Postdoc position in machine learning & image analysis

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

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 🙂

Rethinking productivity

Hello friends,

It goes without saying that I haven’t been on this website much lately. You would maybe expect that the explanation would be that “I’m busy” because I got a new job and moved countries. But while it’s certainly been a moving year (pun intended), that’s not quite it. I had time to blog. I just didn’t want to.

This goes against what I used to be recommend to others from this very website, such as doing a little bit each day. I still agree that’s a good way to get started with a project and to get things done. But I realized it’s not the best strategy for me on a larger scale of things. Even with all my productivity ideas (coping strategies?), my brain gets tired of doing multiple projects at the same time. And with everything happening this year, there was time – but no space – left for other things. But things are slowly converging, which is why I’m writing this 🙂

In general I think quite a few things changed in how I approach productivity compared to a few years ago. I tweeted a bit about this recently, and as you can see, the thought process is still ongoing. But here are things that I’m leaning more towards now, or some things that didn’t work quite as expected.

Having a few focus projects

I need to have only a few things I’m doing on a given day or week. I already liked the idea, as described in my Kanban post. But I try to take it into account more now, and I think I’ve been mildly successful with not starting new projects before I finish existing ones.

In a way, this also means I cannot keep up with all the daily habits I would like to have. If I start writing the first thing in the morning, I will probably end up writing for hours, and maybe forget to eat (and definitely “forget” to exercise). On the positive side, I get more done in that type of day, than if you would just take the hours put together, so I think I’m just going to run with it.

No work email on my phone

I was a big supporter of the “one inbox” principle, but ten years into academia, I decided to give it a try when I started at ITU, and finally use Outlook without forwarding mail to my Gmail. The headspace this gives me on my days off is excellent.

The disadvantages are that Outlook is not great with search, and although there is integration with Todoist, the URLs that are created out of tasks often fail. But if I cannot 100% decide how I want to do email, this will have to do.

Scheduling tasks on the calendar

I already tried to do this with Getting Things Done but I think that level was too fine-grained, and difficult to keep up with. Since I also leveled up to actually using my work’s Outlook calendar, I reserve 3-6 hour blocks to finish tasks which are important and coming up soon, such as preparing talks or grading exams. It often ends up being less hours and ends up getting moved around, but it helps me see how much I have to do in a particular time period.

(Not) capturing everything

Again in the Getting Things Done category, I was happy to have a system to capture everything I might need to think of later. I have relaxed this a bit, some things don’t need to be captured – at least by me. I am still saving a lot of papers I probably won’t read in full, but otherwise I’m not using Evernote quite as much as I used to.

Except Fitbit for health purposes, I’m also not using any previously-tried “productivity apps” that track how long I am using which app, how long I am using my phone, etc.

*****

That’s all I have at this point, but I’m planning to come back a bit more often, so let me know if there’s something specific you’d like to hear more about. For now, I’ll get back to my focus project of organizing my apartment 🙂

Two PhD positions in medical imaging

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 🙂

How I Fail S02E12 – Prof. Lexie Ali (Educator, Diagnostic Radiology / Medical Imaging)

Prof. Lexie Ali is a Deaf-HOH Radiology Educator who runs a free educational organization : MRI Buzz https://www.mribuzz.com – designed to provide educational support, resources, and networking opportunities in one place for students or medical imaging professionals with lesser credentials.  

She has an additional background in Pre-medicine from Loyola University Chicago and University of Wisconsin – Milwaukee. While in the field, Prof. Ali authored many articles endorsing her colleagues and dear friends’ various educational programs. 

Prof. Ali co-owns MRI Buzz with her close friend – Matt Rederer. She is also an avid MR Safety Advocate / Speaker and hosts her own web series – “Let’s Talk MR Safety with Lexie” – on multiple social media channels.  

Furthermore, Prof. Ali sits on the Society of Magnetic Resonance Imaging – International Society of Magnetic Resonance in Medicine : SMRT-ISMRM’s Global Relations Board, helping to translate Radiology-specific Educational Webinars for individuals situated in other countries. She continues to author pending academic papers and/or assist colleagues with such papers/presentations and is also pursuing higher academic/educational prospects at UW-Milwaukee.

Hi Lexie, thanks for joining How I Fail! Next to your official bio, could you say a bit more about yourself? 

I am a Deaf-HOH Radiology Educator. I run my own free Educational Organization : MRI Buzz – https://www.mribuzz.com – and a Podcast: Let’s Talk MR Safety with Lexie –  https://www.youtube.com/c/mribuzz – on my official YouTube channel – to  advocate for safer patient care in MRI – along with side blogs/webcasts for inclusion in Medicine. I am also a DEI advocate with the goal of creating more inclusive spaces for Women and Deaf-HOH in Radiology, ER and OR spaces. That is also the reason why I sit on the SMRT-ISMRM Global Relations Board : I seek to include more diversity-based spaces in Imaging Education. Additionally, I love to expand in terms of academic prospects – so I aim to do more in terms of Diagnostic Radiology and completing the required prerequisites and residency for that. I am a little private with regards to my career and academic prospects but, my overall goal is to go higher than where I am. 

What’s a memorable failure for you?

My most memorable failure would be having had my facility closed for rotations during my final year of med school and then having had to struggle to find placements in time to graduate with my class. 

