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Book ; Online: Optimization Dynamics of Equivariant and Augmented Neural Networks

Flinth, Axel / Ohlsson, Fredrik

2023

Abstract: We investigate the optimization of multilayer perceptrons on symmetric data. We compare the strategy of constraining the architecture to be equivariant to that of using augmentation. We show that, under natural assumptions on the loss and non-linearities, ...

Abstract	We investigate the optimization of multilayer perceptrons on symmetric data. We compare the strategy of constraining the architecture to be equivariant to that of using augmentation. We show that, under natural assumptions on the loss and non-linearities, the sets of equivariant stationary points are identical for the two strategies, and that the set of equivariant layers is invariant under the gradient flow for augmented models. Finally, we show that stationary points may be unstable for augmented training although they are stable for the equivariant models. Comment: v2: Revised manuscript. Mostly small edits, apart from new experiments (see Appendix E)
Keywords	Computer Science - Machine Learning ; Mathematics - Optimization and Control ; 68T07 ; 20C35 ; 37N40
Publishing date	2023-03-23
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Tunable spring balanced magnetic energy harvester for low frequencies and small displacements

Bjurström, Johan / Ohlsson, Fredrik / Vikerfors, Andreas / Rusu, Cristina / Johansson, Christer

Energy conversion and management. 2022 May 01, v. 259

2022

Abstract: In this paper we present a novel concept to efficiently harvest vibrational energy at low frequencies and very small displacement. We describe and evaluate an electromagnetic energy harvester which generates power from a magnetic circuit with motion ... ...

Abstract	In this paper we present a novel concept to efficiently harvest vibrational energy at low frequencies and very small displacement. We describe and evaluate an electromagnetic energy harvester which generates power from a magnetic circuit with motion induced variations of an air gap. External vibrations induce oscillations of the gap length around an equilibrium point, due to a linear spring counteracting the magnetic force. The relative position of the spring can be adjusted to optimize the harvester output for excitation amplitude and frequency. A simulation model is built in COMSOL and verified by comparison with lab measurements. The simulation model is used to determine the potential performance of the proposed concept under both harmonic and non-harmonic excitation. Under harmonic excitation, we achieve a simulated RMS load power of 26.5 μW at 22 Hz and 0.028 g acceleration amplitude. From a set of comparable EH we achieve the highest theoretical power metric of 1712.2 µW/cm³/g² while maintaining the largest relative bandwidth of 81.8%. Using measured non-harmonic vibration data, with a mean acceleration of 0.039 g, resulted in a mean power of 52 μW. Moreover, the simplicity and robustness of our design makes it a competitive alternative for use in practical situations.
Keywords	administrative management ; air ; energy conversion ; magnetism ; simulation models ; spring ; vibration
Language	English
Dates of publication	2022-0501
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2000891-0
ISSN	0196-8904
ISSN	0196-8904
DOI	10.1016/j.enconman.2022.115568
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Symmetry structures in dynamic models of biochemical systems.

Ohlsson, Fredrik / Borgqvist, Johannes / Cvijovic, Marija

Journal of the Royal Society, Interface

2020 Volume 17, Issue 168, Page(s) 20200204

Abstract: Understanding the complex interactions of biochemical processes underlying human disease represents the holy grail of systems biology. When processes are modelled in ordinary differential equation (ODE) fashion, the most common tool for their analysis is ...

