My Research - Detecting Cancer with Positron Emission Tomography

Hi Readers,

I periodically have these blogging sprees like today. It's too bad they don't come more often than they do. Right now, many of you probably know that I am at Stanford University, en route to getting a Ph.D in electrical engineering. However, I don't think I've ever talked about what kind of research I do there.

Like the title suggests, I work in a group  that focuses primarily on a medical imaging method called Positron Emission Tomography (PET). It is a technique commonly used for "functional imaging", which means that you are trying to image a process in the body, instead of the structure of the body. Most conventional imaging, such as CT scans (shooting x-rays through the body), MRIs (using magnetic fields to induce proton rotation in the body), and ultrasounds (bouncing sound waves through the body), use structural imaging to accomplish their task.

Here's a simple explanation of how PET works for cancer imaging. Cancer tumors are simply clumps of cells whose only orders are to grow as fast as they can, and forget about what they were originally supposed to do. To grow, they must have as much sugar as possible, and so they gobble up all the sugars in the body to maximize their growth rate. Therefore, if we can attach some kind of tracking device to sugar, we should be able to see where the tumors are by seeing where the sugars go. This is exactly how PET works.

In the case of PET, the "tracking device" is actually a positron that the specialized sugar (called FDG) releases in the body. When the positron is released, it will hit an electron in the body; since one is matter and one is antimatter, they will disappear into pure energy (called annhilation). In this case, the pure energy is released as two photons, or light particles, which shoot out of the location of annihilation in the complete opposite direction of each other. As these two leave the body, they hit detectors that surround the body, which records down their location. After that, you simply draw a line between these 2 locations (like connect the dot), and now you have a line which shows the possible places the tumor is located. These lines go in every random direction and share only one common trait, which is that they must intersect the tumor somewhere. Therefore, if you draw a million lines, the place where they all cross each other is the place where the tumor is located.

The project that I am working on involves the construction of a PET machine that can be used specifically for breast cancer imaging. There are five members on the project team. I am the person in charge of designing and integrating hardware to monitor the operation of the machine. This involves prototyping different configurations of the signal lines on the machine, sensors for temperature and humidity, as well as the detector-by-detector monitoring. Of course, it involves more than that, and probably has much more in common with an industry job than a university Ph.D, but it is a fulfilling and exciting role on a team of brilliant people.

Till next post!
FCDH

The Coolness of EE 263: Linear Dynamical Systems

Hi Readers,

I am taking a break from the homework in one of my classes at Stanford, EE 263, titled "Linear Dynamical Systems." It is a heavily linear algebra based class. Ah heck, it's all linear algebra. This is my first ever linear algebra class that I've taken, and it is kicking my ass with gusto. In my undergrad, I tried 4 different times to take linear algebra, but each time I ended up dropping the class, because it was just SO DAMN BORING. But this class - wow! It is incredibly interesting, and super applicable too! Let me explain.

When I tell people about this class, the inevitable first question arises - "what is a linear dynamical system?" I'm not 100% sure, but the way I describe it, it's a system that somehow can be formed into the form of y = Ax. To put it in real world terms, it is a system A, which behaves with a linear fashion to input x, such that it can reliably produce output y.

It sounds pretty ridiculous when I first heard it. But it's absolutely unbelievable, the kinds of questions we have put this to use. A lot of systems in the real world are roughly linear, and this class teaches you many methods to resolve problems in real life. Our midterm questions were all applied linear algebra questions. For example, let's say you have an ecosystem where the animal populations were all in equilibrium, and you release some number of animal x into the ecosystem, and watch the fluctuations of all other animals. With linear systems, you can reverse the process. If you wanted animal x to increase by a certain number at a certain time, there are ways to reverse the equation so that you know exactly how many of each animal you need to release into the system at time zero in order to achieve your goal.

This class teaches you a lot of applications of this. The easy one is of course, if you are given the input x and system A, to find output y. Or, given a limited set of input and output, figure out what the system is, and use it to predict what the future outputs will be. Or, given what the output is and how the system behaves, how do you trace it back to the input?

I never really thought linear algebra could be fun. And to be fair, there are times during this class when I just want to bang my head against a wall and just turn in incomplete homeworks (because they are SO long!). However, I think it's fantastically useful, and I hope to be able to use such things to build models of systems in the future. This seems especially apt with medical imaging, since much of medical imaging is based upon the idea of model construction and optimization.

Anyways, it's late and I should go home to sleep. Just wanted to start blogging again - my blog has been so neglected, and I want to revive it.

