Progress reports

Research update – lab website, papers & webinar

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A lot has been happening in research life the last year! In this post I’m sharing a couple of recent updates.

Lab website

In 2022 three people – Bethany, Dovile in January, and Amelia in August, joined the lab. Although I used the name “PURRlab” already when I was in Eindhoven, this time we went a bit further and made our own lab website and everything.

Papers

The latest news is that the paper on shortcuts in chest X-rays (see preprint), led by Amelia, has been accepted at ISBI 2023! Here’s a tweetorial by Amelia about the work.

There are more preprints coming up in the next few months on various topics related to datasets, transfer learning, bias, and understanding ML researchers.

Webinar

We are also organizing a webinar series where we want to take a deeper look into the datasets used in machine learning for healthcare. In the first edition we have three speakers who will talk about their work on skin lesions datasets, but we will be exploring other applications in future editions. If you want to stay updated, we have a newsletter you can sign up for on the webinar page. Thanks to Eike Petersen (DTU) for help with the setup!

-Veronika

I’m on Mastodon, and I love it

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Things are happening quickly on the bird site! Time for a blog.

When the possible acquisition was announced back in April, I created my Mastodon account at scholar.social. (If you haven’t heard of Mastodon, there are various great guides, for example here and here). Back in April it was a bit quiet and I didn’t use it much, but things feel different this time.

My bird account dates back to 2010, but I only really started using it in 2015 or so, as a postdoc. I was struggling in various ways during that time (not a secret, but not the point now, if you are curious you can infer a few things from my shadow CV). But with #AcademicTwitter, I found a community, and it had a lot of impact on me as a person. Being there led to many good things, and I even wrote a paper and gave some talks about it.

Twitter changed a lot since then. I did my best to keep my experience algorithm-free, by using a chronological timeline, muting suggested tweets and such (example). I like to think I was quite successful in this, because my Twitter experience has been good. But the recent activity on Mastodon made me realize that recently my Twitter experience wasn’t great.

I don’t want to get into too many details right now on why I think Twitter is not a good place to stay or trying to convince others about this. Perhaps it’s worth mentioning I hard quit various social apps a few years ago, due to both mental health and ethical considerations, and more recently I’ve replaced many big tech services with open source alternatives. All of this has been great, so if it seems surprising that I’m not so lyrical about Twitter right now, it’s actually not.

With my reasons, a few weeks ago I dusted off my account on scholar.social, and I absolutely love it. I found things that I remember from “early Twitter”, like connecting about niche topics. There are no ads, no algorithmic suggestions, and lots of helpful people. There is a feeling of excitement, like we are all going on a road trip. I genuinely missed this feeling, and didn’t even realize it – until the recent events became the catalyst. I’d like this feeling to stay, and I want to contribute to building the community. I did already move instances to dair-community.social, as I’ve excited to see their local timeline. So from now on you will mainly find me @DrVeronikaCH@dair-community.social, and of course, this blog 🙂

10 things I miss about The Netherlands

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Later this week it will be 1.5 years since I moved to Denmark, and a Twitter poll told me that you would like to hear what I miss about The Netherlands (NL)! It goes without saying that of course I miss many people there who I don’t get to see as often! But here are 10 things about NL that perhaps I was not expecting to miss.

1 – Healthcare professionals who listen to me

I’ve had to deal with a number of both physical and mental health issues in recent years, and in NL I finally felt like I was getting the care that I needed. To put this mildly, the level of ignorance both me and my husband encountered here would be the number one reason for us to go back, and to advise anyone in similar situations to stay away. I don’t want to go into all the details, but perhaps the best example is my psychiatrist saying “I don’t remember what dose you are on but just double it” about lithium, after I had described the adverse side effects I’ve been experiencing.

2 – The train connections

I like travelling by train and although Denmark has good connections to Sweden and Germany, it was easier to reach more places directly from NL – London in 4 hours, Paris in 3, Berlin in 6 and so on.

3 – The tap water

Tap water in Denmark is safe to drink, but has high concentrations of minerals (safe but annoying to deal with due to the limescale build-up) and the tap water in NL just somehow tastes better to me.

