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Tuomo Hartonen @tuomohartonen.bsky.social · 24d

Are you interested in pushing the limits of what population health "foundation model" could be used for? Would you like to study privacy and fairness of generative models that are trained on sensitive health data? Or combine this with your own ideas?

Two weeks left to apply to this PhD position 👇

Tuomo Hartonen @tuomohartonen.bsky.social · Aug 28

I am hiring! 🎓

We offer a fully funded PhD student position to work on exciting machine learning projects utilizing rich, multimodal real-life health data, based at @fimm-uh.bsky.social in Helsinki, Finland, the happiest country in the world 🇫🇮

jobs.helsinki.fi/job/Helsinki...

Feel free to DM me!

Doctoral researcher in generative AI for population health

jobs.helsinki.fi

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Tuomo Hartonen @tuomohartonen.bsky.social · Sep 10

You know those really annoying but really niche tasks? Like ordering a long author list and correctly numbering each affiliation and linking them to correct author to produce the final "authors and affiliations" block in a paper.

I never intent to do this manually again:

github.com/hartonen/mak...

GitHub - hartonen/make_author_list: This repository provides a Bash script that converts two simple text files (one describing authors and their affiliation keys, and another describing affiliation te...

This repository provides a Bash script that converts two simple text files (one describing authors and their affiliation keys, and another describing affiliation texts with keys) into a formatted s...

github.com

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Tuomo Hartonen @tuomohartonen.bsky.social · Sep 8

Thanks Kira!

Tuomo Hartonen @tuomohartonen.bsky.social · Sep 8

A new blog post 💡

Generative AI trained on 100M+ real health trajectories?! 🤖

open.substack.com/pub/tuomohar...

I am experimenting with this "short review" format where I aim at highlighting just a couple of quick point from an interesting paper. Let me know how it works!

Short review: "Generative Medical Event Models Improve with Scale."

This is my first try on this “short review” format.

open.substack.com

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Tuomo Hartonen @tuomohartonen.bsky.social · Sep 1

Here we looked into more automated modelling of EHR data, and also diseases with no clinical risk models. Perhaps this information could be utilized in addition to models we already have? And also where we do not yet have established risk models. In my opinion, both approaches are valuable.

Tuomo Hartonen @tuomohartonen.bsky.social · Sep 1

Absolutely, there are studies combining PGS with risk factors such blood pressure, smoking etc., often focusing on risk of one disease and thus going quite deep into that disease-specific risk factors. And we also mention this in the paper.

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Tuomo Hartonen @tuomohartonen.bsky.social · Sep 1

I could have worded it better I think. The main point we had was to look whether these two sources of information are complementary in prediction models, and it seemed to be the case.

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Tuomo Hartonen @tuomohartonen.bsky.social · Aug 28

I am hiring! 🎓

We offer a fully funded PhD student position to work on exciting machine learning projects utilizing rich, multimodal real-life health data, based at @fimm-uh.bsky.social in Helsinki, Finland, the happiest country in the world 🇫🇮

jobs.helsinki.fi/job/Helsinki...

Feel free to DM me!

Doctoral researcher in generative AI for population health

jobs.helsinki.fi

4 7

Tuomo Hartonen @tuomohartonen.bsky.social · Aug 27

In case you want to check a quick run-through of the main results, I have written a blog post summarizing just these:

tuomohartonen.substack.com/p/medical-re...

Medical records-based information and genetics are orthogonal predictors of disease risk

Instead of a review, this blog entry is a short summary about our own recently published paper.

tuomohartonen.substack.com

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Tuomo Hartonen @tuomohartonen.bsky.social · Aug 27

This was a nice collaborative effort within the INTERVENE consortium which I had the chance to co-lead together with @detroiki.bsky.social and @andganna.bsky.social with strong support from our colleagues from University of Tartu, Estonia!

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Tuomo Hartonen @tuomohartonen.bsky.social · Aug 27

Are electronic health records (EHR) more predictive of disease onset than polygenic scores? Can we transfer EHR-based prediction models between countries? Our study on these questions using 3 biobank-based studies with N>845K, is out in @natgenet.nature.com today:

www.nature.com/articles/s41...

Cross-biobank generalizability and accuracy of electronic health record-based predictors compared to polygenic scores - Nature Genetics

Comparison of electronic health record-based phenotype risk scores (PheRS) and polygenic scores (PGS) across 13 common diseases and three biobank-based studies indicates that PheRS and PGS may provide...

www.nature.com

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Tuomo Hartonen @tuomohartonen.bsky.social · Aug 22

I started an experiment: a blog in substack! My idea is to mainly post short reviews about interesting papers at the interface of AI and health sciences, but also stuff related to other aspects of science life.

The first post actually is of the latter category 👇

open.substack.com/pub/tuomohar...

