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Questions tagged [runumap]

UMAP (Uniform Manifold Approximation and Projection) is a novel manifold manifold learning technique for dimension reduction. The UMAP algorithm is competitive with t-SNE for visualization quality and arguably preserves more of the global structure and superior run time performance. UMAP has not computational restrictions on embedding dimensions making it viable as a general purpose dimension reduction technique for machine learning

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Is there any way to draw UMAP or t-SNE plot for data table?

I have a huge file (below is a small set of data) like below, I would like to draw a PCA, I could draw PCA using PCA function but it looks a bit messy, because I have 200 columns so I think maybe t-SNE or UMAP works better, but I couldn't draw using…
star
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Python Make UMAP fast(er)

I am using UMAP (https://umap-learn.readthedocs.io/en/latest/#) to reduce the dimensions in my data. My dataset contains 4700 samples with 1,2 million features each (which I would like to reduce). However, this takes quite a while despite using 32…
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UMAP "ValueError: cannot assign slice from input of different size"

I am using umap-learn 0.5.3 for dimension reduction of a Numpy array. The array, say arrival_tfidf, is shaped (7898, 2969) and is a TF-IDF transformation of 7898 messages, containing float64 elements. When running the following snippet import…
kohlstein
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Lost information during dimensionality reduction using umap

I am working with spotify tracks database and trying to understand how columns danceability, liveness and energy affect popularity (use discrete popularity: -1, 0, 1). I want to do dimensionality reduction from three columns to two. Here's the…
Mariia Skripchenko
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Clustering with UMAP and HDBScan

I have a somewhat large amount of textual data, input by approximately 5000 people. I've assigned each person a vector using Doc2vec, reduced to two dimensions using UMAP and highlighted groups contained within using HDBSCAN. The intention is to…
Jacob
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Cannot import umap: cannot import name 'structref' from 'numba.experimental'

I tried to import umap in my jupyter notebook but had the following error: ImportError: cannot import name 'structref' from 'numba.experimental' (C:\Users\name\Anaconda3\lib\site-packages\numba\experimental\__init__.py) I tried to update conda but…
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UMAP Error TypeError: a bytes-like object is required, not 'list'

I am trying to run a code that utilizes UMAP for dimensionality reduction based on the work here: https://umap-learn.readthedocs.io/en/latest/basic_usage.html I am running on Spyder (Python 3.7). I get this error: TypeError: a bytes-like object is…
Elizabeth
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RunUMAP gives segmentation fault

I tried the following > my.exp <- RunUMAP(my.exp, dims = 1:30) UMAP(a=None, angular_rp_forest=False, b=None, init='spectral', learning_rate=1.0, local_connectivity=1, metric='correlation', metric_kwds=None, min_dist=0.3, n_components=2,…
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Pipeline for UMAP Clustering

# Import pandas library import pandas as pd initialize list of lists data = {'person_id':[1,1,2,1,2,3,4,5,6,5,6,4,5,4,7,8,8,9,10,1,10,1,10,9,8,7,6,5,4,2], 'condition_concept_id':[43927,5234, 1111, 2222, 5234, 4444000, 67675, 43927, 67890, 5234,…
user22394410
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scRNAseq UMAP error with FindVariableFeatures

I am new to scRNAseq analysis and am self-taught so apologies if this is really basic! I have downloaded metadata and TPM counts for a scRNAseq dataset (https://github.com/Martin-Villalba-lab/Data/tree/master/Cell_2019/SmartSeq2). My goal is to…
Jemima Becker
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How to Systematically Tune UMAP Hyperparameters for Supervised Learning

I have a question about using Uniform Manifold Approximation and Projection (UMAP) for feature extraction. In my project I am using two tabular datasets both containing around 10000 samples. One has 20 features and the other has 550 features. My…
serkanardaa
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TypeError: 'module' object is not callable - while using UMAP

import umap as UMAP import umap retarget = {df_train['target'].value_counts().reset_index()['index'][i]: i for i in range(len(df_train['target'].value_counts()))} retarget2 = {i: k for k, i in retarget.items()} df_train['target'] =…
Babita
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Show legend on UMAP plot

I am making an interactive UMAP plot, where you can hover the mouse over a datapoint to view the sample ID. My code works, showing a plot colour coded by class and with the hover feature working However, I can't figure out how to get it to show a…
TheyTakingTheHobbitsToIsengard
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RSpectra installation had Non zero exit status

I am trying to install umap however the dependency RSpectra needs to be installed to. Whenever I try to install RSpectra, R shows me a result that installation had Non zero exit status. Does any one knows how can I fix this? 18 warnings…
JuanitaMonje
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Seurat UMAP visualization result is mirrored after running in two identical environments

When I run the same R code in my local computer RStudio (R 4.0.2) and on Code Ocean R 4.0.3, I have two different UMAP visualization results and they are mirrored [] I use Seurat 3.2.0 version in both environments and particularly for umap…
Yulia Kentieva
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