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Falk, M., Tobiasson, V., Bock, A., Hansen, C. & Ynnerman, A. (2023). A Visual Environment for Data Driven Protein Modeling and Validation. IEEE Transactions on Visualization and Computer Graphics
Open this publication in new window or tab >>A Visual Environment for Data Driven Protein Modeling and Validation
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2023 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506Article in journal (Refereed) Epub ahead of print
Abstract [en]

In structural biology, validation and verification of new atomic models are crucial and necessary steps which limit the production of reliable molecular models for publications and databases. An atomic model is the result of meticulous modeling and matching and is evaluated using a variety of metrics that provide clues to improve and refine the model so it fits our understanding of molecules and physical constraints. In cryo electron microscopy (cryo-EM) the validation is also part of an iterative modeling process in which there is a need to judge the quality of the model during the creation phase. A shortcoming is that the process and results of the validation are rarely communicated using visual metaphors.

This work presents a visual framework for molecular validation. The framework was developed in close collaboration with domain experts in a participatory design process. Its core is a novel visual representation based on 2D heatmaps that shows all available validation metrics in a linear fashion, presenting a global overview of the atomic model and provide domain experts with interactive analysis tools. Additional information stemming from the underlying data, such as a variety of local quality measures, is used to guide the user's attention toward regions of higher relevance. Linked with the heatmap is a three-dimensional molecular visualization providing the spatial context of the structures and chosen metrics. Additional views of statistical properties of the structure are included in the visual framework. We demonstrate the utility of the framework and its visual guidance with examples from cryo-EM.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2023
Keywords
molecular visualization, cryo-EM, model validation, verification
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-195458 (URN)10.1109/tvcg.2023.3286582 (DOI)37327104 (PubMedID)
Funder
ELLIIT - The Linköping‐Lund Initiative on IT and Mobile CommunicationsSwedish Research Council, 2015-05462Knut and Alice Wallenberg Foundation, KAW 2019.0024NIH (National Institutes of Health), R01EB023947NIH (National Institutes of Health), R01EB031872
Note

The supplemental material is available under https://osf.io/pqymt/ (DOI: 10.17605/OSF.IO/PQYMT).

Available from: 2023-06-20 Created: 2023-06-20 Last updated: 2024-03-28Bibliographically approved
Zohrevandi, E., Brorsson, E., Darnell, A., Bång, M., Lundberg, J. & Ynnerman, A. (2023). Design of an Ecological Visual Analytics Interface for Operators of Time-Constant Processes. In: 2023 IEEE Visualization and Visual Analytics (VIS): . Paper presented at 2023 IEEE Visualization Conference, Melbourne, Australia (Hybrid), 22-27 October 2023 (pp. 131-135). IEEE
Open this publication in new window or tab >>Design of an Ecological Visual Analytics Interface for Operators of Time-Constant Processes
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2023 (English)In: 2023 IEEE Visualization and Visual Analytics (VIS), IEEE, 2023, p. 131-135Conference paper, Published paper (Refereed)
Abstract [en]

In industrial applications where the physical parameters are highly interconnected, keeping the process flow steady is a major concern for the operators. This is caused by the sensitivity of system to the process dynamics. As a result, a slight adjustment to a control parameter can significantly affect the efficiency of the system and thus impact the financial gain. Paper pulp production is an example of such a process, where operators continuously investigate the potential of changes in the process and predict the consequences of an adjustment before making a decision. Process parameter adjustments prescribed by simulated control models cannot be fully trusted as the external disturbances and the process inherent variabilities cannot be fully incorporated into the simulations. Therefore, to assess the viability of a strategy, operators often compare the situation with the historical records and trends during which the processes in the plant ran steadily. While previous research has mostly focused on developing advanced control models to simulate complex pulp production process, this work aims to support operators analytical reasoning by provision of effective data visualization. The contributions of our design study include a domain problem characterization and a linked-view visual encoding design, which aims to enhance operator's mental models independent of particular users or scenarios. Finally, by reflecting on the advantages of our choice of task abstraction technique, inherited from the ecological interface design framework [5], we reason for the generalizability of our approach to similar industrial applications.

