> ## Documentation Index
> Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt
> Use this file to discover all available pages before exploring further.

# PARADE UTR cell-type specificity

> Drive a UTR toward high on-target and low off-target activity using the PARADE model.

<div class="page-hero">
  <img class="page-hero-banner" src="https://proto-bio.github.io/proto-assets/images/constraint/parade-utr-specificity/hero.png" alt="PARADE UTR cell-type specificity" />
</div>

<Note>
  **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](https://github.com/autosome-ru/parade/blob/master/LICENSE) for full terms.
</Note>

<p class="entity-disclaimer">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.</p>

<hr class="entity-rule" />

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<a href="https://github.com/evo-design/proto-language/blob/d3b7822f74ea64747cc751a3b2ab1aa6b799ac47/proto_language/constraint/rna_expression/parade_utr_specificity_constraint.py#L285" target="_blank" class="tab-panel source-panel" data-tab="source-constraint-parade-utr-specificity">
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    ```bibtex theme={null}
    @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}
    }
    ```
  </div>

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<div class="entity-contributors"><span class="entity-contributors-label">Constraint contributors</span><span class="entity-contributors-people"><a class="entity-contributor" href="https://github.com/bviggiano" target="_blank" rel="noopener" title="bviggiano: 1 commit"><img noZoom class="entity-contributor-avatar" src="https://avatars.githubusercontent.com/u/21143637?v=4&s=64" alt="" loading="lazy" /><span class="entity-contributor-login">bviggiano</span></a><a class="entity-contributor" href="https://github.com/dguo8412" target="_blank" rel="noopener" title="dguo8412: 1 commit"><img noZoom class="entity-contributor-avatar" src="https://avatars.githubusercontent.com/u/46211285?v=4&s=64" alt="" loading="lazy" /><span class="entity-contributor-login">dguo8412</span></a><a class="entity-contributor" href="https://github.com/roknabadi" target="_blank" rel="noopener" title="roknabadi: 1 commit"><img noZoom class="entity-contributor-avatar" src="https://avatars.githubusercontent.com/u/74315203?v=4&s=64" alt="" loading="lazy" /><span class="entity-contributor-login">roknabadi</span></a></span></div>
Score UTR proposals with matched maximize-on and minimize-off activity terms.

## API Reference

<div class="api-model-section api-model-static api-config-section">
  <div class="api-model-header"><span class="api-model-badge api-config-badge">Config</span><span class="api-model-name">ParadeUTRSpecificityConfig</span><a href="https://github.com/evo-design/proto-language/blob/d3b7822f74ea64747cc751a3b2ab1aa6b799ac47/proto_language/constraint/rna_expression/parade_utr_specificity_constraint.py#L50" target="_blank" class="func-table-btn func-source-btn api-model-source"><svg width="12" height="12" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><polyline points="16 18 22 12 16 6" /><polyline points="8 6 2 12 8 18" /></svg> Source</a></div>

  Configuration for the PARADE UTR cell-type-specificity constraint.

  <ParamField path="construct_type" type="enum" default="utr5">
    PARADE UTR model to score with: 'utr5' (5' UTR) or 'utr3' (3' UTR).

    Options: `utr5`, `utr3`
  </ParamField>

  <ParamField path="on_target" type="enum" default="c2">
    PARADE cell code whose predicted activity should be maximized.

    Options: `c1`, `c2`, `c4`, `c6`, `c17`, `c13`
  </ParamField>

  <ParamField path="off_target" type="enum" default="c6">
    PARADE cell code whose predicted activity should be minimized.

    Options: `c1`, `c2`, `c4`, `c6`, `c17`, `c13`
  </ParamField>

  <ParamField path="sigmoid_center" type="number" default="2.0">
    Raw PARADE activity at the shared forward/gradient sigmoid midpoint.
  </ParamField>

  <ParamField path="sigmoid_scale" type="number" default="1.0">
    Positive float32-safe width of the shared sigmoid transform; larger is gentler.
  </ParamField>

  <ParamField path="temperature" type="number" default="1.0">
    Fallback softmax temperature for direct gradient calls; optimizer schedules take precedence.
  </ParamField>

  <ParamField path="device" type="string" default="cuda">
    Device used for PARADE inference.
  </ParamField>

  <ParamField path="batch_size" type="integer" default="1">
    Number of sequences scored per PARADE GPU batch.
  </ParamField>
</div>

<div class="api-model-section api-model-static api-output-section">
  <div class="api-model-header"><span class="api-model-badge api-output-badge">Returns</span><span class="api-model-name">ConstraintOutput</span></div>

  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.
</div>

## Usage

```python python icon="python" theme={null}
from proto_language.core import Constraint
from proto_language.constraint import parade_utr_specificity_constraint, ParadeUTRSpecificityConfig

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

scores = constraint.evaluate()
```

## Metadata

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