IRES Students will be posting updates on this page throughout the summer.
Click on the headings to read each blog post!
Emma
My first week of the program has mainly consisted of our orientation weekend, exploring possible directions for my research this summer, and getting settled into Stockholm. Since I just finished my first week, my lab work is still in the beginning stages. I've been reading papers, familiarizing myself with new concepts, and learning how the lab operates. I've also been given cake at work 2 days this week, which I've been told not to get used to.
While most of my experiences exploring Stockholm were throughout the orientation weekend, I have been going on walks around the city, trying to explore as much as I can. One thing I've observed while exploring is how there are so many people hanging out at parks, having picnics, and socializing after work. From talking with people in my lab as well, I've noticed the strong emphasis on work-life balance. This differs from where I grew up, as I feel like there is less of an emphasis on having a good work-life balance and less accessible community-based spaces. While I expected there to be a difference in this area, I've never been able to experience this first-hand. From the number of parks, outdoor gyms, playgrounds, running trails, and more, I really enjoy how Stockholm reflects the importance of life after work and places that build community.
Lyra
Our first week in Stockholm has been amazing so far! We were very lucky to have beautiful weather during our first weekend in the city. Mark took us to some of his favorite tourist-y sites: a lovely café in the Royal Djurgården, the Nobel Prize museum, the royal palace, and more. I especially enjoyed learning a bit of Swedish history on our guided walking tour of Stockholm's old town and seeing some of the gorgeous old artwork in the palace.
The work side of things has been going well, too. This week has largely been about orientation—getting a keycard to the building, reading papers for background on the lab's current projects, meeting with other members of the lab to hear about their personal work, and the like—but I'm excited to nail down the details of what I'll be working on this summer soon so that I can dive into a project of my own.
It might seem a little silly, but some of the differences between Stockholm and home that I've noticed the most have been the smallest things. For example, when you unscrew the cap on any kind of milk or juice carton here, it doesn't come all the way off; one corner of the cap stays connected to the plastic ring around the spout, so you can't set the cap down and walk away from it or misplace it—it's so convenient! I don't know why everyone doesn't make cartons like this. There are also these great little tetrahedral packages of shelf-stable milk that seem to be the norm to use in coffee instead of creamer, and as someone who isn't the greatest fan of creamer, I've been enjoying them. It took me a little while to work out how to open and empty them reliably without spraying milk on myself or on the counter, but I've gotten the hang of it now.
Not all the small technological differences have been quite so delightful, though. For some reason, I and everyone else in the group who I've talked to about it have been having trouble with doors. We keep trying to pull on doors that ought to be pushed, across many different doors and buildings, even when we've gone through that door several times before and really should know better. I haven't figured out yet what the core of the problem is. I think there might be some small difference in the standard way door-frames or hinges are made here that's affecting our learned ability to subconsciously tell which way a door swings based on visual cues, but when I don't have any American doors to compare these ones to, it's hard to confirm or reject that theory.
Despite my minor door- and milk package-related travails, my time here so far has been great! I can't wait to start working in earnest on my project in the Daub lab, and our ten weeks here in Sweden are already starting to feel short what with how many little adventures in Stockholm and across Europe I want to plan. I don't know exactly which ones will end up happening yet, so be sure to check back here around July 4 to find out in my next blog post. I'll see you then!
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Emma
Walking in Old Town
Nobel Prize Museum!
The Royal Palace
Chinese Pagoda in Hagaparken
Lyra
Excellent vegetarian ramen from Rosendals Trädgårdskafé
The chapel at the Royal Palace
Two of the lions that guard Stockholm's pedestrian streets from cars
A pretty street in the Old Town
Rony
We've all been in Stockholm for a mostly lovely, sometimes overwhelming 2 weeks now, and I'm feeling well settled in. Things have begun to take their shape around me, and I no longer eagerly need google maps to be comfortable around Solna.
I've also begun to pick up on the 'little' things that really make Solna feel like home: I now know that you can change the air pressure of the shower, where to dispose my garbage bags, that you have to press the 1hr power button on the kitchen counter in order to use the stove top, and I'm finding shortcuts to many familiar places, such as the gym and my beloved Pita Baren (photo shown below).
I've gotten acquainted with my amazing lab mates, their research and diverse backgrounds, and I look forward to lunch with them every day. On Wednesday, my PI, Fredrik, returned from the International Breast Density & Cancer Risk Assessment Workshop in Hawaii, and I finally got to officially meet him and hear about the perfect weather, magically blue water, and mesmerizing hikes in Hawaii -- and of course about the research being presented at the Conference.
Fast forward to Thursday, After our weekly workshop on Thursday, the group met up with local medical students at Karolinska doing a summer research program. Today was pancake Thursday in the hospital cafeteria, and they excitedly and warmly invited the group to join them for lunch. I learned that pancake Thursday is actually a tradition in Sweden, accompanied with pea soup, and growing up, they'd have it provided by the school. I learned Saturday is when the Swedes have candy, and I can't remember which, but one day is dedicated to Tex-Mex style tacos.
In the virtual training series, Mark told us about the Swedes way of living -- humble and equality, discouraging boasting about one's accomplishments -- and this was confirmed by the local medical students, who told me this concept even has a name: Jantelagen, or the Law of Jante. We discussed the dichotomy of this to other western approaches, such as the largely individualistic and ambitious way of life in America, and how it's encouraged there. One of us had said "ambition is good for yourself, but not for others", to which someone else responded "but good-willed ambition can be good for everyone", which is what, I think, has drawn me into the research I'm conducting here at the Karolinska Institute, my lab is ambitious about helping, diagnosing, and giving true clarity for women undergoing breast screening to prevent disease. To be ambitious for others is to have a good-willed ambition.
