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An ensemble deep learning model for predicting minimum inhibitory concentrations of antimicrobial peptides against pathogenic bacteria

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iscience 2024年第9期27卷

作者： Chung, Chia-Ru Chien, Chung-Yu Tang, Yun Wu, Li-Ching Hsu, Justin Bo-Kai Lu, Jang-Jih Lee, Tzong-Yi Bai, Chen Horng, Jorng-Tzong Department of Computer Science and Information Engineering National Central University Taoyuan Taiwan Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Biomedical Sciences and Engineering National Central University Taoyuan Taiwan Department of Computer Science and Engineering Yuan Ze University Taoyuan Taiwan Department of Laboratory Medicine Chang Gung Memorial Hospital at Linkou Taoyuan City Taiwan School of Medicine Chang Gung University Taoyuan City Taiwan Department of Medical Biotechnology and Laboratory Science Chang Gung University Taoyuan City Taiwan Center for Intelligent Drug Systems and Smart Biodevices (IDS2B) National Yang Ming Chiao Tung University Hsinchu City Taiwan Warshel Institute for Computational Biology School of Medicine The Chinese University of Hong Kong (Shenzhen) Shenzhen 518172 Hong Kong

The rise of antibiotic resistance necessitates effective alternative therapies. Antimicrobial peptides (AMPs) are promising due to their broad inhibitory effects. This study focuses on predicting the minimum inhibitory concentration (MIC) of AMPs against whom-priority pathogens: Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, and Pseudomonas aeruginosa ATCC 27853. We developed a comprehensive regression model integrating AMP sequence-based and genomic features. Using eight AI-based architectures, including deep learning with protein language model embeddings, we created an ensemble model combining bi-directional long short-term memory (BiLSTM), convolutional neural network (CNN), and multi-branch model (MBM). The ensemble model showed superior performance with Pearson correlation coefficients of 0.756, 0.781, and 0.802 for the bacterial strains, demonstrating its accuracy in predicting MIC values. This work sets a foundation for future studies to enhance model performance and advance AMP applications in combating antibiotic resistance. © 2024 The Authors

关键词： Biological sciences Chemistry computer science

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A Full Dive into Realizing the Edge-enabled Metaverse: Visions, Enabling Technologies,and Challenges

arXiv

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arXiv 2022年

作者： Xu, Minrui Ng, Wei Chong Lim, Wei Yang Bryan Kang, Jiawen Xiong, Zehui Niyato, Dusit Yang, Qiang Shen, Xuemin Sherman Miao, Chunyan The School of Computer Science and Engineering Nanyang Technological University Singapore Alibaba Group Alibaba-NTU Joint Research Institute Nanyang Technological University Singapore The School of Automation Guangdong University of Technology China The Pillar of Information Systems Technology and Design Singapore University of Technology and Design Singapore487372 Singapore The Department of Computer Science and Engineering Hong Kong University of Science and Technology Hong Kong Webank China The Department of Electrical and Computer Engineering University of Waterloo WaterlooONN2L 3G1 Canada

Dubbed "the successor to the mobile Internet", the concept of the Metaverse has grown in popularity. While there exist lite versions of the Metaverse today, they are still far from realizing the full vision of an immersive, embodied, and interoperable Metaverse. Without addressing the issues of implementation from the communication and networking, as well as computation perspectives, the Metaverse is difficult to succeed the Internet, especially in terms of its accessibility to billions of users today. In this survey, we focus on the edge-enabled Metaverse to realize its ultimate vision. We first provide readers with a succinct tutorial of the Metaverse, an introduction to the architecture, as well as current developments. To enable ubiquitous, seamless, and embodied access to the Metaverse, we discuss the communication and networking challenges and survey cutting-edge solutions and concepts that leverage next-generation communication systems for users to immerse as and interact with embodied avatars in the Metaverse. Moreover, given the high computation costs required, e.g., to render 3D virtual worlds and run data-hungry artificial intelligence-driven avatars, we discuss the computation challenges and cloud-edge-end computation framework-driven solutions to realize the Metaverse on resource-constrained edge devices. Next, we explore how blockchain technologies can aid in the interoperable development of the Metaverse, not just in terms of empowering the economic circulation of virtual user-generated content but also to manage physical edge resources in a decentralized, transparent, and immutable manner. Finally, we discuss the future research directions towards realizing the true vision of the edge-enabled Metaverse. © 2022, CC BY.

