Linguistics

Contains reports on three research projects.U. S. Air Force (Electronics Systems Division) under Contract AF 19(628)-2487Joint Services Electronics Programs (U. S. Army, U. S. Navy, and U. S. Air Force) under Contract DA 36-039-AMC-03200(E)National Science Foundation (Grant GK-835)National Institutes of Health (Grant 2 P01 MH-04737-06)National Aeronautics and Space Administration (Grant NsG-496

Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results

Systematic research on noncoding RNAs (ncRNAs) has revealed that many ncRNAs are actively involved in various biological networks. Therefore, in order to fully understand the mechanisms of these networks, it is crucial to understand the roles of ncRNAs. Unfortunately, the annotation of ncRNA genes that give rise to functional RNA molecules has begun only recently, and it is far from being complete. Considering the huge amount of genome sequence data, we need efficient computational methods for finding ncRNA genes. One effective way of finding ncRNA genes is to look for regions that are similar to known ncRNA genes. As many ncRNAs have well-conserved secondary structures, we need statistical models that can represent such structures for this purpose. In this paper, we propose a new method for representing RNA sequence profiles and finding structural alignment of RNAs based on profile context-sensitive hidden Markov models (profile-csHMMs). Unlike existing models, the proposed approach can handle any kind of RNA secondary structures, including pseudoknots. We show that profile-csHMMs can provide an effective framework for the computational analysis of RNAs and the identification of ncRNA genes

Linguistics and some aspects of its underlying dynamics

In recent years, central components of a new approach to linguistics, the Minimalist Program (MP) have come closer to physics. Features of the Minimalist Program, such as the unconstrained nature of recursive Merge, the operation of the Labeling Algorithm that only operates at the interface of Narrow Syntax with the Conceptual-Intentional and the Sensory-Motor interfaces, the difference between pronounced and un-pronounced copies of elements in a sentence and the build-up of the Fibonacci sequence in the syntactic derivation of sentence structures, are directly accessible to representation in terms of algebraic formalism. Although in our scheme linguistic structures are classical ones, we find that an interesting and productive isomorphism can be established between the MP structure, algebraic structures and many-body field theory opening new avenues of inquiry on the dynamics underlying some central aspects of linguistics.Comment: 17 page

Towards an implementable dependency grammar

The aim of this paper is to define a dependency grammar framework which is both linguistically motivated and computationally parsable. See the demo at http://www.conexor.fi/analysers.html#testingComment: 10 page

On Descriptive Complexity, Language Complexity, and GB

We introduce $L^2_{K,P}$, a monadic second-order language for reasoning about trees which characterizes the strongly Context-Free Languages in the sense that a set of finite trees is definable in $L^2_{K,P}$ iff it is (modulo a projection) a Local Set---the set of derivation trees generated by a CFG. This provides a flexible approach to establishing language-theoretic complexity results for formalisms that are based on systems of well-formedness constraints on trees. We demonstrate this technique by sketching two such results for Government and Binding Theory. First, we show that {\em free-indexation\/}, the mechanism assumed to mediate a variety of agreement and binding relationships in GB, is not definable in $L^2_{K,P}$ and therefore not enforcible by CFGs. Second, we show how, in spite of this limitation, a reasonably complete GB account of English can be defined in $L^2_{K,P}$. Consequently, the language licensed by that account is strongly context-free. We illustrate some of the issues involved in establishing this result by looking at the definition, in $L^2_{K,P}$, of chains. The limitations of this definition provide some insight into the types of natural linguistic principles that correspond to higher levels of language complexity. We close with some speculation on the possible significance of these results for generative linguistics.Comment: To appear in Specifying Syntactic Structures, papers from the Logic, Structures, and Syntax workshop, Amsterdam, Sept. 1994. LaTeX source with nine included postscript figure

Compiling knowledge-based systems from KEE to Ada

The dominant technology for developing AI applications is to work in a multi-mechanism, integrated, knowledge-based system (KBS) development environment. Unfortunately, systems developed in such environments are inappropriate for delivering many applications - most importantly, they carry the baggage of the entire Lisp environment and are not written in conventional languages. One resolution of this problem would be to compile applications from complex environments to conventional languages. Here the first efforts to develop a system for compiling KBS developed in KEE to Ada (trademark). This system is called KATYDID, for KEE/Ada Translation Yields Development Into Delivery. KATYDID includes early prototypes of a run-time KEE core (object-structure) library module for Ada, and translation mechanisms for knowledge structures, rules, and Lisp code to Ada. Using these tools, part of a simple expert system was compiled (not quite automatically) to run in a purely Ada environment. This experience has given us various insights on Ada as an artificial intelligence programming language, potential solutions of some of the engineering difficulties encountered in early work, and inspiration on future system development

Aspects of the theory of syntax Special technical report no. 11

Formulation of transformational grammar - syntax theor