Abstract	Understanding the complex interactions of biochemical processes underlying human disease represents the holy grail of systems biology. When processes are modelled in ordinary differential equation (ODE) fashion, the most common tool for their analysis is linear stability analysis where the long-term behaviour of the model is determined by linearizing the system around its steady states. However, this asymptotic behaviour is often insufficient for completely determining the structure of the underlying system. A complementary technique for analysing a system of ODEs is to consider the set of symmetries of its solutions. Symmetries provide a powerful concept for the development of mechanistic models by describing structures corresponding to the underlying dynamics of biological systems. To demonstrate their capability, we consider symmetries of the nonlinear Hill model describing enzymatic reaction kinetics and derive a class of symmetry transformations for each order of the model. We consider a minimal example consisting of the application of symmetry-based methods to a model selection problem, where we are able to demonstrate superior performance compared to ordinary residual-based model selection. Moreover, we demonstrate that symmetries reveal the intrinsic properties of a system of interest based on a single time series. Finally, we show and propose that symmetry-based methodology should be considered as the first step in a systematic model building and in the case when multiple time series are available it should complement the commonly used statistical methodologies.
MeSH term(s)	Algorithms ; Humans ; Kinetics ; Models, Biological ; Nonlinear Dynamics ; Systems Biology
Language	English
Publishing date	2020-07-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2156283-0
ISSN	1742-5662 ; 1742-5689
ISSN (online)	1742-5662
ISSN	1742-5689
DOI	10.1098/rsif.2020.0204
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Article ; Online: Arm impairment and walking speed explain real-life activity of the affected arm and leg after stroke.

Andersson, Sofi A / Danielsson, Anna / Ohlsson, Fredrik / Wipenmyr, Jan / Alt Murphy, Margit

Journal of rehabilitation medicine

2021 Volume 53, Issue 6, Page(s) jrm00210

Abstract: Objective: To determine to what extent accelerometer-based arm, leg and trunk activity is associated with sensorimotor impairments, walking capacity and other factors in subacute stroke.: Design: Cross-sectional study.: Patients: Twenty-six ... ...

Abstract	Objective: To determine to what extent accelerometer-based arm, leg and trunk activity is associated with sensorimotor impairments, walking capacity and other factors in subacute stroke. Design: Cross-sectional study. Patients: Twenty-six individuals with stroke (mean age 55.4 years, severe to mild motor impairment). Methods: Data on daytime activity were collected over a period of 4 days from accelerometers placed on the wrists, ankles and trunk. A forward stepwise linear regression was used to determine associations between free-living activity, clinical and demographic variables. Results: Arm motor impairment (Fugl-Meyer Assessment) and walking speed explained more than 60% of the variance in daytime activity of the more-affected arm, while walking speed alone explained 60% of the more-affected leg activity. Activity of the less-affected arm and leg was associated with arm motor impairment (R2 = 0.40) and independence in walking (R2 = 0.59). Arm activity ratio was associated with arm impairment (R2 = 0.63) and leg activity ratio with leg impairment (R2 = 0.38) and walking speed (R2 = 0.27). Walking-related variables explained approximately 30% of the variance in trunk activity. Conclusion: Accelerometer-based free-living activity is dependent on motor impairment and walking capacity. The most relevant activity data were obtained from more-affected limbs. Motor impairment and walking speed can provide some information about real-life daytime activity levels.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Arm Injuries/pathology ; Cross-Sectional Studies ; Female ; Humans ; Male ; Middle Aged ; Stroke/complications ; Stroke Rehabilitation/methods ; Walking Speed/physiology
Language	English
Publishing date	2021-06-23
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	2039427-5
ISSN	1651-2081 ; 1651-2235 ; 0891-060X ; 1650-1977
ISSN (online)	1651-2081 ; 1651-2235
ISSN	0891-060X ; 1650-1977
DOI	10.2340/16501977-2838
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Book ; Online: Equivariance versus Augmentation for Spherical Images

Gerken, Jan E. / Carlsson, Oscar / Linander, Hampus / Ohlsson, Fredrik / Petersson, Christoffer / Persson, Daniel

2022

Abstract: We analyze the role of rotational equivariance in convolutional neural networks (CNNs) applied to spherical images. We compare the performance of the group equivariant networks known as S2CNNs and standard non-equivariant CNNs trained with an increasing ... ...

