We're a little crazy, about science!

Posts tagged “coronavirus

Day #253: A race to the finish

finish line

Well still quite a bit of work to do and some of it was frustrating, but here we are. So let’s run through what I’ve got left to do before the end of the term (ALREADY?!) and talk about the next few posts since I have somewhat of a plan… for once.

(more…)


Day #252: Dead…line

dead...line

Today is the day, my group presentation is due. Is it done? Well… sort of? Okay not quite, but we’re getting there. My group member still sucks, but since I yelled at him (in a professional manner of course), he’s gotten a little better and has been more responsive, so what’s the hold up? What a great question, let me explain.

(more…)


Day #251: Deadline tomorrow

deadline

Well the apocalypse can’t stop the gears of education. Tomorrow is our final presentation for the class I am in, so there is work to be done and expectation maximization will come another day. For now let’s give a quick rundown of what I’m working on.

(more…)


Day #250: Maximum Likelihood Estimation

probability

If we are going to talk about expectation maximization (now that I’m done complaining for a bit), we are going to have to introduce the idea of maximum likelihood. It’s going to be very easy to introduce, but it is a very powerful tool in estimating the state of something. Of course, it takes understanding a little bit of statistics, but trust me, if I can understand it, so can you.

(more…)


Day #249: A stern email later…

angry

Photo of me responding to his email …

I don’t want to jinx it, I really don’t, but I have an update on my group member situation and it isn’t completely awful! I mean, I’m still doing all the work and blah, blah, blah, but I’ve got an interesting story and I hope that things will be better now.

(more…)


Day #248: A Virtual Conference

background

Every zoom meeting I try to break my PI and get him to laugh, this was my last attempt, still nothing… my work continues.

This will be my first conference since the pandemic and it will be a virtual one. To be completely honest, it wasn’t until yesterday that I was reminded we had one today. It’s a little bit different from our normal routine and I think that is what is throwing me off.
(more…)


Day #247: The Kalman filter – Part 2

Kalman filter estimate

The Kalman filter converges on the optimal state estimate using noisy measurements and a model that we create.

Okay I lied, I think we can do a better job explaining the Kalman filter, more importantly I have a fun little demo I can share with everyone. It’s not mine, but I like it a lot and it will give you a feel for what the kalman filter does. So let’s get started!
(more…)


Day #246: The Kalman filter

We have 3-dimensions here even though it is a 2 dimensional problem. the third dimension is time, this way we can see the path over the course of the recorded time. Notice there are no units, becuase in this case we were working with synthetic data so the units were meaningless and I did not include them.
We have 3-dimensions here even though it is a 2 dimensional problem. the third dimension is time, this way we can see the path over the course of the recorded time. Notice there are no units, becuase in this case we were working with synthetic data so the units were meaningless and I did not include them.

This is just one application for the Kalman filter, I estimated a two dimensional position using a random walk model. We have 3-dimensions here even though it is a 2 dimensional problem, the third dimension is time. This way we can see the path over the course of the recorded time. Notice there are no units, becuase in this case we were working with synthetic data so the units were meaningless and I did not include them.

Since we’ve been talking a lot about it, I thought it might be a good idea to formally introduce the Kalman filter. This will be a semi-high level introduction (like my knowing your spinal cord series), but at the end of it you should have a relatively good feel for what a Kalman filter is.
(more…)


Day #245: Fine, I’ll do it myself.

Thanos - I'll do it myself

I will not fail this class becuase of a shitty team member. I will not allow it, I’ve put too much effort and time into this class to do poorly at the last minute because my team member can’t be bothered to do the job he agreed to do. I suppose, this was… inevitable

(more…)


Day #244: The end of the term!?

end of term

Okay, where the hell did that come from?! It’s almost the end of the school term. WHAT THE HELL!? It feels like we just got started, but my instructor just sent out the final assignment, which is due the last week of school… next week. I’m sort of freaking out right now.

(more…)


Day #243: Deadlines approaching!

deadlines

It seems like it’s been non-stop for me left and right. I have experiments to do, papers to write, and classes to work on. With the pandemic I was hoping to get a chance to take a break, but nope it seems like I’m even busier than normal. I HAD thought that I was caught up finally when I finished processing some of the experimental data I had laying around, but nope I was reminded yesterday that I had not one, but two major deadlines coming.

(more…)


Day #242: Experimenting in the time of a pandemic

Experiment-blur

Another day forward in our new normal. I’ve left the house exactly once in the last two weeks and while it’s nice not having to commute to school, I do miss living in a world without the constant fear of catching the virus. What day is it? Who knows, it doesn’t matter anymore. I do have some things coming up though, so let’s talk about experimenting in the age of COVID-19.

(more…)


Day #241: Modeling the COVID-19 Pandemic

COVID-19

COVID-19

Today is the day. I submitted my super high level explainer video on how I modeled the COVID-19 about  a week ago and I got an email from my professor telling me that it was great (yay) and that she had uploaded it to her labs youtube channel. That means I finally get to share it with all of you!

(more…)


Day #240: Conferencing at a distance!

video conferencing
video conferencing

Not everyone has access to such luxurious setups.

It’s that time of the year again, well one of two times of the year really (for us anyway). Unfortunately with the coronavirus conferences are better held virtually than in person. While I have mixed feelings about the usefulness of meeting virtually to share our work, I am grateful that there are workarounds, don’t get me wrong, but there are some logistics that make it, well painful and some things that make this worthwhile.

