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AB0205 A NOVEL METHOD FOR PREDICTING 1-YEAR RETENTION OF ABATACEPT USING machine learning TECHNIQUES: DIRECTIONALITY AND IMPORTANCE OF PREDICTORS

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Annals of the Rheumatic Diseases 2021年 80卷 1127-1128页

作者： R. Alten C. Behar C. Boileau P. Merckaert E. Afari V. Vannier-Moreau S. Connolly A. Najm P.A. Juge A. Rai Y. Elbez K. Lozenski Schlosspark-Klinik University Department of Internal Medicine Rheumatology Berlin Germany Tulsy Co-founder Paris France Excelya N/A Boulogne-Billancourt France Data Revenue GmbH Machine Learning Engineering Department Berlin Germany Private Practice N/A Brunoy France Bristol Myers Squibb Medical Affairs France Rueil-Malmaison France Bristol Myers Squibb Global Drug Development Princeton United States of America University of Glasgow Institute of Infection Immunity and Inflammation College of Medical Veterinary and Life Sciences Glasgow United Kingdom Université de Paris AP-HP Hôpital Bichat Claude-Bernard Department of Rheumatology Paris France Bristol Myers Squibb Global Biometrics and Data Science Princeton United States of America Deepscover Biostatistics Puteaux France Bristol Myers Squibb Immunology and Fibrosis Princeton United States of America

Background: In the ACTION ( NCT02109666 ) study, multivariable Cox proportional hazards regression models showed that the predictors of 1-year retention to abatacept treatment were: patient global pain assessment, country, reason for stopping last biologic, number of prior biologic treatments, abatacept monotherapy, RF/anti-cyclic citrullinated peptide (CCP) status, previous neoplasms, psychiatric disorders and cardiac disorders. 1 machine learning techniques, using the gradient-boosting model, subsequently identified additional predictors of abatacept retention in patients with moderate-to-severe RA enrolled in ACTION; however, the analysis did not show the directionality of the predictors. 2 Objectives: To improve the clinical interpretability of the machine learning model in terms of directionality and the importance of each variable in predicting retention. Methods: Previous analyses using the gradient-boosting model to identify predictors of abatacept retention at 1 year in the ACTION study have been described. 2 This analysis used SHapley Additive exPlanations (SHAP), a mathematical framework, to show how a particular predictor value influences prediction in the context of all other predictors. Higher SHAP values indicate a higher likelihood of retention. The contribution of every variable in the model's prediction (with the exception of country variables) was computed for each data point to capture individual variable impact. This enabled interpretation for level of importance and directionality at a patient level. Results: Using data from 2350 patients enrolled in ACTION (May 2008 to December 2013), the mean retention rate at 1 year was 59.3% (n=1393). Overall variable importance is shown in Figure 1 . After removal of country variables, the top five baseline predictors of retention were: no previous corticosteroid use, ACR functional class II, ≥2 prior biologic treatments prior to abatacept initiation, abatacept monotherapy and HAQ-DI. In terms of direction

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Torus graphs for multivariate phase coupling analysis

arXiv

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arXiv 2019年

作者： Klein, Natalie Orellana, Josue Brincat, Scott Miller, Earl K. Kass, Robert E. Department of Statistics and Data Science Carnegie Mellon University Machine Learning Department Carnegie Mellon University Center for the Neural Basis of Cognition Carnegie Mellon University University of Pittsburgh Department of Brain and Cognitive Science Massachusetts Institute of Technology

Angular measurements are often modeled as circular random variables, where there are natural circular analogues of moments, including correlation. Because a product of circles is a torus, a d-dimensional vector of circular random variables lies on a d-dimensional torus. For such vectors we present here a class of graphical models, which we call torus graphs, based on the full exponential family with pairwise interactions. The topological distinction between a torus and Euclidean space has several important consequences. Our development was motivated by the problem of identifying phase coupling among oscillatory signals recorded from multiple electrodes in the brain: oscillatory phases across electrodes might tend to advance or recede together, indicating coordination across brain areas. The data analyzed here consisted of 24 phase angles measured repeatedly across 840 experimental trials (replications) during a memory task, where the electrodes were in 4 distinct brain regions, all known to be active while memories are being stored or retrieved. In realistic numerical simulations, we found that a standard pairwise assessment, known as phase locking value, is unable to describe multivariate phase interactions, but that torus graphs can accurately identify conditional associations. Torus graphs generalize several more restrictive approaches that have appeared in various scientific literatures, and produced intuitive results in the data we analyzed. Torus graphs thus unify multivariate analysis of circular data and present fertile territory for future research. Copyright © 2019, The Authors. All rights reserved.

