相关论文: Joint Overlap Analysis of Multiple Genomic Interva…

Overlap is a common phenomenon seen when structural components of a digital object are neither disjoint nor nested inside each other. Overlapping components resist reduction to a structural hierarchy, and tree-based indexing and query…

Detecting changepoints in a time series of length $N$ entails evaluating up to $2^{N-1}$ possible changepoint models, making exhaustive enumeration computationally infeasible. Genetic algorithms (GAs) provide a stochastic way to identify…

Identifying intersections among a set of d-dimensional rectangular regions (d-rectangles) is a common problem in many simulation and modeling applications. Since algorithms for computing intersections over a large number of regions can be…

Quantifying how hard it is to build a molecular graph matters for biosignature detection, chemical complexity, and cheminformatics. We present an exact, scalable algorithm to compute the molecular assembly index (MA) which prioritizes the…

Efficient large-scale annotation of genomic intervals is essential for personal genome interpretation in the realm of precision medicine. There are 13 possible relations between two intervals according to Allen's interval algebra.…

Genetic Algorithms (GAs) are used to solve search and optimization problems in which an optimal solution can be found using an iterative process with probabilistic and non-deterministic transitions. However, depending on the problem's…

Automatic protein function prediction (AFP) is classified as a large-scale multi-label classification problem aimed at automating protein enrichment analysis to eliminate the current reliance on labor-intensive wet-lab methods. Currently,…

This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…

Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

The emerging class of instance-optimized systems has shown potential to achieve high performance by specializing to a specific data and query workloads. Particularly, Machine Learning (ML) techniques have been applied successfully to build…

Evolutionary relationships between species are usually inferred through phylogenetic analysis, which provides phylogenetic trees computed from allelic profiles built by sequencing specific regions of the sequences and abstracting them to…

In medicine, visualizing chromosomes is important for medical diagnostics, drug development, and biomedical research. Unfortunately, chromosomes often overlap and it is necessary to identify and distinguish between the overlapping…

This paper studies large-scale dynamical networks where the current state of the system is a linear transformation of the previous state, contaminated by a multivariate Gaussian noise. Examples include stock markets, human brains and gene…

The landscape of deep learning has vastly expanded the frontiers of source code analysis, particularly through the utilization of structural representations such as Abstract Syntax Trees (ASTs). While these methodologies have demonstrated…

Abstract syntax tree (AST) mapping algorithms are widely used to analyze changes in source code. Despite the foundational role of AST mapping algorithms, little effort has been made to evaluate the accuracy of AST mapping algorithms, i.e.,…

Using (a,b)-trees as an example, we show how to perform a parallel split with logarithmic latency and parallel join, bulk updates, intersection, union (or merge), and (symmetric) set difference with logarithmic latency and with information…

Axis-aligned decision trees are fast and stable but struggle on datasets with rotated or interaction-dependent decision boundaries, where informative splits require linear combinations of features rather than single-feature thresholds.…

Graphical modeling is a widely used tool for analyzing conditional dependencies between variables and traditional methods may struggle to capture shared and distinct structures in multi-group or multi-condition settings. Joint graphical…