Related papers: Permutation patterns in genome rearrangement probl…
Permutation testing in linear models, where the number of nuisance coefficients is smaller than the sample size, is a well-studied topic. The common approach of such tests is to permute residuals after regressing on the nuisance covariates.…
Recently, different works proposed a new way to mine patterns in databases with pathological size. For example, experiments in genome biology usually provide databases with thousands of attributes (genes) but only tens of objects…
Open set recognition problems exist in many domains. For example in security, new malware classes emerge regularly; therefore malware classification systems need to identify instances from unknown classes in addition to discriminating…
We initiate the study of sorting permutations using prefix block-interchanges, which exchange any prefix of a permutation with another non-intersecting interval. The goal is to transform a given permutation into the identity permutation…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…
Testing whether the observed data conforms to a purported model (probability distribution) is a basic and fundamental statistical task, and one that is by now well understood. However, the standard formulation, identity testing, fails to…
Compression of integer sets and sequences has been extensively studied for settings where elements follow a uniform probability distribution. In addition, methods exist that exploit clustering of elements in order to achieve higher…
In this paper we present a novel tool to evaluate problem solving systems. Instead of using a system to solve a problem, we suggest using the problem to evaluate the system. By finding a numerical representation of a problem's complexity,…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
The simple permutations in two permutation classes --- the 321-avoiding permutations and the skew-merged permutations --- are enumerated using a uniform method. In both cases, these enumerations were known implicitly, by working backwards…
The genome-wide recombination rate ($RR$) of a species is often described by one parameter, the ratio between total genetic map length ($G$) and physical map length ($P$), measured in centiMorgans per Megabase (cM/Mb). The value of this…
Evolving networks with a constant number of edges may be modelled using a rewiring process. These models are used to describe many real-world processes including the evolution of cultural artifacts such as family names, the evolution of…
Permutation Matrices are a well known class of matrices which encode the elements of the symmetric group on $d$ elements as a square $d\times d$ matrix. Motivated by [4], we define a similar class of matrices which are a generalization of…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
Prefix parsing asks whether an input prefix can be extended to a complete string generated by a given grammar. In the weighted setting, it also provides prefix probabilities, which are central to context-free language modeling,…
In this chapter we provide a theoretically founded investigation of state-of-the-art learning approaches for inverse problems from the point of view of spectral reconstruction operators. We give an extended definition of regularization…
The classes of tree permutations and forest permutations were defined by Acan and Hitczenko (2016). We study random permutations of a given length from these classes, and in particular the number of occurrences of a fixed pattern in one of…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
A permutation of n letters is k-prolific if each (n-k)-subset of the letters in its one-line notation forms a unique pattern. We present a complete characterization of k-prolific permutations for each k, proving that k-prolific permutations…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…