Theoretically Efficient Parallel Graph Algorithms Can Be Fast and Scalable

There has been significant recent interest in parallel graph processing due to the need to quickly analyze the large graphs available today. Many graph codes have been designed for distributed memory or external memory. However, today even the largest publicly-available real-world graph (the Hyperlink Web graph with over 3.5 billion vertices and 128 billion edges) can fit in the memory of a single commodity multicore server. Nevertheless, most experimental work in the literature report results on much smaller graphs, and the ones for the Hyperlink graph use distributed or external memory. Therefore, it is natural to ask whether we can efficiently solve a broad class of graph problems on this graph in memory. This paper shows that theoretically-efficient parallel graph algorithms can scale to the largest publicly-available graphs using a single machine with a terabyte of RAM, processing them in minutes. We give implementations of theoretically-efficient parallel algorithms for 20 important graph problems. We also present the optimizations and techniques that we used in our implementations, which were crucial in enabling us to process these large graphs quickly. We show that the running times of our implementations outperform existing state-of-the-art implementations on the largest real-world graphs. For many of the problems that we consider, this is the first time they have been solved on graphs at this scale. We have made the implementations developed in this work publicly-available as the Graph-Based Benchmark Suite (GBBS).Comment: This is the full version of the paper appearing in the ACM Symposium on Parallelism in Algorithms and Architectures (SPAA), 201

HaTS: Hardware-Assisted Transaction Scheduler

In this paper we present HaTS, a Hardware-assisted Transaction Scheduler. HaTS improves performance of concurrent applications by classifying the executions of their atomic blocks (or in-memory transactions) into scheduling queues, according to their so called conflict indicators. The goal is to group those transactions that are conflicting while letting non-conflicting transactions proceed in parallel. Two core innovations characterize HaTS. First, HaTS does not assume the availability of precise information associated with incoming transactions in order to proceed with the classification. It relaxes this assumption by exploiting the inherent conflict resolution provided by Hardware Transactional Memory (HTM). Second, HaTS dynamically adjusts the number of the scheduling queues in order to capture the actual application contention level. Performance results using the STAMP benchmark suite show up to 2x improvement over state-of-the-art HTM-based scheduling techniques

Novel molecular insights about lactobacillar sortase-dependent piliation

One of the more conspicuous structural features that punctuate the outer cell surface of certain bacterial Gram-positive genera and species is the sortase-dependent pilus. As these adhesive and variable-length protrusions jut outward from the cell, they provide a physically expedient and useful means for the initial contact between a bacterium and its ecological milieu. The sortase-dependent pilus displays an elongated macromolecular architecture consisting of two to three types of monomeric protein subunits (pilins), each with their own specific function and location, and that are joined together covalently by the transpeptidyl activity of a pilus-specific C-type sortase enzyme. Sortase-dependent pili were first detected among the Gram-positive pathogens and subsequently categorized as an essential virulence factor for host colonization and tissue invasion by these harmful bacteria. However, the sortase-dependent pilus was rebranded as also a niche-adaptation factor after it was revealed that “friendly” Gram-positive commensals exhibit the same kind of pilus structures, which includes two contrasting gut-adapted species from the Lactobacillus genus, allochthonous Lactobacillus rhamnosus and autochthonous Lactobacillus ruminis. This review will highlight and discuss what has been learned from the latest research carried out and published on these lactobacillar pilus types.Peer reviewe

A Music Therapy Protocol for Pain Management in Individuals with Cerebral Palsy

The purpose of this project was to develop an individualized Management for Differing Types of Pain in Cerebral Palsy: Music Therapy Protocol on the use of music therapy for pain management and reduction with individuals with cerebral palsy. Most studies addressing pain and music therapy do not investigate the cerebral palsy population. Therefore, a synthesis of the current literature of pain and music therapy informed the development of this protocol. Many individuals in this population experience pain daily and research investigating pain management for this population is needed. The protocol developed outlines interventions to reduce pain specific to the cerebral palsy diagnosis based on a synthesis of the literature from different populations experiencing pain. The sessions outline 30 minutes of music therapy interventions to alleviate specific types of pain for clients with cerebral palsy with reminders to music therapists to constantly assess for pain and discomfort within sessions. Along with the protocol, the music therapist developed five music tracks to accompany the interventions presented within the protocol. The music therapist developed a guided imagery backing track, heartbeat entrainment track, slow breathing music assisted relaxation track, vagus nerve stimulation backing track, and an alternative music engagement backing track. The music therapist synthesized all research found on specific musical elements that reduce pain and used these parameters when creating each track. Each music track can be manipulated within GarageBand to best fit the needs of each client

A Faster Distributed Single-Source Shortest Paths Algorithm

We devise new algorithms for the single-source shortest paths (SSSP) problem with non-negative edge weights in the CONGEST model of distributed computing. While close-to-optimal solutions, in terms of the number of rounds spent by the algorithm, have recently been developed for computing SSSP approximately, the fastest known exact algorithms are still far away from matching the lower bound of $\tilde \Omega (\sqrt{n} + D)$ rounds by Peleg and Rubinovich [SIAM Journal on Computing 2000], where $n$ is the number of nodes in the network and $D$ is its diameter. The state of the art is Elkin's randomized algorithm [STOC 2017] that performs $\tilde O(n^{2/3} D^{1/3} + n^{5/6})$ rounds. We significantly improve upon this upper bound with our two new randomized algorithms for polynomially bounded integer edge weights, the first performing $\tilde O (\sqrt{n D})$ rounds and the second performing $\tilde O (\sqrt{n} D^{1/4} + n^{3/5} + D)$ rounds. Our bounds also compare favorably to the independent result by Ghaffari and Li [STOC 2018]. As side results, we obtain a $(1 + \epsilon)$-approximation $\tilde O ((\sqrt{n} D^{1/4} + D) / \epsilon)$-round algorithm for directed SSSP and a new work/depth trade-off for exact SSSP on directed graphs in the PRAM model.Comment: Presented at the the 59th Annual IEEE Symposium on Foundations of Computer Science (FOCS 2018