Remy Liu

icon indicating a website link https://remylau.github.io/

icon company Carnegie Mellon University icon location Post-doc fellow in the Ray and Stephanie Lane Computational Biology Department at CMU

Results 84 issues of Remy Liu

Add option to `.score` method to take `index` option, which indicates which samples we want to calculate the scores

- [ ] `index` option - [ ] `mask` option

enhancement

Model object abstraction and refactoring

- Model metadata, e.g., description, training info, params - Abstract methods (standardize in/out format) - ``fit(*args, **kwargs) -> None`` - ``predict(*args, **kwargs) -> Union[np.ndarray, torch.Tensor, other?]`` - ``fit_predict`` shortcut function...

Priority-P1

Fix ``scmm`` error due to zero total counts calling ``torch.lgamma`` (called by ``torch.distributions.NegativeBinomial``)

Make util for auto device selection

Add more info about key error from `get_feature`, e.g., what channel type

Exclude benchmark runs from default pytest runs, make `lite-bench` and `full-bench` test options (tox)

- [ ] Update contribution guidelines with notes about bench tests vs. unit tests

DSTG link graph add connections between real spots?

1 comment

According to the link graph construction description from the paper, the graph should also contain interaction between real-spots. However, in the current implementation (modified from the original implementation, see https://github.com/Su-informatics-lab/DSTG/issues/16),...

question

Convention for tensor device

## Problem Currently, there is no convention for which device the data is stored when a function, e.g., `fit()`, is called. For example, even though the computation device to use...

Priority-P1

Add random_state option to PCA transforms

It turns out that the random seed of the SVD solver impacts the PCA loadings (except for the top few) quite a bit, even when the `tol` option is set...

Cell type order file

2 comment

Hi @michellemli! Love your work. Is there any way I can find out the corresponding cell type in the provided embeddings on figshare? Or is it safe to assume that...