Add to Chrome
Add to Firefox
Add to EdgeHMAMP: Hypervolume-Driven Multi-Objective Antimicrobial Peptides Design
May 01, 2024
Antimicrobial peptides (AMPs) have exhibited unprecedented potential as biomaterials in combating multidrug-resistant bacteria. Despite the increasing adoption of artificial intelligence for novel AMP design, challenges pertaining to conflicting attributes such as activity, hemolysis, and toxicity have significantly impeded the progress of researchers. This paper introduces a paradigm shift by considering multiple attributes in AMP design. Presented herein is a novel approach termed Hypervolume-driven Multi-objective Antimicrobial Peptide Design (HMAMP), which prioritizes the simultaneous optimization of multiple attributes of AMPs. By synergizing reinforcement learning and a gradient descent algorithm rooted in the hypervolume maximization concept, HMAMP effectively expands exploration space and mitigates the issue of pattern collapse. This method generates a wide array of prospective AMP candidates that strike a balance among diverse attributes. Furthermore, we pinpoint knee points along the Pareto front of these candidate AMPs. Empirical results across five benchmark models substantiate that HMAMP-designed AMPs exhibit competitive performance and heightened diversity. A detailed analysis of the helical structures and molecular dynamics simulations for ten potential candidate AMPs validates the superiority of HMAMP in the realm of multi-objective AMP design. The ability of HMAMP to systematically craft AMPs considering multiple attributes marks a pioneering milestone, establishing a universal computational framework for the multi-objective design of AMPs.
A Composite Decomposition Method for Large-Scale Global Optimization
Mar 08, 2024
Cooperative co-evolution (CC) algorithms, based on the divide-and-conquer strategy, have emerged as the predominant approach to solving large-scale global optimization (LSGO) problems. The efficiency and accuracy of the grouping stage significantly impact the performance of the optimization process. While the general separability grouping (GSG) method has overcome the limitation of previous differential grouping (DG) methods by enabling the decomposition of non-additively separable functions, it suffers from high computational complexity. To address this challenge, this article proposes a composite separability grouping (CSG) method, seamlessly integrating DG and GSG into a problem decomposition framework to utilize the strengths of both approaches. CSG introduces a step-by-step decomposition framework that accurately decomposes various problem types using fewer computational resources. By sequentially identifying additively, multiplicatively and generally separable variables, CSG progressively groups non-separable variables by recursively considering the interactions between each non-separable variable and the formed non-separable groups. Furthermore, to enhance the efficiency and accuracy of CSG, we introduce two innovative methods: a multiplicatively separable variable detection method and a non-separable variable grouping method. These two methods are designed to effectively detect multiplicatively separable variables and efficiently group non-separable variables, respectively. Extensive experimental results demonstrate that CSG achieves more accurate variable grouping with lower computational complexity compared to GSG and state-of-the-art DG series designs.
Improving Performance Insensitivity of Large-scale Multiobjective Optimization via Monte Carlo Tree Search
Apr 14, 2023
The large-scale multiobjective optimization problem (LSMOP) is characterized by simultaneously optimizing multiple conflicting objectives and involving hundreds of decision variables. Many real-world applications in engineering fields can be modeled as LSMOPs; simultaneously, engineering applications require insensitivity in performance. This requirement usually means that the results from the algorithm runs should not only be good for every run in terms of performance but also that the performance of multiple runs should not fluctuate too much, i.e., the algorithm shows good insensitivity. Considering that substantial computational resources are requested for each run, it is essential to improve upon the performance of the large-scale multiobjective optimization algorithm, as well as the insensitivity of the algorithm. However, existing large-scale multiobjective optimization algorithms solely focus on improving the performance of the algorithms, leaving the insensitivity characteristics unattended. In this work, we propose an evolutionary algorithm for solving LSMOPs based on Monte Carlo tree search, the so-called LMMOCTS, which aims to improve the performance and insensitivity for large-scale multiobjective optimization problems. The proposed method samples the decision variables to construct new nodes on the Monte Carlo tree for optimization and evaluation. It selects nodes with good evaluation for further search to reduce the performance sensitivity caused by large-scale decision variables. We compare the proposed algorithm with several state-of-the-art designs on different benchmark functions. We also propose two metrics to measure the sensitivity of the algorithm. The experimental results confirm the effectiveness and performance insensitivity of the proposed design for solving large-scale multiobjective optimization problems.
