PhD Year 3 In Review

My 3rd year flew by. I still don’t believe it is already over and I feel like I still have not done much research.

Things I accomplished:

1. Got engaged!
2. Completed my comprehensive exams and advanced to PhD Candidacy
3. Completed the UCLA Biodesign Discovery Fellowship
   1. Competed at the Rice Business Plan Competition
4. Completed the Anderson Venture Accelerator
5. Applied to an F31 fellowship (we’ll see if I get it)
6. Published my first first-author manuscript in JAMIA open (covidcompare.io)
7. Found a vendor and organized development of the application for digital phenotyping in a large mental health study
8. Outlined what I want my first paper in my field to be on

Things I thought I’d have done by the end of September:

1. Published in my own field
2. Presented at a conference
3. Formed a company

Things I want to do next year:

1. Publish in my field at least twice
2. Have an expected graduation date
3. Incorporate and raise funding for AiroSolve
4. Talk to a variety of people whom the research I’m doing may effect

Most of my time went towards Biodesign, but it was such a valuable experience. I feel like I really know so much more about the different aspects of medical product development. Enough now to know when to ask for help and importantly where to ask for help. Biodesign has given me access to a network of individuals across UCLA and abroad. I’ve never felt well-networked until now. I have the confidence that for the future activities I do I can talk to and work with the right people to help me efficiently along the path.

A big insecurity that’s been building for me is that I have really not done that much research. I was hoping without classes I could really focus on just research and come through with some great publications and advance the field. In practice I’ve been doing more product development, management, and organizational tasks. That being said this year has cemented in me that my focus is and should be translational research. Its something I’ve half heartedly said but now really believe, that specific personal insight has helped me focus my research and how I frame questions. I am less worried about validity and more about the downstream functionality. I luckily work with great people who can ensure the constructs and building blocks of systems I work with are valid and reliable.

Overall though I feel mixed about my progress. I feel incredibly lucky to be in my PhD program, lab, and Biodesign. However, while I have worked hard I also don’t have much tangible to show for it. It feels like people have invested in my potential and I’m reaching a stage where I should be showing some results. On a day to day I find myself flailing from one task to the next pretty often. However, I’m proud I’ve maintained my personal and social life. This Ph.D. program has given me time, flexibility, and a large degree of freedom but with that comes balancing efforts between my aspirations, daily happiness, and distractions.

Getting engaged this year is definitely the highlight though.

Notes

Below are real time, minimally altered notes taken during the past year. Each paragraph per section corresponds to one of the “updated” times.

Summer 2021

Updated:

• 08-09-2021
• 09-08-2021

Life Context

Moved into apartment with Shar, had wisdom teeth removed, went on vacation to Joshua Tree for a weekend, now living at home for 2 weeks before biodesign bootcamp.

Back in LA, got a dining table and more house stuff set up. Shar and I are actually living together now for a longer period of time.

DGC Research

I’ve primarily just been writing my prospectus. From helping Alex on another grant I gained a better idea of how to literature search and have just been pounding through papers as I refocus my prospectus from metric validation and depression trajectory modeling to individualized mood models + participant clustering. Most days I write a paragraph or so, read a half dozen papers, and reflect on findings. I’m at like 8 pages of content, mostly lit review for my prospectus but feeling much better about the direction. The lab meeting where I presented my old 2 aims was really informative for this new direction. Starting to feel like I actually know things.

Finished the first draft of my prospectus 2 weeks ago (just before biodesign bootcamp) and got feedback from Alex. Main points were digging deeper in to aim 1 similar to what i did for aim 2, and reformat. Also creating figures to better tell a story. I think this next draft is going to be much clearer. The date for my actual prospectus presentation is going to be pre-thanksgiving November.

Biodesign

Biodesign is starting to almost start. In 2 weeks we’ll begin bootcamp, but some prelim emails and slack invites starting now,

Bootcamp was really cool. I was a bit overwhelmed going in to the Medical Center at 8am to professionally socialize with physicians, professors, entrepreneurs, but it was actually pretty fun and intense. Learned so much, especially about team building, company formation, and from the CEO talks. Wild how many really talented and accomplished speakers we got to hear candidly from. The Saturday of Bootcamp was fun since we had a beach retreat after, got to play volleyball with VCs. The fellows are really nice too, played smash ultimate with professors, planning to surf and watch the new marvel movie (Shang-Chi). We had an “innovation sprint” in which we were presented a problem and asked in teams of 4 to go through the full biodesign process in 5-6 days ending with concept generation. Our team did awesome, especially balancing life priorities with work. I missed a PPE training because I didn’t check my calendar and felt really bad about that but hopefully its okay.

