It appears affinity propagation would appear to accept sparse similarity input: X = check_array(X, accept_sparse='csr') But if I try it, I get: ~/.local/lib/python3.7/site- packages/sklearn/cluster/affinity_propagation_.py in affinity_propagation(S, preference, convergence_iter, max_iter, damping, copy, verbose, return_n_iter) 137 138 # Place preference on the diagonal of S --> 139 S.flat[::(n_samples + 1)] = preference 140 141 A = np.zeros((n_samples, n_samples)) ~/.local/lib/python3.7/site-packages/scipy/sparse/base.py in __getattr__(self, attr) 687 return self.getnnz() 688 else: --> 689 raise AttributeError(attr + " not found") 690 691 def transpose(self, axes=None, copy=False): AttributeError: flat not found