arXiv subjects

Da Zheng

Publications and source records attributed to Da Zheng.

68 records · Page 4Linked to original sources

arXiv2020

Few-shot link prediction via graph neural networks for Covid-19 drug-repurposing

Predicting interactions among heterogenous graph structured data has numerous applications such as knowledge graph completion, recommendation systems and drug discovery. Often times, the links to be predicted belong to rare types such as the case in repurposing drugs for novel diseases. This motivates the task of few-shot link prediction. Typically, GCNs are ill-equipped in learning such rare link types since the relation embedding is not learned in an inductive fashion. This paper proposes an inductive RGCN for learning informative relation embeddings even in the few-shot learning regime. The proposed inductive model significantly outperforms the RGCN and state-of-the-art KGE models in few-shot learning tasks. Furthermore, we apply our method on the drug-repurposing knowledge graph (DRKG) for discovering drugs for Covid-19. We pose the drug discovery task as link prediction and learn embeddings for the biological entities that partake in the DRKG. Our initial results corroborate that several drugs used in clinical trials were identified as possible drug candidates. The method in this paper are implemented using the efficient deep graph learning (DGL)

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arXiv2020

DGL-KE: Training Knowledge Graph Embeddings at Scale

Knowledge graphs have emerged as a key abstraction for organizing information in diverse domains and their embeddings are increasingly used to harness their information in various information retrieval and machine learning tasks. However, the ever growing size of knowledge graphs requires computationally efficient algorithms capable of scaling to graphs with millions of nodes and billions of edges. This paper presents DGL-KE, an open-source package to efficiently compute knowledge graph embeddings. DGL-KE introduces various novel optimizations that accelerate training on knowledge graphs with millions of nodes and billions of edges using multi-processing, multi-GPU, and distributed parallelism. These optimizations are designed to increase data locality, reduce communication overhead, overlap computations with memory accesses, and achieve high operation efficiency. Experiments on knowledge graphs consisting of over 86M nodes and 338M edges show that DGL-KE can compute embeddings in 100 minutes on an EC2 instance with 8 GPUs and 30 minutes on an EC2 cluster with 4 machines with 48 cores/machine. These results represent a 2x~5x speedup over the best competing approaches. DGL-KE is available on https://github.com/awslabs/dgl-ke.

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arXiv2019

Graphyti: A Semi-External Memory Graph Library for FlashGraph

Graph datasets exceed the in-memory capacity of most standalone machines. Traditionally, graph frameworks have overcome memory limitations through scale-out, distributing computing. Emerging frameworks avoid the network bottleneck of distributed data with Semi-External Memory (SEM) that uses a single multicore node and operates on graphs larger than memory. In SEM, $\mathcal{O}(m)$ data resides on disk and $\mathcal{O}(n)$ data in memory, for a graph with $n$ vertices and $m$ edges. For developers, this adds complexity because they must explicitly encode I/O within applications. We present principles that are critical for application developers to adopt in order to achieve state-of-the-art performance, while minimizing I/O and memory for algorithms in SEM. We present them in Graphyti, an extensible parallel SEM graph library built on FlashGraph and available in Python via pip. In SEM, Graphyti achieves 80% of the performance of in-memory execution and retains the performance of FlashGraph, which outperforms distributed engines, such as PowerGraph and Galois.

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arXiv2018

Challenges Towards Deploying Data Intensive Scientific Applications on Extreme Heterogeneity Supercomputers

Shrinking transistors, which powered the advancement of computing in the past half century, has stalled due to power wall; now extreme heterogeneity is promised to be the next driving force to feed the needs of ever-increasingly diverse scientific domains. To unlock the potentials of such supercomputers, we identify eight potential challenges in three categories: First, one needs fast data movement since extreme heterogeneity will inevitably complicate the communication circuits -- thus hampering the data movement. Second, we need to intelligently schedule suitable hardware for corresponding applications/stages. Third, we have to lower the programming complexity in order to encourage the adoption of heterogeneous computing.

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arXiv2017

knor: A NUMA-Optimized In-Memory, Distributed and Semi-External-Memory k-means Library

k-means is one of the most influential and utilized machine learning algorithms. Its computation limits the performance and scalability of many statistical analysis and machine learning tasks. We rethink and optimize k-means in terms of modern NUMA architectures to develop a novel parallelization scheme that delays and minimizes synchronization barriers. The \textit{k-means NUMA Optimized Routine} (\textsf{knor}) library has (i) in-memory (\textsf{knori}), (ii) distributed memory (\textsf{knord}), and (iii) semi-external memory (\textsf{knors}) modules that radically improve the performance of k-means for varying memory and hardware budgets. \textsf{knori} boosts performance for single machine datasets by an order of magnitude or more. \textsf{knors} improves the scalability of k-means on a memory budget using SSDs. \textsf{knors} scales to billions of points on a single machine, using a fraction of the resources that distributed in-memory systems require. \textsf{knord} retains \textsf{knori}'s performance characteristics, while scaling in-memory through distributed computation in the cloud. \textsf{knor} modifies Elkan's triangle inequality pruning algorithm such that we utilize it on billion-point datasets without the significant memory overhead of the original algorithm. We demonstrate \textsf{knor} outperforms distributed commercial products like H$_2$O, Turi (formerly Dato, GraphLab) and Spark's MLlib by more than an order of magnitude for datasets of $10^7$ to $10^9$ points.

