Ecosyste.ms: Issues

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GitHub / jlmelville/uwot issues and pull requests

#128 - unrealistic point predict

Issue - State: closed - Opened by mytarmail 3 months ago - 3 comments

#126 - Seurat UMAP crashing with high numbers of cells

Issue - State: open - Opened by ollieeknight 4 months ago - 6 comments

#125 - Error installing uwot into R-4.3.3 of centos-7.9

Issue - State: open - Opened by dfgao 6 months ago - 1 comment

#124 - Error on installing uwot under Microsoft R-4.1.2

Issue - State: open - Opened by yingyin2019 6 months ago - 2 comments

#123 - Umap2

Pull Request - State: closed - Opened by jlmelville 7 months ago

#122 - UMAP trustworthiness and continuity?

Issue - State: open - Opened by davidechicco 7 months ago - 1 comment

#121 - Found more than one class "dist" in cache

Issue - State: closed - Opened by AndiMunteanu 7 months ago - 4 comments

#120 - rnndescent support

Pull Request - State: closed - Opened by jlmelville 8 months ago

#119 - HNSW support

Pull Request - State: closed - Opened by jlmelville 8 months ago

#117 - umap_transform uses a different distance metric if loaded in

Issue - State: closed - Opened by mdrnao 10 months ago - 5 comments
Labels: bug

#116 - maybe unintended data use in examples

Issue - State: closed - Opened by topepo 10 months ago - 2 comments

#115 - irlba as_cholmod_sparse problems

Issue - State: open - Opened by jlmelville 11 months ago - 1 comment

#114 - dgCMatrix_colSums' not found error when using a binary matrix

Issue - State: closed - Opened by rfarouni about 1 year ago - 2 comments

#113 - umap_transform with seurat umap coordinate

Issue - State: closed - Opened by TuoCai2000 over 1 year ago - 2 comments

#112 - Make one more AnnoyIndex use be Annoy::AnnoyIndex

Pull Request - State: closed - Opened by eddelbuettel over 1 year ago - 6 comments

#111 - Accomodate updated (Rcpp)Annoy and the added Annoy namespace

Pull Request - State: closed - Opened by eddelbuettel over 1 year ago - 6 comments

#110 - Reproducibility issue with the same data and OS

Issue - State: closed - Opened by SuhasSrinivasan over 1 year ago - 17 comments
Labels: enhancement

#109 - I can not load the saved model, an example from the help

Issue - State: closed - Opened by mytarmail over 1 year ago - 9 comments

#108 - devtools can no longer build uwot on Windows

Issue - State: closed - Opened by jlmelville over 1 year ago - 5 comments

#107 - What C++ version should CXX_STD have?

Issue - State: open - Opened by jlmelville over 1 year ago - 17 comments

#106 - Weird looking UMAP for spectral flow data

Issue - State: closed - Opened by fingeram over 1 year ago - 3 comments

#105 - Citing {uwot}

Issue - State: closed - Opened by nspies13 almost 2 years ago - 1 comment

#104 - umap transform fuzzy graph

Issue - State: closed - Opened by PedroMilanezAlmeida about 2 years ago - 3 comments
Labels: enhancement

#103 - umap_transform can give odd results with dens_scale

Issue - State: closed - Opened by FemkeSmit about 2 years ago - 17 comments

#102 - umap_transform causes R Studio to abort (R encountered a fatal error.)

Issue - State: closed - Opened by ChVav about 2 years ago - 4 comments
Labels: bug

#101 - Add general_simplicial_set_intersection to the uwot API

Issue - State: closed - Opened by jlmelville about 2 years ago - 3 comments
Labels: enhancement

#100 - Test failure an arm64, ppc64el and s390x

Issue - State: open - Opened by lucaskanashiro about 2 years ago - 8 comments
Labels: bug

#99 - Range scale input before optimization

Issue - State: closed - Opened by jlmelville about 2 years ago - 2 comments
Labels: enhancement

#98 - How to input similarity_graph back into umap parameters?

Issue - State: closed - Opened by Chengwei94 about 2 years ago - 3 comments
Labels: enhancement

#97 - Differences in model parameters when calling umap() causes umap_transform() to error

Issue - State: closed - Opened by AustinHartman about 2 years ago - 3 comments
Labels: bug

#96 - `fuzzy_simplicial_set()` for BBKNN

Issue - State: closed - Opened by ycli1995 about 2 years ago - 5 comments
Labels: enhancement

#95 - retrieve umap parameters

Issue - State: closed - Opened by kjiang18 over 2 years ago - 2 comments

#94 - Does uwot need connecting internet?

