Related papers: Improving spliced alignment for identification of …
The automated assembly of complex products requires a system that can automatically plan a physically feasible sequence of actions for assembling many parts together. In this paper, we present ASAP, a physics-based planning approach for…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
Graph-SLAM is a well-established algorithm for constructing a topological map of the environment while simultaneously attempting the localisation of the robot. It relies on scan matching algorithms to align noisy observations along robot's…
Progressive methods offer efficient and reasonably good solutions to the multiple sequence alignment problem. However, resulting alignments are biased by guide-trees, especially for relatively distant sequences. We propose MSARC, a new…
Context: The huge and still rapidly growing amount of galaxies in modern sky surveys raises the need of an automated and objective classification method. Unsupervised learning algorithms are of particular interest, since they discover…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
In Artificial Intelligence with Coalition Structure Generation (CSG) one refers to those cooperative complex problems that require to find an optimal partition, maximising a social welfare, of a set of entities involved in a system into…
Conformal prediction is a statistical framework that generates prediction sets containing ground-truth labels with a desired coverage guarantee. The predicted probabilities produced by machine learning models are generally miscalibrated,…
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…
Discovering and clustering subspaces in high-dimensional data is a fundamental problem of machine learning with a wide range of applications in data mining, computer vision, and pattern recognition. Earlier methods divided the problem into…
We have formulated the problem of generating periodic dense paritcle packings as an optimization problem called the Adaptive Shrinking Cell (ASC) formulation [S. Torquato and Y. Jiao, Phys. Rev. E {\bf 80}, 041104 (2009)]. Because the…
In this study, we investigate the application of Semidefinite Programming (SDP) to phylogenetics. SDP is a powerful optimization framework that seeks to optimize a linear objective function over the cone of positive semidefinite matrices.…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
We describe a new global multiple alignment program capable of aligning a large number of genomic regions. Our progressive alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic…
Ashtiani et al. (NIPS 2016) introduced a semi-supervised framework for clustering (SSAC) where a learner is allowed to make same-cluster queries. More specifically, in their model, there is a query oracle that answers queries of the form…
Genome sequencing technology has improved significantly in few last years and resulted in abundance genetic data. Artificial intelligence has been employed to analyze genetic data in response to its sheer size and variability. Gene…
In solving hard computational problems, semidefinite program (SDP) relaxations often play an important role because they come with a guarantee of optimality. Here, we focus on a popular semidefinite relaxation of K-means clustering which…
Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence alignments (MSAs) and phylogenetic trees of large datasets.…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
In order to study real-world systems, many applied works model them through signed graphs, i.e. graphs whose edges are labeled as either positive or negative. Such a graph is considered as structurally balanced when it can be partitioned…