## G.2.1 Combinatorics (F.2.2)

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#### Document Type

- Bachelor Thesis (1)
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#### Keywords

- Distributed system (1)
- Earley-Parser (1)
- Hitting families (1)
- Online chain partitioning (1)
- Partially ordered sets (1)
- RNA interaction (1)
- Random testing (1)
- analysis of algorithms (1)
- multiple context free grammar (1)
- semiring parsing (1)

Large-scale distributed systems consist of a number of components, take a number of parameter values as input, and behave differently based on a number of non-deterministic events. All these features—components, parameter values, and events—interact in complicated ways, and unanticipated interactions may lead to bugs. Empirically, many bugs in these systems are caused by interactions of only a small number of features. In certain cases, it may be possible to test all interactions of \(k\) features for a small constant \(k\) by executing a family of tests that is exponentially or even doubly-exponentially smaller than the family of all tests. Thus, in such cases we can effectively uncover all bugs that require up to \(k\)-wise interactions of features.
In this thesis we study two occurrences of this phenomenon. First, many bugs in distributed systems are caused by network partition faults. In most cases these bugs occur due to two or three key nodes, such as leaders or replicas, not being able to communicate, or because the leading node finds itself in a block of the partition without quorum. Second, bugs may occur due to unexpected schedules (interleavings) of concurrent events—concurrent exchange of messages and concurrent access to shared resources. Again, many bugs depend only on the relative ordering of a small number of events. We call the smallest number of events whose ordering causes a bug the depth of the bug. We show that in both testing scenarios we can effectively uncover bugs involving small number of nodes or bugs of small depth by executing small families of tests.
We phrase both testing scenarios in terms of an abstract framework of tests, testing goals, and goal coverage. Sets of tests that cover all testing goals are called covering families. We give a general construction that shows that whenever a random test covers a fixed goal with sufficiently high probability, a small randomly chosen set of tests is a covering family with high probability. We then introduce concrete coverage notions relating to network partition faults and bugs of small depth. In case of network partition faults, we show that for the introduced coverage notions we can find a lower bound on the probability that a random test covers a given goal. Our general construction then yields a randomized testing procedure that achieves full coverage—and hence, find bugs—quickly.
In case of coverage notions related to bugs of small depth, if the events in the program form a non-trivial partial order, our general construction may give a suboptimal bound. Thus, we study other ways of constructing covering families. We show that if the events in a concurrent program are partially ordered as a tree, we can explicitly construct a covering family of small size: for balanced trees, our construction is polylogarithmic in the number of events. For the case when the partial order of events does not have a "nice" structure, and the events and their relation to previous events are revealed while the program is running, we give an online construction of covering families. Based on the construction, we develop a randomized scheduler called PCTCP that uniformly samples schedules from a covering family and has a rigorous guarantee of finding bugs of small depth. We experiment with an implementation of PCTCP on two real-world distributed systems—Zookeeper and Cassandra—and show that it can effectively find bugs.

Recently, a new Quicksort variant due to Yaroslavskiy was chosen as standard sorting
method for Oracle's Java 7 runtime library. The decision for the change was based on
empirical studies showing that on average, the new algorithm is faster than the formerly
used classic Quicksort. Surprisingly, the improvement was achieved by using a dual pivot
approach — an idea that was considered not promising by several theoretical studies in the
past. In this thesis, I try to find the reason for this unexpected success.
My focus is on the precise and detailed average case analysis, aiming at the flavor of
Knuth's series “The Art of Computer Programming”. In particular, I go beyond abstract
measures like counting key comparisons, and try to understand the efficiency of the
algorithms at different levels of abstraction. Whenever possible, precise expected values are
preferred to asymptotic approximations. This rigor ensures that (a) the sorting methods
discussed here are actually usable in practice and (b) that the analysis results contribute to
a sound comparison of the Quicksort variants.

It has been observed that for understanding the biological function of certain RNA molecules, one has to study joint secondary structures of interacting pairs of RNA. In this thesis, a new approach for predicting the joint structure is proposed and implemented. For this, we introduce the class of m-dimensional context-free grammars --- an extension of stochastic context-free grammars to multiple dimensions --- and present an Earley-style semiring parser for this class. Additionally, we develop and thoroughly discuss an implementation variant of Earley parsers tailored to efficiently handle dense grammars, which embraces the grammars used for structure prediction. A currently proposed partitioning scheme for joint secondary structures is transferred into a two-dimensional context-free grammar, which in turn is used as a stochastic model for RNA-RNA interaction. This model is trained on actual data and then used for predicting most likely joint structures for given RNA molecules. While this technique has been widely used for secondary structure prediction of single molecules, RNA-RNA interaction was hardly approached this way in the past. Although our parser has O(n^3 m^3) time complexity and O(n^2 m^2) space complexity for two RNA molecules of sizes n and m, it remains practically applicable for typical sizes if enough memory is available. Experiments show that our parser is much more efficient for this application than classical Earley parsers. Moreover the predictions of joint structures are comparable in quality to current energy minimization approaches.