Passing Inputs Longer Than 512 Tokens After Pretraining a T5 Model: Is It Safe?

Hi,

I have pretrained a T5 model with a maximum window size of 512.
Here is the code:

max_length = 512
config = T5Config(
vocab_size=len(tokenizer),
d_model=768,
d_ff=3072,
num_layers=12,
num_heads=12,
dropout_rate=0.1,
pad_token_id=tokenizer.pad_token_id,
eos_token_id=tokenizer.eos_token_id,
decoder_start_token_id=tokenizer.pad_token_id,
)

expanded_inputs_length, targets_length = compute_input_and_target_lengths(
inputs_length=max_length,
noise_density=args.mlm_probability,
mean_noise_span_length=args.mean_noise_span_length,
)

target_length = 114 and expanded_input_length = 568

data_collator = DataCollatorForT5MLM(
tokenizer=tokenizer,
noise_density=args.mlm_probability,
mean_noise_span_length=args.mean_noise_span_length,
input_length=max_length,
target_length=targets_length,
pad_token_id=model.config.pad_token_id,
decoder_start_token_id=model.config.decoder_start_token_id,
)

I came across this comment in another post:

“The 512 in T5’s config is a bit misleading since it is not a hard limit. T5 was mostly trained using 512 input tokens, but thanks to its use of relative attention it can handle much longer sequences. This means that if you increase the input length, you won’t get an index out of positional embedding matrix error (as you would with absolute position embeddings). Instead, the limit is your GPU memory, and you may eventually get an out-of-memory CUDA error.

T5 uses standard self-attention, so memory consumption scales quadratically (n²) with the input length. Therefore, it’s important to use padding/truncation and group batches by similar lengths.”

Source: Does T5 truncate input longer than 512 internally?

⸻

My question:
Since I pretrained the model with a maximum input length of 512, does this mean I can still pass longer sequences (e.g., 1024 tokens) during fine-tuning and inference, as long as the GPU memory allows it?

Seems yes.


Yes: you can feed your 512-pretrained T5 inputs of length 1024 (and more) at fine-tuning and inference time, as long as:

  • your tokenizer + collator + Trainer are configured to actually produce 1024-token sequences, and
  • your GPU memory can handle the quadratic attention cost.

It will run without positional-embedding errors. The only real caveat is that 1024 is longer than what you pretrained on, so it’s “length extrapolation”: it’s safe but may change quality, and may benefit from some extra training at that length.

Below is the reasoning, step-by-step, tied to your exact setup.


1. Why T5 doesn’t have a hard 512-token limit

1.1 Absolute vs relative positions

Many models (BERT, GPT-2, classic BART) use an absolute positional embedding matrix with a fixed size max_position_embeddings. If you go past that, you get an “index out of range in positional embedding matrix” error.

T5 is different:

  • It uses relative positional bias via a small bucketed table:
    parameters like relative_attention_num_buckets and relative_attention_max_distance define how query–key distance is mapped to a bucket, and each bucket has a learned scalar bias. (Hugging Face)
  • Distances larger than relative_attention_max_distance (typically 128) are all mapped into one “far” bucket.

Because of that:

  • There is no absolute position embedding indexed 0…511 which would overflow at 512+.
  • The attention bias for each (query position, key position) pair is computed on the fly from the distance; that code works for any sequence length the GPU can hold. (GitLab)

The Hugging Face forum thread you quoted says exactly this: T5 was trained mostly with 512-token inputs, but “thanks to its use of relative attention it can handle much longer sequences; the real limit is GPU memory.” (Hugging Face Forums)

1.2 So what did “512” do in practice for you?

In your code, 512 comes from:

  • max_length = 512
  • DataCollatorForT5MLM(... input_length=max_length, ...)

So:

  • Architecturally, the model does not know “512 is my max”; there’s no max_position_embeddings=512 being enforced for T5.

  • The 512 cap is enforced by your data pipeline:

    • the collator produces encoder inputs of length 512;
    • expanded_inputs_length=568 is just internal math for span corruption; it shrinks back to 512 before going into the model.

Conclusion:

  • 512 is a training window size, not a hard architectural ceiling.
  • The model’s weights have only seen sequences up to 512 so far, but the machinery can process longer sequences.

2. Will 1024-token inputs work technically?

Yes.