4 – My go-to shops

In NL I developed a list of places that I’d buy a lot of basics, that I haven’t quite found good replacements for here. My top three are (the links go to Wikipedia for some more information about the stores):

  • Decathlon, which sells sports and hiking equipment, mostly of in-house brands which have great designs but are a lot cheaper. Decathlon exists in 60 countries, but not in Denmark, and none of the neighbouring countries want to ship here.
  • Hema, which sells pretty much everything, again with own designs and great prices. It is a Dutch store that has a few stores in other countries. I haven’t tried shipping yet, but there is also something nice in just browsing there in person.
  • Amazing Oriental, a grocery store with food and drinks from many Asian cuisines. I’ve found smaller stores here in Copenhagen, but none that have quite the same range of products in one place.

5 – The freshest vegetables

NL produces a lot of vegetables, and they stay good longer, compared to some vegetables that Denmark imports from Spain, or, yes, The Netherlands. Or maybe it’s just the grocery store next to my place. I don’t miss a lot of specific foods otherwise, maybe except proper pindakaas (“peanut cheese”).

6 – Sauna complexes

You would think that the proximity to other Nordic countries would mean this is a thing here. Yes, there are saunas, but mostly as a “side” to swimming, and/or by the hour, and/or are “not a real sauna” according to my Swedish husband. I’m talking about complexes where you buy a day pass and can go to multiple saunas, hot baths, cold baths, a restaurant, and so on – popular in NL and I think at least in a part of Germany.

7 – At least 5K EUR extra that used to be in my bank account

Although I received some moving allowance from ITU, it just covered the cost of the movers driving here with our things, and we did all of the packing etc ourselves to reduce costs. But with a few trips back to NL with certified PCR tests at each end, not being to go across country borders when originally planned, and ultimately furnishing an entire apartment in a few days, it was even a more expensive & stressful exercise than moving countries is otherwise. To be fair, this was not entirely unexpected, and one of the reasons I never understood how some senior academics expect juniors to just go and do that multiple times (the other is healthcare, as per point 1).

8 – DIY-ing the place I live

Alterations are not allowed in many? rentals, therefore also not where I live now. I miss being able to attach things to walls, ceilings, and other existing structures. First thing I’m doing when this is possible again, is getting one of those ceiling bridges for the cats.

9 – A scheduled lunch break

Lunch food in Denmark is much better – I was never quite satisfied with NL’s selection of bread with cheese and milk (yes, really). But at least in Dutch universities there is a lunch break, say from 12:30 to 13:30, when no classes are scheduled. If a “lunch meeting” is scheduled, usually said meeting will at least have the bread/cheese/milk on offer. Here classes start at even hour blocks (8am, 10am, 12pm, 2pm, 4pm) and it can be difficult to meet with colleagues who are teaching or have regular meetings without food at 12pm.

10 – Oranjekoorts a.k.a. “Orange fever”

A thing that happens during King’s (previously Queen’s) day, and whenever NL plays football where everybody dresses up in orange and paints Dutch flags on their face and it’s a big party, like so:

A woman and a man in their thirties, wearing orange clothes, red/white/blue flags on their faces and red/white/blue flower guirlands.

Postdoc position in machine learning & image analysis

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Last year next to the NovoNordisk starting grant which funded two PhD positions, I was also lucky enough to be awarded the Inge Lehmann grant from the Independent Research Fund of Denmark, where I will be hiring a postdoc!

The project is titled “Making Metadata Count” and aims to investigate the role of metadata in machine learning methods for medical images. This includes both “traditional” metadata like patient age, and other image information, like the presence surgical markers. This is a 3 year position starting October 2022 (negotiable), and the call closes on the 30th of April – for full details please see the vacancy on ITU’s website.

Please forward to anyone interested in doing research with me in Denmark! To apply, please go through the HR system above, or get in touch via vech AT itu.dk if you have any questions.

7 things I wish I would have done during my tenure track

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Recently I’ve seen some Twitter threads on advice for new PhDs/postdocs/PIs. I’ve shared this about my PhD before (see 7 things I wish I would have done during my PhD), and in my current job I’ve been reflecting a bit about how my previous job went, I thought I would also share the 7 things I wish I would have done during my tenure track!

