Immersive Intelligence Genomic Data Visualisation

Genomics data are very complex and could contain crucial information about a disease or how a treatment method may perform well on one but not on another. Understanding such genomic data would enable better insight into the correlation between genes and diseases, which could facilitate personalised treatments for the patients. Although visualisations have been increasingly used in the genomic analysis, there is still limited research work on interactive visualisations on immersive platforms, such as in Augmented and Virtual Reality. This paper presents a new interactive visualisation and navigation of genomics data in such environments. We provide an overview of the patient cohort in 3D genetic similarity-space as well as the views of the genes of interests for detail study. The visualisation employs avatars to represent the patients to enhance the realistic look-and-feel of the patients in the immersive environments. We illustrate the effectiveness of our platform through a childhood cancer dataset, B-cell Acute Lymphoblastic Leukaemia.

[1]  Albert Rizzo,et al.  Baseline psychophysiological and cortisol reactivity as a predictor of PTSD treatment outcome in virtual reality exposure therapy. , 2016, Behaviour research and therapy.

[2]  Yu Yao,et al.  starmap: Immersive visualisation of single cell data using smartphone-enabled virtual reality , 2018 .

[3]  Matthew Montebello,et al.  A case study inside virtual worlds: use of analytics for immersive spaces , 2013, LAK '13.

[4]  Jarkko Venna,et al.  Comparison of Visualization Methods for an Atlas of Gene Expression Data Sets , 2007, Inf. Vis..

[5]  Robert H. Halstead,et al.  Matrix Computations , 2011, Encyclopedia of Parallel Computing.

[6]  Daniel F. Keefe,et al.  Virtual reality for persistent pain: A new direction for behavioral pain management , 2012, PAIN®.

[7]  Daniel C. Krawczyk,et al.  Virtual Reality Social Cognition Training for children with high functioning autism , 2016, Comput. Hum. Behav..

[8]  Nicholas Polys,et al.  Immersive analytics: Crossing the gulfs with high-performance visualization , 2016, 2016 Workshop on Immersive Analytics (IA).

[9]  P. Bordnick,et al.  Feasibility of Virtual Reality Environments for Adolescent Social Anxiety Disorder , 2016 .

[10]  Ivan Poupyrev,et al.  An Introduction to 3-D User Interface Design , 2001, Presence: Teleoperators & Virtual Environments.

[11]  J. Deutsch,et al.  Virtual Reality for Stroke Rehabilitation , 2011, The Cochrane database of systematic reviews.

[12]  Jih-Hsuan Tammy Lin,et al.  Fear in virtual reality (VR): Fear elements, coping reactions, immediate and next-day fright responses toward a survival horror zombie virtual reality game , 2017, Comput. Hum. Behav..

[13]  Ali Arya,et al.  A framework for an immersive learning environment with telemetries and simulation , 2011 .

[14]  Pietro Cipresso,et al.  Virtual reality : technologies, medical applications and challenges , 2014 .

[15]  Allen Tan Beyond Intuitive UI: Design Considerations for Attention, Rhythm, and Weight , 2014 .

[16]  M. Kempton,et al.  Virtual reality in the psychological treatment for mental health problems: An systematic review of recent evidence , 2016, Psychiatry Research.

[17]  Pedro Gamito,et al.  Cognitive training on stroke patients via virtual reality-based serious games , 2017, Disability and rehabilitation.

[18]  Andrea Turolla,et al.  Virtual Reality for Upper Limb Rehabilitation in Subacute and Chronic Stroke: A Randomized Controlled Trial. , 2018, Archives of physical medicine and rehabilitation.

[19]  Xueni Pan,et al.  Reduced Mimicry to Virtual Reality Avatars in Autism Spectrum Disorder , 2016, Journal of autism and developmental disorders.

[20]  Ben Shneiderman,et al.  Improving Healthcare with Interactive Visualization , 2013, Computer.

[21]  Bennett A Landman,et al.  Immersive virtual reality for visualization of abdominal CT , 2013, Medical Imaging.

[22]  Carolina Cruz-Neira,et al.  Tweek: Merging 2D and 3D Interaction in Immersive Environments , 2002 .

[23]  Quang Vinh Nguyen,et al.  Visual Analytics of Complex Genomics Data to Guide Effective Treatment Decisions , 2016, J. Imaging.

[24]  Marc Baaden,et al.  MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis , 2018, J. Integr. Bioinform..

[25]  D. Chou Health IT and Patient Safety: Building Safer Systems for Better Care , 2012 .

[26]  Nuria Lopez-Bigas,et al.  Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps , 2011, PloS one.

[27]  Todd M. Moore,et al.  The Impact of Virtual Reality on Chronic Pain , 2016, PloS one.

[28]  Hunter G Hoffman,et al.  Water-friendly virtual reality pain control during wound care. , 2004, Journal of clinical psychology.

[29]  Tom Sante,et al.  ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation , 2014, PloS one.

