Frequently Asked Questions

Problem	Cause	Solution
the following arguments are required: --dataset	bsvae-train requires dataset path	Pass --dataset path/to/matrix.csv.
RuntimeError or OOM during training	Batch too large for available memory	Reduce --batch-size; disable CUDA with --no-cuda if needed.
ImportError: faiss-cpu is required for Method B	gamma_knn requested without FAISS	Install faiss-cpu in environment.
ValueError for hierarchical loss mapping	--hier-strength enabled without usable feature index mapping	Provide valid --tx2gene and ensure feature IDs align with dataset rows.
Missing soft_eigengenes.csv	--soft-eigengenes needs --expr	Add --expr <features x samples matrix>.