Travelling to a scientific conference in Italy from Finland - without flying

As a scientist, flying to conferences and international meetings has for some time bothered me.

open.substack.com

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Reposted by Tuomo Hartonen

FinnGen @finngen.bsky.social · Aug 21

We are looking for a Data Scientist to support our clinically oriented research teams in generating insights from decades of rich, longitudinal health data. If you are inspired by the opportunity to contribute to cutting-edge research at a global scale, apply here:
jobs.helsinki.fi/job/Helsinki...

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Reposted by Tuomo Hartonen

Institute for Molecular Medicine Finland (FIMM) @fimm-uh.bsky.social · Aug 18

The Faculty of Biological and Environmental Sciences of @helsinki.fi invites applications for the position of

🟢 ASSISTANT PROFESSOR / ASSOCIATE PROFESSOR / PROFESSOR OF HUMAN GENETICS AND GENOMICS 🟢

with a possibility of a secondary affiliation with FIMM.

➡️ jobs.helsinki.fi/job/Helsinki...

University of Helsinki career ad with a blue chromosome and text: ‘Career Opportunity! Assistant Professor / Associate Professor or Professor of Human Genetics and Genomics. Apply by 10 Oct

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Reposted by Tuomo Hartonen

Institute for Molecular Medicine Finland (FIMM) @fimm-uh.bsky.social · Jun 19

Our warmest congratulations to all FIMM-affiliated researchers who have received funding from the winter call of the Research Council of Finland! 💐

Academy Projects: Olli Kallioniemi, @rafabolism.bsky.social & Esa Pitkänen
Research Fellowship: Tuomo Hartonen
Clinical Researcher: Pauli Pöyhönen

A congratulatory graphic from FIMM (Institute for Molecular Medicine Finland) announcing new grant recipients. The left side features a photo of a colorful bouquet in a white vase, framed by a white jagged border on a teal background. The top-left corner contains a black ribbon banner with a party popper icon and the text "FIMM CONGRATULATES". On the right, white text reads: "The Research Council of Finland has granted funding for new FIMM-driven Academy Projects, Research Fellowships and Clinical Researchers. Warm congratulations to all grant recipients!" Below, the names of the recipients are listed: Olli Kallioniemi, Rafa Najumudeen, Esa Pitkänen, Tuomo Hartonen & Pauli Pöyhönen.

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Tuomo Hartonen @tuomohartonen.bsky.social · May 26

Reminder to come check our work on sex-specific effects in human plasma proteome today at 4pm. The poster is located just behind the break area #eshg2025

Reposted by Tuomo Hartonen

Nature @nature.com · May 25

💍 The Gollum Effect: possessive behaviours, attempts to undermine others, and efforts to restrict access to data, resources or opportunities

https://go.nature.com/4mxAJvG

Science’s ‘Gollum effect’: PhDs bear brunt of territorial behaviour

Nature - Survey respondents at all career stages report colleagues engaging in territorial and possessive behaviours — but early-career researchers are most often affected.

go.nature.com

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Tuomo Hartonen @tuomohartonen.bsky.social · May 24

A big plus is for sure that one gets to enjoy the views much more than when flying! This is me soaking in the last rays of the sun on the sundeck of the ferry to Stockholm 😎 I think for many trips within Europe, flight is not always the only viable option. 13/13.

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Tuomo Hartonen @tuomohartonen.bsky.social · May 24

All in all, for this specific trip overland travel worked out very well without big downsides. Except that booking the trip was much more complicated, and Uni Helsinki travel agent only allows invoicing flight tickets directly from Uni, so overland travel costs one only gets back after the trip 12/n

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Tuomo Hartonen @tuomohartonen.bsky.social · May 24

Arrived to Milan just five minutes behind the original schedule!

In total the trip was around 2,700 km, and the overland travel saved ~70% of carbon emissions compared to flying. I also had to start the trip ~12 hours earlier and I missed the first morning session of the Milan conference. 11/n

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Reposted by Tuomo Hartonen

Andrea Ganna @andganna.bsky.social · May 24

Our team presentations at #eshg25 #eshg2025. looking forward!!

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Tuomo Hartonen @tuomohartonen.bsky.social · May 24

Final leg of the trip to Milan and #eshg2025 is well on its way! Enhoying the beautiful Swiss scenery 😍 10/n

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Reposted by Tuomo Hartonen

Brooke Wolford, PhD @bnwolford.bsky.social · May 23

The abstract deadline for #ASHG25 is fast approaching! Submit your science by June 9! 🧬

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Tuomo Hartonen @tuomohartonen.bsky.social · May 23

Did you know that some genetic males have plasma proteomes similar to those of genetic females and vice versa? What are the consequences of this?

Come discuss with me at our poster number P18.021.D on Monday 26.5. at 4pm-5pm at #ESHG2025

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Tuomo Hartonen @tuomohartonen.bsky.social · May 23

Here are the sources used for the computation. 9/n

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