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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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A sharp interface Lagrangian-Eulerian method for flexible-body fluid-structure interaction

arXiv

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arXiv 2022年

作者： Kolahdouz, Ebrahim M. Wells, David R. Rossi, Simone Aycock, Kenneth I. Craven, Brent A. Griffith, Boyce E. Center for Computational Biology Flatiron Institute Simons Foundation New YorkNY United States Department of Mathematics University of North Carolina Chapel HillNC United States Division of Applied Mechanics Office of Science and Engineering Laboratories Center for Devices and Radiological Health United States Food and Drug Administration Silver SpringMD United States Departments of Mathematics and Biomedical Engineering University of North Carolina Chapel HillNC United States Carolina Center for Interdisciplinary Applied Mathematics University of North Carolina Chapel HillNC United States Computational Medicine Program University of North Carolina Chapel HillNC United States McAllister Heart Institute University of North Carolina Chapel HillNC United States

This paper introduces a sharp-interface approach to simulating fluid-structure interaction (FSI) involving flexible bodies described by general nonlinear material models and across a broad range of mass density ratios. This new flexible-body immersed Lagrangian-Eulerian (ILE) scheme extends our prior work on integrating partitioned and immersed approaches to rigid-body FSI. Our numerical approach incorporates the geometrical and domain solution flexibility of the immersed boundary (IB) method with an accuracy comparable to body-fitted approaches that sharply resolve flows and stresses up to the fluid-structure interface. Unlike many IB methods, our ILE formulation uses distinct momentum equations for the fluid and solid subregions with a Dirichlet-Neumann coupling strategy that connects fluid and solid subproblems through simple interface conditions. As in earlier work, we use approximate Lagrange multiplier forces to treat the kinematic interface conditions along the fluid-structure interface. This penalty approach simplifies the linear solvers needed by our formulation by introducing two representations of the fluid-structure interface, one that moves with the fluid and another that moves with the structure, that are connected by stiff springs. This approach also enables the use of multi-rate time stepping, which allows us to use different time step sizes for the fluid and structure subproblems. Our fluid solver relies on an immersed interface method (IIM) for discrete surfaces to impose stress jump conditions along complex interfaces while enabling the use of fast structured-grid solvers for the incompressible Navier-Stokes equations. The dynamics of the volumetric structural mesh are determined using a standard finite element approach to large-deformation nonlinear elasticity via a nearly incompressible solid mechanics formulation. This formulation also readily accommodates compressible structures with a constant total volume, and it can handle fully compressibl

关键词： Fluid structure interaction

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Biases in Inverse Ising Estimates of Near-Critical Behaviour

arXiv

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arXiv 2023年

作者： Kloucek, Maximilian B. Machon, Thomas Kajimura, Shogo Royall, C. Patrick Masuda, Naoki Turci, Francesco H.H. Wills Laboratory School of Physics University of Bristol Bristol United Kingdom Bristol Centre for Functional Nanomaterials University of Bristol Bristol United Kingdom Faculty of Information and Human Sciences Kyoto Institute of Technology Kyoto606-8585 Japan Gulliver UMR CNRS 7083 ESPCI Paris Université PSL Paris75005 France Department of Mathematics State University of New York BuffaloNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY14260-5030 United States

Inverse Ising inference allows pairwise interactions of complex binary systems to be reconstructed from empirical correlations. Typical estimators used for this inference, such as Pseudo-likelihood maximization (PLM), are biased. Using the Sherrington-Kirkpatrick (SK) model as a benchmark, we show that these biases are large in critical regimes close to phase boundaries, and may alter the qualitative interpretation of the inferred model. In particular, we show that the small-sample bias causes models inferred through PLM to appear closer-to-criticality than one would expect from the data. Data-driven methods to correct this bias are explored and applied to a functional magnetic resonance imaging (fMRI) dataset from neuroscience. Our results indicate that additional care should be taken when attributing criticality to real-world datasets. Copyright © 2023, The Authors. All rights reserved.

