Grad School: What I Wish I Did

You're only stupid enough to get a PhD once. Here are some lessons learned the hard way.
tagged: studying, research
My newest project is, the easiest way to learn pharmacology for USMLE Step 1. Pharm450 packs an entire course on medical pharmacology into a set of entertaining videos that leverage your visual, spatial, and emotional memory so you learn faster and retain more.

I should admit from the start that I didn’t do all of these. If you could manage to do them all, you would be a rock star. These are things I wish I did, in some cases saw others do. Some ideas might resonate with you, others might fall flat. Grad school is a time to find your own path.

Work on important projects

Whatever you do, make sure it’s worth it. You want your time and energy to make a difference. It’s so easy to work on projects that are technically feasible but have no consequence on the world. These will be some of the most focused and productive years of your life, so make them count.

At the start, you’re likely to get swept up in some “awesome” project your advisor or a senior student dreams up. This may seem like a grind and you might not be able to step out. If that’s the case, then keep at it and keep your eyes open for opportunities to breakout in new interesting directions. Use the experience to learn your tools.

Richard Hamming gave a famous lecture entitled “You and your research” (video). I highly recommend pouring over his advice. Among the gems in there, one I want to highlight here is how he would have lunch with people from other departments. Often he would raise the question “What are the important problems in your field?” And soon after that he would prod by asking why they weren’t working on the important problems? Questions like this get under your skin. He wasn’t welcomed at the lunch table anymore. Paul Graham has a good discussion of this.

Elon Musk is another a fascinating individual with wildly ambitious goals. The story goes that he dropped out of the Stanford robotics PhD and ultimately came to focus his energy on the biggest problems facing Earth’s limited resources: energy (solar, electric cars) and space exploration.

Follow rockstars

Study their techniques and writing. Try to distill why they are successful. Maybe you can find a way to relate your work to theirs and forge a joint project. Have a list of rockstars both inside and outside your field.

Every year when the Nobel Prize is announced, understand the technique it highlights enough that you can explain its significance to friends and family. Same goes for the Breakthrough Prize, Fields Medal, Turing Award, Lasker Award, etc.

Choose your advisor carefully

This will in large part determine what you work on, how stable funding is, and overall how friendly the lab will be. Your advisor can control a lot of factors outside your control.

Find a young and hungry advisor. It’s good for the advisor to have a few years at your school already so you can ask around for others’ impressions and enjoy the benefit of an established pipeline of projects already up and running. It’s also good for the advisor to be a few years out from tenure so they are hungry for work and willing to roll up their sleeves to help.

Probably above all else, you want an advisor you get along with, one you’d enjoy grabbing beers with. Ask their students and other faculty for impressions. If your advisor picks up the tab, that’s a good sign that funding is secure.

Review their publication record. Do the topics interest you? Does the quality match your expectations?

Later, when it comes to your committee, that’s the opportunity to get more seasoned professors involved to help make introductions.

Don’t just jump at the first professor offering funding. Take your time here and seek the advice of others.

Consult your advisor

Read all of their major works. Ask them where to start and what to read. You’ll find that a few key papers keep coming up, especially as you prepare background citations in your work and go on to meet former students at conference.

Ask your advisor to sketch out her view of the entire field and how her work fits within it. Which topics should you master and which should you only be familiar? What are new hot areas? Any related fields to pay attention to?

Create a blog

You’re now a knowledge worker and your personal website is your brand. Treat it like an investment: early work pays dividends as you build up a valuable resources for those following in your footsteps. Don’t wait until your final years to advertise yourself.

More important than building a public image, writing is a great way to evolve your thinking, to vet ideas, and practice effective communication. It’s also a great way to show your advisor what you’ve been up to.

In some fields, there’s of course the need to not give away your ideas to competitors, but I wager you can still put valuable information in the public.

Avoid classes

You’ll have some minimal requirements. Get those out of the way as fast as possible. You will be way more productive once you can spend 100% of your brainpower on research, instead of breaking to go to some random class. At this point, with all that’s available online, top students can teach themselves anything necessary. Your advisor can point out most of your deficiencies; ask her what you should take classes in, and what to avoid.

It’s fine to “drop in” on a few lectures here and there that you enjoy, but don’t delude yourself into actually taking the course to learn. Classes, especially those at the grad level, have you jumping through hoops to complete ethereal homework assignments and cramming for exams when you could be putting that energy into a publication that will advance your career. To broaden your horizons, attend some seminar lectures, drop in on some specific classes, have lunch with a particular professor, ask your advisor to point you in the right direction, let yourself wander on the internet for a few hours. But don’t consign yourself to a static lecture every Wednesday afternoon.

If you’re really interested in something, approach the professor personally and ask for any lecture notes or a book recommendation, and then block off several days to work through the first few chapters and associated problems – no research, just working through the book and Wikipedia. Come back to their office for help. I would wager that a professor watching you do this would be ecstatic to see a student with such diligence and true interest. You’ll likely learn more out of a few focused days rather than some sprinkled one hour lectures and a final.

Invest in yourself and understanding how you learn, so that you can forever after teach yourself anything you want.