Opioid Overdose

Met with Collier collective people who seem interested in just staying in contact as our interests align. Submitted covidcompare.io manuscript to JAMIA open as it got rejected from just JAMIA.

Worked on the FORE Grant that Dr. Shover is applying to and me and some others will be co-investigators on. Seems really promising. I’ve done nothing related to this work in a while though.

Fall 2021

Updated:

• 10-10-2021
• 11-17-2021
• 12-09-2022

Life Context

Lots of events (birthdays, holidays, etc.) this quarter so out of LA almost every weekend. Fun but chaotic with everything else going on. Been going to more in person UCLA events as will which has been nice. Things like retreats, lunches, happy hours, and even just meetings.

More birthdays and holidays. Went to Outside Lands all three days, LA Craftoberfest, 3 nights beachside in San Diego for Shar and I’s combined birthday bash with 20 friends.

Winter break went to Montana, got COVID asymptomatic, isolated. Felt really burnt out and tired, got some of that reduced but not all, wish I had another week of break. Omicron variant spreading everywhere → campus remote until Jan 28th now.

DGC Research/Thesis Proposal

I’ve completed my written thesis proposal, submitted it 2 days early (Oct 6th instead of 8th). Now prepping my slide deck and updating figures. I’m both confident in my work and terrified about what I may have missed, but excited to have my committee review and improve my work. For my actual presentation, my advisor will be doing 3 hour long practice sessions with me to make sure I’m ready. First draft of my slides is due October 11th. On the side we (people working on the DGC project) are also working on better organizing the data from the DGC studies to aide analysis efforts.

I passed my Oral qualifying exam on Nov 8th. It was kind of underwhelming, I didn’t get many questions on my methods but more so on what the exact clinical statements I can make are. I definitely didn’t expand on the real limitations of what I propose to do. Overall it seems to have gone well though. Excited to be a candidate, but hard to feel proud of myself because now I’ve spent a lot of time talking about what I’m going to do instead of doing it. I think once I’ve begun implementing I’ll feel better about this whole PhD thing. A lot of what I’m doing now is writing documentation and helping guide database related planning for the full study.

I’ve been getting feedback that mood monitoring isn’t clinically relevant/important and I disagree. I do believe that being able to infer daily mood from fully passive data streams is a big step towards mental health monitoring, although not the full thing on its own. I’ve begun implementing the pipeline for daily data aggregation and mood prediction, but much slower than anticipated with all my other obligations.

Biodesign

Biodesign has been awesome and chaotic. I’ve begun clinical immersion and had experiences in sterile processing, the cath lab, the cardio-thoracic intensive care unit, and the sleep clinic. It has been very eye opening to enter these spaces and observe. I definitely notice that compared to my more clinical colleagues, I am much less comfortable and able to understand whats going on. I do think my observations add something to what our other team members see, but definitely not on the complicated medical procedure details side, I’ve been more useful in observing things like culture and process. Only downside of clinical immersion is that scheduling other meetings is super hard. I don’t know until almost the day before if I have an immersion scheduled or not so I may have to miss a meeting. Part of that is I prioritize very few things over the experience of clinical immersion right now.

Biodesign continues to be a really important experience for me. I’m appreciating more and more the opportunity I was given to be in all these different clinical spaces. We have moved from in patient to more out patient settings (cardiac rehab, sleep clinic, remote patient monitoring) and seeing things come full circle has been super useful. I’ve been asking peers about how to do qualitative and mixed-methods research and its super hard and in depth. I think for a program which is based primarily on solidifying a real clinical need before coming up with solutions we should have an expert at observation as a member.

