Concurrent disjoint set union

We develop and analyze concurrent algorithms for the disjoint set union (“union-find” ) problem in the shared memory, asynchronous multiprocessor model of computation, with CAS (compare and swap) or DCAS (double compare and swap) as the synchronization primitive. We give a deterministic bounded wait-free algorithm that uses DCAS and has a total work bound of $$O\biggl ( m \cdot \left( \log {\left( \frac{np}{m} + 1 \right) } + \alpha {\left( n, \frac{m}{np} \right) } \right) \biggr )$$ O ( m · log np m + 1 + α n , m np ) for a problem with n elements and m operations solved by p processes, where $$\alpha $$ α is a functional inverse of Ackermann’s function. We give two randomized algorithms that use only CAS and have the same work bound in expectation. The analysis of the second randomized algorithm is valid even if the scheduler is adversarial. Our DCAS and randomized algorithms take $$O(\log n)$$ O ( log n ) steps per operation, worst-case for the DCAS algorithm, high-probability for the randomized algorithms. Our work and step bounds grow only logarithmically with p, making our algorithms truly scalable. We prove that for a class of symmetric algorithms that includes ours, no better step or work bound is possible. Our work is theoretical, but Alistarh et al (In search of the fastest concurrent union-find algorithm, 2019), Dhulipala et al (A framework for static and incremental parallel graph connectivity algorithms, 2020) and Hong et al (Exploring the design space of static and incremental graph connectivity algorithms on gpus, 2020) have implemented some of our algorithms on CPUs and GPUs and experimented with them. On many realistic data sets, our algorithms run as fast or faster than all others.

Reversal Distance for Strings with Duplicates: Linear Time Approximation using Hitting Set

In the last decade there has been an ongoing interest in string comparison problems; to a large extend the interest was stimulated by genome rearrangement problems in computational biology but related problems appear in many other areas of computer science. Particular attention has been given to the problem of sorting by reversals (SBR): given two strings, $A$ and $B$, find the minimum number of reversals that transform the string $A$ into the string $B$ (a reversal $\rho(i,j)$, $i < j$, transforms a string $A=a_1\ldots a_n$ into a string $A'=a_1\ldots a_{i-1} a_{j} a_{j-1} \ldots a_{i} a_{j+1} \ldots a_n$). Closely related is the minimum common string partition problem (MCSP): given two strings, $A$ and $B$, find a minimum size partition of $A$ into substrings $P_1,\ldots,P_l$ (i.e., $A=P_1\ldots P_l$) and a partition of $B$ into substrings $Q_1,\ldots,Q_l$ such that $(Q_1,\ldots,Q_l)$ is a permutation of $(P_1,\ldots,P_l)$. Primarily the SBR problem has been studied for strings in which every symbol appears exactly once (that is, for permutations) and only recently attention has been given to the general case where duplicates of the symbols are allowed. In this paper we consider the problem $k$-SBR, a version of SBR in which each symbol is allowed to appear up to $k$ times in each string, for some $k\geq 1$. The main result of the paper is a $\Theta(k)$-approximation algorithm for $k$-SBR running in time $O(n)$; compared to the previously known algorithm for $k$-SBR, this is an improvement by a factor of $\Theta(k)$ in the approximation ratio, and by a factor of $\Theta(k)$ in the running time. We approach the $k$-SBR by finding an approximation for the $k$-MCSP first and then turning it into a solution for $k$-SBR. Crucial ingredients of our algorithm are the suffix tree data structure and a linear time algorithm for a special case of a disjoint set union problem.