research

Cats in my research

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I have had the idea to post this for a while, but now it’s finally happening! Somebody on Mastodon is going to write a review of cats appearing in papers, so the best I can do is provide references 🙂 Here are some ways I added cats to my papers, in chronological order.

2013 – Cat mention

Three years into my PhD is the first mention of cats in my papers. In “Combining Instance Information to Classify Bags” (PDF here) which is about my PhD topic of multiple instance learning, I write “For example, an image labeled as “cat” would have a cat in at least one of its segments, whereas images without this label would not portray any cats at all“.

I’m not sure whether this was a coincidence or intentional. But more cats happened in the years after!

2015

In 2015 I finished my PhD thesis, and the cover of the thesis features a puzzle with cat illustrations! The puzzle could have worked with any kind of illustration, so the cats were definitely intentional. Thanks to Hella Hekkelman who made the illustration.

Unfolded book cover titled "Dissimilarity-Based Multiple Instance Learning" by Veronika Cheplygina, both front and back covers have groups of cartoon cats on them.

I also added my cat Buffy to the thesis acknowledgments!

2019

Probably the biggest achievement of my career – I wrote a paped titled “Cats or CAT scans: transfer learning from medical or natural image source datasets” (PDF here) AND inserted a picture of my cat Buffy (by then over the rainbow) into it. Here is Buffy pretending to be an image from ImageNet:

2020

More images of Buffy, now occupying the whole figure, in “Ten simple rules for getting started on Twitter as an academic“. Now teaching the reader about cat-related hashtags like #AcademicsWithCats and #Caturday.

2021

Based on the work about transfer learning I stared a few years before, I received a grant from the Novo Nordisk Foundation called “CATS: Choosing A Transfer Source for medical image classification”.

2022

More Buffy, promoting self-care in “Ten simple rules for failing successfully in academia“.

More cats?

That’s it as far as I can remember, but Pixel and Dot definitely deserve paper appearances as well, so keep an eye out for that 🙂

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

Reader Q&A: choosing your advisor and topic

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In today’s post I’m answering some questions from readers of this blog, on choosing an advisor and research topics. As a caveat, for me both things just “happened” so I am not the best person to give advice, but I did think of some tips that could be useful.

1. How to choose your advisor?

I think the lab where you will do your PhD is the most important factor for choosing a particular position. A large part of this is the advisor, but also the general atmosphere in the lab. That being said, it can be difficult to figure these things out in advance, if you are not already familiar with the lab. Nevertheless, there are a couple of things you can do:

  • Do people in the lab have social media accounts? The absense of social media probably doesn’t tell you much, but if one or more people have accounts perhaps you can learn a bit about the lab culture.
  • Look at publications lists – do the students get a chance to publish? Are there publications with multiple students, indicating more collaborations in the lab? Do students publish on their own topics, or only extend the work of the advisor?
  • Look at videos or slides from the advisor’s talks, if you can find any – do they credit their trainees for the work?
  • Get in touch with current or former trainees of the advisor – how is/was their experience in the lab?
  • Ask questions during the interview – what are the expectations of students in the lab? Are there any group meetings (such as a journal club) or other lab activities?

2. How to choose a research topic?

In the Netherlands (and several other countries in Europe) the topic will already be somewhat defined when you start a project. However, within that topic you should still have freedom to explore different questions. Here are some things that worked for me:

  • Just start somewhere. Read papers and implement them, and be critical about what you see. Are there some limitations, for example datasets that would not be suitable for the method?
  • Start writing as soon as possible, for example your thoughts about the papers you read. Are there any trends you start noticing?
  • Talk to others, both within and outside your field. Explaining research to others can often bring you to new thoughts
  • Ask yourself, “Am I building another hammer instead of investigating whether the problem is a nail?”
  • Ask yourself, “If my work was going to change a sentence in a textbook, what would that textbook/sentence be?” (Paraphrased from talk by Robert Williamson)

As with everything on this blog, my final piece of advice is – don’t stop here, but search for more different people giving different types of advice. If you know of a great blog post, or have your own advice to share, please comment below!

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