nmslib (https://github.com/nmslib/nmslib) supports sparse vectors for some of its spaces. It has fewer indexing methods than faiss, though.

https://github.com/nmslib/nmslib/blob/master/manual/spaces.m...

Welcome! Unfortunately faiss doesn't support sparse vectors. If you're using sparse vectors I would either not use faiss (there are better options like Elasticsearch) - or convert them into dense for use with faiss