This was memorable for me because I was depressed to the point where I lost faith in God and felt the futility behind hard work. However, my Grandpa, who passed from COVID would always say things happen for a reason and that closed doors, lead to better windows of opportunities. This rang true – because after months of searching – I was able to find a teaching hospital with hands-on experience in terms of patient care and medical imaging. Being deaf, it is twice as hard to learn patient care, in fast and noisy spaces as hospitals. However, I was quite fortunate to have found a teaching hospital that was very accommodating to my communication needs as a deaf healthcare professional. Closed doors really lead to better windows. 

What do you think about sharing failures?

I think sharing failures is, uniformly, a good thing in the sense of inspiration to others who might have similar lived experiences. However, there are some caveats in that it might lead to judgment or micro-aggressions from some individuals who might view such openness as sensitivity or vulnerability. 

Are there any other topics we (collectively) are avoiding, that we need to discuss more often?

I think we are avoiding solution-oriented approach to social / political issues around us today – and instead – resort to negativity/ ‘bashing’ of said issues. For instance;  there’s more talk of ‘why racism is an evil virtue’ or ‘why Black Lives Matter dialogue is essential’ than ‘what training can be offered’ or ‘how law enforcement officials can be screened’ prior to being placed in service. We need to be discussing / having more solution-oriented dialogues. Everyone knows and talks about why something is happening but no one is talking about what can be done to prevent the something that’s happening. 

Is the situation changing? Do you see differences, for example across different fields? 

Yes, especially in Radiology, I am seeing more inclusive spaces for Women Radiologists. In an industry, that is heavily male-dominated, I am seeing a change in attitudes/mindset and acceptance/inclusion in spaces/field traditionally reserved for men. 

Is there anything that you are currently failing at yourself? 

At the moment, I am failing at striking the right balance between work and personal life. As with the pandemic, things are slower and it takes longer to finish tasks these days. So; that is the thing I am definitely failing at. 

If your ideas about failure have changed since you started doing research, who or what has been influential for this?

My Grandpa and my parents have been influential in changing my mindset and attitude towards failure. I used to think of failures as the end of everything that should have been going for you.  But really, it is the beginning of long-term success / success in the long run. 

Are failures something you discuss with the people you supervise/mentor?

Yes, I do. I have a lot of mentor figures in my field – Diagnostic Radiology. My first ever mentor was – Notable Radiologist – Dr. Emanuel Kanal – And everything I have learned and achieved today with regards to Diagnostic Medicine – Medical Imaging – is because he too – taught me to view failures as an opportunity to reinvent myself and come back stronger, harder. 

What types of things – successes, failures, habits, mood etc – do you keep track regularly, why/why not?

The one habit I keep track of daily is : Reading. 

And it is this habit that brought about my hidden talent for writing – which has gone a long way – in terms of collaborations with notable individuals across various fields. 

Keeping track of anything: be it success, failure, or a habit does go a long way in helping you accomplish what you set out for and more. 

Should we be sharing more successes? Not just traditional ones like jobs or papers, but what you are proud of today ?

Yes, we should be sharing more successes. Even the small ones. 

I remember – in the early 90s – in India : when I used to visit my Grandpa – those days we had a dial-up landline phone: which would randomly stop working. And the same happened, one such day. My grandpa walked all the way to the operator headquarters to get the service back. And when he returned, it did: we celebrated our phone working with great pomp and show. When you celebrate the smaller successes, they actually help you be satisfied if failures come your way and/or enjoy bigger successes better. 

What is such a non-traditional, recent success for you?

Being surprisingly good at hip-hop dancing. I actually do a lot of such dance duets with notable choreographers on TikTok and I never, in my wildest dreams, thought I would be good at setting up my TikTok page. 

Are there also reasons to not share (some) successes?

While sharing successes is a good thing in terms of inspiration for those struggling to achieve the same – there comes a point – where you deliberately DO NOT want to share the same successes : because sometimes the same success can remain incomplete in the form of obstacles because of the rush to take up space and competition as thus.

What would a ten year younger you think of you now? 

A ten year younger me would think of me as a stronger, emotionally mature person, who is satisfied with both failures and success – rather than the rush to ‘be something’.

What advice would you give to that person? 

I would advise the younger me to exercise more patient and be satisfied with what comes my way. 

How I Fail S02E11: Pradeep Reddy Raamana (PhD’14, Medical Imaging and Machine Learning)

Dr. Pradeep Reddy Raamana is an Assistant Professor at the University of Pittsburgh. He is interested in developing multimodal biomarkers for brain disorders, and the necessary data science tools to realize personalized medicine. He founded the special interest group on neuroimaging quality control (niQC) at the International Neuroinformatics Coordinating Facility. He is a passionate advocate for quality, reproducible and open science. He leads the Open MINDS lab @ Pitt (now hiring!), where they develop multidisciplinary techniques for computer-aided diagnosis (CAD) and precision medicine, with a motivation to improve data quality, reproducibility, performance of predictive models and their potential for clinical translation.

Hi Pradeep, thanks for joining How I Fail! Next to your official bio, could you say a bit more about yourself?

Thanks for inviting me, Veronika! I would like to think I am a simple straightforward guy trying to improve the world around me in various ways I can. I think a good way to be happy is to make others happy! They sound cliché but that is in fact where I derive my motivation to find value in my actions, work and life in general.

That is also a key motivation for me to choose the academic career, which I believe would give me the opportunity to 1) develop necessary techniques and tools to improve healthcare, and 2) [at some point soon] provide a sufficiently stable and independent platform to speak my mind and pursue solving whichever problems (broadly speaking) I believe would make the most impact. I hope to pursue it by rejecting the traditional careerist approach, and help reform it by eliminating various sources of toxicity in academic life for all stakeholders involved including trainees and faculty.