Looking ahead, this weekend, I'll be flying to Paris to meet up with my girlfriend, Maggie, who's currently in Spain doing an internship. Friends from my home university have been traveling through Europe, and had just come from Paris, telling me about the wondrous suggestions they got from a Parisian to explore the city. I'm excited to take some of those suggestions and do some exploring of our own with Maggie.
Until next time, farväl! :)
Julia
My first weeks in Stockholm could be best described as an exploration period. Exploring the city, the culture, and being introduced to what seems like an endless amount of people and options for projects as well. The first few days were spent completely adjusting my sleep schedule (I was waking up at 4 am everyday for the first 5 days), learning words like Utgang, Meny, and Hemköp, and remembering to press automated door buttons as I adjusted to life in Stockholm. The first weekend, we took tours of parks and Gamla Stan, learning about how Stockholm gained it's charm and history.
We visited the Royal Palace which was covered in gold and renaissaunce-esk paintings, followed by me and Elle having 8 cups of coffee over the course of the weekend. Stockholm really knows how to get their Fika on.
Following the first weekend, I met my PI, Magnus, who is more of a jack of all trades when it comes to AI and ML applications. He works on projects spanning from topics around education to finance to mental health to cancer. It seemed as if I was learning about a completely different division of ML application everyday as I followed him to each and every meeting over the course of 2 weeks. I had the opportunity to attend the AI@KI retreat to meet even more people and learn even more about how AI can be applied in clinical settings and with that was able to make some new Swedish and non-Swedish friends over some perspective altering conversations. From this I picked up the friendly and agreeable 'hmm, hmm' ad lib to indicate my intentional listening. It was enlightening to be greeted with such respect and curiosity from people who I perceive to be experts in everything. My previous interpretation of the academic world took a positive shift as my previously heirarchical notions began to crumble.
Finally, a few friends and I left for Barcelona where we spent the at Sónar music festival and the days exploring all the art, architecture and culture we could possibly ask for in the span of 2 days.
Overall, the first two weeks have been an incredible experience and there's been so much information to take in. Life-long learning I suppose.
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Rony
Pita Baren -- fantastical chicken gyros. My current favorite local food a walk away from the residence
Late night near Gamla Stan
The world's third largest IKEA store in Älmhult with friends from my home university
Eating some home-made lingenberry jam sandwiches at a beautiful and calm lake halfway through a hike
Julia
Painting on the Royal Palace Ceiling
One of my 27 coffees this week
Casa Milá Rooftop in Barcelona
AI-UPP Squad in Djurgarden :D
Jooeun
I can’t believe we’ve already finished our third week in Sweden! This was also our last three-day weekend during the 10-week program. Since Saturday was Midsummer’s Day, the town we’re staying in was nearly empty as most people had gone out to celebrate. Unfortunately, I wasn’t feeling well on Friday and Saturday, so I didn’t join the festivities. I mostly stayed in and took a quiet walk around town to do some grocery shopping, but the streets were practically deserted.
I did make a solo trip to IKEA to pick up a few things for my apartment. It was fun seeing the same items I’ve seen in the U.S., but priced in Swedish krona instead of dollars. I didn’t take any photos, but I did get to try authentic Swedish meatballs—right here in Sweden! I bought some items I need for kitchen, trashcan, and some cute little plushies for myself.
With Mark heading back to the United States, we had a farewell pizza dinner with everyone on Wednesday night. The pizza was absolutely delicious, and it was such a nice way to spend time together as a group. Partway through dinner, it started to rain—but instead of heading inside, we decided to stay outside. After we finished eating, we all went out for ice cream together. It was such a fun and memorable experience!
Elle
I’m super excited to finally be here in Stockholm! I’ve loved meeting everyone in the program in person and getting to explore the city. My favorites so far have been the Rosendals Tradgarden cafe on the Djurgarden island and Gamla Stan (old town). I’ve also been loving all of the running trails. On Sundays I go on trail running adventures where I take public transit to a trailhead, and do my long run form there. It’s a great way to explore the city and find beautiful trails. I've also been able to travel to Barcelona with som eof the people I met here. It was definitely an eventful trip! As for my lab work, I was lucky that my advisor gave me a project topic and my data right away. I have been doing a lot of background research and some coding practice, but I’ve also been able to jump right into some analysis. So far I’m super interested in my project topic and excited for the work I will be doing.
One practice in Sweden that I love is fika, where you take a little break to have coffee and pastries and chat. There actually aren’t any Swedish people in my lab, but it’s still nice that they take fika breaks every once in a while. I have also made some friends in the lab by suggesting fika and having some nice conversations. My reaction when I noticed this difference was to be happy that there is a less rigid work culture in Sweden when compared to the U.S.
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Jooeun
Solna Centrum Metro Station
Dinner with lab member at restaurant Voodoo Room
IKEA
Pizza dinner with everyone at
800° Grader
Elle
Very fun trip to Barelona! Highlights: Sagrada Familia, Sonar festival, beach!
Maypole dancing in Skansen for Midsummer! Don't watch the movie 🫣
A very lovely sunset on a run in Hagaparken
On Sundays I go on trail running adventures. This was especially beautiful, but I could not tell you where I was!
Josh
When I got to the lab, I had already been given a project with the option to be the project lead. Since then I have been working with the data and been analyzing it and creating visualizations for the findings that should be conveyed. The next steps for me is to finalize the visualizations then begin writing a paper on the data and findings which I find a little bit frightening. As for exploring Sweden most of the exploring is being done on the weekends, but I love going into the city and just being around different people. My favorite place in Stockholm so far is either the old town area or just being on public transportation and seeing so many people. I have also started to do some exploring of Europe, as I have been to Barcelona and have plans to go to Copenhagen, Amsterdam, and hopefully another big city.
