Instructions to use dnagpt/laya-bio-models with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Laya
How to use dnagpt/laya-bio-models with Laya:
# No code snippets available yet for this library. # To use this model, check the repository files and the library's documentation. # Want to help? PRs adding snippets are welcome at: # https://github.com/huggingface/huggingface.js
- Notebooks
- Google Colab
- Kaggle
File size: 12,572 Bytes
d35dd87 | 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 | """Matched raw-input / full biological BPE supervision, without CPT or test access."""
from __future__ import annotations
import argparse
from collections import Counter, defaultdict
import gc
import hashlib
import json
from pathlib import Path
import random
import shutil
import torch
import laya_formal_experiment as core
from laya_direct_bpe import DirectBPE, DEFAULT, digest
def parse_args():
p = argparse.ArgumentParser(description=__doc__)
p.add_argument('--condition', choices=['raw', 'full_bpe'], default='raw')
p.add_argument('--representation-dir', type=Path, default=DEFAULT)
p.add_argument('--output-dir', type=Path, required=True)
p.add_argument('--eligible-ids', default='artifacts/laya_formal_data/eligible_ids.json')
p.add_argument('--seed', type=int, default=20260922)
p.add_argument('--updates', type=int, default=3005)
p.add_argument('--micro-batch', type=int, default=8)
p.add_argument('--grad-accum', type=int, default=4)
p.add_argument('--eval-batch', type=int, default=16)
p.add_argument('--device', default='cuda')
p.add_argument('--audit-only', action='store_true')
p.add_argument('--smoke', action='store_true', help='4 train and 2 eval rows/class; never a formal result')
return p.parse_args()
def load_rows(a):
eligible = core.load_eligible_ids(a.eligible_ids)
rows = {s: [r for r in core.load_split(core.ROOT/'artifacts/laya_formal_data', 'both', s)
if r['id'] in eligible] for s in ('train','selection_dev','calibration')}
if a.smoke:
for split, values in rows.items():
groups = defaultdict(list)
for r in values:
groups[(r['task'], r['label'])].append(r)
n = 4 if split == 'train' else 2
rows[split] = [r for group in groups.values() for r in group[:n]]
return rows
def make_items(rows, rep, condition, builder, seed, shuffle=False):
items = []
for row in rows:
order = list(range(len(row['choices'])))
if shuffle:
h = hashlib.sha256(f"{seed}:{row['id']}".encode()).digest()
random.Random(int.from_bytes(h[:8], 'big')).shuffle(order)
ids, markers = rep.build(row, condition, builder, order)
items.append({'ids': ids, 'markers': markers, 'qtype': 0,
'label': order.index(row['label']), 'task': row['task'], 'id': row['id'],
'n_tokens': len(ids), 'full_tokens': len(ids), 'truncated': False})
return items
def stats(items):
values = sorted(x['n_tokens'] for x in items)
return {'n': len(values), 'length_p50': values[len(values)//2],
'length_p95': values[max(0, int(len(values)*.95)-1)],
'length_max': max(values), 'truncated_count': 0,
'membership_sha256': hashlib.sha256('\n'.join(x['id'] for x in items).encode()).hexdigest()}
def audit(a, rep, rows, builder):
report = {'no_cpt': True, 'test_access': False, 'seed': a.seed,
'eligibility_policy': 'same frozen common-complete sample IDs as first 64-token pair',
'representation_sha256': digest(rep.root/'metadata.json'), 'conditions': {}}
all_sets = {}
for condition in ('raw','full_bpe'):
all_sets[condition] = {s: make_items(values, rep, condition, builder, a.seed, s == 'train')
for s, values in rows.items()}
report['conditions'][condition] = {s: {task: stats([x for x in items if x['task']==task])
for task in sorted({x['task'] for x in items})}
for s,items in all_sets[condition].items()}
print(f'Audited {condition}: '+str({s: stats(v) for s,v in all_sets[condition].items()}), flush=True)
for split in rows:
for raw, expanded in zip(all_sets['raw'][split],all_sets['full_bpe'][split]):
assert (raw['id'],raw['label'],raw['markers']) == (expanded['id'],expanded['label'],expanded['markers'])
end = raw['markers'][-1]
assert raw['ids'][:end+1] == expanded['ids'][:end+1]
old_size = len(rep.base)
counts = Counter(i for x in all_sets['full_bpe']['train'] for i in x['ids'] if i >= old_size)
report['train_token_coverage'] = {k: {'added': len(rep.maps[k]),