Cheers,
FCDH

Oh hello, Student Government!

Hi Readers,

I'd say I was pretty involved during my undergraduate years at the University of Illinois. However, there was one area where I wasn't, which was student government. However, that all changed here at Stanford! A few months ago, while I was taking a break from studying, I saw an email from the Stanford elections commission, telling graduate students to "apply now!" to be on Stanford's Graduate Student Council. I almost closed the page, but then I was like, "meh, if I close this window now I'll probably just waste more time on Facebook anyways. It's not like I'm wasting time by filling this out..." So I filled out the application, wrote a brief (and somewhat BS paragraph) about what I wanted to do on the GSC, and didn't give it any more thought.

Well, turns out there were only 16 graduate students who were competing for 14 spots on the GSC, and I suppose I was lucky enough to be one of the 14 who were elected to be on the GSC. At the time, I really had no idea what I had gotten myself into. I didn't really even know what the GSC did, other than that they threw pretty big parties and planned other events for the graduate students here at Stanford. All that changed quickly with the transition meetings with the old GSC, where we learned all about what student government is (supposed to be) about. 

While the general election only elected people onto the GSC, the GSC held an internal election afterward to determine the new leadership team of the GSC, namely the chairs that would help guide the GSC. Here was where things began getting more intense. The initial front-runners for the chair positions had a falling-out a couple of days before the internal election, so another GSC member tapped me to run with him as co-chairs. We did, and managed to win the internal election! So now I am one of the co-chairs of the new GSC!

So far it has been an exhilarating ride. I've had a blast learning about the inner workings of the university, and I am very excited to be able to work at making a difference to the students!

That's it for now!

-FCDH

Stanford Quals!

Hi Readers,

I started writing this post 35 days ago, before I actually took quals and found out my results. The fact that I haven't finished it until today speaks volumes as to how busy I have been. This quarter has just been waves and waves of shazam and I'm finally starting to dig myself out of all this crap. I just turned in 2 final projects, and I have another final project and final hw set due on Monday. After that, 2 finals stand in my way of snowboarding and other spring break plans. Yippee!

AND I PASSED THE QUALS!! FIRST TIME TOO!!! I was unbelievably happy when that email came. =)

Anyways, this post is going to talk about my experiences taking the qualifying exams at Stanford. When I came to Stanford , the EE department head (Professor Mark Horowitz) was very adamant about it not being a big deal. He said that first years should not worry about passing or failing their first time, and that they should just treat it as a practice their first year. I think he's slightly out of touch with the EE students. When do we not freak out about anything? Especially a test that is, even if only symbolic, a somewhat traumatic experience for all who go through it.

Here's what the quals nominally entail:
-10 oral exams with 10 different professors, each 12 minutes long.

Here's what the quals actually entail:
-at least a month of frantic studying
-a complete 8-hour day of running around to different rooms
-lots of sighing
-sarcastic professors making fun of you
-well-meaning professors unintentionally making fun of you
-having absolutely no idea if you passed or failed

Here are some tips and hindsight:

Studying
-A quals study group is a great idea. I usually don't work in groups, but studying for quals in a group is a phenomenal idea, since there are many people at Stanford who are smarter than you.
-I started really studying for the quals a month before I took them. This really was not enough, and I should have started studying earlier, so I could cover more. It was pure luck that I passed the first time.
-Do not study your group 3 and 4 more than your group 1 and 2, even though you might not be very good at them. The group I ended up doing the worst on was group 1, while groups 2, 3, and 4 ensured that I passed.

Professor Selection
For quals, you must make your professor selections from the list that is given to you that year. There are many different fields your professors can be chosen from. All quals students have to choose 20 professors to distribute into 4 groups, and 10 quals professors will be chosen from those 4. Students will rank their groups from 1-4, with 1 being the most preferred, and 4 being the least preferred. 4 professors will be chosen from group 1, 3 from group 2, 2 from group 3, and 1 from group 4. The maximum professors from any one field that can be chosen is 4.

Given knowledge of this, it is possible to "game" the system a bit, by selecting professors in special ways. For example, if there are 6 professors in the field that you specialize in, you can put 5 of them in group 1, which will ensure that the 6th will not be picked if placed in any other group (because the maximum 4 professors from group 1 will have been picked already). If you game the selection process carefully, it is possible to minimize your chances of getting professors in areas that you don't want. My four areas were devices, physics, E&M, and circuits, and yet I managed to escape with 4 professors in devices, 4 in physics, and 2 in E&M. Sheer luck! I would have performed poorly on circuits.