关键词： Blockchain

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Studying speed-accuracy trade-offs in best-of-n collective decision-making through heterogeneous mean-field modeling

arXiv

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arXiv 2023年

作者： Reina, Andreagiovanni Njougouo, Thierry Tuci, Elio Carletti, Timoteo Université Libre de Bruxelles Brussels Belgium Centre for the Advanced Study of Collective Behaviour Universität Konstanz Konstanz Germany Department of Collective Behavior Max Planck Institute of Animal Behavior Konstanz Germany Faculty of Computer Science Namur Institute for Complex Systems naXys Université de Namur Rue Grandgagnage 21 NamurB5000 Belgium Department of Mathematics Namur Institute for Complex Systems naXys Université de Namur Rue Grafé 2 NamurB5000 Belgium

To succeed in their objectives, groups of individuals must be able to make quick and accurate collective decisions on the best option among a set of alternatives with different qualities. Group-living animals aim to do that all the time. Plants and fungi are thought to do so too. Swarms of autonomous robots can also be programmed to make best-of-n decisions for solving tasks collaboratively. Ultimately, humans critically need it and so many times they should be better at it! Thanks to their mathematical tractability, simple models like the voter model and the local majority rule model have proven useful to describe the dynamics of such collective decision-making processes. To reach a consensus, individuals change their opinion by interacting with neighbors in their social network. At least among animals and robots, options with a better quality are exchanged more often and therefore spread faster than lower-quality options, leading to the collective selection of the best option. With our work, we study the impact of individuals making errors in pooling others’ opinions caused, for example, by the need to reduce the cognitive load. Our analysis is grounded on the introduction of a model that generalizes the two existing models (local majority rule and voter model), showing a speed-accuracy trade-off regulated by the cognitive effort of individuals. We also investigate the impact of the interaction network topology on the collective dynamics. To do so, we extend our model and, by using the heterogeneous mean-field approach, we show the presence of another speed-accuracy trade-off regulated by network connectivity. An interesting result is that reduced network connectivity corresponds to an increase in collective decision accuracy. © 2023, CC BY.

关键词： Decision making

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Experimental demonstration of the advantage of adaptive quantum circuits

arXiv

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arXiv 2023年

作者： Foss-Feig, Michael Tikku, Arkin Lu, Tsung-Cheng Mayer, Karl Iqbal, Mohsin Gatterman, Thomas M. Gerber, Justin A. Gilmore, Kevin Gresh, Dan Hankin, Aaron Hewitt, Nathan Horst, Chandler V. Matheny, Mitchell Mengle, Tanner Neyenhuis, Brian Dreyer, Henrik Hayes, David Hsieh, Timothy H. Kim, Isaac H. Quantinuum 303 S. Technology Ct. BroomfieldCO80021 United States Centre for Engineered Quantum Systems University of Sydney SydneyNSW2006 Australia Perimeter Institute for Theoretical Physics WaterlooONN2L 2Y5 Canada Quantinuum Leopoldstrasse 180 Munich80804 Germany Department of Computer Science UC Davis DavisCA95616 United States

Adaptive quantum circuits employ unitary gates assisted by mid-circuit measurement, classical computation on the measurement outcome, and the conditional application of future unitary gates based on the result of the classical computation. In this paper, we experimentally demonstrate that even a noisy adaptive quantum circuit of constant depth can achieve a task that is impossible for any purely unitary quantum circuit of identical depth: the preparation of long-range entangled topological states with high fidelity. We prepare a particular toric code ground state with fidelity of at least 76.9 ± 1.3% using a constant depth (d = 4) adaptive circuit, and rigorously show that no unitary circuit of the same depth and connectivity could prepare this state with fidelity greater than 50%. Copyright © 2023, The Authors. All rights reserved.

关键词： Ground state

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Semantic surprise predicts the N400 brain potential

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Neuroimage: Reports 2023年第1期3卷 100161-100161页

作者： Lindborg, Alma Musiolek, Lea Ostwald, Dirk Rabovsky, Milena Department of Psychology University of Potsdam Karl-Liebknecht-Str. 24-25 Potsdam 14476 Germany Adaptive Systems Group Department of Computer Science Humboldt-Universitaet zu Berlin Unter den Linden 6 Berlin 10099 Germany Institute of Psychology Otto von Guericke Universitaet Magdeburg Universitaetsplatz 2 Magdeburg 39106 Germany

Language is central to human life;however, how our brains derive meaning from language is still not well understood. A commonly studied electrophysiological measure of on-line meaning related processing is the N400 component, the computational basis of which is still actively debated. Here, we test one of the recently proposed, computationally explicit hypotheses on the N400 – namely, that it reflects surprise with respect to a probabilistic representation of the semantic features of the current stimulus in a given context. We devise a Bayesian sequential learner model to derive trial-by-trial semantic surprise in a semantic oddball like roving paradigm experiment, where single nouns from different semantic categories are presented in sequences. Using experimental data from 40 subjects, we show that model-derived semantic surprise significantly predicts the N400 amplitude, substantially outperforming a non-probabilistic baseline model. Investigating the temporal signature of the effect, we find that the effect of semantic surprise on the EEG is restricted to the time window of the N400. Moreover, comparing the topography of the semantic surprise effect to a conventional ERP analysis of predicted vs. unpredicted words, we find that the semantic surprise closely replicates the N400 topography. Our results make a strong case for the role of probabilistic semantic representations in eliciting the N400, and in language comprehension in general. © 2023 The Authors

