tabulm / code /finetune_tabqa.py
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Add TabuLM training and evaluation code
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#!/usr/bin/env python3
"""Fine-tune TabuLM for cell-selection on TabQA-kin (526 Kinyarwanda table QA pairs).
Strategy: Given a (table, question) pair, encode both through the TabuLM encoder
and predict which table cell (row_id, col_id) contains the answer via a linear
scoring head over per-cell pooled hidden states.
"""
import argparse
import json
import os
import random
import sys
from datetime import datetime
from typing import Dict, List, Optional, Tuple
import numpy as np
import torch
import torch.nn as nn
from torch.nn.utils import clip_grad_norm_
# ── Server paths ───────────────────────────────────────────────────────────────
CODE_DIR = '/shared/scratch/0/tmp/v_ireddi_rakshitha_results/tabulm/code'
DATA_DIR = '/shared/scratch/0/tmp/v_ireddi_rakshitha_results/tabulm/data'
CHECKPOINT = os.path.join(DATA_DIR, 'tabulm_model_2026-05-13_pos@1_stem@1_afsets@False@10000.pt')
TABQA_FILE = os.path.join(DATA_DIR, 'tabqa_kin.json')
CSV_DIR = os.path.join(DATA_DIR, 'tables')
BEST_MODEL = os.path.join(DATA_DIR, 'finetune_tabqa_best.pt')
RESULTS = os.path.join(DATA_DIR, 'finetune_tabqa_results.json')
sys.path.insert(0, CODE_DIR)
import youtokentome as yttm
from morpho_data_loaders import KBVocab
from tabular_serializer import serialize_csv, table_cells_to_text, TableCell
from morpho_stub import parse_text_stub
from tabulm_model import TabuLM, tabulm_base
# ── Architecture auto-detection ────────────────────────────────────────────────
def detect_arch_from_state(state: dict) -> argparse.Namespace:
"""Infer all architecture hyperparameters by inspecting checkpoint tensor shapes."""
ns = argparse.Namespace()
# Sequence transformer model dimension
ns.seq_tr_d_model = int(state['encoder.row_embedding.weight'].shape[1])
d = ns.seq_tr_d_model
# Stem / morpho dims
ns.stem_dim = int(state['encoder.s_stem_embedding.weight'].shape[1])
if 'encoder.m1_pos_embedding.weight' in state:
ns.morpho_dim = int(state['encoder.m1_pos_embedding.weight'].shape[1])
elif 'encoder.m_stem_embedding.weight' in state:
ns.morpho_dim = int(state['encoder.m_stem_embedding.weight'].shape[1])
else:
ns.morpho_dim = 128
# Sequence transformer layers
layer_ids = {
int(k.split('.layers.')[1].split('.')[0])
for k in state
if 'encoder.seq_transformer_encoder.layers.' in k and '.layers.' in k
}
ns.seq_tr_nlayers = max(layer_ids) + 1 if layer_ids else 12
# Heads from tabular bias parameter
if 'encoder.row_attn_bias' in state:
ns.seq_tr_nhead = int(state['encoder.row_attn_bias'].shape[0])
else:
ns.seq_tr_nhead = 8
# Feed-forward dim
ff_key = 'encoder.seq_transformer_encoder.layers.0.linear1.weight'
ns.seq_tr_dim_feedforward = int(state[ff_key].shape[0]) if ff_key in state else d * 4
# Morpho transformer layers
m_ids = {
int(k.split('.layers.')[1].split('.')[0])
for k in state
if 'encoder.morpho_transformer_encoder.layers.' in k and '.layers.' in k
}
ns.morpho_tr_nlayers = max(m_ids) + 1 if m_ids else 4
mff_key = 'encoder.morpho_transformer_encoder.layers.0.linear1.weight'
ns.morpho_tr_dim_feedforward = int(state[mff_key].shape[0]) if mff_key in state else ns.morpho_dim * 4
ns.morpho_tr_nhead = max(1, ns.morpho_dim // 32) # head_dim=32 default
