# /// script # requires-python = ">=3.10" # dependencies = [ # "datasets", # "sentence-transformers>=5.0.0", # "torch", # "numpy", # "pillow", # "einops", # "huggingface-hub", # ] # /// """ Generate embeddings for a Hugging Face dataset (text OR images) with sentence-transformers, and push the result back to the Hub as a new dataset with an `embeddings` column. This is the simple, ergonomic default. It runs as one command on the bare uv image, on CPU or any GPU flavor. For maximum throughput on large *decoder* embedding models (e.g. Qwen3-Embedding), see the vLLM variant; to get a searchable vector index as a Hub dataset, see the Lance variant. PROMPTS (retrieval correctness — read this): Many embedding models need a DIFFERENT prefix/instruction for documents vs queries, and getting it wrong silently degrades retrieval. This script embeds a *document corpus* by default, via sentence-transformers' native encode_document()/encode_query() (which also route Router models by task), picking the right document convention for you: 1. the model's REGISTERED prompt if it ships one (e.g. Qwen3-Embedding) — selected natively by encode_document/encode_query, else 2. a small built-in table of well-known families (e5, nomic, bge), else 3. no prefix. Heads-up: current sentence-transformers injects a placeholder prompts dict {"query": "", "document": ""} even for models that register NOTHING — so e5 ("passage: "), nomic ("search_document: ") etc. look prompt-less via `.prompts`; their real prefixes live only in the model card. The built-in table handles that. Override with --prompt '' or --prompt-name ; embed a query set with --query-mode; force no prefix with --prompt ''. The chosen prompt is logged and recorded in the dataset card. Benchmarks (20k rows, seq-cap 512): all-MiniLM-L6-v2 ~900 rows/s on an L4 (~$0.24/1M rows); bge-base-en-v1.5 ~120 rows/s. L4 is the cheapest flavor for these encoder models. Examples: # Text (default). Document convention auto-picked. hf jobs uv run --flavor l4x1 -s HF_TOKEN generate-embeddings.py \\ stanfordnlp/imdb your-name/imdb-embeddings \\ --column text --model sentence-transformers/all-MiniLM-L6-v2 # e5: docs auto-get "passage: ". (--prompt 'passage: ' would be the explicit form.) hf jobs uv run --flavor l4x1 -s HF_TOKEN generate-embeddings.py \\ stanfordnlp/imdb your-name/imdb-e5 --model intfloat/multilingual-e5-large # Images (CLIP) — prompts don't apply. hf jobs uv run --flavor l4x1 -s HF_TOKEN generate-embeddings.py \\ your-name/photos your-name/photos-embeddings \\ --modality image --column image --model clip-ViT-B-32 # Test on a small slice first, keep the output private hf jobs uv run --flavor l4x1 -s HF_TOKEN generate-embeddings.py \\ stanfordnlp/imdb your-name/imdb-emb --max-samples 100 --private """ import argparse import logging import os import re import sys import time logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s") logger = logging.getLogger("generate-embeddings") def find_batch_size(model, sample, normalize, candidates=(32, 64, 128, 256)): """Probe for the fastest batch that fits (used by --batch-size auto). Throughput is NOT monotonic in batch size, so we time a few on a warmup sample and keep the fastest that doesn't OOM. Why bigger isn't better: for text, larger batches pad to the longest member + add overhead; for images, the ViT forward already saturates the GPU by ~batch 32. Works for text and images.""" import time import torch warm = sample[: min(1024, len(sample))] try: # one untimed warmup so cudnn autotune doesn't penalise the first probe model.encode(warm[:32], batch_size=32, show_progress_bar=False, convert_to_numpy=True, normalize_embeddings=normalize) except Exception: pass best_bs, best_rps = candidates[0], 0.0 for bs in candidates: try: if torch.cuda.is_available(): torch.cuda.empty_cache() torch.cuda.synchronize() t = time.perf_counter() model.encode(warm, batch_size=bs, show_progress_bar=False, convert_to_numpy=True, normalize_embeddings=normalize) if torch.cuda.is_available(): torch.cuda.synchronize() rps = len(warm) / (time.perf_counter() - t) logger.info(f" auto-batch probe bs={bs}: {rps:.0f} rows/s") if rps > best_rps: best_rps, best_bs = rps, bs except RuntimeError as e: if "out of memory" in str(e).lower(): logger.info(f" auto-batch bs={bs} OOM → stopping probe") if torch.cuda.is_available(): torch.cuda.empty_cache() break raise logger.info(f"auto-batch chose bs={best_bs} ({best_rps:.0f} rows/s on warmup)") return best_bs def known_convention(model_id): """Best-effort (query_prefix, doc_prefix) for common families whose convention is documented in the model card but NOT registered in config_sentence_transformers.json. Returns None if unknown. Overridable with --prompt / --no-auto-prompt. Verified 2026-07-03 on HF Jobs: of e5 / nomic / bge-en / bge-m3 / Qwen3-Embedding, only Qwen3-Embedding registers real ST prompts; the rest ship none and rely on manual prefixes. """ m = model_id.lower() # Instruction-style embedders (e5-*-instruct, gte-Qwen, ...): prefer the model's REGISTERED # prompt or an explicit --prompt; don't guess a literal prefix. if "instruct" in m: return None if "nomic-embed-text" in m: return ("search_query: ", "search_document: ") if "bge-m3" in m: # bge-m3 uses no prompts return ("", "") # e5 family (e5-base/large/small, multilingual-e5-*), boundaried so e.g. "table5" or a # model with "e5" mid-word can't silently pick up "query:/passage:" prefixes. if re.search(r"(^|[/_-])e5([_-]|$)", m): return ("query: ", "passage: ") if "bge" in m and "-en" in m: # English bge retrieval: query instruction, docs raw return ("Represent this sentence for searching relevant passages: ", "") return None def resolve_prompt(model, model_id, is_query, args): """Decide the EXPLICIT prefix to pass to encode_query()/encode_document(), or None to let the native method choose. sentence-transformers' encode_query/encode_document already select the model's REGISTERED query/document prompt and set the Router task — we lean on that, and only supply a prefix ourselves for (a) explicit --prompt/--prompt-name, (b) the known-family table covering models that register nothing (e5, nomic, bge-en — their prefixes live only in the model card, so the native fallback would silently apply NO prefix).""" registered = dict(getattr(model, "prompts", {}) or {}) # Current sentence-transformers injects a placeholder {"query":"","document":""} for models # with no config prompts; only non-empty values are real conventions. real = {k: v for k, v in registered.items() if v} logger.info(f"Registered prompts: {registered} · real (non-empty): {real or 'none'} · " f"default_prompt_name={getattr(model, 'default_prompt_name', None)}") side = "query" if is_query else "document" if args.prompt is not None: # includes --prompt '' to force no prefix logger.info(f"Prompt: raw --prompt → {args.prompt!r}") return args.prompt if args.prompt_name: if args.prompt_name not in registered: logger.error(f"--prompt-name {args.prompt_name!r} not registered ({list(registered)}); " f"use --prompt '' instead.") sys.exit(1) logger.info(f"Prompt: registered prompt_name={args.prompt_name!r} → {registered[args.prompt_name]!r}") return registered[args.prompt_name] native_keys = ("query",) if is_query else ("document", "passage", "corpus") if any(real.get(k) for k in native_keys): # Model ships a real prompt for this side (e.g. Qwen3 query) → encode_query/encode_document # selects it natively (and routes Router models by task). logger.info(f"Prompt: model-registered — selected natively by encode_{side}()") return None kc = known_convention(model_id) if kc is not None: chosen = kc[0] if is_query else kc[1] if args.no_auto_prompt: if chosen: logger.warning(f"--no-auto-prompt set: NOT applying the known {side} prefix {chosen!r} for " f"{model_id}. Retrieval may degrade unless you pass --prompt.") return "" logger.info(f"Prompt: known-family {side} prefix → {chosen!r} (override with --prompt)" if chosen else f"Prompt: known-family → no {side} prefix needed") return chosen logger.info(f"Prompt: none registered or known for {model_id} — encode_{side}() applies no prefix. " f"If it's a retrieval model needing a query/document prefix, pass --prompt.") return None def