We finally reached the stage where we have a problem space we want to work in. Our team is excited about it and seems like our mentors/advisors are as well. Took a lot of work to see if different need areas are feasible especially in the context of a 10 month program to work on. Learned so much about how to do market and business related research. I think understanding regulatory pathways and reimbursement is still our weakest area, but we’re trying to improve that. Began working on an equity in Biodesign paper with Laura and others affiliated with Biodesign. It’s an interesting gap in that typically medical innovation and the biodesign process doesn’t focus on equitable access and performance. I think we’ll be able to contribute something new. Glad Laura asked if I was interested in helping, but also a little overwhelmed with tasks.

Overdose Work

No update

Fixed the NEMSIS scraper so that it works with the new UI changes. Hoping to have a full visualization for the overdose now-casting platform by end of this year.

I’ve been working on creating a front end viz tool for now- casted and forecasted U.S. opioid overdose data. Also been building integrations with the CDC Wonder API to pull the data we need, but their API is a little buggy for the provisional dataset that was just released. In contact with the CDC technical support and they responded super quick, was pleasantly surprised. The issue remains unsolved but glad they are aware of and working on it.

Winter 2022

Updated

• Feb 10th 2022
• March 7th 2022

Life Context

Been going on a good amount of trips/events these last couple of weeks. Surfing in San Onofre, Ski trip in Mammoth, had friends visit for 5 days, partied in Cabo for 3 nights. Also lots of hanging out with friends on the weekends and weekdays between those trips. I’m kind of socialized out. Definitely not the most COVID-responsible thing but I have all 3 shots and got COVID asymptomatically in December so I feel dangerously immune. Also I have been routinely testing myself to ensure I’m not an absolute hazard to the world. Been feeling on-and-off burnt out from working non-stop many days and not letting myself really relax on the weekends. Even the weekends we had trips and such I spent good chunks working as well. I think I may have taken on a little too much where I don’t feel like I’m making enough progress on any particular domain.

Continued to socialize a good amount, beach days, valentines day celebration (Sharvari treated me to an amazing Omikase sushi experience), visited home, adventures in downtown LA, went to small concert. I know I said after Cabo I was “socialized out” but there are so many fun things happening. I do need to spend more heads down working time, the weekends leave me a bit strained on Mondays. Shar just left for 10 days for work/fun travel which does give me some time to re-center as my social calendar will lighten a bit.

DGC Research

I have barely done any of the implementation of the things I proposed. I have put together a preliminary pipeline for doing mood prediction from wearable device data and analyzed missingness within sensor data for the studies I am working on, but also I thought I’d just be so much farther by now. This work is something I need to prioritize harder, but lacks a firm deadline. A lot of my time has recently gone to figuring out application development for how we will collect sensor data for another digital phenotyping project under the Depression Grand Challenge at UCLA. I’ve been in contact with 3 companies who may be potential vendors as well as trying to estimate if we could implement the app ourselves in a reasonable time period using tools like CardinalKit. Been a pretty cool experience talking at such a high level with established companies. Last thing I’ve been working on is reformatting my thesis proposal in to a 6 page document to submit as an NIH F-31 grant. Surprisingly hard to condense information, I got it from 13 pages with figures to 6 without figures so far.

Honestly I have not made much progress still. Much of my time still goes to figuring out details of the new research project thats in the works. I have written much of my F-31 grant submission, almost done with applicant background which is the second 6-page part and have some results to add to the research portion. I am not satisfied with my pace of work though, and need to allocate much more dedicated time to my research.

Biodesign

I’ve been alternating between putting 80% and 20% of my time in a given week to biodesign. Our team had a really exciting brainstorming session to figure out some potential embodiments of our product. I’ve also been doing more clinical immersion and even shadowed nurses during the night shift til midnight. We’re slowly getting somewhere, but I’m a little surprised that I still don’t know where. We are still far from a prototype or product idea and I think we may pivot in many directions. We also began working with people from quality improvement initiatives at UCLA Health to collaborate on data analysis that would also benefit our team as the initiative is within the problem space we also want to work on. Also my reports on biodesign will get progressively vaguer as we enter the ~IP~ territory.

Large update here is that I’ve brought up switching teams and discussed this with both my team and the second Biodesign team. I really like working with my team, the only motivation of the switch is that the second team is just working on a problem space in which I have real expertise, the specific expertise their team also is lacking. I think I could really contribute there more so than my current team. Had a lot of honest conversations and we may move forward with a team switch after the formal biodesign program. Our current project got really kicked in to gear though as we are now officially accepted to compete in the Rice Business Plan Competition. We have a really aggressive timeline to get some provisional IP filed within a month.