'observed': sum(i in counts for i in rep.maps[k].values()),
'occurrences': sum(counts[i] for i in rep.maps[k].values())} for k in rep.maps}
report['same_samples_labels_candidate_markers'] = True
report['full_sequence_reconstruction_checked'] = True
a.output_dir.mkdir(parents=True,exist_ok=True)
(a.output_dir/'input_audit.json').write_text(json.dumps(report,indent=2)+'\n')
return all_sets
def initialize(model, rep):
old_size = len(rep.base)
old = model.encoder.get_input_embeddings().weight.detach().clone()
model.encoder.resize_token_embeddings(len(rep.expanded), mean_resizing=False)
emb = model.encoder.get_input_embeddings().weight
maximum_error = 0.0
with torch.no_grad():
for start in range(0,len(rep.entries),512):
entries = rep.entries[start:start+512]
width = max(len(e['base_ids']) for e in entries)
indexes = torch.zeros((len(entries),width),dtype=torch.long,device=emb.device)
mask = torch.zeros((len(entries),width),dtype=emb.dtype,device=emb.device)
for j,e in enumerate(entries):
indexes[j,:len(e['base_ids'])] = torch.tensor(e['base_ids'],device=emb.device)
mask[j,:len(e['base_ids'])] = 1
means = (old[indexes]*mask[:,:,None]).sum(1)/mask.sum(1)[:,None]
dst = torch.tensor([e['expanded_id'] for e in entries],device=emb.device)
emb[dst] = means
maximum_error = max(maximum_error,float((emb[dst]-means).abs().max().cpu()))
old_preserved = torch.equal(emb[:old_size],old)
if not old_preserved or maximum_error != 0 or not torch.isfinite(emb).all():
raise ValueError('Embedding initialization verification failed')
return {'old_vocab_size': old_size, 'new_vocab_size': len(rep.expanded),
'added_by_modality': rep.meta['added_by_modality'],
'raw_fragment_mean_initialization': True, 'old_rows_unchanged_at_initialization': old_preserved,
'maximum_initialization_error': maximum_error, 'fallback_initializations': 0}
def gradient_probe(model, rep, items, device):
out = {}
old_size = len(rep.base)
model.eval()
for task in sorted({x['task'] for x in items}):
model.zero_grad(set_to_none=True)
chosen = [x for x in items if x['task']==task][:2]
batch = core.move(core.collate(chosen, rep.expanded.pad_token_id),device)
with core.autocast_context(device,torch.bfloat16):
logits,_ = model(batch['input_ids'],batch['attention_mask'],batch['marker_pos'],batch['marker_mask'],batch['qtype'])
loss = torch.nn.functional.cross_entropy(logits.masked_fill(~batch['marker_mask'],-1e4),batch['label'])
loss.backward()
grad = model.encoder.get_input_embeddings().weight.grad
active = sorted({i for x in chosen for i in x['ids'] if i >= old_size})
norm = float(grad[active].norm().detach().cpu())
if not torch.isfinite(loss) or not torch.isfinite(grad).all() or not norm > 0:
raise ValueError('New embedding receives no finite task gradient')
out[task] = {'active_new_ids': len(active),'gradient_norm': norm}
model.zero_grad(set_to_none=True)
return out
def main():
a = parse_args()
if (a.output_dir/'summary.json').exists():
raise FileExistsError('Completed run exists; choose a new output directory')
core.set_seed(a.seed)
rep = DirectBPE(a.representation_dir)
rows = load_rows(a)
_, builder_model, builder_sequence = core.import_laya('vendor/laya')
if a.audit_only:
audit(a,rep,rows,builder_sequence)
return
items = {s: make_items(values, rep, a.condition, builder_sequence, a.seed, s=='train')
for s,values in rows.items()}
a.output_dir.mkdir(parents=True,exist_ok=True)
item_stats = {s:stats(v) for s,v in items.items()}
print(json.dumps({'condition':a.condition,'smoke':a.smoke,'item_stats':item_stats},indent=2),flush=True)
model_dir = core.ROOT/'artifacts/laya_model'
cfg = json.loads((model_dir/'rl_agent_config.json').read_text())
cfg.update(max_len=1024,head_max_len=256,gradient_checkpointing=True)
device = torch.device(a.device)
model = core.load_model(model_dir,cfg,builder_model,device,trainable=True)
expansion = initialize(model,rep) if a.condition=='full_bpe' else None
token = rep.expanded if a.condition=='full_bpe' else rep.base
probes = gradient_probe(model,rep,items['train'],device) if expansion else None
trainable = sum(p.numel() for p in model.parameters() if p.requires_grad)
core.set_seed(a.seed) # Equal dropout RNG start after representation-specific initialization/probes.
