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  1. Bender, M. ; Gilbert, J. ; Hendrickson, B. ; Sullivan, B. (Ed.)
    We design new serial and parallel approximation algorithms for computing a maximum weight b-matching in an edge-weighted graph with a submodular objective function. This problem is NP-hard; the new algorithms have approximation ratio 1/3, and are relaxations of the Greedy algorithm that rely only on local information in the graph, making them parallelizable. We have designed and implemented Local Lazy Greedy algorithms for both serial and parallel computers. We have applied the approximate submodular b-matching algorithm to assign tasks to processors in the computation of Fock matrices in quantum chemistry on parallel computers. The assignment seeks to reduce the run time by balancing the computational load on the processors and bounding the number of messages that each processor sends. We show that the new assignment of tasks to processors provides a four fold speedup over the currently used assignment in the NWChemEx software on 8000 processors on the Summit supercomputer at Oak Ridge National Lab.
  2. We consider how to generate graphs of arbitrary size whose chromatic numbers can be chosen (or are well-bounded) for testing graph coloring algorithms on parallel computers. For the distance-1 graph coloring problem, we identify three classes of graphs with this property. The first is the Erdős-Rényi random graph with prescribed expected degree, where the chromatic number is known with high probability. It is also known that the Greedy algorithm colors this graph using at most twice the number of colors as the chromatic number. The second is a random geometric graph embedded in hyperbolic space where the size of the maximum clique provides a tight lower bound on the chromatic number. The third is a deterministic graph described by Mycielski, where the graph is recursively constructed such that its chromatic number is known and increases with graph size, although the size of the maximum clique remains two. For Jacobian estimation, we bound the distance-2 chromatic number of random bipartite graphs by considering its equivalence to distance-1 coloring of an intersection graph. We use a “balls and bins” probabilistic analysis to establish a lower bound and an upper bound on the distance-2 chromatic number. The regimes of graph sizes and probabilitiesmore »that we consider are chosen to suit the Jacobian estimation problem, where the number of columns and rows are asymptotically nearly equal, and have number of nonzeros linearly related to the number of columns. Computationally we verify the theoretical predictions and show that the graphs are often be colored optimally by the serial and parallel Greedy algorithms.« less
  3. We present the augmented matrix for principal submatrix update (AMPS) algorithm, a finite element solution method that combines principal submatrix updates and Schur complement techniques, well-suited for interactive simulations of deformation and cutting of finite element meshes. Our approach features real-time solutions to the updated stiffness matrix systems to account for interactive changes in mesh connectivity and boundary conditions. Updates are accomplished by an augmented matrix formulation of the stiffness equations to maintain its consistency with changes to the underlying model without refactorization at each timestep. As changes accumulate over multiple simulation timesteps, the augmented solution algorithm enables tens or hundreds of updates per second. Acceleration schemes that exploit sparsity, memoization and parallelization lead to the updates being computed in real-time. The complexity analysis and experimental results for this method demonstrate that it scales linearly with the number of nonzeros of the factors of the stiffness matrix. Results for cutting and deformation of 3D elastic models are reported for meshes with up to 50,000 nodes, and involve models of surgery for astigmatism and the brain.
