MANIFOLD LEARNING, GRAPH EMBEDDING

megaman Metric Manifold Learning for Million data points in python written by Marina Meila, James McQueen, Zhongyue Zhang and Jacob VanderPlas. Other substantial contributors are Samson Koelle and Yu-Chia Chen. [Overview] [Download] [Paper]


montlake by Samson Koelle. Manifold coordinates with phyiscal meaning, feature construction from molecular configurations (JMLR'22)

github.com/yuchaz/homology_emb Estimation of higher-order Laplacians, smoothing and analyzing vector fields 1-st order (co)-homology embedding, finding shortest loops (Neurips'21) by Yu-Chia Chen.

github.com/yuchaz/independent_coordinate_search Selecting the independent coordinates of manifolds with large aspect ratios" (NeurIPS'19) by Yu-Chia Chen.

STABILITY GUARANTEES FOR CLUSTERING

admm_ss_sdp - Distribution free stability guarantees for clustering written in Matlab by Gang Cheng,
based on the Sublevel Set (SS) method introduced in this paper
[Overview/Manual][Download]

SPECTRAL CLUSTERING

SpectraLIB - Package for symmetric spectral clustering in Matlab written by Deepak Verma. Updated by Tatiana Maravina and Marina Meila
[Overview/Manual] [Download SpectraLIB]

SpectraLIB_A - Package for asymmetric spectral clustering in Matlab written by Marina Meila and Tatiana Maravina (an extension to SpectraLIB)
[Overview/Manual] [Download SpectraLIB_A]

RSL_library_beta - Package for spectral Learning written by Susan Shortreed and Marina Meila
[Overview/Manual][Download RSL_Library](temporarily unavailable)

PREFERENCES, RANKINGS AND INTRANSITIVITY

RIM Recursive Inversion Models in C++/R written by Luca Weihs

Recursive Inversion Models in Java written by Marina Meila (TB Posted) and by Anne Wagner
[Download] [Paper]

dpmm-gmm Dirichlet Process Mixtures of Mallows Models in Matlab/C written by Harr Chen
[Download] [Paper]

GMM - Estimation of Generalized Mallows Models in Java written by Bhushan Mandhani
[Overview/Manual] [Download] [Paper]

MS -- Exponential Blurring Mean-Shift for Rankings in Matlab written by Le Bao and Marina Meila
[Overview] [Download] [Paper]

OTHER TOOLS

LazyRunner framework for organized scientific computing; in python, written by Hoyt Koepke

TreeDict fast, flexible and full-featured hierarchical python container that makes simple and sophisticated bookkeeping easy; in python, written by Hoyt Koepke

pyksvd highly optimized, parallel version of the Batch-OMP version of the KSVD learning algorithm; written by Hoyt Koepke