Quantum Kolmogorov Complexity Based on Classical Descriptions

We develop a theory of the algorithmic information in bits contained in an individual pure quantum state. This extends classical Kolmogorov complexity to the quantum domain retaining classical descriptions. Quantum Kolmogorov complexity coincides with the classical Kolmogorov complexity on the classical domain. Quantum Kolmogorov complexity is upper bounded and can be effectively approximated from above under certain conditions. With high probability a quantum object is incompressible. Upper- and lower bounds of the quantum complexity of multiple copies of individual pure quantum states are derived and may shed some light on the no-cloning properties of quantum states. In the quantum situation complexity is not sub-additive. We discuss some relations with ``no-cloning'' and ``approximate cloning'' properties.Comment: 17 pages, LaTeX, final and extended version of quant-ph/9907035, with corrections to the published journal version (the two displayed equations in the right-hand column on page 2466 had the left-hand sides of the displayed formulas erroneously interchanged

Algorithmic Identification of Probabilities

TThe problem is to identify a probability associated with a set of natural numbers, given an infinite data sequence of elements from the set. If the given sequence is drawn i.i.d. and the probability mass function involved (the target) belongs to a computably enumerable (c.e.) or co-computably enumerable (co-c.e.) set of computable probability mass functions, then there is an algorithm to almost surely identify the target in the limit. The technical tool is the strong law of large numbers. If the set is finite and the elements of the sequence are dependent while the sequence is typical in the sense of Martin-L\"of for at least one measure belonging to a c.e. or co-c.e. set of computable measures, then there is an algorithm to identify in the limit a computable measure for which the sequence is typical (there may be more than one such measure). The technical tool is the theory of Kolmogorov complexity. We give the algorithms and consider the associated predictions.Comment: 19 pages LaTeX.Corrected errors and rewrote the entire paper. arXiv admin note: text overlap with arXiv:1208.500

The Google Similarity Distance

Words and phrases acquire meaning from the way they are used in society, from their relative semantics to other words and phrases. For computers the equivalent of `society' is `database,' and the equivalent of `use' is `way to search the database.' We present a new theory of similarity between words and phrases based on information distance and Kolmogorov complexity. To fix thoughts we use the world-wide-web as database, and Google as search engine. The method is also applicable to other search engines and databases. This theory is then applied to construct a method to automatically extract similarity, the Google similarity distance, of words and phrases from the world-wide-web using Google page counts. The world-wide-web is the largest database on earth, and the context information entered by millions of independent users averages out to provide automatic semantics of useful quality. We give applications in hierarchical clustering, classification, and language translation. We give examples to distinguish between colors and numbers, cluster names of paintings by 17th century Dutch masters and names of books by English novelists, the ability to understand emergencies, and primes, and we demonstrate the ability to do a simple automatic English-Spanish translation. Finally, we use the WordNet database as an objective baseline against which to judge the performance of our method. We conduct a massive randomized trial in binary classification using support vector machines to learn categories based on our Google distance, resulting in an a mean agreement of 87% with the expert crafted WordNet categories.Comment: 15 pages, 10 figures; changed some text/figures/notation/part of theorem. Incorporated referees comments. This is the final published version up to some minor changes in the galley proof

A New Quartet Tree Heuristic for Hierarchical Clustering

We consider the problem of constructing an an optimal-weight tree from the 3*(n choose 4) weighted quartet topologies on n objects, where optimality means that the summed weight of the embedded quartet topologiesis optimal (so it can be the case that the optimal tree embeds all quartets as non-optimal topologies). We present a heuristic for reconstructing the optimal-weight tree, and a canonical manner to derive the quartet-topology weights from a given distance matrix. The method repeatedly transforms a bifurcating tree, with all objects involved as leaves, achieving a monotonic approximation to the exact single globally optimal tree. This contrasts to other heuristic search methods from biological phylogeny, like DNAML or quartet puzzling, which, repeatedly, incrementally construct a solution from a random order of objects, and subsequently add agreement values.Comment: 22 pages, 14 figure

A Fast Quartet Tree Heuristic for Hierarchical Clustering

The Minimum Quartet Tree Cost problem is to construct an optimal weight tree from the $3{n \choose 4}$ weighted quartet topologies on $n$ objects, where optimality means that the summed weight of the embedded quartet topologies is optimal (so it can be the case that the optimal tree embeds all quartets as nonoptimal topologies). We present a Monte Carlo heuristic, based on randomized hill climbing, for approximating the optimal weight tree, given the quartet topology weights. The method repeatedly transforms a dendrogram, with all objects involved as leaves, achieving a monotonic approximation to the exact single globally optimal tree. The problem and the solution heuristic has been extensively used for general hierarchical clustering of nontree-like (non-phylogeny) data in various domains and across domains with heterogeneous data. We also present a greatly improved heuristic, reducing the running time by a factor of order a thousand to ten thousand. All this is implemented and available, as part of the CompLearn package. We compare performance and running time of the original and improved versions with those of UPGMA, BioNJ, and NJ, as implemented in the SplitsTree package on genomic data for which the latter are optimized. Keywords: Data and knowledge visualization, Pattern matching--Clustering--Algorithms/Similarity measures, Hierarchical clustering, Global optimization, Quartet tree, Randomized hill-climbing,Comment: LaTeX, 40 pages, 11 figures; this paper has substantial overlap with arXiv:cs/0606048 in cs.D