A recent step I am taking in that direction is to “boycott” all interactions (reviewing, editing and submitting any academic outputs including papers and books) with for-profit publishing businesses like Elsevier. The motivation is to eliminate the subjective (and arguably disproven) concepts of “prestigious” and “high-impact” journals (by relying on high rejection rates and impact factors etc) from our peer-review discourse as well as in hiring and promotion policies.

I believe sticking to publishing only in society-run journals that are accountable to the members of their scientific society would give us the power to choose the peer review criteria (focus on validity, not on accumulating citations to charge higher subscription fees), and optimize them towards what is ethical and best for science. This would also reduce the costs for publication and be more inclusive.

Given great adoption of open science we are seeing which includes transparency in peer review, we can adapt the policies of a society-run journal based on the best available evidence. Within a society-run journal, members would have option to reject many unethical and toxic practices we notice in many for-profit journal businesses such as

  1. picking for “shiny” topics and encouraging authors make inflated claims,
  2. extracting within-same-journal citations from authors (to manipulate their IF),
  3. unnecessarily large number of revisions to leech off many-fold submission fees as well as to
  4. create a false appearance of faster processing time from submission to publication.

I urge everyone to join me, esp. those with sufficient job security. 

What’s a memorable failure for you?

Great question! Besides the typical failures we all face, I think the most memorable for me would go back all the way to the first year of my PhD where I felt the euphoria of building a “perfect biomarker” to diagnose AD “accurately”. Like 100% accuracy in my evaluation (using an SVM classifier I think – they were all the rage then!). I thought I won the jackpot and was super happy. That lasted only 10 minutes or so until I discovered I was totally double dipping!

On Twitter you shared about null results during your postdoc – can you explain more about this?

I was referring to a key project in my postdoc to build neuroimaging “biomarkers” (loosely speaking) for Major Depressive Disorder (MDD). When I was just getting started on it, there were few review papers implying the possibility and potential of neuroimaging to predict response to treatment.  I did have sufficient expertise with both machine learning and imaging-derived features: the focus of my PhD thesis was exactly that but focused on Alzheimer’s disease (AD) and related neurological disorders.

I picked it up with enthusiasm but after a long series of attempts to evaluate the predictive utility of know biomarker candidates as well as some new ideas we had, I realized neuroimaging-based features (various versions of morphometric and functional connectivity) were no better or only slightly than chance. As you know it’s harder or impossible to publish null results, except in specialized/non-popular venues. Hence, I kept digging deeper and wider to try find a “somewhat positive” result, and I must say I failed thoroughly. However, I must say I succeeded in thoroughly understanding various challenges related to predicting response to treatment in MDD well.

If you ask me how I viewed it differently then and now: then, I saw it as an exciting, important, high-risk high-reward challenge, that will demonstrate my expertise and diversify research “portfolio” so to say. I was skeptical of the published results (based on my previous understanding of the AD literature that most biomarker studies reported inflated and/or overfitted results).

But looking back I feel I didn’t think sufficiently through various possible outcomes and whether they align with my career plan i.e. I should have asked the hard questions first: 1) will the results be publishable, and 2) do they add to and merge as a coherent part of my research program in my job talk etc? However, I don’t regret that effort at all! I learnt a lot from this exercise that I wouldn’t have learnt otherwise esp. challenges in in the world of psychiatric disorders. But I am thoroughly disappointed in the system, structure and community around us that would rate that effort (without big papers to show) towards nothing.

Is there a story behind your name “Future Distinguished Emeritus Prof” and bio “without an agenda”? 🙂

LOL, that title is a joke on the high prevalence of Named Professors / Chairs in the academy, which I believe are related to donations into the university. Given the already-hierarchical nature of the academy and concentration of power into few rich clubs, this never-ending quest for more titles incentivizes “generation of money” from new sources proposing all sorts of research. This quest to climb the ladder higher and higher leads to piles of papers in flimsy fields that don’t really move the needle in the context of larger challenges to society, that they are supposed to help with.

This is also related to some traditional biography pages I read which are just a really long list of such “titles”, and I remember saying to myself “OK.. that’s a stack of “trophies”, but tell me what you actually do?”. I personally believe titles shouldn’t get in the way of a good conversation or a debate, and we must evaluate comments on their substance and merit. So, the prefix is just to indicate I will also have few titles in the future. Some on Twitter told me it made them chuckle! J

The “without an agenda” in my Twitter profile is to clarify how I try to conduct myself there: to keep it real, unfiltered and without a specific agenda towards promoting a certain set of topics or people. Few years after I started using Twitter routinely, I’ve noticed how some powerful people promote only those (people or papers) that suit their agenda, and not all the good work that exists. That is really upsetting when it is done by those claiming to be a champion of open science. This saddened me deeply, and I decided to try keep it real and be myself.

The “without an agenda” is also a disclaimer and “warning” of sort for people thinking of following me (many find me based on my research) on what sort of content/feed they can expect when they follow me. I am not trying to virtue signal here, and I probably have blindspots and biases myself. I hope to learn them and correct them to the extent possible.

It seems that you are pretty open about topics others might be avoiding. How do people usually respond to this?

