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When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may…
Decision trees and randomized forests are widely used in computer vision and machine learning. Standard algorithms for decision tree induction optimize the split functions one node at a time according to some splitting criteria. This greedy…
The evolution of parallel I/O library as well as new concepts such as 'in transit' and 'in situ' visualization and analysis have been identified as key technologies to circumvent I/O bottleneck in pre-exascale applications. Nevertheless,…
In this work, we bridge standard adaptive mesh refinement and coarsening on scalable octree background meshes and robust unfitted finite element formulations for the automatic and efficient solution of large-scale nonlinear solid mechanics…
We propose efficient parallel algorithms and implementations on shared memory architectures of LU factorization over a finite field. Compared to the corresponding numerical routines, we have identified three main difficulties specific to…
In this thesis, Minimal Partitioning (MP) algorithm, an innovative algorithm for enumerating all the spanning trees in an undirected graph is presented. While MP algorithm uses a computational tree graph to traverse all possible spanning…
Tree ensembles are powerful models that achieve excellent predictive performances, but can grow to unwieldy sizes. These ensembles are often post-processed (pruned) to reduce memory footprint and improve interpretability. We present…
In this paper, we present a new algorithm for computing the linear recurrence relations of multi-dimensional sequences. Existing algorithms for computing these relations arise in computational algebra and include constructing structured…
Current popular methods for Magnetic Resonance Fingerprint (MRF) recovery are bottlenecked by the heavy computations of a matched-filtering step due to the growing size and complexity of the fingerprint dictionaries in multi-parametric…
K-nearest neighbor (kNN) search has wide applications in many areas, including data mining, machine learning, statistics and many applied domains. Inspired by the success of ensemble methods and the flexibility of tree-based methodology, we…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
Parallel implementation of numerical adaptive mesh refinement (AMR)strategies for solving 3D elastostatic contact mechanics problems is an essential step toward complex simulations that exceed current performance levels. This paper…
We present parallel algorithms for constructing and traversing sparse octrees on graphics processing units (GPUs). The algorithms are based on parallel-scan and sort methods. To test the performance and feasibility, we implemented them in…
To answer traffic engineering goals, current backbone networks use expensive and sophisticated equipments, that run distributed algorithms to imple- ment dynamic multi-path routing (e.g., MPLS tunnels and dynamic trunk rerout- ing). We…
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
Many of the distributed localization algorithms are based on relaxed optimization formulations of the localization problem. These algorithms commonly rely on first-order optimization methods, and hence may require many iterations or…
The Aho, Hopcroft and Ullman (AHU) algorithm has been the state of the art since the 1970s for determining in linear time whether two unordered rooted trees are isomorphic or not. However, it has been criticized (by Campbell and Radford)…
We introduce a deep recursive octree network for the compression of 3D voxel data. Our network compresses a voxel grid of any size down to a very small latent space in an autoencoder-like network. We show results for compressing 32, 64 and…
When considering the number of subtrees of trees, the extremal structures which maximize this number among binary trees and trees with a given maximum degree lead to some interesting facts that correlate to other graphical indices in…
We describe a framework for maintaining forest algebra representations that are of logarithmic height for unranked trees. Such representations can be computed in O(n) time and updated in O(log(n)) time. The framework is of potential…