Utils

Utility functions for models and metrics. Plotting functionality for models mapping sequences to either embedding- or property-space. Diagnostics to evaluate embedding models alignment with the feature(s) of interest.

Projections

Projection and visualization of sequence embeddings.

seqme.utils.pca	Project embeddings into 2D using PCA.
seqme.utils.tsne	Project embeddings into 2D using t-SNE.
seqme.utils.umap	Project embeddings into 2D using UMAP.
seqme.utils.plot_embeddings	Plot projections for one or more groups.

Diagnostics

Helpers to select an appropriate embedding model.

seqme.utils.spearman_alignment_score	Compute the Spearman correlation coefficient using the pairwise distance between embedding spaces.
seqme.utils.knn_alignment_score	Compute the k-NN feature alignment score of an embedding model.
seqme.utils.plot_knn_alignment_score	Plot the k-NN feature alignment score of an embedding model using variable-number of neighbors.

Sequence Operations

Helpers for generating and transforming sequence data.

seqme.utils.shuffle_characters	Randomly shuffle characters within each sequence.
seqme.utils.subsample	Sample a subset of the sequences without replacement.