffix = " focal" if loss.startswith("focal_loss") else ""
return {
"Protocol": "P4",
"Method": f"{model_family} top{top_k}{qa_suffix}{loss_suffix} weighted sampler rescue",
"Evidence source": "retrieved evidence",
"Notes": "AVeriTeC rescue candidate with weighted sampler; official dev used as local_test; hidden test excluded",
}
if top_k == "10":
loss_suffix = " focal" if loss.startswith("focal_loss") else ""
return {
"Protocol": "P4",
"Method": f"{model_family} top{top_k}{qa_suffix}{loss_suffix} weighted rescue",
"Evidence source": "retrieved evidence",
"Notes": "AVeriTeC rescue candidate; official dev used as local_test; hidden test excluded",
}
return {
"Protocol": "P4",
"Method": "ModernBERT baseline",
"Evidence source": "retrieved evidence",
"Notes": "official dev used as local_test; hidden test excluded",
}
def run_seed(cfg: dict[str, Any], seed: int, output_dir: Path) -> dict[str, Any]:
random.seed(seed)
np.random.seed(seed)
torch.manual_seed(seed)
set_seed(seed)
dataset_name = cfg["dataset"]
model_name = cfg["model_name"]
label_set = list(cfg["label_set"])
label2id = {label: idx for idx, label in enumerate(label_set)}
id2label = {idx: label for label, idx in label2id.items()}
training_cfg = cfg["training"]
train_rows = [row for row in read_jsonl(Path(cfg["input"]["train"])) if row.get("label") in label2id]
dev_rows = [row for row in read_jsonl(Path(cfg["input"]["dev"])) if row.get("label") in label2id]
test_rows = [row for row in read_jsonl(Path(cfg["input"]["test"])) if row.get("label") in label2id]
tokenizer = load_tokenizer(model_name)
requested_max_length = int(training_cfg.get("max_length", 512))
max_length = effective_max_length(tokenizer, requested_max_length)
model = load_sequence_classifier(model_name, len(label_set), label_set)
train_dataset = VerifierDataset(train_rows, tokenizer, label2id, max_length=max_length)
dev_dataset = VerifierDataset(dev_rows, tokenizer, label2id, max_length=max_length)
test_dataset = VerifierDataset(test_rows, tokenizer, label2id, max_length=max_length)
loss_cfg = cfg.get("loss") or {}
loss_type = loss_cfg.get("type", "cross_entropy")
focal_gamma = float(loss_cfg.get("gamma", 2.0))
class_weight_mode = loss_cfg.get("class_weight_mode")
if class_weight_mode is None:
class_weight_mode = training_cfg.get("class_weight")
if loss_type not in {"cross_entropy", "weighted_cross_entropy", "focal_loss"}:
raise ValueError(f"Unsupported loss type: {loss_type}")
if loss_type == "weighted_cross_entropy" and not class_weight_mode:
raise ValueError("loss.type=weighted_cross_entropy requires loss.class_weight_mode")
weights = class_weights_for(train_rows, label_set, label2id, class_weight_mode)
train_sampler = sampler_for(train_rows, label2id, cfg.get("sampler"))
args = TrainingArguments(
output_dir=str(output_dir / "trainer"),
num_train_epochs=float(training_cfg.get("epochs", 3)),
per_device_train_batch_size=int(training_cfg.get("batch_size", 8)),
per_device_eval_batch_size=int(training_cfg.get("eval_batch_size", training_cfg.get("batch_size", 8))),
gradient_accumulation_steps=int(training_cfg.get("gradient_accumulation_steps", 1)),
learning_rate=float(training_cfg.get("learning_rate", 2e-5)),
weight_decay=float(training_cfg.get("weight_decay", 0.01)),
warmup_ratio=float(training_cfg.get("warmup_ratio", 0.06)),
eval_strategy="epoch",
save_strategy="epoch",
logging_strategy="steps",
logging_steps=int(training_cfg.get("logging_steps", 25)),
load_best_model_at_end=True,
metric_for_best_model=str(training_cfg.get("metric_for_best_model", "macro_f1")),
greater_is_better=True,
save_total_limit=1,
