HICT: Doctoral Candidate in Deep generative modeling for 1) precision medicine and 2) continuous-time dynamical systems

Updated: 4 months ago

The Helsinki Doctoral Education Network in Information and Communications Technology (HICT) is a collaborative doctoral education network hosted jointly by Aalto University and the University of Helsinki, the two leading universities within this area in Finland. The network serves as a collaboration platform for doctoral education combining all the relevant subfields of computer science and information technology at Aalto University and the University of Helsinki. It involves at present 80 professors and almost 300 doctoral students, and the participating units graduate altogether more than 40 new doctors each year.

We offer the possibility to join world-class research groups in both universities with multiple interesting research projects to choose from. The list of all open Doctoral Candidate positions in this joint call can be found here: https://hict.fi/admissions/

HICT Doctoral Candidate in Deep generative modeling for 1) precision medicine and 2) continuous-time dynamical systems

Supervisor(s): Harri Lähdesmäki (Aalto University)

We are looking for a doctoral student to develop novel probabilistic machine learning methods for large-scale health datasets from biobanks, clinical trials and/or single-cell sequencing experiments. This project develops novel deep generative modeling methods to (i) predict adverse drug effects using longitudinal/time-series data from large-scale biobanks and clinical trials, and to (ii) harmonize large-scale health data sets for AI-assisted decision making to revolutionize future clinical trials. Methodologically this project includes e.g. VAEs, GANs, Bayesian NNs, domain adaptation, Gaussian processes and causal analysis. The work will be done in collaboration with research groups from the Finnish Center for Artificial Intelligence, and the novel methods will be tested using unique real-world data sets from our collaborators in university hospitals and big pharma company.

Our recent work:
[1] http://proceedings.mlr.press/v130/ramchandran21b.html
[2] http://proceedings.mlr.press/v130/ramchandran21a.html
[3] https://arxiv.org/abs/2111.02019
[4] https://academic.oup.com/bioinformatics/article/37/13/1860/6104850

Recent machine learning breakthroughs include black-box modeling methods for differential equations, such as Gaussian process ODEs [1] and neural ODEs. These methods are particularly useful in learning arbitrary continuous-time dynamics from data, either directly in the data space [1] or in a latent space in case of very high-dimensional data [3]. We are looking for a doctoral student to join our current efforts to (i) develop efficient yet calibrated Bayesian methods for learning such black-box ODE models, (ii) develop neural ODEs to learn arbitrary dynamics of high-dimensional systems (e.g. in robotics, biology, physics or video applications) using a low-dimensional latent space representation, and (iii) further developing these methods for reinforcement learning and causal analysis.

Our recent work:
[1] http://proceedings.mlr.press/v80/heinonen18a.html
[2] http://proceedings.mlr.press/v89/hegde19a.html
[3] https://papers.nips.cc/paper/9497-ode2vae-deep-generative-second-order-odes-with-bayesian-neural-networks
[4] https://openreview.net/forum?id=aUX5Plaq7Oy
[5] https://proceedings.mlr.press/v139/yildiz21a.html
[6] http://arxiv.org/abs/2106.10905

For more information: https://research.cs.aalto.fi/csb/publications.shtml
Contact: harri.lahdesmaki@aalto.fi

Please list which project you are applying for in your application.

Ready to apply?

If you want to join our community and start your journey towards Doctoral dissertation submit your application via our electronic recruitment system. The application form will close 6th February 2022 at 23:59 Finnish time (UTC +2).

If you are currently working at Aalto University, please submit your application via HR System Workday (Career – Find jobs – Apply).

Please be prepared to add the following attachments:

  • Cover letter
  • CV
  • Transcript of your Master’s studies

You will be asked to provide also the contact details of 2-3 academic referees.

What we offer?

HICT is a network of world-class professors and researchers with huge passion for their field of study. In HICT you will become part of enthusiastic and professional team of bold and innovative thinkers.

During your Doctoral studies you will be a full-time employee in either Aalto University or the University of Helsinki depending on the supervisor and the research area. You will be covered by occupational health care based on the employment contract.

More information:

General information about the joint HICT call and HICT: https://hict.fi/

General questions about HICT: Christina Sirviö, HICT team

General questions about recruitment process: Sanni Kirmanen, Aalto University HR


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