Severin Dicks

rank_genes_groups fix

1

Dear all, I fixed the `rank_genes_groups` function. However I change quit a bit of the preprocessing e.g. masking from cupy to numpy. In the notebooks that I was able to...

CUDARuntimeError in Notebooks

15

Hello everyone, I'm having trouble running the notebooks on our institutes server (64 Core Epyc and 2 Quadro RTX 6000), however when I'm at home running them on my personal...

MultiGPU notebooks calculated differentially expressed PCAs

1

Hey Nvidia Genomics Team, In the Multi GPU Notebook the AnnData object post PCA is created with the PCA in `.X`. Therefore when you later later perform the differential gene...

CSR & CSC sum along Axis slow

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### Description I recently had a user notice a slowdown while summing a sparse CSR matrix along the major axis. After some tinkering, I created a new method for summing...

[FEA] Sparse multi-GPU PCA

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**Is your feature request related to a problem? Please describe.** I have developed a multi-GPU implementation for Dask-based sparse PCA. This implementation closely aligns with the sparse single GPU PCA...

[BUG] Dense PCA fails with CUDA12

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**Describe the bug** Dense PCA fails for larger Datasets with the following error. RuntimeError: cuSOLVER error encountered at: file=/home/sdicks/micromamba/envs/rapids-23.08_12/include/raft/linalg/detail/eig.cuh line=118: With CUDA 11.8 and Rapids-23.08 it works. **Steps/Code to reproduce...

**Describe the bug** `kneighbors_graph` with `algorithm="ivfflat"` fails because `_fit_X` gives and AttributeError. ``` /home/severin/conda/envs/rapids-23.10/lib/python3.10/site-packages/cuml/internals/api_decorators.py:190: UserWarning: Warning: Approximate Nearest Neighbor methods might be unstable in this version of cuML. This is...

log1p return matrix

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### What kind of feature would you like to request? Additional function parameters / changed functionality / changed defaults? ### Please describe your wishes I think it would be good...

[FEA]: Spatial Autocorrelation

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### Is this a new feature, an improvement, or a change to existing functionality? New Feature ### How would you describe the priority of this feature request Low (would be...

anndata optional dependency import system can behave poorly with autodoc_mock_imports

4

### Please make sure these conditions are met - [X] I have checked that this issue has not already been reported. - [X] I have confirmed this bug exists on...