Abstract	We analyze the role of rotational equivariance in convolutional neural networks (CNNs) applied to spherical images. We compare the performance of the group equivariant networks known as S2CNNs and standard non-equivariant CNNs trained with an increasing amount of data augmentation. The chosen architectures can be considered baseline references for the respective design paradigms. Our models are trained and evaluated on single or multiple items from the MNIST or FashionMNIST dataset projected onto the sphere. For the task of image classification, which is inherently rotationally invariant, we find that by considerably increasing the amount of data augmentation and the size of the networks, it is possible for the standard CNNs to reach at least the same performance as the equivariant network. In contrast, for the inherently equivariant task of semantic segmentation, the non-equivariant networks are consistently outperformed by the equivariant networks with significantly fewer parameters. We also analyze and compare the inference latency and training times of the different networks, enabling detailed tradeoff considerations between equivariant architectures and data augmentation for practical problems. The equivariant spherical networks used in the experiments are available at https://github.com/JanEGerken/sem_seg_s2cnn . Comment: Accepted to ICML2022, updated according to ICML-reviewer comments, 18 pages of which 9 in main body, 16 figures
Keywords	Computer Science - Machine Learning ; Computer Science - Computer Vision and Pattern Recognition
Subject code	004
Publishing date	2022-02-08
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: HEAL-SWIN

Carlsson, Oscar / Gerken, Jan E. / Linander, Hampus / Spieß, Heiner / Ohlsson, Fredrik / Petersson, Christoffer / Persson, Daniel

A Vision Transformer On The Sphere

2023

Abstract: High-resolution wide-angle fisheye images are becoming more and more important for robotics applications such as autonomous driving. However, using ordinary convolutional neural networks or vision transformers on this data is problematic due to ... ...

Abstract	High-resolution wide-angle fisheye images are becoming more and more important for robotics applications such as autonomous driving. However, using ordinary convolutional neural networks or vision transformers on this data is problematic due to projection and distortion losses introduced when projecting to a rectangular grid on the plane. We introduce the HEAL-SWIN transformer, which combines the highly uniform Hierarchical Equal Area iso-Latitude Pixelation (HEALPix) grid used in astrophysics and cosmology with the Hierarchical Shifted-Window (SWIN) transformer to yield an efficient and flexible model capable of training on high-resolution, distortion-free spherical data. In HEAL-SWIN, the nested structure of the HEALPix grid is used to perform the patching and windowing operations of the SWIN transformer, resulting in a one-dimensional representation of the spherical data with minimal computational overhead. We demonstrate the superior performance of our model for semantic segmentation and depth regression tasks on both synthetic and real automotive datasets. Our code is available at https://github.com/JanEGerken/HEAL-SWIN. Comment: Main body: 10 pages, 7 figures. Appendices: 4 pages, 2 figures
Keywords	Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning
Subject code	004
Publishing date	2023-07-14
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Friends With Benefits: Exploring the Phycosphere of the Marine Diatom

Johansson, Oskar N / Pinder, Matthew I M / Ohlsson, Fredrik / Egardt, Jenny / Töpel, Mats / Clarke, Adrian K

Frontiers in microbiology

2019 Volume 10, Page(s) 1828

Abstract: Marine diatoms are the dominant phytoplankton in the temperate oceans and coastal regions, contributing to global photosynthesis, biogeochemical cycling of key nutrients and minerals and aquatic food chains. Integral to the success of marine diatoms is a ...

Abstract	Marine diatoms are the dominant phytoplankton in the temperate oceans and coastal regions, contributing to global photosynthesis, biogeochemical cycling of key nutrients and minerals and aquatic food chains. Integral to the success of marine diatoms is a diverse array of bacterial species that closely interact within the diffusive boundary layer, or phycosphere, surrounding the diatom partner. Recently, we isolated seven distinct bacterial species from cultures of
Language	English
Publishing date	2019-08-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2019.01828
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Article ; Online: Comparison of accelerometer-based arm, leg and trunk activity at weekdays and weekends during subacute inpatient rehabilitation after stroke.