Place, publisher, year, edition, pages
IEEE, 2023
Series
IEEE Visualization Conference, ISSN 2771-9537, E-ISSN 2771-9553
Keywords
Visual analytics interfaces; Design study; Focus+context techniques; Linked-view interfaces; Time-constant processes
National Category
Production Engineering, Human Work Science and Ergonomics Computer Systems
Identifiers
urn:nbn:se:liu:diva-199828 (URN)10.1109/VIS54172.2023.00035 (DOI)001137142800027 ()9798350325577 (ISBN)9798350325584 (ISBN)
Conference
2023 IEEE Visualization Conference, Melbourne, Australia (Hybrid), 22-27 October 2023
Note

Funding agencies: The Sweden’s Innovation Agency (Vinnova) under the project EXPLAIN (2021-04336) and the Knutand Alice Wallenberg Foundation (grant KAW 2019.0024).

Available from: 2023-12-22 Created: 2023-12-22 Last updated: 2024-02-09
Elmquist, E., Bock, A., Lundberg, J., Ynnerman, A. & Rönnberg, N. (2023). SonAir: the design of a sonification of radar data for air traffic control. Journal on Multimodal User Interfaces, 17(3), 137-149
Open this publication in new window or tab >>SonAir: the design of a sonification of radar data for air traffic control
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2023 (English)In: Journal on Multimodal User Interfaces, ISSN 1783-7677, E-ISSN 1783-8738, Vol. 17, no 3, p. 137-149Article in journal (Refereed) Published
Abstract [en]

Along with the increase of digitalization and automation, a new kind of working environment is emerging in the field of air traffic control. Instead of situating the control tower at the airport, it is now possible to remotely control the airport at any given location, i.e. in a remote tower center (RTC). However, by controlling the airport remotely, the situational awareness and sense of presence might be compromised. By using directional sound, a higher situational awareness could potentially be achieved while also offloading the visual perception which is heavily used in air traffic control. Suitable use cases for sonification in air traffic control were found through workshops with air traffic controllers. A sonification design named SonAir was developed based on the outcome of the workshops, and was integrated with an RTC simulator for evaluating to what degree SonAir could support air traffic controllers in their work. The results suggest that certain aspects of SonAir could be useful for air traffic controllers. A continuous sonification where the spatial positioning of aircraft were conveyed was experienced to be partially useful, but the intrusiveness of SonAir should be further considered to fit the air traffic controllers’ needs. An earcon that conveyed when an aircraft enters the airspace and from which direction was considered useful to support situational awareness.

Place, publisher, year, edition, pages
SPRINGER, 2023
Keywords
Sonification; Air traffic control; Situational awareness; User evaluation
National Category
Media Engineering
Identifiers
urn:nbn:se:liu:diva-196256 (URN)10.1007/s12193-023-00404-x (DOI)001021523300001 ()
Note

Funding: Swedish Transport Authority [TRV-2019/53555]; Knut and Alice Wallenberg Foundation [KAW 2019.0024]

Available from: 2023-07-08 Created: 2023-07-08 Last updated: 2023-12-07
Besançon, L., Schönborn, K., Sundén, E., Yin, H., Rising, S., Westerdahl, P., . . . Ynnerman, A. (2022). Exploring and Explaining Climate Change: Exploranation as a Visualization Pedagogy for Societal Action. In: : . Paper presented at VIS4GOOD, a workshop on Visualization for Social Good, held as part of IEEE VIS 2022. Institute of Electrical and Electronics Engineers (IEEE)
Open this publication in new window or tab >>Exploring and Explaining Climate Change: Exploranation as a Visualization Pedagogy for Societal Action
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2022 (English)Conference paper, Oral presentation only (Other academic)
Abstract [en]

Engaging mass audiences with crucial societal issues, such as cli-mate change, can be provided through interactive exhibits designed around the paradigm of exploranation. We present example inter-active installations in the newly founded Wadstr¨oms Exploranation Laboratory that explain various aspects of climate change while allowing public participants to explore the real scientific data. We describe how effects and causes of climate change can be communi-cated by two of the installations that allow for interactive opportuni-ties to explore the underlying data while gaining insight into climate change sources and effects. We close with implications for future work on exploranation as an emerging visualization pedagogy in public spaces.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2022
National Category
Climate Research
Identifiers
urn:nbn:se:liu:diva-194046 (URN)
Conference
VIS4GOOD, a workshop on Visualization for Social Good, held as part of IEEE VIS 2022
Available from: 2023-05-22 Created: 2023-05-22 Last updated: 2023-10-10Bibliographically approved
Skånberg, R., Falk, M., Linares, M., Ynnerman, A. & Hotz, I. (2022). Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions. IEEE Transactions on Visualization and Computer Graphics, 28(9), 3126-3137
Open this publication in new window or tab >>Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions
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2022 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 28, no 9, p. 3126-3137Article in journal (Refereed) Published
Abstract [en]

