Precision Health – improving the understanding of underlying mechanisms through the analysis of temporal and multi-modal data
April 22-23, 2024, Simula Research Lab, Kristian Augusts gate 23, Oslo, Norway
Data sets from diverse sources are collected in multi-omics studies with the goal of bringing together various aspects of genomics, phenomics and environment in the quest for precision medicine. Such data sets are heterogeneous – they are often a collection of static and dynamic data sets with different characteristics such as different data/noise distributions, different temporal resolutions. For instance, some data sets are dynamic as a result of repeated sampling every few months in longitudinal cohorts, every few hours in meal challenge tests, every few seconds through wearable sensors or simply as a result of the temporal nature of electronic health records.
Integrating such heterogeneous data sets in an explainable way is one of the main pillars of precision medicine in order to find better stratifications of disease groups, reveal biomarkers, understand individual differences, predict early signs of diseases, and design precision therapy.
However, integration – in other words, jointly analyzing data from multiple sources (also referred to as data fusion) - is challenging due to the different nature of these data sets. Dynamic data sets can often be arranged as a multiway array, e.g., participants by metabolites by time tensor, while static data sets can be in the form of matrices, e.g., participants by genes. Tensor factorizations, which are extensions of matrix factorizations (e.g., principal component analysis) to multiway data sets, have been successfully used to reveal the underlying patterns in such higher-order/multiway data sets. For instance, tensor factorizations have been used to analyze gut microbiome data collected from infants over time and capture birth mode-related microbial changes, have shown promising performance in terms of revealing temporal phenotypes from electronic health records as well as capturing metabolic differences among participants in terms of their response to a meal challenge test. Tensor factorizations have been extended to joint analysis of data sets from multiple sources through coupled matrix and tensor factorizations, and such coupled factorization-based approaches have also started to be used in systems biology applications.
In this workshop, we will bring together a selection of studies (where integration of such heterogeneous data is of interest) and the researchers working on developing methods based on tensor factorizations and their extensions to joint analysis of data from multiple sources with a particular interest in omics data analysis. We expect the workshop to facilitate the synergy between different disciplines and pave the way to effective methods to address data analysis challenges, especially in terms of integration of data sets, in precision health.
Organizers
Evrim Acar, Simula Metropolitan Center for Digital Engineering
Age K. Smilde, University of Amsterdam
Morten A. Rasmussen, COPSAC & University of Copenhagen
Confirmed Speakers & Participants
Speakers
Evrim Acar, Simula Metropolitan Center for Digital Engineering, Norway
Francesco Asnicar, University of Trento & Zoe
Oleksandr Frei, University of Oslo, Norway
Joyce Ho, Emory University, US
Lu Li, Simula Metropolitan Center for Digital Engineering, Norway
Roel van der Ploeg & Fred White, University of Amsterdam, The Netherlands
Liat Shenhav, NYU, US
Erick Armingol, Wellcome Sanger Institute, UK
Timothy Ebbels, Imperial College London, UK
Hilde Herrema, Amsterdam UMC, The Netherlands
Rasmus Jakobsen, University of Copenhagen, Denmark
Aaron Meyer, University of California, Los Angeles, US
Morten A. Rasmussen, COPSAC & University of Copenhagen, Denmark
Maria Karoline Andersen, NTNU, Norway
Zhi Zhao, University of Oslo, Norway
Attendees
David Barnett, Maastricht University, The Netherlands
Ingunn Berget, Nofima, Norway
Christos Chatzis, SimulaMet, Norway
Balazs Erdos, SimulaMet, Norway
Jon Alm Eriksen, Bio-Me, Norway
Mikkel Lepperød, Simula Research Laboratory, Norway
Ingrid Måge, Nofima, Norway
Naimahmed Nesaragi, Oslo University Hospital
Biswa Sahu, University of Oslo
Viktor Skantze, Fraunhofer-Chalmers Centre, Sweden
Magne Thoresen, University of Oslo
Manuela Zucknick, University of Oslo
Rasmus Bro, University of Copenhagen
Charlotte Castel, Oslo Centre for Biostatistics and Epidemiology
Matteo D'Alessandro, Oslo Centre for Biostatistics and Epidemiology
Parvaneh Ebrahimi, University of Copenhagen & COPSAC
Mari Myhrstad, Oslo Metropolitan University
Marco Molinari, University of Oslo
Marie E. Rognes, Simula Research Laboratory, Norway
Carla Schenker, SimulaMet, Norway
Age Smilde, University of Amsterdam & SimulaMet
Charles Stabell, Bio-Me, Norway
Serdar Özsezen, TNO, The Netherlands
Zhi Ye, University of Copenhagen
Workshop Schedule
The workshop will take place in HPL’s Lecture Hall on 8th Floor, Kristian Augusts gate 23, Oslo.