关键词： Criticality (nuclear fission)

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

arXiv

引用

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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Widely Tunable Berry Curvature in the Magnetic Semimetal Cr1+δTe2

引用

Advanced Materials 2023年第12期35卷

作者： Fujisawa, Yuita Pardo-Almanza, Markel Hsu, Chia-Hsiu Mohamed, Atwa Yamagami, Kohei Krishnadas, Anjana Chang, Guoqing Chuang, Feng-Chuan Khoo, Khoong Hong Zang, Jiadong Soumyanarayanan, Anjan Okada, Yoshinori Okinawa904-0495 Japan Department of Physics National Sun Yat-sen University Kaohsiung80424 Taiwan Physics Division National Center for Theoretical Sciences Taipei10617 Taiwan Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University Singapore637371 Singapore Center for Theoretical and Computational Physics National Sun Yat-sen University Kaohsiung80424 Taiwan Institute of High Performance Computing Agency for Science Technology and Research Singapore138632 Singapore Department of Physics and Astronomy University of New Hampshire DurhamNH 03824 United States Materials Science Program University of New Hampshire DurhamNH 03824 United States Department of Physics National University of Singapore Singapore117551 Singapore Institute of Materials Research and Engineering Agency for Science Technology and Research Singapore138634 Singapore

Magnetic semimetals have increasingly emerged as lucrative platforms hosting spin-based topological phenomena in real and momentum spaces. Cr1+δTe2 is a self-intercalated magnetic transition metal dichalcogenide (TMD), which exhibits topological magnetism and tunable electron filling. While recent studies have explored real-space Berry curvature effects, similar considerations of momentum-space Berry curvature are lacking. Here, the electronic structure and transport properties of epitaxial Cr1+δTe2 thin films are systematically investigated over a range of doping, δ (0.33 – 0.71). Spectroscopic experiments reveal the presence of a characteristic semi-metallic band region, which shows a rigid like energy shift with δ. Transport experiments show that the intrinsic component of the anomalous Hall effect (AHE) is sizable and undergoes a sign flip across δ. Finally, density functional theory calculations establish a link between the doping evolution of the band structure and AHE: the AHE sign flip is shown to emerge from the sign change of the Berry curvature, as the semi-metallic band region crosses the Fermi energy. These findings underscore the increasing relevance of momentum-space Berry curvature in magnetic TMDs and provide a unique platform for intertwining topological physics in real and momentum spaces. © 2023 The Authors. Advanced Materials published by Wiley-VCH GmbH.

关键词： Density functional theory

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Google COVID-19 community mobility reports: Insights from multi-criteria decision making

arXiv

引用

arXiv 2020年

作者： da Silva, Gabriela Cavalcante Oliveira, Sabrina Wanner, Elizabeth F. Bezerra, Leonardo C.T. Brazil Postgraduate Program in Mathematical and Computational Modeling CEFET-MG Brazil Computer Engineering Dept. CEFET-MG Brazil Computer Science Group Aston University United Kingdom

Social distancing (SD) has been critical in the fight against the novel coronavirus disease (COVID-19). To aid SD monitoring, many technology companies have made available mobility data, the most prominent example being the community mobility reports (CMR) provided by Google. Given the wide range of research fields that have been drawing insights from CMR data, there has been a rising concern for methodological discussion on how to use them. Indeed, Google recently released their own guidelines, concerning the nature of the place categories and the need for calibrating regional values. In this work, we discuss how measures developed in the field of multi-criteria decision making (MCDM) might benefit researchers analyzing this data. Concretely, we discuss how Pareto dominance and performance measures adopted in MCDM enable the mobility evaluation for (i) multiple categories for a given time period and (ii) multiple categories over multiple time periods. We empirically demonstrate these approaches conducting both a region- and country-level analysis, comparing some of the most relevant outbreak examples from different continents. Copyright © 2020, The Authors. All rights reserved.

关键词： Coronavirus

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Effective approaches to disaster evacuation during a COVID-like pandemic

arXiv

引用

arXiv 2022年

作者： Tsai, Yi-Lin Sitepu, Dymasius Y. Chappell, Karyn E. Mediratta, Rishi P. Wang, C. Jason Kitanidis, Peter K. Field, Christopher B. Department of Civil and Environmental Engineering Stanford University StanfordCA United States Department of Engineering Science National University of Singapore Singapore Department of Engineering Imperial College London London United Kingdom Department of Pediatrics Stanford University School of Medicine StanfordCA United States Department of Health Policy Stanford University School of Medicine StanfordCA United States Woods Institute for the Environment Stanford University StanfordCA United States Bio-X Stanford University StanfordCA United States Institute for Computational and Mathematical Engineering Stanford University StanfordCA United States Department of Biology Stanford University StanfordCA United States Department of Earth System Science Stanford University StanfordCA United States Interdisciplinary Environmental Studies Program Stanford University StanfordCA United States

