Results 1 
5 of
5
The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment
 Journal of Computational Biology
, 1997
"... Multiple alignment is an important problem in computational biology. It is well known that it can be solved exactly by a dynamic programming algorithm which in turn can be interpreted as a shortest path computation in a directed acyclic graph. The A algorithm (or goal directed unidirectional search ..."
Abstract

Cited by 19 (3 self)
 Add to MetaCart
(Show Context)
Multiple alignment is an important problem in computational biology. It is well known that it can be solved exactly by a dynamic programming algorithm which in turn can be interpreted as a shortest path computation in a directed acyclic graph. The A algorithm (or goal directed unidirectional search) is a technique that speeds up the computation of a shortest path by transforming the edge lengths without losing the optimality of the shortest path. We implemented the A algorithm in a computer program similar to MSA [GKS95] and FMA [SI97b]. We incorporated in this program new bounding strategies for both, lower and upper bounds and show that the A algorithm, together with our improvements, can speed up computations considerably. Additionally we show that the A algorithm together with a standard bounding technique is superior to the well known CarilloLipman bounding since it excludes more nodes from consideration. 1 Introduction One of the most prominent problems in computational mo...
Fachbereich Mathematik und Informatik
"... In this thesis, we propose a method for modeling utility (rating) functions based on a novel concept called Fuzzy Operator Tree (FOT for short). As the notion suggests, this method makes use of techniques from fuzzy set theory and implements a fuzzy rating function, that is, a utility function that ..."
Abstract
 Add to MetaCart
(Show Context)
In this thesis, we propose a method for modeling utility (rating) functions based on a novel concept called Fuzzy Operator Tree (FOT for short). As the notion suggests, this method makes use of techniques from fuzzy set theory and implements a fuzzy rating function, that is, a utility function that maps to the unit interval, where 0 corresponds to the lowest and 1 to the highest evaluation. Even though the original motivation comes from quality control, FOTs are completely general and widely applicable. Our approach allows a human expert to specify a model in the form of an FOT in a quite convenient and intuitive way. To this end, he simply has to split evaluation criteria into subcriteria in a recursive manner, and to determine in which way these subcriteria ought to be combined: conjunctively, disjunctively, or by means of an averaging operator. The result of this process is the qualitative structure of the model. A second step, then, it is to parameterize the model. To support or even free the expert form this step, we develop a method for calibrating the model on the basis of
Graph Alignment: Robust Data Mining on Structured Objects
, 2004
"... In bioinformatics and chemoinformatics, one is often concerned with the study of objects that have a complex and variable internal structure, e.g. protein structures or small organic molecules. The structure of such objects is frequently correlated with their relevant properties (e.g., biological fu ..."
Abstract
 Add to MetaCart
(Show Context)
In bioinformatics and chemoinformatics, one is often concerned with the study of objects that have a complex and variable internal structure, e.g. protein structures or small organic molecules. The structure of such objects is frequently correlated with their relevant properties (e.g., biological function or toxicity), although the connection between structural features and properties is often complex. Graphs offer an appropriate formalism for modeling structured objects, as they allow a representation of structural features free from losses. Therefore, we propose a method that allows one to examine relationships among the existence of structural patterns in graphs and their membership in certain classes. The method is designed to be very robust against errors and noise as these occur frequently
Sequence Comparison: close and open problems
, 1998
"... Comparing sequences is a very important activity, both in computer science and in many other subjects: for example, thanks to the success of text editors everyone knows the particular instance of sequence comparing problem, known as string matching problem, consisting in searching a word, eventu ..."
Abstract
 Add to MetaCart
(Show Context)
Comparing sequences is a very important activity, both in computer science and in many other subjects: for example, thanks to the success of text editors everyone knows the particular instance of sequence comparing problem, known as string matching problem, consisting in searching a word, eventually with errors, in a very long text.
1 Hybrid DNA Sequence Similarity Scheme for Training Support Vector Machines *
"... Similarity between two DNA sequences is based on alignment. There are different approaches of alignments; each has its own specialty of bearing different information on DNA sequence. This paper presents a study on similarity kernels based on different similarity schemes and proposes a hybrid one. Si ..."
Abstract
 Add to MetaCart
(Show Context)
Similarity between two DNA sequences is based on alignment. There are different approaches of alignments; each has its own specialty of bearing different information on DNA sequence. This paper presents a study on similarity kernels based on different similarity schemes and proposes a hybrid one. Similarity Kernel is required in order to represent the distance or similarity between two DNA sequences. The different schemes of alignments and the cost of computing them, make it further more difficult to decide what scheme to use. In this study we combine different similarity schemes; each scheme is deduced based on alignment. We demonstrate that combining different similarity scheme does in fact generalize well in machine learning. The scoring scheme also turned to have impact on generalization. 1.