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Accurately predicting anticancer peptide using an ensemble of heterogeneously trained classifiers

Informatics in Medicine Unlocked 2023年 42卷

作者： Azim, Sayed Mehedi Sabab, Noor Hossain Nuri Noshadi, Iman Alinejad-Rokny, Hamid Sharma, Alok Shatabda, Swakkhar Dehzangi, Iman Center for Computational and Integrative Biology Rutgers University Camden 08102 NJ United States Department of Computer Science and Engineering United International University Plot 2 United City Madani Avenue BaddaDhaka 1212 Bangladesh Department of Bioengineering University of California Riverside 92507 CA United States BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering The University of New South Wales (UNSW Sydney) Sydney NSW 2052 Australia UNSW Data Science Hub UNSW Sydney Sydney NSW 2052 Australia Health Data Analytics Program AI-enabled Processes Research Centre Macquarie University Sydney 2109 Australia Institute for Integrated and Intelligent Systems Griffith University Brisbane Australia Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama 230-0045 Japan Department of Computer Science Rutgers University Camden 08102 NJ United States

The use of therapeutic peptides for the treatment of cancer has received tremendous attention in recent years. Anticancer peptides (ACPs) are considered new anticancer drugs which have several advantages over chemistry-based drugs including high specificity, strong tumor penetration capacity, and low toxicity level for normal cells. Due to the rise of experimentally verified bioactive peptides, several in silico approaches became imperative for the investigation of the characteristics of ACPs. In this paper, we proposed a new machine learning tool named iACP-RF that uses a combination of several sequence-based features and an ensemble of three heterogeneously trained Random Forest classifiers to accurately predict anticancer peptides. Experimental results show that our proposed model achieves an accuracy of 75.9% which outperforms other state-of-the-art methods by a significant margin. We also achieve 0.52, 75.6%, and 76.2% in terms of Matthews Correlation Coefficient (MCC), Sensitivity, and Specificity, respectively. iACP-RF as a standalone tool and its source code are publicly available at: https://***/MLBC-lab/iACP-RF. © 2023 The Authors

关键词： Anticancer peptides Ensemble learning Feature extraction Heterogeneous classifiers Machine learning Random Forest

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Iterative quantum optimization of spin glass problems with rapidly oscillating transverse fields

arXiv

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arXiv 2024年

作者： Barton, Brandon Sagal, Jacob Feeney, Sean Grattan, George Patnaik, Pratik Oganesyan, Vadim Carr, Lincoln D. Kapit, Eliot Quantum Engineering Program Colorado School of Mines 1523 Illinois St GoldenCO80401 United States Department of Applied Mathematics and Statistics Colorado School of Mines 1500 Illinois St GoldenCO80401 United States Center for Computational Quantum Physics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Department of Physics Colorado School of Mines 1523 Illinois St GoldenCO80401 United States Department of Computer Science Colorado School of Mines 1500 Illinois St GoldenCO80401 United States Department of Physics and Astronomy College of Staten Island City University of New York Staten IslandNY10314 United States Physics program and Initiative for the Theoretical Sciences The Graduate Center City University of New York New YorkNY10016 United States

In this work, we introduce a new iterative quantum algorithm, called Iterative Symphonic Tunneling for Satisfiability problems (IST-SAT), which solves quantum spin glass optimization problems using high-frequency oscillating transverse fields. IST-SAT operates as a sequence of iterations, in which bitstrings returned from one iteration are used to set spin-dependent phases in oscillating transverse fields in the next iteration. Over several iterations, the novel mechanism of the algorithm steers the system toward the problem ground state. We benchmark IST-SAT on sets of hard MAX-3-XORSAT problem instances with exact state vector simulation, and report polynomial speedups over trotterized adiabatic quantum computation (TAQC) and the best known semi-greedy classical algorithm. When IST-SAT is seeded with a sufficiently good initial approximation, the algorithm converges to exact solution(s) in a polynomial number of iterations. Our numerical results identify a critial Hamming radius(CHR), or quality of initial approximation, where the time-to-solution crosses from exponential to polynomial scaling in problem size. By combining IST-SAT with future classical or quantum approximation algorithms, larger gains may be achieved. The mechanism we present in this work thus presents a new path toward achieving quantum advantage in optimization. © 2024, CC BY.

