v0.0.34

Fast-tracking to v0.0.34 from v0.0.20

Enhancements

Pruning Support:

• Enabled pruning in bnmf, wnmf, and nmf_recommender.
• Added pruning of additional matrices, e.g., MASK, based on X.
• Included pruned_cols and pruned_rows in saved outputs.

Matrix Factorization:

• Introduced new submodule BNMFk under NMFk with nmf_method='bnmf'.
• Added WEIGHT and MASK keys for WNMFk and BNMFk.
• Implemented matrix deletion in subroutines to reduce memory consumption.
• Added factor_thresholding parameter to perform thresholding over NMFk factors, making them boolean. Options include:
  • coord_desc_thresh
  • WH_thresh
• Introduced factor_thresholding_obj_params for configuring thresholding subroutines.
• Added clustering_method parameter with options:
  • kmeans
  • bool or boolean (both are equivalent).
• Introduced clustering_obj_params to configure clustering subroutines.
• Added new perturbation type for boolean matrices: perturb_type='boolean' or perturb_type='bool'.
• Updated examples to reflect new boolean-specific features.
• Path compatibility using os.path.join.

Thresholding and Clustering:

• Added factor_thresholding_H_regression with options:
  • otsu_thresh
  • coord_desc_thresh
  • kmeans_thresh
• Default factor_thresholding_H_regression set to kmeans_thresh.
• Default factor_thresholding set to otsu_thresh.
• Introduced factor_thresholding_H_regression_obj_params to configure parameters.
• Added K-means-based boolean thresholding for W and H matrices:
  • Clusters values in each row of W and H into two groups; then the boolean threshold is the midpoint of cluster centroids.

Hardware and Device Management:

• Added device parameter to NMFk for GPU management:
  • device=-1: Use all GPUs.
  • device=0: Use the GPU with ID 0.
  • device=[0,1,...]: Use a specific list of GPUs.
  • Negative values other than -1: Use (number of GPUs + device + 1).

Hierarchical NMFk (HNMFk) Improvements:

• Added new variables for nodes:
  • parent_node_factors_path
  • parent_node_k
  • factors_path
• Enabled dynamic renaming of paths when loading HNMFk models from different directories.
• Improved decomposition behavior:
  • Nodes with fewer samples than the sample threshold no longer decompose unnecessarily.
• Added signature, centroid, and probabilities from parent nodes to child nodes.
• Introduced graph iterator methods for navigating to specific nodes by name.
• Updated node naming conventions to use ancestor-based indexing.

Result Storage:

• Added W_all to saved outputs of NMFk.

Installation and Documentation

• Migrated to a new installation system using pip and Poetry.
• Added a post-installation script for simplifying setup on different systems.
• Updated documentation for:
  • New installation methods on Chicoma and Darwin.

Bug Fixes

• Corrected HNMFk behavior to return total data indices instead of indices of indices.
• Corrected naming inconsistencies in pruning variables in NMFk.
• Fixed error calculation to consider only known locations when masking is applied.
• Resolved GPU transfer conflicts when using MASK.
• Fixed default device parameter in NMFk to be -1 (use all devices).
• Addressed issues in WNMFk and BNMFk examples.
• Fixed checkpointing bugs:
  • Made saving checkpoints true by default.
  • Resolved issues when loading an HNMFk model during an ongoing process.
• Fixed scalar addition error with sparse matrices in kl_mu.
• Resolved dependency conflicts with numpy and numba.
• Updated HPC documentation for T-ELF installation.