Related papers: MaxSSmap: A GPU program for mapping divergent shor…
Maxflow is a fundamental problem in graph theory and combinatorial optimisation, used to determine the maximum flow from a source node to a sink node in a flow network. It finds applications in diverse domains, including computer networks,…
Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long…
The ability of Gaussian processes (GPs) to predict the behavior of dynamical systems as a more sample-efficient alternative to parametric models seems promising for real-world robotics research. However, the computational complexity of GPs…
GPS receivers embedded in cell phones and connected vehicles generate a series of location measurements that can be used for various analytical purposes. A common pre-processing step of this data is the so-called map matching. The goal of…
Globally consistent dense maps are a key requirement for long-term robot navigation in complex environments. While previous works have addressed the challenges of dense mapping and global consistency, most require more computational…
Max-product Belief Propagation (BP) is a popular message-passing algorithm for computing a Maximum-A-Posteriori (MAP) assignment over a distribution represented by a Graphical Model (GM). It has been shown that BP can solve a number of…
The problem of finding a maximum size matching in a graph (known as the maximum matching problem) is one of the most classical problems in computer science. Despite a significant body of work dedicated to the study of this problem in the…
Energy consumption of memory accesses dominates the compute energy in energy-constrained robots which require a compact 3D map of the environment to achieve autonomy. Recent mapping frameworks only focused on reducing the map size while…
In this paper, we address a long-standing challenge: how to achieve both efficiency and scalability in solving semidefinite programming problems. We propose breakthrough acceleration techniques for a wide range of low-rank…
Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis. This step -- called sequence alignment -- is the computational bottleneck because: (1) it is…
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…
Pansharpening aims to generate high-resolution multispectral (HRMS) images by fusing low-resolution multispectral (LRMS) and high-resolution panchromatic (PAN) images while preserving both spectral and spatial information. Although deep…
Maximum Inner Product Search or top-k retrieval on sparse vectors is well-understood in information retrieval, with a number of mature algorithms that solve it exactly. However, all existing algorithms are tailored to text and…
We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…
Most genetic algorithms (GAs) used in literature to solve control problems are time consuming and involve important storage memory requirements. In fact, the search in GAs is iteratively performed on a population of chromosomes (control…
In recent years graphical processing units (GPUs) have become a powerful tool in scientific computing. Their potential to speed up highly parallel applications brings the power of high performance computing to a wider range of users.…
We study the problem of maximizing a monotone submodular set function subject to linear packing constraints. An instance of this problem consists of a matrix $A \in [0,1]^{m \times n}$, a vector $b \in [1,\infty)^m$, and a monotone…
Planning long-horizon robot manipulation requires making discrete decisions about which objects to interact with and continuous decisions about how to interact with them. A robot planner must select grasps, placements, and motions that are…
In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…