They are:

  1. Being in the office less
  2. Not agreeing to only teach undergraduate courses
  3. Spending less energy on grants
  4. Divorcing my email accounts
  5. Getting a Macbook
  6. More papers with people from Twitter
  7. Sharing more work online

1 Being in the office less

After starting my tenure track in February 2017, my best-case scenario day would look like this: I would leave my house in Rotterdam at 7:20, to take the train and get to the office at 9:00. Similarly I would leave at 16:50 and get home at 18:30, in time for dinner. There were sometimes disruptions, with me arriving 1-2 hours late in either direction. Maybe not too bad considering depending from where in the world you are reading. And as a plus I could work in the train – I would often read or draft blog posts.

After two years of working at home, I cannot imagine being able to do these kind of hours again. Although I was already quite mindful of the hours I would spend on my job, I didn’t realize that doing productive things in the train also counted, and that I probably was not getting enough rest. I also don’t really understand why I felt it was necessary, as I wasn’t required to be in the office on specific days or hours unless I was teaching or had other meetings.

2 Not agreeing to only teach undergraduate courses

For the first three years, I was the course manager of a first year BSc project and taught in another third year BSc course. I enjoy teaching at multiple levels, but I think I shot myself in the foot a bit here. As I had no start-up, PhD students to co-supervise, etc, the main way to start new projects was to supervise MSc students. But since I wasn’t a person the then-MSc students were aware of, recruiting such students was rather difficult.

3 Spending less energy on grants

Funny given that during my PhD I wish I had “applied to all the things”! As part of my tenure track conditions I had to apply for two “medium” (1 PhD position size) grants a year, which was reasonable, and it was useful to think about the project proposal. But several of these applications were doomed to fail, as even with a perfect score on the research proposal, my CV just was not “good enough” to get funding. Given that there weren’t many other opportunities to apply for, I guess overall this was still a useful experience, but I definitely could have spent less time on writing workshops, endless revisions etc.

Another advice was to apply for all possible small grants (workshops, collaborations) that I could get. I did that and actually got several of the things I applied for. But this was too much – relative to larger proposals, these cost more time to write, AND require more work from you after, without the option of hiring somebody to help.

4 Divorcing my email accounts

I used be very much a “one inbox” kind of person, and forwarded my university email to my Gmail. But with a new job and email account, I decided to try it out. Although Gmail has a much better interface than Outlook (don’t get me started on this…), I like it a lot. I don’t have Outlook on my phone, so I mainly have access to my work email during my work hours. This frees up a bit of headspace during time off, which I would often already use to mentally draft emails, thus spending way more energy on emails overall.

5. Getting a Macbook

Similarly to me trying out a different strategy with emails, I felt brave enough to try out a Macbook after a lifetime of Windows. It’s kind of great, I’m still pretty inept at using shortcuts etc, but I don’t imagine going back anytime soon.

6. Starting more papers with people from Twitter

One of the most satisfying things in my career has been to work with people met on Twitter. The prime example is probably this paper about Twitter – some of us have met each other beforehand but I feel safe to say this was a Twitter collaboration.

Another highlight was this preprint with Gaël – it started because I agreed with him about AI being hyped too much and said “we should write a paper about this”. A longer revised version has just been accepted so keep an eye out.

I like slow science, so there are other projects that are amazing and that started on Twitter but are not out yet. Stay tuned 🙂

7.Sharing more work online

This perhaps sounds surprising since I share preprints, slides etc and would even write blog posts on a more-regular basis. But I still see so many things that I’ve done that could be possibly useful to others, that I did not share, either because the thing needed a bit more input (for example going from an undergraduate project to a preprint), or simply because I didn’t get around to it (for example rejected grant proposals).

I am not sure I will ever get to a point where I’m doing this better, but as usual, if there is something I have that might be helpful to you, just ask.

***

This is just my list! There are also a few issues others mentioned in the Twitter discussion that maybe I did OK with? and are therefore not on this page – but that’s for another blog post 🙂

Two PhD positions in medical imaging

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I’m happy to announce that NovoNordisk Fonden recently funded by project “CATS: Choosing a Transfer Source for medical image classification”, which means I will be hiring two PhD students in the coming months!

