arXiv subjects

Zexuan Zhu

Publications and source records attributed to Zexuan Zhu.

24 records · Page 2Linked to original sources

arXiv2024

Dockformer: A transformer-based molecular docking paradigm for large-scale virtual screening

Molecular docking is a crucial step in drug development, which enables the virtual screening of compound libraries to identify potential ligands that target proteins of interest. However, the computational complexity of traditional docking models increases as the size of the compound library increases. Recently, deep learning algorithms can provide data-driven research and development models to increase the speed of the docking process. Unfortunately, few models can achieve superior screening performance compared to that of traditional models. Therefore, a novel deep learning-based docking approach named Dockformer is introduced in this study. Dockformer leverages multimodal information to capture the geometric topology and structural knowledge of molecules and can directly generate binding conformations with the corresponding confidence measures in an end-to-end manner. The experimental results show that Dockformer achieves success rates of 90.53% and 82.71% on the PDBbind core set and PoseBusters benchmarks, respectively, and more than a 100-fold increase in the inference process speed, outperforming almost all state-of-the-art docking methods. In addition, the ability of Dockformer to identify the main protease inhibitors of coronaviruses is demonstrated in a real-world virtual screening scenario. Considering its high docking accuracy and screening efficiency, Dockformer can be regarded as a powerful and robust tool in the field of drug design.

cs.LG↗

arXiv2024

Parameter Efficient Adaptation for Image Restoration with Heterogeneous Mixture-of-Experts

Designing single-task image restoration models for specific degradation has seen great success in recent years. To achieve generalized image restoration, all-in-one methods have recently been proposed and shown potential for multiple restoration tasks using one single model. Despite the promising results, the existing all-in-one paradigm still suffers from high computational costs as well as limited generalization on unseen degradations. In this work, we introduce an alternative solution to improve the generalization of image restoration models. Drawing inspiration from recent advancements in Parameter Efficient Transfer Learning (PETL), we aim to tune only a small number of parameters to adapt pre-trained restoration models to various tasks. However, current PETL methods fail to generalize across varied restoration tasks due to their homogeneous representation nature. To this end, we propose AdaptIR, a Mixture-of-Experts (MoE) with orthogonal multi-branch design to capture local spatial, global spatial, and channel representation bases, followed by adaptive base combination to obtain heterogeneous representation for different degradations. Extensive experiments demonstrate that our AdaptIR achieves stable performance on single-degradation tasks, and excels in hybrid-degradation tasks, with fine-tuning only 0.6% parameters for 8 hours.

cs.CV↗

arXiv2020

A Two stage Adaptive Knowledge Transfer Evolutionary Multi-tasking Based on Population Distribution for Multi/Many-Objective Optimization

Multi-tasking optimization can usually achieve better performance than traditional single-tasking optimization through knowledge transfer between tasks. However, current multi-tasking optimization algorithms have some deficiencies. For high similarity problems, the knowledge that can accelerate the convergence rate of tasks has not been fully taken advantages of. For low similarity problems, the probability of generating negative transfer is high, which may result in optimization performance degradation. In addition, some knowledge transfer methods proposed previously do not fully consider how to deal with the situation in which the population falls into local optimum. To solve these issues, a two-stage adaptive knowledge transfer evolutionary multi-tasking optimization algorithm based on population distribution, labeled as EMT-PD, is proposed. EMT-PD can accelerate and improve the convergence performance of tasks based on the knowledge extracted from the probability model that reflects the search trend of the whole population. At the first transfer stage, an adaptive weight is used to adjust the step size of individual's search, which can reduce the impact of negative transfer. At the second stage of knowledge transfer, the individual's search range is further adjusted dynamically, which can improve the diversity of population and be beneficial for jumping out of local optimum. Experimental results on multi-tasking multi-objective optimization test suites show that EMT-PD is superior to other six state-of-the-art evolutionary multi/single-tasking algorithms. To further investigate the effectiveness of EMT-PD on many-objective optimization problems, a multi-tasking many-objective test suite is also designed in this paper. The experimental results on the new test suite also demonstrate the competitiveness of EMT-PD.

cs.NE↗

arXiv2020

Multi-factorial Optimization for Large-scale Virtual Machine Placement in Cloud Computing

The placement scheme of virtual machines (VMs) to physical servers (PSs) is crucial to lowering operational cost for cloud providers. Evolutionary algorithms (EAs) have been performed promising-solving on virtual machine placement (VMP) problems in the past. However, as growing demand for cloud services, the existing EAs fail to implement in large-scale virtual machine placement (LVMP) problem due to the high time complexity and poor scalability. Recently, the multi-factorial optimization (MFO) technology has surfaced as a new search paradigm in evolutionary computing. It offers the ability to evolve multiple optimization tasks simultaneously during the evolutionary process. This paper aims to apply the MFO technology to the LVMP problem in heterogeneous environment. Firstly, we formulate a deployment cost based VMP problem in the form of the MFO problem. Then, a multi-factorial evolutionary algorithm (MFEA) embedded with greedy-based allocation operator is developed to address the established MFO problem. After that, a re-migration and merge operator is designed to offer the integrated solution of the LVMP problem from the solutions of MFO problem. To assess the effectiveness of our proposed method, the simulation experiments are carried on large-scale and extra large-scale VMs test data sets. The results show that compared with various heuristic methods, our method could shorten optimization time significantly and offer a competitive placement solution for the LVMP problem in heterogeneous environment.

cs.NE↗

arXiv2017

Evolutionary Multitasking for Single-objective Continuous Optimization: Benchmark Problems, Performance Metric, and Baseline Results

In this report, we suggest nine test problems for multi-task single-objective optimization (MTSOO), each of which consists of two single-objective optimization tasks that need to be solved simultaneously. The relationship between tasks varies between different test problems, which would be helpful to have a comprehensive evaluation of the MFO algorithms. It is expected that the proposed test problems will germinate progress the field of the MTSOO research.

cs.NE↗

arXiv2017

Concept Drift Adaptation by Exploiting Historical Knowledge

Incremental learning with concept drift has often been tackled by ensemble methods, where models built in the past can be re-trained to attain new models for the current data. Two design questions need to be addressed in developing ensemble methods for incremental learning with concept drift, i.e., which historical (i.e., previously trained) models should be preserved and how to utilize them. A novel ensemble learning method, namely Diversity and Transfer based Ensemble Learning (DTEL), is proposed in this paper. Given newly arrived data, DTEL uses each preserved historical model as an initial model and further trains it with the new data via transfer learning. Furthermore, DTEL preserves a diverse set of historical models, rather than a set of historical models that are merely accurate in terms of classification accuracy. Empirical studies on 15 synthetic data streams and 4 real-world data streams (all with concept drifts) demonstrate that DTEL can handle concept drift more effectively than 4 other state-of-the-art methods.

cs.LG↗