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Getting Started

  • Installation
    • From PyPI
    • From Source
    • With Numba Acceleration
    • With Rust Backend
    • Dependencies
  • Quick Start
    • Loading Data
    • Training
    • Gene Embeddings
    • Cell Embeddings & Annotation

User Guide

  • MI Computation Backends
    • How MI Computation Works
    • Backend Dispatch
    • Selecting a Backend
    • Checking Available Backends
    • Practical Runtimes
    • Architecture
  • Co-expression Targets
    • Built-in Targets
    • Usage
    • Graph-Aware Targets
    • Custom Targets
    • Caching
  • Synthetic dataset templates
    • Templates
    • Shared contract

API Reference

  • genevector.data
    • GeneVectorDataset
      • GeneVectorDataset.__init__()
      • GeneVectorDataset.create_inputs_outputs()
      • GeneVectorDataset.get_batches()
      • GeneVectorDataset.get_gene_entropy()
      • GeneVectorDataset.load_target_scores()
      • GeneVectorDataset.load_targets()
      • GeneVectorDataset.quality_control()
      • GeneVectorDataset.save_target_scores()
  • genevector.model
    • GeneVector
      • GeneVector.__init__()
      • GeneVector.load()
      • GeneVector.plot()
      • GeneVector.save()
      • GeneVector.train()
    • GeneVectorModel
      • GeneVectorModel.__init__()
      • GeneVectorModel.forward()
      • GeneVectorModel.save_embedding()
  • genevector.embedding
    • CellEmbedding
      • CellEmbedding.__init__()
      • CellEmbedding.batch_correct()
      • CellEmbedding.cell_distance()
      • CellEmbedding.cluster()
      • CellEmbedding.compare_classification()
      • CellEmbedding.compare_expression_to_similarity()
      • CellEmbedding.entmax_15()
      • CellEmbedding.get_adata()
      • CellEmbedding.get_expression()
      • CellEmbedding.get_inverse_predictive_genes()
      • CellEmbedding.get_predictive_genes()
      • CellEmbedding.module_score_r2()
      • CellEmbedding.normalized_exponential_vector()
      • CellEmbedding.normalized_marker_expression()
      • CellEmbedding.phenotype_probability()
      • CellEmbedding.phenotype_qc()
      • CellEmbedding.plot_confusion_matrix()
      • CellEmbedding.plot_probabilities()
    • GeneEmbedding
      • GeneEmbedding.__init__()
      • GeneEmbedding.average_vector_results()
      • GeneEmbedding.compute_similarities()
      • GeneEmbedding.generate_network()
      • GeneEmbedding.generate_vector()
      • GeneEmbedding.generate_weighted_vector()
      • GeneEmbedding.get_adata()
      • GeneEmbedding.get_metagenes()
      • GeneEmbedding.get_similar_genes()
      • GeneEmbedding.get_vector()
      • GeneEmbedding.plot_metagene()
      • GeneEmbedding.plot_metagenes_scores()
      • GeneEmbedding.plot_similarities()
      • GeneEmbedding.read_embedding()
      • GeneEmbedding.read_vector()
      • GeneEmbedding.score_metagenes()
  • genevector.metrics
    • compute_mi_gpu()
    • compute_mi_numba()
    • compute_mi_rust()
    • compute_mi_vectorized()
    • discretize_genes()
    • get_target_function()
    • register_target()
    • target_cosine()
    • target_jaccard()
    • target_mi()
    • target_pearson()
    • target_spearman()
  • genevector.cache
    • clear_cache()
    • compute_cache_key()
    • get_cache_path()
    • load_scores()
    • save_scores()
  • genevector.aggregation
    • aggr_mean()
    • get_aggregation()
    • register_aggregation()
    • target_graph_xcorr()

About

  • Citation
    • BibTeX
    • Links
  • Changelog
    • v1.0.0 (2026)
    • v0.3.0
    • v0.2.0
GeneVector
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