During my first week, I think one of the biggest differences I noticed was the amount of people using public transportation and biking. In the US, a lot of people will ride around in cars, but here it is nice to see a lot more people out and about outside of a car. I wasn't surprised, but was kind of happy to see people biking and getting some exercise while getting to where they need to go. I have since hopped on the wave and rented a bike. I very much enjoy it and maybe will keep up with cycling in the future.
Eric
My project this summer involves using spatial transcriptomics data obtained from breast cancer tissue to characterize various subtypes of the disease. If this sounds vague in terms of a research question, it’s be cause it is. I found out on my first day at work that the specific question that I wanted to answer would ultimately be up to me. This was quite different from my other research experiences in which I was given a question to answer by my PI. So, my first several weeks in the Daub lab have consisted of doing a literature review of the topic as well as a survey of the data that was available to me. I have a decent background in immunology, so I wanted my project to be related to immune cells in some way. I discovered that B-cells have unpredictable effects on how breast cancers progress. I also discovered that the transition from in situ ductal breast cancer (DCIS) to invasive ductal breast cancer (IDC) was not well understood. My idea for a research question after all this was to characterize the activity of B-cells in DCIS vs. IDC tissue. I had data that was available to me that could be used to answer these questions. I really enjoyed this process of getting to design my own experimental question. In turn, I think I will enjoy more the process of answering this question. This week, I finished my (intended) workflow to answer my experimental question and have started to analyze some data.
Outside of the lab, the AI-UPP cohort has gone out on weekends to explore more of Stockholm. Upon arriving in Sweden, we first explored Gamla Stan (the old town part of Stockholm). During subsequent weekends, we’ve also explored the museum art in the various train stations across Sweden and when thrift shopping in the south side of the city. For national day, we went to an outdoor celebration/orchestra concert at Hagaparken. For midosmmar, we went to Skansen danced around the May pole. We even took a trip to Barcelona and will soon take a trip to the Tatra Mountains in Poland. My PI hosted a lab dinner and took also took us rock climbing. I most recently went to the national museum of art with some members of my lab. Evidently, a good work-life balance is easily achievable in Sweden. My favorite aspect of work culture is having fika in the afternoons of occasional work days. Fika is an afternoon coffee with pastries and snacks. In the Daub lab, we have fika whenever someone has successfully defended their thesis or if someone is moving away soon. I also enjoy how the lab has lunch together. All these make for the opportunity to take a short but effective break from work during the day.
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Josh
Lovely Night in Stockholm
Skansen for Midsommar
Old Town Stockholm
La Sagrada Familia
Eric
Lunch at Rosendals Trädgårdskafé
Midsommar Sunset
Rock Climbing with Lab
Swedish National Museum of Art
Emma
Since my last blog post, I’ve been up to lots of exploring and even some traveling! I’ve gone to Barcelona, Spain, and just got back from Kraków and Zakopane, Poland. I hiked the most I ever have this weekend! During the weekdays, I’ve also been trying to explore new areas in Stockholm. In the lab, I’ve been attending a variety of meetings and starting to get deeper into the work on my project. My main focus in the lab has been analyzing methylated and unmethylated DNA to estimate methylation at CpG regions. Additionally, I have been learning about DNA motif analysis and new tools to analyze this data. I also went to my lab’s 10-year anniversary at Kastellet in Stockholm!
Since starting my research work, I’ve often found that there are so many different directions you can go, questions to investigate, and ways to view a problem. To overcome this, I’ve focused on finding ways I can expand upon the tasks I’m given, finding more ways to analyze and view questions. This has taught me about the endless possibilities in research, along with growing my abilities to think in diverse ways. I’m fortunate that my lab has given me the freedom to investigate my project from many perspectives, allowing me to grow in my critical thinking and as a researcher. One challenge that I’ve been struggling to overcome is figuring out some analysis when I don’t have enough data. While this has taught me many different ways I can look at the data I’ve been given, it also has made it difficult to know if the work I’m doing is relative to my specific samples, or has the potential to be generalized further. In the future, I will try to deal with this type of challenge by actively seeking out what type of analysis is appropriate for the samples I have and seeing if I can find similar data.
Lyra
Hello again! It's only been four weeks since my last blog post here, but somehow it feels like it's been way longer and way shorter at the same time. I've been getting up to a lot of exploring in my free time, both around Stockholm and outside of Sweden. So far, I've managed to visit Barcelona and Paris on two of my more action-packed weekends, and both were lovely—the highlights of each trip for me were probably the Palau de la Música Catalana in Barcelona and a tie between Sainte-Chapelle and the Palais Garnier in France. What can I say, I love some impressive stained glass. On the home front, my favorite recent discovery in Stockholm is Java Whiskers cat café, where I met an absolute sweetheart of a tabby named Trouble. I'm not sure where she got the name, since she seemed very calm and cuddly to me!
On the research front, most of my work up until this point has just been figuring out what my summer's project will be. Unlike some of my peers, my PI, Carsten Daub, didn't offer me a pre-designed project, so I've had both the privilege and the challenge of coming up with my own plan for what to work on. Since all my previous work in labs has involved projects my PIs handed me from the beginning, designing one from scratch has been a new experience, but a valuable one for me to carry into future academic pursuits. It's been a long road of diving into background research, meeting with other past and present members of the Daub lab to hear about their work, and attending Karolinska seminars for inspiration, but I've ultimately settled on a plan as of just a week or so ago, so I can move forward with the project proper!