Overdose Work

Been slowly fleshing out a data visualization tool for the overdose now-casting and fore-casting platform Joe and I are working on. Able circumvent needing a SQL database for this project by just using a Gatsby based static website and github pages. Ran out of free credits for covidcompare.io so the database is down :(. Hoping to find a new way to host that without tapping in to my luxurious grad student stipend again.

Able to covidcompare.io back up and running. Also secured a website domain for the overdose tracking site Joe and I have been putting together. Most of the components are functional, now I just also need to link together the data scraping pipeline with Joe’s analysis code and have that run monthly or so with automated data updates to the visualization tool.

Spring 2022

Updated:

• April 18th 2022
• June 4th 2022

Biodesign

Our team Airosolve had a whirlwind of a time getting prepped for the Rice Business Plan Competition. We defined our product, made 3D renderings, branding, product specifications, a pricing strategy, regulatory strategy, filed a provisional patent, put together a pitch deck, and sent it. Learned an incredible amount from the competition, made friends with many of the other teams competing and broadly had a great experience. The week of the RBPC was the hardest I have ever worked and maintained functional capacity. No longer will be switching teams as I’m way too invested in our current product and problem space. I’ve continued to look at the hyper-oxygenation dataset at UCLA and come out with some preliminary results that we are now refining.

The rush to keep pitching we felt post RBPC slowly faded as our team began focusing on all the things we still had to do work wise. We’ve hit a strange spot where pitches truly feel like a distraction. I’m building out our first prototype after we’ve gone back and forth on if we really need a prototype, but its really a good grounding component to have if we can produce it in house. As we prep for biodesign graduation on June 23rd conversations over what we’ll really be doing post-grad on Airosolve have been more and more real. With two of our team members being full time doctors, its effectively going to be just me and our fourth team member (who is also a full time physician and MBA student) working on the project next year which honestly scares me, I don’t want the responsibility of being the backstop of progress. A couple times this year we’ve had many of our members be fully occupied with clinical or other duties which has left it often to me to be the one doing all the “keeping it running” tasks like prepping for our weekly meetings and such. Overall though I still feel really happy with what we’ve done and the promise of our product and would love to see this through, however I won’t be the champion of it, its too far outside my area of expertise and where I see myself working in the future (digital health). I also am liking the data analysis I’ve been doing looking at hyper-oxygenation in UCLA ICUs.

Depression Grand Challenge Research

I definitely neglected my PhD dissertation topic during prep for the business plan competition. For a lab meeting presentation I put together more results and presented on the use of mixed effect models for daily mood prediction from Apple watch data. This was happening during our prep for Rice and so I was very pressed for time but having the lab meeting presentation deadline was really good to get me back to working on my primary research. I re-remembered that I really like this work. I’m also no longer submitted for the April deadline for the F-31 grant and will be aiming for the August submission.

Once more i feel like I wish I had more time to work on DGC related research. One of my peers has been absolutely killing it and doing really good/rigorous work on the datasets. I’m honestly a little jealous but excited for when Biodesign slows down so I can once again try to focus on a main project. I’m at a point where I have a rough idea for a paper I want to write in the mental health/digital health space though and excited to flesh that out.

Overdose Work

Have not really done much. Put together a preliminary UI but need to now build a pipeline to get data end-to-end and feed in to the data visualization. Meeting with Joe to get back on it soon.

The CDC api I was having trouble with works now! Emailed the CDC Wonder team and they fully helped me debug my API call with their updates and it was successful. Now we just have to put our full data aggregation + forecasting/nowcast pipeline together and get a website running before we submit a manuscript on the work.

Summer 2022

Updated

• July 5th 2022
• August 16th 2022
• September 25th 2022

Life Context

I am actively flying back from a trip to New York where I had quite a blast for 5 straight days. My body is tired and I’m ready to head home. Been pretty deep in planning out how to propose to my partner as well, most things assembled and rings ordered. We’ve had a lot of social activity these last couple weeks, I even went on a retreat to Santa Barbara for the bioinformatics program which was also real fun but I barely slept. Before that went home to Northern California and before that we were in San Diego for a weekend. Going to unwind and re-work for a week before heading to Chicago on July 12th.