关键词： Graphic methods

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Deep CNN: A machine learning approach for driver drowsiness detection based on eye state

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Revue d'Intelligence Artificielle 2019年第6期33卷 461-466页

作者： Reddy Chirra, Venkata Rami Uyyala, Srinivasulu Reddy Kishore Kolli, Venkata Krishna Department of Computer Applications National Institute of Technology Tiruchirappalli620015 India Machine Learning and Data Analytics Lab Department of Computer Applications National Institute of Technology Tiruchirappalli620015 India Department of Computer Science and Engineering VFSTR Guntur522213 India

Driver drowsiness is one of the reasons for large number of road accidents these days. With the advancement in Computer Vision technologies, smart/intelligent cameras are developed to identify drowsiness in drivers, thereby alerting drivers which in turn reduce accidents when they are in fatigue. In this work, a new framework is proposed using deep learning to detect driver drowsiness based on Eye state while driving the vehicle. To detect the face and extract the eye region from the face images, Viola-Jones face detection algorithm is used in this work. Stacked deep convolution neural network is developed to extract features from dynamically identified key frames from camera sequences and used for learning phase. A SoftMax layer in CNN classifier is used to classify the driver as sleep or non-sleep. This system alerts driver with an alarm when the driver is in sleepy mood. The proposed work is evaluated on a collected dataset and shows better accuracy with 96.42% when compared with traditional CNN. The limitation of traditional CNN such as pose accuracy in regression is overcome with the proposed Staked Deep CNN. © 2019 Lavoisier. All rights reserved.

关键词： Face recognition

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Efficient Algorithms for Set-Valued Prediction in Multi-Class Classification

arXiv

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arXiv 2019年

作者： Mortier, Thomas Wydmuch, Marek Dembczyński, Krzysztof Hüllermeier, Eyke Waegeman, Willem Department of Data Analysis and Mathematical Modelling Ghent University Belgium Institute of Computing Science Poznań University of Technology Poland Intelligent Systems and Machine Learning Universität Paderborn Germany

In cases of uncertainty, a multi-class classifier preferably returns a set of candidate classes instead of predicting a single class label with little guarantee. More precisely, the classifier should strive for an optimal balance between the correctness (the true class is among the candidates) and the precision (the candidates are not too many) of its prediction. We formalize this problem within a general decision-theoretic framework that unifies most of the existing work in this area. In this framework, uncertainty is quantified in terms of conditional class probabilities, and the quality of a predicted set is measured in terms of a utility function. We then address the problem of finding the Bayes-optimal prediction, i.e., the subset of class labels with highest expected utility. For this problem, which is computationally challenging as there are exponentially (in the number of classes) many predictions to choose from, we propose efficient algorithms that can be applied to a broad family of utility scores. Two of these algorithms make use of structural information in the form of a class hierarchy, which is often available in prediction problems with many classes. Our theoretical results are complemented by experimental studies, in which we analyze the proposed algorithms in terms of predictive accuracy and runtime efficiency. Copyright © 2019, The Authors. All rights reserved.

关键词： Forecasting

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A multi-objective deep reinforcement learning algorithm for spatio-temporal latency optimization in mobile IoT-enabled edge computing networks

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Simulation Modelling Practice and Theory 2025年 143卷