bf16=bool(training_cfg.get("precision") == "bf16" and torch.cuda.is_available()),
fp16=bool(training_cfg.get("precision") == "fp16" and torch.cuda.is_available()),
report_to=[],
seed=seed,
dataloader_num_workers=int(training_cfg.get("dataloader_num_workers", 0)),
)
def compute_metrics(eval_pred: Any) -> dict[str, float]:
logits, labels = eval_pred
pred_ids = np.asarray(logits).argmax(axis=1)
y_true = [id2label[int(idx)] for idx in labels]
y_pred = [id2label[int(idx)] for idx in pred_ids]
metrics = classification_metrics(label_set, y_true, y_pred)
return {
"accuracy": metrics["accuracy"],
"macro_f1": metrics["macro_f1"],
"weighted_f1": metrics["weighted_f1"],
}
trainer = WeightedTrainer(
model=model,
args=args,
train_dataset=train_dataset,
eval_dataset=dev_dataset,
processing_class=tokenizer,
compute_metrics=compute_metrics,
callbacks=[EarlyStoppingCallback(early_stopping_patience=int(training_cfg.get("early_stopping_patience", 2)))],
class_weights=weights,
train_sampler=train_sampler,
loss_type=loss_type,
focal_gamma=focal_gamma,
)
trainer.train()
dev_metrics = evaluate_split(trainer, dev_rows, dev_dataset, "dev", output_dir, label_set, id2label, model_name, seed)
test_metrics = evaluate_split(trainer, test_rows, test_dataset, "test", output_dir, label_set, id2label, model_name, seed)
train_token_stats = token_length_stats(train_rows, tokenizer, max_length)
dev_token_stats = token_length_stats(dev_rows, tokenizer, max_length)
test_token_stats = token_length_stats(test_rows, tokenizer, max_length)
training_log = trainer.state.log_history
write_jsonl(output_dir / "training_log.jsonl", training_log)
metrics = {
"dataset": dataset_name,
"model_name": model_name,
"seed": seed,
"label_set": label_set,
"requested_max_length": requested_max_length,
"effective_max_length": max_length,
"train_size": len(train_rows),
"loss": {
"type": loss_type,
"gamma": focal_gamma if loss_type == "focal_loss" else None,
"class_weight_mode": class_weight_mode,
"class_weights": [round(float(value), 6) for value in weights.tolist()] if weights is not None else None,
},
"sampler": cfg.get("sampler"),
"dev": dev_metrics,
"test": test_metrics,
"token_stats": {
"train": train_token_stats,
"dev": dev_token_stats,
"test": test_token_stats,
},
}
write_json(output_dir / "metrics.json", metrics)
return metrics
def update_summary_tables(cfg: dict[str, Any], model_dir_name: str, seed_results: list[dict[str, Any]], output_root: Path) -> None:
dataset = cfg["dataset"]
model_name = cfg["model_name"]
test_seed_metrics = [row["test"] for row in seed_results]
acc_mean, acc_std = aggregate_seed_metrics(test_seed_metrics, "accuracy")
f1_mean, f1_std = aggregate_seed_metrics(test_seed_metrics, "macro_f1")
per_class = test_seed_metrics[-1].get("per_class_f1", "{}")
input_meta = input_metadata(cfg)
top_k = input_meta["top_k"]
input_format = input_meta["input_format"]
loss = loss_name(cfg)
meta = method_metadata(dataset, model_name, top_k, loss, cfg.get("sampler"), input_format)
seed_count = len(seed_results)
last_per_class = test_seed_metrics[-1].get("per_class", {})
collapse_labels = [
label
for label, values in last_per_class.items()
if float(values.get("f1", 0.0)) < 0.1 and (dataset == "averitec" or float(values.get("support", 0)) > 0)
]
collapse_warning = "No" if not collapse_labels else f"YES: {'/'.join(collapse_labels)} collapse"
averitec_rescue_minimum_pass = True
if dataset == "averitec":
nei_f1 = float(last_per_class.get("NEI", {}).get("f1", 0.0))
conflicting_f1 = float(last_per_class.get("CONFLICTING", {}).get("f1", 0.0))
