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Increasing the robustness of the automatic IMU calibration for lower Extremity Motion Analysis

Current Directions in Biomedical Engineering 2018年第1期4卷 439-442页

作者： Küderle, Arne Becker, Sebastian Disselhorst-Klug, Catherine Machine Learning and Data Analytics Lab. University of Erlangen-Nürnberg (FAU) Carl-Thiersch-Strasse 2b Erlangen Germany Department of Rehabilitation and Prevention Engineering Institute of Applied Medical Engineering RWTH Aachen University Aachen Germany

With the advances of IMU-based human motion tracking, joint angle tracking in an home environment has become a realistic goal. Achieving it, could enable novel applications in rehabilitation and sports medicine. However, in existing systems the process of aligning the mounted sensors with the body coordinate system is either not robust enough or to complicated for fully unsupervised usage. In this publication the performance of a promising existing algorithm is evaluated with a range of different calibration motions. Further, an extension to this implementation is proposed, aiming to improve its stability when only non-ideal calibration data is available. It could be validated that the modification of the algorithm can increase the stability and reduce the dependency of the calibration on specific calibration motions. Based on these results, we recommend the proposed extension of the algorithm as a drop-in replacement for the existing implementation. © 2018 Arne Küderle et al.

关键词： Calibration

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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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The state-of-the-art in Cardiac MRI Reconstruction: Results of the CMRxRecon Challenge in MICCAI 2023

arXiv

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arXiv 2024年

作者： Lyu, Jun Qin, Chen Wang, Shuo Wang, Fanwen Li, Yan Wang, Zi Guo, Kunyuan Ouyang, Cheng Tänzer, Michael Liu, Meng Sun, Longyu Sun, Mengting Li, Qin Shi, Zhang Hua, Sha Li, Hao Chen, Zhensen Zhang, Zhenlin Xin, Bingyu Metaxas, Dimitris N. Yiasemis, George Teuwen, Jonas Zhang, Liping Chen, Weitian Pang, Yanwei Liu, Xiaohan Razumov, Artem Dylov, Dmitry V. Dou, Quan Yan, Kang Xue, Yuyang Du, Yuning Dietlmeier, Julia Garcia-Cabrera, Carles Hemidi, Ziad Al-Haj Vogt, Nora Xu, Ziqiang Zhang, Yajing Chu, Ying-Hua Chen, Weibo Bai, Wenjia Zhuang, Xiahai Qin, Jing Wu, Lianmin Yang, Guang Qu, Xiaobo Wang, He Wang, Chengyan Psychiatry Neuroimaging Laboratory Brigham and Women’s Hospital Harvard Medical School 399 Revolution Drive BostonMA02215 United States Department of Electrical and Electronic Engineering & I-X Imperial College London United Kingdom Digital Medical Research Center School of Basic Medical Sciences Fudan University Shanghai China Department of Bioengineering & I-X Imperial College London LondonW12 7SL United Kingdom Cardiovascular Magnetic Resonance Unit Royal Brompton Hospital Guy’s and St Thomas’ NHS Foundation Trust LondonSW3 6NP United Kingdom Department of Radiology Ruijin Hospital Shanghai Jiao Tong University School of Medicine Shanghai China Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance National Institute for Data Science in Health and Medicine Institute of Artificial Intelligence Xiamen University Xiamen361102 China Department of Computing Department of Brain Sciences Imperial College London LondonSW7 2AZ United Kingdom Human Phenome Institute Fudan University 825 Zhangheng Road Pudong New District Shanghai201203 China Department of Radiology Zhongshan Hospital Fudan University Shanghai China Department of Cardiovascular Medicine Ruijin Hospital Lu Wan Branch Shanghai Jiao Tong University School of Medicine Shanghai China Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Shanghai200433 China Department of Computer Science Rutgers University PiscatawayNJ08854 United States AI for Oncology Netherlands Cancer Institute Plesmanlaan 121 Amsterdam1066 CX Netherlands Department of Imaging and Interventional Radiology The Chinese University of Hong Kong Hong Kong TJK-BIIT Lab School of Electrical and Information Engineering Tianjin University Tianjin300072 China Skolkovo Institute Of Science And Technology Center for Artificial Intelligence Technology 30/1 Bolshoy blvd. Moscow121205 Russia Department of Biomedical Engineering University of Virginia