Great question! I’d love to hear from the community what they think of my timeline 🙂

As a true believer in open science, I think it is essential to be as open and as honest as possible. As is true in broader life (relationships, politics etc), only honest discourse from everyone leads to real and sustainable progress for all stakeholders involved.  So, I try not to filter any comments or questions I have and try providing an open outlet/forum to discuss all topics, regardless of whether I think that particular tweet or topic would be well-received or not. This process of sharing (past some basic filtering) also helps me a keep a journal of sort over time, and over multiple debates on similar topics.

As for how people respond to this, I think there is definitely those who listen to what I have to say, offer thoughtful responses, advice and support in their own ways. I’d like to sincerely thank them, and consider them my friends! They certainly keep me going, as I don’t think I’d have decided to pursue the academic career if I didn’t find that open and supportive community in time.

That said, they are more on the smaller minority, and I feel there is a clear and strong tendency to avoid any “negative” and non-work topics. Engaging in these debates is considered “unproductive” by some. I might be wrong but one of the reasons for this is many researchers treat academic Twitter as another social media channel to promote their work or themselves (“brand management” comes to mind). That is their choice, and that is not wrong, but it doesn’t help with facilitating important open conversations to be had.

There is also a clear and noticeable tendency to popularize who are already popular e. g. an identical idea or comment from a “well-known senior researcher” would get disproportionately more attention than otherwise. I don’t claim to understand how or why that happens, but I think the tweet should matter much more than the tweeter.

Are there any other topics we (collectively) are avoiding, that we need to discuss more often?

Yes – there are a few (which I have been trying to shout out loud and often):

  1. More debate and realization towards how we the academics are squarely the source of many of the fundamental issues in science
  2. More honest communication with prospective PhD students on what academic life is really like, and the bleak prospects for many towards a traditional Professorial career, and why we should strongly discourage many to pursue a PhD in the first place
  3. Why we should eliminate the concepts of “prestige” and ranks in our discourse, starting with journals (Impact Factor etc), and then universities

Is the situation changing? Do you see differences, for example across different fields?

Yes! Based on my experience and bubbles (which is arguably limited and likely not representative of the full academia at large), the “computer sciences” seem to be more open compared to the more “clinical” and life-sciences fields. This may be due to differences in training, and perhaps because the tools and platforms to share (relating to computers and software) are much more natural and integrated to them. I have definitely noticed “hierarchy” and “authority” play a bigger role in the more clinical / “hardware” fields relative to the “software” fields. Again, I could be less than accurate as this was based on my own observations and anecdata.

Is there anything that you are currently failing at yourself?

Yes! I suck at time-management and sticking to my plans and priorities esp. in the medium term.

Do you have a success that is not a traditional one, like jobs or papers, that you are proud of today?

As I participated in the American Elections debates online over the years, I noticed they were only worsening the political divide and weren’t helping with bridging the gap! Hence, I’ve been itching to meet the real American voters in the real world and something “real” instead of another Twitter debate. While the pandemic didn’t really help this cause, I was able to visit many poll centers in the Greater Pittsburgh area to distribute water and food on the historic 2020 American Election Day.

The original idea was to help the voters stay in line and make sure they vote as Pennsylvania was a critical swing state. However, as large numbers voted by mail, the lines weren’t as long as expected. So, I was able to help the poll workers themselves! They were visibly and clearly delighted to see somebody offer them water and chocolates. And that was an experience I wouldn’t forget for sometime.

How I Fail S02E10: Charles T. Gray (PhD’21, Interdisciplinary Computational Metascience)

Charles T. Gray is a reformed musicologist, one-time fire twirler, former inter-library loans officer, and intermittent typist. She spent the nineties immersed in Melbourne’s vibrant street-punk scene, and it was every bit as fun, confronting, and political as it sounds. She is currently a postdoctoral scholar with Newcastle University’s Evidence Synthesis Lab, where she specialises in Bayesian network meta-analysis for Cochrane intervention reviews. She has three bachelor degrees: music, arts, and mathematics. None of these prepared her formally for her current occupation. Nevertheless, she believes that working in the performing arts is the perfect precursor to academia.

Hi Charles, thanks for joining How I Fail! Next to your official bio, could you say a bit more about yourself? 

It shouldn’t be shameful or taboo that I had a shitty childhood, nor that this continues to shape my adult life today. I manage with a variety of practices: medication, yoga, VR fitness, therapy, literature, bullet journalling, and peer support groups. 

We need to change the dichotomised understanding of people as broken or crazy and others as normal. We’re all capable of being irrational, overwhelmed by past feelings. 

No one is irreparably broken, and having experienced hardship, even rape and physical abuse, does not mean we cannot contribute meaningfully to society. Indeed, if we listened to survivors more, I believe we’d all learn a great deal. 

Everyone experiences trauma; people with my past simply have a masterclass in it.  

What’s a memorable failure for you?

Getting through high school was a huge effort, finding myself homeless and on the streets at fifteen after life with my parents became untenable. Despite dropping out for half of school, I got myself into a top university.

I supported myself through my degrees by working as a piano accompanist and teacher, enduring gruelling hours, and when I finally finished with a double degree and a thesis, I thought my fortunes would change. Instead, I graduated into the 2008 Global Financial Crisis, and discovered that society didn’t much value my music degree, nor my arts degree. 

I cast wider and wider nets trying to find work; a low point was not even getting an interview for a two-hour a week cleaning job. I applied for everything and couldn’t seem to get interviews. I found myself careening towards the age of thirty feeling as if I’d completely failed in adulting.

