$\textit{De Novo}$ Genome assembly is one of the most important tasks in computational biology. ELBA is the state-of-the-art distributed-memory parallel algorithm for overlap detection and layout simplification steps of $\textit{De Novo}$ genome assembly but exists a performance bottleneck in pairwise alignment. In this work, we proposed 3 GPU schedulers for ELBA to accommodate multiple MPI processes and multiple GPUs. The GPU schedulers enable multiple MPI processes to perform computation on GPUs in a round-robin fashion. Both strong and weak scaling experiments show that 3 schedulers are able to significantly improve the performance of baseline while there is a trade-off between parallelism and GPU scheduler overhead. For the best performance implementation, the one-to-one scheduler achieves $\sim$7-8$\times$ speed-up using 25 MPI processes compared with the baseline vanilla ELBA GPU scheduler.
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Top-$k$ frequent items detection is a fundamental task in data stream mining. Many promising solutions are proposed to improve memory efficiency while still maintaining high accuracy for detecting the Top-$k$ items. Despite the memory efficiency concern, the users could suffer from privacy loss if participating in the task without proper protection, since their contributed local data streams may continually leak sensitive individual information. However, most existing works solely focus on addressing either the memory-efficiency problem or the privacy concerns but seldom jointly, which cannot achieve a satisfactory tradeoff between memory efficiency, privacy protection, and detection accuracy. In this paper, we present a novel framework HG-LDP to achieve accurate Top-$k$ item detection at bounded memory expense, while providing rigorous local differential privacy (LDP) protection. Specifically, we identify two key challenges naturally arising in the task, which reveal that directly applying existing LDP techniques will lead to an inferior ``accuracy-privacy-memory efficiency'' tradeoff. Therefore, we instantiate three advanced schemes under the framework by designing novel LDP randomization methods, which address the hurdles caused by the large size of the item domain and by the limited space of the memory. We conduct comprehensive experiments on both synthetic and real-world datasets to show that the proposed advanced schemes achieve a superior ``accuracy-privacy-memory efficiency'' tradeoff, saving $2300\times$ memory over baseline methods when the item domain size is $41,270$. Our code is open-sourced via the link.
Let $\Omega = [0,1]^d$ be the unit cube in $\mathbb{R}^d$. We study the problem of how efficiently, in terms of the number of parameters, deep neural networks with the ReLU activation function can approximate functions in the Sobolev spaces $W^s(L_q(\Omega))$ and Besov spaces $B^s_r(L_q(\Omega))$, with error measured in the $L_p(\Omega)$ norm. This problem is important when studying the application of neural networks in a variety of fields, including scientific computing and signal processing, and has previously been solved only when $p=q=\infty$. Our contribution is to provide a complete solution for all $1\leq p,q\leq \infty$ and $s > 0$ for which the corresponding Sobolev or Besov space compactly embeds into $L_p$. The key technical tool is a novel bit-extraction technique which gives an optimal encoding of sparse vectors. This enables us to obtain sharp upper bounds in the non-linear regime where $p > q$. We also provide a novel method for deriving $L_p$-approximation lower bounds based upon VC-dimension when $p < \infty$. Our results show that very deep ReLU networks significantly outperform classical methods of approximation in terms of the number of parameters, but that this comes at the cost of parameters which are not encodable.
It is common to model a deterministic response function, such as the output of a computer experiment, as a Gaussian process with a Mat\'ern covariance kernel. The smoothness parameter of a Mat\'ern kernel determines many important properties of the model in the large data limit, including the rate of convergence of the conditional mean to the response function. We prove that the maximum likelihood estimate of the smoothness parameter cannot asymptotically undersmooth the truth when the data are obtained on a fixed bounded subset of $\mathbb{R}^d$. That is, if the data-generating response function has Sobolev smoothness $\nu_0 > d/2$, then the smoothness parameter estimate cannot be asymptotically less than $\nu_0$. The lower bound is sharp. Additionally, we show that maximum likelihood estimation recovers the true smoothness for a class of compactly supported self-similar functions. For cross-validation we prove an asymptotic lower bound $\nu_0 - d/2$, which however is unlikely to be sharp. The results are based on approximation theory in Sobolev spaces and some general theorems that restrict the set of values that the parameter estimators can take.
Lexical ambiguity is a challenging and pervasive problem in machine translation (\mt). We introduce a simple and scalable approach to resolve translation ambiguity by incorporating a small amount of extra-sentential context in neural \mt. Our approach requires no sense annotation and no change to standard model architectures. Since actual document context is not available for the vast majority of \mt training data, we collect related sentences for each input to construct pseudo-documents. Salient words from pseudo-documents are then encoded as a prefix to each source sentence to condition the generation of the translation. To evaluate, we release \docmucow, a challenge set for translation disambiguation based on the English-German \mucow \cite{raganato-etal-2020-evaluation} augmented with document IDs. Extensive experiments show that our method translates ambiguous source words better than strong sentence-level baselines and comparable document-level baselines while reducing training costs.