I proposed to my now Fiancée on August 6th 2022! The event went amazingly, we had a really nice afterparty with close friends after and a lunch with our families the day after. Shar has since gone to Houston for one of our close friends white coat ceremony and unfortunately got COVID and is stuck there quarantining. One day I’ll see my fiancée again.

Have been engaged now for almost 2 months, a lot has happened since then. Finally got some time with my Fiancée after she came back from COVID quarentine in Houston. My cat (Noodle) had to go to the ER for a couple of days but is luckily fine now, my partner’s family dog passed away, had guests for a couple weekends, went to a concert, and just recently got back from a trip with my family to Alaska.

Biodesign

We graduated late June! I’m now going from 50+% of time to Biodesign to just 10 or so percent. I’m proud of what we accomplished in the year. I was successfully able to build our proof of concept device. I am a little mad that I still haven’t been reimbursed the almost $3000 for travel and prototyping expenses. This has been such a great learning experience overall, I do hope AiroSolve and our product ends up continuing and from the team discussions we’ve now had and equity split discussions we finally settled on sounds like we will. I was pretty scared a lot of work would be my responsibility, but the team did end up taking on a good amount of tasks outside of the product development arena. We’re onboarding a new team member for the summer and I really hope I am able to provide them a good experience as they would be working primarily with me on engineering. It has been nice these last two weeks not doing much biodesign. I have done more analysis of the hyper-oxygenation dataset, hoping to push that to a manuscript soon while figuring out some more of the complexities, sanity checks with EHR data analysis. We are surprised we didn’t see more mechanical ventilation patients in the dataset so really need to investigate that.

Progress has been slow, but that was by design, we all needed a bit of a break from AiroSolve and also started some important next life steps. We are back on it though, part of the Anderson Activate program in UCLA’s business school and will be part of the Biodesign Accelerator program next academic year. We wanted to have a new team member onboarded but due to the fact we are actively building out our patents, it isn’t really possible to have a member on board until we finish incorporating. This is due to a flurry of legal reasons surrounding intellectual property ownership between us, UCLA, and a new team member. That being said we are also in the process of recruiting other key holes in our team to ensure we continue making progress. I’ve also continued doing data analysis work on oxygen therapy in the ICUs, but we’ve learned that there must have been an issue in the data requested as there are way too few COVID and mechanically ventilated patients in the data set given the time period. Going back now to contact the team that pulled the data to help out.

Our team (AiroSolve) completed the Anderson Activate summer accelerator and started the Biodesign Accelerator program which kicked off with a week of bootcamp consisting of 8am-5pm+ daily talks, lectures, panels, and activities including a tour of Edward’s Life Sciences. The bootcamp was great to meet the new fellows and get refreshed on all the different aspects that go in to medical innovation. It was overwhelming last year as a discovery fellow and only kind of overwhelming this year. I was able to ask more questions since the talks on things like incorporation and intellectual property were relevant to the stage we are at with AiroSolve. We’ve solidified our equity split and are in the process of finalizing paperwork to incorporate and bring on new team members. Progress has slowed but we’re figuring out how to work best as a team with all the founders having a full time jobs especially given the three other founders are all medical doctors. I go through waves of feeling like we’ve done so much and everything is possible countered by waves of feeling like its too much work and no longer relevant to my research on wearables for mental health monitoring and broadly digital health. That being said I do think this is a worthwhile endeavor and a big unmet need which has kept me focused, excited and ready to work on it. Communication within our team has been very strong and worked to help keep us all aligned and honest.

