04301 Abstracts Collection -- Cache-Oblivious and Cache-Aware Algorithms

The Dagstuhl Seminar 04301 ``Cache-Oblivious and Cache-Aware Algorithms\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl, from 18.07.2004 to 23.07.2004. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

On-the-Fly Maintenance of Series-Parallel Relationships in Fork-Join Multithreaded Programs

A key capability of data-race detectors is to determine whether one thread executes logically in parallel with another or whether the threads must operate in series. This paper provides two algorithms, one serial and one parallel, to maintain series-parallel (SP) relationships "on the fly" for fork-join multithreaded programs. The serial SP-order algorithm runs in O(1) amortized time per operation. In contrast, the previously best algorithm requires a time per operation that is proportional to Tarjan’s functional inverse of Ackermann’s function. SP-order employs an order-maintenance data structure that allows us to implement a more efficient "English-Hebrew" labeling scheme than was used in earlier race detectors, which immediately yields an improved determinacy-race detector. In particular, any fork-join program running in T₁ time on a single processor can be checked on the fly for determinacy races in O(T₁) time. Corresponding improved bounds can also be obtained for more sophisticated data-race detectors, for example, those that use locks. By combining SP-order with Feng and Leiserson’s serial SP-bags algorithm, we obtain a parallel SP-maintenance algorithm, called SP-hybrid. Suppose that a fork-join program has n threads, T₁ work, and a critical-path length of T[subscript â]. When executed on P processors, we prove that SP-hybrid runs in O((T₁/P + PT[subscript â]) lg n) expected time. To understand this bound, consider that the original program obtains linear speed-up over a 1-processor execution when P = O(T₁/T[subscript â]). In contrast, SP-hybrid obtains linear speed-up when P = O(√T₁/T[subscript â]), but the work is increased by a factor of O(lg n).Singapore-MIT Alliance (SMA

Key Extraction from the Primary Side of a Switched-Mode Power Supply

In this paper we detail techniques that can be used to analyze and attack an AES implementation on an FPGA from the primary (i.e., external) side of a switched-mode power supply. Our attack only requires measurements of the duty cycle of the power supply, and then increases the signal-to-noise ratio (SNR) though averaging, deconvolution and wavelet based detrending. The result is an exploitable source of leakage that allows a secret key to be determined from low-frequency power measurements. The techniques and procedures provide a general approach to performing differential power analysis (DPA) from a single point of information for any single hypothesized intermediate value, suggesting their potential for improving other types of side-channel analysis

Adversarial Analyses of Window Backoff Strategies for Simple Multiple-Access Channels

Backoff strategies have typically been analyzed by making statistical assumptions on the distribution of problem inputs. Although these analyses have provided valuable insights into the efficacy of various backoff strategies, they leave open the question as to which backoff algorithms perform best in the worst case or on inputs, such as bursty inputs, that are not covered by the statistical models. This paper analyzes randomized backoff strategies using worst-case assumptions on the inputs. Specifically, we analyze algorithms for simple multiple-access channels, where the only feedback from each attempt to send a packet is a single bit indicating whether the transmission succeeded or the packet collided with another packet. We analyze a class of strategies, called window strategies, where each packet partitions time into a sequence (W₁, W₂,...) of windows. Within each window, the packet makes an access attempt during a single randomly selected slot. If its transmission is unsuccessful, it waits for its slot in the next window before retrying. We use delay-sequence arguments to show that for the batch problem, in which n packets all arrive at time 0, if every window has size W = Θ(n), then with high probability, all packets successfully transmit with makespan n lg lg n ± O(n). We use this result to analyze window backoff strategies with varying window sizes. Specifically, we show that the familiar binary exponential backoff algorithm, where Wk = Θ(2k), has makespan Θ(n lg n), and that more generally, for any constant r > 1, the r-exponential backoff algorithm in which Wk = Θ(rk) has makespan Θ(n lglg rn). We also show that for any constant r > 1, the r-polynomial backoff algorithm, in which Wk = Θ(kr), has makespan Θ((n/lg n)¹⁺¹/r). All of these batch strategies are monotonic, in the sense that the window size monotonically increases over time. We exhibit a monotonic backoff algorithm that achieves makespan Θ(n lg lg n/lg lg lg n). We prove that this algorithm, whose backoff is superpolynomial and subexponential, is optimal over all monotonic backoff schemes. In addition, we exhibit a simple backoff/backon algorithm, having window sizes that vary nonmonotonically according to a "sawtooth" pattern, that achieves the optimal makespan of Θ(n). We study the online setting using an adversarial queueing model. We define a (λ,T)-stream to be an input stream of packets in which at most n = λT packets arrive during any time interval of size T. In this model, to evaluate a given backoff algorithm (which does not know λ or T), we analyze the worst-case behavior of the algorithm over the class of (λ,T)-streams. Our results for the online setting focus on exponential backoff. We show that for any arrival rate λ, there exists a sufficiently large interval size T such that the throughput goes to 0 for some (λ,T)-stream. Moreover, there exists a sufficiently large constant c such that for any interval size T, if λ ⥠c lg lg n/lg n, the system is unstable in the sense that the arrival rate exceeds the throughput in the worst case. If, on the other hand, we have λ ⤠c/lg n for a sufficiently small constant c, then the system is stable. Surprisingly, the algorithms that guarantee smaller makespans in the batch setting require lower arrival rates to achieve stability than does exponential backoff, but when they are stable, they have better response times.Singapore-MIT Alliance (SMA