At this point, to make things worse, I finally accepted that I didn’t enjoy practicing music anymore. Indeed, my passion was theory, not performance, but there was no work in music theory. My only source of income was something that I was not only bad at, but lacked the drive to become good at it. At this point, I’d been practicing music for twenty years, and I was fatally bored. 

I wasn’t sure I’d ever find the strength to get myself out of that situation, after struggling so hard to get myself into those courses in the first place. It is, however, astonishing what inner resources one can muster when the alternatives are so much worse. I took action, beginning studies in mathematics at thirty, when I began to suffer insomnia so badly that I was struggling with the basics of life.  

You’ve had a major career change, that people have told you would not be possible – how does that affect you going forward? What would be the advice you would give others in a similar situation?

There are widely-held beliefs about fixed and innate skills, but most skills are learnt through hard work and perseverance. There will always be outliers with amazing abilities: five-year olds who can play Mozart piano concertos or solve complex equations. However, this does not mean that one shouldn’t try. 

To combat the gnawing, ever-present anxiety surrounding being good enough in my ten years of mathematics study, spanning my thirties, I reminded myself constantly that my goals are modest. All I want is to work in mathematical science, ideally research. There’s a reason research isn’t performed by five-year old prodigies; it wasn’t a requirement that I be gifted, merely competent

Working long hours meant I was forced to accept my marks would be lower, that I wouldn’t be top of the class. Rather than comparing myself to others, I ask myself over and over, is what I’m achieving good enough for the next step toward my goal of working in mathematical science?

Code like a girl poster with Charles Gray

You will soon give a talk on failing at reproducibility at the R-Ladies Toolbox Series, can you say something more about that?

Reproducibility is a hot topic right now. If the twittersphere is anything to go by, psychology seems to be consumed by flame wars surrounding replication of results and preregistration. 

Computational reproducibility is analogous in statistical science. We are witnessing a dizzying proliferation of software tools and methodological standards of best practice. 

I tried and consummately failed at creating a reproducible doctoral project. I want to save others from the internal agony of feeling they’re failing at keeping up with the Joneses of reproducible science

Why is reproducibility important in science? We wish to provide both means of validating our scientific results and extending on the work we’ve done. My thesis is a hot mess of TeX, .Rmd, .R, and data files. I doubt, even in the unimaginable event someone was inclined to reproduce that work, they could. However, by trying and failing, I learnt many skills and workflows that make my life so much easier now in my current research. 

I believe even so-called good enough scientific practice is unattainable. There’ll always be a tool or workflow one hasn’t mastered, let alone heard of. But by trying and failing, we inch all scientific practice toward better standards, and we learn beneficial skills. 

You have a bullet journal featured on your Twitter profile- what types of things do you track there, and how does it relate to success/failure for you?

My bullet journal is an integral part of my daily workflow to help me centre in the moment. I manage complex post-traumatic stress disorder, experiencing visceral flashbacks; my time on the streets as an adolescent, and the circumstances that brought me there, will always shape my adult life in large and small ways. Bullet journalling helps me to focus on setting daily, small-scale goals; and to somewhat mitigate the past distorting my feelings of success and failure. 

Paper bullet journal with a pen and a ruler

Keep putting one paw in front of the other, it’s all any of us can do. 

Practice diaries are common in music. We don’t need them for the flow-state days where we play Scriabin’s Etude in C# minor for 6 hours straight because we simply cannot get enough of the feel of keys under our fingers conjuring such transcendent music. 

Anything we have to do every day begins to feel like a chore, and it’s hard to stay motivated day to day, even if we do appreciate it when we achieve flow state. Practice diaries and schedules are for the uninspired, overwhelmed, and tired days.  

What’s a recent success, and one thing you are “successfully failing” at 🙂 

Last year I decided to take things easy. My scholarship had run out, but I had data engineering work on a large open science project. I ignored the hyperventilating from others about my timeline and decided I’d work part time and complete my doctorate in a relaxed manner. 

In part, the pandemic helped make this decision easy; if I had rushed, I would have graduated into a time where research was being slashed and few positions advertised. I decided it would take as long as it would take, provided I kept writing my dissertation fairly consistently, albeit part-time. 

My advisors noted how polished it was, and provided very few comments. Indeed, only one examiner had two small amendments. I was waiting until I submitted for examination before looking for work, but managed to obtain a postdoctoral position before this, that is, before I’d begun the job hunt. 

In some ways, this feels like the greatest achievement of all: a stress-free submission and avoiding the ontological angst of reimagining oneself for position after position, only to have those hopes dashed.  

The inspiration for this talk on failing at reproducibility is my newfound calm in the face of a torrent of scientific tools, workflows, and theory, that I’ll never possibly master sufficiently to all standards. As I try in earnest to be a good scientist, I know I’ll fail, but I also know the next attempt will be a bit easier. 

As I used to tell my piano students, you have to hit the wrong notes to learn to hit the right ones; what holds us back is fear of trying. 

How I Fail S02E09: Bernhard Egger (PhD’17, Computer Science)

Bernhard Egger is a postdoc at the Computational Cognitive Science Lab at MIT. His research is focused around inverse graphics in Computer Vision and Computational Cognitive Science. You can find out more about him on his website https://eggerbernhard.ch/ or on Twitter https://twitter.com/VisionBernie.

Hi Bernhard, thanks for joining How I Fail! Next to your official bio, could you say a bit more about yourself, and what made you join this series? 