2.1 No positional-embedding crash

For Hugging Face’s T5ForConditionalGeneration / T5Model:

  • The forward pass accepts input_ids shaped [batch_size, seq_len] with arbitrary seq_len.
  • Relative attention biases are computed for that seq_len Ă— seq_len shape; there’s no index into a [max_len, dim] position-embedding table that would overflow at >512. (GitLab)
  • HF maintainers explicitly confirm in that “Does T5 truncate input longer than 512 internally?” thread that T5 does not internally truncate or error at >512; the limit is memory. (Hugging Face Forums)

So if you construct input_ids with length 1024, the model will run.

2.2 The real constraint: GPU memory and n2 attention

T5 uses standard full self-attention:

  • Every encoder layer builds an attention matrix of shape seq_len Ă— seq_len.
  • Memory and compute therefore scale as O(n2) in sequence length. (Hugging Face Forums)

If you go from 512 → 1024:

  • The attention matrix becomes 4Ă— larger.
  • Roughly, memory and time for the attention part also grow by ~4Ă— (plus some overhead).

Practically, when you move to 1024:

  • You’ll almost certainly need to reduce batch size.

  • You should strongly consider:

    • mixed precision (fp16/bf16),
    • gradient checkpointing,
    • and length-based batching (group sequences of similar lengths, to avoid padding everything to 1024). (Hugging Face)

3. How to actually get 1024 tokens through HF today

One subtle part is the tooling: recent HF versions changed some defaults around tokenizers and truncation. If you don’t wire things explicitly, you may think you are using 1024 but still be capped at 512 (or something else) by the tokenizer/collator.

3.1 Tokenizer: always set max_length + truncation

The tokenizer controls how long your input sequences are before they reach the model.

  • Padding/truncation docs show that padding and truncation combine with max_length to produce fixed-size batches. (Hugging Face)
  • The tokenizer API docs say: if max_length is not set, it uses an internal “predefined model maximum length” if the model specifies one; if not, no max-length truncation happens. (Hugging Face)

Because you have a custom T5 config/tokenizer, that “model max length” may be missing or not set to 512. You should therefore always be explicit:

enc = tokenizer(
    texts,
    padding="max_length",
    truncation=True,
    max_length=1024,      # <- your new window size
    return_tensors="pt",
)
assert enc.input_ids.shape[1] == 1024

Key point:

  • If you don’t pass max_length=1024 (or don’t set tokenizer.model_max_length = 1024 yourself), you can’t rely on the tokenizer using 1024 for you; it might stay at some default 512, or use no truncation at all. (Hugging Face)

3.2 Your pretraining collator: bump input_length to 1024

Your current collator:

data_collator = DataCollatorForT5MLM(
    tokenizer=tokenizer,
    noise_density=args.mlm_probability,
    mean_noise_span_length=args.mean_noise_span_length,
    input_length=max_length,      # 512 now
    target_length=targets_length,
    pad_token_id=model.config.pad_token_id,
    decoder_start_token_id=model.config.decoder_start_token_id,
)

To continue pretraining or fine-tuning at 1024:

  1. Recompute expanded_inputs_length, targets_length with inputs_length=1024.
  2. Recreate the collator with input_length=1024.

That way:

  • The encoder sees inputs of length 1024, not 512.
  • The decoder still sees span-corrupted targets of whatever target_length your helper calculates for 1024.

If you keep input_length=512, the collator will keep cropping/padding back to 512 even if the tokenizer produced 1024-token sequences.

3.3 Trainer / generation: don’t forget output lengths

Two separate “lengths” to care about:

  1. Encoder input length: controlled via max_length at tokenization / input_length in your collator.
  2. Decoder output length: controlled via max_new_tokens or max_length in model.generate.

There’s a common gotcha where outputs look “oddly short” because generate defaults are small; StackOverflow answers show that you need to raise max_length in generate explicitly when you want longer outputs. (Stack Overflow)

Example for generation:

outputs = model.generate(
    **enc,
    max_new_tokens=128,  # or max_length for total sequence length
)

This generation limit is independent of your encoder input length (512 vs 1024).


4. What changes semantically when you go from 512 → 1024?

T5’s relative positional bias scheme:

  • Uses ~32 buckets (relative_attention_num_buckets) to encode relative distances.
  • Distances are exact for small offsets and merged into logarithmic ranges up to relative_attention_max_distance (usually 128); beyond that, all distances share the final “far” bucket. (Hugging Face)

In your training at 512:

  • The model has already seen:

    • many tokens with distances ≤128, using fine-grained buckets;
    • many tokens with distances >128, all mapped to that same “far” bucket.