Alt Murphy, Margit / Andersson, Sofi / Danielsson, Anna / Wipenmyr, Jan / Ohlsson, Fredrik

Journal of rehabilitation medicine

2019 Volume 51, Issue 6, Page(s) 426–433

Abstract: Objective: To determine whether there are differences in arm, leg and trunk activity measured by acceleration between weekdays and weekends in people undergoing rehabilitation in the subacute stage after stroke.: Design: Cross-sectional study.: ... ...

Abstract	Objective: To determine whether there are differences in arm, leg and trunk activity measured by acceleration between weekdays and weekends in people undergoing rehabilitation in the subacute stage after stroke. Design: Cross-sectional study. Patients: Twenty-eight individuals with stroke (mean age 55.4 years; severe to mild impairment) and 10 healthy controls. Methods: A set of 5 3-axial accelerometers were used on the trunk, wrists and ankles during 2 48-h sessions at weekdays and over a weekend. Day-time acceleration raw data were expressed as the signal magnitude area. Asymmetry between the affected and less-affected limb was calculated as a ratio. Results: Participants with stroke used their both arms and legs less at weekends than on weekdays (p< 0.05, effect size 0.32-0.57). Asymmetry between the affected and less-affected arm was greater at weekends (p < 0.05, effect size 0.32). All activity measures, apart from the less-affected arm on weekdays, were lower in stroke compared with controls (p < 0.05, effect size 0.4-0.8). No statistically significant differences were detected between weekday and weekend activity for the control group. One-third of participants perceived the trunk sensor as inconvenient to wear. Conclusion: Increased focus needs to be applied on activities carried out during weekends at rehabilitation wards.
MeSH term(s)	Accelerometry/statistics & numerical data ; Aged ; Arm/physiopathology ; Cross-Sectional Studies ; Female ; Humans ; Inpatients/statistics & numerical data ; Leg/physiopathology ; Male ; Middle Aged ; Stroke/physiopathology ; Stroke Rehabilitation/statistics & numerical data ; Time Factors ; Torso/physiopathology
Language	English
Publishing date	2019-04-05
Publishing country	Sweden
Document type	Evaluation Study ; Journal Article
ZDB-ID	2039427-5
ISSN	1651-2081 ; 1651-2235 ; 0891-060X ; 1650-1977
ISSN (online)	1651-2081 ; 1651-2235
ISSN	0891-060X ; 1650-1977
DOI	10.2340/16501977-2553
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Article ; Online: An upper body garment with integrated sensors for people with neurological disorders - early development and evaluation.

Alt Murphy, Margit / Bergquist, Filip / Hagström, Bengt / Hernández, Niina / Johansson, Dongni / Ohlsson, Fredrik / Sandsjö, Leif / Wipenmyr, Jan / Malmgren, Kristina

BMC biomedical engineering

2019 Volume 1, Page(s) 3

Abstract: Background: In neurology and rehabilitation the primary interest for using wearables is to supplement traditional patient assessment and monitoring in hospital settings with continuous data collection at home and in community settings. The aim of this ... ...