...Well, I would be able to move forward with the project proper, if I weren't having an unfortunate series of technical issues accessing the lab's remote server that are so far stumping even the IT department. Since I can't get much done on my project without the server, I'm lucky that the connection problems are only intermittent, but it's still an annoying drain on my time to sometimes be randomly locked out of my work for no clear reason and with nothing I can do about it. On the bright side, the troubleshooting process has forced me to learn more about how remote servers work than I otherwise might have if I could just use them without issue, so I suppose it's not a total loss. Still, though, I can't say I wouldn't be happy to solve my connection issues permanently. So, here's hoping that I or IT will summon up some miracle to fix the problem properly before I return to you with my final update of the summer. See you in August!
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Emma
The Royal Mounds in Gamla Uppsala
Pretty flowers I found in Rosendals Trädgård
Lots of hiking in Zakopane, Poland!
Bridge in the Bergius Botanic Garden
Lyra
Palau de la Música Catalana
Palais Garnier
Sainte-Chapelle
My new best friend <3
Rony
I can't believe the last I wrote in this blog was when I was flying out to Paris. Sure, because time flies, but also because everything around me feels different -- like my time before Paris in Stockholm was a different world. That's partially because since then, my world has grown. I've seen so many more things, been to so many more places, both nearby, and far away. Paris was stormy when I arrived, the AC in our AirBnB kept malfunctioning, and I was up in the middle of the night deciphering a French-written manual debugging the machine (it worked!). My favorite part of the trip was sitting on a stone ledge atop the Montmartre hill with my girlfriend, Maggie, under the night sky, watching faint fireworks going off in central Paris. Then, in late June, I went to Bilbao, Spain, to see Maggie for her birthday. Many hikes, beach days, museums visits ensued. We visited Santoña, a nearby coastal town, and hiked to this beautiful water body. There was a large rock, which we used to swing and jump into the deep blue, cool water. Later, a boat of tourists came and cheered anyone jumping off the rock -- standing, clapping, and yelling encouraging things like "¡Salta!" (jump!). Lastly -- to not make this sound like a travel blog I'll keep it short -- I visited family friends in Vaasa, Finland, and swam out on the islands.
Now let's zoom back into Stockholm. I've not been able to include pictures as my travel took up my 4 spots, but I've been deeply exploring the Solna area and have found many mesmerizing rock outlooks into the city, where I read a book, or listen to my language-learning courses. Research has been well, and my lab is made up of amazing people -- this week I ranted about a language model malfunction to some lab peers, and they suggested advice that fixed the error. One particular thing I've grown to learn is to ensure you understand your research question. I have been doing some post-processing from model inferences, but realized I was uncovering model deficiencies that needed to be manually debugged. Post-processing shouldn't be a 'cover' for model errors -- we should tackle the model itself, such as better understand what it's getting wrong, and find ways to increase its generalization. For example, one language model I'm using is "speaking too much", leading to errors in processing. I fixed this by creating a parse function that will search through the output of the model for what is relevant, but instead of creating a post-processing manual extraction function, the end-goal should be to fix the malfunction of the model (which I have been unsuccessfully attempting to -- but I have ideas...) it unveils that this language model cannot perform the task accurately.
My abstract for BMES has been written -- excited to hopefully present at the conference in San Diego. I'm going to Amsterdam this weekend, Vienna the next. I've loved my time in Stockholm, and I know I'll miss it when I have to wave goodbye. But for now, there are still many ventures in the city and countryside for the rest of my time here. Farväl! :)
Julia
Since my last update, I've solidified my project topic, united with some long lost cousins in the UK, met so many interesting people, and experienced many rainy days. My days consist of sitting on the patio with two of my team-members (which Magnus has decided to name the Power Rangers) as we collectively contribute to an ongoing protocol and 'set up' paper for a novel project which will take years to complete if successful. It's a long road ahead but we're quickly making progress as we bridge the gap between science and proving 'science fiction'. We're working on identifying a group of universal 'off-switch' mutations in cancer cells using ML methods. We call this new category of mutations 'Goners' because they're deleterious and when present in pan-cancer cells, we theorize that the cell self-destructs.
We've been working on a scoping review, trying to read up and synthesize all the current work with genetic buffering and synthetic lethality while simultaneously searching for publicaly available data sets, genes to test simulations on, and different classification and prediction models to use for identifying Goner mutations and predicting cell viability as a result of these types of mutations.
A challenge that I overcame during this 'project definition' and open ended search process has been imposter syndrome. When I initially met some of the other students in the AI-UPP program I was blown away by their work ethic and accomplishments so far. Then, as Magnus is bringing me to retreats and meetings and I'm speaking with former CEOs of medtech companies, the departmental heads of medical clinics, or numerous people who have both their PhD and their MD and are working on projects that seem like science fiction, I'd been completely taken aback. I had never imagined I'd be surrounded by so many bright minds and inspiring people and in a way, that was really intimidating. I felt like I didn't belong or I wasn't necessarily on their level, or that I'd never achieve what they had achieved. I was comparing myself to people who had 10, 20, or 30+ years of experience in academia but also generally in life. It definitely took some mental recallibration to realize that I was selected for this program because I'm enough and exactly at the point I should be.
After talking to what seems like a billion people (really it was probably 50 maximum) and doing some self reflection, I came to realize that not only was I 'smart and accomplished' enough to be here, but I am absolutely capable of making significant contributions to my research, despite not being an 'expert' in what we've been studying. It's not that these people are smarter than me (some of them are forces of nature though: I met this woman who is a neuro-radiologist, pursuing a PhD in ML and diagnostics, runs her own business, is a mother of three, and used to be a world-class Heliskiier(jumps out of Helicopters to ski down a mountain)), they've just had more time and experience to learn and create their lives. This sort of reality checked me and helped me become more confident intellectually while also providing inspiration and examples of how much opportunity I have. I've always thought that my career would be in 'something that I don't even know exists' and some of these people were doing exactly that.