averitec_rescue_minimum_pass = f1_mean >= 0.4 and nei_f1 > 0.1 and conflicting_f1 > 0.1
if dataset == "averitec" and (collapse_labels or not averitec_rescue_minimum_pass):
gate = "NEEDS_RESCUE"
strong_gate_status = "PENDING_AVERITEC_RESCUE"
elif dataset == "averitec" and seed_count < 3:
gate = "RESCUE_MINIMUM_PASS"
strong_gate_status = "PENDING_3_SEEDS"
elif seed_count >= 3:
gate = "STRONG_PASS_CANDIDATE"
strong_gate_status = "READY_FOR_STRONG_GATE_REVIEW"
else:
gate = "MINIMUM_PASS"
strong_gate_status = "PENDING_3_SEEDS"
t11_row = {
"Dataset": dataset,
"Protocol": meta["Protocol"],
"Method": meta["Method"],
"Evidence source": meta["Evidence source"],
"Verifier": model_name,
"KG/path": "No",
"Top-k": top_k,
"input_top_k": top_k,
"input_format": input_format,
"loss_type": loss,
"Acc": acc_mean,
"Acc std": acc_std,
"Macro-F1": f1_mean,
"Macro-F1 std": f1_std,
"Per-class F1": per_class,
"Seeds": ",".join(str(row["seed"]) for row in seed_results),
"seed_count": seed_count,
"collapse_warning": collapse_warning,
"strong_gate_status": strong_gate_status,
"Gate": gate,
"Notes": meta["Notes"],
}
update_csv_by_key(
output_root / "tables" / "T11_main_verification.csv",
[t11_row],
key_fields=["Dataset", "Method", "Verifier", "Top-k", "loss_type", "input_format"],
)
training = cfg["training"]
t5_row = {
"Dataset": dataset,
"Verifier": model_name,
"Model dir": model_dir_name,
"Top-k": top_k,
"input_format": input_format,
"max_length": training.get("max_length"),
"batch_size": training.get("batch_size"),
"gradient_accumulation_steps": training.get("gradient_accumulation_steps"),
"learning_rate": training.get("learning_rate"),
"epochs": training.get("epochs"),
"precision": training.get("precision"),
"loss_type": loss,
"sampler": json.dumps(cfg.get("sampler"), sort_keys=True) if cfg.get("sampler") else "",
"seeds": ",".join(str(seed) for seed in cfg["training"].get("seeds", [])),
}
update_csv_by_key(
output_root / "tables" / "T5_training_config.csv",
[t5_row],
key_fields=["Dataset", "Verifier", "Model dir", "Top-k"],
)
def main() -> None:
parser = argparse.ArgumentParser()
parser.add_argument("--config", type=Path, required=True)
parser.add_argument("--output-root", type=Path, default=Path("outputs"))
parser.add_argument("--seeds", type=int, nargs="*", default=None)
parser.add_argument("--refresh-summary-only", action="store_true")
args = parser.parse_args()
cfg = yaml.safe_load(args.config.read_text(encoding="utf-8"))
seeds = args.seeds if args.seeds else list(cfg["training"].get("seeds", [13]))
cfg["training"]["seeds"] = seeds
model_dir_name = str(cfg.get("output_name") or sanitize_model_name(cfg["model_name"])).replace("/", "__")
base_dir = args.output_root / "baselines" / cfg["dataset"] / "encoder_verifier" / model_dir_name
base_dir.mkdir(parents=True, exist_ok=True)
seed_results: list[dict[str, Any]] = []
if not args.refresh_summary_only:
for seed in seeds:
seed_dir = base_dir / f"seed_{seed}"
seed_dir.mkdir(parents=True, exist_ok=True)
seed_results.append(run_seed(cfg, seed, seed_dir))
all_seed_results = load_available_seed_results(base_dir, seed_results)
if not all_seed_results:
raise FileNotFoundError(f"No seed metrics found under {base_dir}")
cfg["training"]["seeds"] = [int(row["seed"]) for row in all_seed_results]
write_json(base_dir / "summary.json", {"config": cfg, "seeds": cfg["training"]["seeds"], "results": all_seed_results})
update_summary_tables(cfg, model_dir_name, all_seed_results, args.output_root)
print(f"Wrote encoder verifier outputs to {base_dir}")
if __name__ == "__main__":
main()
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