关键词： Bayesian modelling Electrophysiology Language N400 Semantics

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New antenna selection schemes for full-duplex cooperative MIMO-NOMA systems

arXiv

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arXiv 2022年

作者： Mobini, Zahra Mohammadi, Mohammadali Tsiftsis, Theodoros A. Ding, Zhiguo Tellambura, Chintha Faculty of Engineering Shahrekord University Shahrekord115 Iran School of Intelligent Systems Science and Engineering Jinan University Zhuhai519070 China Department of Computer Science and Telecommunications University of Thessaly Lamia35131 Greece School of Electrical and Electronic Engineering The University of Manchester Manchester United Kingdom Department of Electrical and Computer Engineering University of Alberta EdmontonABT6G 2V4 Canada

In this paper, we address the antenna selection (AS) problem in full-duplex (FD) cooperative non-orthogonal multiple access (NOMA) systems, where a multi-antenna FD relay bridges the connection between the multiantenna base station and NOMA far user. Specifically, two AS schemes, namely max-U1 and max-U2, are proposed to maximize the end-to-end signal-to-interference-plus-noise ratio at either or both near and far users, respectively. Moreover, a two-stage AS scheme, namely quality-of-service (QoS) provisioning scheme, is designed to realize a specific rate at the far user while improving the near user's rate. To enhance the performance of the QoS provisioning AS scheme, the idea of dynamic antenna clustering is applied at the relay to adaptively partition the relay's antennas into transmit and receive subsets. The proposed AS schemes' exact outage probability and achievable rate expressions are derived. To provide more insight, closed-form asymptotic outage probability expressions for the max-U1 and max-U2 AS schemes are obtained. Our results show that while the QoS provisioning AS scheme can deliver a near-optimal performance for static antenna setup at the relay, it provides up to 12% average sum rate gain over the optimum AS selection with fixed antenna setup. © 2022, CC BY.

关键词： Antennas

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Determination of the spectral dispersion for the heart muscle – a Kramers-Kronig approach

Determination of the spectral dispersion for the heart muscl...

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International Conference on Laser Optics

作者： Luís M. Oliveira Maria R. Pinheiro Hélder P. Oliveira Maria I. Carvalho Valery V. Tuchin Physics Department Rua Dr. António Bernardino de Almeida 431 Polytechnic of Porto School of Engineering Porto Portugal Institute for Systems and Computer Engineering Technology and Science (INESC TEC) Rua Dr. Roberto Frias Porto Portugal Department of Computer Science Rua do Campo Alegre 1021 Faculty of Science Porto University Porto Portugal Faculty of Engineering Rua Dr. Roberto Frias Porto University Porto Portugal Institute of Physics and Science Medical Center Saratov State University 83 Astrakhanskaya str. Saratov Russia Laboratory of Laser Molecular Imaging and Machine Learning Tomsk State University 36 Lenin ave. Tomsk Russia RC “Biotechnology of the Russian Academy of Sciences” 33 Leninsky prospect build 2 A.N. Bach Institute of Biophotonics Moscow Russia

ISBN: (数字)9798350390674

ISBN: (纸本)9798350390681

The refractive index of the pigs heart was measured at wavelengths between 255 and 850 nm to calculate the dispersion. The total transmittance and total reflectance spectra of the pig heart were measured between 200 and 1000 nm to calculate the spectral absorption coefficient. Using Kramers-Kronig relations, the dispersion of the heart was matched to experimental refractive index values.

关键词： Heart Reflectivity Absorption Wavelength measurement Refractive index Measurement by laser beam Muscles

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Evaluation of the Montenegrin Academic Digital Innovation Hub

Evaluation of the Montenegrin Academic Digital Innovation Hu...

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International Scientific-Professional Conference on Information Technology (IT)

作者： Luka Laković Peter A. Kara Ivana Ognjanović Laszlo Bokor Ramo Šendelj Christoph Reich Milovan Roganović Emmanouil Zoulias Jevto Eraković Tanja Radusinović Nada Rakočević Aniko Simon Faculty for Information Systems and Technologies University of Donja Gorica 81000 Podgorica Montenegro Department of Networked Systems and Services Faculty of Electrical Engineering and Informatics Budapest University of Technology and Economics 1111 Budapest Hungary Department of Computer Science School of Computer Science and Mathematics Wireless Multimedia and Networking Research Group Faculty of Science Engineering and Computing Kingston University London KT1 2EE UK Humanistic Studies University of Donja Gorica 81000 Podgorica Montenegro Institute of Data Science Cloud Computing and IT Security Furtwangen University 78120 Furtwangen Germany Clinic for Neurology Clinical Centre of Montenegro 81000 Podgorica Montenegro Faculty of Nursing School of Health Sciences National and Kapodistrian University of Athens 11527 Goudi Greece Chamber of Economy of Montenegro 81000 Podgorica Montenegro Sigma Technology 1093 Budapest Hungary