So that was a very enlightening life-lesson. I'm still working through my next life-lesson now about patience, advocacy, and learning my work and 'learning' styles. If I'm being honest, my first few weeks of my research felt a bit rocky. Up until this point, I was used to working with clearly defined goals, deadlines, and a clear cut path on how to accomplish these tasks. This summer has been somewhat the opposite, I've had to get creative but I for once, have a voice in the directionality of a serious project. I mean of course in the past I've 'had a voice in projects' but that's more in a 'class project' sense. You have a rubric, you've learned methods in lecture, provided with resources, then boom, 4 weeks later you have a 37 page paper about an expandable leg implant. It seems now, that I'm in much more of a lawless land. The project I'm working on has so many unknowns that it's been difficult to even know where to begin at times. I look to my Power Rangers Team for guidance but their individual expertises (one in AI and ML and the other in precision genetics) only extend as far as they've learned so far. I'm used to all of my questions being answered, being told exactly how to accolmplish tasks, and having a linear workflow with a clear end. My research experience hasn't been like this and with that comes good days, bad days, and a duality of perspectives. I realize how much freedom comes with the work that I'm doing, I have the leisure of falling down rabbit holes and coming back out to share whatever I've found. Sometimes the rabbit holes lead to a dead end, sometimes they cause a pivot in our entire project, and sometimes they advance our project forward. I'm learning to be creative and enjoy the freedom of research without guardrails but sometimes that freedom can be a lot and take a very very long time to see and end product. I've had to advocate for what I feel is the right next step and I'm happy that I'm in a space where I'm listened to. At the end of the day, I'm getting paid to learn as much as I can and then tell people about it, so really I should just have fun with it. But alas, perfectionism.
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Rony
Somewhere in Paris
Faro del Caballo in Santoña, Spain
Vaasa, Finland -- out on the islands with family friends
Lunch at a Helsinki, Finland Food Hall
Julia
Meeting my cousins in the UK for the first time!!
Hike to a waterfall in the English country side
Magnus gave me a season pass ticket to a Hummelby soccer game, 3rd row!!
Goners Research - drawing out our workflow
Jooeun
I can’t believe it’s already our seventh week in Sweden! I’ve spent much of my free time exploring Stockholm on my own, navigating the city by bus and metro. It’s been exciting to visit different markets in various neighborhoods—and I was especially surprised to find American candy in Swedish stores (and even more surprised by the prices!). On the work side, my direct supervisor, Emma, has just left for her vacation. Before leaving, she gave me some instructions, but now it’s up to me to figure things out on my own.
The main challenge I had to overcome was familiarizing myself with Variational Autoencoders and learning PyTorch. In my previous coursework, we used TensorFlow, so PyTorch was pretty new to me. Since my direct supervisor Emma was working in PyTorch, I needed to get myself familiarized with PyTorch. She encouraged me to seek out tutorials and learning resources on my own, as she was unsure of my current skill level. Over the course of several weeks, I spent time to studying tutorials, experimenting with code, and seeking occasional guidance from others. Through this process, I can confidently say that I became comfortable using PyTorch. This experience strengthened my ability to troubleshoot and solve problems independently.
One challenge I have not yet been able to resolve is building the Variational Autoencoder itself. Although we are still actively working on it, I often feel like I am not making much progress. I do not have an answer on how to build the good autoencoder. The process involves determining the optimal architecture, such as the right size and number of layers, as well as tuning parameters like the ideal weights for loss functions. Because I am still in the process of building the model, I am also still learning from this challenge. In the future, I plan to approach similar challenges by not giving up. I believe that as long as I do not give up, every attempt brings me one step closer to finding the right solution.
Elle
Since my last post, I have gotten up to lots of travel both in Sweden/Stockholm area and around Europe. The places I have been to (since Barcelona) are Uppsala, Zakopane/Tatra Mountains (Poland), Copenhagen and Venice. I also have a solo trip to Norway planned so I am looking forward to that. In the lab, my work is going really well. I’ve done lots of analysis and am starting to consolidate everything into a final presentation to give to my PI.
One significant challenge that I have overcome was struggling with having more independent work. My direct supervisor left for a two week vacation, so during that time it was harder for me to ask her questions directly. She is the most knowledgeable about my project, so it felt harder to ask others for help. While she was away, I did have more freedom to explore the data in new ways that were different from the pipeline that I was given. I feel like I learned a lot and also had multiple ways I could have looked at the data. This experience has taught me that in the future, I should take time to explore different perspectives on how to analyze data before sticking to one specific pipeline.
One challenge I have not been able to resolve is feeling stressed about the outcome of my project. While I enjoy the computational aspects, my project also has a wet lab component at the end to verify my computational work. This makes me feel nervous because until I completely finish the computational analysis and get the wet lab results back, I won’t know if my project has been “successful” or not. What I have learned is to be patient with science and to be thorough in my analysis so that my results at the end are as biologically accurate as possible. I also have to remember that even if the wet lab experiments don’t validate my dry lab findings, the research experience I’ve gained is still valuable and “successful”.
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Jooeun
Cat I met near the KI Housing!
Malatang I tried in Stockholm! It was different from what I had back in US
Dubai Crepe I had after the trip to Museum
Escalators. I took photo of it because light made them look rainbow colored!
Elle
Tatra mountains, Zakopane, Poland
Copenhagen, Denmark
Venice, Italy
Medieval/Viking themed dinner in Gamla Stan
Josh
Since my last post, I have travelled with my lab to Copenhagen, started writing my paper, and been going to some soccer games. In Copenhagen we did a big data collection over two days, and I was really happy to have been apart of that. As for the rest of my lab work, I am doing a lot of reading to familiarize myself with the literature related to my field, and I have written the hardest sections of the paper, so now I am finishing that up and creating my final presentation. In the city, I have been going to multiple soccer games, and I also had my sister and cousin visit, and we went to Amsterdam for the weekend.