Cardiac magnetic resonance imaging (MRI) provides detailed and quantitative evaluation of the heart’s structure, function, and tissue characteristics with high-resolution spatial-temporal imaging. However, its slow imaging speed and motion artifacts are notable limitations. Undersampling reconstruction, especially data-driven algorithms, has emerged as a promising solution to accelerate scans and enhance imaging performance using highly under-sampled data. Nevertheless, the scarcity of publicly available cardiac k-space datasets and evaluation platform hinder the development of data-driven reconstruction algorithms. To address this issue, we organized the Cardiac MRI Reconstruction Challenge (CMRxRecon) in 2023, in collaboration with the 26th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI). CMRxRecon presented an extensive k-space dataset comprising cine and mapping raw data, accompanied by detailed annotations of cardiac anatomical structures. With overwhelming participation, the challenge attracted more than 285 teams and over 600 participants. Among them, 22 teams successfully submitted Docker containers for the testing phase, with 7 teams submitted for both cine and mapping tasks. All teams use deep learning based approaches, indicating that deep learning has predominately become a promising solution for the problem. The first-place winner of both tasks utilizes the E2E-VarNet architecture as backbones. In contrast, U-Net is still the most popular backbone for both multi-coil and single-coil reconstructions. This paper provides a comprehensive overview of the challenge design, presents a summary of the submitted results, reviews the employed methods, and offers an in-depth discussion that aims to inspire future advancements in cardiac MRI reconstruction models. The summary emphasizes the effective strategies observed in Cardiac MRI reconstruction, including backbone architecture, loss function, pre-processing techn

关键词： Mapping

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Evaluating the Accuracy and Reliability of Real-World Digital Mobility Outcomes in Older Adults After Hip Fracture: Cross-Sectional Observational Study

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JMIR Formative Research 2025年 9卷 e67792页

作者： Berge, Martin A. Paraschiv-Ionescu, Anisoara Kirk, Cameron Küderle, Arne Micó-Amigo, Encarna Becker, Clemens Cereatti, Andrea Del Din, Silvia Engdal, Monika Garcia-Aymerich, Judith Grønvik, Karoline B. Hansen, Clint Hausdorff, Jeffrey M. Helbostad, Jorunn L. Jansen, Carl-Philipp Johnsen, Lars Gunnar Klenk, Jochen Koch, Sarah Maetzler, Walter Megaritis, Dimitrios Müller, Arne Rochester, Lynn Schwickert, Lars Taraldsen, Kristin Vereijken, Beatrix Department of Neuromedicine and Movement Science Norwegian University of Science and Technology Trondheim Norway Laboratory of Movement Analysis and Measurement Ecole Polytechnique Federale de Lausanne Lausanne Switzerland Translational and Clinical Research Institute Faculty of Medical Sciences Newcastle University Newcastle Upon Tyne United Kingdom Machine Learning and Data Analytics Lab Department Artificial Intelligence in Biomedical Engineering Friedrich-Alexander-Universität Erlangen-Nürnberg Erlangen Germany Geriatric Center Medical Faculty Heidelberg Heidelberg University Heidelberg Germany Department of Geriatrics and Rehabilitation Robert Bosch Hospital Stuttgart Germany Department of Electronics and Telecommunications Politecnico di Torino Turin Italy National Institute for Health and Care Research Newcastle Biomedical Research Centre Newcastle University The Newcastle Upon Tyne Hospitals NHS Foundation Trust Newcastle Upon Tyne United Kingdom Barcelona Institute for Global Health Barcelona Spain Department of Medicine and Life Sciences Universitat Pompeu Fabra Catalonia Barcelona Spain CIBER Epidemiología y Salud Pública Madrid Spain Department of Neurology University Hospital Schleswig-Holstein Kiel University Kiel Germany Center for the Study of Movement Cognition and Mobility Neurological Institute Tel Aviv Medical Center Tel Aviv Israel Department of Physical Therapy Faculty of Medical & Health Sciences Tel Aviv University Tel Aviv Israel Sagol School of Neuroscience Tel Aviv University Tel Aviv Israel Rush Alzheimer’s Disease Center Rush University Medical Center Chicago IL United States Department of Orthopedic Surgery Rush Medical College Rush University Chicago IL United States Department of Orthopaedic Surgery St. Olav’s Hospital Trondheim Norway Institute of Epidemiology and Medical Biometry Ulm University Ulm Germany IB University of Health and Social Sciences Study Centre Stuttgart Stuttgart Germany Department of Sport