Linear regression is one of the most fundamental linear algebra problems. Given a dense matrix $A \in \mathbb{R}^{n \times d}$ and a vector $b$, the goal is to find $x'$ such that $ \| Ax' - b \|_2^2 \leq (1+\epsilon) \min_{x} \| A x - b \|_2^2 $. The best classical algorithm takes $O(nd) + \mathrm{poly}(d/\epsilon)$ time [Clarkson and Woodruff STOC 2013, Nelson and Nguyen FOCS 2013]. On the other hand, quantum linear regression algorithms can achieve exponential quantum speedups, as shown in [Wang Phys. Rev. A 96, 012335, Kerenidis and Prakash ITCS 2017, Chakraborty, Gily{\'e}n and Jeffery ICALP 2019]. However, the running times of these algorithms depend on some quantum linear algebra-related parameters, such as $\kappa(A)$, the condition number of $A$. In this work, we develop a quantum algorithm that runs in $\widetilde{O}(\epsilon^{-1}\sqrt{n}d^{1.5}) + \mathrm{poly}(d/\epsilon)$ time. It provides a quadratic quantum speedup in $n$ over the classical lower bound without any dependence on data-dependent parameters. In addition, we also show our result can be generalized to multiple regression and ridge linear regression.
Radio Frequency Interference (RFI) detection and mitigation is critical for enabling and maximising the scientific output of radio telescopes. The emergence of machine learning methods capable of handling large datasets has led to their application in radio astronomy, particularly in RFI detection. Spiking Neural Networks (SNNs), inspired by biological systems, are well-suited for processing spatio-temporal data. This study introduces the first application of SNNs to an astronomical data-processing task, specifically RFI detection. We adapt the nearest-latent-neighbours (NLN) algorithm and auto-encoder architecture proposed by previous authors to SNN execution by direct ANN2SNN conversion, enabling simplified downstream RFI detection by sampling the naturally varying latent space from the internal spiking neurons. We evaluate performance with the simulated HERA telescope and hand-labelled LOFAR dataset that the original authors provided. We additionally evaluate performance with a new MeerKAT-inspired simulation dataset. This dataset focuses on satellite-based RFI, an increasingly important class of RFI and is, therefore, an additional contribution. Our SNN approach remains competitive with the original NLN algorithm and AOFlagger in AUROC, AUPRC and F1 scores for the HERA dataset but exhibits difficulty in the LOFAR and MeerKAT datasets. However, our method maintains this performance while completely removing the compute and memory-intense latent sampling step found in NLN. This work demonstrates the viability of SNNs as a promising avenue for machine-learning-based RFI detection in radio telescopes by establishing a minimal performance baseline on traditional and nascent satellite-based RFI sources and is the first work to our knowledge to apply SNNs in astronomy.
Spectral clustering (SC) is a popular clustering technique to find strongly connected communities on a graph. SC can be used in Graph Neural Networks (GNNs) to implement pooling operations that aggregate nodes belonging to the same cluster. However, the eigendecomposition of the Laplacian is expensive and, since clustering results are graph-specific, pooling methods based on SC must perform a new optimization for each new sample. In this paper, we propose a graph clustering approach that addresses these limitations of SC. We formulate a continuous relaxation of the normalized minCUT problem and train a GNN to compute cluster assignments that minimize this objective. Our GNN-based implementation is differentiable, does not require to compute the spectral decomposition, and learns a clustering function that can be quickly evaluated on out-of-sample graphs. From the proposed clustering method, we design a graph pooling operator that overcomes some important limitations of state-of-the-art graph pooling techniques and achieves the best performance in several supervised and unsupervised tasks.
Incompleteness is a common problem for existing knowledge graphs (KGs), and the completion of KG which aims to predict links between entities is challenging. Most existing KG completion methods only consider the direct relation between nodes and ignore the relation paths which contain useful information for link prediction. Recently, a few methods take relation paths into consideration but pay less attention to the order of relations in paths which is important for reasoning. In addition, these path-based models always ignore nonlinear contributions of path features for link prediction. To solve these problems, we propose a novel KG completion method named OPTransE. Instead of embedding both entities of a relation into the same latent space as in previous methods, we project the head entity and the tail entity of each relation into different spaces to guarantee the order of relations in the path. Meanwhile, we adopt a pooling strategy to extract nonlinear and complex features of different paths to further improve the performance of link prediction. Experimental results on two benchmark datasets show that the proposed model OPTransE performs better than state-of-the-art methods.
It is important to detect anomalous inputs when deploying machine learning systems. The use of larger and more complex inputs in deep learning magnifies the difficulty of distinguishing between anomalous and in-distribution examples. At the same time, diverse image and text data are available in enormous quantities. We propose leveraging these data to improve deep anomaly detection by training anomaly detectors against an auxiliary dataset of outliers, an approach we call Outlier Exposure (OE). This enables anomaly detectors to generalize and detect unseen anomalies. In extensive experiments on natural language processing and small- and large-scale vision tasks, we find that Outlier Exposure significantly improves detection performance. We also observe that cutting-edge generative models trained on CIFAR-10 may assign higher likelihoods to SVHN images than to CIFAR-10 images; we use OE to mitigate this issue. We also analyze the flexibility and robustness of Outlier Exposure, and identify characteristics of the auxiliary dataset that improve performance.
Neural machine translation (NMT) is a deep learning based approach for machine translation, which yields the state-of-the-art translation performance in scenarios where large-scale parallel corpora are available. Although the high-quality and domain-specific translation is crucial in the real world, domain-specific corpora are usually scarce or nonexistent, and thus vanilla NMT performs poorly in such scenarios. Domain adaptation that leverages both out-of-domain parallel corpora as well as monolingual corpora for in-domain translation, is very important for domain-specific translation. In this paper, we give a comprehensive survey of the state-of-the-art domain adaptation techniques for NMT.
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