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.

Physics of Sound Fall 2018 Fall Projects

 

This fall, I taught a revised physics of sound course. The revision was due to changes to Wheaton’s core curriculum program. The course expanded from 2 to 4 credit hours. It also took on new content, since it has both a Science Practice and an Advanced Integrative Seminar tag.

For the first half of the course, the students engaged with physics of sound content in a standards based grading manner. Then, at mid-term we switched to project and seminar mode. The students devised projects and revised them twice. We tried as hard as possible to maintain a true lab-like environment, with lab meetings and everything. The students also read primary sources such as On the Sensations of Tone by Hermann von Helmholtz and Sensation and Perception in the History of Experimental Psychology by Edward Boring, as well as newer texts on psychoacoustics, which fostered discussions on how humans hear. (We found some really interesting coverage of this by Aristotle, too!)

Below are pictures of the student projects. In years past, students in my two credit hour physics of music course made projects as well, but the longer term allowed us to have more time to design, test, and refine the instruments. The students also were able to make use of the very excellent engineering lab at Wheaton.

It is interesting to me how sometimes a course will take on themes that I don’t plan for. From these projects, I believe the students and I all gained a greater appreciation for the role of resonance to make sounds louder and the challenges with the choice of materials that will enhance resonance while being easy to work with and affordable. The hardware store is a natural place for students to first look for materials, but that largely restricts them to materials like PVC. When I teach the course again next fall, we’ll focus initial design on identifying and selecting materials that will enhance resonance.

 

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.

 

An update (and a recommendation)

It has been a busy fall semester. I know it is for everyone, not just me, though! We have handled a lot personally and professionally and it is now mid-semester. At Wheaton, we have quad courses which meet for half a semester. I’m in the usually dreaded position of adding a course at mid-term, instead of dropping one, but I am adding my Intro to Medical Physics course, so that is not a bother at all.

One particular professional challenge was converting my Physics of Music course, which previously had been a 2 credit hour course, to Physics of Sound, which is a 4 credit hour course with two tags in our new core system, Advanced Integrative Seminar and Scientific Practice. But it is a good challenge - good for me to grow, and I hope it is good for the students! I am really enjoying working with this group of students in particular.

On the research front, my abstract submission to SPIE Medical Imaging 2019 was accepted, so I am very excited about that. To be honest, I’m worried about the funding for travel: our institution has travel funds for faculty but I have already exhausted my allotment for the year. I want to be honest about it because it’s a reality of doing research at small institutions. So I’m crossing my fingers for a couple of options that might come through. More immediately, I am prepping a talk for the 2019 meeting of the Radiological Society of North America, which is conveniently held in Chicago every year. I also have a poster and that is all done.

Lastly, I want to share something I recently purchased that has been a big help to me. I feel like I am always on the search for a practical but nice bag for work. The lines between work and personal life are so blurred that I really need a bag that can handle everything. And I really needed something that could be a backpack. I recently purchased the bag below, by Timbuk2. And it has been awesome. It holds a lot but since the bag is lightweight in the first place, it never feels like too much. Somehow, when it is backpack mode, the weight distribution is especially good and it doesn’t feel heavy at all.

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 Work by Time of Day

In my last post, I shared where my work time went over the Spring 2018 semester. I was curious about when I was doing most of my work, so I broke down the numbers even more. I was interested in knowing how much I spent working before 8 AM, between 8 AM - 5 PM ("normal" working hours), between 5-8 PM (work that would have been going on during the critical kid hours of dinner, bath time, and bedtime), and after 8 PM.

Where did the (Spring 2018 work) time go?

I enjoy reading materials by Laura Vanderkam about managing time. She is a big advocate for tracking time, among several other strategies, especially in light of the fact that most people overestimate the time they spend in different activities (especially work). By tracking your time, you can think objectively about how to change things up. 

I've done a few time tracking challenges in the past, usually for durations of one week. This past spring, I decided to track my time for the whole semester.