In molecular analysis, Spatial Distribution Functions (SDF) are fundamental instruments in answering questions related to spatial occurrences and relations of atomic structures over time. Given a molecular trajectory, SDFs can, for example, reveal the occurrence of water in relation to particular structures and hence provide clues of hydrophobic and hydrophilic regions. For the computation of meaningful distribution functions, the definition of molecular reference structures is essential. Therefore we introduce the concept of an internal frame of reference (IFR) for labeled point sets that represent selected molecular structures, and we propose an algorithm for tracking the IFR over time and space using a variant of Kabschs algorithm. This approach lets us generate a consistent space for the aggregation of the SDF for molecular trajectories and molecular ensembles. We demonstrate the usefulness of the technique by applying it to temporal molecular trajectories as well as ensemble datasets. The examples include different docking scenarios with DNA, insulin, and aspirin.

Place, publisher, year, edition, pages
IEEE COMPUTER SOC, 2022
Keywords
Distribution functions, Trajectory, Visualization, Graphical models, Numerical models, Shape, Periodic structures
National Category
Chemical Sciences Mathematics Computer and Information Sciences
Identifiers
urn:nbn:se:liu:diva-174336 (URN)10.1109/TVCG.2021.3051632 (DOI)000833767700005 ()33444141 (PubMedID)
Note

Funding agencies: Excellence Center at Linkoping and Lund in Information Technology (ELLIIT); Swedish e-Science Research Centre (SeRC)

Available from: 2021-03-20 Created: 2021-03-20 Last updated: 2023-01-13
Gawel, D., Bojner Horwitz, E., Sysoev, O., Jacobsson, B., Jönsson, J.-I., Melén, E., . . . Benson, M. (2021). Stor potential när genomikdatakan implementeras i klinisk rutin: [Clinical translation of genomic medicine]. Läkartidningen, 118
Open this publication in new window or tab >>Stor potential när genomikdatakan implementeras i klinisk rutin: [Clinical translation of genomic medicine]
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2021 (Swedish)In: Läkartidningen, ISSN 0023-7205, E-ISSN 1652-7518, Vol. 118Article, review/survey (Refereed) Published
Abstract [en]

Recent technical developments and early clinical examples support that precision medicine has potential to provide novel diagnostic and therapeutic solutions for patients with complex diseases, who are not responding to existing therapies. Those solutions will require integration of genomic data with routine clinical, imaging, sensor, biobank and registry data. Moreover, user-friendly tools for informed decision support for both patients and clinicians will be needed. While this will entail huge technical, ethical, societal and regulatory challenges, it may contribute to transforming and improving health care towards becoming predictive, preventive, personalised and participatory (4P-medicine).

Abstract [sv]

Ett av de största problemen för många patienter är attde inte förbättras av läkemedelsbehandling. Detta orsakar, förutom lidande, stora samhällskostnader. Viktigaorsaker är sjukdomars molekylära komplexitet samt sendiagnostik och behandling.

Precisionsmedicin kan bidra till att lösa problem genom att karakterisera och tolka denna komplexitet. Ettexempel är att läkemedelsbehandling kan provas ut ochindividualiseras genom datorsimuleringar.

Precisionsmedicin har potential att påtagligt förbättrabåde hälsa och ekonomi. Detta kräver en bred IT-strategi för att integrera genomik- och andra storskaligadatakällor, som inkluderar nationella superdator-,visualiserings- och AI-centrum.

Place, publisher, year, edition, pages
Sveriges Läkarförbund, 2021
National Category
Medical Ethics
Identifiers
urn:nbn:se:liu:diva-185093 (URN)33977515 (PubMedID)
Available from: 2022-05-17 Created: 2022-05-17 Last updated: 2022-05-31Bibliographically approved
Eilertsen, G., Jönsson, D., Ropinski, T., Unger, J. & Ynnerman, A. (2020). Classifying the classifier: dissecting the weight space of neural networks. In: Giuseppe De Giacomo, Alejandro Catala, Bistra Dilkina, Michela Milano, Senén Barro, Alberto Bugarín, Jérôme Lang (Ed.), Proceedings of the 24th European Conference on Artificial Intelligence (ECAI 2020): . Paper presented at European Conference on Artificial Intelligence (ECAI 2020) (pp. 1119-1126). IOS PRESS, 325, Article ID FAIA200209.
Open this publication in new window or tab >>Classifying the classifier: dissecting the weight space of neural networks
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2020 (English)In: Proceedings of the 24th European Conference on Artificial Intelligence (ECAI 2020) / [ed] Giuseppe De Giacomo, Alejandro Catala, Bistra Dilkina, Michela Milano, Senén Barro, Alberto Bugarín, Jérôme Lang, IOS PRESS , 2020, Vol. 325, p. 8p. 1119-1126, article id FAIA200209Conference paper, Published paper (Refereed)
Abstract [en]

