moscot

moscot copied to clipboard

Add Sparse Geodesic Cost Support

7

Here are the steps I planned. I first want to ensure the tests work with this version and I am currently on that step. - [x] make sure it works...

selmanozleyen

Fix TranslationProblem and xy being set when alpha is 1 then improve tests

2

I did thes things in this PR: - Fix and test https://github.com/theislab/moscot/issues/687 - Add another error case for https://github.com/theislab/moscot/issues/680 i.e. throw error when xy is given and alpha is 1...

selmanozleyen

Add user guide

1

ArinaDanilina

prepare method does not warn about unknown parameters

3

I was just wondering why `problem.prepare` recomputes a PCA, even though I pre-computed one and passed `join_attr='X_pca'` until I realized that I had a typo in there. The `prepare` method...

Marius1311

updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.2 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.2...v0.4.3)

pre-commit-ci[bot]

Exhaust memory when using Eucidean cost.

3

Hi there, I notice that I encoutered the exhaust memory error when using the Euclidean cost, but not when Im using SqEuclidean cost. I am running on MOSTA and it...

Chengwei94

Unbalance FGW full rank marginal normalization issue

1

xlink https://github.com/theislab/moscot/pull/686

giovp

(feat): Linear GENOT

8

We add two main new classes here: 1. `GENOTLinSolver` wraps the underlying OTT-Jax solver in a moscot-usable way 2. `GENOTLinProblem` at the next level of abstraction up, allowing users to...

ilan-gold

`TranslationProblem.prepare` method can't set `joint_attr={"attr":"X"}`

2

When I try to run this ```python tp = tp.prepare(batch_key="batch", src_attr=src_attr, tgt_attr=tgt_attr, joint_attr={"attr": "X"}) ``` TemporalProblem will give an error because of this line https://github.com/theislab/moscot/blob/3151da7b324672fab6757b8a84bcd1d0bcb9f027/src/moscot/problems/cross_modality/_translation.py#L167 with the message `KeyError: 'x_key'`

selmanozleyen

change `batch_size` in `sparsify`

11

Needed for keeping solver fast (high batch size), but prevent OOM in `sparsify` (need low batch size), see https://github.com/theislab/cellrank/issues/1146#issuecomment-1856213099

MUCDK