Dynamic-shape tensor computation poses challenges for shape-specific compilation due to variable input dimensions. Existing compilers rely on shape samples, incurring high tuning costs and performance degradation on unseen inputs. We present Helix, a dynamic tensor compilation framework with sample-free compilation and architecture-guided optimization to achieve both compilation efficiency and shape-general performance. To avoid shape sampling, Helix constructs shape-agnostic compilation by decomposing computations across architectural layers. A bidirectional strategy combines top-down abstraction to align tensor computations with architectural hierarchies, and bottom-up kernel construction to build efficient execution strategies from reusable, architecture-aligned micro-kernels. A hybrid analyzer ensures accuracy through profiling at lower architectural levels, and achieves scalability through architecture-informed modeling at higher levels and runtime. This hierarchical design eliminates shape-specific tuning and enables shape-adaptive execution. Evaluations conducted on x86 CPUs, ARM CPUs, and NVIDIA GPUs demonstrate that Helix reduces compilation time by 174 × over the existing compilers and delivers 2.26 × and 3.29 × execution speedups over vendor libraries and dynamic-shape compilers, respectively.

In this paper, we propose a highly efficient computing method for game character control with phase-functioned neural networks (PFNN). The primary challenge to accelerate PFNN on mobile platforms is that PFNN dynamically produces weight matrices with an argument, phase, which is individual to each game character. Therefore existing libraries that generally assume frozen weight matrices are inefficient to accelerate PFNN. The situation becomes even worse when multiple characters are present. To address the challenges, we reformulate the equations and leverage the deep learning compiler stack TVM to build a cross-platform, high-performance implementation. Evaluations reveal that our solutions deliver close-to-peak performance on various platforms, from high-performance servers to energy-efficient mobile platforms. This work is publicly available at https://github.com/turbo0628/pfnn_tvm.

Scoring functions are important components in molecular docking for structure-based drug discovery. Traditional scoring functions, generally empirical- or force field-based, are robust and have proven to be useful for identifying hits and lead optimizations. Although multiple highly accurate deep learning- or machine learning-based scoring functions have been developed, their direct applications for docking and screening are limited. We describe a novel strategy to develop a reliable protein-ligand scoring function by augmenting the traditional scoring function Vina score using a correction term (OnionNet-SFCT). The correction term is developed based on an AdaBoost random forest model, utilizing multiple layers of contacts formed between protein residues and ligand atoms. In addition to the Vina score, the model considerably enhances the AutoDock Vina prediction abilities for docking and screening tasks based on different benchmarks (such as cross-docking dataset, CASF-2016, DUD-E and DUD-AD). Furthermore, our model could be combined with multiple docking applications to increase pose selection accuracies and screening abilities, indicating its wide usage for structure-based drug discoveries. Furthermore, in a reverse practice, the combined scoring strategy successfully identified multiple known receptors of a plant hormone. To summarize, the results show that the combination of data-driven model (OnionNet-SFCT) and empirical scoring function (Vina score) is a good scoring strategy that could be useful for structure-based drug discoveries and potentially target fishing in future.

We presentFastConv, a template-based code auto-generation open-source library that can automatically generate high-performance deep learning convolution kernels of arbitrary matrices/tensors shapes. FastConv is based on the Winograd algorithm, which is reportedly the highest performing algorithm for the time-consuming layers of convolutional neural networks. ARM CPUs cover a wide range of designs and specifications, from embedded devices to HPC-grade CPUs. The leads to the dilemma of how to consistently optimize Winograd-based convolution solvers for convolution layers of different shapes. FastConv addresses this problem by using templates to auto-generate multiple shapes of tuned kernels variants suitable for skinny tall matrices. As a performance portable library, FastConv transparently searches for the best combination of kernel shapes, cache tiles, scheduling of loop orders, packing strategies, access patterns, and online/offline computations. Auto-tuning is used to search the parameter configuration space for the best performance for a given target architecture and problem size. Results show 1.02x to 1.40x, 1.14x to 2.17x, and 1.22x and 2.48x speedup is achieved over NNPACK, ARM NN, and FeatherCNN on Kunpeng 920. Furthermore, performance portability experiments with various convolution shapes show that FastConv achieves 1.2x to 1.7x speedup and 2x to 22x speedup over NNPACK and ARM NN inference engine using Winograd on Kunpeng 920. CPU performance portability evaluation on VGG–16 show an average speedup over NNPACK of 1.42x, 1.21x, 1.26x, 1.37x, 2.26x, and 11.02x on Kunpeng 920, Snapdragon 835, 855, 888, Apple M1, and AWS Graviton2, respectively.

