Chromatic scheduling of dynamic data-graph computations

Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2013.Cataloged from PDF version of thesis.Includes bibliographical references (pages 67-73).Data-graph computations are a parallel-programming model popularized by programming systems such as Pregel, GraphLab, PowerGraph, and GraphChi. A fundamental issue in parallelizing data-graph computations is the avoidance of races between computation occurring on overlapping regions of the graph. Common solutions such as locking protocols and bulk-synchronous execution often sacrifice performance, update atomicity, or determinism. A known alternative is chromatic scheduling which uses a vertex coloring of the conflict graph to divide data-graph updates into sets which may be parallelized without races. To date, however, only static data-graph computations, which do not schedule updates at runtime, have employed chromatic scheduling. I introduce PRISM, a work-efficient scheduling algorithm for dynamic data-graph computations that uses chromatic scheduling. For a collection of four application benchmarks on a modern multicore machine, chromatic scheduling approximately doubles the performance of the lock-based GraphLab implementation, and triples the performance of GraphChi's update execution phase when enforcing determinism. Chromatic scheduling motivates the development of efficient deterministic parallel coloring algorithms. New analysis of the Jones-Plassmann message-passing algorithm shows that only O([Delta] + In A in V/ In ln V) rounds are needed to color a graph G = (V, E) with max vertex degree [Delta], generalizing previous results for bounded degree graphs. A new log-degree ordering heuristic is described which can reduce the number of colors used in practice, while only increasing the number of rounds by a logrithmic factor. An efficient implementation for the shared-memory setting is described and analyzed using the CRQW contention model, showing that this algorithm performs [Theta](V + E) work and has expected span O([Delta] In [Delta]A + 1n 2[Delta] In V/In In V). Benchmarks on a set of real world graphs show that, in practice, these parallel algorithms achieve modest speedup over optimized serial code (around 4x on a 12-core machine).by Tim Kaler.M. Eng

EvolveGCN: Evolving Graph Convolutional Networks for Dynamic Graphs

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at \url{https://github.com/IBM/EvolveGCN}.Comment: AAAI 2020. The code is available at https://github.com/IBM/EvolveGC

Rotation of young stars in Cepheus OB3b

We present a photometric study of I-band variability in the young association Cepheus OB3b. The study is sensitive to periodic variability on time-scales of less than a day, to more than 20 d. After rejection of contaminating objects using V, I, R and narrow-band Hα photometry, we find 475 objects with measured rotation periods, which are very likely pre-main-sequence members of the Cep OB3b star-forming region. We revise the distance and age to Cep OB3b, putting it on the self-consistent age and distance ladder of Mayne & Naylor. This yields a distance modulus of 8.8 ± 0.2 mag, corresponding to a distance of 580 ± 60 pc, and an age of 4–5 Myr. The rotation period distribution confirms the general picture of rotational evolution in young stars, exhibiting both the correlation between accretion (determined in this case through narrow-band Hα photometry) and rotation expected from disc locking, and the dependence of rotation upon mass that is seen in other star-forming regions. However, this mass dependence is much weaker in our data than found in other studies. Comparison to the similarly aged NGC 2362 shows that the low-mass stars in Cep OB3b are rotating much more slowly. This points to a possible link between star-forming environment and rotation properties. Such a link would call into question models of stellar angular momentum evolution, which assume that the rotational period distributions of young clusters and associations can be assembled into an evolutionary sequence, thus ignoring environmental effects

Adjunctive rifampicin for Staphylococcus aureus bacteraemia (ARREST): a multicentre, randomised, double-blind, placebo-controlled trial.

