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Here you can read about everything that's happening in the ISB Group.

Two-hour STRATIF-AI session in ISMH conference

Uncategorised Posted on Thu, May 23, 2024 16:17:07

Two days after STRATIF-AI was featured at the BME@LIU-day in Linköping, Sweden, it is featured again in the ISMH conference in Technirghiol, Rumania. In Linköping, we had a shared booth with SUND (the spin-off company that converts the digital twins to eHealth products), and produced a roll-up and a poster. This roll-up has now been transported to Rumania, together with Gunnar Cedersund, to be displayed at a 2h session at the ISMH conference. This happens today May 23, at 17-19, CET, and can be viewed online.

ISMH stands for the International Society of Medical Hydrology and Climatology. In other words, the conference deals with water-based treatments, such as spas (German: kurort), mineral waters, mud baths, as well as temperature-based treatments, such as saunas, ice-baths, etc. These are old traditional treatments, that dates back to ancient Greek, at the least, but there is also a growing scientific interest, with 10 times more papers published per year today, compared to 20 years ago. Still, the ISMH is old, by scientific standards, and the conference celebrated its 125th birthday yesterday. In the picture below, you see Prof, MD Gelu Onose, one of our main collaborators in STRATIF-AI, and also one of the the main organizer of the event, who cut the first piece of the cake, during yesterday’s celebration.

While the official motto of the conference is “Evidence-based balneology”, while there are lots of medical doctors and professors here, and while balneology is an established speciality in medicine in quite a few countries in Europe, it is still a field that lies on the fringes of medicine. For instance, in Sweden, balneology is not an established discipline of medicine, and MDs cannot become specialized in this field, as they can in e.g. cardiology, or hepatology. Therefore, balneology is to some extent similar to other alternative treatments, such as yoga, regular exercise and gym-based personal trainers, health coaches, etc. They exist in society, they work with health, there is some scientific support for the health benefits of these activities, but they are to a large extent not integrated in conventional healthcare. This is where the activities and visions of STRATIF-AI can contribute. Our ambition is to go from a doctor-centric fragmented system, to an integrated patient-centric eco-system system (see picture below). In this eco-system, e.g. personal trainers can take over where nurses leave a patient, following a health conversation (as in our clinical study 2 in STRATIF-AI). And in this eco-system, one can add new actors, such as spas and kurorts, as long as there is evidence that their methods work, and as long as the underlying mechanisms can be added to the digital twin’s models and visualizations.

The 2h session we will have is structured as follows: First, Gunnar Cedersund, the coordinator of STRATIF-AI gives an overview of STRATIF-AI, and of the digital twins, which converts knowledge and data to computational models. Thereafter Prof Gelu Onose from SCUBA (in the picture above), and his colleagues Constantin Munteanu and Cristina Popescu (both MDs), give an overview of the scientific basis for prevention and treatment of stroke using different modalities, including balneology. Thereafter, we look at the data integration aspects: Jesper Fellenius from Z2 gives an overview of the personal data vault, Cati Martinez from University of Murcia talks about their work with semantic harmonization and inter-operability, and SIMAVI talk about their work on Electronic Healthcare Records, and app developments, e.g. for rehabilitation of stroke. The session is concluded with a round-table discussion. All things can be followed online, at this link. The general link to the conference is available here.

BME@LIU day 2024

Uncategorised Posted on Mon, May 20, 2024 23:42:45

Tomorrow, May 21, 2024, we are arranging a new edition of the BME@LIU-day. BME stands for biomedical engineering, i.e. the interplay between biomedicine (from basic science to clinical practice) and engineering. In practice, BME, entails fields such as modelling and AI, digital twins, wearable sensors, new biomaterials, eHealth, bioinformatics, imaging, bio-optics, etc etc. BME is therefore also one of the core areas of LIU, and it is – in fact – one of the reasons why Linköping university (LIU) was founded, in 1975: to create a bridge between the needs for new engineers at SAAB, and the need for new biomedical research and personnel at the hospital. Around this need, LIU was founded, and at the heart of this dream of a bridge between these two worlds was the Department of Biomedical Engineering (IMT).