Issue - State: closed - Opened by summerghw over 2 years ago - 4 comments

#93 - Licensing model for uwot and umappp

Issue - State: closed - Opened by dsudar over 2 years ago - 3 comments

#92 - Support binary metric

Issue - State: open - Opened by frederikziebell over 2 years ago - 2 comments
Labels: enhancement

#91 - Can't install on CentOS server machine

Issue - State: closed - Opened by MiguelRodo over 2 years ago - 2 comments

#90 - Help needed . How to parallel RcppANNOY

Issue - State: closed - Opened by jianshu93 over 2 years ago - 1 comment

#89 - Optimization of n_components and spread

Issue - State: closed - Opened by felipe-mansoldo almost 3 years ago - 2 comments

#88 - Saving a loaded uwot model

Issue - State: closed - Opened by ilyakorsunsky almost 3 years ago - 2 comments
Labels: bug

#87 - use Rcpphnsw instead of Rcppannoy to accelerate nearest neighbor search

Issue - State: open - Opened by jianshu93 almost 3 years ago - 20 comments

#86 - check_graph in umap_transform

Issue - State: closed - Opened by yuhanH almost 3 years ago - 2 comments
Labels: bug

#85 - Behavior with equidistant data

Issue - State: closed - Opened by jlmelville almost 3 years ago - 5 comments

#84 - batch mode with Adam optimization

Pull Request - State: closed - Opened by jlmelville almost 3 years ago

#83 - Parallelizing the optimization step (redux)

Issue - State: closed - Opened by LTLA about 3 years ago - 27 comments
Labels: enhancement

#82 - Order of elements is not preserved in subgraph_init

Issue - State: closed - Opened by LTLA about 3 years ago - 3 comments

#81 - keep the rownames

Issue - State: closed - Opened by jwijffels about 3 years ago - 7 comments
Labels: bug

#80 - Rolling out uwot's C++ code as a header-only library

Issue - State: open - Opened by LTLA about 3 years ago - 10 comments

#79 - 3 questions from running this online tutorial

Issue - State: closed - Opened by jielab over 3 years ago - 4 comments

#78 - can't find object 'mnist'

Issue - State: closed - Opened by jielab over 3 years ago - 1 comment

#77 - Can't open saved models if they are larger than 8GB

Issue - State: open - Opened by jlmelville over 3 years ago - 1 comment
Labels: bug

#76 - `umap_transform` does not validate input sufficiently

Issue - State: open - Opened by jlmelville over 3 years ago - 2 comments

#75 - compilation issue and possible output issue with different version

Issue - State: closed - Opened by mpr121 over 3 years ago - 6 comments

#73 - densMAP implementation?

Issue - State: closed - Opened by barveaditya almost 4 years ago - 7 comments
Labels: enhancement

#72 - Use RcppAnnoy header with 0.0.17

Pull Request - State: closed - Opened by jlmelville almost 4 years ago - 23 comments

#71 - How to cite?

Issue - State: closed - Opened by momeara almost 4 years ago - 1 comment

#70 - Accomodate RcppAnnoy 0.16.2 or later with Annoy 1.17 (closes #69)

Pull Request - State: closed - Opened by eddelbuettel almost 4 years ago

#69 - Change for next (Rcpp)Annoy version

Issue - State: closed - Opened by eddelbuettel almost 4 years ago - 30 comments

#68 - Error in model$nn_index$getNTrees() : external pointer is not valid

Issue - State: closed - Opened by RyanYip-Kat about 4 years ago - 2 comments

#67 - feature request: aligned UMAP

Issue - State: open - Opened by StaffanBetner about 4 years ago
Labels: enhancement

#66 - Added a quick check to make sure "pca" is not too large

Pull Request - State: closed - Opened by khughitt about 4 years ago - 3 comments

#65 - feature request: UMAP connectivity and diagnostic plotting

Issue - State: open - Opened by maddyduran over 4 years ago - 7 comments
Labels: enhancement

