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PARADE UTR cell-type specificity
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evo-design/proto-language/proto_language/constraint/rna_expression/parade_utr_specificity_constraint.py
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Constraint contributors
Score UTR proposals with matched maximize-on and minimize-off activity terms.

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API Reference

ConfigParadeUTRSpecificityConfig Source
Configuration for the PARADE UTR cell-type-specificity constraint.
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enum
default:"utr5"
PARADE UTR model to score with: ‘utr5’ (5’ UTR) or ‘utr3’ (3’ UTR).Options: utr5, utr3
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enum
default:"c2"
PARADE cell code whose predicted activity should be maximized.Options: c1, c2, c4, c6, c17, c13
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enum
default:"c6"
PARADE cell code whose predicted activity should be minimized.Options: c1, c2, c4, c6, c17, c13
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number
default:"2.0"
Raw PARADE activity at the shared forward/gradient sigmoid midpoint.
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number
default:"1.0"
Positive float32-safe width of the shared sigmoid transform; larger is gentler.
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number
default:"1.0"
Fallback softmax temperature for direct gradient calls; optimizer schedules take precedence.
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string
default:"cuda"
Device used for PARADE inference.
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integer
default:"1"
Number of sequences scored per PARADE GPU batch.
ReturnsConstraintOutput
One result per proposal. score is the mean of the maximize-on-target and minimize-off-target sigmoid energies in [0.0, 1.0]; metadata carries both raw activities and their difference.

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Usage

python

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Metadata