MOTIVATION: Modern sequencing technologies continue to revolutionize many areas of biology and medicine. Since the generated datasets are error-prone, downstream applications usually require quality control methods to pre-process FASTQ files. However, existing tools for this task are currently not able to fully exploit the capabilities of computing platforms leading to slow runtimes. RESULTS: We present RabbitQC, an extremely fast integrated quality control tool for FASTQ files, which can take full advantage of modern hardware. It includes a variety of operations and supports different sequencing technologies (Illumina, Oxford Nanopore and PacBio). RabbitQC achieves speedups between one and two orders-of-magnitude compared to other state-of-the-art tools. AVAILABILITY AND IMPLEMENTATION: C++ sources and binaries are available at https://github.com/ZekunYin/RabbitQC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Deep Learning is ubiquitous in a wide field of applications ranging from research to industry. In comparison to timeconsuming iterative training of convolutional neural networks (CNNs), inference is a relatively lightweight operation making it amenable to execution on mobile devices. Nevertheless, lower latency and higher computation efficiency are crucial to allow for complex models and prolonged battery life. Addressing the aforementioned challenges, we propose FeatherCNN- a fast inference library for ARM CPUs - targeting the performance ceiling of mobile devices. FeatherCNN employs three key techniques: 1) A highly efficient TensorGEMM (generalized matrix multiplication) routine is applied to accelerate Winograd convolution on ARM CPUs, 2) General layer optimization based on custom high performance kernels improves both the computational efficiency and locality of memory access patterns for non-Winograd layers. 3) The framework design emphasizes joint layer-wise optimization using layer fusion to remove redundant calculations and memory movements. Performance evaluation reveals that FeatherCNN significantly outperforms state-ofthe-art libraries. A forward propagation pass of VGG-16 on a 64-core ARM server is 48, 14, and 12 times faster than Caffe using OpenBLAS, Caffe2 using Eigen, and NNPACK, respectively. In addition, FeatherCNN is 3.19 times faster than the recently released TensorFlow Lite library on an iPhone 7 plus. In terms of GEMM performance, FeatherCNN achieves 14.8 and 39.0 percent higher performance than Apple's Accelerate framework on an iPhone 7 plus and Eigen on a Samsung Galaxy S8, respectively. The source code of FeatherCNN library is publicly available at https://github.com/tencent/feathercnn.

MOTIVATION: Modern bioinformatics tools for analyzing large-scale NGS datasets often need to include fast implementations of core sequence alignment algorithms in order to achieve reasonable execution times. We address this need by presenting the BGSA toolkit for optimized implementations of popular bit-parallel global pairwise alignment algorithms on modern microprocessors. RESULTS: BGSA outperforms Edlib, SeqAn and BitPAl for pairwise edit distance computations and Parasail, SeqAn and BitPAl when using more general scoring schemes for pairwise alignments of a batch of sequence reads on both standard multi-core CPUs and Xeon Phi many-core CPUs. Furthermore, banded edit distance performance of BGSA on a Xeon Phi-7210 outperforms the highly optimized NVBio implementation on a Titan X GPU for the seed verification stage of a read mapper by a factor of 4.4. AVAILABILITY AND IMPLEMENTATION: BGSA is open-source and available at https://github.com/sdu-hpcl/BGSA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The progress of next-generation sequencing has a major impact on medical and genomic research. This technology can now produce billions of short DNA fragments (reads) in a single run. One of the most demanding computational problems used by almost every sequencing pipeline is short-read alignment; i.e. determining where each fragment originated from in the original genome. Most current solutions are based on a seed-and-extend approach, where promising candidate regions (seeds) are first identified and subsequently extended in order to verify whether a full high-scoring alignment actually exists in the vicinity of each seed. Seed verification is the main bottleneck in many state-of-the-art aligners and thus finding fast solutions is of high importance. We present a parallel un gapped-alignment-featured seed verification (PUNAS) algorithm, a fast filter for effectively removing the majority of false positive seeds, thus significantly accelerating the short-read alignment process. PUNAS is based on bit-parallelism and takes advantage of SIMD vector units of modern microprocessors. Our implementation employs a vectorize-and-scale approach supporting multi-core CPUs and many-core Knights Landing (KNL)-based Xeon Phi processors. Performance evaluation reveals that PUNAS is over three orders-of-magnitude faster than seed verification with the Smith-Waterman algorithm and around one order-of-magnitude faster than seed verification with the banded version of Myers bit-vector algorithm. Using a single thread it achieves a speedup of up to 7.3, 27.1, and 11.6 compared to the shifted Hamming distance filter on a SSE, AVX2, and AVX-512 based CPU/KNL, respectively. The speed of our framework further scales almost linearly with the number of cores. PUNAS is open-source software available at https://github.com/Xu-Kai/PUNASfilter.

