On Empirical Entropy

We propose a compression-based version of the empirical entropy of a finite string over a finite alphabet. Whereas previously one considers the naked entropy of (possibly higher order) Markov processes, we consider the sum of the description of the random variable involved plus the entropy it induces. We assume only that the distribution involved is computable. To test the new notion we compare the Normalized Information Distance (the similarity metric) with a related measure based on Mutual Information in Shannon's framework. This way the similarities and differences of the last two concepts are exposed.Comment: 14 pages, LaTe

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

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

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

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