What is multi-hot encoding?
Without having read the paper, from the name I would say a multi-hot encoding is a matrix $X \in \{0,1\}^{n \times m }$, with $\sum_{i = 1}^{n} X_{i,j} = 1, \forall j = 1,\ldots,m$.
You obtain the normal hot-encoding by setting $m=1$.