When you switch to 1024:

  • No new distance buckets are introduced; farther tokens still land in the same “far” bucket.
  • From the perspective of the relative position module, 1024 isn’t qualitatively new; it just has more “far” relationships.

However, length extrapolation work shows that:

  • Even with relatively robust positional encodings like T5’s RPE, performance can degrade as you go far beyond the training length, because the model never learned how to use very distant context in that regime. (arXiv)

So:

  • 512 → 1024 is usually moderate extrapolation (reasonably safe).
  • 512 → 4096+ is aggressive and often needs special architectures like LongT5 (which modifies attention to handle 4k–16k efficiently). (Hugging Face)

5. Best-practice strategies for your situation

5.1 If you “just want to try 1024”

This is often enough if you mainly want more context, and your tasks are not hyper-sensitive to the very longest spans.

  1. Change tokenizer + collator to 1024 (as above).
  2. Reduce batch size and enable memory-saving tricks.
  3. Fine-tune directly on your downstream task with 1024 inputs.

You’ll likely see:

  • No crashes.
  • Usable performance, often close to 512-based performance, sometimes better for tasks that genuinely benefit from extra context.

5.2 If long context is core: do a short “continued pretraining”

If long range is central (e.g. long-doc summarization, retrieval-augmented generation with big concatenated passages):

  1. Run continued pretraining (same span-corruption objective) at longer lengths, with your existing weights:

    • e.g. a few thousand steps at 768, then at 1024.
  2. Use a lower LR than initial pretraining (you’re refining, not starting from scratch).

  3. Then fine-tune on your task at 1024.

This is analogous to context-extension techniques for other LLMs: a small amount of training at the new length helps the model adapt its attention patterns to the bigger window. (arXiv)

5.3 When to switch to LongT5 or other long-context models

If you start needing 4k–16k inputs consistently, vanilla T5’s full attention becomes:

  • Very expensive (n2).
  • Less effective, because everything beyond 128 positions is in that single “far” bucket.

LongT5 re-architects attention (local + transient-global) to handle up to 16k tokens more efficiently and comes with configs that explicitly expect long contexts. (Hugging Face)

For 1024, you are still firmly in “vanilla T5 is okay” territory; for 8k, something like LongT5 is much more attractive.


6. Direct answer to your question

Since I pretrained the model with a maximum input length of 512, does this mean I can still pass longer sequences (e.g., 1024 tokens) during fine-tuning and inference, as long as the GPU memory allows it?

Summarizing:

  1. Yes, you can.

    • T5’s relative positional attention does not impose a hard 512 limit.
    • Feeding 1024 tokens is architecturally safe; the main limit is GPU memory. (Hugging Face Forums)
  2. You must configure HF to actually use 1024.

    • Set max_length=1024, truncation=True in the tokenizer. (Hugging Face)
    • Recreate your DataCollatorForT5MLM with input_length=1024 and recomputed target_length.
    • Set appropriate max lengths in your Trainer / generation code.
  3. Quality-wise, 1024 is length extrapolation, not magic.

    • T5’s RPE tends to generalize beyond training length reasonably well, but performance can still change or degrade as you go longer. (arXiv)
    • For important long-context use cases, a bit of continued pretraining (or at least fine-tuning) at 1024 is recommended.

So as long as you handle the tokenizer/collator/Trainer lengths explicitly and watch your GPU memory, you are free to use 1024-token inputs with your 512-pretrained T5.

