Related papers: Sequence alignment, mutual information, and dissim…
Background: Alignment of biological sequences such as DNA, RNA or proteins is one of the most widely used tools in computational bioscience. All existing alignment algorithms rely on heuristic scoring schemes based on biological expertise.…
Motivation: Clustering is a frequently used concept in variety of bioinformatical applications. We present a new method for hierarchical clustering of data called mutual information clustering (MIC) algorithm. It uses mutual information…
A new class of distances appropriate for measuring similarity relations between sequences, say one type of similarity per distance, is studied. We propose a new ``normalized information distance'', based on the noncomputable notion of…
We present a method for hierarchical clustering of data called {\it mutual information clustering} (MIC) algorithm. It uses mutual information (MI) as a similarity measure and exploits its grouping property: The MI between three objects $X,…
Information distance is a parameter-free similarity measure based on compression, used in pattern recognition, data mining, phylogeny, clustering, and classification. The notion of information distance is extended from pairs to multiples…
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…
Enormous volumes of short reads data from next-generation sequencing (NGS) technologies have posed new challenges to the area of genomic sequence comparison. The multiple sequence alignment approach is hardly applicable to NGS data due to…
Clustering is a concept used in a huge variety of applications. We review a conceptually very simple algorithm for hierarchical clustering called in the following the {\it mutual information clustering} (MIC) algorithm. It uses mutual…
Normalized information distance (NID) uses the theoretical notion of Kolmogorov complexity, which for practical purposes is approximated by the length of the compressed version of the file involved, using a real-world compression program.…
Multimodal image alignment is the process of finding spatial correspondences between images formed by different imaging techniques or under different conditions, to facilitate heterogeneous data fusion and correlative analysis. The…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Normalized information distance (NID) uses the theoretical notion of Kolmogorov complexity, which for practical purposes is approximated by the length of the compressed version of the file involved, using a real-world compression program.…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
In this paper we exploit concepts of information theory to address the fundamental problem of identifying and defining the most suitable tools to extract, in a automatic and agnostic way, information from a generic string of characters. We…
The ability of machine learning (ML) algorithms to generalize well to unseen data has been studied through the lens of information theory, by bounding the generalization error with the input-output mutual information (MI), i.e., the MI…
The mutual information (MI) between two random variables is an important correlation measure in data analysis. The Shannon entropy of a joint probability distribution is the variable part under fixed marginals. We aim to minimize and…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
The normalized information distance is a universal distance measure for objects of all kinds. It is based on Kolmogorov complexity and thus uncomputable, but there are ways to utilize it. First, compression algorithms can be used to…