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arXiv2017

FlashR: R-Programmed Parallel and Scalable Machine Learning using SSDs

R is one of the most popular programming languages for statistics and machine learning, but the R framework is relatively slow and unable to scale to large datasets. The general approach for speeding up an implementation in R is to implement the algorithms in C or FORTRAN and provide an R wrapper. FlashR takes a different approach: it executes R code in parallel and scales the code beyond memory capacity by utilizing solid-state drives (SSDs) automatically. It provides a small number of generalized operations (GenOps) upon which we reimplement a large number of matrix functions in the R base package. As such, FlashR parallelizes and scales existing R code with little/no modification. To reduce data movement between CPU and SSDs, FlashR evaluates matrix operations lazily, fuses operations at runtime, and uses cache-aware, two-level matrix partitioning. We evaluate FlashR on a variety of machine learning and statistics algorithms on inputs of up to four billion data points. FlashR out-of-core tracks closely the performance of FlashR in-memory. The R code for machine learning algorithms executed in FlashR outperforms the in-memory execution of H2O and Spark MLlib by a factor of 2-10 and outperforms Revolution R Open by more than an order of magnitude.

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arXiv2016

Semi-External Memory Sparse Matrix Multiplication for Billion-Node Graphs

Sparse matrix multiplication is traditionally performed in memory and scales to large matrices using the distributed memory of multiple nodes. In contrast, we scale sparse matrix multiplication beyond memory capacity by implementing sparse matrix dense matrix multiplication (SpMM) in a semi-external memory (SEM) fashion; i.e., we keep the sparse matrix on commodity SSDs and dense matrices in memory. Our SEM-SpMM incorporates many in-memory optimizations for large power-law graphs. It outperforms the in-memory implementations of Trilinos and Intel MKL and scales to billion-node graphs, far beyond the limitations of memory. Furthermore, on a single large parallel machine, our SEM-SpMM operates as fast as the distributed implementations of Trilinos using five times as much processing power. We also run our implementation in memory (IM-SpMM) to quantify the overhead of keeping data on SSDs. SEM-SpMM achieves almost 100% performance of IM-SpMM on graphs when the dense matrix has more than four columns; it achieves at least 65% performance of IM-SpMM on all inputs. We apply our SpMM to three important data analysis tasks--PageRank, eigensolving, and non-negative matrix factorization--and show that our SEM implementations significantly advance the state of the art.

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arXiv2016

An SSD-based eigensolver for spectral analysis on billion-node graphs

Many eigensolvers such as ARPACK and Anasazi have been developed to compute eigenvalues of a large sparse matrix. These eigensolvers are limited by the capacity of RAM. They run in memory of a single machine for smaller eigenvalue problems and require the distributed memory for larger problems. In contrast, we develop an SSD-based eigensolver framework called FlashEigen, which extends Anasazi eigensolvers to SSDs, to compute eigenvalues of a graph with hundreds of millions or even billions of vertices in a single machine. FlashEigen performs sparse matrix multiplication in a semi-external memory fashion, i.e., we keep the sparse matrix on SSDs and the dense matrix in memory. We store the entire vector subspace on SSDs and reduce I/O to improve performance through caching the most recent dense matrix. Our result shows that FlashEigen is able to achieve 40%-60% performance of its in-memory implementation and has performance comparable to the Anasazi eigensolvers on a machine with 48 CPU cores. Furthermore, it is capable of scaling to a graph with 3.4 billion vertices and 129 billion edges. It takes about four hours to compute eight eigenvalues of the billion-node graph using 120 GB memory.

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arXiv2015

Tensor Products of the Operator System Generated by the Cuntz Isometries

We study tensor products and nuclearity-related properties of the operator system $\mathcal S_n$ generated by the Cuntz isometries. By using the nuclearity of the Cuntz algebra, we can show that $\mathcal{S}_n$ is $C^*$-nuclear, and this implies a dual row contraction version of Ando's theorem characterizing operators of numerical radius 1. On the other hand, without using the nuclearity of the Cuntz algebra, we are still able to show directly this Ando type property of dual row contractions and conclude that $\mathcal{S}_n$ is $C^*$-nuclear, which yields a new proof of the nuclearity of the Cuntz algebras. We prove that the dual operator system of $\mathcal{S}_n$ is completely order isomorphic to an operator subsystem of $M_{n+1}$. Finally, a lifting result concerning Popescu's joint numerical radius is proved via operator system techniques.