IMT eventually attracted Gunnar Cedersund, who started there gradually from around 2011, and then gradually moved his research group over to this department. IMT has since then also expanded its mission to support biomedical engineering beyond its own department, i.e. at the university level. And the arrangement of this BME@LIU-day is a central part of this new broader mission.

In practice, the day will feature a lot of activities at LiU, and also a lot of our own activities. For instance: at 10-10.30, postdoc William Lövfors and MD/Ph.D. student Valentin Kindesjö will introduce the latest developments of our digital twins, using a so-called double presentation where a clinician and an engineer each presents from their specific perspective. In the same session on modelling and AI, at 10.50-11.10, we also see presentations by our newly transitioned postdoc Nicolas Sundqvist, who will present a new story, where we quantify the importance of different cell types for the neurovascular coupling. Finally, also in that session, at 11.20-11.40, we have one of our newest postdocs, Dirk de Weerd, who presents a work he has done together with our incoming postdoc Rasmus Magnusson, on the usage of Variational AutoEncoders, to identify a compressed space for gene expression variations, and apply this to disease modelling. A final oral presentation, not by us, but by one of our closest collaborators, is that 10.50-11.10 by Jesper Fellenius, who will present his perspectives from 20 years of app developments for commercial companies (Ericsson, Swedbank etc) and his 75 MSEK development of a personal data vault. Link to the modelling presentation is here and link to Jesper’s session is here.

Finally, apart from oral presentations, we will also be featured in various places in the poster session combined with the arena. There will be 6 student-based posters, who present 6 large B.Sc. projects, on various modelling tasks within the digital twin development: i) on blood pressure and exercise, ii) on exercise and VO2max, iii) on dysfunctional fat storage in large adipocytes and liver fat, iv) on the neurovascular coupling, v) on drugs and cognitive function, and vi) on alcohol metabolism. Apart from that, there will be many other research-based posters from our group. Finally, we will also – for the first time – be featured not only by our original spin-off company SUND sound medical decisions, but by the newly created daughter company with Z2 and Johan Holmsäter – with the working title Lev Skönare.

All these companies and research projects will be featured with oral presentations, posters, or exhibitions, where you also can test to create your own digital twin, if you want.


Gunnar Cedersund, chair of the program committee

Lecture on Friday May 17 in the NBIS AI seminar series

Events, News, Systems biology and science Posted on Thu, May 16, 2024 11:25:59

On Friday, Gunnar Cedersund will give a lecture in the NBIS AI seminar series. NBIS is the National Bioinformatics Infrastructure Sweden, which is a core-facility spread out over all universities in Sweden. In other words, at each university in Sweden, there are some local bioinformaticians located, which helps out in projects. NBIS also arranges a seminar series on artificial intelligence (AI), and the next such lecture – on Friday May 17, at 10AM CET – features Gunnar Cedersund. Gunnar will talk about our digital twins, and about how they can be used to integrate a variety of data, both classical bioinformatics multi-omics data and behavioral and imaging data, into a personal data vault, and into a personalized copy of a patients. More information, abstract, and link to the online lecture is available here:

Double jackpot from Swedish Research Council – glowing 3R project reviews

Uncategorised Posted on Tue, November 07, 2023 02:25:35

This year, we got a double jackpot from the Swedish Research Council – who gave us glowing reviews for the 3R project, scaling from microphysiological in vitro systems to humans using scalable digital twins.

In Sweden, the Swedish Research Council (Swe: Vetenskapsrådet, VR), is the most central research grant, and it is often considered a key quality stamp of a top researcher to have at least one grant from VR. Therefore, competition is usually fierce (acceptance rate usually is 5-15%), and it is not at all guaranteed that you get money, even if you have a competitive application. Therefore, I am proud to say that this year, I got not only one grant, but two – and that the evaluation from the reviewers was unusually high and glowing.