Hi Veronika, 

I want to figure out how vision works: how human vision works, and how we can build computer vision systems that generalize. I choose to perform computer vision research based on an inverse rendering approach. I am convinced that Analysis-by-Synthesis is the way human vision works and the way we should build machines that perform vision in such a way. This idea puts me in an interesting niche in the community. During my PhD it sometimes felt like fighting a lonely battle against a huge flood of supervised deep learning research in the community – however over the last few years inverse rendering, 3D Morphable Models (3DMMs) and in general more model based approaches to vision are coming back. Even conferences like CVPR (the most important one in my field) are going more and more in that direction. I might have chosen a path that is not particularly fruitful when it comes to citations, but it definitely enabled a lot of steps in my career. Whilst a career in academia was less a master plan, than a “just in time” evaluation at each step, I would say it mainly worked out because of the niche I’m working in, that I found for myself. This niche for me is fun and therefore I can make an excellent, motivated story for a presentation – which I think is crucial for i.e. (faculty) interviews. 

I wanted to join this series mainly with the intention to show that not everything is as smooth as it might look in my CV, a lot of things that are important cornerstones in my CV had a significant component of luck involved – and there is also a lot of failures or drawbacks that are just not mentioned.

What’s a memorable failure for you?

My biggest failure was probably my first attempt to get a personal career funding grant –  I was following my partner to Boston, so I cold-called professors at MIT to get a postdoc position (a cold-call is how more than 40% of the postdocs get into MIT). I intended to get my own funding, by applying for a grant for 18 months, with an acceptance rate of about 50%

After visiting a lab at MIT and having support from a professor for the grant I was super pumped and confident that it would work out. I wrote the grant during a ski vacation (spending the days on the slopes). I then got feedback from the professor and also from my peers that it needs some work. I had one week to go – but I was super confident that with MIT as an institution and this high acceptance rate it should work out. So I did a little bit of work, but did not invest as much time as my peers would have recommended. 

In the interview (which is short <10 minutes) they basically took me apart and isolated the weaknesses of my proposal. They caught my vague formulations and found that for some essential parts of the proposal, I was just not certain enough how to do it. 

I was first disappointed and angry at the reviewers – but then quickly realized that this was my own fault – I took it too lightly and felt like a small kid testing his boundaries of what is acceptable and what not.

When preparing the revision for the grant, I realized how sloppy it was – I spent a whole month writing a proper proposal and got it funded in the second attempt. This however also led to a delay of my start at MIT and I moved to the US with a delay of 3 months after my partner.

Another big failure was an attempt to organize a workshop on 3DMMs at a major conference. We had a group of organizers together and wrote a decent proposal. It was rejected from both CVPR and ECCV (two major conferences in the field) in years where there were tons of workshops on “deep learning for x”. This was very frustrating, especially because a workshop should add content in an area that is not covered enough by the main conference. So in my eyes a deep learning for x workshop might not add much value to a conference that is anyway 80% deep learning for x.

After those two rejections, I basically gave up – but a senior person among the organizers told me “Let’s try to do a Dagstuhl seminar instead” and that worked out and was my best scientific experience so far!

Guess which conference added 3DMMs as an area two years later? CVPR… But it is not good enough as a CVPR workshop 🙂

What kind of topics are associated with failure, and are not talked about enough? What problems does this create for early career researchers?

I think academia just has this huge illusion of a perfect world: perfect CVs, perfect projects. When listening to a presentation, especially from a senior person the story will be so smooth it just sounds like everything was always planned that way. Some people include some failures in their presentation, but then more in a funny way than formulated as a real failure.

I really appreciate that you added a CV of failure to your website – I think it takes a lot of courage. It is refreshingly transparent and it would probably be valuable if more people would do so. However it might come at a cost: Will I be judged by others based on sharing my failures? And especially if there are only a few people sharing their failures it is easy to judge them. I don’t know what the right solution here is – everything public and transparent might be a bit much, but sharing failures within the lab, especially from the most senior person might be  valuable and create a culture of sharing failure. 

One other key topic that is prominent in academia is the imposter syndrome. I stumbled on an online test recently on twitter (http://impostortest.nickol.as/). And if you check #ImpostorSyndrome you will see tons of results from researchers with high scores in this test. We are in an environment where smart people come together, and almost always you will find somebody appearing smarter and more successful. It is sometimes really hard to not feel stupid in this environment. One important message here is that ~ 70% of people in academia feel that way – we can’t all be that bad 🙂 

Is the situation changing? And are there differences between different fields, countries etc?

I have hope that things are changing slowly. The first important step is probably awareness. Some institutions put big efforts into the mental health of their students and employers but some of the issues might be in the structure of how academia is set up at the moment. So fixing the final problem might not be as good as trying to change the cause. 

The main responsibility in my eyes lies with the advisors/mentors. I think the moment we mentor someone (starting from an undergrad level, over PhD students and including young faculty), we actively propagate the way we think academia should work to our students. A lot of my behavior and the way I see academia I learned from mentors I valued. If a mentor is particularly bad when it comes to real life challenges like mental health issues that is likely to dramatically affect the career of the mentee and pushes especially minorities out of the field. I also believe some of this can start with small things. I try to make authentic and honest statements that signal that there is room for discussions or self-care and hope this helps to do a small step in the right direction.

Is there anything that you are currently failing at yourself?

Yes – focusing. Over my PhD and postdoc I however started to accept it and just ignore all this self-optimization stuff 🙂 I still see it as kind of failing, mainly because it is easy to spot that I just lost some hours doing X (or nothing) and it feels like there is a constant drain of potential.

Are there specific people who have been influential to how you approach setbacks?