This paper presents an empirical study on the weights of neural networks, where we interpret each model as a point in a high-dimensional space – the neural weight space. To explore the complex structure of this space, we sample from a diverse selection of training variations (dataset, optimization procedure, architecture,etc.) of neural network classifiers, and train a large number of models to represent the weight space. Then, we use a machine learning approach for analyzing and extracting information from this space. Most centrally, we train a number of novel deep meta-classifiers withthe objective of classifying different properties of the training setup by identifying their footprints in the weight space. Thus, the meta-classifiers probe for patterns induced by hyper-parameters, so that we can quantify how much, where, and when these are encoded through the optimization process. This provides a novel and complementary view for explainable AI, and we show how meta-classifiers can reveal a great deal of information about the training setup and optimization, by only considering a small subset of randomly selected consecutive weights. To promote further research on the weight space, we release the neural weight space (NWS) dataset – a collection of 320K weightsnapshots from 16K individually trained deep neural networks.

Place, publisher, year, edition, pages
IOS PRESS, 2020. p. 8
Series
Frontiers in Artificial Intelligence and Applications, ISSN 1879-8314 ; 325
Keywords
machine learning, deep learning, ai, computer vision
National Category
Computer Vision and Robotics (Autonomous Systems) Computer Sciences
Identifiers
urn:nbn:se:liu:diva-169431 (URN)10.3233/FAIA200209 (DOI)000650971301047 ()9781643681016 (ISBN)
Conference
European Conference on Artificial Intelligence (ECAI 2020)
Note

Funding: Wallenberg Autonomous Systems and Software Program (WASP); strategic research environment ELLIIT

Available from: 2020-09-15 Created: 2020-09-15 Last updated: 2021-09-20
Dieckmann, M. E., Falk, M., Folini, D., Walder, R., Steneteg, P., Hotz, I. & Ynnerman, A. (2020). Collisionless Rayleigh–Taylor-like instability of the boundary between a hot pair plasma and an electron–proton plasma: The undular mode. Physics of Plasmas, 27(11), 1-14, Article ID 112106.
Open this publication in new window or tab >>Collisionless Rayleigh–Taylor-like instability of the boundary between a hot pair plasma and an electron–proton plasma: The undular mode
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2020 (English)In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 27, no 11, p. 1-14, article id 112106Article in journal (Refereed) Published
Abstract [en]

We study with a two-dimensional particle-in-cell simulation the stability of a discontinuity or piston, which separates an electron–positron cloud from a cooler electron–proton plasma. Such a piston might be present in the relativistic jets of accreting black holes separating the jet material from the surrounding ambient plasma and when pair clouds form during an x-ray flare and expand into the plasma of the accretion disk corona. We inject a pair plasma at a simulation boundary with a mildly relativistic temperature and mean speed. It flows across a spatially uniform electron–proton plasma, which is permeated by a background magnetic field. The magnetic field is aligned with one simulation direction and oriented orthogonally to the mean velocity vector of the pair cloud. The expanding pair cloud expels the magnetic field and piles it up at its front. It is amplified to a value large enough to trap ambient electrons. The current of the trapped electrons, which is carried with the expanding cloud front, drives an electric field that accelerates protons. A solitary wave grows and changes into a piston after it saturated. Our simulations show that this piston undergoes a collisionless instability similar to a Rayleigh–Taylor instability. The undular mode grows and we observe fingers in the proton density distribution. The effect of the instability is to deform the piston but it cannot destroy it.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2020
Keywords
PIC simulation, collisionless plasma, shock
National Category
Fusion, Plasma and Space Physics
Identifiers
urn:nbn:se:liu:diva-171119 (URN)10.1063/5.0018321 (DOI)000591344800002 ()
Note

Funding agencies:Ecole Nationale Superieure de Lyon, Universite de Lyon; French National Program of High Energy (PNHE); EPOCH [EP/P02212X/1]; French supercomputing facilities GENCI [A0070406960]