if device.type=='cuda':
torch.cuda.reset_peak_memory_stats()
torch.cuda.synchronize()
updates = 2 if a.smoke else a.updates
training = core.train_model(model,items['train'],token,device,updates,a.micro_batch,a.grad_accum,
2e-5,.01,a.seed,25,3,.05)
if device.type=='cuda':
training['peak_allocated_gib'] = torch.cuda.max_memory_allocated()/2**30
training['peak_reserved_gib'] = torch.cuda.max_memory_reserved()/2**30
predictions = {s:core.evaluate(model,items[s],token,device,a.eval_batch) for s in ('selection_dev','calibration')}
groups = defaultdict(list)
for r in predictions['calibration']:
groups[r['task']].append(r)
temps = {t: core.fit_metric_temperature([r['logits'] for r in values],[r['label'] for r in values],
n_classes=values[0]['n_classes']) for t,values in groups.items()}
temperature_values = {t:v['temperature'] for t,v in temps.items()}
metrics = {s:{'raw':core.metric_from_records(records),
'calibrated':core.metric_from_records(records,temperature_values)} for s,records in predictions.items()}
if any(not torch.isfinite(torch.tensor(r['logits'])).all() for records in predictions.values() for r in records):
raise FloatingPointError('Non-finite evaluation logits')
checkpoint = a.output_dir/'checkpoint'
core.save_checkpoint(model,token,cfg,checkpoint)
shutil.copytree(rep.root,checkpoint/'representation')
disk_rep = DirectBPE(checkpoint/'representation')
disk_items = make_items(rows['selection_dev'],disk_rep,a.condition,builder_sequence,a.seed)
if disk_items != items['selection_dev']:
raise ValueError('Saved representation changed evaluation IDs or candidate markers')
del model
gc.collect()
if device.type=='cuda':torch.cuda.empty_cache()
reloaded = core.fresh_reload(checkpoint,cfg,builder_model,device)
again = core.evaluate(reloaded,disk_items,token,device,a.eval_batch)
match = len(again)==len(predictions['selection_dev']) and all(
x['id']==y['id'] and len(x['logits'])==len(y['logits']) and
max(abs(l-r) for l,r in zip(x['logits'],y['logits'])) < 1e-5
for x,y in zip(again,predictions['selection_dev']))
if not match:raise ValueError('Checkpoint reload changed logits')
for split,records in predictions.items():
(a.output_dir/f'{split}_predictions.jsonl').write_text(''.join(json.dumps(r)+'\n' for r in records))
summary = {'formal':not a.smoke,'smoke_only':a.smoke,'condition':a.condition,'seed':a.seed,
'no_cpt':True,'test_access':False,'evaluated_splits':['selection_dev','calibration'],
'representation_sha256':digest(rep.root/'metadata.json'),'eligible_id_filter':a.eligible_ids,
'n_rows':{s:len(v) for s,v in rows.items()},'item_stats':item_stats,'training':training,
'trainable_parameters':trainable,'embedding_trainable':True,'evaluation':metrics,
'calibration_temperature':temps,'calibration_temperature_fit_on':'calibration',
'expansion':expansion,'new_embedding_gradient_probe':probes,
'checkpoint':str(checkpoint),'checkpoint_reload_input_ids_match':True,
'checkpoint_reload_logits_match':match,'selection_policy':'final fixed-budget checkpoint'}
(a.output_dir/'summary.json').write_text(json.dumps(summary,indent=2)+'\n')
print(json.dumps(summary,indent=2),flush=True)
if __name__=='__main__':
main()
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