One significant challenge I have overcome is just not knowing enough about molecular exercise physiology. The data I got was ready for me to use and it was easy enough to create results and then research different bioinformatic ways to present results, but the hardest part has always been interpreting the meaning behind everything. To overcome this I have done A LOT of reading, and that is one of the biggest things I've learned is research is a lot of reading. This helps though, especially with paper writing since it helps with citations.
One significant challenge I have not been able to overcome is getting FGSEA to work on my dataset. FGSEA is fast gene set enrichment which would take a ranked list of genes (that encode for the proteins I'm working with), and it would map those genes onto different biological pathways giving a higher level meaning. I learned many ways to trouble shoot and try and change different parameters, so I think I am pretty good at FGSEA as a whole now even though I never got it to work fully. I learned that you can't fix everything and sometimes its best to move on and not let something frustrate you too much. With this type of challenge in the future, hopefully it will not happen again, since it only didn't seem to work since the panel I was looking at was very specified.
Eric
When I wrote my last blog post, I had just decided that I wanted to investigate the role of B-cells during the transition from in situ breast cancer to invasive breast cancer. Since then, I have been analyzing data to answer this question. I happened to encounter a challenge right at the beginning of this process: the format of the spatial transcriptomics data sets was not compatible with RStudio. After trying to make it work and not succeeding, I had to switch to python. This was intimidating as I was not as familiar with working in python. But, I picked it up pretty quickly, so I now know a new coding language which will definitely be helpful in future computational research projects. I selected data sets and spots based off of some gene expression criteria, and performed differential expression and gene set enrichment analysis, comparing expression of B-cells in in situ breast cancer tissues and invasive breast cancer samples. Throughout this analysis, it seemed there were several ways to proceed at a particular step. Most of my time was spent exploring these different paths and determining which one was best for the question I wanted to answer. I now have some pretty cool results, and am working on summarizing my work and findings in a poster and presentation.
Besides working on my project, I’ve spent the weekends traveling. Right after my last blog post, I traveled to Zakopane, Poland and did some hiking. I summited my first mountain on this trip! I am just now wrapping up a trip to Copenhagen, Denmark and Bergen, Norway. Copenhagen is a city rich with culture and art and has interesting architectural designs. I visited some palaces/castles and did some walking around the new parts of the city. Bergen is a great town for hiking as it is surrounded by seven mountains. I just completed a hike up Mount Ulriken, the tallest of these seven mountains. My favorite part of this trip was a hike from Trengereid, a small village east of Bergen, to Hananipa, a location in the mountains. There were incredible views of the fjords at Hananipa, and I definitely saw more sheep than people on this hike. (I also really like fog, and there was tons of it in the mountains in Norway, and it made everything look really cool.) Within Sweden, I visited Vaxholm and Sandhamm in the Swedish archipelago. These are great places to go for a day trip and do some swimming.
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Josh
AIK game
Vasa Museum
Amsterdam
Copenhagen
Eric
View from the top of Mt. Koscielec in Zakopane, Poland
Trouville beach at Sandhamm Island in the Swedish Archipelago
Rosenborg Castle in Copenhagen, Denmark
Selfie with sheep in Hananipa near Bergen, Norway
Emma
Firstly, what an amazing 10 weeks! I am beyond grateful for the opportunity to work and experience life in Sweden. I’ve learned so much both in and out of the lab.
During my time in the research lab, I was fortunate to work on a variety of projects and tasks. Since my background lies primarily in computer science, data science, and statistics, this summer was an excellent opportunity to combine these skills with biology concepts. I am proud that I have been able to pick up on the biology and start to make connections between concepts! Additionally, I am thankful for all of the mentorship I received in the lab. From technical to conceptual help, I was able to grow while feeling extremely welcomed.
Through traveling and being immersed in a new culture, I’ve grown tremendously as a person and in my perspective on the world. Before this summer, I hadn’t been out of the country much in my life. Now I’ve experienced more places than I would’ve imagined. Beyond traveling, I absolutely loved living in Stockholm. Some of my favorite things about living in Stockholm include the amazing public transportation, emphasis on work-life balance, and the amount of community spaces. One of the most challenging parts of living abroad was not having my support system as readily available as back home. Especially with the 7-hour time difference, most of my friends and family didn't wake up until 3 pm my time. While this was challenging, it also pushed me to grow in ways I wouldn’t have imagined. I learned how to do new, challenging things independently and when to ask for help. I was also able to branch out and meet so many amazing people abroad that I am so grateful for!
Lyra
Here we are at the end of the summer already! Now that I have the full program behind me, I can say categorically that it's been an incredible experience. Academics-wise, it's been very helpful to me in figuring out my plans for the future to experience research at the intersection of computer science and biology—especially in as welcoming and supportive a group as the Daub lab. On the personal level, my time living in Stockholm and exploring Europe this summer has given me the chance to become a much more confident solo traveler and trip planner, and made more comfortable with the idea of living, studying, or working somewhere other than the US in the longer term.
Living abroad has been so much less challenging or intimidating than I thought it might be, in many ways. Going into this summer, I was most worried about things like the language barrier, or feeling isolated from my friends and family back home, but those didn't end up affecting me nearly as much as they might have. I'm fortunate to be able to say that the worst problems I've had over the course of this summer have been the weird door thing at the very beginning of my stay before I memorised which way all of my commonly-used doors at home and work open (though I still maintain that they're weird) and a sprained ankle while I was camping out on the west coast, which could have just as well happened anywhere in the world—it had nothing to do with being abroad.
