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Long single-molecular sequencing technologies, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine in CpGs (5mCpGs), especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. Here, we present ccsmeth, a deep-learning method to detect DNA 5mCpGs using CCS reads. We sequence polymerase-chain-reaction treated and M.SssI-methyltransferase treated DNA of one human sample using PacBio CCS for training ccsmeth. Using long (≥10 Kb) CCS reads, ccsmeth achieves 0.90 accuracy and 0.97 Area Under the Curve on 5mCpG detection at single-molecule resolution. At the genome-wide site level, ccsmeth achieves >0.90 correlations with bisulfite sequencing and nanopore sequencing using only 10× reads. Furthermore, we develop a Nextflow pipeline, ccsmethphase, to detect haplotype-aware methylation using CCS reads, and then sequence a Chinese family trio to validate it. ccsmeth and ccsmethphase can be robust and accurate tools for detecting DNA 5-methylcytosines.

 

Due to improvements in high-performance computing (HPC) capabilities, many of today’s applications produce petabytes worth of data, causing bottlenecks within the system. Importance-based sampling methods, including our spatio-temporal hybrid data sampling method, are capable of resolving these bottlenecks. While our hybrid method has been shown to outperform existing methods, its effectiveness relies heavily on user parameters, such as histogram bins, error threshold, or number of regions. Moreover, the throughput it demonstrates must be higher to avoid becoming a bottleneck itself. In this article, we resolve both of these issues. First, we assess the effects of several user input parameters and detail techniques to help determine optimal parameters. Next, we detail and implement accelerated versions of our method using OpenMP and CUDA. Upon analyzing our implementations, we find 9.8× to 31.5× throughput improvements. Next, we demonstrate how our method can accept different base sampling algorithms and the effects these different algorithms have. Finally, we compare our sampling methods to the lossy compressor cuSZ in terms of data preservation and data movement.

 

Lossy compressors are increasingly adopted in scientific research, tackling volumes of data from experiments or parallel numerical simulations and facilitating data storage and movement. In contrast with the notion of entropy in lossless compression, no theoretical or data-based quantification of lossy compressibility exists for scientific data. Users rely on trial and error to assess lossy compression performance. As a strong data-driven effort toward quantifying lossy compressibility of scientific datasets, we provide a statistical framework to predict compression ratios of lossy compressors. Our method is a two-step framework where (i) compressor-agnostic predictors are computed and (ii) statistical prediction models relying on these predictors are trained on observed compression ratios. Proposed predictors exploit spatial correlations and notions of entropy and lossyness via the quantized entropy. We study 8+ compressors on 6 scientific datasets and achieve a median percentage prediction error less than 12%, which is substantially smaller than that of other methods while achieving at least a 8.8× speedup for searching for a specific compression ratio and 7.8× speedup for determining the best compressor out of a collection.

 

This study presents a new method for modeling the interaction between compressible flow, shock waves, and deformable structures, emphasizing destructive dynamics. Extending advances in time-splitting compressible flow and the Material Point Methods (MPM), we develop a hybrid Eulerian and Lagrangian/Eulerian scheme for monolithic flow-structure interactions. We adopt the second-order WENO scheme to advance the continuity equation. To stably resolve deforming boundaries with sub-cell particles, we propose a blending treatment of reflective and passable boundary conditions inspired by the theory of porous media. The strongly coupled velocity-pressure system is discretized with a new mixed-order finite element formulation employing B-spline shape functions. Shock wave propagation, temperature/density-induced buoyancy effects, and topology changes in solids are unitedly captured.