ns.morpho_tr_dropout = 0.1
ns.seq_tr_dropout = 0.1
ns.layernorm_epsilon = 1e-6
ns.max_seq_len = 512
# Tabular embedding flags
ns.num_pos_m_embeddings = 1
ns.num_stem_m_embeddings = 1
ns.use_afsets = False
ns.afset_dict_size = 10000
ns.use_morpho_encoder = True
morpho_part = d - ns.stem_dim
tot_morpho_vecs = morpho_part // ns.morpho_dim if ns.morpho_dim else 2
tot_morpho_idx = ns.num_pos_m_embeddings + ns.num_stem_m_embeddings
ns.use_affix_bow_m_embedding = (tot_morpho_vecs > tot_morpho_idx)
ns.use_tupe_rel_pos_bias = 'encoder.tupe_rel_pos_bias.weight' in state \
or any('tupe' in k for k in state)
ns.use_pos_aware_rel_pos_bias = any('pos_aware' in k for k in state)
ns.use_pos_aware_rel = ns.use_pos_aware_rel_pos_bias
ns.predict_affixes = False
# Needed by tabulm_base factory
ns.gpus = 0
ns.world_size = 1
ns.exploratory_model_load = None
return ns
# ── Gold cell lookup via text matching ────────────────────────────────────────
def find_gold_cell(cells: List[TableCell], answer_text: str,
question_text: str = '') -> Optional[Tuple[int, int]]:
"""
Find the (row_id, col_id) of the cell whose content matches answer_text.
When multiple cells share the same value, uses question-word overlap against
both first-column row labels AND header-row column names to disambiguate.
"""
answer_norm = answer_text.strip().lower()
# Pass 1: exact match
matches = [(c.row_id, c.col_id) for c in cells
if c.row_id > 1 and c.col_id > 0 and c.content.strip() == answer_text.strip()]
if len(matches) == 1:
return matches[0]
# Pass 2: case-insensitive
if not matches:
matches = [(c.row_id, c.col_id) for c in cells
if c.row_id > 1 and c.col_id > 0 and c.content.strip().lower() == answer_norm]
if not matches:
return None
if len(matches) == 1:
return matches[0]
# Multiple cells match β€” score by (row overlap, col overlap) jointly
if question_text:
q_words = set(question_text.lower().split())
row_labels = {c.row_id: c.content.strip().lower()
for c in cells if c.col_id == 1 and c.row_id > 1}
col_headers = {c.col_id: c.content.strip().lower()
for c in cells if c.row_id == 1 and c.col_id > 0}
best, best_score = None, (-1, -1)
for (row_id, col_id) in matches:
r_sc = len(q_words & set(row_labels.get(row_id, '').split()))
c_sc = len(q_words & set(col_headers.get(col_id, '').split()))
if (r_sc, c_sc) > best_score:
best_score, best = (r_sc, c_sc), (row_id, col_id)
if best_score[0] > 0 or best_score[1] > 0:
return best
return min(matches, key=lambda rc: (rc[0], rc[1]))
# ── Sequence encoding (no masking) ────────────────────────────────────────────
def _add_special(key, kv, pos_tags, stems, tokens_lengths, row_ids, col_ids, cell_types):
pos_tags.append(kv.pos_tag_vocab[key])
stems.append(kv.reduced_stem_vocab[key])
tokens_lengths.append(0)
row_ids.append(0)
col_ids.append(0)
cell_types.append(0)
def encode_item(
cells,
question_text: str,
kv: KBVocab,
bpe,
max_seq_len: int = 512,
) -> Optional[Tuple]:
"""
Encode a table (List[TableCell]) + question string into flat lists for the
TabuLM encoder. Returns None if the table serialization fails.
Returns:
pos_tags, stems, affixes, tokens_lengths,
row_ids, col_ids, cell_types,
ordered_cells, cell_to_positions
where ordered_cells is a sorted list of unique (row_id, col_id) tuples, and
cell_to_positions maps each (row_id, col_id) β†’ [token_idx, ...].