Computer architectures continue to develop rapidly towards massively parallel and heterogeneous systems. Thus, easily extensible yet highly efficient parallelization approaches for a variety of platforms are urgently needed. In this paper, we present SWhybrid, a hybrid computing framework for large-scale biological sequence database search on heterogeneous computing environments with multi-core or many-core processing units (PUs) based on the Smith- Waterman (SW) algorithm. To incorporate a diverse set of PUs such as combinations of CPUs, GPUs and Xeon Phis, we abstract them as SIMD vector execution units with different number of lanes. We propose a machine model, associated with a unified programming interface implemented in C++, to abstract underlying architectural differences. Performance evaluation reveals that SWhybrid (i) outperforms all other tested state-of-the-art tools on both homogeneous and heterogeneous computing platforms, (ii) achieves an efficiency of over 80% on all tested CPUs and GPUs and over 70% on Xeon Phis, and (iii) achieves utlization rates of over 80% on all tested heterogeneous platforms. Our results demonstrate that there is enough commonality between vector-like instructions across CPUs and GPUs that one can develop higher-level abstractions and still specialize with close-to-peak performance. SWhybrid is open-source software and freely available at https://github.com/turbo0628/swhybrid.

BACKGROUND: Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. RESULTS: This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data parallelism, thread-level coarse-grained parallelism, and vector-level fine-grained parallelism. Furthermore, we re-organize the sequence datasets and use Xeon Phi shuffle operations to improve I/O efficiency. CONCLUSIONS: Evaluations show that our method achieves a peak overall performance up to 220 GCUPS for scanning real protein sequence databanks on a single node consisting of two Intel E5-2620 CPUs and two Intel Xeon Phi 7110P cards. It also exhibits good scalability in terms of sequence length and size, and number of compute nodes for both database scanning and multiple sequence alignment. Furthermore, the achieved performance is highly competitive in comparison to optimized Xeon Phi and GPU implementations. Our implementation is available at https://github.com/turbo0628/LSDBS-mpi .

In this paper we present new parallelization techniques for searching large-scale biological sequence databases with the Smith-Waterman algorithm on Xeon Phi-based neoheterogenous architectures. In order to make full use of the compute power of both the multi-core CPU and the many-core Xeon Phi hardware, we use a collaborative computing scheme as well as hybrid parallelism. At the CPU side, we employ SSE intrinsics and multi-threading to implement SIMD parallelism. At the Xeon Phi side, we use Knights Corner vector instructions to gain more data parallelism. We have presented two dynamic task distribution schemes (thread level and device level) in order to achieve better load balancing. Furthermore, a multi-threaded asynchronous scheme is used to overlap communication and computation between CPUs and Xeon Phis. Evaluations on real protein sequence databases show that our method achieves a peak overall performance up to 220 GCUPS on a neo-heterogeneous platform consisting of two Intel E5-2620 CPUs and two Intel Xeon Phi 7110P cards. It also exhibits good scalability in terms of database size and query length. Our implementation is available at: http://turbo0628.github.io/LSBDS/.

PROSITE provides rich documentation entries describing protein domains, families and functional sites, associated patterns as well as generalized profiles to identify them. Generalized profiles in PROSITE are often used to detect distantly related proteins by doing sequence comparison. The developments of the PROSITE have increased the discriminatory power of generalized profiles. However in practice, comparing PROSITE profiles to large protein databases, such as GenBank, usually requires long runtimes on sequential architectures. Due to the continuing rapid growth of sequence databases, there is a high demand to accelerate this task. In this paper we present XPFS, a new parallel algorithm for searching generalized profiles against protein sequence databases based on Xeon Phi which is Intel's first generation Many Integrated Core product. To our knowledge this is the first reported implementation of the PROSITE profile search algorithm on Xeon Phi. The executable binary code of XPFS is available at http://xpfs.sdu-hpcl.org/.