The Arbitrary Scores
I tried to smile the entire way through my quals, but it was hard for many reasons. For one, you have absolutely no idea what criteria by which the professors are judging you on. You don't know what the right answer is, whether or not there were more parts to the problem that you didn't answer, or whether you made a good impression on the professor or not. You are struck by the arbitrariness of it all.

And that's really the word of the day: arbitrariness. When I received the final breakdown of grades by professor, it completely floored me. Here were the big shocks in the scores:

1. My group 1 professors (Devices) gave me the lowest scores. I had Professor X (anonymized in case we were not supposed to reveal this information), who I thought I did relatively well on. 1.2/10 after curving. How I got that, I had no idea, and still have no idea. Professor Y asked me if I was in signals and systems at the end of our session. Ouch.
2. Physics and E&M profs love me. At least, I did better than 75% percentile of students on all of them. I had no idea how to answer Professor Z's question, and made up an answer, and the professor told me at the end of the session: "your answer was wrong. You may leave now." 8/10. WTF?
3. I performed either extremely well or extremely poorly. It was either below 25th percentile, or above 75th.

I lost complete faith in the quals system after the scores were published. Some professors that I thought I did well on didn't give me good scores. Some professors that I thought I failed gave me fantastic scores. How this is supposed to measure your ability to do research, I have no idea.

But that's over. It was a very traumatic experience, but one that all Ph.D EE students will be able to complain about for years to come. And I passed! That's the important thing. =)

Till next post!
-FCDH

The Free Food Bible

Hi Readers,

I am taking a break from my homework on noise processes. Because even though I've spent 5 hours on it, I have made nil progress. As in, I still have no idea how to approach the problem. Blah. The white board in lab is littered with my equations, each of which hit a dead end. Nope, no idea.

So here's one interesting note about how I eat here at Stanford. Most of the dinners that I eat during the week are free. This is because Silicon Valley companies and startups love to flood Stanford with info sessions, each of which comes with free food. At the U of I, it was (comparatively) very hard to eat for free; if you did get free food, there was a 99% chance it was pizza.

This is not true of Stanford. Here, our info sessions have a smorgasbord of food. In a short span of 2 months, I've seen the following appear at info sessions: Thai, Mediterranean, Chinese, Mexican, American (sandwiches), Italian, pizza, and burgers. Most of the time, you can stuff your face and not have to worry about the food running out for other people. It is quite a luxury. But there is an art to free-food hopping!

Though the frequency of the sessions have been dying out as the recruitment cycle slowly comes to an end, throughout the first month and a half of classes, you could predictably count on at least 2 meals a day. There was always a lunch session at noon, followed by 2 afternoon/evening sessions at 5pm and 6:30pm. There would be a million emails sent out about the sessions, so everyone on the mailing list knew  about them.

There are two types of people that hit up these sessions. The first type is people who actually want a job or internship. These flood to the high-profile companies such as Google, Microsoft, Yahoo, Facebook, etc. The second type is people who want free food. These flood to the lowest-profile companies they can find, where there is always guaranteed to be food no matter how late you walk in. I am a type 2, and as many type 2s, I hate going to a type 1 situation because the food will always run out super quickly. Then you're stuck between a rock (staying and being hungry) and a hard place (loudly shuffling out of the room during the presentation to dirty looks from people).

Here are some tips and basic etiquette for free food:

1. Leave your dignity at the door. If you're still hungry after one plate, stand up during the presentation and get some more immediately! Since grad students are characterized by bosons and not fermions, you will notice that you will create a domino "bunching" effect as others will see your audaciousness and copy you. Better yet, load up on a huge plate of food your first round. Just don't accidentally spill it everywhere. And if you do spill, CLEAN IT UP.

2. Free food "etiquette" dictates that if the food is almost out, you should take less and leave some for others. Please feel free to blatantly ignore this rule, since you will never see it applied to yourself when the person in front of you takes the rest of the food and leaves you pissed off and hungry.

3. For type 1 companies, get there 10 minutes early. For type 2 companies, get there on time. The earliest you should leave a session can be determined by applying the minimum function to "halfway through the allotted time" and "first person leaves the room."

4. If the food is discrete and fungible (sandwiches, burritos), feel free to wrap some up and take it to go if it is convenient to do so. Again, check your dignity at the door. Food is your priority, and the dirty looks you are getting from other grad students are actually tinged with admiration because they wish they had the balls to do what you just did. Company reps actually admire students who do this, because it shows they are not afraid of making themselves look bad in pursuit of a goal. (Being serious here - I've gotten compliments before).