The project is inspired by my earlier paper “Cats or CAT scans: Transfer learning from natural or medical image source data sets?” [also on arXiV] where I showed that there is no consensus on how to select a source dataset to initialize weights of a model, that will be further trained on medical imaging.

The project will focus on investigating dataset similarities, which will help us define how to select a good source dataset, and PhDs 1 & 2 will investigate different approaches to defining this similarity.

I am looking for two PhD students with different backgrounds (math/computer science, and psychology/computational social sciences) for the project. You can view the vacancies here (closing date July 31st):

  • PhD 1 (maths/computer science)
  • PhD 2 (psychology/social sciences)

Please forward to any interested candidates! To apply, please go through the HR system above, but I am happy to answer questions about the project, just drop me an email 🙂

Hello, tenure!

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I’m excited to announce that as of 1st of February 2021, I will start as a tenured associate professor at the IT University of Copenhagen!

How?

This is an unexpected turn of events, even for myself. When I announced I was leaving my tenure track position in May, I was not planning to look for a faculty position. I was still interested in doing research, but also thought I’d look at positions in data science or research support.

My announcement led to a lot of people on Twitter suggesting different (both academic and non-academic) positions to me. Among these were three faculty positions that were strongly recommended to me AND which seemed to have better conditions than my tenure track. As I already had an updated CV, I decided to apply, and was successful in getting an interview at all three. In two cases, the conditions were not as I imagined after all, and I stepped out of the interview process.

At ITU the process was a lot slower than what I’m used to, so I sort of forgot about it. Instead I was focusing on positions related to open science, and got to know a great community in the Netherlands, which I would still wholeheartedly recommend. Just as I decided this would be my next job, I got notified that I qualified for a tenured associate position.

Why?

This is a big deal! But given my experiences in academia, I was still quite skeptical whether this was something I wanted to do at all. But, still hurting from failing my tenure track, I was also intrigued to find out why they wanted to hire me 🙂 What’s another virtual interview, after all?

The interviews changed my mind. I haven’t felt this much “at home” in a while – I could just be myself, with all my opinions about machine learning and academia, and they still wanted to have me. About half of the interview time was spent on values, which tells me this is a good place.

So although I never searched for this, feeling valued like this gives me motivation to try again. It’s ironic that all of this happened while all Dutch universities are discussing “recognition and rewards” and how to increase the numbers of women. It turns out you can just do it. Of course I can’t predict how things will be going forward, but I’m grateful for the support and trust I received from ITU so far.

What’s next?

Going forward, I will still do research on learning with limited labeled data, but I will be focusing on understanding similarities and differences between datasets (meta-learning), but also on a more abstract level, between communities (science of science or meta-science). I believe it’s important to understand what is (not) being studied and why, so that we can make science more open and inclusive.

I will also still be continuing with workshops on failure, although things might be a little slower as I get settled in. And of course, you can always following my updates on this blog and on Twitter.

Goodbye, tenure track

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I wasn’t sure about sharing this, but in the original spirit of my blog, that I ought to. 

I am leaving my tenure track position. 

There it is. It feels good to write it down. There are a lot of failure related thoughts here, which I will be sharing in future posts. But first, a bit of background about what happened. 

Tenure criteria 

In the previous post I wrote about starting my tenure track position and what I was planning to achieve in 4 years. To recap, here is summary of the goals, which were approved by the department

  • Get teaching certificate
  • Setup and teach a course, co-teach in other courses
  • Supervise at least 2 MSc and 4 BSc students
  • Co-supervise a PhD researcher
  • Co-author of at least 5 peer-reviewed publications in high impact, relevant journals
  • Setup collaborations with other departments 
  • Apply for 2 medium-sized (1 PhD or postdoc) grants per year
  • Apply to small grants, for example for workshops, when possible
  • Give talks at (local) conferences, or invited talks if possible
  • Outreach about academia through blog and Twitter 

Progress so far

As far as teaching goes, all goals are achieved. I setup a course, taught in another course (both 3 years in a row now), and recently gave a number of lectures in a MSc course. So far I supervised 5 MSc students and 12 BSc students. I’m the daily supervisor of two PhD researchers, one based on my own funding efforts.  I also received my university teaching qualification in 2019. 

