AlphaGenome Interval Track

Score AlphaGenome track signal over one or more intervals by minimizing or maximizing mean value.

License: AlphaGenome uses Apache-2.0 for code and Custom (AlphaGenome Terms of Use) for model weights and has restrictions around commercial use and may require explicit attribution when utilized. Model weights are gated and require accepting the provider’s terms and authenticating with a HuggingFace token. 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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proto-bio/proto-language/proto_language/constraint/sequence_annotation/alphagenome_interval_track_constraint.py

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@article{avsec2026alphagenome,
  title={Advancing regulatory variant effect prediction with AlphaGenome},
  author={Avsec, {\v{Z}}iga and Latysheva, Natasha and Cheng, Jun and Novati, Guido and Taylor, Kyle R and Ward, Tom and Bycroft, Clare and Nicolaisen, Lauren and Arvaniti, Eirini and Pan, Joshua and Thomas, Raina and Dutordoir, Vincent and Perino, Matteo and De, Soham and Karollus, Alexander and Gayoso, Adam and Sargeant, Toby and Mottram, Anne and Wong, Lai Hong and Drot{\'a}r, Pavol and Kosiorek, Adam and Senior, Andrew and Tanburn, Richard and Applebaum, Taylor and Basu, Souradeep and Hassabis, Demis and Kohli, Pushmeet},
  journal={Nature},
  year={2026},
  volume={649},
  number={8099},
  pages={1206--1218},
  doi={10.1038/s41586-025-10014-0}
}

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Score mean AlphaGenome track signal over one or more intervals.

API Reference

ConfigAlphaGenomeIntervalTrackConfig Source

Configuration for interval track-value scoring with AlphaGenome.

intervals · List[array] · required

0-based half-open intervals scored on the predicted track.

ontology_terms · List[string] · required

AlphaGenome ontology term(s) to score.

requested_output · enum · default: "RNA_SEQ"

AlphaGenome output type to score.

Options: ATAC, CAGE, DNASE, RNA_SEQ, CHIP_HISTONE, CHIP_TF, SPLICE_SITES, SPLICE_SITE_USAGE, SPLICE_JUNCTIONS, CONTACT_MAPS, PROCAP

direction · enum · default: "maximize"

Whether to maximize or minimize the interval mean signal.

Options: maximize, minimize

maximize_inflection_value · number · default: "5.0"

Signal value where maximize-mode sigmoid has its inflection.

maximize_sigmoid_scale · number · default: "1.0"

Scale for maximize-mode sigmoid transform.

minimize_threshold_value · number · default: "1.0"

Upper bound for minimize-mode linear score; values above are clipped.

model_version · string · default: "all_folds"

AlphaGenome model version.

organism · enum · default: "human"

Organism for AlphaGenome prediction.

Options: human, mouse

device · string · default: "cuda"

Device for AlphaGenome prediction.

prediction_timeout · integer · default: "3600"

Timeout (seconds) for each AlphaGenome prediction call.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import alphagenome_interval_track_constraint, AlphaGenomeIntervalTrackConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	alphagenome-interval-track
Function	alphagenome_interval_track_constraint
Category	sequence_annotation
Mode	discrete
Uses GPU	True
Supported Types	dna