Combined Data Structure for Previous- and Next-Smaller-Values

Let $A$ be a static array storing $n$ elements from a totally ordered set. We present a data structure of optimal size at most $n\log_2(3+2\sqrt{2})+o(n)$ bits that allows us to answer the following queries on $A$ in constant time, without accessing $A$: (1) previous smaller value queries, where given an index $i$, we wish to find the first index to the left of $i$ where $A$ is strictly smaller than at $i$, and (2) next smaller value queries, which search to the right of $i$. As an additional bonus, our data structure also allows to answer a third kind of query: given indices $i<j$, find the position of the minimum in $A[i..j]$. Our data structure has direct consequences for the space-efficient storage of suffix trees.Comment: to appear in Theoretical Computer Scienc

Observation and Distinction. Representing Information in Infinite Games

We compare two approaches for modelling imperfect information in infinite games by using finite-state automata. The first, more standard approach views information as the result of an observation process driven by a sequential Mealy machine. In contrast, the second approach features indistinguishability relations described by synchronous two-tape automata. The indistinguishability-relation model turns out to be strictly more expressive than the one based on observations. We present a characterisation of the indistinguishability relations that admit a representation as a finite-state observation function. We show that the characterisation is decidable, and give a procedure to construct a corresponding Mealy machine whenever one exists

Entropy-scaling search of massive biological data

Many datasets exhibit a well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here, we introduce a framework for similarity search based on characterizing a dataset's entropy and fractal dimension. We prove that searching scales in time with metric entropy (number of covering hyperspheres), if the fractal dimension of the dataset is low, and scales in space with the sum of metric entropy and information-theoretic entropy (randomness of the data). Using these ideas, we present accelerated versions of standard tools, with no loss in specificity and little loss in sensitivity, for use in three domains---high-throughput drug screening (Ammolite, 150x speedup), metagenomics (MICA, 3.5x speedup of DIAMOND [3,700x BLASTX]), and protein structure search (esFragBag, 10x speedup of FragBag). Our framework can be used to achieve "compressive omics," and the general theory can be readily applied to data science problems outside of biology.Comment: Including supplement: 41 pages, 6 figures, 4 tables, 1 bo