Abstract	Background: In neurology and rehabilitation the primary interest for using wearables is to supplement traditional patient assessment and monitoring in hospital settings with continuous data collection at home and in community settings. The aim of this project was to develop a novel wearable garment with integrated sensors designed for continuous monitoring of physiological and movement related variables to evaluate progression, tailor treatments and improve diagnosis in epilepsy, Parkinson's disease and stroke. In this paper the early development and evaluation of a prototype designed to monitor movements and heart rate is described. An iterative development process and evaluation of an upper body garment with integrated sensors included: identification of user needs, specification of technical and garment requirements, garment development and production as well as evaluation of garment design, functionality and usability. The project is a multidisciplinary collaboration with experts from medical, engineering, textile, and material science within the wearITmed consortium. The work was organized in regular meetings, task groups and hands-on workshops. User needs were identified using results from a mixed-methods systematic review, a focus group study and expert groups. Usability was evaluated in 19 individuals (13 controls, 6 patients with Parkinson's disease) using semi-structured interviews and qualitative content analysis. Results: The garment was well accepted by the users regarding design and comfort, although the users were cautious about the technology and suggested improvements. All electronic components passed a washability test. The most robust data was obtained from accelerometer and gyroscope sensors while the electrodes for heart rate registration were sensitive to motion artefacts. The algorithm development within the wearITmed consortium has shown promising results. Conclusions: The prototype was accepted by the users. Technical improvements are needed, but preliminary data indicate that the garment has potential to be used as a tool for diagnosis and treatment selection and could provide added value for monitoring seizures in epilepsy, fluctuations in PD and activity levels in stroke. Future work aims to improve the prototype further, develop algorithms, and evaluate the functionality and usability in targeted patient groups. The potential of incorporating blood pressure and heart-rate variability monitoring will also be explored.
Language	English
Publishing date	2019-01-30
Publishing country	England
Document type	Journal Article
ISSN	2524-4426
ISSN (online)	2524-4426
DOI	10.1186/s42490-019-0002-3
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Article ; Online: Tonic-clonic seizure detection using accelerometry-based wearable sensors: A prospective, video-EEG controlled study.

Johansson, Dongni / Ohlsson, Fredrik / Krýsl, David / Rydenhag, Bertil / Czarnecki, Madeleine / Gustafsson, Niclas / Wipenmyr, Jan / McKelvey, Tomas / Malmgren, Kristina

Seizure

2018 Volume 65, Page(s) 48–54

Abstract: Purpose: The aim of this prospective, video-electroencephalography (video-EEG) controlled study was to evaluate the performance of an accelerometry-based wearable system to detect tonic-clonic seizures (TCSs) and to investigate the accuracy of different ...

Abstract	Purpose: The aim of this prospective, video-electroencephalography (video-EEG) controlled study was to evaluate the performance of an accelerometry-based wearable system to detect tonic-clonic seizures (TCSs) and to investigate the accuracy of different seizure detection algorithms using separate training and test data sets. Methods: Seventy-five epilepsy surgery candidates undergoing video-EEG monitoring were included. The patients wore one three-axis accelerometer on each wrist during video-EEG. The accelerometer data was band-pass filtered and reduced using a movement threshold and mapped to a time-frequency feature space representation. Algorithms based on standard binary classifiers combined with a TCS specific event detection layer were developed and trained using the training set. Their performance was evaluated in terms of sensitivity and false positive (FP) rate using the test set. Results: Thirty-seven available TCSs in 11 patients were recorded and the data was divided into disjoint training (27 TCSs, three patients) and test (10 TCSs, eight patients) data sets. The classification algorithms evaluated were K-nearest-neighbors (KNN), random forest (RF) and a linear kernel support vector machine (SVM). For the TCSs detection performance of the three algorithms in the test set, the highest sensitivity was obtained for KNN (100% sensitivity, 0.05 FP/h) and the lowest FP rate was obtained for RF (90% sensitivity, 0.01 FP/h). Conclusions: The low FP rate enhances the clinical utility of the detection system for long-term reliable seizure monitoring. It also allows a possible implementation of an automated TCS detection in free-living environment, which could contribute to ascertain seizure frequency and thereby better seizure management.
MeSH term(s)	Accelerometry/methods ; Adolescent ; Adult ; Aged ; Algorithms ; Electroencephalography/methods ; False Positive Reactions ; Female ; Humans ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Seizures/diagnosis ; Seizures/diagnostic imaging ; Video Recording ; Wearable Electronic Devices ; Young Adult
Language	English
Publishing date	2018-12-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1137610-7
ISSN	1532-2688 ; 1059-1311
ISSN (online)	1532-2688
ISSN	1059-1311
DOI	10.1016/j.seizure.2018.12.024
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