Jintao Meng
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View article: Decoding circRNA translation: challenges and advances in computational method development
Decoding circRNA translation: challenges and advances in computational method development Open
In recent years, numerous studies have demonstrated that circRNAs play crucial biological roles through their capacity to encode functional proteins. Computational methods have become essential for investigating circRNA translation. In thi…
View article: Learning the native-like codons with a 5'UTR and RNA secondary structure aided species-informed transformer model
Learning the native-like codons with a 5'UTR and RNA secondary structure aided species-informed transformer model Open
Efficient protein expression across heterologous hosts remains a major challenge in synthetic biology, largely due to species-specific differences in codon usage and regulatory sequence context. A key difficulty lies in reconstructing the …
View article: A Comparative Study of Sequence Clustering Algorithms
A Comparative Study of Sequence Clustering Algorithms Open
Sequence clustering software is essential in bioinformatics. However, selecting the appropriate one can be challenging due to its diverse algorithms and targeted applications. This paper analyzes and evaluates eight representative software…
View article: Correction: Wang et al. Deep Learning-Based Cloud Detection for Optical Remote Sensing Images: A Survey. Remote Sens. 2024, 16, 4583
Correction: Wang et al. Deep Learning-Based Cloud Detection for Optical Remote Sensing Images: A Survey. Remote Sens. 2024, 16, 4583 Open
There was an error in the original publication [...]
View article: NM-SpMM: Accelerating Matrix Multiplication Using \textit{N:M} Sparsity with GPGPU
NM-SpMM: Accelerating Matrix Multiplication Using \textit{N:M} Sparsity with GPGPU Open
Deep learning demonstrates effectiveness across a wide range of tasks. However, the dense and over-parameterized nature of these models results in significant resource consumption during deployment. In response to this issue, weight prunin…
View article: Deep Learning-Based Cloud Detection for Optical Remote Sensing Images: A Survey
Deep Learning-Based Cloud Detection for Optical Remote Sensing Images: A Survey Open
In optical remote sensing images, the presence of clouds affects the completeness of the ground observation and further affects the accuracy and efficiency of remote sensing applications. Especially in quantitative analysis, the impact of …
View article: Distributed Heterogeneous Spiking Neural Network Simulator Using Sunway Accelerators
Distributed Heterogeneous Spiking Neural Network Simulator Using Sunway Accelerators Open
Spiking Neural Network (SNN) simulation is very important for studying brain function and validating the hypotheses for neuroscience, and it can also be used in artificial intelligence. Recently, GPU-based simulators have been developed to…
View article: OpenDock: a pytorch-based open-source framework for protein–ligand docking and modelling
OpenDock: a pytorch-based open-source framework for protein–ligand docking and modelling Open
Motivation Molecular docking is an invaluable computational tool with broad applications in computer-aided drug design and enzyme engineering. However, current molecular docking tools are typically implemented in languages such as C++ for …
View article: Vortex: Efficient Sample-Free Dynamic Tensor Program Optimization via Hardware-aware Strategy Space Hierarchization
Vortex: Efficient Sample-Free Dynamic Tensor Program Optimization via Hardware-aware Strategy Space Hierarchization Open
Dynamic-shape deep neural networks (DNNs) are rapidly evolving, attracting attention for their ability to handle variable input sizes in real-time applications. However, existing compilation optimization methods for such networks often rel…
View article: Autism Spectrum Disorder Classification with Interpretability in Children Based on Structural MRI Features Extracted Using Contrastive Variational Autoencoder
Autism Spectrum Disorder Classification with Interpretability in Children Based on Structural MRI Features Extracted Using Contrastive Variational Autoencoder Open
Autism Spectrum Disorder (ASD) is a highly disabling mental disease that brings significant impairments of social interaction ability to the patients, making early screening and intervention of ASD critical. With the development of the mac…
View article: Research and application of adaptive anti-interference based VU-fuzzy-PID algorithm in temperature control system of platic extruder
Research and application of adaptive anti-interference based VU-fuzzy-PID algorithm in temperature control system of platic extruder Open
Plastic profiles, as the basic material for social and economic development, are mainly processed and moulded by plastic extruders. In the production process of plastic profiles, the temperature precision control of plastic extruder direct…
View article: A Weakly Supervised Learning Method for Cell Detection and Tracking Using Incomplete Initial Annotations
A Weakly Supervised Learning Method for Cell Detection and Tracking Using Incomplete Initial Annotations Open
