Wavelet Trees Meet Suffix Trees

We present an improved wavelet tree construction algorithm and discuss its applications to a number of rank/select problems for integer keys and strings. Given a string of length n over an alphabet of size $\sigma\leq n$, our method builds the wavelet tree in $O(n \log \sigma/ \sqrt{\log{n}})$ time, improving upon the state-of-the-art algorithm by a factor of $\sqrt{\log n}$. As a consequence, given an array of n integers we can construct in $O(n \sqrt{\log n})$ time a data structure consisting of $O(n)$ machine words and capable of answering rank/select queries for the subranges of the array in $O(\log n / \log \log n)$ time. This is a $\log \log n$-factor improvement in query time compared to Chan and P\u{a}tra\c{s}cu and a $\sqrt{\log n}$-factor improvement in construction time compared to Brodal et al. Next, we switch to stringological context and propose a novel notion of wavelet suffix trees. For a string w of length n, this data structure occupies $O(n)$ words, takes $O(n \sqrt{\log n})$ time to construct, and simultaneously captures the combinatorial structure of substrings of w while enabling efficient top-down traversal and binary search. In particular, with a wavelet suffix tree we are able to answer in $O(\log |x|)$ time the following two natural analogues of rank/select queries for suffixes of substrings: for substrings x and y of w count the number of suffixes of x that are lexicographically smaller than y, and for a substring x of w and an integer k, find the k-th lexicographically smallest suffix of x. We further show that wavelet suffix trees allow to compute a run-length-encoded Burrows-Wheeler transform of a substring x of w in $O(s \log |x|)$ time, where s denotes the length of the resulting run-length encoding. This answers a question by Cormode and Muthukrishnan, who considered an analogous problem for Lempel-Ziv compression.Comment: 33 pages, 5 figures; preliminary version published at SODA 201

Query Learning with Exponential Query Costs

In query learning, the goal is to identify an unknown object while minimizing the number of "yes" or "no" questions (queries) posed about that object. A well-studied algorithm for query learning is known as generalized binary search (GBS). We show that GBS is a greedy algorithm to optimize the expected number of queries needed to identify the unknown object. We also generalize GBS in two ways. First, we consider the case where the cost of querying grows exponentially in the number of queries and the goal is to minimize the expected exponential cost. Then, we consider the case where the objects are partitioned into groups, and the objective is to identify only the group to which the object belongs. We derive algorithms to address these issues in a common, information-theoretic framework. In particular, we present an exact formula for the objective function in each case involving Shannon or Renyi entropy, and develop a greedy algorithm for minimizing it. Our algorithms are demonstrated on two applications of query learning, active learning and emergency response.Comment: 15 page

Identifiability of Large Phylogenetic Mixture Models

Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The fundamental question of whether parameters of such a model are identifiable is difficult to address, due to the complexity of the parameterization. We analyze mixture models on large trees, with many mixture components, showing that both numerical and tree parameters are indeed identifiable in these models when all trees are the same. We also explore the extent to which our algebraic techniques can be employed to extend the result to mixtures on different trees.Comment: 15 page