Since COVID-19 vaccines became available, no studies have quantified how different disaster evacuation strategies can mitigate pandemic risks in shelters. Therefore, we applied an age-structured epidemiological model, known as the Susceptible-Exposed-Infectious-Recovered (SEIR) model, to investigate to what extent different vaccine uptake levels and the Diversion protocol implemented in Taiwan decrease infections and delay pandemic peak occurrences. Taiwan’s Diversion protocol involves diverting those in self-quarantine due to exposure, thus preventing them from mingling with the general public at a congregate shelter. The Diversion protocol, combined with sufficient vaccine uptake, can decrease the maximum number of infections and delay outbreaks relative to scenarios without such strategies. When the diversion of all exposed people is not possible, or vaccine uptake is insufficient, the Diversion protocol is still valuable. Furthermore, a group of evacuees that consists primarily of a young adult population tends to experience pandemic peak occurrences sooner and have up to 180% more infections than does a majority elderly group when the Diversion protocol is implemented. However, when the Diversion protocol is not enforced, the majority elderly group suffers from up to 20% more severe cases than the majority young adult group. Copyright © 2022, The Authors. All rights reserved.

关键词： COVID-19

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Position: Bayesian Deep Learning is Needed in the Age of Large-Scale AI

arXiv

引用

arXiv 2024年

作者： Papamarkou, Theodore Skoularidou, Maria Palla, Konstantina Aitchison, Laurence Arbel, Julyan Dunson, David Filippone, Maurizio Fortuin, Vincent Hennig, Philipp Hernández-Lobato, José Miguel Hubin, Aliaksandr Immer, Alexander Karaletsos, Theofanis Khan, Mohammad Emtiyaz Kristiadi, Agustinus Li, Yingzhen Mandt, Stephan Nemeth, Christopher Osborne, Michael A. Rudner, Tim G.J. Rügamer, David Teh, Yee Whye Welling, Max Wilson, Andrew Gordon Zhang, Ruqi Department of Mathematics The University of Manchester Manchester United Kingdom Eric and Wendy Schmidt Center Broad Institute of MIT and Harvard Cambridge United States Spotify London United Kingdom Computational Neuroscience Unit University of Bristol Bristol United Kingdom Centre Inria de l'Université Grenoble Alpes Grenoble France Department of Statistical Science Duke University United States Statistics Program KAUST Saudi Arabia Helmholtz AI Munich Germany Department of Computer Science Technical University of Munich Munich Germany Munich Center for Machine Learning Munich Germany Tübingen AI Center University of Tübingen Tübingen Germany Department of Engineering University of Cambridge Cambridge United Kingdom Department of Mathematics University of Oslo Oslo Norway Bioinformatics and Applied Statistics Norwegian University of Life Sciences Ås Norway Department of Computer Science ETH Zurich Switzerland Chan Zuckerberg Initiative CA United States Center for Advanced Intelligence Project RIKEN Tokyo Japan Vector Institute Toronto Canada Department of Computing Imperial College London London United Kingdom Department of Computer Science UC Irvine Irvine United States Department of Mathematics and Statistics Lancaster University Lancaster United Kingdom Department of Engineering Science University of Oxford Oxford United Kingdom Center for Data Science New York University New York United States Department of Statistics LMU Munich Munich Germany DeepMind London United Kingdom Department of Statistics University of Oxford Oxford United Kingdom Informatics Institute University of Amsterdam Amsterdam Netherlands Courant Institute of Mathematical Sciences Center for Data Science Computer Science Department New York University New York United States Department of Computer Science Purdue University West Lafayette United States

In the current landscape of deep learning research, there is a predominant emphasis on achieving high predictive accuracy in supervised tasks involving large image and language datasets. However, a broader perspective reveals a multitude of overlooked metrics, tasks, and data types, such as uncertainty, active and continual learning, and scientific data, that demand attention. Bayesian deep learning (BDL) constitutes a promising avenue, offering advantages across these diverse settings. This paper posits that BDL can elevate the capabilities of deep learning. It revisits the strengths of BDL, acknowledges existing challenges, and highlights some exciting research avenues aimed at addressing these obstacles. Looking ahead, the discussion focuses on possible ways to combine large-scale foundation models with BDL to unlock their full potential. © 2024, CC BY-NC-ND.