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arXiv2015

Optimize Unsynchronized Garbage Collection in an SSD Array

Solid state disks (SSDs) have advanced to outperform traditional hard drives significantly in both random reads and writes. However, heavy random writes trigger fre- quent garbage collection and decrease the performance of SSDs. In an SSD array, garbage collection of individ- ual SSDs is not synchronized, leading to underutilization of some of the SSDs. We propose a software solution to tackle the unsyn- chronized garbage collection in an SSD array installed in a host bus adaptor (HBA), where individual SSDs are exposed to an operating system. We maintain a long I/O queue for each SSD and flush dirty pages intelligently to fill the long I/O queues so that we hide the performance imbalance among SSDs even when there are few parallel application writes. We further define a policy of select- ing dirty pages to flush and a policy of taking out stale flush requests to reduce the amount of data written to SSDs. We evaluate our solution in a real system. Experi- ments show that our solution fully utilizes all SSDs in an array under random write-heavy workloads. It improves I/O throughput by up to 62% under random workloads of mixed reads and writes when SSDs are under active garbage collection. It causes little extra data writeback and increases the cache hit rate.

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arXiv2015

The Operator System Generated by Cuntz Isometries

In this paper we consider the operator system $\cl{S}_n$ generated by $n$ Cuntz isometries, i.e. the span of the generators of the Cuntz algebra $\cl{O}_n$ together with their adjoints and the identity. We define an operator subsystem $\cl{E}_n\subseteq M_{n+1}$ and then prove that $\cl{S}_n$ is completely order isomorphic to a quotient of $\cl{E}_n$. This result implies a characterization of positive elements in $M_p(\cl{S}_n)$.

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arXiv2015

Active Community Detection in Massive Graphs

A canonical problem in graph mining is the detection of dense communities. This problem is exacerbated for a graph with a large order and size -- the number of vertices and edges -- as many community detection algorithms scale poorly. In this work we propose a novel framework for detecting active communities that consist of the most active vertices in massive graphs. The framework is applicable to graphs having billions of vertices and hundreds of billions of edges. Our framework utilizes a parallelizable trimming algorithm based on a locality statistic to filter out inactive vertices, and then clusters the remaining active vertices via spectral decomposition on their similarity matrix. We demonstrate the validity of our method with synthetic Stochastic Block Model graphs, using Adjusted Rand Index as the performance metric. We further demonstrate its practicality and efficiency on a most recent real-world Hyperlink Web graph consisting of over 3.5 billion vertices and 128 billion edges.

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arXiv2015

FlashGraph: Processing Billion-Node Graphs on an Array of Commodity SSDs

Graph analysis performs many random reads and writes, thus, these workloads are typically performed in memory. Traditionally, analyzing large graphs requires a cluster of machines so the aggregate memory exceeds the graph size. We demonstrate that a multicore server can process graphs with billions of vertices and hundreds of billions of edges, utilizing commodity SSDs with minimal performance loss. We do so by implementing a graph-processing engine on top of a user-space SSD file system designed for high IOPS and extreme parallelism. Our semi-external memory graph engine called FlashGraph stores vertex state in memory and edge lists on SSDs. It hides latency by overlapping computation with I/O. To save I/O bandwidth, FlashGraph only accesses edge lists requested by applications from SSDs; to increase I/O throughput and reduce CPU overhead for I/O, it conservatively merges I/O requests. These designs maximize performance for applications with different I/O characteristics. FlashGraph exposes a general and flexible vertex-centric programming interface that can express a wide variety of graph algorithms and their optimizations. We demonstrate that FlashGraph in semi-external memory performs many algorithms with performance up to 80% of its in-memory implementation and significantly outperforms PowerGraph, a popular distributed in-memory graph engine.

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arXiv2014

Hadoop in Low-Power Processors

In our previous work we introduced a so-called Amdahl blade microserver that combines a low-power Atom processor, with a GPU and an SSD to provide a balanced and energy-efficient system. Our preliminary results suggested that the sequential I/O of Amdahl blades can be ten times higher than that a cluster of conventional servers with comparable power consumption. In this paper we investigate the performance and energy efficiency of Amdahl blades running Hadoop. Our results show that Amdahl blades are 7.7 times and 3.4 times as energy-efficient as the Open Cloud Consortium cluster for a data-intensive and a compute-intensive application, respectively. The Hadoop Distributed Filesystem has relatively poor performance on Amdahl blades because both disk and network I/O are CPU-heavy operations on Atom processors. We demonstrate three effective techniques to reduce CPU consumption and improve performance. However, even with these improvements, the Atom processor is still the system's bottleneck. We revisit Amdahl's law, and estimate that Amdahl blades need four Atom cores to be well balanced for Hadoop tasks.

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