5. If there are lots of food leftover and you are not in a rush, stay until the end of the session and take the rest of the food trays home. If you go to the session moderator and ask confidently whether you can take it home, there's a 99% chance they will say yes. Voila - that's more free food to tide you over when you can't find any free food for the day.

That's all for now. This was actually one of the most fun blog posts I've written in awhile. And I'm completely serious with these 5 rules. If you want to eat freely and well, commit these rules to heart.

-FCDH

Reflections on Stanford Visit

Hi Readers,

I am currently at the airport in Dallas, waiting for my connecting flight back to CU. Literally just 5 seconds ago, I ran into AX here, which was a nice surprise. AX flew out of Champaign on the same flight as me on Wednesday, except he was going to Intel for an interview and I was going to Stanford for my visit. What a coincidence that we ended up on the same flight again on the way back!

Anyways, back on topic. I visited Stanford on the DiscoverEE visitation trip for Electrical Engineers these past 2 days, and it was very, very eye-opening. Now I understand why people are encouraged to visit a campus before making their decision. My experience was a very mixed pot, and I am now feeling slightly stressed out about going to grad school (already).

Because Stanford couldn’t find a student host for me, I ended up finding one for myself. I crashed at my friend NJ’s place, where he had graciously taken me in and set up an air mattress for me. It was comfortable and he had a really nice studio (certainly much nicer than the studio that I used to live in). It ended up being really nice, because I could see the living conditions of the grad students, and NJ also took me around and told me a lot about things that I should expect and look for when I do come here.

Since I visited Stanford with JC and we had mutual friends there (including NJ), we ended up going out to dinner afterward at a place called the Straits. It was actually very nice and I thoroughly enjoyed it.

Here’s a short summary of the positives and negatives I felt about Stanford.

Positives – Research

-I am really excited about the research opportunities that will be available at Stanford. There are so many professors there, and Stanford is really unique in that they encourage multidisciplinary and cross-discipline research. So I could literally go in and join a professor in the school of business, or agriculture, or physics, or any other major, as long as it is even tangentially related to Electrical Engineering.

-Stanford professors really encourage students to “hop” between different research groups in their first year, until they find a group that suits them. They even go as far as to say, “No I will not take you into my group immediately upon your entrance to grad school. But you can join my group temporarily to try it out first, and if it is a good match then I will take you.” This was really a big relief to me, because one of the things that I worried about was choosing a group that you are not compatible in, and then being miserable for the rest of your years while you try to battle out your research project and graduate. I always thought that it was a huge risk that I would have to take, but Stanford really minimizes this, which makes me feel better.

Negatives – Living

-Stanford’s campus seems somewhat boring. When I arrived at midnight on Wednesday, I did not see a single other person on the street apart from NJ, or cars as well. Though others told me that parties did happen in the dorms, it is still a big change from Illinois.

-Where are the restaurants and bars? After the student union closes at 10, the closest places to eat/drink are like 15-20 minutes away. No more Green St. and its bars and restaurants that are readily accessible and stay open till like 2am.

-HOUSING PRICES?!?! It seems universally agreed that at Stanford $600 is the lowest you can get, while on average it is around $1000 and can go up to $1600. And here I'm paying $320 a month. Ahhh that monthly rent payment will be so painful now!

I'm still pretty sure that I'll end up going to Stanford (since UC Santa Barbara seems to have rejected me, from its lack of response), despite JJ's attempts to convince me to go to UCSB. I'm just hoping that I won't regret it, since I turned down a full-time job at National Instruments to go to graduate school. It seems like the research is positive while the living is negative, which should balance out to neutral. I hope it'll all be great in the end.

Toodles for now! Next post on Japan earthquake.

-FCDH

Birthday Smatterings

Hi Readers,

TODAY'S MY BIRTHDAY!!!!!!!!!!!!!!! I'm 22 now. SO OLD. Ugh.

Anyways, here is just a short entry about recent happenings and plans, along with a short political note.

Politics first. I hold no grudge toward Republicans that are jumping on Obama's statement about the unconstitutionality of the Defense of Marriage Act (DOMA), and the fact that the government will stop defending it in court. However, those Republicans that are flat-out LYING and saying that Obama is not enforcing the law can go to hell. Boehner, this is looking at you.

Obama is required by law to enforce the law until it is repealed by either Congress, or ruled unconstitutional by the judicial system. He is doing exactly what he is supposed to do. But I know that conservative news networks are going to spread this lie like all the other lies, under the guise of the freedom of speech. This supposed "freedom of speech" is what grates on my nerves about the US, and probably the biggest deterrent to me settling down long-term here in the US.