关键词： Combinatorial optimization

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Terahertz chiral photonic-crystal cavities with broken time-reversal symmetry

arXiv

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arXiv 2024年

作者： Tay, Fuyang Sanders, Stephen Baydin, Andrey Song, Zhigang Welakuh, Davis M. Alabastri, Alessandro Rokaj, Vasil Dag, Ceren B. Kono, Junichiro Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley–Curl Institute Rice University HoustonTX77005 United States Smalley–Curl Institute Rice University HoustonTX77005 United States John A. Paulson School of Engineering and Applied Sciences Harvard University CambridgeMA02139 United States Max Planck Institute for The Structure and Dynamics of Matter Luruper Chaussee 149 Hamburg22761 Germany ITAMP Harvard-Smithsonian Center for Astrophysics CambridgeMA02138 United States Department of Physics Harvard University CambridgeMA02138 United States Department of Physics Villanova University VillanovaPA19085 United States Department of Physics and Astronomy Rice University HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States

Strong coupling between matter and vacuum electromagnetic fields in a cavity can induce novel quantum phases in thermal equilibrium via symmetry breaking. Particularly, coupling with circularly polarized fields can break time-reversal symmetry, leading to topological modifications in the band structure. Therefore, chiral optical cavities that host chiral vacuum fields are being sought, especially in the terahertz (THz) frequency range, where various large-oscillator-strength resonances exist. Here, we present a novel approach to achieving THz chiral photonic-crystal cavities (PCCs) with high-quality factors (>400) using a magnetoplasma in a lightly doped semiconductor. Numerical simulations of an optimized structure based on InSb in a small perpendicular magnetic field (∼0.2 T) show chiral cavity resonances with near-perfect ellipticity at the surfaces of the central dielectric layer, where one can place atomically thin materials like monolayer graphene. We theoretically estimate an energy gap on the order of 1 meV in graphene when coupled to our proposed chiral cavity, which is potentially measurable in experiments. These THz chiral PCCs offer a promising platform for exploring new phases in cavity-dressed condensed matter with broken time-reversal symmetry. Copyright © 2024, The Authors. All rights reserved.

关键词： Crystal symmetry

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Topological Metamaterials

arXiv

引用

arXiv 2022年

作者： Ni, Xiang Yves, Simon Krasnok, Alex Alu, Andrea Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States Department of Electrical and Computer Engineering Florida International University MiamiFL33174 United States Department of Electrical Engineering City College The City University of New York 160 Convent Avenue New York10031 United States Physics Program The Graduate Center The City University of New York 365 Fifth Avenue New York10016 United States

Unlike geometrical features, such as shape or volume, the topological properties of an object do not change continuously, but only due to abrupt transitions associated with a change in the integer quantities that describe these properties - known as topological invariants. In turn, this resilience of topological features is associated with intrinsic robustness. For example, the topological invariant known as the Chern number, associated with the quantization of the Hall conductance in a two-dimensional electron gas, supports disorder-immune electron transport at the surface of topological insulators (TIs). One of the most significant breakthroughs in physics of the last decade has been the discovery that materials with non-trivial topological properties for electronic, electromagnetic, acoustic and mechanical responses can be designed and manufactured at our will through engineered metamaterials (MMs). Here, we review the foundation and the state-of-the-art advances of topological photonics, acoustics and mechanical MMs. We discuss how topological MMs enable nontrivial wave phenomena in physics, engineering, of great interest for a broad range of interdisciplinary science disciplines such as classical and quantum chemistry. We first introduce the foundations of topological materials and the main concepts behind their peculiar features, including the concepts of topological charge and geometric phase. We then discuss the topology of electronic band structures in natural topological materials, like topological insulators and gapless Dirac and Weyl semimetals. Based on these concepts, we review the concept, design and response of topologically nontrivial MMs in photonics and phononics, including topological phases in 2D MMs with and without time-reversal symmetry, Floquet TIs based on spatial and temporal modulation, topological phases in 3D MMs, higher-order topological phases in MMs, non-Hermitian and nonlinear topological MMs and the topological features of scatteri

