New paper published!

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I’m pleased to announce the publication of a new journal article resulting from my work in the Giger Lab at the University of Chicago. This article, “Effect of biopsy on the MRI radiomics classification of benign lesions and luminal A cancers” investigates radiomic feature distributions of benign lesions and luminal A cancers of the breast from a database involving lesions imaged EITHER pre-biopsy OR post-biopsy (it’s very hard to locate cases in which a person was imaged with MRI both before and after biopsy.) Our hypothesis was that some features will change as a result of the biopsy process or the presence of a biopsy clip. Because it is so hard to collect single cases in both conditions, we took an approach of comparing groups of lesions. It’s part of an overall effort by our lab to understand the effects of what goes into machine learning algorithms for the purposes of computer-aided diagnosis. A lesion could be the same as another one nominally but have experienced differences in its physical state (such as in biopsy) or in imaging protocol, and we want to better understand the possible impacts on computer-aided diagnosis.

As always, peer-review made a useful impact on the paper. One of the reviewers encouraged us to look at precision-recall curve performance in addition to the usual AUC metrics our lab uses, especially because the cancer prevalence was so different in our pre-biopsy and post-biopsy sets. So you’ll see that extension to the paper.

I always get a lot of questions from fellow conference goers about what it is like to work on research at a primarily undergraduate institution. It’s not easy with a full teaching load, 12 credit hours each semester! I’m very proud that this paper was produced almost entirely from conception to publication without any kind of teaching release. I worked hard but also was able to work with the extraordinary folks at the University of Chicago. It takes a collection of people to do good research!

SPIE Medical Imaging 2019

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SPIE Medical Imaging has come and gone. My trip to San Diego for the conference was very nice. I love that this particular meeting has different tracks (or conferences, as it is actually called within the meeting) and generally all the talks in a given track are in the same room. (But of course you can always dip your toe into the other topics, as you wish.) Another nice feature of SPIE Medical Imaging is that lunch is included each day. This means that you can prioritize meeting with other people and not having to track down food in the middle of the day. Plus, the food is always actually good!

This year I presented about the work I am doing in the Giger lab on developing a radiomics methodology for computer-aided diagnosis using two different populations of patients with breast lesions, one in the United States and one in China. Here’s the formal title and author information:

Effect of diversity of patient population and acquisition systems on the use of radiomics and machine learning for classification of 2,397 breast lesions. 
Whitney, H M., Ji, Y., Li, H., Edwards, A., Papaioannou, J., Liu, P., Giger, M L.

I also helped out with a poster on multi-parametric MRI for breast cancer diagnosis. There were lots of other good talks to see. I was especially interested in the presentations on using computer-aided diagnosis in ophthalmology.

Onward to AAPM and RSNA abstract season!

R15 grant awarded!

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I am so excited to share that I have been awarded a grant from the National Cancer Institute at the National Institutes of Health. The grant will support investigations into understanding the repeatability and robustness of radiomics in breast cancer (just as the title says!). It is for a three-year period. I’m excited that collaborators from the University of Chicago are co-investigators, and Darcie Delzell, a professor of statistics at Wheaton, is also on the personnel. Most importantly, the grant will support four students, two physics students and two from the life sciences, to work on the grant. The grant releases me from teaching obligations in Spring 2019, and provides a course release in years 2 and 3. That is a bit unusual for a professor at a primarily undergraduate institution, but it’s true to the level of involvement I will have on the research. (Although I will add: this spring I hope to have just as many deliverables on research as I did last spring, while teaching a full load!)

This marks the culmination of over 2.5 years of work and four submissions to the NIH. I have learned a lot over these years! True to the nature of peer review, each time we resubmitted, the application represented growth for me, in knowledge and in communication. I am very grateful to those who have supported me in this endeavor. My collaborators at UChicago are unparalleled in their excellence and I am grateful to be able to make use of the resources in the Giger lab in this work. The grants officer at Wheaton is an unsung hero of encouragement. Even my PhD advisor supported me by writing letters of support, even though I completed my dissertation now ten years ago. And my family has been there all the way too. When I did my first application, my kids were so little! My older son, who was (just barely!) three at the time, felt that I needed to wear a construction helmet while working on the grant, so I did so dutifully for much of that writing work. A pleasant side benefit is that my husband has been hired at Wheaton to be full time for this semester to cover my classes, so we also get a semester’s reprieve from the two body problem.

Let’s get to work.

RSNA 2018

 
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RSNA 2018 is in the books. As always, there was a dizzying array of fantastic presentations, posters, and vendors.

