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Gaussian Process (GP) formulation of continuoustime trajectory offers a fast solution to the motion planning problem via probabilistic inference on factor graph. However, often the solution converges to in-feasible local minima and the…
In the context of the genome-wide association studies (GWAS), one has to solve long sequences of generalized least-squares problems; such a task has two limiting factors: execution time --often in the range of days or weeks-- and data…
The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a…
The horseshoe prior is frequently employed in Bayesian analysis of high-dimensional models, and has been shown to achieve minimax optimal risk properties when the truth is sparse. While optimization-based algorithms for the extremely…
DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive…
Model selection in Gaussian processes scales prohibitively with the size of the training dataset, both in time and memory. While many approximations exist, all incur inevitable approximation error. Recent work accounts for this error in the…
A fundamental problem in supervised learning is to find a good set of features or distance measures. If the new set of features is of lower dimensionality and can be obtained by a simple transformation of the original data, they can make…
Span programs are a model of computation that have been used to design quantum algorithms, mainly in the query model. For any decision problem, there exists a span program that leads to an algorithm with optimal quantum query complexity,…
We study the Shortest-Walk Problem (SWP) in a Graph of Convex Sets (GCS). A GCS is a graph where each vertex is paired with a convex program, and each edge couples adjacent programs via additional costs and constraints. A walk in a GCS is a…
Recently, graphics processors (GPUs) have been increasingly leveraged in a variety of scientific computing applications. However, architectural differences between CPUs and GPUs necessitate the development of algorithms that take advantage…
Genome sequence analysis is a powerful tool in medical and scientific research. Considering the inevitable sequencing errors and genetic variations, approximate string matching (ASM) has been adopted in practice for genome sequencing.…
With the advance in genome sequencing technology, the lengths of deoxyribonucleic acid (DNA) sequencing results are rapidly increasing at lower prices than ever. However, the longer lengths come at the cost of a heavy computational burden…
Graph Convolutional Networks (GCNs) are recently getting much attention in bioinformatics and chemoinformatics as a state-of-the-art machine learning approach with high accuracy. GCNs process convolutional operations along with graph…
Genomics is the foundation of precision medicine, global food security and virus surveillance. Exact-match is one of the most essential operations widely used in almost every step of genomics such as alignment, assembly, annotation, and…
We present an improved inverse ray-shooting code based on GPUs for generating microlensing magnification maps. In addition to introducing GPUs for acceleration, we put the efforts in two aspects: (i) A standard circular lens plane is…
Subgraph matching has garnered increasing attention for its diverse real-world applications. Given the dynamic nature of real-world graphs, addressing evolving scenarios without incurring prohibitive overheads has been a focus of research.…
Biclustering techniques have been widely used to identify homogeneous subgroups within large data matrices, such as subsets of genes similarly expressed across subsets of patients. Mining a max-sum sub-matrix is a related but distinct…
Small Angle Scattering (SAS) of X-rays or neutrons is an experimental technique that provides valuable structural information for biological macromolecules under physiological conditions and with no limitation on the molecular size. In…
This paper presents a novel approach, named the Group Marching Tree (GMT*) algorithm, to planning on GPUs at rates amenable to application within control loops, allowing planning in real-world settings via repeated computation of…
3D Gaussian Splatting (3DGS) has attracted great attention in novel view synthesis because of its superior rendering efficiency and high fidelity. However, the trained Gaussians suffer from severe zooming degradation due to non-adjustable…