"""
text, word_meta = table_cells_to_text(cells)
parsed_table = parse_text_stub(text, kv, bpe)
if len(parsed_table) != len(word_meta):
return None
parsed_question = parse_text_stub(question_text, kv, bpe)
pos_tags, stems, affixes, tokens_lengths = [], [], [], []
row_ids, col_ids, cell_types = [], [], []
cell_to_positions: Dict[Tuple[int, int], List[int]] = {}
# CLS
_add_special('<CLS>', kv, pos_tags, stems, tokens_lengths, row_ids, col_ids, cell_types)
# Table tokens β€” each ParsedToken may have multiple sub-stems (BPE)
for pt, (r, c, ct) in zip(parsed_table, word_meta):
for sidx in pt.stem_idx:
seq_idx = len(pos_tags)
pos_tags.append(pt.pos_tag_idx)
stems.append(kv.mapped_stem_vocab_idx[sidx])
affixes.extend(pt.affixes_idx)
tokens_lengths.append(len(pt.affixes_idx))
row_ids.append(r)
col_ids.append(c)
cell_types.append(ct)
if r > 0 and c > 0:
cell_to_positions.setdefault((r, c), []).append(seq_idx)
# SEP between table and question
_add_special('<SEP>', kv, pos_tags, stems, tokens_lengths, row_ids, col_ids, cell_types)
# Question tokens (row_id=0, col_id=0 β†’ not scored as table cells)
for pt in parsed_question:
for sidx in pt.stem_idx:
pos_tags.append(pt.pos_tag_idx)
stems.append(kv.mapped_stem_vocab_idx[sidx])
affixes.extend(pt.affixes_idx)
tokens_lengths.append(len(pt.affixes_idx))
row_ids.append(0)
col_ids.append(0)
cell_types.append(0)
# Final SEP
_add_special('<SEP>', kv, pos_tags, stems, tokens_lengths, row_ids, col_ids, cell_types)
# Truncate to max_seq_len
if len(pos_tags) > max_seq_len:
pos_tags = pos_tags[:max_seq_len]
stems = stems[:max_seq_len]
tokens_lengths = tokens_lengths[:max_seq_len]
row_ids = row_ids[:max_seq_len]
col_ids = col_ids[:max_seq_len]
cell_types = cell_types[:max_seq_len]
affixes = affixes[:sum(tokens_lengths)]
cell_to_positions = {
k: [p for p in v if p < max_seq_len]
for k, v in cell_to_positions.items()
}
cell_to_positions = {k: v for k, v in cell_to_positions.items() if v}
ordered_cells = sorted(cell_to_positions.keys(),
key=lambda rc: min(cell_to_positions[rc]))
return (pos_tags, stems, affixes, tokens_lengths,
row_ids, col_ids, cell_types,
ordered_cells, cell_to_positions)
# ── Fine-tuning model ──────────────────────────────────────────────────────────
class TabQAModel(nn.Module):
"""TabuLM encoder + linear cell-selection head."""
def __init__(self, tabulm: TabuLM):
super().__init__()
self.encoder = tabulm.encoder
d = self.encoder.seq_tr_d_model
self.cell_head = nn.Linear(d, 1)
nn.init.normal_(self.cell_head.weight, std=0.02)
nn.init.zeros_(self.cell_head.bias)
def get_hidden(self, args, pos_tags, stems, affixes,
tokens_lengths, row_ids, col_ids, cell_types, device):
pos_t = torch.tensor(pos_tags, dtype=torch.long, device=device)
stem_t = torch.tensor(stems, dtype=torch.long, device=device)
afx_t = (torch.tensor(affixes, dtype=torch.long, device=device)
if affixes else torch.zeros(0, dtype=torch.long, device=device))
row_t = torch.tensor(row_ids, dtype=torch.long, device=device)
col_t = torch.tensor(col_ids, dtype=torch.long, device=device)
ct_t = torch.tensor(cell_types, dtype=torch.long, device=device)
hidden = self.encoder.forward(
args,
rel_pos_arr=None,
tokens_lengths=tokens_lengths,
input_sequence_lengths=[len(pos_tags)],
pos_tags=pos_t, stems=stem_t, afsets=None, affixes=afx_t,
row_ids=row_t, col_ids=col_t, cell_types=ct_t,
) # (S, 1, d)
return hidden[:, 0, :] # (S, d)
def forward(self, args, pos_tags, stems, affixes,
tokens_lengths, row_ids, col_ids, cell_types,
ordered_cells, cell_to_positions, device):
"""
Returns (scores, valid_cells) where scores is a (C,) tensor of logits
and valid_cells is the subset of ordered_cells that had token positions.