关键词： Metamaterials

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Beyond Bounds on Light Scattering with Complex Frequency Excitations

arXiv

引用

arXiv 2022年

作者： Kim, Seunghwi Lepeshov, Sergey Krasnok, Alex Alù, Andrea Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States DTU Electro Department of Electrical and Photonics Engineering Technical University of Denmark Ørsteds Plads 343 Kgs. LyngbyDK-2800 Denmark Department of Electrical and Computer Engineering Florida International University MiamiFL33174 United States Physics Program Graduate Center City University of New York New YorkNY10016 United States

Light scattering is one of the most established wave phenomena in optics, lying at the heart of light-matter interactions and of crucial importance for nanophotonic applications. Passivity, causality and energy conservation imply strict bounds on the degree of control over scattering from small particles, with implications on the performance of many optical devices. Here, we demonstrate that these bounds can be surpassed by considering excitations at complex frequencies, yielding extreme scattering responses as tailored nanoparticles reach a quasi-steady-state regime. These mechanisms can be used to engineer light scattering of nanostructures beyond conventional limits for noninvasive sensing, imaging, and nanoscale light manipulation. Copyright © 2022, The Authors. All rights reserved.

关键词： Light scattering

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Application of Genetic Algorithms to the Multiple Team Formation Problem

arXiv

引用

arXiv 2019年

作者： Esgario, Jose G. M. Da Silva, Iago E. Krohling, Renato A. Program in Computer Science Federal University of Espirito Santo Brazil Department of Production Engineering Federal University of Espirito Santo Brazil Department of Production Engineering and Graduate Program in Computer Science Federal University of Espirito Santo

Allocating of people in multiple projects is an important issue considering the efficiency of groups from the point of view of social interaction. In this paper, based on previous works, the Multiple Team Formation Problem (MTFP) based on sociometric techniques is formulated as an optimization problem taking into account the social interaction among team members. To solve the resulting optimization problem we propose a Genetic Algorithm due to the NP-hard nature of the problem. The social cohesion is an important issue that directly impacts the productivity of the work environment. So, maintaining an appropriate level of cohesion keeps a group together, which will bring positive impacts on the results of a project. The aim of the proposal is to ensure the best possible effectiveness from the point of view of social interaction. In this way, the presented algorithm serves as a decision-making tool for managers to build teams of people in multiple projects. In order to analyze the performance of the proposed method, computational experiments with benchmarks were performed and compared with the exhaustive method. The results are promising and show that the algorithm generally obtains near-optimal results within a short computational time. Copyright © 2019, The Authors. All rights reserved.

关键词： Genetic algorithms

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A Vehicle Forensics framework with Post-Quantum Cryptography and Blockchain

A Vehicle Forensics framework with Post-Quantum Cryptography...

引用

IEEE International Symposium on Intelligent Signal Processing and Communication Systems (ISPACS)

作者： Chien-Lung Hsu Yi-Cheih Hsu Yu-Jen Shih Cheng-Wei Wu Fu-Hau Hsu Graduate Institute of Management Chang Gung University Taiwan Taoyuan R.O.C Department of Information Management Chang Gung University Taiwan Taoyuan R.O.C Healthy Aging Research Center Chang Gung University Taiwan Taoyuan R.O.C Department of Visual Communication Design Ming-Chi University of Technology Taiwan Taoyuan R.O.C Chang-Gung Memorial Hospital Taiwan Taoyuan R.O.C Department of Master of Science Degree Program in Innovation for Smart Medicine Chang Gung University Taiwan Taoyuan R.O.C Computer Science& Information Engineering National Central University Taiwan Taoyuan R.O.C Information Management Chang Gung University Taiwan Taoyuan R.O.C

ISBN: (数字)9798350389210

ISBN: (纸本)9798350389227

With the recent rapid development of the Internet of Vehicles and autonomous driving technology, the demand for digital vehicle identification has also increased. Coupled with the gradual maturity of quantum technology, the Internet of Vehicles, which mainly uses wireless communication technology for data transmission, will face the threat of quantum computing and privacy issues. This research proposes the Vehicle Forensics Cloud System (VFCS), a framework combining post-quantum cryptography and blockchain technology to address these issues and provide a comprehensive solution for vehicle digital forensics.