The project I have gotten the review responses for so far is a special call on 3R, i.e. Replacement, Reduction and Refinement of animal experiments. This is a topic, I have been very active in ever since 2015, when I was awarded the first edition of the prize “Nytänkaren” (the thinker of new ideas), by the Swedish Fund for Research without Animal Experiments. The project extends on our experimental work, both within the group, doing cell biology cultures using 13C-labelled metabolites on liver and adipose tissue taken from surgery), and that in collaboration with AstraZeneca, centered around organs-on-a-chip, i.e. small microphysiological systems (MPS), with organoids and spheroids consisting of human cells (Fig A, recent paper). In the project, we will i) analyse these in vitro data using mechanistic modelling to get more information out of the data (e.g. metabolic fluxes), ii) plan new experiments, by first doing the experiments in the computer, and iii) translate the results to humans, by e.g. scaling the volumes of the spheroids to human sizes, and by adding the missing organs, which allows us to re-assemble the digital twin in the computer (Fig B-C, Step 1 and 2). The project will evaluate and quantify the benefits of this for e.g. drug development, and we will disseminate the results to pharma, scientists, and regulatory agencies (Fig C, Step 3).

In the evaluation, we only got 6s and 7s, which means that we were among the highest rated of all applicants, even among the few who got money (6 out of 56). The ranking is from 1-7, where a “normal, decent” scientist usually get a 3 (meaning “good”), and where you need at least a mixture of 5s and 6s to have any chance of getting money. If you get all 6s, you are usually getting the money for sure, and 7 is only very rarely given out (I was a reviewer for ~60 applicants two years ago, and then I think only one or possibly two got a 7 on any criterion). Therefore, I am very grateful that this year, I got only 6s and higher, and that two(!) categories got a 7: “merits of applicant” and “relevance for 3R” (Fig D). If the rating levels were the same as when I was a reviewer, I would – I think – have been number one of all applicants that year, and in any case, I must have been among the very top of all the 56 applicants also this year.

The life of a scientist is filled with many many rejected applications, so when you get a jackpot once in a while, it is important to stop a bit – and celebrate! Because tomorrow, it is time to get started working on the new exciting research projects! 🙂

Concluding keynote at Data-driven mechanistic modelling in life sciences

Uncategorised Posted on Mon, October 30, 2023 17:00:09

Last week, I had the honor of giving the concluding keynote lecture at the event “Data-driven mechanistic modelling in life sciences”. This follows a trend of being invited to give more and more keynote and plenary lectures at events, for which I am very grateful. Such longer lectures also give me the chance to expand a little bit more on my point-of-view. The focus of this particular workshop is also something I am very keen to promote, since I think that this particular overlap (mechanistic and data-driven modelling) is under-represented in many communities and conferences.

The centrality of this overlap is actually seen even in our group logo (Fig A). a) The fact that it has an open non-black box, represents the fact that we do mechanistic modelling. b) The data-driven aspect of our models is represent by the purple core in the middle, which represents the fact that we always look for core predictions. Core predictions are predictions that are well-determined from the current prior knowledge and data, even when taking all uncertainties in data and prior knowledge into account.

While I personally think that this is the way to work, and while we have a very well-established workflow for how to develop models in this fashion, mechanistic modelling and data-driven modelling are unfortunately often done in two disjoint communities, with too little overlap (Fig B). Mechanistic modelling often results in mere simulation-based results, which have not been validated using independent data, i.e. data that has not been used to train the model. This is often the case for e.g. PDE and agent-based models, but also common in e.g. theoretical ecology, theoretical biology, etc. It was therefore encouraging too see that one of the presentations at the workshop (by Joshua Bull) looked at spatial models, and on how to quantify the comparison between simulations and data also for spatial models. Data-driven modelling is too often interpreted to mean only machine-learning, narrow AI, and other black-box modelling techniques. While these are big and very hyped communities and approaches at the moment, they are not the only techniques that can be used to do data-driven modelling. In other words, while these black-box models include important techniques, which are useful if one has standardized large-scale data, they also have critical short-comings. Black-box models e.g. have big problems incorporating the type of data that is present in most biological papers, including the prior that is knowledge available. For these reasons, explainability and trustworthiness are challenges. I therefore think that hybrid modelling is the way forward (see e.g. this review, and this example). At the conference, there was also an excellent opening keynote of day 2, by Alvaro Köhn-Luque, which showed some additional and interesting examples of hybrid models.