For me it is not really a specific person, but probably each one of my peers. The longer I stay in academia the more I realize that nobody is perfect, everybody gets grants or papers rejected. This definitely helps in the moments where a setback happens to normalize it and look forward. One of the most important strategies that I think I learned from others is to always look ahead – and usually some of the feedback of a review process is useful to improve the work to submit it again. And no, reviewer 2, I don’t think that I should just do deep learning instead!

Are failures something you discuss with the people you supervise/mentor?

I realized that failures like rejected grants or paper annoy me a lot, especially at the moment of the rejection. However after a few days I’m over it and either resubmit it or forget about it. I’m however terrible at giving good advice in discussing failure or rejections. When submitting a paper I already know that there is a big chance of getting a rejection, especially when aiming at the top venues – so once the rejection is in the inbox I’m not really surprised, usually annoyed about at least one reviewer, but I’m just bad in finding the right words to express my thoughts to the first author(s). I try of course to motivate them, and tell them that this just belongs to the experience in academia but what do you say the second or third time – especially if you are convinced that the paper is actually solid?

What types of things do you track regularly?

I’m crazy about my google scholar profile – I check it way too often and am always super curious who is citing which work. This was especially frustrating earlier in my career where it took super long till something changed and some citations even wrote something wrong when citing the work in their related works section. But recently it changed from being frustrating to be motivating – mainly caused by a nice survey paper that gets lots of citations!

That sounds familiar! 🙂

What about successes, should we be sharing more non-traditional ones, not like jobs or papers, but what you are proud of today?

I think such things can be very valuable, especially in a lab setting. Share success or setbacks with the lab in regular meetings. Here I really like the idea of a common coffee break which is common in Europe and not so common in the US. Such a coffee break is usually the point where smaller or different successes and smaller setbacks are shared and discussed and this interaction is definitely highly valuable since it is much more granular and also more personal than a paper acceptance or rejection. If somebody tried a new recipe at home and thinks everybody in the lab should know it – the coffee break is exactly the right platform. Or if you were waiting in line to submit a certain bureaucratic form for 30 minutes just to learn that you also need another one – that is another thing I think can find space in the coffee break. And there will still be enough space for scientific discussions or programming questions even with these little bits of personal success or drawbacks.

What is such a non-traditional, recent success for you?

I ran a marathon during my PhD and I was not shy about sharing it with everybody 🙂 The best part of it however was the training. It was together with a postdoc friend in the same lab and we did all the long runs on the weekends together. I really enjoyed all the conversations, especially since the brain seems to work really well when my body is busy with some other work 🙂 The final moment of then running a marathon and being able to actually finish it was a moment where I was proud of myself and just enjoyed that I actually did something that felt impossible half a year before (I could not run through a half marathon before training and it is not that I didn’t try).

If you’ve been a reader of How I Fail last season, what are your favorite lessons from the series?

I really enjoyed learning about the posters centered around mental health from Dr. Zoë Ayres:

This is an excellent and valuable resource that I plan to share with all my incoming future students since they bring a lot of things on the point that people rarely talk about.

What would a ten year younger you think of you now? What advice would you give to that person?

I tried plenty of those self-optimization and productivity tools. I would tell myself to just not care about all of that and not stress out about (productive) procrastination.

How I Fail S02E08 – Jen Heemstra (PhD’05, Chemistry)

Jen Heemstra is an Associate Professor of Chemistry at Emory University. Research in the Heemstra lab is focused on harnessing the molecular recognition and self-assembly properties of nucleic acids for applications in biosensing and bioimaging. Outside of work, Jen enjoys spending time with her husband and two sons, as well as rock climbing, cycling, and running. You can find out more about her and the members of the Heemstra Lab on her website or on Twitter.

Hi Jen, thanks for joining How I Fail! Next to your official bio, could you say a bit more about yourself?

Hi Veronika, 

It’s great to join you to talk about failure! This is a topic that I know well. From my 8th grade teacher telling me I wasn’t good at science to the grant proposal that was rejected last month, it is a topic that has significantly shaped my life and who I am as a person. The “unofficial” bio is that I’m someone who never thought I could be a scientist or a faculty member, so I still wake up every day in awe of where I am. And, while most people would call me a scientist, at this point in my career, I see myself more as a mentor and leader – science is just the vehicle for me to empower others to build their careers. To that end, my favorite thing about my job is getting to work with all of the students and postdocs who are my colleagues in the Heemstra Lab. People who know me on Twitter also know that I’m pretty outspoken about changing academic culture.

What’s a memorable failure for you?

Probably the most impactful failure of my career was my tenure vote at my former institution. It was not an outright failure (and I did ultimately get tenure) but it did not go as I had expected. It was definitely the most painful failure of my life, as I felt like I had let down my family and my research group members – basically all of the people I care most about. For anyone who hasn’t experienced that, it is a truly horrible feeling. But, it can also be a beautifully humbling experience as well. Seeing how all of those people stood by me in the midst of the struggle ended up seismically shifting my worldview and priorities. It gave me a new view of what academia could be and a fire to make that into a reality. It also made me fearless. This specific failure that I had long been afraid of ended up happening to me. It was the exact thing that I had deeply dreaded, and I found myself suddenly thrust into it and with no choice but to cope and keep moving forward. As I continued to work hard and succeed in spite of that and eventually came out of the situation, I realized that I’m stronger than I ever thought I was and that people’s opinions of me don’t have to define me.

On Twitter you have “embrace failure” in your bio. What does failure mean to you? Is there a story that made you add this line?