Background: Algorithms estimating real-world digital mobility outcomes (DMOs) are increasingly validated in healthy adults and various disease cohorts. However, their accuracy and reliability in older adults after hip fracture, who often walk slowly for short durations, is underexplored. Objective: This study examined DMO accuracy and reliability in a hip fracture cohort considering walking bout (WB) duration, physical function, days since surgery, and walking aid use. Methods: In total, 19 community-dwelling participants were real-world monitored for 2.5 hours using a lower back wearable device and a reference system combining inertial modules, distance sensors, and pressure insoles. A total of 6 DMO estimates from 164 WBs from 58% (11/19) of the participants (aged 71-90 years;assessed 32-390 days after surgery;Short Physical Performance Battery [SPPB] scores of 3-12;gait speed range 0.39-1.34 m/s) were assessed against the reference system at the WB and participant level. We stratified by WB duration (all WBs, WBs of >10 seconds, WBs of 10-30 seconds, and WBs of >30 seconds) and lower versus higher SPPB scores and observed whether days since surgery and walking aid use affected DMO accuracy and reliability. Results: Across WBs, walking speed and distance ranged from 0.25 to 1.29 m/s and from 1.7 to 436.5 m, respectively. Estimation of walking speed, cadence, stride duration, number of steps, and distance stratified by WB duration showed intraclass correlation coefficients (ICCs) ranging from 0.50 to 0.99 and mean relative errors (MREs) from –6.9% to 12.8%. Stride length estimation showed poor reliability, with ICCs ranging from 0.30 to 0.49 and MREs from 6.1% to 13.2%. Walking speed and distance ICCs in the higher–SPPB score group ranged from 0.85 to 0.99, and MREs ranged from –10.1% to –1.7%. In the lower–SPPB score group, walking speed and distance ICCs ranged from 0.17 to 0.99, and MREs ranged from 13.5% to 32.6%. There was no discernible effect of time since s

关键词： active aging cadence digital mobility assessment distance free living gait walking speed wearable device

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machine learning Techniques for Stress Prediction in Working Employees

Machine Learning Techniques for Stress Prediction in Working...

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IEEE International Conference on Computational Intelligence and Computing Research

作者： U Srinivasulu Reddy Aditya Vivek Thota A Dharun Department of Computer Applications Machine Learning and Data Analytics Lab National Institute of Technology Trichy ECE National Institute of Technology Trichy

ISBN: (纸本)9781538615096

Stress disorders are a common issue among working IT professionals in the industry today. With changing lifestyle and work cultures, there is an increase in the risk of stress among the employees. Though many industries and corporates provide mental health related schemes and try to ease the workplace atmosphere, the issue is far from control. In this paper, we would like to apply machine learning techniques to analyze stress patterns in working adults and to narrow down the factors that strongly determine the stress levels. Towards this, data from the OSMI mental health survey 2017 responses of working professionals within the tech-industry was considered. Various machine learning techniques were applied to train our model after due data cleaning and preprocessing. The accuracy of the above models was obtained and studied comparatively. Boosting had the highest accuracy among the models implemented. By using Decision Trees, prominent features that influence stress were identified as gender, family history and availability of health benefits in the workplace. With these results, industries can now narrow down their approach to reduce stress and create a much comfortable workplace for their employees.

