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What is the relationship between the MCL process, the MCL algorithm, and the ’mcl’ implementation?

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What is the relationship between the MCL process, the MCL algorithm, and the ’mcl’ implementation?

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mcl is what you use for clustering. It implements the MCL algorithm, which is a cluster algorithm for graphs. The MCL algorithm is basically a shell in which the MCL process is computed and interpreted. I will describe them in the natural, reverse, order. The MCL process generates a row of stochastic matrices given some initial stochastic matrix. The elements with even index are obtained by expanding the previous element, and the elements with odd index are obtained by inflating the previous element given some inflation constant. Expansion is nothing but normal matrix squaring, and inflation is a particular way of rescaling the entries of a stochastic matrix such that it remains stochastic. The row of MCL elements (from the MCL process) is in principle without end, but what happens is that the elements converge to some specific kind of matrix, called the limit of the process. The heuristic underlying MCL predicts that the interaction of expansion with inflation will lead to a limit exh

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