Esra Erdem

2005

Proceedings of the Seventh International Symposium on Practical Aspects of Declarative Languages (PADL), pages 37--51, 2005

We describe the reconstruction of a phylogeny for a set of taxa, with a character-based cladistics approach, in a declarative knowledge representation formalism, and show how to use computational methods of answer set programming to generate conjectures about the evolution of the ...MORE ⇓

We describe the reconstruction of a phylogeny for a set of taxa, with a character-based cladistics approach, in a declarative knowledge representation formalism, and show how to use computational methods of answer set programming to generate conjectures about the evolution of the given taxa. We have applied this computational method in two domains: to historical analysis of languages, and to historical analysis of parasite-host systems. In particular, using this method, we have computed some plausible phylogenies for Chinese dialects, for Indo-European language groups, and for Alcataenia species. Some of these plausible phylogenies are different from the ones computed by other software. Using this method, we can easily describe domain specific information (e.g. temporal and geographical constraints), and thus prevent the reconstruction of some phylogenies that are not plausible.

Theory and Practice of Logic Programming, 2005

The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities are in contact, and also that a contact ...MORE ⇓

The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities are in contact, and also that a contact is only possible when the languages are spoken at the same time. We show how computational methods of answer set programming and constraint logic programming can be used to generate plausible conjectures about contacts between prehistoric linguistic communities, and illustrate our approach by applying it to the evolutionary history of Indo-European languages.

2003

Reconstructing the evolutionary history of Indo-European languages using answer set programmingdoi.orgPDF

Proceedings of the 5th International Symposium on Practical Aspects of Declarative Languages (PADL 03), 2003

The evolutionary history of languages can be modeled as a tree, called a phylogeny, where the leaves represent the extant lan- guages, the internal vertices represent the ancestral languages, and the edges represent the genetic relations between the languages. Languages not only ...MORE ⇓

The evolutionary history of languages can be modeled as a tree, called a phylogeny, where the leaves represent the extant lan- guages, the internal vertices represent the ancestral languages, and the edges represent the genetic relations between the languages. Languages not only inherit characteristics from their ancestors but also sometimes borrow them from other languages. Such borrowings can be represented by additional non-tree edges. This paper addresses the problem of com- puting a small number of additional edges that turn a phylogeny into a 'perfect phylogenetic network'. To solve this problem, we use answer set programming, which represents a given computational problem as a logic program whose answer sets correspond to solutions. Using the answer set solver smodels, with some heuristics and optimization tech- niques, we have generated a few conjectures regarding the evolution of Indo-European languages.