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enable per output token likelihood prediction for evo2 #1057

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Merged
yzhang123 merged 1 commit into from
Aug 25, 2025
Merged

enable per output token likelihood prediction for evo2 #1057

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18 changes: 11 additions & 7 deletions sub-packages/bionemo-evo2/src/bionemo/evo2/run/predict.py
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Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ def parse_args():
)
ap.add_argument(
"--log-prob-collapse-option",
choices=["sum", "mean"],
choices=["sum", "mean", "per_token"],
default="mean",
help="How to collapse the log probabilities across the sequence dimension.",
)
Expand Down Expand Up @@ -160,7 +160,7 @@ def __init__(
self,
*args,
output_log_prob_seqs: bool = False,
log_prob_collapse_option: Literal["sum", "mean"] = "mean",
log_prob_collapse_option: Literal["sum", "mean", "per_token"] = "mean",
**kwargs,
):
"""Initialize the predictor with our needs around computing log probabilities."""
Expand Down Expand Up @@ -195,10 +195,14 @@ def predict_step(self, batch, batch_idx: int | None = None) -> Tensor:
2, # along the vocab dimension...
input_ids.unsqueeze(-1), # using the token ids to index.
).squeeze(-1)
log_prob_seqs = torch.sum(logprobs * batch["loss_mask"][:, 1:].float(), dim=-1)
if self.log_prob_collapse_option == "mean":
log_prob_seqs = log_prob_seqs / (batch["loss_mask"][:, 1:].float().sum(dim=-1) + 1e-8)
return {"log_probs_seqs": log_prob_seqs.cpu(), "seq_idx": batch["seq_idx"].cpu()}
log_prob_per_token = logprobs * batch["loss_mask"][:, 1:].float()
if self.log_prob_collapse_option == "per_token":
return {"log_probs_seqs": log_prob_per_token.cpu(), "seq_idx": batch["seq_idx"].cpu()}
else:
log_prob_seqs = torch.sum(log_prob_per_token, dim=1)
if self.log_prob_collapse_option == "mean":
log_prob_seqs = log_prob_seqs / (batch["loss_mask"][:, 1:].float().sum(dim=-1) + 1e-8)
return {"log_probs_seqs": log_prob_seqs.cpu(), "seq_idx": batch["seq_idx"].cpu()}
else:
# If the user wants to match back to logits, then they will need to do the offsetting logic themselves.
return {
Expand Down Expand Up @@ -504,7 +508,7 @@ def __init__(
config,
tokenizer=None,
output_log_prob_seqs: bool = False,
log_prob_collapse_option: Literal["sum", "mean"] = "mean",
log_prob_collapse_option: Literal["sum", "mean", "per_token"] = "mean",
):
"""Initialize the MambaPredictor, which wraps the mamba model for prediction handling model parallelism.

Expand Down