Research-wise, things are alright. I published six journal papers and one preprint, but it could be argued that some of these do not count. For example three were started during my postdoc, although I put in more hours during my tenure track. There’s also the Twitter paper, which is not on the topic of my research, but probably has had more impact than the others combined. I am also quite happy with my Google scholar numbers.

I am not sure about the funding. I applied for two larger grants per year as agreed, and 1 of these was funded. The others are in my failure CV. This is in line with the overall success rate, and several smaller grants were funded as well. But I have the feeling this is not sufficient, even though the tenure criteria do not specify it.

In terms of visibility, things are good. Especially in the first two years when I was blogging regularly, my website and Twitter were growing steadily. I think this has contributed to invitations for talks, and I have given more talks, including international ones, than I ever expected. I’ve also been invited as an associate editor, social media chair and other similar roles. 

So overall, not bad, considering that in my third year I was seriously ill and I spent several months recovering, which was extremely difficult. Even so I did get a few things done in that time, such as the teaching certificate. Overall, things could have been better, but given that I had no start-up nor PhD researchers I could co-supervise from the start, overall I’m actually quite happy with what I achieved.

Perhaps here I should mention two other developments. The first is the artificial intelligence “brain drain” in the Netherlands, limiting the number of people willing to teach. The second is a position paper by several organizations (including funding agencies), that aims to redesign how researchers are evaluated, and to recognize factors other than the h-index. Music to my ears.

Midway evaluation 

As I explained in the previous post, traditionally there is a midway evaluation halfway through the tenure track, to see what else is needed to fulfill the tenure criteria. My midway evaluation was scheduled for May 2019, but a month before that I became ill, so this was cancelled.

Towards the end of 2019 I was working full-time again. The idea was to schedule an unofficial midway evaluation, a year ahead of the final evaluation. I gave a talk about my research and updated my CV and progress document (summarized above).   

Given this information, the committee advised that, I will probably not get tenure if I have the final evaluation as planned in 2021. The proposed solution was to give me a temporary contract and have the final evaluation later, so that I have more time for, between the lines, getting funding and writing more papers. 

Tenure clock extension, that’s good right?

Although to many readers this extension might sound good, I declined the offer. I will therefore be leaving my tenure track position.

The first reason for this decision is the uncertainty. I believe that the trigger for my manic episode was staying up at night to write grants, and I don’t want my life to depend on a lottery. There is also no definition of what “enough” would be, and that once I achieve those things, I would get tenure.

Secondly, I feel like my illness is a bad excuse that there wasn’t enough time to evaluate me. But people are at times evaluated after two or three years – researchers who are employed by the same university before starting a tenure track position, due to the labor laws.

But most importantly, I don’t want to be in a place with such priorities. I have achieved most goals on my list – goals that were agreed upon at the beginning – despite having a major illness. I will not be an award-winning researcher, but I feel – and people have told me – that the things I do are valuable. If the university does not see this, I need to find a place that does.

What next?

My current contract runs out at the start of 2022, but since I made this decision already, I will probably leave earlier.

For now I will be finishing up various projects, and slowly searching for a job.

So dear readers, I am now officially open for job opportunities! I don’t want to limit myself to specific job titles or sectors just yet. So if you think you could use my research, teaching, outreach, organizing, blogging skills (academic CV here), please get in touch.

That’s it for now, but expect more failure-inspired content soon!

Year in review: 2019 – tenure track year 3

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Although I wrote yearly reviews on this blog for several years, I wasn’t expecting to do one this year for two reasons. The first, simple, reason is that I haven’t been blogging recently, and just doing nothing is easier than doing something. The second, more complex reason, is that I might have been afraid to think about this year as a whole. But that is exactly the type of thing that I find important to write about, so here we go.

Mental health

The first thing I have to think about is the manic episode I had in spring which I wrote about earlier, and my diagnosis as bipolar. Mental health issues were not new to me, but this experience was extreme. Although I was stable once I got medication, it felt like parts of my brain had shut off.

