PARADE UTR activity

License: PARADE is open source and free for academic and commercial use under an MIT license and may require explicit attribution when utilized. Please refer to the license for full terms.

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evo-design/proto-language/proto_language/constraint/rna_expression/parade_utr_activity_constraint.py

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@article{khoroshkin2024parade,
  title={A generative framework for enhanced cell-type specificity in rationally designed mRNAs},
  author={Khoroshkin, Matvei and Zinkevich, Arsenii and Aristova, Elizaveta and Yousefi, Hassan and Lee, Sean B. and Mittmann, Tabea and Manegold, Karoline and Penzar, Dmitry and Raleigh, David R. and Kulakovskiy, Ivan V. and Goodarzi, Hani},
  journal={bioRxiv},
  year={2024},
  publisher={Cold Spring Harbor Laboratory},
  doi={10.1101/2024.12.31.630783}
}

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Constraint contributors

Score UTR proposals by predicted single-cell activity.

API Reference

ConfigParadeUTRActivityConfig Source

Configuration for the single-cell PARADE UTR activity constraint.

enum

default:"utr5"

PARADE UTR model to score with: ‘utr5’ (5’ UTR) or ‘utr3’ (3’ UTR).Options: utr5, utr3

enum

default:"c2"

PARADE cell code whose predicted activity is scored.Options: c1, c2, c4, c6, c17, c13

enum

default:"max"

Whether to maximize (‘max’) or minimize (‘min’) the activity.Options: max, min

number

default:"2.0"

Raw PARADE activity mapped to energy 0.5.

number

default:"1.0"

Positive float32-safe width of the sigmoid transform; larger is gentler.

number

default:"1.0"

Fallback softmax temperature for direct gradient calls; optimizer schedules take precedence.

string

default:"cuda"

Device used for PARADE inference.

integer

default:"1"

Number of sequences scored per PARADE GPU batch.

ReturnsConstraintOutput

One result per proposal. score is in [0.0, 1.0] (lower is better in the requested direction); metadata carries the raw activity.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import parade_utr_activity_constraint, ParadeUTRActivityConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	`parade-utr-activity`
Function	`parade_utr_activity_constraint`
Category	`rna_expression`
Mode	`dual`
Uses GPU	`True`
Supported Types	`dna`, `rna`

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PARADE UTR activity

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