Overall, my summer in Sweden has been absolutely wonderful. It's hard to pick one favorite thing about Stockholm, but some highlights that I haven't yet mentioned here include: the traditional Thursday pancake lunch, all the art in the subways (especially Kungsträdgården station!), Fabrique bakery's to-die-for olive-gruyere bread, the public ferry system, and fika hours with my lab group.
The AI-UPP program may be over now, but since I have one last trip around Scandinavia in the works before I return to the US for the fall semester, I need to finish writing this blog post and go pack. Since this is the last you'll hear from me here: thanks for coming along with me (and everyone else in AI-UPP 2025) on this summer's adventures! I hope it's been at least a fraction as fun to read about as it was to experience in person. Goodbye!
Rony
I had saved my last few weeks here to spend time solely exploring Stockholm, and I can without doubt say it has become like a second home. My time here has reinforced my interest in impactful research, and I am fortunate to say I have made so many friends, both in my time in the lab and in the adventures with my peers in the AI-UPP program. More specifically, I've learned how to better read, question, and analyze contemporary research papers, effective visualization, and honest development of LLMs for applied tasks such as data extraction.
The adjustment of living in a city like Stockholm has taught me a lot. Sure, to use the public transit system, learn a greater independence, and to seek local communities out on my own. Academically, I've also learned the importance of documenting your error and your daily work progress, which ultimately saved me so much time when running into the same issue.
All in all, it was the people around me who have made this summer amazing. I'd like to thank our program director, Mark, for the opportunity to conduct research in such a welcoming, vibrant intellectual environment. I tried to make the most out of my time here -- travelling to cities around Sweden and the greater region of Europe -- and for the chance to meet so many people. Thank you to Fredrik for welcoming me to his awesome lab, and to Apostolia, Taeyang, Lorenzo, Gurwinder, Shreya, and Jose, for your kindness and the delicious princess cake. Thank you to Josh, Julia, Elle, Emma, Lyra, Eric, and Jooeun, who reminded me I was not alone in my experience, and for those amazing Thursday pancake lunches. Lastly, thank you to Maggie, who came to visit, and made exploring all of Europe and all of Sweden, like the Vasa musuem, the Sandhamn beach, and even the simple trip to the grocery store to make a fun dinner the treat of a lifetime.
Julia
Wow.
I never knew I could learn so much in such a short period of time. The AI-UPP program has been an invaluable experience, granting me an exponential pot of knowledge to draw from. It feels like every pillar of my identity was enhanced in some way. Professionally, academically, and personally I've experienced so much growth and have found a love for research, traveling, and making international connections. My ability to communicate complex concepts, overcome challenges, and connect computational findings with conceptual/biological findings, and then organize a research workflow are skills that transcend this program. Participation in this program and contributing within my work environment has changed my way of thinking and has helped me re-evaluate my strengths and weaknesses from a professional and personal perspective. I found comfort in working together with my team to find answers to seemingly impossible questions and found that there's always a solution, I just have to dig for it.
Personally, I've absolutely loved living in Europe. Stockholm felt like a utopia somedays. I really found an appreciation for my daily walks to work, spending the days outside, having access to quality and affordable food, and PUBLIC TRANSPORTATION. Stockholm's infastructure seems to be build with so much intentionality, from the bike routes throughout the city, to their method of hot water dispersal, one of the biggest things I'm missing now as I'm back in California is the lifestyle and the culture. While abroad, I had the opportunity to travel to seven countries, each of which were completely different experiences. I solo traveled to the Czech Republic and stayed in a 36 person hostel in a castle dungeon then the week following, stayed in a apartment in Paris overlooking the Seine, across the street from the Notre Dame. I had the chance to meet up with extended family for the first time, visit the Louvre, see one of my favorite artists at a music festival, meet people from all over the world, and make some long time friends. This summer has been the best yet, the first where I've had complete independence and have been able to do whatever I want, whenever I want. It's sparked my solo travel bug but also deepened my understanding of the importance of friendship (cheesy I know but I need my socialization fix). This summer has taught me to overcome the fear of the unknown and find grounding in completely new experiences. This summer was filled with so many 'firsts' and 'unknowns' and at first, it was really scary. But now I get an adrenaline rush experiencing a new city, navigating public transportation in Czech, trying to speak a language, understanding new research concepts, and making new friends. Something just clicked for me and I feel like I'm capable of adjusting, learning, and achieving anything as long as I have enough time on my hands. Definitely an empowering experience and I absolutely cannot wait to see what more I'm capable of.
Jooeun
I can’t believe how fast these ten weeks went by! This was my very first time living outside the U.S. (other than Korea, where I was born), and it was a fantastic experience for me! When I first stepped into the lab, I had no idea what to expect. I didn’t really know what people in science labs did or what my role would be. But along the way, I figured out how to work together with others on a project, how to run data on lab workstations instead of just my own laptop, and how to stay on top of my schedule. I also got to learn about Variational Autoencoders (VAEs)—what makes them different from regular machine learning models, and why they’re the right fit for our project. Before all this, I didn’t even know what Multiple Sclerosis was, or how you could study cells to learn about it, but now I feel much more informed and engaged with the research process.
I was really nervous at first, since I had lived with my parents almost my whole life, and this was my very first time living outside the U.S. on my own. It was also my first time flying through an airport by myself! I remember worrying about getting on the right plane at the right time and then figuring out how to find the right building once I arrived. In fact, I actually got lost on my way to the dorm and I got help from other members!
