When an individual's DNA is sequenced, sensitive medical information becomes available to the sequencing laboratory.
Information Theory Cryptography and Security Information Theory
In these experiments, we observe that BanditPAM returns the same results as state-of-the-art PAM-like algorithms up to 4x faster while performing up to 200x fewer distance computations.
The second ingredient is to utilise a multi-armed bandit algorithm to adaptively refine this spectral estimator only for read pairs that are likely to have large alignments.
Current state-of-the-art $k$-medoids clustering algorithms, such as Partitioning Around Medoids (PAM), are iterative and are quadratic in the dataset size $n$ for each iteration, being prohibitively expensive for large datasets.