"""
hidden = self.get_hidden(args, pos_tags, stems, affixes,
tokens_lengths, row_ids, col_ids, cell_types, device)
S = hidden.size(0)
cell_embeds, valid_cells = [], []
for rc in ordered_cells:
positions = [p for p in cell_to_positions[rc] if p < S]
if not positions:
continue
h = hidden[positions].mean(0)
cell_embeds.append(h)
valid_cells.append(rc)
if not cell_embeds:
return None, []
cell_embeds = torch.stack(cell_embeds) # (C, d)
scores = self.cell_head(cell_embeds).squeeze(-1) # (C,)
return scores, valid_cells
# ── Evaluation ────────────────────────────────────────────────────────────────
def _predict_lookup(scores, valid_cells, cells, question_text):
"""For lookup questions: restrict to (best_row, best_col) using question-word
overlap against row labels (first column) and column headers (header row)."""
q_words = set(question_text.lower().split())
row_labels = {c.row_id: c.content.strip().lower()
for c in cells if c.col_id == 1 and c.row_id > 1}
col_headers = {c.col_id: c.content.strip().lower()
for c in cells if c.row_id == 1 and c.col_id > 0}
if not q_words:
return valid_cells[scores.argmax().item()]
row_score = {r: len(q_words & set(lbl.split())) for r, lbl in row_labels.items()}
col_score = {c: len(q_words & set(hdr.split())) for c, hdr in col_headers.items()}
best_row = max(row_score, key=row_score.get) if row_score else None
best_col = max(col_score, key=col_score.get) if col_score else None
has_row = best_row is not None and row_score[best_row] > 0
has_col = best_col is not None and col_score[best_col] > 0
if not has_row and not has_col:
return valid_cells[scores.argmax().item()]
# Narrow to best row first
if has_row:
row_indices = [i for i, rc in enumerate(valid_cells) if rc[0] == best_row]
else:
row_indices = list(range(len(valid_cells)))
if not row_indices:
return valid_cells[scores.argmax().item()]
# Further narrow to best column if signal available
if has_col:
both = [i for i in row_indices if valid_cells[i][1] == best_col]
if both:
return valid_cells[max(both, key=lambda i: scores[i].item())]
return valid_cells[max(row_indices, key=lambda i: scores[i].item())]
def _predict_comparison(scores, valid_cells, cells, question_text):
"""For comparison questions: restrict to col-1 (entity name) cells of the
top-2 question-relevant rows. The answer is the winning entity name."""
q_words = set(question_text.lower().split())
row_labels = {c.row_id: c.content.strip().lower()
for c in cells if c.col_id == 1 and c.row_id > 1}
if not q_words or not row_labels:
return valid_cells[scores.argmax().item()]
row_score = {r: len(q_words & set(lbl.split())) for r, lbl in row_labels.items()}
top2 = sorted([r for r, s in row_score.items() if s > 0],
key=lambda r: row_score[r], reverse=True)[:2]
if not top2:
return valid_cells[scores.argmax().item()]
# Prefer col-1 cells (entity names) in those rows; fall back to any cell
cand = [i for i, (r, c) in enumerate(valid_cells) if r in top2 and c == 1]
if not cand:
cand = [i for i, (r, c) in enumerate(valid_cells) if r in top2]
if not cand:
return valid_cells[scores.argmax().item()]
return valid_cells[max(cand, key=lambda i: scores[i].item())]
def evaluate(model, args, items, kv, bpe, csv_dir, device, split='dev'):
model.eval()
correct = 0
total = 0
skipped = 0
by_type: Dict[str, List[int]] = {}
with torch.no_grad():
for item in items:
csv_path = os.path.join(csv_dir, item['table_file'])
if not os.path.exists(csv_path):
skipped += 1
continue
cells = serialize_csv(csv_path)
if not cells:
skipped += 1
continue
question = item['question']
atype = item.get('answer_type', 'unknown')
# Find gold cell β€” use question context to resolve duplicate values
gold_rc = find_gold_cell(cells, item['answer'], question_text=question)
if gold_rc is None:
skipped += 1
continue
enc = encode_item(cells, question, kv, bpe)
if enc is None:
skipped += 1
continue
(pos_tags, stems, affixes, tokens_lengths,
row_ids, col_ids, cell_types, ordered_cells, cell_to_positions) = enc
if gold_rc not in cell_to_positions:
skipped += 1
continue
scores, valid_cells = model(args, pos_tags, stems, affixes,
tokens_lengths, row_ids, col_ids, cell_types,
ordered_cells, cell_to_positions, device)
if scores is None or gold_rc not in valid_cells:
skipped += 1
continue
if atype == 'lookup':
pred_rc = _predict_lookup(scores, valid_cells, cells, question)
elif atype == 'comparison':
pred_rc = _predict_comparison(scores, valid_cells, cells, question)
else:
pred_rc = valid_cells[scores.argmax().item()]
hit = int(pred_rc == gold_rc)
correct += hit
total += 1
by_type.setdefault(atype, []).append(hit)
em = correct / total if total > 0 else 0.0
ts = datetime.now().strftime('%H:%M:%S')
print(f' [{ts}] {split} EM={em:.4f} ({correct}/{total} correct, {skipped} skipped)')
for atype, hits in sorted(by_type.items()):
print(f' {atype}: {sum(hits)}/{len(hits)} = {sum(hits)/len(hits):.3f}')
return em
# ── Training ──────────────────────────────────────────────────────────────────
def train_finetune(args, model, train_items, dev_items, kv, bpe, csv_dir, device,
num_epochs=20, lr=2e-5, best_model_path=BEST_MODEL):
# Fine-tune top-4 seq transformer layers + cell head; freeze the rest
for name, p in model.named_parameters():
if 'cell_head' in name:
p.requires_grad = True
elif 'seq_transformer_encoder.layers.' in name:
# Extract layer index
try:
layer_idx = int(name.split('seq_transformer_encoder.layers.')[1].split('.')[0])
total_layers = model.encoder.seq_tr_nlayers \
if hasattr(model.encoder, 'seq_tr_nlayers') else 12
p.requires_grad = (layer_idx >= total_layers - 4)
except (IndexError, ValueError):
p.requires_grad = False
else:
p.requires_grad = False
trainable = sum(p.numel() for p in model.parameters() if p.requires_grad)
print(f'[FT] Trainable parameters: {trainable:,}')
optimizer = torch.optim.AdamW(
[p for p in model.parameters() if p.requires_grad],
lr=lr, weight_decay=0.01,
)
criterion = nn.CrossEntropyLoss()
best_em = 0.0
history = []
for epoch in range(1, num_epochs + 1):
model.train()
random.shuffle(train_items)
total_loss = 0.0
n_ok = 0
n_skip = 0
for item in train_items:
csv_path = os.path.join(csv_dir, item['table_file'])
if not os.path.exists(csv_path):
n_skip += 1
continue
cells = serialize_csv(csv_path)
if not cells:
n_skip += 1
continue
# Find gold cell by text matching (bypasses broken coord system)
gold_rc = find_gold_cell(cells, item['answer'])
if gold_rc is None:
n_skip += 1
continue
enc = encode_item(cells, item['question'], kv, bpe)
if enc is None:
n_skip += 1
continue
(pos_tags, stems, affixes, tokens_lengths,
row_ids, col_ids, cell_types, ordered_cells, cell_to_positions) = enc
if gold_rc not in cell_to_positions:
n_skip += 1
continue
scores, valid_cells = model(args, pos_tags, stems, affixes,
tokens_lengths, row_ids, col_ids, cell_types,
ordered_cells, cell_to_positions, device)
if scores is None or gold_rc not in valid_cells:
n_skip += 1
continue
gold_idx = torch.tensor([valid_cells.index(gold_rc)],
dtype=torch.long, device=device)