sniff_token_lengths(model, texts, max_seq_len, sample=512): """Tokenize a sample to report the token-length distribution + how much --max-seq-len truncates, and return the median length (used to pick the auto-batch candidate range: short texts under-use the GPU at small batch, long texts waste compute on padding). Text only; returns None on failure.""" try: tok = model.tokenizer except Exception: return None s = texts[: min(sample, len(texts))] lens = sorted(len(tok.encode(t, add_special_tokens=True)) for t in s) n = len(lens) if not n: return None median, p90, mx = lens[n // 2], lens[min(n - 1, int(n * 0.9))], lens[-1] pct_over = 100 * sum(1 for L in lens if L > max_seq_len) / n note = (f" → {pct_over:.0f}% exceed --max-seq-len {max_seq_len} and are truncated " f"(raise it to keep more, at higher cost/slower)" if pct_over >= 5 else f" (all within --max-seq-len {max_seq_len})") logger.info(f"Token lengths (sample {n}): median {median}, p90 {p90}, max {mx}{note}") return median def main(): p = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) p.add_argument("input_dataset", help="Input dataset ID on the Hugging Face Hub") p.add_argument("output_dataset", help="Output dataset ID to create on the Hub") p.add_argument("--model", default="sentence-transformers/all-MiniLM-L6-v2", help="sentence-transformers model (text or CLIP image model)") p.add_argument("--modality", choices=["text", "image"], default="text") p.add_argument("--column", default="text", help="Input column (text string, or image)") p.add_argument("--output-column", default="embeddings") p.add_argument("--config", default=None, help="Dataset config name (e.g. wikipedia needs one)") p.add_argument("--split", default="train") p.add_argument("--max-samples", type=int, default=None, help="Limit rows (for testing)") p.add_argument("--batch-size", default="auto", help="'auto' probes for the fastest batch that fits, or pass an int") p.add_argument("--prompt", default=None, help="Raw prefix to prepend to every text (e.g. 'passage: '). Highest precedence. " "Use --prompt '' to force NO prefix.") p.add_argument("--prompt-name", default=None, help="Name of a prompt REGISTERED by the model (e.g. 'query'); errors if not registered.") p.add_argument("--query-mode", action="store_true", help="Embed inputs as QUERIES, not documents (flips the auto-picked convention).") p.add_argument("--no-auto-prompt", action="store_true", help="Disable the built-in known-family prefix table (still honours registered prompts).") p.add_argument("--max-seq-len", type=int, default=512, help="Truncate text to this many tokens (predictable cost; RAG-typical)") p.add_argument("--normalize", action="store_true", default=True) p.add_argument("--no-normalize", dest="normalize", action="store_false") p.add_argument("--private", action="store_true", help="Make the output dataset private") args = p.parse_args() import torch from datasets import load_dataset from huggingface_hub import DatasetCard, login from sentence_transformers import SentenceTransformer token = os.environ.get("HF_TOKEN") if token: login(token=token) if not torch.cuda.is_available(): logger.warning("No CUDA — running on CPU (much slower). Prefer a GPU flavor, e.g. --flavor l4x1.") logger.info(f"Loading {args.input_dataset} [{args.split}]") ds = (load_dataset(args.input_dataset, args.config, split=args.split) if args.config else load_dataset(args.input_dataset, split=args.split)) if args.column not in ds.column_names: logger.error(f"Column {args.column!r} not found. Available: {ds.column_names}") sys.exit(1) if args.output_column in ds.column_names: logger.error(f"Output column {args.output_column!r} already exists — choose another --output-column.") sys.exit(1) if args.max_samples: ds = ds.select(range(min(args.max_samples, len(ds)))) logger.info(f"{len(ds)} rows; modality={args.modality}") device = "cuda" if torch.cuda.is_available() else "cpu" model = SentenceTransformer(args.model, device=device, trust_remote_code=True) if args.modality == "text" and getattr(model, "max_seq_length", None): model.max_seq_length = min(model.max_seq_length, args.max_seq_len) dim = model.get_sentence_embedding_dimension() logger.info(f"Model {args.model} on {device}; dim={dim}") # Prompt handling — many retrieval models need a query vs document/passage prefix (text only). prompt_str = None # None = let encode_query/encode_document choose natively if args.modality == "text": prompt_str = resolve_prompt(model, args.model, is_query=args.query_mode, args=args) items = [t if isinstance(t, str) and t.strip() else " " for t in ds[args.column]] else: if args.prompt or args.prompt_name: logger.warning("--prompt/--prompt-name ignored for image modality.") items = [im.convert("RGB") if hasattr(im, "convert") else im for im in ds[args.column]] median_tok = sniff_token_lengths(model, items, args.max_seq_len) if args.modality == "text" else None if str(args.batch_size).lower() == "auto": # Pick the probe range from the data shape. Images: the ViT forward saturates the GPU by # ~batch 32, so bigger only adds memory — probe low. Text: short texts under-use the GPU at # small batch (probe bigger); long texts pad-waste at big batch (stay modest). Probe verifies. if args.modality == "image": candidates = (32, 64, 128) elif median_tok is None or median_tok >= 256: candidates = (32, 64, 128, 256) elif median_tok >= 64: candidates = (64, 128, 256, 512) else: candidates = (128, 256, 512, 1024) logger.info(f"Finding batch size (--batch-size auto; candidates {candidates})...") batch_size = find_batch_size(model, items, args.normalize, candidates=candidates) else: batch_size = int(args.batch_size) # Text goes through encode_query/encode_document (native registered-prompt selection + Router # task routing); our resolved prefix, when not None, overrides via prompt=. Images use encode(). if args.modality == "text": encode_fn = model.encode_query if args.query_mode else model.encode_document encode_kwargs = {"prompt": prompt_str} if prompt_str is not None else {} else: encode_fn = model.encode encode_kwargs = {} t0 = time.perf_counter() emb = encode_fn(items, batch_size=batch_size, show_progress_bar=True, convert_to_numpy=True, normalize_embeddings=args.normalize, **encode_kwargs) secs = time.perf_counter() - t0 logger.info(f"Embedded {len(items)} in {secs:.1f}s ({len(items)/secs:.0f} rows/s), dim={dim}") ds = ds.add_column(args.output_column, [e.tolist() for e in emb]) # For the card: record the effective prefix (explicit, else the model's registered one). side_keys = ("query",) if args.query_mode else ("document", "passage", "corpus") effective = prompt_str if prompt_str is not None else next( (v for k in side_keys if (v := (getattr(model, "prompts", {}) or {}).get(k))), "") prompt_line = f"`{effective}`" if effective else "(none)" card = DatasetCard( f"# {args.output_dataset}\n\n" f"Embeddings of [`{args.input_dataset}`](https://huggingface.co/datasets/{args.input_dataset}) " f"column `{args.column}`.\n\n" f"- Model: [`{args.model}`](https://huggingface.co/{args.model}) (dim {dim})\n" f"- Column: `{args.output_column}` · normalized: {args.normalize}\n" f"- Prompt prepended ({'query' if args.query_mode else 'document'} side): {prompt_line}\n\n" f"Produced on Hugging Face Jobs with `uv-scripts/embeddings/generate-embeddings.py`.\n" ) # Retry the push with an XET-disable fallback: a transient upload failure here would # otherwise lose the whole (paid) embedding run. logger.info(f"Pushing to {args.output_dataset} (private={args.private})") max_retries = 3 for attempt in range(1, max_retries + 1): try: if attempt > 1: logger.warning("Disabling XET (fallback to HTTP upload)") os.environ["HF_HUB_DISABLE_XET"] = "1" ds.push_to_hub(args.output_dataset, private=args.private) break except Exception as e: logger.error(f"Upload attempt {attempt}/{max_retries} failed: {e}") if attempt < max_retries: delay = 30 * (2 ** (attempt - 1)) logger.info(f"Retrying in {delay}s...") time.sleep(delay) else: logger.error("All upload attempts failed. Results are lost.") sys.exit(1) try: card.push_to_hub(args.output_dataset, repo_type="dataset") except Exception as e: logger.warning(f"card push skipped: {e}") logger.info(f"✅ https://huggingface.co/datasets/{args.output_dataset}") if __name__ == "__main__": main()