相关论文: SOPanG 2: online searching over a pan-genome witho…

We model and discuss advantages of pan-editing, the complex way of expressing mitochondrial genes in kinetoplastids. The rapid spread and preservation of pan-editing seems to be due to its concomitant fragment dispersal. Such dispersal…

We consider a method to jointly estimate sparse precision matrices and their underlying graph structures using dependent high-dimensional datasets. We present a penalized maximum likelihood estimator which encourages both sparsity and…

This paper proposes a novel Extended Particle Swarm Optimization model (EPSO) that potentially enhances the search process of PSO for optimization problem. Evidently, gene expression profiles are significantly important measurement factor…

Coding over subsets (known as generations) rather than over all content blocks in P2P distribution networks and other applications is necessary for a number of practical reasons such as computational complexity. A penalty for coding only…

Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two…

Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…

The motivation of this work is to improve the performance of standard stacking approaches or ensembles, which are composed of simple, heterogeneous base models, through the integration of the generation and selection stages for regression…

Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…

A hypergraph is a generalization of a graph, in which a hyperedge can connect multiple vertices, modeling complex relationships involving multiple vertices simultaneously. Hypergraph pattern matching, which is to find all isomorphic…

Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…

The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…

Transcriptional profiling on microarrays to obtain gene expressions has been used to facilitate cancer diagnosis. We propose a deep generative machine learning architecture (called DeepCancer) that learn features from unlabeled microarray…

Generative approaches have been recently shown to be effective for both Entity Disambiguation and Entity Linking (i.e., joint mention detection and disambiguation). However, the previously proposed autoregressive formulation for EL suffers…

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…

Research on overlapped and discontinuous named entity recognition (NER) has received increasing attention. The majority of previous work focuses on either overlapped or discontinuous entities. In this paper, we propose a novel span-based…

In the genomic era, the identification of gene signatures associated with disease is of significant interest. Such signatures are often used to predict clinical outcomes in new patients and aid clinical decision-making. However, recent…

Resting-state EEG offers a non-invasive view of spontaneous brain activity, yet the extraction of meaningful patterns is often constrained by limited availability of high-quality data, and heavy reliance on manually engineered EEG features.…

In medical documents, it is possible that an entity of interest not only contains a discontiguous sequence of words but also overlaps with another entity. Entities of such structures are intrinsically hard to recognize due to the large…

We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…

Pattern matching of streaming time series with lower latency under limited computing resource comes to a critical problem, especially as the growth of Industry 4.0 and Industry Internet of Things. However, against traditional single pattern…