Available from: 2020-11-05 Created: 2020-11-05 Last updated: 2020-12-16Bibliographically approved
Zohrevandi, E., Westin, C., Lundberg, J. & Ynnerman, A. (2020). Design of a Real Time Visual Analytics Support Tool for Conflict Detection and Resolution in Air Traffic Control. In: EuroVis 2020 - Short Papers: . Paper presented at EuroVis, Norrköping, Sweden, May 25-29, 2020. Eurographics - European Association for Computer Graphics
Open this publication in new window or tab >>Design of a Real Time Visual Analytics Support Tool for Conflict Detection and Resolution in Air Traffic Control
2020 (English)In: EuroVis 2020 - Short Papers, Eurographics - European Association for Computer Graphics, 2020Conference paper, Published paper (Refereed)
Abstract [en]

Air traffic control is a safety critical high-risk environment where operators need to analyse and interpret traffic dynamics of spatio-temporal data in real-time. To support the air traffic controller in safely separating traffic, earlier research has applied real-time visualisation techniques that explore the constraints and solution spaces of separation problems. Traditionally, situation displays for conflict detection and resolution have used visualisations that convey information about the relative horizontal position between aircraft. Although vertical solutions for solving conflicts are common, and often a preferred among controllers, visualisations typically provide limited information about the vertical relationship between aircraft. This paper presents a design study of an interactive conflict detection and resolution support tool and explores techniques for real-time visualisation of spatio-temporal data. The design evolution has incorporated several activities, including an initial work domain analysis, iterative rounds of programming, design, and evaluations with a domain expert, and an evaluation with eight active controllers. The heading-time-altitude visualisation system is developed based on formulating and solving aircraft movements in a relative coordinate system. A polar-graph visualisation technique is used to construct a view of conflicting aircraft vertical solution spaces in the temporal domain. Using composite glyphs, the final heading-time-altitude visualisation provides a graphical representation of both horizontal and vertical solution spaces for the traffic situation.

Place, publisher, year, edition, pages
Eurographics - European Association for Computer Graphics, 2020
National Category
Media and Communication Technology
Identifiers
urn:nbn:se:liu:diva-179234 (URN)10.2312/evs.20201044 (DOI)
Conference
EuroVis, Norrköping, Sweden, May 25-29, 2020
Funder
Swedish Research Council
Available from: 2021-09-14 Created: 2021-09-14 Last updated: 2022-09-14Bibliographically approved
Falk, M., Ljung, P., Lundström, C., Ynnerman, A. & Hotz, I. (2020). Feature Exploration in Medical Volume Data using Local Frequency Distributions. In: B. Kozlíková, M. Krone, and N. N. Smit (Ed.), : . Paper presented at Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), Tübingen, Germany, September 28 – October 1, 1010.
Open this publication in new window or tab >>Feature Exploration in Medical Volume Data using Local Frequency Distributions
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2020 (English)In: / [ed] B. Kozlíková, M. Krone, and N. N. Smit, 2020Conference paper, Published paper (Refereed)
Abstract [en]

Frequency distributions (FD) are an important instrument when analyzing and investigating scientific data. In volumetric visualization, for example, frequency distributions visualized as histograms, often assist the user in the process of designing transfer function (TF) primitives. Yet a single point in the distribution can correspond to multiple features in the data, particularly in low-dimensional TFs that dominate time-critical domains such as health care. In this paper, we propose contributions to the area of medical volume data exploration, in particular Computed Tomography (CT) data, based on the decomposition of local frequency distributions (LFD). By considering the local neighborhood utilizing LFDs we can incorporate a measure for neighborhood similarity to differentiate features thereby enhancing the classification abilities of existing methods. This also allows us to link the attribute space of the histogram with the spatial properties of the data to improve the user experience and simplify the exploration step. We propose three approaches for data exploration which we illustrate with several visualization cases highlighting distinct features that are not identifiable when considering only the global frequency distribution. We demonstrate the power of the method on selected datasets.

Keywords
Scientific Visualization, Frequency Distributions, Volume Rendering
National Category
Media and Communication Technology
Identifiers
urn:nbn:se:liu:diva-170755 (URN)10.2312/vcbm.20201166 (DOI)
Conference
Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), Tübingen, Germany, September 28 – October 1, 1010
Funder
Swedish e‐Science Research CenterELLIIT - The Linköping‐Lund Initiative on IT and Mobile Communications
Available from: 2020-10-20 Created: 2020-10-20 Last updated: 2021-09-23Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-9466-9826

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