1 Like

Thank you so much for such a detailed answer. If I have understood correctly, I don’t need to change anything in my pretraining script if I don’t want to set a max window size of 1024 for the pretrained model. The only change I need to make in my fine-tuning script is inside the tokenize function.

def tokenize_function(examples,max_length=1024):

        """Tokenize inputs and targets"""

        

        # Tokenize inputs

        inputs = []

        targets = []

        

        # We'll use a single loop to find the correct pairs

        # Note: the dataset is already mixed with both directions

        for i in range(len(examples['genome'])):

            dna_seq = examples['genome'][i]

            prot_seq = examples['protein'][i]

            

            # Check for the DNA2Prot token in the DNA sequence

            if args.mode == "DNA2Prot":

                inputs.append(control_tokens[0]+" "+preprocess_kmer(dna_seq))

                targets.append(preprocess_kmer(prot_seq))

        tokenized_ex = tokenizer(

            inputs,

            text_target=targets,

            max_length=max_length,

            truncation=True,

            padding='max_length'

        )

         return tokenized_ex

Everything else stays as it is.

collator = DataCollatorForSeq2Seq(tokenizer, model=model, pad_to_multiple_of=8)
training_args = Seq2SeqTrainingArguments(

        output_dir=f"./finetuning/model/{args.mode}/{output_path}",

        predict_with_generate=True,

        per_device_train_batch_size=args.batch_size,

        per_device_eval_batch_size=args.batch_size//2,

        weight_decay=0.01,

        eval_strategy="steps",      # Evaluate every N steps

        save_strategy="steps",      # Save every N steps

        logging_strategy="steps",

        save_steps=step_count,

        logging_steps=step_count,

        eval_steps = step_count,

        max_steps=step_count*args.e,

        load_best_model_at_end=True,

        metric_for_best_model=args.validation,

        save_total_limit=2,

        report_to="tensorboard",

        logging_dir=f"./finetuning/logs/{args.mode}/{output_path}",

        gradient_checkpointing=True,

        fp16=True,

        gradient_accumulation_steps=2,

        greater_is_better=True,

    )
1 Like

Yeah.


Your understanding is essentially correct for encoder input length. You do not need to change your pretraining script or model config. To use a 1024-token window during fine-tuning:

  • You only need to ensure that your tokenization step produces sequences with max_length=1024 and truncation=True. (Hugging Face)
  • DataCollatorForSeq2Seq and Seq2SeqTrainingArguments do not impose an additional 512-token limit by themselves; they will work with whatever lengths come from tokenization (subject to GPU memory). (Kaggle)

Below is a more detailed breakdown, including a small checklist and a couple of “nice to have” tweaks.


1. Pretraining script and model config

You do not need to modify:

  • The pretraining script that used input_length=512 in DataCollatorForT5MLM.
  • The T5Config you created (no need to add n_positions or anything similar).

Reason:

  • T5 uses relative positional bias, not a fixed [0..max_pos] embedding table, so there is no architectural 512-token cap to “resize” or re-pretrain.
  • 512 was just the training window enforced by your pretraining collator, not a structural limit in the model.
  • At fine-tuning time, you are free to feed longer sequences as long as the rest of the pipeline (tokenizer/collator) produces them.

So your pretraining code can stay as-is.


2. Fine-tuning: what you changed and why it’s enough

Your tokenize function:

def tokenize_function(examples, max_length=1024):
    """Tokenize inputs and targets"""
    inputs = []
    targets = []

    for i in range(len(examples['genome'])):
        dna_seq = examples['genome'][i]
        prot_seq = examples['protein'][i]

        if args.mode == "DNA2Prot":
            inputs.append(control_tokens[0] + " " + preprocess_kmer(dna_seq))
            targets.append(preprocess_kmer(prot_seq))

    tokenized_ex = tokenizer(
        inputs,
        text_target=targets,
        max_length=max_length,
        truncation=True,
        padding="max_length",
    )
    return tokenized_ex

Key points:

  1. max_length=max_length + truncation=True means both inputs and targets are truncated/padded to exactly max_length tokens. This is the documented way to enforce a fixed window with Hugging Face tokenizers. (Hugging Face)

  2. Because you pass max_length=1024 explicitly, you override any default model_max_length the tokenizer might have. Even if your tokenizer had no predefined max length (common for custom models), providing max_length directly is supported and recommended. (Hugging Face)

So from the tokenizer’s perspective, you have correctly “switched” the encoder window from 512 to 1024 for fine-tuning.