Depression Grand Challenge Research

These last 2 weeks post Biodesign I’ve felt a lot better about my research direction and pace. We are now creating a slide deck to actually present to Apple with goals of fostering collaboration and discussing the research. I definitely have been re-focusing a lot of my research now-a-days. In my prospectus I centered on higher level pipeline development for predicting daily mood but I think I need to now go back and do more granular theory driven research to see if measured behaviors linked to the phenomena we think we’re measuring → looking deeper in the psychology literature and theories to drive analysis. It’s interesting because when I started writing my prospectus I did begin with a desire to start from theory and ask targeted questions derived from the causal diagram or potential mechanism. I shifted away from that in favor of centering on creation of a system to do mood monitoring as I do personally like focusing on the more translational side of research. I’ll need to meet somewhere in the middle, and I’m enjoying this re-exploration. Kerneau, one of the main people I work with has done a lot of this theory driven/targeted analysis and has been very influential now to where I see myself focusing, somewhere between system implementation and psychiatry research.

A lot of my time in the last month has been dedicated to fleshing out my F31 fellowship application. It requires tons of documents to be written. I thought that since I had written my research strategy portion, I was mostly set, but I was wrong. So much writing. Got it submitted on time (August 8th) so hopeful it goes well. In the process of writing I did begin to feel like I had somehow carved a logical path in the last three years, centered on translating research in to clinical impact. With that finding its helped my refocus the actual analysis I want to do now. I was pretty burnt out after the grant, Biodesign, and getting engaged so took a couple days to fully do nothing but watch anime and this last week have really started digging in to the methods I think of most interest to me. In particular I am focusing on the implementation of anomaly detection and use of detected anomalies as a feature in mental health related prediction tasks. Its crazy to me how much not being burnt out makes me enjoy the work I do and focus more naturally.

After proposing to my fiancée i had a good two weeks were I did so much research. Since then other tasks have overtaken a majority of my time. A big one being Wellcome leap project management type work. I have however made steps to maturing my understanding how to incorporate anomaly detection and had great conversations about the methods and am fleshing out and expanding the scope of my work in a direction I’m excited about. I just need to do the work. Another barrier to the work is that the computational environment we are supposed to be working on has been delayed for over a month from the last set of delays so haven’t really touched the data in a while. Big goal is to publish in my field by the end of Fall quarter. I reviewed and revised my Notion set up to better align with my work and keep track of my big goals and deadlines. Made me feel much clearer about progress.

Overdose work

No real update honestly, Joe has restarted med-school post getting his PhD and I definitely need to follow up.

Still no real updates.

Also no updates.

Wellcome Leap Work

The last couple months I’ve also been tasked with working with a company called Ethica to develop the data collecting phone app used for a study the DGC is doing funded by the Wellcome leap foundation. We were supposed to have the app ready to enroll patients by April… we are not ready yet. I’ve been pretty intensely emailing and coordinating with many different players, UCLA’s app development team, the back end UCLA AWS team, Ethica’s app dev team, and the DGC leadership to ensure things keep moving forward. I didn’t really realize how much work it would be or how much can go wrong and also didn’t really realize what my own role in this was for too long. I entered as “grad student trying to find company to do app dev” and am now the central information point for the bottleneck holding up a large study. As a side i’ve also been trying to implement an algorithm called DPSleep that calculates sleep/activity metrics and was created by other researchers in the WL foundation. I’m trying this to see if we can apply it to Apple watch data as the package is built for GeneActiv watches. As part of this trial, me and 2 others will be wearing both an Apple Watch and a GeneActiv watch and rigorously tracking our days for ~3 days to compare the outputs. I have failed to get DPsleep to work for weeks, a lot of version issues and package issues as DPSleep uses Matlab wrapped in python.

There was some serious pressure from DGC leadership to push application development quick, I was sending daily updates up until we learned that the big issue with getting the application developed for the study was related to an approval needed from Apple. After a month more of delays we finally have that approval and I’ve asked the Ethica team to get the full featured application out as soon as they can which hopefully should take less than a week.

This experience of kind of managing the application development for a digital health study has taught about many of the ways things can always go wrong and that delay’s are to be expected and planned for. We still don’t have an App that can collect all the data we need but feel like we’re almost there. I have gained a pretty intimate understanding of how Apple’s metric collection functions though which has been valuable as well as better grasp of systems used for data handling in digital phenotyping. We need an app by next week or risk funding getting pulled so curious how that will all go. My trip to Alaska coincided with what ended up being a critical period for deadlines on application development and I feel bad I didn’t handle letting people know early enough. I had informed Alex well in advance but not really the rest of the people I work with in an explicit way (mentioned in meetings and such). I need to definitely do a better job of that next time.