The automatic detection of cells in microscopy image sequences is a significant task in biomedical research. However, routine microscopy images with cells, which are taken during the process whereby constant division and differentiation oc…
View article: <scp>zPoseScore</scp> model for accurate and robust protein–ligand docking pose scoring in <scp>CASP15</scp>
<span>zPoseScore</span> model for accurate and robust protein–ligand docking pose scoring in <span>CASP15</span> Open
We introduce a deep learning‐based ligand pose scoring model called zPoseScore for predicting protein–ligand complexes in the 15th Critical Assessment of Protein Structure Prediction (CASP15). Our contributions are threefold: first, we gen…
View article: Research and Application of Plastic Extruder Temperature System Based on Variable Universe Fuzzy PID Control
Research and Application of Plastic Extruder Temperature System Based on Variable Universe Fuzzy PID Control Open
Plastic profiles, as the basic material for social and economic development, are mainly processed and moulded by plastic extruders. In the production process of plastic profiles, the temperature precision control of plastic extruder direct…
View article: Revisiting Temporal Blocking Stencil Optimizations
Revisiting Temporal Blocking Stencil Optimizations Open
Iterative stencils are used widely across the spectrum of High Performance\nComputing (HPC) applications. Many efforts have been put into optimizing\nstencil GPU kernels, given the prevalence of GPU-accelerated supercomputers. To\nimprove …
View article: PERKS: a Locality-Optimized Execution Model for Iterative Memory-bound GPU Applications
PERKS: a Locality-Optimized Execution Model for Iterative Memory-bound GPU Applications Open
Iterative memory-bound solvers commonly occur in HPC codes. Typical GPU implementations have a loop on the host side that invokes the GPU kernel as much as time/algorithm steps there are. The termination of each kernel implicitly acts the …
View article: zPoseScore model for accurate and robust protein-ligand docking pose scoring in CASP15
zPoseScore model for accurate and robust protein-ligand docking pose scoring in CASP15 Open
We introduce a deep learning-based ligand pose scoring model called zPoseScore for predicting protein-ligand complexes in the 15th Critical Assessment of Protein Structure Prediction (CASP15). Our contributions are three-fold: firstly, we …
View article: Exploiting Scratchpad Memory for Deep Temporal Blocking
Exploiting Scratchpad Memory for Deep Temporal Blocking Open
General Purpose Graphics Processing Units (GPGPU) are used in most of the top systems in HPC. The total capacity of scratchpad memory has increased by more than 40 times in the last decade. However, existing optimizations for stencil compu…
View article: Efficient Phase-Functioned Real-time Character Control in Mobile Games: A TVM Enabled Approach
Efficient Phase-Functioned Real-time Character Control in Mobile Games: A TVM Enabled Approach Open
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 ma…
View article: Inter-Residue Distance Prediction From Duet Deep Learning Models
Inter-Residue Distance Prediction From Duet Deep Learning Models Open
Residue distance prediction from the sequence is critical for many biological applications such as protein structure reconstruction, protein–protein interaction prediction, and protein design. However, prediction of fine-grained distances …
View article: PERKS: a Locality-Optimized Execution Model for Iterative Memory-bound GPU Applications
PERKS: a Locality-Optimized Execution Model for Iterative Memory-bound GPU Applications Open
Iterative memory-bound solvers commonly occur in HPC codes. Typical GPU implementations have a loop on the host side that invokes the GPU kernel as much as time/algorithm steps there are. The termination of each kernel implicitly acts the …
View article: Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term
Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term Open
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 …
View article: Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning
Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning Open
In this work, we present FastConv, 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 …
View article: Structure prediction of the entire proteome of monkeypox variants
Structure prediction of the entire proteome of monkeypox variants Open
Recently, the monkeypox virus has begun to spread in many countries worldwide [1]. The genome sequence of the monkeypox virus variant responsible for the current outbreak has been reported, thus providing an important resource for better u…
View article: Evaluating Interfacial Stability in Solid-State Pouch Cells Via Ultrasonic Imaging
Evaluating Interfacial Stability in Solid-State Pouch Cells Via Ultrasonic Imaging Open
Chemical/electrochemical stability at the interfaces greatly affects the performance of solid-state batteries (SSBs). However, the interfacial behavior in SSBs remains elusive due to the subsurface nature of interfaces and the lack of prop…