loss = criterion(scores.unsqueeze(0), gold_idx)
optimizer.zero_grad()
loss.backward()
clip_grad_norm_(model.parameters(), 1.0)
optimizer.step()
total_loss += loss.item()
n_ok += 1
ts = datetime.now().strftime('%H:%M:%S')
avg_loss = total_loss / max(n_ok, 1)
print(f'[{ts}] Epoch {epoch}/{num_epochs} loss={avg_loss:.4f} '
f'trained={n_ok} skipped={n_skip}')
em = evaluate(model, args, dev_items, kv, bpe, csv_dir, device, split='dev')
history.append({'epoch': epoch, 'train_loss': avg_loss, 'dev_em': em})
if em > best_em:
best_em = em
torch.save({
'epoch': epoch,
'model_state_dict': model.state_dict(),
'dev_em': em,
}, best_model_path)
print(f' ** New best EM={best_em:.4f} saved to {best_model_path}')
return best_em, history
# ── Main ──────────────────────────────────────────────────────────────────────
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--checkpoint', type=str, default=CHECKPOINT,
help='Path to pre-trained TabuLM checkpoint (.pt)')
parser.add_argument('--output-prefix', type=str, default='finetune_tabqa',
help='Prefix for best-model and results files (no extension)')
cli = parser.parse_args()
best_model_path = os.path.join(DATA_DIR, f'{cli.output_prefix}_best.pt')
results_path = os.path.join(DATA_DIR, f'{cli.output_prefix}_results.json')
random.seed(42)
np.random.seed(42)
torch.manual_seed(42)
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
print(f'[FT] Device: {device}')
# Load vocab + BPE
print('[FT] Loading vocab and BPE...')
bpe = yttm.BPE(model=os.path.join(DATA_DIR, 'BPE-30k.mdl'))
kv = KBVocab()
kv.load_state_dict(torch.load(os.path.join(DATA_DIR, 'kb_vocab_state_dict_2021-02-07.pt'),
map_location='cpu'))
# Load checkpoint and detect architecture
print(f'[FT] Loading checkpoint from {cli.checkpoint}')
ckpt = torch.load(cli.checkpoint, map_location='cpu')
state = ckpt['model_state_dict']
if all(k.startswith('module.') for k in state):
state = {k[len('module.'):]: v for k, v in state.items()}
args = detect_arch_from_state(state)
print(f'[FT] Detected: d_model={args.seq_tr_d_model} nlayers={args.seq_tr_nlayers} '
f'nhead={args.seq_tr_nhead} ff={args.seq_tr_dim_feedforward} '
f'morpho_dim={args.morpho_dim} stem_dim={args.stem_dim} '
f'bow={args.use_affix_bow_m_embedding}')
# Build model and load weights
tabulm = tabulm_base(kv, None, None, device, args, saved_model_file=None)
missing, unexpected = tabulm.load_state_dict(state, strict=False)
print(f'[FT] Loaded encoder: {len(missing)} missing, {len(unexpected)} unexpected keys')
model = TabQAModel(tabulm).to(device)
# Load and split TabQA-kin
print(f'[FT] Loading TabQA-kin from {TABQA_FILE}')
with open(TABQA_FILE) as f:
all_items = json.load(f)
print(f'[FT] {len(all_items)} QA items total')
random.shuffle(all_items)
split_n = int(0.8 * len(all_items))
train_items = all_items[:split_n]
dev_items = all_items[split_n:]
print(f'[FT] Train={len(train_items)} Dev={len(dev_items)}')
print('[FT] Baseline (pre-training weights, no task training):')
evaluate(model, args, dev_items, kv, bpe, CSV_DIR, device, split='dev-baseline')
best_em, history = train_finetune(
args, model, train_items, dev_items, kv, bpe, CSV_DIR, device,
num_epochs=20, lr=2e-5, best_model_path=best_model_path,
)
print(f'\n[FT] Done. Best dev EM = {best_em:.4f}')
with open(results_path, 'w') as f:
json.dump({'best_em': best_em, 'epochs': history,
'train_size': len(train_items), 'dev_size': len(dev_items)}, f, indent=2)
print(f'[FT] Results saved to {results_path}')
if __name__ == '__main__':
main()