I presented my research in two venues:

(1) a talk in the Breast Series: Hot Topics forum in Arie Crown Theatre, seen above. The authors and title were Whitney H M, Li H, Ji Y, Edwards A, Papaioannou J, Liu P, Giger M L. “Robustness of Computer-aided Diagnosis of Breast Cancer Using Radiomics and Machine Learning Classification of 3,158 Lesions across Populations in China and the United States."

(2) a poster, coauthors and title were Ji Y,Whitney H M, Li H, Edwards A, Papaioannou J, Drukker K, Liu P, Giger M L. “Does Biopsy Influence Effectiveness of Radiomics in the Classification of Benign Lesions and Cancers on Breast MRI?"

Both of these projects were a result of the collaboration the Giger Lab has been doing with investigators from Tianjin Cancer Hospital and Institute.

Another highlight was having students in my Introduction to Medical Physics course attend the conference. The students are required to attend one “big talk” (i.e., plenary), one science session of talks, a poster session, and a vendor. It is always so interesting to read their reflections. Many are quite captivated by the dual role of science and business that is a part of the implementation of medical physics in medicine.

Finally, I want to give a shout out to my husband, who held down the fort while I was at the conference. For Chicagolanders, RSNA is the conference that is so close but yet so far away. It takes me about 1.5 hours to drive to McCormick Place each day for the conference, which is not trivial. But this year, on top of that daily drive, there was a blizzard on Sunday night. So I packed a bag for my Sunday trek over, just in case, and when the news came out about how the blizzard warning would extend into the time when I was going to present, I got a hotel room close to the conference center so I wouldn’t have to worry about getting snowed out. Meanwhile, my husband handled the overnight with a 14 hour power outage with two small kids in the house - not a trivial matter! It’s always important to give credit to what’s going on in the background to make the good things happen.

 

Summer conferences

This summer I traveled to two conferences.

The first was the International Workshop on Breast Imaging, held at Emory University in Atlanta, GA. It was a small conference, with just one series of talks. I really like that kind of format: you don't have to worry about fear of missing out (FOMO) on talks you want to hear, and it is a little easier to get to know people. I gave a talk on understanding how biopsy affects using radiomics for imaged-based classification of breast lesions. A highlight was our conference dinner at the Fernbank Museum of Natural History (seen above in the picture), where I got to chat with the representatives from Planmed, who are from Finland.

Later, I went to the annual meeting of the American Association of Physicists in Medicine, held in Nashville, TN. It was a big treat to get to back to where I lived for grad school and my first teaching job, although the city is has changed so much since then. I gave a poster presentation of my work on using deep learning to classify breast lesions by molecular subtype. Poster formats are changing up all the time. I was assigned an "ePoster", which involved submitting a powerpoint slide version of my poster a few weeks ahead of time, which was magically transformed into sections that I could zoom in on by touching a button. I felt a little like Vanna White, but I think it did help facilitate discussion in some novel ways. Plus, it is always nice to not have to lug a poster tube around. A highlight of AAPM was seeing a college classmate who is now a medical physicist in Michigan and a former research student of mine who is now in medical physics graduate school.

Classes at Wheaton don't start until August 29, but that doesn't mean I'm in vacation mode. Right now the lab is working on tomorrow's SPIE Medical Imaging 2019 abstract deadline, and then I hope to get two manuscripts submitted by the start of classes for peer review. Busy but good times.

Is a PUI registration fee category possible for conferences?

I'm really fortunate in how well my collaboration is going. We've had several conference abstract acceptances for my work and am hoping for more. Before the collaboration, I would go to 1-2 conferences per year, and the costs would generally fit within my institutional faculty development grant allotment, helped dramatically by the fact that one conference was in Chicago and had no registration fee, due to my AAPM membership. 

However, in this calendar year, I have attended one conference already and have three more to attend for the remainder of the year. And the costs are stacking up. Here's an outlay of the conference registration fees I will have for the year, even after taking advantage of early registration savings, one-day rates when I can swing it, etc.:

Conference 1: $815
Conference 2: $575
Conference 3: $695 (I'm sneaking in with the one-day rate, $340)
Conference 4: free (but I otherwise pay $447 for yearly membership, out of my personal funds)

Registration fees for conferences 1 and 2 are more than my faculty development grant fund amount from my college for the entire year. These costs listed above do not include airfare, hotel, and food. And they're lower than they could be, because I pay more than $1000 out of personal funds each year for professional society memberships. I have some remaining funds from my start up that I can draw from, but that won't last forever. My department chipped in to help with costs for Conference 1, but they of course can't do that for everything, and the other faculty members deserve any additional support we can give them as well. Another obvious place for getting funds is from fringe funds from grants, but I haven't yet been able to land an external one (although I'm feeing a teensy bit positive about my last application round).