关键词： data handling decision trees DP management employee welfare ergonomics gender issues health care learning (artificial intelligence) occupational stress organisational aspects personnel psychology risk analysis computer installation management Decision Trees Organizational aspects gender issue data processing stress at work Ergonomics Psychology Risk Management risk analysis Personnel Employees Health Care data cleaning learning methods

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Reducing over-smoothness in speech synthesis using Generative Adversarial Networks

arXiv

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arXiv 2018年

作者： Sheng, Leyuan Pavlovskiy, Evgeniy N. Department of Mathematics and Mechanics Novosibirsk State University Novosibirsk Russia Stream Data Analytics and Machine Learning laboratory Novosibirsk State University Novosibirsk Russia

Speech synthesis is widely used in many practical applications. In recent years, speech synthesis technology has developed rapidly. However, one of the reasons why synthetic speech is unnatural is that it often has over-smoothness. In order to improve the naturalness of synthetic speech, we first extract the mel-spectrogram of speech and convert it into a real image, then take the over-smooth mel-spectrogram image as input, and use image-to-image translation Generative Adversarial Networks(GANs) framework to generate a more realistic mel-spectrogram. Finally, the results show that this method greatly reduces the over-smoothness of synthesized speech and is more close to the mel-spectrogram of real speech. Copyright © 2018, The Authors. All rights reserved.

关键词： Generative adversarial networks

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Indoor Positioning Using OFDM-Based Visible Light Communication System

Indoor Positioning Using OFDM-Based Visible Light Communicat...

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International Conference on Indoor Positioning and Indoor Navigation (IPIN)

作者： Birendra Ghimire Jochen Seitz Christopher Mutschler Precise Positioning and Analytics Department Fraunhofer Institute for Integrated Circuits IIS Nürnberg Germany Machine Learning and Data Analytics Lab Friedrich-Alexander University Erlangen-Nürnberg (FAU) Erlangen Germany

Precise indoor positioning is essential to support emerging applications of location aware mobile computing. Current positioning techniques that use signals transmitted in the Gigahertz region of radio-frequency spectrum do not provide highly accurate position estimates due to multipath propagation of signals. This paper proposes a novel positioning system which uses the entities of visible light communication (VLC) system as anchors and tags. Our technique scales with the number of tags and the VLC network provides both positioning and communication capabilities. The anchor points transmit the OFDM-based VLC signals synchronously, and we estimate the time differences of arrival between anchor points and tags using positioning reference signals embedded into the air-interface of the VLC system. Simulation results show that positioning accuracy of 10 cm or better is possible for over 95% of users if the sampling clock offset is better that 10 ppm, clock jitter is below 1 ps, and a bit resolution of at least 16 bits is available.

关键词： Light emitting diodes OFDM Optical receivers Adaptive optics Optical filters Measurement uncertainty

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Smart Annotation Tool for Multi-sensor Gait-based Daily Activity data

Smart Annotation Tool for Multi-sensor Gait-based Daily Acti...

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IEEE International Conference on Pervasive Computing and Communications

作者： Christine F. Martindale Nils Roth Julius Hannink Sebastijan Sprager Bjoern M. Eskofier Machine Learning and Data Analytics Lab Computer Science Department Friedrich-Alexander University Erlangen-Nürnberg Germany Faculty of Computer and Information Science University of Ljubljana Slovenia

ISBN: (纸本)9781538632284

The monitoring of patients within a natural, home environment is important in order to close knowledge gaps in the treatment and care of neurodegenerative diseases, such as quantifying the daily fluctuation of Parkinson's patients' symptoms. The combination of machine learning algorithms and wearable sensors for gait analysis is becoming capable of achieving this. However, these algorithms require large, labelled, realistic datasets for training. Most systems used as a ground truth for labelling are restricted to the laboratory environment, as well as being large and expensive. We propose a study design for a realistic activity monitoring dataset, collected with inertial measurement units, pressure insoles and cameras. It is not restricted by a fixed location or capture volume and still enables the labelling of gait phases or, where non-gait movement such as jumping occur: on-the-ground, off-the-ground phases. Additionally, this paper proposes a smart annotation tool which reduces annotation cost by more than 80%. This smart annotation is based on edge detection within the pressure sensor signal. The tool also enables annotators to perform assisted correction of these labels in a post-processing step. This system enables the collection and labelling of large, fairly realistic datasets where 93% of the automatically generated labels are correct and only an additional 10% need to be inserted manually. Our tool and protocol, as a whole, will be useful for efficiently collecting the large datasets needed for training and validation of algorithms capable of cyclic human motion analysis in natural environments.

