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Register a new userCommunication-Efficient Jaccard Similarity for High-Performance Distributed Genome Comparisons
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Added by
Maciej Besta
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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The Jaccard similarity index is an important measure of the overlap of two sets, widely used in machine learning, computational genomics, information retrieval, and many other areas. We design and implement SimilarityAtScale, the first communication-efficient distributed algorithm for computing the Jaccard similarity among pairs of large datasets. Our algorithm provides an efficient encoding of this problem into a multiplication of sparse matrices. Both the encoding and sparse matrix product are performed in a way that minimizes data movement in terms of communication and synchronization costs. We apply our algorithm to obtain similarity among all pairs of a set of large samples of genomes. This task is a key part of modern metagenomics analysis and an evergrowing need due to the increasing availability of high-throughput DNA sequencing data. The resulting scheme is the first to enable accurate Jaccard distance derivations for massive datasets, using largescale distributed-memory systems. We package our routines in a tool, called GenomeAtScale, that combines the proposed algorithm with tools for processing input sequences. Our evaluation on real data illustrates that one can use GenomeAtScale to effectively employ tens of thousands of processors to reach new frontiers in large-scale genomic and metagenomic analysis. While GenomeAtScale can be used to foster DNA research, the more general underlying SimilarityAtScale algorithm may be used for high-performance distributed similarity computations in other data analytics application domains.
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Large-scale distributed training of neural networks is often limited by network bandwidth, wherein the communication time overwhelms the local computation time. Motivated by the success of sketching methods in sub-linear/streaming algorithms, we introduce Sketched SGD, an algorithm for carrying out distributed SGD by communicating sketches instead of full gradients. We show that Sketched SGD has favorable convergence rates on several classes of functions. When considering all communication -- both of gradients and of updated model weights -- Sketched SGD reduces the amount of communication required compared to other gradient compression methods from $mathcal{O}(d)$ or $mathcal{O}(W)$ to $mathcal{O}(log d)$, where $d$ is the number of model parameters and $W$ is the number of workers participating in training. We run experiments on a transformer model, an LSTM, and a residual network, demonstrating up to a 40x reduction in total communication cost with no loss in final model performance. We also show experimentally that Sketched SGD scales to at least 256 workers without increasing communication cost or degrading model performance.
We investigate fast and communication-efficient algorithms for the classic problem of minimizing a sum of strongly convex and smooth functions that are distributed among $n$ different nodes, which can communicate using a limited number of bits. Most previous communication-efficient approaches for this problem are limited to first-order optimization, and therefore have emph{linear} dependence on the condition number in their communication complexity. We show that this dependence is not inherent: communication-efficient methods can in fact have sublinear dependence on the condition number. For this, we design and analyze the first communication-efficient distributed variants of preconditioned gradient descent for Generalized Linear Models, and for Newtons method. Our results rely on a new technique for quantizing both the preconditioner and the descent direction at each step of the algorithms, while controlling their convergence rate. We also validate our findings experimentally, showing fast convergence and reduced communication.
When the data is distributed across multiple servers, lowering the communication cost between the servers (or workers) while solving the distributed learning problem is an important problem and is the focus of this paper. In particular, we propose a fast, and communication-efficient decentralized framework to solve the distributed machine learning (DML) problem. The proposed algorithm, Group Alternating Direction Method of Multipliers (GADMM) is based on the Alternating Direction Method of Multipliers (ADMM) framework. The key novelty in GADMM is that it solves the problem in a decentralized topology where at most half of the workers are competing for the limited communication resources at any given time. Moreover, each worker exchanges the locally trained model only with two neighboring workers, thereby training a global model with a lower amount of communication overhead in each exchange. We prove that GADMM converges to the optimal solution for convex loss functions, and numerically show that it converges faster and more communication-efficient than the state-of-the-art communication-efficient algorithms such as the Lazily Aggregated Gradient (LAG) and dual averaging, in linear and logistic regression tasks on synthetic and real datasets. Furthermore, we propose Dynamic GADMM (D-GADMM), a variant of GADMM, and prove its convergence under the time-varying network topology of the workers.
Distributed implementations of gradient-based methods, wherein a server distributes gradient computations across worker machines, need to overcome two limitations: delays caused by slow running machines called stragglers, and communication overheads. Recently, Ye and Abbe [ICML 2018] proposed a coding-theoretic paradigm to characterize a fundamental trade-off between computation load per worker, communication overhead per worker, and straggler tolerance. However, their proposed coding schemes suffer from heavy decoding complexity and poor numerical stability. In this paper, we develop a communication-efficient gradient coding framework to overcome these drawbacks. Our proposed framework enables using any linear code to design the encoding and decoding functions. When a particular code is used in this framework, its block-length determines the computation load, dimension determines the communication overhead, and minimum distance determines the straggler tolerance. The flexibility of choosing a code allows us to gracefully trade-off the straggler threshold and communication overhead for smaller decoding complexity and higher numerical stability. Further, we show that using a maximum distance separable (MDS) code generated by a random Gaussian matrix in our framework yields a gradient code that is optimal with respect to the trade-off and, in addition, satisfies stronger guarantees on numerical stability as compared to the previously proposed schemes. Finally, we evaluate our proposed framework on Amazon EC2 and demonstrate that it reduces the average iteration time by 16% as compared to prior gradient coding schemes.
Information compression is essential to reduce communication cost in distributed optimization over peer-to-peer networks. This paper proposes a communication-efficient linearly convergent distributed (COLD) algorithm to solve strongly convex optimization problems. By compressing innovation vectors, which are the differences between decision vectors and their estimates, COLD is able to achieve linear convergence for a class of $delta$-contracted compressors. We explicitly quantify how the compression affects the convergence rate and show that COLD matches the same rate of its uncompressed version. To accommodate a wider class of compressors that includes the binary quantizer, we further design a novel dynamical scaling mechanism and obtain the linearly convergent Dyna-COLD. Importantly, our results strictly improve existing results for the quantized consensus problem. Numerical experiments demonstrate the advantages of both algorithms under different compressors.
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