PyHySCO: GPU-enabled susceptibility artifact distortion correction in seconds.

Over the past decade, reversed gradient polarity (RGP) methods have become a popular approach for correcting susceptibility artifacts in echo-planar imaging (EPI). Although several post-processing tools for RGP are available, their implementations do not fully leverage recent hardware, algorithmic, and computational advances, leading to correction times of several minutes per image volume. To enable 3D RGP correction in seconds, we introduce PyTorch Hyperelastic Susceptibility Correction (PyHySCO), a user-friendly EPI distortion correction tool implemented in PyTorch that enables multi-threading and efficient use of graphics processing units (GPUs). PyHySCO uses a time-tested physical distortion model and mathematical formulation and is, therefore, reliable without training. An algorithmic improvement in PyHySCO is its use of the one-dimensional distortion correction method by Chang and Fitzpatrick to initialize the non-linear optimization. PyHySCO is published under the GNU public license and can be used from the command line or its Python interface. Our extensive numerical validation using 3T and 7T data from the Human Connectome Project suggests that PyHySCO can achieve accuracy comparable to that of leading RGP tools at a fraction of the cost. We also validate the new initialization scheme, compare different optimization algorithms, and test the algorithm on different hardware and arithmetic precisions.

An efficient swarm intelligence approach to the optimization on high-dimensional solutions with cross-dimensional constraints, with applications in supply chain management.

Introduction: The Swarm Intelligence Based (SIB) method has widely been applied to efficient optimization in many fields with discrete solution domains. E-commerce raises the importance of designing suitable selling strategies, including channel- and direct sales, and the mix of them, but researchers in this field seldom employ advanced metaheuristic techniques in their optimization problem due to the complexities caused by the high-dimensional problems and cross-dimensional constraints. Method: In this work, we introduce an extension of the SIB method that can simultaneously tackle these two challenges. To pursue faster computing, CPU parallelization techniques are employed for algorithm acceleration. Results: The performance of the SIB method is examined on the problems of designing selling schemes in different scales. It outperforms the Genetic Algorithm (GA) in terms of both the speed of convergence and the optimized capacity as measured using improvement multipliers.

Upscaled Production of Satellite-Free Droplets: Step Emulsification with Deterministic Lateral Displacement.

Step emulsification is a key technique for achieving scalable production of monodisperse emulsion droplets owing to its resilience to flow fluctuations. However, the persistent issue of satellite droplets, an inherent byproduct of main droplets, poses challenges for achieving truly uniform product sizes. In a previous study, we introduced a module with step-emulsifier nozzles upstream and deterministic lateral displacement (DLD) micropillar arrays downstream to generate satellite-free droplets at a low throughput. In this study, we demonstrate an upscaled parallelized setup with ten modules that were designed to produce satellite-free droplets. Each module integrated 100 step-emulsification nozzles in the upstream region with DLD micropillar arrays downstream. We conducted 3D flow simulations to ensure homogeneous distribution of the input fluids. Uniformly supplying an aqueous polyvinyl alcohol solution and an acrylate monomer as continuous and dispersed phases into the ten modules, the nozzles in each module exhibited a production rate of 539.5 ± 28.6 drop/s (n = 10). We successfully isolated the main droplets with a mean diameter of 66 µm and a coefficient of variation of 3.1% from satellite droplets with a mean diameter of 3 µm. The total throughput was 3.0 mL/h. The high yield and contamination-free features of our approach are promising for diverse industrial applications.

A vulnerability detection method for IoT protocol based on parallel fuzzy algorithm.

The Internet of Things communication protocol is prone to security vulnerabilities when facing increasing types and scales of network attacks, which can affect the communication security of the Internet of Things. It is crucial to effectively detect these vulnerabilities in order to improve the security of IoT communication protocols and promptly fix them. Therefore, this study proposes a distributed IoT communication protocol vulnerability detection method based on an improved parallelized fuzzy testing algorithm. Firstly, based on design principles and by comparing different communication protocols, a communication architecture for the distribution network's Internet of Things was constructed, and the communication protocols were formalized and decomposed. Next, preprocess the vulnerability detection samples, and then use genetic algorithm to improve the parallelized fuzzy testing algorithm to perform vulnerability detection. Through this improved algorithm, the missed detection rate and false detection rate can be effectively reduced, thereby improving the security of IoT communication protocols. The experimental results show that the highest missed detection rate of this method is only 4.0 %, and the false detection rate is low, with high detection efficiency. This indicates that the method has good performance and reliability in detecting vulnerabilities in IoT communication protocols.

Distributed Acceleration of Adhesive Dynamics Simulations.

Cell adhesion plays a critical role in processes ranging from leukocyte migration to cancer cell transport during metastasis. Adhesive cell interactions can occur over large distances in microvessel networks with cells traveling over distances much greater than the length scale of their own diameter. Therefore, biologically relevant investigations necessitate efficient modeling of large field-of-view domains, but current models are limited by simulating such geometries at the sub-micron scale required to model adhesive interactions which greatly increases the computational requirements for even small domain sizes. In this study we introduce a hybrid scheme reliant on both on-node and distributed parallelism to accelerate a fully deformable adhesive dynamics cell model. This scheme leads to performant system usage of modern supercomputers which use a many-core per-node architecture. On-node acceleration is augmented by a combination of spatial data structures and algorithmic changes to lessen the need for atomic operations. This deformable adhesive cell model accelerated with hybrid parallelization allows us to bridge the gap between high-resolution cell models which can capture the sub-micron adhesive interactions between the cell and its microenvironment, and large-scale fluid-structure interaction (FSI) models which can track cells over considerable distances. By integrating the sub-micron simulation environment into a distributed FSI simulation we enable the study of previously unfeasible research questions involving numerous adhesive cells in microvessel networks such as cancer cell transport through the microcirculation.

A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets.

As the volume of next generation sequencing data increases, an urgent need for algorithms to efficiently process the data arises. Universal hitting sets (UHS) were recently introduced as an alternative to the central idea of minimizers in sequence analysis with the hopes that they could more efficiently address common tasks such as computing hash functions for read overlap, sparse suffix arrays, and Bloom filters. A UHS is a set of k-mers that hit every sequence of length L, and can thus serve as indices to L-long sequences. Unfortunately, methods for computing small UHSs are not yet practical for real-world sequencing instances due to their serial and deterministic nature, which leads to long runtimes and high memory demands when handling typical values of k (e.g. k>13). To address this bottleneck, we present two algorithmic innovations to significantly decrease runtime while keeping memory usage low: (i) we leverage advanced theoretical and architectural techniques to parallelize and decrease memory usage in calculating k-mer hitting numbers; and (ii) we build upon techniques from randomized Set Cover to select universal k-mers much faster. We implemented these innovations in PASHA, the first randomized parallel algorithm for generating nearoptimal UHSs, which newly handles k>13. We demonstrate empirically that PASHA produces sets only slightly larger than those of serial deterministic algorithms; moreover, the set size is provably guaranteed to be within a small constant factor of the optimal size. PASHA's runtime and memory-usage improvements are orders of magnitude faster than the current best algorithms. We expect our newly-practical construction of UHSs to be adopted in many high-throughput sequence analysis pipelines.