3. Data collator and trainer: why they don’t need changes

You have:

collator = DataCollatorForSeq2Seq(tokenizer, model=model, pad_to_multiple_of=8)

and

training_args = Seq2SeqTrainingArguments(
    # ...
    predict_with_generate=True,
    per_device_train_batch_size=args.batch_size,
    per_device_eval_batch_size=args.batch_size//2,
    # ...
    gradient_checkpointing=True,
    fp16=True,
    gradient_accumulation_steps=2,
    # ...
)

3.1 DataCollatorForSeq2Seq

DataCollatorForSeq2Seq:

  • Takes already-tokenized input_ids and labels from your dataset.
  • Dynamically pads them to the length of the longest sequence in the batch (or to pad_to_multiple_of if specified), but does not re-apply any max_length truncation of its own. (Kaggle)

Implication:

  • As long as your tokenize function outputs 1024-length sequences, the collator will simply pad to 1024 (or the longest in batch) and respect that length.
  • You do not need to pass a separate max_length into the collator for this.

3.2 Seq2SeqTrainingArguments

Seq2SeqTrainingArguments mainly cares about:

  • Batch sizes, gradient accumulation, fp16/bf16, gradient checkpointing, etc.
  • Generation behavior during evaluation/prediction: predict_with_generate=True makes the trainer call model.generate(); the maximum output length is controlled via generation_max_length or the model’s generation config, not via your tokenize max_length. (Hugging Face)

So:

  • Nothing in Seq2SeqTrainingArguments is silently capping your encoder input at 512.
  • You don’t have to modify training_args to “enable 1024”, at least for the encoder side.

The only caveat is:

  • If you want longer decoder outputs than whatever the default generation_max_length / config allows, you may want to set generation_max_length explicitly (e.g., 256 or 512), but that is independent of the encoder window size.

4. Two optional improvements / checks

Your current plan is “only change max_length in tokenization”. That is enough to get 1024-token inputs into the encoder, but there are two practical things worth considering.

4.1 Separate max length for input and target

Right now you pass the same max_length to both inputs and text_target. For many seq2seq tasks, it is common to separate them:

  • max_source_length (e.g. 1024) for the encoder input.
  • max_target_length (often much smaller, e.g. 256) for the decoder target. (Educative)

For example:

def tokenize_function(examples, max_source_length=1024, max_target_length=256):
    inputs, targets = [], []
    for i in range(len(examples["genome"])):
        dna_seq = examples["genome"][i]
        prot_seq = examples["protein"][i]
        if args.mode == "DNA2Prot":
            inputs.append(control_tokens[0] + " " + preprocess_kmer(dna_seq))
            targets.append(preprocess_kmer(prot_seq))

    model_inputs = tokenizer(
        inputs,
        max_length=max_source_length,
        truncation=True,
        padding="max_length",
    )

    with tokenizer.as_target_tokenizer():
        labels = tokenizer(
            targets,
            max_length=max_target_length,
            truncation=True,
            padding="max_length",
        )

    model_inputs["labels"] = labels["input_ids"]
    return model_inputs

This is not required for “making 1024 work”, but it:

  • Avoids wasting memory on unnecessarily long label sequences.
  • Reduces the chance of target truncation if protein sequences are known to be much shorter.

4.2 Batch size and memory

When you go from 512 → 1024:

  • Attention cost grows ~4Ă—; GPU memory usage will rise accordingly. (Hugging Face)

You already set:

  • fp16=True and gradient_checkpointing=True, which are good for memory.

You should still be prepared to:

  • Reduce args.batch_size if you hit CUDA OOMs.
  • Possibly increase gradient_accumulation_steps to keep the same effective batch size.

No code change for lengths, but important for training stability.


5. Summary relative to your exact question

“If I have understood correctly, I don’t need to change anything in my pretraining script if I don’t want to set a max window size of 1024 for the pretrained model. The only change I need to make in my fine-tuning script is inside the tokenize function. Everything else stays as it is.”

For encoder input window size, this understanding is correct:

  • You do not need to change the pretraining script or model config to “declare” a 1024 max window for T5.
  • Setting max_length=1024 and truncation=True in your fine-tuning tokenization is enough to feed 1024-token sequences into the model. (Hugging Face)
  • DataCollatorForSeq2Seq and Seq2SeqTrainingArguments will respect those longer sequences; there is no hidden 512-token cap there. (Kaggle)

Additional, optional steps that are not required but often useful:

  • Use separate max_source_length / max_target_length for inputs and labels.
  • Set generation_max_length if you need longer decoder outputs at evaluation.
  • Adjust batch size and memory settings for 1024-length training.

If you do those checks and the training fits in GPU memory, you are correctly running fine-tuning with a 1024-token window, even though the model was originally pretrained with 512-token sequences.

1 Like