关键词： Large datasets

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Rabi antenna using microstrip add-drop multiplexer for electron warp speed investigation

引用

Chinese Optics Letters 2022年第7期20卷 80-87页

作者： Somchat Sonasang Prakasit Prabpal Piya Sirikan Pratimakorn Hakaew Nhat Truong Pham Preecha Yupapin Kanad Ray Sarawoot Boonkirdram Department of Electronic Technology Faculty of Industrial TechnologyNakhon Phanom UniversityNakhon Phanom 48000Thailand Department of Electrical Technology School of Industrial TechnologySakonnakhon Technical CollegeInstitute of Vocational Education Northeastern Region 2Sakonnakhorn 47000Thailand Division of Computational Mechatronics Institute for Computational ScienceTon Duc Thang UniversityHo Chi Minh City 72915Vietnam Faculty of Electrical and Electronics Engineering Ton Duc Thang UniversityHo Chi Minh City 72915Vietnam Amity School of Applied Sciences Amity University RajasthanJaipurIndia Faubert Lab Universitéde MontréalH3T 1P1 MontréalCanada Facultad de CienciasFisico-Matematicas Benemérita Universidad Autónoma de PueblaAv.San Claudio y Av.18 surCol.San Manuel Ciudad UniversitariaPuebla Pue 72570Mexico Program of Electrical and Electronics Faculty of Industrial TechnologySakon Nakhon Rajabhat UniversitySakon Nakhon 47000Thailand

This work presents experimental results of Rabi antenna characteristics using the coupled line microstrip *** was constructed by a modified coupled line microstrip four-port network,which is known as an add-drop *** driven AC input enters the device via an input port using the suitable frequency and coupled line microstrip ring *** multilevel system is generated by a wave-particle aspect before the two-level system is *** the resonance,the transitions of the states induce the energy called whispering gallery mode(WGM)at the circuit center,which is the squeezed *** generated electron oscillation within the WGM envelope oscillated by the frequency is known as the Rabi *** the successive filtering with continuous AC input via the selected port,the electron cloud warp speed can be generated and achieved inside the two-level *** constructed microstrip ring radius is 25 mm,and the experimental results of the Rabi antenna characteristics are in good agreement with the simulation *** obtained resonant antenna oscillation frequency is 2.103 *** electron cloud warp speed of 1.100c and time dilation of 0.006μs are obtained.

关键词： integrated photonics waveguide microwave photonics Rabi antenna

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Question-Answering System Extracts Information on Injection Drug Use from Clinical Notes

arXiv

引用

arXiv 2023年

作者： Mahbub, Maria Goethert, Ian Danciu, Ioana Knight, Kathryn Srinivasan, Sudarshan Tamang, Suzanne Rozenberg-Ben-Dror, Karine Solares, Hugo Martins, Susana Trafton, Jodie Begoli, Edmon Peterson, Gregory D. Cyber Resilience and Intelligence Division Oak Ridge National Laboratory Oak RidgeTN United States Information Technology Services Division Oak Ridge National Laboratory Oak RidgeTN United States Computational Sciences and Engineering Division Oak Ridge National Laboratory Oak RidgeTN United States Department of Biomedical Informatics Vanderbilt University NashvilleTN United States Program Evaluation and Resource Center Office of Mental Health and Suicide Prevention Department of Veterans Affairs United States Department of Medicine Stanford University School of Medicine StanfordCA United States Veterans Affairs Great Lakes Health Care System WestchesterIL United States Department of Electrical Engineering and Computer Science University of Tennessee Knoxville KnoxvilleTN United States

Background: Injection drug use (IDU) is a dangerous health behavior that increases mortality and morbidity. Identifying IDU early and initiating harm reduction interventions can benefit individuals at risk. However, extracting IDU behaviors from patients’ electronic health records (EHR) is difficult because there is no International Classification of Disease (ICD) code and the only place IDU information can be indicated is unstructured free-text clinical notes. Although natural language processing can efficiently extract this information from unstructured data, there are no validated tools. Methods: To address this gap in clinical information, we design and demonstrate a question-answering (QA) framework to extract information on IDU from clinical notes. Our framework involves two main steps: (1) generating a gold-standard QA dataset and (2) developing and testing the QA model. We utilize 2323 clinical notes of 1145 patients sourced from the VA Corporate Data Warehouse to construct the gold-standard dataset for developing and evaluating the QA model. We also demonstrate the QA model’s ability to extract IDU-related information on temporally out-of-distribution data. Results: Here we show that for a strict match between gold-standard and predicted answers, the QA model achieves 51.65% F1 score. For a relaxed match between the gold-standard and predicted answers, the QA model obtains 78.03% F1 score, along with 85.38% Precision and 79.02% Recall scores. Moreover, the QA model demonstrates consistent performance when subjected to temporally out-of-distribution data. Conclusions: Our study introduces a QA framework designed to extract IDU information from clinical notes, aiming to enhance the accurate and efficient detection of people who inject drugs, extract relevant information, and ultimately facilitate informed patient care. © 2023, CC BY-NC-ND.

关键词： Data warehouses

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