关键词： Image edge detection Tools Cameras Labeling Pressure sensors Intelligent sensors Edge detection Pressure Sensor Device Component Cameras intelligent sensors ANNOTATIONS laboratory environment dataset Wearable sensors Measurement units Research Design INSOLE Packaging

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DOP57 Predictive modelling to examine long term treatment effectiveness of darvadstrocel in patients with complex perianal fistulas in Crohn’s Disease

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Journal of Crohn's and Colitis 2021年第SUPPLEMENT_1期15卷 S092-S093页

作者： Maruszczak, M Genenz, K Turkstra, E Fenu, E Hantsbarger, G Gilaberte, I Karki, C Panes, J Parexel International Data Analytics and Machine Learning Uxbridge United Kingdom Takeda Pharmaceuticals Takeda Pharmaceuticals Zurich Switzerland Parexel International Parexel Access Consulting Uxbridge United Kingdom Takeda Pharmaceuticals USA- Inc Statistical and Quantitative Sciences Cambridge United States Takeda Pharmaceuticals USA- Inc Clinical Sciences Cambridge United States Takeda Pharmaceuticals USA- Inc Global Evidence and Outcomes Cambridge United States Hospital Clínic de Barcelona- IDIBAPS Gastroenterology Department Barcelona Spain

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Why is the Winner the Best?

Why is the Winner the Best?

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Conference on Computer Vision and Pattern Recognition (CVPR)

作者： M. Eisenmann A. Reinke V. Weru M. D. Tizabi F. Isensee T. J. Adler S. Ali V. Andrearczyk M. Aubreville U. Baid S. Bakas N. Balu S. Bano J. Bernal S. Bodenstedt A. Casella V. Cheplygina M. Daum M. De Bruijne A. Depeursinge R. Dorent J. Egger D. G. Ellis S. Engelhardt M. Ganz N. Ghatwary G. Girard P. Godau A. Gupta L. Hansen K. Harada M. Heinrich N. Heller A. Hering A. Huaulmé P. Jannin A. E. Kavur O. Kodym M. Kozubek J. Li H. Li J. Ma C. Martín-Isla B. Menze A. Noble V. Oreiller N. Padoy S. Pati K. Payette T. Rädsch J. Rafael-Patiño V. Singh Bawa S. Speidel C. H. Sudre K. Van Wijnen M. Wagner D. Wei A. Yamlahi M. H. Yap C. Yuan M. Zenk A. Zia D. Zimmerer D. Aydogan B. Bhattarai L. Bloch R. Brüngel J. Cho C. Choi Q. Dou I. Ezhov C. M. Friedrich C. Fuller R. R. Gaire A. Galdran Á. García Faura M. Grammatikopoulou S. Hong M. Jahanifar I. Jang A. Kadkhodamohammadi I. Kang F. Kofler S. Kondo H. Kuijf M. Li M. Luu T. Martinčič P. Morais M. A. Naser B. Oliveira D. Owen S. Pang J. Park S. Park S. Płotka E. Puybareau N. Rajpoot K. Ryu N. Saeed A. Shephard P. Shi D. Štepec R. Subedi G. Tochon H. R. Torres H. Urien J. L. Vilaça K. A. Wahid H. Wang J. Wang L. Wang X. Wang B. Wiestler M. Wodzinski F. Xia J. Xie Z. Xiong S. Yang Y. Yang Z. Zhao K. Maier-Hein P. F. Jäger A. Kopp-Schneider L. Maier-Hein Division of Intelligent Medical Systems German Cancer Research Center (DKFZ) Heidelberg Germany Helmholtz Imaging German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany Division of Medical Image Computing German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Engineering and Physical Sciences School of Computing University of Leeds Leeds UK Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Sierre Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Lausanne Switzerland Technische Hochschule Ingolstadt Ingolstadt Germany Center for Artificial Intelligence and Data Science for Integrated Diagnostics (AI2D) and Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology University of Washington Seattle WA USA Department of Computer Science Wellcome/EPSRC Centre for Interventional and Surgical Sciences (WEISS) University College London London UK Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Division of Translational Surgical Oncology National Center for Tumor Diseases (NCT/UCC) Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy Department of Electronics Information and Bioengineering Politecnico di Milano Milan Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Department of Radiology and Nuc

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multicenter study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and post-processing (66%). The “typical” lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

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