  4. We consider the maximum vertex-weighted matching problem (MVM), in which non-negative weights are assigned to the vertices of a graph, and the weight of a matching is the sum of the weights of the matched vertices. Although exact algorithms for MVM are faster than exact algorithms for the maximum edge-weighted matching problem, there are graphs on which these exact algorithms could take hundreds of hours. For a natural number k, we design a k/(k + 1)approximation algorithm for MVM on non-bipartite graphs that updates the matching along certain short paths in the graph: either augmenting paths of length at most 2k + 1 or weight-increasing paths of length at most 2k. The choice of k = 2 leads to a 2/3-approximation algorithm that computes nearly optimal weights fast. This algorithm could be initialized with a 2/3-approximate maximum cardinality matching to reduce its runtime in practice. A 1/2-approximation algorithm may be obtained using k = 1, which is faster than the 2/3-approximation algorithm but it computes lower weights. The 2/3-approximation algorithm has time complexity O(Δ2m) while the time complexity of the 1/2-approximation algorithm is O(Δm), where m is the number of edges and Δ is the maximum degree of a vertex.more »Results from our serial implementations show that on average the 1/2-approximation algorithm runs faster than the Suitor algorithm (currently the fastest 1/2-approximation algorithm) while the 2/3-approximation algorithm runs as fast as the Suitor algorithm but obtains higher weights for the matching. One advantage of the proposed algorithms is that they are well-suited for parallel implementation since they can process vertices to match in any order. The 1/2- and 2/3-approximation algorithms have been implemented on a shared memory parallel computer, and both approximation algorithms obtain good speedups, while the former algorithm runs faster on average than the parallel Suitor algorithm. Care is needed to design the parallel algorithm to avoid cyclic waits, and we prove that it is live-lock free.« less
  5. We survey recent work on approximation algorithms for computing degree-constrained subgraphs in graphs and their applications in combinatorial scientific computing. The problems we consider include maximization versions of cardinality matching, edge-weighted matching, vertex-weighted matching and edge-weighted $b$ -matching, and minimization versions of weighted edge cover and $b$ -edge cover. Exact algorithms for these problems are impractical for massive graphs with several millions of edges. For each problem we discuss theoretical foundations, the design of several linear or near-linear time approximation algorithms, their implementations on serial and parallel computers, and applications. Our focus is on practical algorithms that yield good performance on modern computer architectures with multiple threads and interconnected processors. We also include information about the software available for these problems.
  6. We explore the problem of sharing data that pertains to individuals with anonymity guarantees, where each user requires a desired level of privacy. We propose the first shared-memory as well as distributed memory parallel algorithms for the k-anonimity problem that achieves this goal, and produces high quality anonymized datasets. The new algorithm is based on an optimization procedure that iteratively computes weights on the edges of a dissimilarity matrix, and at each iteration computes a minimum weighted b-edgecover in the graph. We describe how a 2-approximation algorithm for computing the b-edgecover can be used to solve the adaptive anonymity problem in parallel. We are able to solve adaptive anonymity problems with hundreds of thousands of instances and hundreds of features on a supercomputer in under five minutes. Our algorithm scales up to 8000 cores on a distributed memory supercomputer, while also providing good speedups on shared memory multiprocessors. On smaller problems where an a Belief Propagation algorithm is feasible, our algorithm is two orders of magnitude faster.
  7. We present an automated pipeline capable of distinguishing the phenotypes of myeloid-derived suppressor cells (MDSC) in healthy and tumor-bearing tissues in mice using flow cytometry data. In contrast to earlier work where samples are analyzed individually, we analyze all samples from each tissue collectively using a representative template for it. We demonstrate with 43 flow cytometry samples collected from three tissues, naive bone-marrow, spleens of tumor-bearing mice, and intra-peritoneal tumor, that a set of templates serves as a better classifier than popular machine learning approaches including support vector machines and neural networks. Our "interpretable machine learning" approach goes beyond classification and identifies distinctive phenotypes associated with each tissue, information that is clinically useful. Hence the pipeline presented here leads to better understanding of the maturation and differentiation of MDSCs using high-throughput data.
  8. We describe two new 3/2-approximation algorithms and a new 2-approximation algorithm for the minimum weight edge cover problem in graphs. We show that one of the 3/2-approximation algorithms, the Dual cover algorithm, computes the lowest weight edge cover relative to previously known algorithms as well as the new algorithms reported here. The Dual cover algorithm can also be implemented to be faster than the other 3/2-approximation algorithms on serial computers. Many of these algorithms can be extended to solve the 6-Edge cover problem as well. We show the relation of these algorithms to the K-Nearest Neighbor graph construction in semi-supervised learning and other applications.