相关论文: Celer: an Efficient Program for Genotype Eliminati…

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…

In this paper, we propose semiparametric efficient estimators of genetic relatedness between two traits in a model-free framework. Most existing methods require specifying certain parametric models involving the traits and genetic variants.…

Many interesting program properties involve the execution of multiple programs, including observational equivalence, noninterference, co-termination, monotonicity, and idempotency. One strategy for verifying such relational properties is to…

Machine learning models make mistakes, yet sometimes it is difficult to identify the systematic problems behind the mistakes. Practitioners engage in various activities, including error analysis, testing, auditing, and red-teaming, to form…

Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…

Computer Algebra systems are widely spread because of some of their remarkable features such as their ease of use and performance. Nonetheless, this focus on performance sometimes leads to unwanted consequences: algorithms and computations…

Some methods aim to correct or test for relationships or to reconstruct the pedigree, or family tree. We show that these methods cannot resolve ties for correct relationships due to identifiability of the pedigree likelihood which is the…

Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…

Enumerating all 3-manifold triangulations of a given size is a difficult but increasingly important problem in computational topology. A key difficulty for enumeration algorithms is that most combinatorial triangulations must be discarded…

Next-generation sequencing techniques have facilitated a large scale analysis of human genetic variation. Despite the advances in sequencing speeds, the computational discovery of structural variants is not yet standard. It is likely that…

Many Mendelian randomization (MR) papers have been conducted only in people of European ancestry, limiting transportability of results to the global population. Expanding MR to diverse ancestry groups is essential to ensure equitable…

With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…

Identification of cognates across related languages is one of the primary problems in historical linguistics. Automated cognate identification is helpful for several downstream tasks including identifying sound correspondences,…

The regression test suite, a key resource for managing program evolution, needs to achieve 100% coverage, or very close, to be useful. Devising a test suite manually is unacceptably tedious, but existing automated methods are often…

In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels…

In this paper we describe SYNERGY, which is a highly parallelizable, linear planning system that is based on the genetic programming paradigm. Rather than reasoning about the world it is planning for, SYNERGY uses artificial selection,…

In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…

Learning neural program embeddings is key to utilizing deep neural networks in program languages research --- precise and efficient program representations enable the application of deep models to a wide range of program analysis tasks.…

Identifying differentially expressed genes from RNA sequencing data remains a challenging task because of the considerable uncertainties in parameter estimation and the small sample sizes in typical applications. Here we introduce Bayesian…