In short, these costs are really tough for faculty from primarily undergraduate institutions! Travel costs, such as airfare or food aren't controllable from a faculty status perspective, but I wonder if conference fees could be.

A natural question is to wonder if I really do need to go to "all these" conferences. In my mind, yes. One focuses on imaging from a clinical perspective, one on the field of medical physics primarily from the view of physicists, a third is broadly about medical imaging, and the fourth is a biennial gathering focused solely on breast imaging. These are all elements of what it means to be involved in medical imaging.

 I know absolutely nothing about planning and executing conferences, but I wonder: is there a place for a middle tier of registration costs for faculty at PUIs, somewhere between trainee and full faculty cost? If you have experience planning conferences, especially large-scale mainstream science ones, I'd love to hear about the plausibility.

Spring 2018 Review

My presentation at SPIE Medical Imaging 2018. Image Credit: Hui Li

My presentation at SPIE Medical Imaging 2018. Image Credit: Hui Li

With one final exam yet to administer, the Spring 2018 Semester is almost completely done. It has been a very busy, but very fulfilling semester.

Spring brings a whirlwind of abstract deadlines in the medical imaging community. Since January, I have prepared two conference proceedings papers, given a presentation (at SPIE Medical Imaging), written six conference abstracts (two have been accepted, four pending review), and sent in revisions on a manuscript and had it accepted (update on that soon!). It's all a big increase in productivity for me compared to my pre-tenure time, when I was completely solo. My collaboration at the University of Chicago has been very fruitful and really fun. I enjoy working with the group and I love that there is an opportunity for me to contribute (with my imaging physics background) and for me to learn (deep learning! statistical interpretations of imaging beyond model fitting! and so much more.) I am really grateful for the opportunity to be associated with the Giger Lab. 

My courses were fairly uneventful. None of them were new, but as always, there are approaches to revise and even a chance for me to understand the material better. Next academic year brings some new preps, as I will be teaching what we call an "advanced integrative course" on the physics of sound (which replaces my old physics of music course) and my department's new data analysis and presentation course (we finally split our two-credit-hour advanced lab-type course into two, two-hour courses). And this fall I am looking forward to my husband getting some adjunct hours in our department, because he will be teaching the labs for a course for which I am the course instructor. I love teaching with him. I'm biased, but we make a good team. I'll need to shake a bit of dust out of my brain, though, because I haven't taught first-semester intro physics since 2014, I believe.

Blogging has been light because of the many good things of this semester, but I hope to get back to it. I keep going back and forth between not believing I have anything valuable to throw out to the blogosphere, and remembering what it was like, pre-tenure, to feel like I might be the only one feeling challenged by this process. Even now, as a parent in a male-dominated field (and department) things feel off sometimes, harder than they should be, so I'm still stumbling about in some ways. And I constantly feel guilt from being on the employed side of our two-body problem. So we'll see where the blog leads. At the very least, I want to share more about research, as it has become a very fulfilling part of my academic (and personal!) life. I'm really excited about the work I am able to produce, especially because I am currently carrying a full teaching load. It is not easy, but it is fun. It brings some tensions of living between two worlds (for example, one-day registrations at two conferences this summer will take up more than half my academic year's faculty travel grant money from my institution) but I have been so energized by the work, and I am so grateful for the opportunity of my collaboration. I can't wait to share more.

Tell your students about the 2018 Summer Fellowships from the American Association of Physicists in Medicine

The American Association of Physicists in Medicine has announced its call for applications for its 2018 summer undergraduate fellowship programs. I want to make sure as many physics professors as possible know about this offering. The announcement usually comes out a bit later than the NSF REU announcements, and so I think it can get missed.

If you have a student even marginally interested in medical physics, I hope you will let them know about the opportunity. You can click on the image above to go to a program flyer.  In addition to the program linked to in that image, there is another wonderful program, the Diversity Recruitment through Education and Mentoring (DREAM) program. Click the image below to go to the flyer for the DREAM program.

And here is a link to the full webpage. (Scroll down to get to the undergraduate fellowship information.) 

There are several nice features about the programs. The stipends are $5,000 and the ten week term can be flexible, determined by the student and the faculty sponsor. The deadline for student applications is February 2, 2018.