Ok, now updates. First, grad schools:

I found out that I was rejected by MIT, which was not a big deal for me. Actually, it came as more of a relief, because now I won't be plagued by the "California or Boston" debate. It's settled: I'm going to California for grad school. Now, as for where...only time will tell. Apart from Stanford, I've also heard back from UC San Diego (accepted with 1 year fellowship), which I'm 99% sure I will decline. The only way I'll go to UCSD would be if I visited (unlikely since their visitation dates conflict with Stanford's) and fell in love with it. Highly unlikely, especially since the only reason I applied in the first place was because my friend MW at UCSD encouraged me to do so.

I'm still waiting to hear back from Berkeley, UC Santa Barbara, and Caltech. At the moment, assuming I had gotten into all of these schools, I will probably choose between Stanford and UCSB. But honestly, I'm not sure which one yet, but I'll have to see what their offers are.

Now, onto plans.

I'm planning on visiting Stanford during Mar. 10-11, for their DiscoverEE days. I'm so excited! I last visited California when I was 7, and I have long since forgotten that experience. My only knowledge of California right now is LAX, and transferring from the domestic terminal to the international terminal. Horrible experiences there, bleh.

A mere week after the Stanford visit, I'll be heading to California again, this time during spring break. The ECE department is sending 2 students (I'm one of them) to the Google headquarters in San Francisco, and Microsoft headquarters in Seattle, for alumni events. Since that's taking place from Monday-Thursday, I'm hoping to squeeze in a trip to Santa Barbara before it, and an EWB conference in Louisville after it. Here's to hoping everything works out with the trip!

That's all right now. It's 6am. It's my birthday. I've spent 8 hours working on homework today. No parties. I need to go home to sleep ughhhh. Tomorrow will be a tiring day.

-FCDH

Stanford!

Hi Readers,

I got exciting news yesterday! A day after posting that last depressing post about not hearing back from grad schools, I got the good news from Stanford!

I was sitting in my digital signals processing class when I opened my email and saw the innocuous-looking email, titled "Stanford Electrical Engineering - (name)", and immediately though "oh crap, I got rejected from Stanford. No big deal - I wasn't expecting it anyways. My application was kinda crappy. Maybe if...." All these flashed through my mind as I clicked the email open, reading to be disappointed.

At the first word, "Congratulations!", my heart jumped. I was like "omg, I got in!" As I began skimming farther, the next thing that caught my eye was the word "fellowship". My heart jumped again - did I really get a fellowship? The answer - YES!

Apparently I was one of the lucky students to be awarded with the Stanford Graduate Fellowship, which will support my work at Stanford for three years. It's the highest fellowship that they can give out - so I was, and still am, extremely excited about it. Now I know what option I'll probably take if MIT turns out not to accept me!

More to follow! Just wanted a brief update on grad schools. So excited!

-FCDH

Tomorrow Can't Come Any Faster

Hi Readers,

I'm totally crashing right now. I think I'm in denial over the amount of work that I have. This semester sucks so much. I hate my life right now. I've got my 536 book open, but I've only managed to read like 5 pages in the last hour. It is incomprehensible. Why do I do this to myself?

I just want out of here. I just wish I had a concrete yes or no for either grad school or full time work. Two of my friends got acceptances today, to Stanford and Columbia. I've gotten nothing, heard nothing.

People always say that I will get into anywhere I want. I used to believe it, but now I don't anymore. I wish I had spent more time on my grad school applications, maybe made them better. Or perhaps if I had started interviewing for full time jobs in the fall instead of waiting until now.

I can't go out anymore on the weekends. I have gotten no work done over the last 3 weekends while I had fun. I'm paying for it right now, but I've almost used up all my credits.

I feel so happy for my friends who have gotten into their dream grad schools.

I no longer know if I will even go to grad school. What is the point? Everybody I know is more miserable in grad school than they would be working in industry. So I'm interviewing for full-time positions, to the shock of my friends. Some of the jobs seem like a step-down for the skills I have developed doing research. Should I care that anyone could do this job? Should I settle for less?

I no longer know. What is "less"? How is it even defined?

Why am I even speculating when I know nothing? I hate the wait. I need to stop checking facebook and seeing other people's happy statuses.

Tomorrow will be better. I hope.

Hotel California just came on my iTunes. Fuck yeah. I can deal with the damn waveguide physics now.

-FCDH