Comments (5)
uwot 0.1.8 is on CRAN with this feature available.
from uwot.
Hello, right now the fuzzy simplicial set is not available for output. But it could be added as a new option in the next release.
from uwot.
OK, thanks! I think this would be a great feature for the next release :)
from uwot.
@twhiscock the github version of uwot now has the option to return the fuzzy simplicial set by using:
res <- umap(X, ret_extra = c("fgraph"))
The coordinates will be in res$embedding
and the graph in res$fgraph
. It's a sparse dgCMatrix
from the Matrix package.
This will show up in the next CRAN version, whenever that is.
Note that the graph is further sparsified by dropping low-weight edges that would not be sampled during optimization. That is determined by the n_epochs
parameter. If you only care about the graph and not the embedded coordinates, set n_epochs = 0
and no edges are removed.
The effect of the sparsifying is small with default values. I looked at n_epochs = 200
and n_epochs = 500
with MNIST (a largeish dataset) and iris
(a very small one) and the number of edges that are dropped is always < 1%.
from uwot.
Awesome :)
from uwot.
Related Issues (20)
- Test failure an arm64, ppc64el and s390x HOT 8
- Add general_simplicial_set_intersection to the uwot API HOT 3
- umap_transform causes R Studio to abort (R encountered a fatal error.) HOT 4
- umap_transform can give odd results with dens_scale HOT 17
- umap transform fuzzy graph HOT 3
- Citing {uwot} HOT 1
- Weird looking UMAP for spectral flow data HOT 3
- What C++ version should CXX_STD have? HOT 14
- devtools can no longer build uwot on Windows HOT 5
- I can not load the saved model, an example from the help HOT 9
- Reproducibility issue with the same data and OS HOT 17
- umap_transform with seurat umap coordinate HOT 2
- dgCMatrix_colSums' not found error when using a binary matrix HOT 2
- irlba as_cholmod_sparse problems
- Does uwot need connecting internet? HOT 4
- retrieve umap parameters HOT 2
- `fuzzy_simplicial_set()` for BBKNN HOT 5
- Differences in model parameters when calling umap() causes umap_transform() to error HOT 3
- How to input similarity_graph back into umap parameters? HOT 3
- Range scale input before optimization HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from uwot.