关键词： Wireless communication Quantum computing Digital forensics Insurance Signal processing Blockchains Safety Autonomous vehicles Interoperability Internet of Vehicles

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Author Correction: Dynamical flexible inference of nonlinear latent factors and structures in neural population activity

引用

Nature biomedical engineering 2025年第2期9卷 283页

作者： Hamidreza Abbaspourazad Eray Erturk Bijan Pesaran Maryam M Shanechi Ming Hsieh Department of Electrical and Computer Engineering Viterbi School of Engineering University of Southern California Los Angeles CA USA. Departments of Neurosurgery Neuroscience and Bioengineering University of Pennsylvania Philadelphia PA USA. Ming Hsieh Department of Electrical and Computer Engineering Viterbi School of Engineering University of Southern California Los Angeles CA USA. shanechi@usc.edu. Thomas Lord Department of Computer Science Alfred E. Mann Department of Biomedical Engineering Neuroscience Graduate Program University of Southern California Los Angeles CA USA. shanechi@usc.edu.

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Voltage Levels and Reactive Power in Distribution Networks with High Integration of Distributed Photovoltaic Generation

Voltage Levels and Reactive Power in Distribution Networks w...

引用

2019 IEEE PES Conference on Innovative Smart Grid Technologies, ISGT Latin America 2019

作者： Darui, Caroline B. F. Lucca, Tiago G. Abaide, Alzenira Da R. Da Veiga, Matheus F. Da Cruz, Matheus S. Knak Neto, Nelson Wüst, Lucas L. Figueiró, Iuri C. Federal University of Santa Maria Graduate Program in Electrical Engineering Santa Maria Brazil URI Santo Ângelo Department of Engineering and Computer Science Santo Ângelo Brazil

ISBN: (纸本)9781538695678

The Brazilian electrical system is undergoing many changes due to the exponential growth of photovoltaic systems connected to the grid (PV). This increase may affect power quality parameters, such as reduction of power factor and increase of voltage levels. This work aims to model and simulate a low voltage distribution network with high levels of integration of PV systems in order to verify how the voltage and reactive parameters behave in these cases. It was used new load curve models, the Monte Carlo method and the OpenDSS software. © 2019 IEEE.

关键词： Monte Carlo methods

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An artificial intelligence method for vessel detection in images of cardiac catheterization

引用

Informatics in Medicine Unlocked 2023年 39卷

作者： Chien, Ting-Ying Ting, Hsien-Wei Li, Hao-Wei Chang, Hsiao-Huang Department of Computer Science and Engineering Yuan Ze University 320 Taoyuan City Taiwan Graduate Program in Biomedical Informatics Yuan Ze University 320 Taoyuan City Taiwan Innovation Center for Big Data and Digital Convergence Yuan Ze University 320 Taoyuan City Taiwan Department of Neurosurgery Taipei Hospital Ministry of Health and Welfare 242 New Taipei City Taiwan Division of Cardiovascular Surgery Department of Surgery Taipei Veterans General Hospital Taipei 11217 Taiwan Department of Surgery School of Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan

Coronary artery disease (CAD) is one of the top ten leading causes of death in countries worldwide. There are several methods used by physicians to diagnose CAD. One common method is the use of X-ray angiogram (XRA) images. When employing a computer-aided automatic analysis method to locate blood vessels in XRA images, problems such as complex background noise, low contrast, and difficulty in separating blood vessels from the background are encountered, especially for blood vessels with a low contrast to the background noise. In this study, we used various image preprocessing methods to highlight blood vessels from complex backgrounds and different types of blood vessel, followed by the employment of four superpixel segmentation methods to partition an image into multiple segments, and finally the utilization of Weighted Voting to determine the best superpixel algorithm. A genetic algorithm was used to identify the best weights by which to determine the locations of blood vessels in images of cardiac catheterization. Our proposed method achieved an average F1-score of 73.4% in the analysis of five patients, which was better than the other superpixel algorithms tested. The results of this research will be helpful for future SYNTAX score analysis. © 2023

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