作者： Parisa Khoshvaght Amir Haider Amir Masoud Rahmani Farhad Soleimanian Gharehchopogh Ferzat Anka Jan Lansky Mehdi Hosseinzadeh Institute of Research and Development Duy Tan University Da Nang Vietnam School of Engineering & Technology Duy Tan University Da Nang Vietnam Centre for Research Impact & Outcome Chitkara University Institute of Engineering and Technology Chitkara University Rajpura 140401 Punjab India Department of AI and Robotics Sejong University Seoul 05006 Republic of Korea Future Technology Research Center National Yunlin University of Science and Technology Yunlin Taiwan Department of Computer Engineering Ur. C. Islamic Azad University Urmia Iran Data Science Application and Research Center (VEBIM) Fatih Sultan Mehmet Vakif University Istanbul Türkiye Department of Computer Science and Mathematics Faculty of Economic Studies University of Finance and Administration Prague Czech Republic Pattern Recognition and Machine Learning Laboratory School of Computing Gachon University Seongnam Republic of Korea

The rapid increase in Mobile Internet of Things (IoT) devices requires novel computational frameworks. These frameworks must meet strict latency and energy efficiency requirements in Edge and Mobile Edge Computing (MEC) systems. Spatio-temporal dynamics, which include the position of edge servers and the timing of task schedules, pose a complex optimization problem. These challenges are further exacerbated by the heterogeneity of IoT workloads and the constraints imposed by device mobility. The balance between computational overhead and communication challenges is also a problem. To solve these issues, advanced methods are needed for resource management and dynamic task scheduling in mobile IoT and edge computing environments. In this paper, we propose a Deep Reinforcement learning (DRL) multi-objective algorithm, called a Double Deep Q-learning (DDQN) framework enhanced with Spatio-temporal mobility prediction, latency-aware task offloading, and energy-constrained IoT device trajectory optimization for federated edge computing networks. DDQN was chosen for its optimize stability and reduced overestimation in Q-values. The framework employs a reward-driven optimization model that dynamically prioritizes latency-sensitive tasks, minimizes task migration overhead, and balances energy efficiency across devices and edge servers. It integrates dynamic resource allocation algorithms to address random task arrival patterns and real-time computational demands. Simulations demonstrate up to a 35 % reduction in end-to-end latency, a 28 % improvement in energy efficiency, and a 20 % decrease in the deadline-miss ratio compared to benchmark algorithms.

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Field-level simulation-based inference of galaxy clustering with convolutional neural networks

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Physical Review D 2024年第8期109卷 083536-083536页

作者： Pablo Lemos Liam Parker ChangHoon Hahn Shirley Ho Michael Eickenberg Jiamin Hou Elena Massara Chirag Modi Azadeh Moradinezhad Dizgah Bruno Régaldo-Saint Blancard David Spergel Department of Physics Université de Montréal Montréal 1375 Avenue Thérèse-Lavoie-Roux Montréal QC H2V 0B3 Canada Mila—Quebec Artificial Intelligence Institute Montréal 6666 Rue Saint-Urbain Montréal QC H2S 3H1 Canada Ciela—Montreal Institute for Astrophysical Data Analysis and Machine Learning Montréal Canada Center for Computational Astrophysics Flatiron Institute 162 5th Avenue New York New York 10010 USA Department of Physics Princeton University Princeton New Jersey 08544 USA Center for Cosmology and Particle Physics Department of Physics New York University New York New York 10003 USA Department of Physics Carnegie Mellon University Pittsburgh Pennsylvania 15213 USA Center for Computational Mathematics Flatiron Institute 162 5th Avenue New York New York 10010 USA Department of Astronomy University of Florida 211 Bryant Space Science Center Gainesville Florida 32611 USA Max-Planck-Institut für Extraterrestrische Physik Postfach 1312 Giessenbachstrasse 1 85748 Garching bei München Germany Waterloo Centre for Astrophysics University of Waterloo 200 University Avenue W. Waterloo Ontario N2L 3G1 Canada Department of Physics and Astronomy University of Waterloo 200 University Avenue W. Waterloo Ontario N2L 3G1 Canada Département de Physique Théorique Université de Genève 24 quai Ernest Ansermet 1211 Genève 4 Switzerland