Living in Sweden turned out to be such a great experience. The buildings were beautiful, and the public transportation was incredible compared to what we have in Los Angeles. I was amazed at how clean the water was. Everyone was drinking straight from fountains! As a Southern Californian, I couldn’t quite bring myself to drink from the tap, so I stuck with bottled water for the whole ten weeks. I had always heard that Sweden’s weather is bad, but while I was there, it was absolutely amazing. Every week I got to explore new places using train, subways and buses. The only downside was how expensive everything was. I think I spent almost everything I earned while I was there. Still, the time I spent in Sweden was truly wonderful. I would love to come back, not only to travel but maybe even to live there one day. I’m so grateful to this program for giving me the chance to experience Sweden and learn so much along the way.
Elle
I learned so much during my time in the research lab. My lab was made up of people from many different cultures and who spoke different languages besides English as their first language. This was a great chance to learn how to work and communicate with diverse people. It was really fun to exchange stories and culture during our breaks :) I also gained a lot of technical coding knowledge and biological knowledge. Every time I completed a new analysis, there was so much to learn about the biological basis of my results. I also learned how to manage my time to complete a research project and stay (mostly) organized.
Personally, my favorite thing about living in Stockholm was feeling independent and being able to find my own routines. Sweden has amazing running trails, which was a great plus. I also loved being in Europe. There is such a strong travel culture, and flights are (somewhat) cheap, so it really encourages you to get out and explore. The most challenging part of the summer was balancing work, running + gym, sleep, eating, and other chores during the week. I really loved my research project and wanted to spend more time in the lab working. But when I did that I would have no time for the other things that are important to me. Also, because I was so busy with these things it was hard for me to know what to do when I did have free time. I think I am still trying to find the balance, but living abroad showed that I am capable of doing it, even when it is hard.
Josh
Professionally, I learned so much. Coming into this program I had little to no true research experience and this experience taught me so much. I wasn't really sure what bioengineering could be used for in the research space, and I found that my lab was a mix of people from different backgrounds. I had the opportunity to learn from exercise physiologists, sports scientists, molecular biologists, and many medical doctors. Everyone coming together really inspired me to learn more about the human body. I learned how to really utilize code to power a project. Additionally, I have learned a lot more about different biological applications like about the proteins in the project that I was working on. I learned that research is a tough process that does require a lot of time and can be very frustrating, but if you are surrounded with the right people it can be made a lot easier.
Personally, I also learned a lot. It was the first time I have been in Europe and the longest I have been away from my parents with a very difficult time change. My favorite thing about living in Stockholm was just seeing a lot of people outside using public transportation or cycling to work. I have grown up in a very car heavy place, and it was really nice to see the Swedish people getting outside and exercising or opting to utilize public transportation. I think the hardest part for me was balancing everyday life at first, but I luckily did get the hang of it. I had never worked a 9-5 job before, never had to cook completely for myself, and have not lived completely on my own. All of this was new and scary at first, but I learned how to be completely self-sufficient which is very empowering in a way.
Eric
My time in Sweden is coming to an end, and I couldn't be happier with all that I accomplished and experienced. First and foremost, I would like to thank Rasha Aljelaify, Carsten Daub PhD, and the rest of the CDA lab for hosting me and for being incredibly welcoming and supportive during my research experience. With their guidance, I conducted a research project that allowed me to explore my interests, learned a wealth of information about breast cancer, gained clarity on my career and next steps, and was able to work in a wonderful lab environment every day. The most unqiue part of this research experience was that I got to (some would say had to) formulate my own research question. While this was a challenging process, I learned that research isn't just about getting results, it is also about knowing how to ask the right questions and finding the motivation within one's self to answer this question. I liked the sense of ownership and self-motivation I had with my project this summer. This made for an overall positive, meaningful, and inspiring research experience, and it will for sure be remembered going forward.
This research experience was also made unqiue by virtue of it being an international research experience. I spent the summer in Sweden. This is a crazy thing for me to think about, even now when it's almost over. I've always wanted to explore Scandinavia, so my favorite part about living in Sweden was in fact simply being in Sweden. However, the more time I spent in Sweden, the more I came to appreciate the richness and depth of Swedish history. Since this insternship was based in Stockholm, I was surrounded by a culture and environemnt which was the culmination of centuries of Swedish existance. This was a pretty cool feeling. Living abroad didn't come without challenges. For one, I did not know Swedish. Even thought Sweden is an English speaking country, Swedish is still the default. After having lived most of my life in the US, I think I was used to everything being in English all the time. Language is an integral part of culture, so not knowing the Swedish language made me feel like I was missing out on Swedish culture a bit. With that being said, there's so much more left to experience in Sweden. So will I return to Sweden one day? Definitely.
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Emma
Hiking through snow in Bergen
Weekend at Losten Island in the archipelago
Post intern presentations!
Exploring Riga, Latvia
Lyra
One corner of the Kungsträdgården subway station art
Thursday pancakes!
A weekend trip to Amsterdam
A pretty sunset from outside my apartment
Rony
AIK Match at the Strawberry Arena in Solna
Exhibition at the Fotografiska Musuem
Outlook near Ivar Lo's Park
The Vasa Musuem!
Julia
The Goner Team: Magnus, Me, and Eleni
Solo Trip to Prague
My 'office' this summer
-I worked outside in the courtyard for 80% of my time here
A family of ducks along the shore of Hornsgatan during my last week in Sweden. Soldermalm is my favorite spot in Stockholm.
Jooeun
Summergate!
My flight back to Los Angeles!
Inside the Subway
All Swedish buildings looked amazing
Elle
Stockholm at night
Norway Fjords
More Norway because this trip was amazing
Grona Lund post intern presentations!
Josh
Lab trip
Viking art
Final swedish sunset
Back in SD
Eric
Taken during a run around Lake Brunnsviken before final presentations
Taken during final presentations
Taken after several roller-coaster rides at Gröna Lund after final presentations