Felix Held

About me

I did my doctoral studies at the Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, with advisor Rebecka Jörnsten.

My research addresses aspects of unsupervised exploratory analysis for biomedical data. Most of the data considered in my PhD project comes from the domain of braincancer research. The methodological focus of my work has been on

• Integrated analysis of multiple data sources through joint matrix factorisation, with emphasis on flexibility, scalability, and interpretability.
• Integrated gene clustering and regulatory program estimation.

Previously, I worked with dynamical models of pharmacological process and parameter estimation in both frequentist and Bayesian settings.

Degrees

• [2024] Doctor of Philosopy in Mathematical Statistics from University of Gothenburg
  • Thesis: Unsupervised methods for integrative data analysis (pdf)
• [2018] Licentiate in Advanced Engineering Mathematics from Chalmers University of Technology with work performed at Fraunhofer Chalmers Research Centre for Industrial Mathematics
  • Thesis: Modelling of drug-effect on time-varying biomarkers (pdf)
• [2016] Master of Science in Mathematics from Chalmers University of Technology with work performed at SAFER – Vehicle and Traffic Safety Centre at Chalmers
  • Thesis: Investigation of under-reporting and the consistency of injury severity classifications in Swedish police crash data compared to hospital injury data based on the Swedish Traffic Accident Data Acquisition (STRADA) (pdf)
• [2013] Bachelor of Science in Mathematics with subsidiary subject Physics from University of Würzburg, Germany
  • Thesis: Introduction to the theory of Bergman spaces with emphasis on their dual spaces

Positions

• [2018-2024] Doctoral Student at the University of Gothenburg
• [2016–2018] Project employee at Fraunhofer Chalmers Research Centre for Industrial Mathematics
• [2015] Data Analyst at SAFER – Vehicle and Traffic Safety Centre at Chalmers
• [2015–2016] Consultant at Chalmers teknologkonsulter
• [2010–2011] Software engineer for the Faculty of Physics and Astronomy, University of Würzburg

Teaching

I was responsible for the lectures and course coordination for

• [2021] MSA220/MVE441 Statistical Learning for Big Data at Chalmers/University of Gothenburg (about 130 students, fully digital course)
• [2020] MSA220/MVE440 Statistical Learning for Big Data at Chalmers/University of Gothenburg (about 120 students, fully digital course due to the Covid-19 pandemic)
• [2019] MSA220/MVE440 Statistical Learning for Big Data at Chalmers/University of Gothenburg (about 90 students, Slides)

and did a lot of teaching assistance (e.g. holding exercise classes, correcting submissions) over the years since 2011. Examples of subjects I was involved in are

Mathematical Statistics, Probability Theory, Linear Algebra, and Calculus.

I supervised the following students during their master thesis projects

• [2020] Selma Tabakovic, Co-clustering of tensor data using sparse tensor factorisation
• [2020, co-supervised with Rebecka Jörnsten] Oskar Liew and Per Edwardsson, Deep learning models for data integration and surrogate models for interpretable predictions with applications in integromics and recommender system

Extra-curricular activities

Co-founder and organiser for a workshop on Modelling in Biology and Medicine

• [2020] Workshop held digitally (30+ participants, see recording on YouTube)
• [2019] Workshop held at the Wallenberg Conference Centre in Gothenburg, Sweden (60+ participants)

Member of organising committee for

• [2019] a poster conference for doctoral students at the University of Gothenburg

Python package author and maintainer

• [Since 2024] solrcmf package (GitHub).
• [Since 2024] lscmf package (GitHub).

R package maintainer

• [Since 2023] scregclust package (GitHub). Authors: Felix Held, Ida Larsson, Sven Nelander
• [Since 2022] mmpca package (CRAN or GitHub). Original author: Jonatan Kallus
• [Since 2020] CMF package (CRAN or GitHub). Original authors: Arto Klami and Lauri Väre

Other activities

• [2020-2022] Chair of the PhD Student Council at the Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg (GU)
• [2018–2021] Member of the PhD Student Council and Research and Education Committee at the Department of Mathematical Sciences, Chalmers and GU

Publications

Peer-reviewed articles

• Larsson I*, Held F* (* shared first authorship), Popova G, Koc A, Soumi K, Jörnsten R, Nelander S (2024) Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers Nature Communications 15, 9699
• Obradović G, Strömberg AB, Held F, Lundberg K (2024) Approximating the Pareto frontier for bi-objective preventive maintenance and workshop scheduling. A Lagrangean lower bounding methodology for evaluating contracting forms Annals of Operations Research
• Gustafsson J, Held F, Robinson JL, Björnson E, Jörnsten R, Nielsen J (2020) Sources of variation in cell-type RNA-Seq profiles PLoS ONE 15(9):e0239495
• Held F, Hoppe E, Cvijovic M, Jirstrand M, Gabrielsson J (2019) Challenge model of TNF_α turnover at varying LPS and drug provocations. Journal of Pharmacokinetics and Pharmacodynamics 46:223–240
• Held F, Ekstrand C, Cvijovic M, Gabrielsson J, Jirstrand M (2019) Modelling of oscillatory cortisol response in horses using a Bayesian population approach for evaluation of dexamethasone suppression test protocols. Journal of Pharmacokinetics and Pharmacodynamics 46:75–87
• Loryan L, Hoppe E, Hansen K, Held F, Kless A, Linz K, Marossek V, Nolte B, Ratcliffe P, Saunders D, Terlinden R, Wegert A, Welbers A, Will O, Hammarlund-Udenaes M (2017) Quantitative Assessment of Drug Delivery to Tissues and Association with Phospholipidosis: A Case Study with Two Structurally Related Diamines in Development. Molecular Pharmaceutics 14(12):4362–4373

Preprints

• Held F (2024) Large-scale Data Integration using Matrix Denoising and Geometric Factor Matching arXiv
• Held F, Lindbäck J, Jörnsten R (2024) Sparse and Orthogonal Low-rank Collective Matrix Factorization (solrCMF): Efficient data integration in flexible layouts arXiv

Talks & Posters

Invited Talks

• [June 2023] Interpretable multi-omics integration using sparse joint matrix factorization. 9th Nordic-Baltic Biometric Conference, Gothenburg, Sweden
• [March 2019] Pharmacokinetic/pharmacodynamic modelling in a Bayesian hierarchical framework. Yearly meeting of the Swedish Society for Medical Statistics, Gothenburg, Sweden
• [July 2018] Bayesian hierarchical model of oscillatory cortisol response during drug intervention. Stan Workshop on Pharmacometrics, INSERM and University Paris Diderot, Paris, France

Research Presentations

• [June 2023] Simultaneous gene clustering and regulatory program reconstruction reveals insight into the phenotypic plasticity of neural cancers. Gothenburg Statistics Seminar, Gothenburg, Sweden
• [November 2019] Scalable integration of sparse data sources. Workshop in Data Science, Halden, Norway

Posters

• [June 2019] A challenge model of TNF_α turnover with LPS provocations and drug intervention. PAGE Meeting 2019, Stockholm, Sweden
• [May 2018] Bayesian hierarchical model of oscillatory cortisol response during drug intervention. PAGE Meeting 2018, Montreux, Switzerland