In the era of global digitalization, digital innovation hubs have become essential, as they function as transforming forces. In this paper, we provide an analysis of the Montenegrin Academic Digital Innovation Hub by applying multi-criteria qualitative evaluation over several criteria: process flow of fully digitized operations of the Hub (with aspects of the innovation life-cycle, ethics, and security), resource management, strategic goals, and feasibility. The paper also proposes a model of comprehensive resource management via the perspective of smart specialization priorities of Montenegro.

关键词： Technological innovation Ethics Resource management Security Information technology

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Assistive Technical Communication of Montenegrin eServices: a Case Study

Assistive Technical Communication of Montenegrin eServices: ...

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International Scientific-Professional Conference on Information Technology (IT)

作者： Aniko Simon Luka Laković Pavle Kovačević Peter A. Kara Ivana Ognjanović Ramo Šendelj Christoph Reich Milovan Roganović John Mantas Laszlo Bokor Sigma Technology 1093 Budapest Hungary Faculty for Information Systems and Technologies University of Donja Gorica 81000 Podgorica Montenegro Budapest University of Technology and Economics 1111 Budapest Hungary Department of Networked Systems and Services Faculty of Electrical Engineering and Informatics Budapest University of Technology and Economics 1111 Budapest Hungary Department of Computer Science School of Computer Science and Mathematics Faculty of Science Engineering and Computing Wireless Multimedia and Networking Research Group Kingston University London KT1 2EE UK Humanistic Studies University of Donja Gorica 81000 Podgorica Montenegro Institute of Data Science Cloud Computing and IT Security Furtwangen University 78120 Furtwangen Germany Clinic for Neurology Clinical Centre of Montenegro 81000 Podgorica Montenegro Faculty of Nursing School of Health Sciences National and Kapodistrian University of Athens 11527 Goudi Greece

With the advancement of information technology in the recent decades, digital and online services have become essential components of everyday life in Europe. Montenegro is no different in this regard. However, as digital literacy in the country is still in a developing phase in comparison with most countries of the EU, a higher portion of its citizens may rely on assistive technical communication. In this paper, we provide a case study on the assistive technical communication of Montenegrin eServices. The work addresses the sectors of online banking, healthcare services, higher education, national administrative services, and utilities. Our findings highlight the diversity in terms of implemented assistive technical communication, and distinguish usage contexts on the level of adequacy. Yet as the functionalities of Montenegrin eServices are expected to gradually expand in the upcoming years, assistive technical communication must aim to handle the higher extents of service complexity.

关键词： Online banking Education Europe Medical services Complexity theory Information technology

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Object-Based Tree Stump Detection Fusing RGB and Multispectral Data

Object-Based Tree Stump Detection Fusing RGB and Multispectr...

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International Conference on Software, Telecommunications and computer Networks (SoftCOM)

作者： Pranisha Chaturvedi Maximilian Johenneken Ahmad Drak Sebastian Houben Alexander Asteroth Department of Computer Science Bonn-Rhein-Sieg University of Applied Sciences Sankt Augustin Germany Institute of Technology Resource and Energy-efficient Engineering (TREE) Bonn-Rhein-Sieg University of Applied Sciences Sankt Augustin Germany institute for Artificial Intelligence and Autonomous Systems (A2S) Bonn-Rhein-Sieg University of Applied Sciences Sankt Augustin Germany

Over the past few years, forests have become increasingly susceptible to various natural stress factors, mainly due to climate change induced events such as drought. Quantifying the objects that lay on the forest floor such as soil, vegetation, wooden debris and tree stumps is a viable method for estimating the extent of the stress factors. Remote sensing is an established modus operandi for collecting data in forest environments. In this work, we focus on Unmanned Aerial Vehicles (UAV) as remote sensing platforms aiming to detect tree stumps in varying stages of decay within a forest calamity area. The platform provides us with both high-resolution images from RGB and multispectral cameras and height data. In addition, a vegetation index for wood is proposed to better highlight the presence of tree stumps using multispectral data. Object detection is performed with feature-level fusion after which Object-Based Image Analysis (OBIA) is carried out. The fused multispectral and RGB data resulted in 53.68% recall and 31.0% precision in detecting tree stumps. In comparison, the fused RGB and height data resulted in 50.0% recall and 20.9% precision.

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