We present the first simulation-based inference (SBI) of cosmological parameters from field-level analysis of galaxy clustering. Standard galaxy clustering analyses rely on analyzing summary statistics, such as the power spectrum Pℓ, with analytic models based on perturbation theory. Consequently, they do not fully exploit the nonlinear and non-Gaussian features of the galaxy distribution. To address these limitations, we use the SimBIG forward modeling framework to perform SBI using normalizing flows. We apply SimBIG to a subset of the Baryon Oscillation Spectroscopic Survey CMASS galaxy sample using a convolutional neural network with stochastic weight averaging to perform massive data compression of the galaxy field. We infer constraints on Ωm=0.267−0.029+0.033 and σ8=0.762−0.035+0.036. While our constraints on Ωm are in line with standard Pℓ analyses, ours on σ8 are 2.65× tighter. Our analysis also provides constraints on the Hubble constant H0=64.5±3.8 km/s/Mpc from galaxy clustering alone. This higher constraining power comes from additional non-Gaussian cosmological information, inaccessible with Pℓ. We demonstrate the robustness of our analysis by showcasing our ability to infer unbiased cosmological constraints from a series of test simulations that are constructed using different forward models than the one used in our training dataset. This work not only presents competitive cosmological constraints but also introduces novel methods for leveraging additional cosmological information in upcoming galaxy surveys like the Dark Energy Spectroscopic Instrument, Prime Focus Spectrograph, and Euclid.

关键词： Cosmology Dark energy Dark matter Large scale structure of the Universe Astrophysical & cosmological simulations Bayesian methods Deep learning machine learning Numerical simulations in gravitation & astrophysics

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Depth selection for deep ReLU nets in feature extraction and generalization

arXiv

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arXiv 2020年

作者： Han, Zhi Yu, Siquan Lin, Shao-Bo Zhou, Ding-Xuan State Key Laboratory of Robotics Shenyang Institute of Automation Chinese Academy of Sciences Shenyang China Institutes for Robotics and Intelligent Manufacturing Chinese Academy of Sciences Shenyang China School of Information Science and Engineering Northeastern University Shenyang China Center of Intelligent Decision-Making and Machine Learning School of Management Xi'an Jiaotong University Xi'an China School of Data Science Department of Mathematics City University of Hong Kong Hong Kong

Deep learning is recognized to be capable of discovering deep features for representation learning and pattern recognition without requiring elegant feature engineering techniques by taking advantage of human ingenuity and prior knowledge. Thus it has triggered enormous research activities in machine learning and pattern recognition. One of the most important challenge of deep learning is to figure out relations between a feature and the depth of deep neural networks (deep nets for short) to reflect the necessity of depth. Our purpose is to quantify this feature-depth correspondence in feature extraction and generalization. We present the adaptivity of features to depths and vice-verse via showing a depth-parameter trade-off in extracting both single feature and composite features. Based on these results, we prove that implementing the classical empirical risk minimization on deep nets can achieve the optimal generalization performance for numerous learning tasks. Our theoretical results are verified by a series of numerical experiments including toy simulations and a real application of earthquake seismic intensity prediction. Copyright © 2020, The Authors. All rights reserved.

关键词： Feature extraction

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Roaming leads to amino acid photodamage: A deep learning study of tyrosine

arXiv

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arXiv 2021年

作者： Westermayr, Julia Gastegger, Michael Vörös, Dora Panzenboeck, Lisa Joerg, Florian González, Leticia Marquetand, Philipp University of Warwick Department of Chemistry Gibbet Hill Rd CoventryCV4 7AL United Kingdom Technical University of Berlin Machine Learning Group Berlin10587 Germany University of Vienna Faculty of Chemistry Institute of Theoretical Chemistry Währinger Str. 17 Vienna1090 Austria University of Vienna Vienna Research Platform on Accelerating Photoreaction Discovery Währinger Str. 17 Vienna1090 Austria University of Vienna Faculty of Chemistry Data Science @ Uni Vienna Währinger Str. 29 Vienna1090 Austria

Although the amino acid tyrosine is among the main building blocks of life, its photochemistry is not fully understood. Traditional theoretical simulations are neither accurate enough, nor computationally efficient to provide the missing puzzle pieces to the experimentally observed signatures obtained via time-resolved pump-probe spectroscopy or mass spectroscopy. In this work, we go beyond the realms of possibility with conventional quantum chemical methods and develop as well as apply a new technique to shed light on the photochemistry of tyrosine. By doing so, we discover roaming atoms in tyrosine, which is the first time such a reaction is discovered in biology. Our findings suggest that roaming atoms are radicals that could play a fundamental role in the photochemistry of peptides and proteins, offering a new perspective. Our novel method is based on deep learning, leverages the physics underlying the data, and combines different levels of theory. This combination of methods to obtain an accurate picture of excited molecules could shape how we study photochemical systems in the future and how we can overcome the current limitations that we face when applying quantum chemical methods. Copyright © 2021, The Authors. All rights reserved.

