scarches

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Issue with expimap model

1

`early_stopping_kwargs = { "early_stopping_metric": "val_unweighted_loss", # val_unweighted_loss "threshold": 0, "patience": 50, "reduce_lr": True, "lr_patience": 13, "lr_factor": 0.1, }` `intr_cvae.train( n_epochs=400, alpha_epoch_anneal=100, alpha=ALPHA, alpha_kl=0.5, weight_decay=0., early_stopping_kwargs=early_stopping_kwargs, use_early_stopping=True, monitor_only_val=False, seed=2024, )` `Preparing...

MoLuLuMo

Hi, I am trying to follow this tutorial: https://github.com/theislab/scarches/blob/master/notebooks/scpoli_surgery_pipeline.ipynb. matplotlib==3.8.2 numpy==1.24.4 pandas==1.5.3 scArches==0.5.10 scanpy==1.9.6 scikit-learn==1.3.2 seaborn==0.13.1 torch==2.1.2 When I try to train the model I run into this error: Traceback...

lsw0825

Potential bugs for label transfer

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Dear HLCA team, Thanks for developing the HLCA. I met a bug when I tried to query my data to the reference using the code in scarches/notebook/hlca_map_classify.ipynb. combined_emb.obs = combined_emb.obs.join(labels)...

shuailinli

First of all, thank you for developing this impressive toolkit. Much appreciated! I encountered a problem when using scPoli for cell-type annotation. When I first trained the model on my...

xr-song

Choice of reference and query data sets

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Hello, Thanks for the nice software. I have 2 data sets A and B annotated separately, and I am using `scArches` for a label transfer analysis from one data set...

hl-xue

scPoli Model for Unsupervised Use

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# Version history scarches: 0.5.10 # Issue When attempting to initialize the scPoli model for unsupervised learning, the constructor seems to require a `label_indices=[]` argument to be passed as an...

ShreyParikh07

scGen model is very slow

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Thanks for the great tools! Is the scGen model in scArches using the newest scGen version? I can run scGen no problem and it runs pretty fast, but when I...

joseph-siefert

fail to use the sca.models.SCVI

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vae = sca.models.SCVI( adata_ref, n_layers=2, encode_covariates=True, deeply_inject_covariates=False, use_layer_norm="both", use_batch_norm="none", ) ValueError: Expected parameter loc (Tensor of shape (128, 10)) of distribution Normal(loc: torch.Size([128, 10]), scale: torch.Size([128, 10])) to satisfy the...

melancholy12

Speed improvement

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Speed improvement in: 1. Data Splitting (scPoli when cell_types are available) 2. Ptorch data loader: Now we fetch cells in batches when using `MultiConditionAnnotatedDataset` rather than cell-by-cell and then combining...

moinfar

For sergei

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MohammedZidane