相关论文: Robust Seriation and Applications to Cancer Genomi…

Seriation seeks to reconstruct a linear order between variables using unsorted, pairwise similarity information. It has direct applications in archeology and shotgun gene sequencing for example. We write seriation as an optimization problem…

We describe a seriation algorithm for ranking a set of items given pairwise comparisons between these items. Intuitively, the algorithm assigns similar rankings to items that compare similarly with all others. It does so by constructing a…

Seriation is a problem consisting of seeking the best enumeration order of a set of units whose interrelationship is described by a bipartite graph, that is, a graph whose nodes are partitioned in two sets and arcs only connect nodes in…

The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…

Matrix seriation, the problem of permuting the rows and columns of a matrix to uncover latent structure, is a fundamental technique in data science, particularly in the visualization and analysis of relational data. Applications span…

Linear discrimination, from the point of view of numerical linear algebra, can be treated as solving an ill-posed system of linear equations. In order to generate a solution that is robust in the presence of noise, these problems require…

Grouping elements into families to analyse them separately is a standard analysis procedure in many areas of sciences. We propose herein a new algorithm based on the simple idea that members from a family look like each other, and don't…

The seriation problem is an important ordering issue which consists of finding the best ordering of a set of units whose interrelationship is defined by a bipartite graph. It has important applications in, e.g., archaeology, anthropology,…

The genomic profile underlying an individual tumor can be highly informative in the creation of a personalized cancer treatment strategy for a given patient; a practice known as precision oncology. This involves next generation sequencing…

Sorting a permutation by reversals is a famous problem in genome rearrangements. Since 1997, quite some biological evidence were found that in many genomes the reversed regions are usually flanked by a pair of inverted repeats. This type of…

Recent advancements in quantum computing and quantum-inspired algorithms have sparked renewed interest in binary optimization. These hardware and software innovations promise to revolutionize solution times for complex problems. In this…

The emerging field of precision oncology relies on the accurate pinpointing of alterations in the molecular profile of a tumor to provide personalized targeted treatments. Current methodologies in the field commonly include the application…

Active seriation aims at recovering an unknown ordering of $n$ items by adaptively querying pairwise similarities. The observations are noisy measurements of entries of an underlying $n$ x $n$ permuted Robinson matrix, whose permutation…

Many nuclear safety applications need fast, portable, and accurate imagers to better locate radiation sources. The Rotating Scatter Mask (RSM) system is an emerging device with the potential to meet these needs. The main challenge is the…

We study the problem of circular seriation, where we are given a matrix of pairwise dissimilarities between $n$ objects, and the goal is to find a {\em circular order} of the objects in a manner that is consistent with their dissimilarity.…

Complex structures are typical in machine learning. Tailoring learning algorithms for every structure requires an effort that may be saved by defining a generic learning procedure adaptive to any complex structure. In this paper, we propose…

Seriation methods order a set of descriptions given some criterion (e.g., unimodality or minimum distance between similarity scores). Seriation is thus inherently a problem of finding the optimal solution among a set of permutations of…

Near term quantum computers suffer from the presence of different noise sources. In order to mitigate for this effect and acquire results with significantly better accuracy, there is the urge of designing efficient error correction or error…

We introduce the strongly NP-complete pagination problem, an extension of BIN PACKING where packing together two items may make them occupy less volume than the sum of their individual sizes. To achieve this property, an item is defined as…

Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…