Things that were simple before – organizing my todo list, for example – felt completely impossible. I also had let go of many good habits, like running, eating healthy or blogging – pretty much anything I used to write about. I’ve also isolated myself from a lot of people, and felt insecure about most things that I’m normally comfortable with. While my ability to do such things has improved somewhat, more general qualities, like creativity and motivation, did not.

I was only part of the person that I used to be, and this was extremely hard to deal with.

The fact that I am writing this now, probably means that these things are improving too, just at a slower pace. But not feeling this improvement had a huge effect on how I felt this year. Even though a lot of positive things happened, I was often feeling too miserable to properly appreciate them.

Successes

To try to beat that overall feeling, here are a few professional things that went well this year:

  • Received my University Teaching Qualification (a prerequisite for tenure at Dutch universities)
  • Two MSc students graduated!
  • Started supervising two PhD researchers four MSc students (one of whom graduated)
  • My papers on not-so-supervised learning and “Cats or CAT scans” were published and gained a few citations so far (checking Google Scholar way too often)
  • Together with Felienne Hermans, Casper Albers, Natalia Bielczyk and Ionica Smeets, our paper “10 simple rules for starting on Twitter as a scientist” was accepted (online soon!).
  • Together with Natalia Bielczyk, Aidan Budd and Stephan Heunis we got a Mozilla mini-grant and organized a workshop about open & inclusive academia.
  • Visited several places where I gave talks, both on machine learning and topics related to this blog.

Also, an important personal milestone – I got married!

Failures?

When I first started summarizing the positive things I felt guilty. There are many things to be grateful for, but my brain just couldn’t see it that way. In the transition from manic to depressed, I felt bad about many ideas I initiated, but couldn’t follow through on. Afterwards, I felt bad about not doing my part, or not keeping up with my responsibilities. I felt anxious about things I’ve done lots of times.

In retrospect perhaps these things themselves are not failures, the overall failure is that I expected too much of myself. It would have been much better for me to accept how much I’m (not) able to do, let go of everything else, and have patience. Which is why crucial part to this year were the people who experienced me from up close – they were understanding and patient and kind. It’s thanks to them that I’m actually doing alright after what happened, and I’m grateful they are in my life.

Happy new year!

How I was diagnosed as bipolar

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If you read this blog more often, you might have noticed that it went silent in March 2019. I’ve taken breaks from blogging before, but no break was quite like this, and in this post I explain why.

Although I never wrote about it in detail, I also never made a secret out of the fact that I have been struggling with depression since my postdoc. I had therapy for some of the time and was in general managing things quite well – doing my job, blogging, doing sports, having a social life. The current me almost can’t believe I was able to do all those things. 

In the second half of 2018 things started getting worse. After my cat Buffy passed away in October 2018, I was at an extremely low point and finally decided therapy alone wouldn’t do. My GP prescribed me antidepressants and I started a period of sick leave (full-time at first, part-time later) to adjust.

The antidepressants seemed to be doing an amazing job – the start was slow, but then I started feeling better and better. I soon went back to working full-time, was getting a lot done and had a lot of fresh ideas. I realized I was probably depressed for longer than I thought, and that I was now returning to the “normal” me. This was exciting for me, but somewhat confusing for many people around me, many of whom had not known me that long. 

Eventually – around March – I started feeling a bit too good. The ideas were coming at me so fast I couldn’t keep up, and neither could people interacting with me. My partner recognized this as hypomania, and following a GP visit I was told to stop the antidepressants. The GP also gave me a referral to the psychiatrist, but I ended up on a waiting list. Meanwhile, I was getting more and more out of balance.

The grand finale was a psychotic episode, during which I was convinced that people I’ve never met were giving me clues I had to follow. To top it off, this happened while I was travelling alone. After a few days in a psychiatric facility in France, I was able to return home again, going back on sick leave full-time. The bright side of this episode is that I could see a psychiatrist immediately, who diagnosed me with bipolar disorder.

Now I am getting used to the new medication to stabilize my mood. Although the effects were noticeable straight away and I feel “normal” again, it has been difficult to go back to my regular life with work, blogging, sports, etc, feeling like an impostor in everything. I’m trying to accept that this is normal, and slowly building things up again. I am therefore not sure when the next post might be – but I’ll celebrate that this post is a win.

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