Cache Oblivious Algorithms for Computing the Triplet Distance Between Trees

We study the problem of computing the triplet distance between two rooted unordered trees with n labeled leafs. Introduced by Dobson 1975, the triplet distance is the number of leaf triples that induce different topologies in the two trees. The current theoretically best algorithm is an O(nlogn) time algorithm by Brodal et al. [SODA 2013]. Recently Jansson et al. proposed a new algorithm that, while slower in theory, requiring O(n log^3 n) time, in practice it outperforms the theoretically faster O(n log n) algorithm. Both algorithms do not scale to external memory. We present two cache oblivious algorithms that combine the best of both worlds. The first algorithm is for the case when the two input trees are binary trees and the second a generalized algorithm for two input trees of arbitrary degree. Analyzed in the RAM model, both algorithms require O(n log n) time, and in the cache oblivious model O(n/B log_{2}(n/M)) I/Os. Their relative simplicity and the fact that they scale to external memory makes them achieve the best practical performance. We note that these are the first algorithms that scale to external memory, both in theory and practice, for this problem

Phylogenetic CSPs are Approximation Resistant

We study the approximability of a broad class of computational problems -- originally motivated in evolutionary biology and phylogenetic reconstruction -- concerning the aggregation of potentially inconsistent (local) information about $n$ items of interest, and we present optimal hardness of approximation results under the Unique Games Conjecture. The class of problems studied here can be described as Constraint Satisfaction Problems (CSPs) over infinite domains, where instead of values $\{0,1\}$ or a fixed-size domain, the variables can be mapped to any of the $n$ leaves of a phylogenetic tree. The topology of the tree then determines whether a given constraint on the variables is satisfied or not, and the resulting CSPs are called Phylogenetic CSPs. Prominent examples of Phylogenetic CSPs with a long history and applications in various disciplines include: Triplet Reconstruction, Quartet Reconstruction, Subtree Aggregation (Forbidden or Desired). For example, in Triplet Reconstruction, we are given $m$ triplets of the form $ij|k$ (indicating that ``items $i,j$ are more similar to each other than to $k$'') and we want to construct a hierarchical clustering on the $n$ items, that respects the constraints as much as possible. Despite more than four decades of research, the basic question of maximizing the number of satisfied constraints is not well-understood. The current best approximation is achieved by outputting a random tree (for triplets, this achieves a 1/3 approximation). Our main result is that every Phylogenetic CSP is approximation resistant, i.e., there is no polynomial-time algorithm that does asymptotically better than a (biased) random assignment. This is a generalization of the results in Guruswami, Hastad, Manokaran, Raghavendra, and Charikar (2011), who showed that ordering CSPs are approximation resistant (e.g., Max Acyclic Subgraph, Betweenness).Comment: 45 pages, 11 figures, Abstract shortened for arxi

Efficient Indexing for Structured and Unstructured Data

The collection of digital data is growing at an exponential rate. Data originates from wide range of data sources such as text feeds, biological sequencers, internet traffic over routers, through sensors and many other sources. To mine intelligent information from these sources, users have to query the data. Indexing techniques aim to reduce the query time by preprocessing the data. Diversity of data sources in real world makes it imperative to develop application specific indexing solutions based on the data to be queried. Data can be structured i.e., relational tables or unstructured i.e., free text. Moreover, increasingly many applications need to seamlessly analyze both kinds of data making data integration a central issue. Integrating text with structured data needs to account for missing values, errors in the data etc. Probabilistic models have been proposed recently for this purpose. These models are also useful for applications where uncertainty is inherent in data e.g. sensor networks. This dissertation aims to propose efficient indexing solutions for several problems that lie at the intersection of database and information retrieval such as joining ranked inputs, full-text documents searching etc. Other well-known problems of ranked retrieval and pattern matching are also studied under probabilistic settings. For each problem, the worst-case theoretical bounds of the proposed solutions are established and/or their practicality is demonstrated by thorough experimentation