### PARADE UTR Activity (`parade-activity`) Predicts cell-type-specific activity for one or more 5' or 3' UTR sequences, returning one value per requested cell code. #### API Reference

Source UTR sequence(s). A single string is normalized to a one-item list. `U` is mapped to `T` and `N` is allowed; mixed lengths are fine (the tool batches per length group).

Source Which UTR model to use — `"utr5"` (5' UTR) or `"utr3"` (3' UTR). Selects the checkpoint and the cell-code panel. Matching the upstream predictor, the model scores the bare insert (no reporter flanks are added). Available options: `utr5`, `utr3` PARADE cell codes to return. Empty means the full panel for `construct_type`. Requested codes must belong to that panel. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device used for inference. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded. Optional override for the pinned checkpoint — a local `.ckpt` path or an `https` link (a schemeless `host.tld/path` is accepted). Caller overrides run on local devices only (rejected on `device="cloud"`). Empty uses the pinned per-target checkpoint. Number of sequences to run per GPU batch.

Source Per-sequence PARADE predictions. The only stored field, so the output survives the framework's iterable-cache reconstruction (which preserves only the iterable field). UTR sequence that was scored (DNA alphabet). Length of the scored sequence. UTR model that produced these scores. Carried per-result so the provenance survives iterable-cache reconstruction. Predicted activity keyed by cell code. **Metrics** (one set per `results` item) | Metric | Type | Range | Availability | | ------ | ----- | --------- | -------------- | | `c1` | float | unbounded | when requested | | `c2` | float | unbounded | when requested | | `c4` | float | unbounded | when requested | | `c6` | float | unbounded | when requested | | `c17` | float | unbounded | when requested | | `c13` | float | unbounded | when requested |

#### Applications Use this tool to rank UTR designs by predicted activity, screen candidate UTRs for a target cell line, or quantify the activity differential between cell types for cell-type-specific mRNA design. #### Usage Tips * **Pick the construct type.** Set `construct_type` to `utr5` or `utr3`; it selects the matching checkpoint and cell-code panel. * **Cell codes are panel-specific.** `c13` exists only for `utr3`. Leave `cell_types` empty to return the full panel for the construct type. * **Match the training length.** Upstream trained the 5' UTR model on \~50-nt inserts and the 3' UTR model on \~240-nt (roughly 200–300 nt) inserts; the model accepts any length (adaptive pooling) but predictions are only meaningful near the training regime. * **Mixed lengths batch together.** Different-length sequences in one call are batched per length group; RNA input (`U`) is accepted and mapped to `T`.

### PARADE mRNA Stability (`parade-stability`) Predicts 3' UTR mRNA stability as an RNA/gDNA log-ratio for one or more sequences; higher is more stable. #### API Reference

Source UTR sequence(s). A single string is normalized to a one-item list. `U` is mapped to `T` and `N` is allowed; mixed lengths are fine (the tool batches per length group).

Source Optional override for the pinned upstream checkpoint — a local `.ckpt` path or an `https` link (a schemeless `host.tld/path` is accepted and normalized to `https://`). A caller override runs on local devices only (rejected on `device="cloud"`, since a checkpoint is an executable pickle). Empty uses the pinned per-target checkpoint, verified against its built-in checksum. Number of sequences to run per GPU batch. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device used for inference. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source Per-sequence PARADE stability predictions. 3' UTR sequence that was scored (DNA alphabet). Length of the scored sequence. Stability metrics; the `log_ratio` metric (RNA/gDNA log-ratio, higher means more stable) is also exposed via the `log_ratio` convenience property. **Metrics** (one set per `results` item) | Metric | Type | Range | Availability | | ----------- | ----- | --------- | ------------ | | `log_ratio` | float | unbounded | always |

#### Applications Use this tool to rank 3' UTR designs by predicted mRNA stability or to pair stability with cell-type-specific activity when selecting UTRs for downstream validation. #### Usage Tips * **Stability has no cell conditioning.** The model returns a single log-ratio per sequence. * **Use the training length.** Upstream trained this stability model on 186-nt sequences (its `seqsize`); score near that length. Mixed lengths in one call are batched per length group. * **Higher is more stable.** The `log_ratio` output is directly comparable across candidates.

### PARADE UTR Activity Gradient (`parade-gradient`) Computes a weighted differentiable UTR-activity objective and, by default, returns the gradient with respect to batched relaxed UTR logits. #### API Reference

Source Batched relaxed UTR logits with shape `(B, L, 4)` in `A,C,G,T` order. Use `B=1` for a single design candidate. Softmax temperature used to relax logits.

Source UTR model to use — `"utr5"` or `"utr3"`. Available options: `utr5`, `utr3` Per-cell objective terms summed into one scalar loss. PARADE cell code to optimize; must be in the configured `construct_type` panel. Available options: `c1`, `c2`, `c4`, `c6`, `c17`, `c13` `"max"` minimizes `1 - sigmoid((raw - center) / scale)`; `"min"` minimizes `sigmoid((raw - center) / scale)`. Available options: `max`, `min` Non-negative scalar applied before terms are summed. Raw activity value where the sigmoid is 0.5. Positive scale for the raw activity transform. Optional override for the pinned checkpoint — a local `.ckpt` path or an `https` link (a schemeless `host.tld/path` is accepted). Caller overrides run on local devices only (rejected on `device="cloud"`). Empty uses the pinned per-target checkpoint. Blend hard argmax one-hot (0) to softmax probabilities (1). Straight-through hard-forward coefficient. Run backward pass and return gradient. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device used for inference and backpropagation. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source Per-sample metric containers with scalar loss and raw per-cell activity. Per-objective-term metadata, including direction, weight, sigmoid transform, and weighted score. Name of the metric that best summarizes the result overall (e.g. `"avg_plddt"` for AlphaFold2). Used by downstream UI and reporting to pick a headline value. Concrete Metrics subclass tag; enables typed reconstruction after a serialization round-trip. Gradient tensor matching input UTR logits, or `None` when `compute_gradient=False`. Sum of per-sample weighted scalar objective values. Per-sample values are available in `sample_metrics`. Auxiliary metadata bundle from the standalone worker, including raw scores, objective-term metadata, and relaxation parameters. DNA column ordering for logits and gradient. **Metrics** | Metric | Type | Range | Availability | | ------ | ----- | --------- | -------------- | | `loss` | float | ≥ 0.0 | always | | `c1` | float | unbounded | when requested | | `c2` | float | unbounded | when requested | | `c4` | float | unbounded | when requested | | `c6` | float | unbounded | when requested | | `c17` | float | unbounded | when requested | | `c13` | float | unbounded | when requested |

#### Applications Use this tool inside gradient-based UTR design loops (e.g. Fast SeqProp) to maximize activity in an on-target cell line while minimizing it in off-target cell lines. It is designed for optimizer calls rather than final biological validation. #### Usage Tips * **Logits are batched.** Pass logits with shape `B x L x 4` in `A,C,G,T` order; use `B=1` for a single candidate. * **Terms target cell codes.** Each loss term names a `cell_type`, a `direction` (`max`/`min`), and a `weight`; all codes must be in the `construct_type` panel. * **Soft/hard mixing controls relaxation.** `soft=1.0, hard=0.0` is fully soft; increasing `hard` uses a straight-through hard-forward estimator.