Inducing and exploiting activation sparsity for fast neural network inference

Optimizing convolutional neural networks for fast inference has recently become an extremely active area of research. One of the go-to solutions in this context is weight pruning, which aims to reduce computational and memory footprint by removing large subsets of the connections in a neural network. Surprisingly, much less attention has been given to exploiting sparsity in the activation maps, which tend to be naturally sparse in many settings thanks to the structure of rectified linear (ReLU) activation functions. In this paper, we present an in-depth analysis of methods for maximizing the sparsity of the activations in a trained neural network, and show that, when coupled with an efficient sparse-input convolution algorithm, we can leverage this sparsity for significant performance gains. To induce highly sparse activation maps without accuracy loss, we introduce a new regularization technique, coupled with a new threshold-based sparsification method based on a parameterized activation function called Forced-Activation-Threshold Rectified Linear Unit (FATReLU). We examine the impact of our methods on popular image classification models, showing that most architectures can adapt to significantly sparser activation maps without any accuracy loss. Our second contribution is showing that these these compression gains can be translated into inference speedups: we provide a new algorithm to enable fast convolution operations over networks with sparse activations, and show that it can enable significant speedups for end-to-end inference on a range of popular models on the large-scale ImageNet image classification task on modern Intel CPUs, with little or no retraining cost

Integrated analysis of germline and somatic variants in ovarian cancer

We report the first large-scale exome-wide analysis of the combined germline-somatic landscape in ovarian cancer. Here we analyze germline and somatic alterations in 429 ovarian carcinoma cases and 557 controls. We identify 3,635 high confidence, rare truncation and 22,953 missense variants with predicted functional impact. We find germline truncation variants and large deletions across Fanconi pathway genes in 20% of cases. Enrichment of rare truncations is shown in BRCA1, BRCA2, and PALB2. Additionally, we observe germline truncation variants in genes not previously associated with ovarian cancer susceptibility (NF1, MAP3K4, CDKN2B, and MLL3). Evidence for loss of heterozygosity was found in 100% and 76% of cases with germline BRCA1 and BRCA2 truncations respectively. Germline-somatic interaction analysis combined with extensive bioinformatics annotation identifies 237 candidate functional germline truncation and missense variants, including 2 pathogenic BRCA1 and 1 TP53 deleterious variants. Finally, integrated analyses of germline and somatic variants identify significantly altered pathways, including the Fanconi, MAPK, and MLL pathways

Characterizing genomic alterations in cancer by complementary functional associations.

Systematic efforts to sequence the cancer genome have identified large numbers of mutations and copy number alterations in human cancers. However, elucidating the functional consequences of these variants, and their interactions to drive or maintain oncogenic states, remains a challenge in cancer research. We developed REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene dependency of oncogenic pathways or sensitivity to a drug treatment. We used REVEALER to uncover complementary genomic alterations associated with the transcriptional activation of β-catenin and NRF2, MEK-inhibitor sensitivity, and KRAS dependency. REVEALER successfully identified both known and new associations, demonstrating the power of combining functional profiles with extensive characterization of genomic alterations in cancer genomes

The Integrated Genomic Landscape of Thymic Epithelial Tumors

Thymic epithelial tumors (TETs) are one of the rarest adult malignancies. Among TETs, thymoma is the most predominant, characterized by a unique association with autoimmune diseases, followed by thymic carcinoma, which is less common but more clinically aggressive. Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype. We further demonstrate a marked prevalence of a thymoma-specific mutated oncogene, GTF2I, and explore its biological effects on multi-platform analysis. We further observe enrichment of mutations in HRAS, NRAS, and TP53. Last, we identify a molecular link between thymoma and the autoimmune disease myasthenia gravis, characterized by tumoral overexpression of muscle autoantigens, and increased aneuploidy

Patterns and functional implications of rare germline variants across 12 cancer types

Large-scale cancer sequencing data enable discovery of rare germline cancer susceptibility variants. Here we systematically analyse 4,034 cases from The Cancer Genome Atlas cancer cases representing 12 cancer types. We find that the frequency of rare germline truncations in 114 cancer-susceptibility-associated genes varies widely, from 4% (acute myeloid leukaemia (AML)) to 19% (ovarian cancer), with a notably high frequency of 11% in stomach cancer. Burden testing identifies 13 cancer genes with significant enrichment of rare truncations, some associated with specific cancers (for example, RAD51C, PALB2 and MSH6 in AML, stomach and endometrial cancers, respectively). Significant, tumour-specific loss of heterozygosity occurs in nine genes (ATM, BAP1, BRCA1/2, BRIP1, FANCM, PALB2 and RAD51C/D). Moreover, our homology-directed repair assay of 68 BRCA1 rare missense variants supports the utility of allelic enrichment analysis for characterizing variants of unknown significance. The scale of this analysis and the somatic-germline integration enable the detection of rare variants that may affect individual susceptibility to tumour development, a critical step toward precision medicine