This is actually a phrase that I think about quite a bit and I’m not sure if I will always “embrace.” As researchers, we often talk about failure being a necessary part of the discovery process, but at the same time we know that we all need at least some success to move forward. As we’ve gotten involved with research on the psychology of failure, I’ve been able to better understand this dichotomy. Where I land right now is recognizing that failure is not inherently good, but rather being willing to fail can make us more likely to succeed. For example, if we are willing to dive into the hard experiment that might kill a project rather than saving it for the end because we’re afraid of the failure, we are ultimately more likely to advance our research in a meaningful way. All of that being said, the character limit for a bio on Twitter is pretty limiting, so I’m guessing I’ll keep the phrase there.

You are quite outspoken about various problems in academia. Can you say a bit more about how you got started with this? 

People who know me know that I’ve always been outspoken – Twitter and other media have just given me a public platform for sharing my thoughts more broadly. The motivation for talking about academia comes from realizing that early-career researchers should be at the center of all that we do in the context of academic research – after all, we work at institutions of higher education, not institutions of higher productivity. However, we have a reward system that primarily focuses on publications, grants, and awards, and this unfortunately can allow faculty to thrive in their own careers even if they don’t support the researchers working in their groups. I feel a responsibility to address this, not only by growing my own mentoring and leadership skills so that I can create a healthy and supportive culture in my own lab, but also by advocating for wider scale change.

Should everybody share failures, and/or be more open in general? What would your advice be for somebody who wants to be more open, but is afraid of the negative consequences?

This is a tricky one. I think we should have a culture in science and academia where people can be open about their failures without consequences. But, until we get there, I’ll say that our responsibility to share our failures is proportional to the amount of power we have in the academic system. For tenured faculty, when we are willing to share there is very little to be lost, but much to be gained in encouraging and supporting the next generation of scientists. I’ve also found that when other people are authentic about their failures, it actually increases my respect for them, rather than decreasing it.

Is there anything that you are currently failing at yourself?

As we stretch into month 8 of the COVID-19 spike in the US, am I allowed to say “everything”? I know it’s not true, but it’s tough to not feel like I’m simultaneously failing as a leader, teacher, mentor, and parent. There is more than ever that needs to be done, and trying to get all of that done in the online environment is often far less effective. And, the stress of everyday life right now makes it more challenging to show up and be the person that I want to be.

What types of things – successes or failures, big or small – do you keep track over time? Why / how does it help you?

That’s a very interesting question, and it makes me realize that I’m probably not great about doing this. I definitely keep track of my growth in key areas such as communication and leadership, but I tend to celebrate the successes and mourn the failures in real-time, then let them go and keep moving. For me, the more important questions are “did I improve myself today?” and “did I improve the world around me today?” and those are often agnostic to failure or success. That being said, part of my job as a faculty member is to fill out an annual report where I cut and paste every publication and talk into a website to be tabulated and analyzed by my institution, so I guess I do sort of use that to keep track.

Should we be sharing more of such (small, non-traditional) successes and failures too? 

I think this is incredibly important. We tend to define success and failure pretty narrowly in academia – the experiment worked or it didn’t, the paper got accepted or rejected, the grant got funded or not funded, etc. In our education research, we define failure as “not achieving a desired outcome” and that can look like many things – it can be not having a conference talk go as smoothly as you wanted or feeling like you didn’t handle a crucial conversation well. Along the same lines, the successes that we should celebrate are also much broader and we’re missing out by not recognizing those.

What is such a recent, small success for you?

I cracked a joke in an email this morning that made someone laugh. We all need laughter right now.

Are there any resources on failure you would recommend to early career researchers?

The book I most highly recommend is Mindset by Carol Dweck. It’s not directly about failure, but rather about how we view our abilities. However, her research suggests that this deeply impacts how we view failure, and ultimately, how likely we are to achieve success. Even more importantly, I’ve found that her research can hugely impact my happiness and sense of satisfaction in my work, and that is even more important to me than the classical metrics of success.

What would a ten year younger you think of you now? What advice would you give to that person?

Ten years younger me would think “No way! It is absolutely impossible that you are doing this.” I spent way too much time thinking that I could never have the career that I do, and I’m constantly amazed that I’ve made it here and have the opportunity to help others identify and work toward their career goals.

The advice I would give to ten years younger me is twofold: (1) it’s easier to live with failure than regret; (2) go out and find yourself some leadership skills – you’re going to need them. The second one I say somewhat jokingly, but also being completely serious. We tend to view academic jobs as “research jobs” while at the same time they require skills in people management, budget and finances, conflict resolution, strategic planning, etc and there is little in the typical trajectory that prepares you for that. But, that’s also why I’m writing a book! It will be all of the leadership advice I wish I had when I started my faculty career.

A song about academic rejection

So far I’ve only used YouTube to share talks, for example about my research or failure in academia. Today is different, because I’m proud to share with my latest project – Jolene, a song about academic rejection!

I wrote the lyrics back in 2017, and several people on Twitter suggested I should also record myself singing. The idea sounded great but I was also too scared of even trying.

Image

But 2020 is the year this changed! After Matt Wall shared his MRI song (a cover of “You shook me all night long” by AC/DC), I talked to him about an academic version of Jolene. As things often go on Twitter, turned into a project! Having another person involved made it easier for me to actually get it done, and Matt’s music & production skills made me confident enough to share this with all of you 🙂

Please enjoy Jolene – a song about academic rejection!

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