mtopic.tl.sMTM

mtopic.tl.sMTM#

class mtopic.tl.sMTM(mdata, n_topics=20, radius=0.05, n_neighbors=None, seed=2291, spatial_key='coords', verbose=True, n_jobs=10)#

Spatial Multimodal Topic Model.

This class implements a Spatial Multimodal Topic Model (sMTM) designed for analyzing single-cell spatial data across multiple modalities. The model captures spatial relationships by constructing a spatial neighborhood graph and uses Variational Inference (VI) to identify spatially-aware topics. These topics represent patterns across features and modalities while incorporating spatial information.

Parameters:

  • mdata (muon.MuData) – A MuData object containing multimodal single-cell spatial data, including spatial coordinates in the obsm attribute.

  • n_topics (int, optional) – Number of topics to infer. Each topic represents a distinct spatial pattern across features and modalities. Default is 20.

  • radius (float, optional) – Radius for constructing a spatial neighborhood graph. Used if n_neighbors is None. Default is 0.05.

  • n_neighbors (int, optional) – Number of neighbors to consider when constructing the spatial neighborhood graph. Overrides radius if set. Default is None.

  • seed (int, optional) – Random seed for reproducibility. Ensures consistent initialization and results. Default is 2291.

  • spatial_key (str, optional) – Key in the obsm attribute of MuData specifying spatial coordinates. Default is ‘coords’.

  • verbose (bool, optional) – If True, displays a progress bar during training. Default is True.

  • n_jobs (int, optional) – Number of CPU cores to use for parallel computation. If set to -1, all available cores are used. Default is 10.

Variables:

  • n_topics (int) – Number of topics initialized in the model.

  • radius (float) – Radius used for spatial neighborhood graph construction.

  • seed (int) – Random seed used for initializing the model.

  • rng (numpy.random.Generator) – Random number generator initialized with the seed.

  • n_jobs (int) – Number of parallel jobs used for computation.

  • spatial_key (str) – Key for accessing spatial coordinates in MuData.

  • modalities (list) – List of modalities in the dataset.

  • features (dict) – Dictionary of feature names for each modality.

  • barcodes (list) – List of barcodes corresponding to the samples.

  • D (int) – Number of samples (observations) in the dataset.

  • M (int) – Number of modalities in the dataset.

  • N (dict) – Dictionary with the number of features per modality.

  • coords (numpy.ndarray) – Spatial coordinates of the samples.

  • coords_scaled (numpy.ndarray) – Scaled spatial coordinates normalized to [0, 1].

  • neighborhood_dist (numpy.ndarray) – Distances between each sample and its neighbors.

  • neighborhood_graph (numpy.ndarray) – Indices of neighbors for each sample.

  • gamma (numpy.ndarray) – Variational parameters for topic distributions.

  • lambda (dict) – Variational parameters for topics across modalities.

  • exp_E_log_beta (dict) – Expected log topic distributions.

Methods:
VI(n_iter=20, max_iter_d=100)#
Perform Variational Inference (VI) to fit the model to the data.
Parameters:

  • n_iter (int, optional) – Number of iterations for the VI algorithm. Default is 20.

  • max_iter_d (int, optional) – Maximum number of iterations for the E-step in each VI update. Default is 100.

Returns:

None

Return type:

None

Example:
model = mtopic.tl.spatialMTM(mdata, n_topics=20, radius=0.05)
model.VI(n_iter=20)
Example:
import mtopic

# Load spatial multimodal single-cell data
mdata = mtopic.read.h5mu("path/to/file.h5mu")

# Initialize and train the model
model = mtopic.tl.spatialMTM(mdata, n_topics=20, radius=0.05)
model.VI(n_iter=20)
__init__(mdata, n_topics=20, radius=0.05, n_neighbors=None, seed=2291, spatial_key='coords', verbose=True, n_jobs=10)#

Methods

VI([n_iter, max_iter_d])

__init__(mdata[, n_topics, radius, ...])