arXiv subjects

Wenjie Wei

Publications and source records attributed to Wenjie Wei.

22 records · Page 2Linked to original sources

arXiv2024

wgatools: an ultrafast toolkit for manipulating whole genome alignments

Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment (WGA) formats, offering practical tools for conversion, processing, statistical evaluation, and visualization of alignments, thereby facilitating population-level genome analysis and advancing functional and evolutionary genomics. Availability and Implementation: wgatools supports diverse formats and can process, filter, and statistically evaluate alignments, perform alignment-based variant calling, and visualize alignments both locally and genome-wide. Built with Rust for efficiency and safe memory usage, it ensures fast performance and can handle large datasets consisting of hundreds of genomes. wgatools is published as free software under the MIT open-source license, and its source code is freely available at https://github.com/wjwei-handsome/wgatools. Contact: weiwenjie@westlake.edu.cn (W.W.) or liuhaijun@yzwlab.cn (H.-J.L.).

q-bio.GN↗

arXiv2024

Global-Local Convolution with Spiking Neural Networks for Energy-efficient Keyword Spotting

Thanks to Deep Neural Networks (DNNs), the accuracy of Keyword Spotting (KWS) has made substantial progress. However, as KWS systems are usually implemented on edge devices, energy efficiency becomes a critical requirement besides performance. Here, we take advantage of spiking neural networks' energy efficiency and propose an end-to-end lightweight KWS model. The model consists of two innovative modules: 1) Global-Local Spiking Convolution (GLSC) module and 2) Bottleneck-PLIF module. Compared to the hand-crafted feature extraction methods, the GLSC module achieves speech feature extraction that is sparser, more energy-efficient, and yields better performance. The Bottleneck-PLIF module further processes the signals from GLSC with the aim to achieve higher accuracy with fewer parameters. Extensive experiments are conducted on the Google Speech Commands Dataset (V1 and V2). The results show our method achieves competitive performance among SNN-based KWS models with fewer parameters.

cs.SD↗

arXiv2024

Event-Driven Learning for Spiking Neural Networks

Brain-inspired spiking neural networks (SNNs) have gained prominence in the field of neuromorphic computing owing to their low energy consumption during feedforward inference on neuromorphic hardware. However, it remains an open challenge how to effectively benefit from the sparse event-driven property of SNNs to minimize backpropagation learning costs. In this paper, we conduct a comprehensive examination of the existing event-driven learning algorithms, reveal their limitations, and propose novel solutions to overcome them. Specifically, we introduce two novel event-driven learning methods: the spike-timing-dependent event-driven (STD-ED) and membrane-potential-dependent event-driven (MPD-ED) algorithms. These proposed algorithms leverage precise neuronal spike timing and membrane potential, respectively, for effective learning. The two methods are extensively evaluated on static and neuromorphic datasets to confirm their superior performance. They outperform existing event-driven counterparts by up to 2.51% for STD-ED and 6.79% for MPD-ED on the CIFAR-100 dataset. In addition, we theoretically and experimentally validate the energy efficiency of our methods on neuromorphic hardware. On-chip learning experiments achieved a remarkable 30-fold reduction in energy consumption over time-step-based surrogate gradient methods. The demonstrated efficiency and efficacy of the proposed event-driven learning methods emphasize their potential to significantly advance the fields of neuromorphic computing, offering promising avenues for energy-efficiency applications.

cs.NE↗

arXiv2023

Unconventionally Fast Transport through Sliding Dynamics of Rodlike Particles in Macromolecular Networks

Transport of rodlike particles in confinement environments of macromolecular networks plays crucial roles in many important biological processes and technological applications. The relevant understanding has been limited to thin rods with diameter much smaller than network mesh size, although the opposite case, of which the dynamical behaviors and underlying physical mechanisms remain unclear, is ubiquitous. Here, we solve this issue by combining experiments, simulations and theory. We find a nonmonotonic dependence of translational diffusion on rod length, characterized by length commensuration-governed unconventionally fast dynamics which is in striking contrast to the monotonic dependence for thin rods. Our results clarify that such a fast diffusion of thick rods with length of integral multiple of mesh size follows sliding dynamics and demonstrate it to be "anomalous yet Brownian". Moreover, good agreement between theoretical analysis and simulations corroborates that the sliding dynamics is an intermediate regime between hopping and Brownian dynamics, and provides a mechanistic interpretation based on the rod-length dependent entropic free energy barrier. The findings yield a principle, that is, length commensuration, for optimal design of rodlike particles with highly efficient transport in confined environments of macromolecular networks, and might enrich the physics of the diffusion dynamics in heterogeneous media.

cond-mat.soft↗