Put everything under version control

Version control is like today’s version of the lab notebook: a record of everything tried. Version control both code and data. This way every experiment is repeatable: every experiment is uniquely identified by a SHA indicating a specific version of the code and data. If you’re using a database, get your database under version control. Put your papers in source control. Don’t put source code in Dropbox.

This is a great way to show your advisor you’re working: point him to the commit log. But of course, just making commits do not mean you’re being productive.

Get your research group collaborating this way. It’s a great way to ensure proper hand-offs of code and projects between students. If you need private repos to keep work confidential (pre-publication?), then ask your advisor to spring for it. GitHub is making strides to support academics.

Other great ways to collaborate may include using Google docs for real-time collaboration between coauthors or drafting. You can now track changes and accept/reject suggested edits. Several platforms exist for collaborating with LaTeX documents. Mendeley lets you share papers among colleagues and quickly assemble bibliographies in MS Word. Authorea is a project to make it easier to interact and share scientific ideas.

Any time you’re dealing with code – your own or from a colleague – you want to get that done in source control. Suppose an older grad student hands you a bunch of code. If it wasn’t through github or such, you should start by putting the files into a fresh repo, before you make any edits. Unzip and make that the initial commit. Only after that initial commit should you make any changes to get the code to run, e.g. changing hard coded values/parameters.

More: Stealing Google’s Coding Practices for Academia

Every project needs its own page

Every project should have its own online page where people can learn more. At a minimum this should have the paper itself, but consider making available code/data for those wishing to replicate/extend your work, high resolution figures, any slides or poster you created, full citation already formated for BibTeX or similar, etc. Make it easy for those wishing to learn more and extend your work. Maybe some student wants to present your work to his/her lab group, so having a ready-made slide deck makes this easy. This is a great way to spread the word about your code and there are many benefits to open sourcing everything. You’re more likely to get cited and for others to build upon your results. When you package up code, set it up so it runs right out of the box on some sample image/data.

Make it accessible to the non-technical readers too. Your research was likely funded by taxpayers, so make some effort to cut out jargon. Make it easy for anyone to quickly grasp the importance of your result and the basic technique.

Contribute to Wikipedia

Evangelize about your research area. Link it into other relevant topics. Link to seminal research and online resources. Provide a road map for newbies and generations to come. This will help you organize your own thoughts and mental map of the research landscape. If you’re going to be spending a lot of time on Wikipedia, customize the user interface for efficiency.

Papers and publishing

Figure out your target conferences and journals, and then obsess over those. Skim the last few years proceedings to get an idea of where the bar is at and what’s hot. Some journals have RSS feeds so you can keep up.

Pick some target conferences and workshops (ones with great locations!) and work backward from those submission dates. Put them on your calendar. Map out the Program Committee members, and be sure you’re familiar with their interests and cite their papers where relevant. A PC member will easily frown upon a paper that fails to mention their relevant work.

Increase your network and chance of publication by teaming up with colleagues. Each of you submits as a primary author but have the other as coauthor (with appropriate contribution). Hopefully at least one of you gets a paper accepted.

Know what a “Win” looks like to your advisor. Where do they want to publish? What do they need to move their own career forward?

Good scholarship is the difference between tinkering on a project and pushing the boundaries of knowledge.

Read more: “How to write and publish a scientific paper”, “How to write a systematic review and meta-analysis”, “30 Tips on writing”, and more posts on writing.


Build your network. Look through the attendee list (if available) and email anyone whose work you build on to see if you can grab coffee or sit together at a session. It’s a conference, not a vacation.

Read through the program. Circle anything interesting. For anything related to your work, reach out those authors. They put as much time into the topic as you did so there will definitely be something to talk about, and you will likely want to cite each other if relevant. Maybe you can coauthor something.

Poster sessions. Print copies of your poster and paper/abstract, and pin these up in a folder underneath your poster for anyone to take for later. Print like 30 copies of the poster/abstract, fewer of a multi-page paper; lots will be wasted but people will be less sheepish about taking one if there are plenty. Double-sided. Balance time in front of your poster and time walking around to interact with other presenters.

What can I say I learned from it all?

I learned how to frame and solve problems. I no longer fear a research paper or get intimidated by big fancy science. When faced with the uncertainty of new topic, I can come up with a research plan and milestones. I can develop convincing experiments. And I can craft an efficient and comprehensive writeup.

My story

I completed a PhD in medical imaging and computer vision with the Department of Electrical & Computer Engineering at Georgia Tech. My advisors provided excellent guidance and support in both life and academia: Yogesh Rathi and Allen Tannenbaum. My committee included some of the most superb scientists I have ever worked with: Tony Yezzi, Patricio Vela, and Sylvain Bouix. I worked and shared an office with some amazing friends: Gallagher Pryor, John Melonakos, Shawn Lankton, Rome Sandhu, Matt Might, and more. Afterward I had the opportunity to focus on diffusion MRI as a research fellow at Brigham and Women’s Hospital. You can see more about the techniques and papers we developed.

During the course of all of that, I worked with fellow students Gallagher Pryor and John Melonakos to build Jacket and ArrayFire, both software libraries for high performance technical computing.

After all that, I’m now pursuing a lifelong dream as a medical student in Atlanta.

tagged: studying, research