[30]  N. Newbutt,et al.  Brief Report: A Pilot Study of the Use of a Virtual Reality Headset in Autism Populations , 2016, Journal of autism and developmental disorders.

[31]  Joan Llobera,et al.  Virtual reality for assessment of patients suffering chronic pain: a case study , 2012, Experimental Brain Research.

[32]  Daniel O. David,et al.  Virtual reality exposure therapy in flight anxiety: A quantitative meta-analysis , 2017, Comput. Hum. Behav..

[33]  Leo Breiman,et al.  Random Forests , 2001, Machine Learning.

[34]  Dieter Schmalstieg,et al.  Caleydo: Design and evaluation of a visual analysis framework for gene expression data in its biological context , 2010, 2010 IEEE Pacific Visualization Symposium (PacificVis).

[35]  Spiros Sirmakessis,et al.  A Comparative Study of Skeuomorphic and Flat Design from a UX Perspective , 2018, Multimodal Technol. Interact..

[36]  Katrin Amunts,et al.  Interactive 3D visualization of structural changes in the brain of a person with corticobasal syndrome , 2014, Front. Neuroinform..

[37]  Pierre Boudoin,et al.  Design of a 3D Navigation Technique Supporting VR Interaction , 2008 .

[38]  David A. Thomas,et al.  The Neurobiology of Virtual Reality Pain Attenuation , 2007, Cyberpsychology Behav. Soc. Netw..

[39]  Oliver G. Staadt,et al.  On Spatial Perception Issues In Augmented Reality Based Immersive Analytics , 2016, ISS Companion.

[40]  Juri G. Gelovani,et al.  Methodological and practical challenges for personalized cancer therapies , 2011, Nature Reviews Clinical Oncology.

[41]  Mao Lin Huang,et al.  Interactive Visualization for Patient-to-Patient Comparison , 2014, Genomics & informatics.

[42]  Jeremy Kepner,et al.  Improving Big Data visual analytics with interactive virtual reality , 2015, 2015 IEEE High Performance Extreme Computing Conference (HPEC).

[43]  David B. Douglas,et al.  Augmented Reality: Advances in Diagnostic Imaging , 2017, Multimodal Technol. Interact..

[44]  Nicholas Ho,et al.  Visual Analytics of Clinical and Genetic Datasets of Acute Lymphoblastic Leukaemia , 2011, ICONIP.

[45]  Min Chen,et al.  Glyph-based Visualization: Foundations, Design Guidelines, Techniques and Applications , 2013, Eurographics.

[46]  Hyo Jeong Kang,et al.  Designing next generation marketplace: The effect of 3D VR store interface design on shopping behavior , 2017, 2017 IEEE Virtual Reality (VR).

[47]  Thomas Ertl,et al.  Interactive Molecular Graphics for Augmented Reality Using HoloLens , 2018, J. Integr. Bioinform..

[48]  Hunter G Hoffman,et al.  Virtual reality pain control during burn wound debridement of combat-related burn injuries using robot-like arm mounted VR goggles. , 2011, The Journal of trauma.

[49]  Ali Arya,et al.  DATA-DRIVEN FRAMEWORK FOR AN ONLINE 3D IMMERSIVE ENVIRONMENT FOR EDUCATIONAL APPLICATIONS , 2010 .

[50]  A. Mirelman,et al.  Virtual reality for rehabilitation in Parkinson's disease. , 2014, The Cochrane database of systematic reviews.

[51]  W. Veling,et al.  Social environments and interpersonal distance regulation in psychosis: A virtual reality study , 2017, Schizophrenia Research.

[52]  Ulrich Engelke,et al.  Collaborative Framework Design for Immersive Analytics , 2016, 2016 Big Data Visual Analytics (BDVA).

[53]  Wei Hu,et al.  Navigation modes, operation methods, observation scales and background options in UI design for high learning performance in VR-based architectural applications , 2018, J. Comput. Des. Eng..

[54]  Heikki Lehväslaiho,et al.  Three‐dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues , 2015, The Journal of comparative neurology.

[55]  Paul T. Spellman,et al.  GenomeGraphs: integrated genomic data visualization with R , 2009, BMC Bioinformatics.

[56]  Shamit Soneji,et al.  CellexalVR: A virtual reality platform to visualise and analyse single-cell data , 2018, bioRxiv.

[57]  Hunter G Hoffman,et al.  Combining ketamine and virtual reality pain control during severe burn wound care: one military and one civilian patient. , 2011, Pain medicine.

[58]  L. Cohen,et al.  Effectiveness of Virtual Reality Exercises in STroke Rehabilitation (EVREST): Rationale, Design, and Protocol of a Pilot Randomized Clinical Trial Assessing the Wii Gaming System , 2010, International journal of stroke : official journal of the International Stroke Society.

[59]  K. Schughart,et al.  Computer-based three-dimensional visualization of developmental gene expression , 2000, Nature Genetics.

[60]  Anderson Maciel,et al.  Medical imaging VR: can immersive 3D aid in diagnosis? , 2016, VRST.