sparank.ModalityConfig

class sparank.ModalityConfig(name='rna', top_k=500, k_feat=50, cl_dropout_rate=0.3, mrp_mask_rate=0.3, depth=None, heads=None)[source]

Bases: object

Specification for one omics modality (RNA, ADT, ATAC, …).

Each modality owns its own vocabulary, token-sequence length, number of top markers, and optional per-tower architecture overrides.

Parameters:

  • name (str)

  • top_k (int)

  • k_feat (int | None)

  • cl_dropout_rate (float)

  • mrp_mask_rate (float)

  • depth (int | None)

  • heads (int | None)

__init__(name='rna', top_k=500, k_feat=50, cl_dropout_rate=0.3, mrp_mask_rate=0.3, depth=None, heads=None)
Parameters:

  • name (str)

  • top_k (int)

  • k_feat (int | None)

  • cl_dropout_rate (float)

  • mrp_mask_rate (float)

  • depth (int | None)

  • heads (int | None)

Return type:

None

Methods

__init__([name, top_k, k_feat, ...])

Attributes

cl_dropout_rate

Dropout rate for the contrastive learning layer.

depth

Override depth for this modality's tower.

heads

Override attention heads.

k_feat

Number of features to use for marker selection.

mrp_mask_rate

Mask rate for masked region prediction (MRP).

name

Name of the modality (e.g., "rna", "adt").

top_k

Number of top features to retain.
cl_dropout_rate: float = 0.3

Dropout rate for the contrastive learning layer.

depth: int | None = None

Override depth for this modality’s tower. If None, inherits from ExpConfig.

heads: int | None = None

Override attention heads. If None, inherits from ExpConfig.

k_feat: int | None = 50

Number of features to use for marker selection.

mrp_mask_rate: float = 0.3

Mask rate for masked region prediction (MRP).

name: str = 'rna'

Name of the modality (e.g., “rna”, “adt”).

top_k: int = 500

Number of top features to retain.