#64 - transform nn

Pull Request - State: closed - Opened by yuhanH over 4 years ago - 2 comments

#63 - return model with precalculated nearest neighbor

Issue - State: closed - Opened by yuhanH over 4 years ago - 2 comments

#62 - uwot with distance matrix impossible to retain embedding

Issue - State: open - Opened by luciat-92 over 4 years ago - 4 comments
Labels: enhancement

#61 - uwot fails with a 5Mx27 matrix

Issue - State: closed - Opened by qihaocytobank over 4 years ago - 1 comment

#59 - Using sparse or distance matrices as the input data yields unexpected clustering

Issue - State: open - Opened by erzakiev over 4 years ago - 2 comments
Labels: bug

#58 - uwot 0.1.8 doesn't install on Debian 9.5

Issue - State: closed - Opened by friedpine over 4 years ago - 2 comments

#57 - umap_transform function

Issue - State: closed - Opened by DanSchnell over 4 years ago - 2 comments

#56 - Error in FNN::get.knn(X, k) : Data include NAs

Issue - State: closed - Opened by akhst7 over 4 years ago - 6 comments

#55 - Reproducibility issue with cosine metric

Issue - State: open - Opened by juba over 4 years ago - 4 comments

#54 - uwot 0.1.8 doesn't install on MacOS 10.14.6

Issue - State: closed - Opened by MarekGierlinski over 4 years ago - 6 comments

#53 - Use RcppParallel subset directly

Pull Request - State: closed - Opened by jlmelville over 4 years ago

#52 - UBSAN issues: RcppParallel

Issue - State: closed - Opened by jlmelville over 4 years ago - 2 comments

#51 - Error when input data is not of a right-numbered column?

Issue - State: closed - Opened by heelarryous over 4 years ago - 3 comments

#50 - Work around Annoy UBSAN issues

Issue - State: closed - Opened by jlmelville over 4 years ago - 31 comments

#47 - Return UMAP graph?

Issue - State: closed - Opened by twhiscock over 4 years ago - 5 comments
Labels: enhancement

#46 - Reproducibility issues

Issue - State: closed - Opened by juba almost 5 years ago - 35 comments
Labels: bug

#45 - Distance metric match argument error

Issue - State: closed - Opened by Harini-107 almost 5 years ago

#44 - Installation error

Issue - State: closed - Opened by nsheff almost 5 years ago - 3 comments

#43 - possible to use multiple y variables ?

Issue - State: closed - Opened by akhst7 almost 5 years ago - 2 comments

#42 - To run umap using external pca components

Issue - State: closed - Opened by Harini-107 almost 5 years ago - 9 comments

#41 - uwot::umap_transform not producing same results as those in python implementation

Issue - State: closed - Opened by moldach almost 5 years ago - 2 comments

#40 - Sample weights

Issue - State: open - Opened by ilyakorsunsky almost 5 years ago - 1 comment
Labels: enhancement

#39 - Uwot/umap crashes when run twice ....

Issue - State: closed - Opened by aldojongejan almost 5 years ago - 40 comments

#38 - Integrating HSNE?

Issue - State: closed - Opened by SamGG about 5 years ago - 2 comments
Labels: enhancement

#37 - Add my info to the list of contributors

Pull Request - State: closed - Opened by sirusb about 5 years ago

#36 - Add github contributors to DESCRIPTION

Issue - State: closed - Opened by jlmelville about 5 years ago - 4 comments

#35 - Binary search and more relaxed .Rprofile advice

Pull Request - State: closed - Opened by LTLA about 5 years ago - 1 comment

#34 - Potential optimization opportunity in supervised.cpp

Issue - State: closed - Opened by LTLA about 5 years ago - 1 comment

#33 - inverse transform?

Issue - State: open - Opened by romainFr about 5 years ago - 3 comments
Labels: enhancement

#32 - uwot 0.1.4 is failing to compile on RStudio Server Pro (RHEL 7)

Issue - State: closed - Opened by mjsteinbaugh about 5 years ago - 7 comments

#31 - Model loading is incompatible with newer RcppAnnoy

Issue - State: closed - Opened by jlmelville about 5 years ago - 14 comments
Labels: bug

#30 - umap_transform and tumap

Issue - State: closed - Opened by jeky82 about 5 years ago - 3 comments

#29 - fail to install uwot on linux server due to path fault

Issue - State: closed - Opened by AlfredShawn about 5 years ago - 9 comments