We study the problem of learning regular tree languages from text. We show that the framework of function distinguishability, as introduced by the author in [Theoret. Comput. Sci.290 (2003) 1679–1711], can be generalized from the case of string languages towards tree languages. This provides a large source of identifiable classes of regular tree languages. Each of these classes can be characterized in various ways. Moreover, we present a generic inference algorithm with polynomial update time and prove its correctness. In this way, we generalize previous works of Angluin, Sakakibara and ourselves. Moreover, we show that this way all regular tree languages can be approximately identified.

The HP model is one of the most popular discretized models for attacking the protein folding problem, i.e., for the computational prediction of the tertiary structure of a protein from its amino acid sequence. It is based on the assumption that interactions between hydrophobic amino acids are the main force in the folding process. Therefore, it distinguishes between polar and hydrophobic amino acids only and tries to embed the amino acid sequence into a two- or three-dimensional grid lattice such as to maximize the number of contacts, i.e., of pairs of hydrophobic amino acids that are embedded into neighboring positions of the grid. In this paper, we propose a new generalization of the HP model which overcomes one of the major drawbacks of the original HP model, namely the bipartiteness of the underlying grid structure which severely restricts the set of possible contacts. Moreover, we introduce the (biologically well-motivated) concept of weighted contacts, where each contact gets assigned a weight depending on the spatial distance between the embedded amino acids. We analyze the applicability of existing approximation algorithms for the original HP model to our new setting and design a new approximation algorithm for this generalized model.

We consider the defect theorem in the context of labelled polyominoes, i.e., two-dimensional figures. The classical version of this property states that if a set of n words is not a code then the words can be expressed as a product of at most n - 1 words, the smaller set being a code. We survey several two-dimensional extensions exhibiting the boundaries where the theorem fails. In particular, we establish the defect property in the case of three dominoes (n × 1 or 1 × n rectangles).

Duplication is the replacement of a factor w within a word by ww. This operation can be used iteratively to generate languages starting from words or sets of words. By undoing duplications, one can eventually reach a square-free word, the original word's duplication root. The duplication root is unique, if the length of duplications is fixed. Based on these unique roots we define the concept of duplication code. Elementary properties are stated, then the conditions under which infinite duplication codes exist are fully characterized; the relevant parameters are the duplication length and alphabet size. Finally, some properties of the languages generated by duplication codes are investigated.

Nous établissons quelques propriétés des mots sturmiens et classifions, ensuite, les mots infinis qui possèdent, pour tout entier naturel non nul n, exactement n+2 facteurs de longueur n. Nous définissons également la notion d'insertion k à k sur les mots infinis puis nous calculons la complexité des mots obtenus en appliquant cette notion aux mots sturmiens. Enfin nous étudions l'équilibre et la palindromie d'une classe particulière de mots de complexité n+2 que nous appelons mots quasi-sturmiens par insertion et que nous caractérisons à l'aide des vecteurs de Parikh.

For finitary set functors preserving inverse images, recursive coalgebras A of Paul Taylor are proved to be precisely those for which the system described by A always halts in finitely many steps.