Comments (1)
This seems to be an error with PaCMAP. Probably they updated the library and now it takes a different format for initialization. TopOMetry uses spectral initialization for all projections, while PaCMAP defaults to PCA initialization. In most systems, this shouldn't cause really big differences.
I'll update the Projector
class to handle whatever updates they might have done and should push a fixed version later today.
For now, you could try running PaCMAP on the latent eigenspace you learned with topometry:
# I suppose this is the eigenspace you're using, from your input:
latent_eigenspace = tg.EigenbasisDict['msDM with bw_adaptive'].results()
embedding = pacmap.PaCMAP(n_components=2, n_neighbors=None, MN_ratio=0.5, FP_ratio=2.0)
X_transformed = embedding.fit_transform(latent_eigenspace, init="pca")
Alternatively, use the spectral initialization:
spectral_init = tg.spectral_layout()
X_transformed = embedding.fit_transform(latent_eigenspace, init=spectral_init)
Let me know if this workaround works for now :)
from topometry.
Related Issues (12)
- Input parameter `X` in Diffusor.transform HOT 1
- When to consider using TopOMetry over UMAP? HOT 2
- Evaluating embedding based on how good the embedding explains a continuous/binary column
- PacMAP error HOT 1
- Conda Forge build HOT 1
- module 'topo' has no attribute 'sc' HOT 7
- comparing classic umap and topometry HOT 2
- Map projection looks odd with high number of cells HOT 1
- library integration
- trustworthiness function missing
- eval_models_layouts throws an error for sparse csr_matrix
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 topometry.