Efficient Evaluation Methods for Neural Architecture Search: A Survey
Jan 14, 2023
Neural Architecture Search (NAS) has received increasing attention because of its exceptional merits in automating the design of Deep Neural Network (DNN) architectures. However, the performance evaluation process, as a key part of NAS, often requires training a large number of DNNs. This inevitably causes NAS computationally expensive. In past years, many Efficient Evaluation Methods (EEMs) have been proposed to address this critical issue. In this paper, we comprehensively survey these EEMs published up to date, and provide a detailed analysis to motivate the further development of this research direction. Specifically, we divide the existing EEMs into four categories based on the number of DNNs trained for constructing these EEMs. The categorization can reflect the degree of efficiency in principle, which can in turn help quickly grasp the methodological features. In surveying each category, we further discuss the design principles and analyze the strength and weaknesses to clarify the landscape of existing EEMs, thus making easily understanding the research trends of EEMs. Furthermore, we also discuss the current challenges and issues to identify future research directions in this emerging topic. To the best of our knowledge, this is the first work that extensively and systematically surveys the EEMs of NAS.
Analysis of Expected Hitting Time for Designing Evolutionary Neural Architecture Search Algorithms
Oct 11, 2022
Evolutionary computation-based neural architecture search (ENAS) is a popular technique for automating architecture design of deep neural networks. In recent years, various ENAS algorithms have been proposed and shown promising performance on diverse real-world applications. In contrast to these groundbreaking applications, there is no theoretical guideline for assigning a reasonable running time (mainly affected by the generation number, population size, and evolution operator) given both the anticipated performance and acceptable computation budget on ENAS problems. The expected hitting time (EHT), which refers to the average generations, is considered to analyze the running time of ENAS algorithms. This paper proposes a general framework for estimating the EHT of ENAS algorithms, which includes common configuration, search space partition, transition probability estimation, and hitting time analysis. By exploiting the proposed framework, we consider the so-called ($\lambda$+$\lambda$)-ENAS algorithms with different mutation operators and manage to estimate the lower bounds of the EHT {which are critical for the algorithm to find the global optimum}. Furthermore, we study the theoretical results on the NAS-Bench-101 architecture searching problem, and the results show that the one-bit mutation with "bit-based fair mutation" strategy needs less time than the "offspring-based fair mutation" strategy, and the bitwise mutation operator needs less time than the $q$-bit mutation operator. To the best of our knowledge, this is the first work focusing on the theory of ENAS, and the above observation will be substantially helpful in designing efficient ENAS algorithms.
Learn to Adapt for Monocular Depth Estimation
Mar 26, 2022
Monocular depth estimation is one of the fundamental tasks in environmental perception and has achieved tremendous progress in virtue of deep learning. However, the performance of trained models tends to degrade or deteriorate when employed on other new datasets due to the gap between different datasets. Though some methods utilize domain adaptation technologies to jointly train different domains and narrow the gap between them, the trained models cannot generalize to new domains that are not involved in training. To boost the transferability of depth estimation models, we propose an adversarial depth estimation task and train the model in the pipeline of meta-learning. Our proposed adversarial task mitigates the issue of meta-overfitting, since the network is trained in an adversarial manner and aims to extract domain invariant representations. In addition, we propose a constraint to impose upon cross-task depth consistency to compel the depth estimation to be identical in different adversarial tasks, which improves the performance of our method and smoothens the training process. Experiments demonstrate that our method adapts well to new datasets after few training steps during the test procedure.
BenchENAS: A Benchmarking Platform for Evolutionary Neural Architecture Search
Aug 14, 2021
Neural architecture search (NAS), which automatically designs the architectures of deep neural networks, has achieved breakthrough success over many applications in the past few years. Among different classes of NAS methods, evolutionary computation based NAS (ENAS) methods have recently gained much attention. Unfortunately, the issues of fair comparisons and efficient evaluations have hindered the development of ENAS. The current benchmark architecture datasets designed for fair comparisons only provide the datasets, not the ENAS algorithms or the platform to run the algorithms. The existing efficient evaluation methods are either not suitable for the population-based ENAS algorithm or are too complex to use. This paper develops a platform named BenchENAS to address these issues. BenchENAS aims to achieve fair comparisons by running different algorithms in the same environment and with the same settings. To achieve efficient evaluation in a common lab environment, BenchENAS designs a parallel component and a cache component with high maintainability. Furthermore, BenchENAS is easy to install and highly configurable and modular, which brings benefits in good usability and easy extensibility. The paper conducts efficient comparison experiments on eight ENAS algorithms with high GPU utilization on this platform. The experiments validate that the fair comparison issue does exist, and BenchENAS can alleviate this issue. A website has been built to promote BenchENAS at https://benchenas.com, where interested researchers can obtain the source code and document of BenchENAS for free.
