Borzoi Track Activity

License: Borzoi uses Apache-2.0 for code and CC-BY-4.0 for model weights and may require explicit attribution when utilized. Please refer to the code license and model weights license for full terms.

This constraint is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.

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evo-design/proto-language/proto_language/constraint/sequence_annotation/borzoi_track_activity_constraint.py

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@article{linder2025borzoi,
  title={Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation},
  author={Linder, Johannes and Srivastava, Divyanshi and Yuan, Han and Agarwal, Vikram and Kelley, David R},
  journal={Nature Genetics},
  volume={57},
  number={4},
  pages={949--961},
  year={2025},
  publisher={Nature Publishing Group},
  doi={10.1038/s41588-024-02053-6}
}

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Constraint contributors

Score target proposals for selected Borzoi output tracks.

API Reference

ConfigBorzoiTrackActivityConfig Source

Configuration for Borzoi track-activity scoring.

enum

default:"human"

Borzoi species head to use: human or mouse.Options: human, mouse

List[integer]

default:"[0]"

Borzoi output track IDs to average before scoring.

array

Optional target-relative intervals to score. If omitted, scores the full target segment.

enum

default:"maximize"

Whether high activity or low activity is preferred.Options: maximize, minimize

number

default:"200.0"

Activity value treated as saturating success for the objective.

enum

default:"mean"

How to combine Borzoi replicate signals.Options: mean, min, std, lcb

string

default:"cuda"

CUDA device for Borzoi inference.

integer

default:"1"

Candidate sequences per Borzoi model batch.

integer

default:"0"

Leading target bases to ignore before Borzoi scoring.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import borzoi_track_activity_constraint, BorzoiTrackActivityConfig

constraint = Constraint(
    inputs=[segment],
    function=borzoi_track_activity_constraint,
    function_config=BorzoiTrackActivityConfig(
        # Configure parameters here
    ),
)

scores = constraint.evaluate()

Metadata

Property	Value
Key	`borzoi-track-activity`
Function	`borzoi_track_activity_constraint`
Category	`sequence_annotation`
Mode	`discrete`
Uses GPU	`True`
Supported Types	`dna`

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Borzoi Track Activity

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