Invited lecture (and possibly teaser-performance) in upcoming MBM workshop

Events, News Posted on Thu, September 10, 2020 00:57:45

There are quite a few public lectures planned for this autumn, and one of the ones I am looking forward to a little bit extra is the MBM workshop, in Gothenburg, on October 15-16, 2020. MBM stands for Modelling in Biology and Medicine, and this is the second edition of the workshop. The workshop started as an initiative by a couple of enthusiastic Ph.D. students at the Math Department at Chalmers/Gothenburg University. But since it turned out so successful, they easily got both the support by the more senior leadership at the department, and enough positive feedback to decide to do a second edition. I really liked attending it last year, both since it was a Swedish workshop on systems biology, which means that it helps foster and grow the Swedish systems biology community, and since they managed to create a nice and cosy athmosphere. Partially because of this, the post-conference informal conversations last year led to me mentioning some of the bigger plans I am working on, which are going to become more public this year.

My dual life: scientist by day, pianist by night. Now they are starting to come together at last!

Those plans involve me combining my science and create careers into one, by doing joint lecture-performances, mixing piano, dancing, and digital twin-based stories. The original plan for this year’s workshop was to do some version of such a lecture-performance at the physical workshop. But since the physical edition had to be cancelled – due to the pandemic – the lecture will be held online. Nevertheless, in the presentation text of me at the home page, my CV covers – for the first time in a scientific event! – both my science and creative careers are mentioned side by side, and as two parts of the same thing. Already this feels really cool! And during the lecture, I plan to say, and probably also show, something short about those new and border-crossing plans in action. The workshop is held completely online, so you will be able to see it, also if you are not living in Sweden. And, later in the autumn, a more proper trailer for the first such lecture-performance will be released. The first proper such lecture-performance is planned be held during the autumn of 2021.

An exciting autumn awaits! And, the workshop is still open for abstract submissions!


New grant: 2 MSEK from ELLIIT “Usable digital twins in healthcare”

News Posted on Tue, September 08, 2020 00:28:07

We have gotten a new grant! The money this time comes from ELLIIT, which is a joint technology programme for Linköping, Lund, Halmstad University, and Blekinge Institute of Technology. The project we applied for is called “Usable digital twins in healthcare“, and it will focus on solving the many different practical challenges involved in bringing our digital twins into actual clinical practice: involving e.g. legal, technical, and ethical issues. A summary of the project and its main steps is given in the figure below. The funding is 2 MSEK, i.e. 200 kEUR/kUSD over a two-year period.

Upcoming lecture in new European webinar series on 3R, Sept 22-24

3R and animal experiments, Events, News Posted on Sun, September 06, 2020 22:56:51

A new international webinar series on 3R – replacement, reduction, and refinement of animal experiments – is about to start! And we are present with a lecture!

From our group, Gunnar Cedersund and Elin Nyman are members of the National Committee on 3Rs, which also serves as the steering committee for the Swedish 3R center (S3RC). Our S3RC has now joined forces with a few other corresponding national centres, and this has led to the launch of a new webinar series. The first edition of this will take place on Sept 22-24, lunch times i.e. 12.30-13.30 CET. Gunnar will present a lecture on digital twins on the last day, i.e. Sept 24.

This is a great initiative, and I hope it will be the start of more collaborations between the centres!

More info, and sign-up here.

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