Snippet Policy Network for Multi-class Varied-length ECG Early Classification
Jul 28, 2021
Arrhythmia detection from ECG is an important research subject in the prevention and diagnosis of cardiovascular diseases. The prevailing studies formulate arrhythmia detection from ECG as a time series classification problem. Meanwhile, early detection of arrhythmia presents a real-world demand for early prevention and diagnosis. In this paper, we address a problem of cardiovascular disease early classification, which is a varied-length and long-length time series early classification problem as well. For solving this problem, we propose a deep reinforcement learning-based framework, namely Snippet Policy Network (SPN), consisting of four modules, snippet generator, backbone network, controlling agent, and discriminator. Comparing to the existing approaches, the proposed framework features flexible input length, solves the dual-optimization solution of the earliness and accuracy goals. Experimental results demonstrate that SPN achieves an excellent performance of over 80\% in terms of accuracy. Compared to the state-of-the-art methods, at least 7% improvement on different metrics, including the precision, recall, F1-score, and harmonic mean, is delivered by the proposed SPN. To the best of our knowledge, this is the first work focusing on solving the cardiovascular early classification problem based on varied-length ECG data. Based on these excellent features from SPN, it offers a good exemplification for addressing all kinds of varied-length time series early classification problems.
An Online Prediction Approach Based on Incremental Support Vector Machine for Dynamic Multiobjective Optimization
Feb 24, 2021
Real-world multiobjective optimization problems usually involve conflicting objectives that change over time, which requires the optimization algorithms to quickly track the Pareto optimal front (POF) when the environment changes. In recent years, evolutionary algorithms based on prediction models have been considered promising. However, most existing approaches only make predictions based on the linear correlation between a finite number of optimal solutions in two or three previous environments. These incomplete information extraction strategies may lead to low prediction accuracy in some instances. In this paper, a novel prediction algorithm based on incremental support vector machine (ISVM) is proposed, called ISVM-DMOEA. We treat the solving of dynamic multiobjective optimization problems (DMOPs) as an online learning process, using the continuously obtained optimal solution to update an incremental support vector machine without discarding the solution information at earlier time. ISVM is then used to filter random solutions and generate an initial population for the next moment. To overcome the obstacle of insufficient training samples, a synthetic minority oversampling strategy is implemented before the training of ISVM. The advantage of this approach is that the nonlinear correlation between solutions can be explored online by ISVM, and the information contained in all historical optimal solutions can be exploited to a greater extent. The experimental results and comparison with chosen state-of-the-art algorithms demonstrate that the proposed algorithm can effectively tackle dynamic multiobjective optimization problems.
System Design and Analysis for Energy-Efficient Passive UAV Radar Imaging System using Illuminators of Opportunity
Oct 01, 2020
Unmanned ariel vehicle (UAV) can provide superior flexibility and cost-efficiency for modern radar imaging systems, which is an ideal platform for advanced remote sensing applications using synthetic aperture radar (SAR) technology. In this paper, an energy-efficient passive UAV radar imaging system using illuminators of opportunity is first proposed and investigated. Equipped with a SAR receiver, the UAV platform passively reuses the backscattered signal of the target scene from an external illuminator, such as SAR satellite, GNSS or ground-based stationary commercial illuminators, and achieves bi-static SAR imaging and data communication. The system can provide instant accessibility to the radar image of the interested targets with enhanced platform concealment, which is an essential tool for stealth observation and scene monitoring. The mission concept and system block diagram are first presented with justifications on the advantages of the system. Then, the prospective imaging performance and system feasibility are analyzed for the typical illuminators based on signal and spatial resolution model. With different illuminators, the proposed system can achieve distinct imaging performance, which offers more alternatives for various mission requirements. A set of mission performance evaluators is established to quantitatively assess the capability of the system in a comprehensive manner, including UAV navigation, passive SAR imaging and communication. Finally, the validity of the proposed performance evaluators are verified by numerical simulations.