关键词： Amino acids

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Epitopedia: identifying molecular mimicry between pathogens and known immune epitopes

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ImmunoInformatics 2023年 9卷

作者： Christian A Balbin Janelle Nunez-Castilla Vitalii Stebliankin Prabin Baral Masrur Sobhan Trevor Cickovski Ananda Mohan Mondal Giri Narasimhan Prem Chapagain Kalai Mathee Jessica Siltberg-Liberles Department of Biological Sciences College of Arts Science and Education Florida International University Miami United States Bioinformatics Research Group (BioRG) Knight Foundation School of Computing and Information Sciences Florida International University Miami United States Department of Physics College of Arts Science and Education Florida International University Miami United States Machine Learning and Data Analytics Group (MLDAG) Knight Foundation School of Computing and Information Sciences Florida International University Miami United States Biomolecular Sciences Institute Florida International University Miami United States Department of Human and Molecular Genetics Herbert Wertheim College of Medicine Florida International University Miami United States

Upon infection, foreign antigenic proteins stimulate the host's immune system to produce antibodies targeting the pathogen. These antibodies bind to regions on the antigen called epitopes. Structural similarity (molecular mimicry) of epitopes between an infecting pathogen and host proteins or other pathogenic proteins the host has previously encountered can impact the host immune response to the pathogen and may lead to cross-reactive antibodies. The ability to identify potential regions of molecular mimicry in a pathogen can illuminate immune effects which are especially important to pathogen treatment and vaccine design. Here we present Epitopedia, a software pipeline that facilitates the identification of regions that may exhibit potential three-dimensional molecular mimicry between an antigenic pathogen protein and known immune epitopes as catalogued by the Immune Epitope database (IEDB). Epitopedia is open-source software released under the MIT license and is freely available on GitHub, including a Docker container with all other software dependencies preinstalled. We performed an analysis describing how various secondary structure states, identity between pentapeptide pairs, and identity between the parent sequences of pentapeptide pairs affects RMSD. We found that pentapeptides pairs in a helical conformation had considerably lower RMSD values than those in extended or coil conformations. We also found that RMSD is significantly increased when pentapeptide pairs are from non-homologous sequences.

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Erratum to ‘Model-Based Cost-Utility Analysis of Combined Low-Dose Computed Tomography Screening for Lung Cancer, Chronic Obstructive Pulmonary Disease, and Cardiovascular Disease’ [JTO Clinical and Research Reports Volume 6 Issue 5 (2025) 100813]

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JTO Clinical and Research Reports 2025年第7期6卷

作者： Carina M. Behr Maarten J. IJzerman Michelle M.A. Kip Harry J.M. Groen Marjolein A. Heuvelmans Maarten van den Berge Pim van der Harst Marleen Vonder Rozemarijn Vliegenthart Hendrik Koffijberg Health Technology and Services Research TechMed Centre University of Twente Enschede The Netherlands Erasmus School of Health Policy & Management Erasmus University Rotterdam Rotterdam The Netherlands Department of Pulmonary Diseases and Tuberculosis UMCG - University Medical Center Groningen Groningen The Netherlands Department of Epidemiology University Medical Center of Groningen University of Groningen Groningen The Netherlands Department of Pulmonary Diseases University of Groningen University Medical Center Groningen Groningen The Netherlands Groningen Research Institute for Asthma and COPD University of Groningen University Medical Center Groningen Groningen The Netherlands Department of Cardiology University Medical Center Utrecht Utrecht The Netherlands Department of Radiology Medical Imaging Center University Medical Center Groningen University of Groningen Groningen The Netherlands Machine Learning Lab Data Science Center in Health (DASH) University Medical Center Groningen University of Groningen Groningen The Netherlands

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