34 questions
0
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38
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Cluster Analysis after a process
I have a dataset with 535 samples, 63 dimensions and 7 clusters (labels). I am going to run some processes on my dataset and then track the impact of the process on the dataset.
What approach would ...
- 1
0
votes
1
answer
695
views
bokeh HoverTool and tooltips not working correctly
Hi there I just got the plot I wanted with some help and tweaks here and there using bokeh; however, I can't figure out how to add information of interest to my tooltips navigation/hover tool.
...
- 221
0
votes
2
answers
103
views
legend in bokeh UMAP shows only one entry
Hi there I just managed to get this plot done in bokeh, so I imagine there are many things that could be improved. Nonetheless, what bothers me the most is that I cannot figure out how to have all ...
- 221
0
votes
0
answers
61
views
how to plot in bokeh
Hi there I'm quite new to Python plotting in general but somehow I can get the gist of things from examples; however, I couldn't find anything useful/helpful to understand how to use bokeh to plot a ...
- 221
3
votes
1
answer
1k
views
Can the results of UMAP for HDBScan clustering be made more consistent?
I have a set of ~40K phrases which I'm clustering with HDBScan after using UMAP for dimensionality reduction. The steps are:
Generate embeddings using a fine-tuned BERT model
Reduce dimensions with ...
- 165
0
votes
0
answers
779
views
Applying UMAP to a distance matrix
I am working on a clustering analysis and computed a distance matrix with a custom metric (it is the fusion of three differently weighted distance matrices) and I am trying to get components out of it ...
- 1
3
votes
2
answers
2k
views
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. ...
- 35
0
votes
1
answer
112
views
How do I compute LSC scores ("stemness") onto a UMAP in Seurat?
In Seurat, I am working with a UMAP of blast cells and would like to use the LSC17 coefficients to produce a feature plot with "stemness" scores generated from the LSC17 onto the UMAP. I'm ...
- 3
1
vote
1
answer
494
views
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/...
0
votes
0
answers
282
views
Latest version of RAPIDS cuML in Kaggle notebooks
First of all, I am fairly new to running models on GPU, so sorry in advance for stupid questions.
I use RAPIDS cuML to GPU-accelerate some algorithms, but I noticed I cannot use the latest version (23....
- 1
0
votes
1
answer
168
views
Clustering text. Chatintets library Python. HBDSCAN, UMAP
I'm using chatintents (https://github.com/dborrelli/chat-intents) for automatically clustering. To embed sentences I use sentence transformers. The problem is when I set the maximum and minimum number ...
1
vote
0
answers
802
views
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 ...
- 11
1
vote
0
answers
295
views
UMAP validation to calculate trustworthiness_vector problem
I have a dataset with over 200.000 data samples with 256 features, then, I used UMAP with n_components = 8, 16, 32, 64, to reduce data dimension fron 256 to 64, 32, 16, 8, respectively. I do not have ...
- 21
0
votes
1
answer
267
views
Best parameters for UMAP + HistGradientBoostingClassifier
I'm trying to find the best parameters for the UMAP (dimensionality reduction) model together with HistGradientBoostingClassifier.
The loop I have created is:
vectorizer = TfidfVectorizer(use_idf=True,...
- 343
1
vote
1
answer
767
views
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 ...
- 39
1
vote
1
answer
637
views
How to perform Weighted dimensionality reduction with Umap
The title pretty much says it all, I have a df with 40+ dimension which I'd like to process into the Umap algorithm in order to have a 2-d output.
I would like to know if it is possible to weight the ...
- 29
1
vote
2
answers
3k
views
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
...
2
votes
0
answers
259
views
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 ...
- 51
0
votes
1
answer
1k
views
'what' must be a function or character string in R error message [closed]
I am plotting different umaps.
I have a part of the code that worked yesterday, however today I get the error message: Error in do.call(c, lapply(2:ncol(nn_idx), function(i) as.vector(rbind(nn_idx[, : ...
- 13
0
votes
0
answers
168
views
How to fix UMAP layout?
I am trying to use UMAP through umap-learn. And I am running 2,000,000 cells with 16 dimensions as my training dataset and another 1,000,000 cells with 16 dimensions as my testing dataset. However, ...
0
votes
0
answers
814
views
UMAP not working on Jupyter (thru Anaconda)
I'm trying to use UMAP in Jupyter (on Anaconda's environment) but something is not working properly. Below is the code I used.
# INSTALL UMAP
conda install -c conda-forge umap-learn # this was what ...
- 17
3
votes
0
answers
231
views
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 ...
0
votes
0
answers
193
views
My mac doesn't show seaborn plot without error message?
In [14]: import seaborn as sns
...: import matplotlib.pyplot as plt
...:
...: l = [41, 44, 46, 46, 47, 47, 48, 48, 49, 51, 52, 53, 53, 53, 53, 55, 55, 55,
...: 55, 56, 56, 56, 56,...
- 7,555
0
votes
2
answers
2k
views
Can I save the coordinates for a UMAP embedding?
I am running a UMAP model as follows:
embedding = umap.UMAP(n_components=2,n_neighbors=30, min_dist=0.0, metric='euclidean').fit(data)
And plotting:
f = umap.plot.points(embedding, labels=df['...
- 77
3
votes
0
answers
2k
views
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 ...
- 53
4
votes
2
answers
5k
views
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). ...
- 157
0
votes
1
answer
3k
views
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\...
- 395
1
vote
1
answer
2k
views
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 ...
- 710
1
vote
1
answer
613
views
UMAP PicklingError: ("Can't pickle <class 'numpy.dtype[float32]'>: ...)
Trying to run UMAP causes an error:
import pandas as pd
import numpy as np
import umap
df = pd.DataFrame(np.arange(25).reshape(-1,5))
um = umap.UMAP(random_state=0)
um.fit(df)
PicklingError: ("...
- 7,215
2
votes
2
answers
2k
views
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 ...
- 31
1
vote
1
answer
165
views
Using map function from purrr to test 2 parameters on one UMAP function in R
newbie need help again.I'm playing around a dataset with UMAP, a dimension reduction tool. Things like this will have 2 parameters that need to tune and look. Previously I have used tSNE, and it ...
- 405
0
votes
1
answer
694
views
umap highlighting two different models
I'm trying to create a umap for single cell data from human samples and ptx samples. I can get the umap plot showing the different clusters but I want to show where the ptx samples and human samples ...
- 123
5
votes
1
answer
6k
views
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-...
- 775
2
votes
0
answers
541
views
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',
...
- 8,172