BACKGROUND: Staphylococcus aureus bacteraemia is a common cause of severe community-acquired and hospital-acquired infection worldwide. We tested the hypothesis that adjunctive rifampicin would reduce bacteriologically confirmed treatment failure or disease recurrence, or death, by enhancing early S aureus killing, sterilising infected foci and blood faster, and reducing risks of dissemination and metastatic infection. METHODS: In this multicentre, randomised, double-blind, placebo-controlled trial, adults (≥18 years) with S aureus bacteraemia who had received ≤96 h of active antibiotic therapy were recruited from 29 UK hospitals. Patients were randomly assigned (1:1) via a computer-generated sequential randomisation list to receive 2 weeks of adjunctive rifampicin (600 mg or 900 mg per day according to weight, oral or intravenous) versus identical placebo, together with standard antibiotic therapy. Randomisation was stratified by centre. Patients, investigators, and those caring for the patients were masked to group allocation. The primary outcome was time to bacteriologically confirmed treatment failure or disease recurrence, or death (all-cause), from randomisation to 12 weeks, adjudicated by an independent review committee masked to the treatment. Analysis was intention to treat. This trial was registered, number ISRCTN37666216, and is closed to new participants. FINDINGS: Between Dec 10, 2012, and Oct 25, 2016, 758 eligible participants were randomly assigned: 370 to rifampicin and 388 to placebo. 485 (64%) participants had community-acquired S aureus infections, and 132 (17%) had nosocomial S aureus infections. 47 (6%) had meticillin-resistant infections. 301 (40%) participants had an initial deep infection focus. Standard antibiotics were given for 29 (IQR 18-45) days; 619 (82%) participants received flucloxacillin. By week 12, 62 (17%) of participants who received rifampicin versus 71 (18%) who received placebo experienced treatment failure or disease recurrence, or died (absolute risk difference -1·4%, 95% CI -7·0 to 4·3; hazard ratio 0·96, 0·68-1·35, p=0·81). From randomisation to 12 weeks, no evidence of differences in serious (p=0·17) or grade 3-4 (p=0·36) adverse events were observed; however, 63 (17%) participants in the rifampicin group versus 39 (10%) in the placebo group had antibiotic or trial drug-modifying adverse events (p=0·004), and 24 (6%) versus six (2%) had drug interactions (p=0·0005). INTERPRETATION: Adjunctive rifampicin provided no overall benefit over standard antibiotic therapy in adults with S aureus bacteraemia. FUNDING: UK National Institute for Health Research Health Technology Assessment

Communication-Efficient Graph Neural Networks with Probabilistic Neighborhood Expansion Analysis and Caching

Training and inference with graph neural networks (GNNs) on massive graphs has been actively studied since the inception of GNNs, owing to the widespread use and success of GNNs in applications such as recommendation systems and financial forensics. This paper is concerned with minibatch training and inference with GNNs that employ node-wise sampling in distributed settings, where the necessary partitioning of vertex features across distributed storage causes feature communication to become a major bottleneck that hampers scalability. To significantly reduce the communication volume without compromising prediction accuracy, we propose a policy for caching data associated with frequently accessed vertices in remote partitions. The proposed policy is based on an analysis of vertex-wise inclusion probabilities (VIP) during multi-hop neighborhood sampling, which may expand the neighborhood far beyond the partition boundaries of the graph. VIP analysis not only enables the elimination of the communication bottleneck, but it also offers a means to organize in-memory data by prioritizing GPU storage for the most frequently accessed vertex features. We present SALIENT++, which extends the prior state-of-the-art SALIENT system to work with partitioned feature data and leverages the VIP-driven caching policy. SALIENT++ retains the local training efficiency and scalability of SALIENT by using a deep pipeline and drastically reducing communication volume while consuming only a fraction of the storage required by SALIENT. We provide experimental results with the Open Graph Benchmark data sets and demonstrate that training a 3-layer GraphSAGE model with SALIENT++ on 8 single-GPU machines is 7.1 faster than with SALIENT on 1 single-GPU machine, and 12.7 faster than with DistDGL on 8 single-GPU machines.Comment: MLSys 2023. Code is available at https://github.com/MITIBMxGraph/SALIENT_plusplu

A Multicore Path to Connectomics-on-Demand

The current design trend in large scale machine learning is to use distributed clusters of CPUs and GPUs with MapReduce-style programming. Some have been led to believe that this type of horizontal scaling can reduce or even eliminate the need for traditional algorithm development, careful parallelization, and performance engineering. This paper is a case study showing the contrary: that the benefits of algorithms, parallelization, and performance engineering, can sometimes be so vast that it is possible to solve "cluster-scale" problems on a single commodity multicore machine. Connectomics is an emerging area of neurobiology that uses cutting edge machine learning and image processing to extract brain connectivity graphs from electron microscopy images. It has long been assumed that the processing of connectomics data will require mass storage, farms of CPU/GPUs, and will take months (if not years) of processing time. We present a high-throughput connectomics-on-demand system that runs on a multicore machine with less than 100 cores and extracts connectomes at the terabyte per hour pace of modern electron microscopes.National Science Foundation (U.S.) (grant IIS-1447786)National Science Foundation (U.S.) (grant CCF1563880)United States. Intelligence Advanced Research Projects Activity (grant 138076-5093555