(more…)


Day #238: Well spoke too soon…

USS Roosevelt Outbreak Navy Guam

USS Roosevelt Outbreak Navy Guam

Yesterday I gave an update on the USS Roosevelt situation. It was basically an update to the predictions I made about how the military was going to handle it and it turns out I was on point. Today is going to be a short post, but I guess there is more to add to the story so let’s just go ahead and get started.

(more…)


Day #237: Coronavirus and the military response – Part 3

USS Theodore Roosevelt

USS Theodore Roosevelt

Well it’s been ten days since I made my predictions about what would happen with the crew of the USS Theodore Roosevelt and it looks like we have some updates so let’s see how close I was to guessing what was going to happen. Let me just start by saying, I hate it when I’m right about this stuff. Some of the things I predicted were longer term, but some of the shorter things we can compare.

(more…)


Day #236: Ugh, coder’s block

coder's block

Okay, maybe not just coder’s block, but I feel like I’ve hit a wall. Every homework assignment I’m given for this class includes a “create your own problem and solve it,” element and for the first two assignments I feel like the topic sort of found me. We can talk about what those two projects were, but let’s first talk about this latest assignment.

(more…)


Day #235: Video making issues

microphone

microphone

I’m not normally one for making videos, in this case I have to make (or rather narrate) two videos for this class. The first one was for our big class project and the second was explaining the COVID-19 model I created. It turns out narating isn’t as easy as it looks, even with a script.

(more…)


Day #234: Learning… at a distance

distance learning

distance learning

Believe it or not, I don’t mind the quarantine. I mean sure going out without the fear of catching the coronavirus is nice, but I’m not generally a social person. There is one thing that has taken some getting used to however, that would be the education portion of the quarantine. Distance learning isn’t particularly enjoyable for me and I’m fairly sure I’m not the only one.

(more…)


Day #233: Coronavirus modeling – Part 6

DeathsModel-NEW

Model estimated death rate plotted in blue compared to the actual death rate plotted in purple. The model predicts deaths based on the previous infected datapoint, so it’s only predicting 1 day ahead, which is not very helpful. However, it lets me check that my model is running correctly.

Another day another unfortunate datapoint for my model validation. On one hand it’s good to be able to further validate my model, on the other, it’s heartbreaking to see it coming to pass. My model prediction isn’t pretty and the trend so far has been very similar to the model. Let’s talk about how we validate the model.

(more…)


Day #232: Coronavirus modeling – Part 5

SEIR flowchart

Well I did it! I finished my model to the best of my abilities. There are a few things I wish I had time to change or do differently, but I think that just comes from actually doing it and not having a clear idea of how I wanted to do it when I started. Let’s take a little look at some of the outputs from the model and I’ll talk a little bit on what the model is designed for, it’s limitations, and the things I wish I could’ve done differently

(more…)


Day #231: Coronavirus modeling – Part 4

Deadline

Still working on my model. It’s taking a little bit longer than I wanted it to take, but I’m getting somewhere finally… I think. In any case, I don’t have a lot of time for an update. So for now this is it. I’m making progress, but I still need to get it done before my deadline, which is fast approaching. Hopefully I can manage before then. Back to work I go!


Day #230: Coronavirus modeling – Part 3

Models

Comic by: XKCD

Well today will need to be short. I broke my model… on purpose, but it still broke. That means I need to go back and check my equations, make sure my assumptions are correct, then figure out why the heck I’m getting the results I’m getting. I have a good idea about what the problem is, I’m just not sure how I want to try to fix it.

(more…)


Day #229: Coronavirus modeling – Part 2

Here we have my estimated exposed population vs the measured infected population, the exposed population is calculated two ways, the first using our susceptible population dynamics (blue) and the second is using our measured infected rate (orange). This is compared to our measured infected since we would expect to see a much higher exposed (asymptomatic) population than infected (symptomatic) population, which we do.
Here we have my estimated exposed population vs the measured infected population, the exposed population is calculated two ways, the first using our susceptible population dynamics (blue) and the second is using our measured infected rate (orange). This is compared to our measured infected since we would expect to see a much higher exposed (asymptomatic) population than infected (symptomatic) population, which we do.

Here we have my estimated exposed population vs the measured infected population, the exposed population is calculated two ways, the first using our susceptible population dynamics (blue) and the second is using our measured infected rate (orange). This is compared to our measured infected since we would expect to see a much higher exposed (asymptomatic) population than infected (symptomatic) population, which we do.

I’ve made a lot of progress! Unfortunately, my model needs some more work and the code is pretty messy right now. For now, I’ll share some of my outputs and discuss what I need to do to finish my assignment. It turns out I have a few extra days to finish the work, I thought it was due Monday, instead it is due Wednesday. The slides and write up are going to take the longest so I’m still crunched for time even though I am mostly done. Let’s go over it.

(more…)


Day #228: Coronavirus modeling – Part 1

Coronavirus modeling

Well the CO of the Roosevelt just got reprimanded just like I predicted. Ever predictable as usual, thanks military. In any case, that isn’t what we are talking about today. Today we are discussing the coronavirus model I’m creating, why it’s important and why no one should believe a model. I’m being slightly facetious, but read on and I’ll explain. I’ll even share some of my model results, it’s not finished, but I thought it would be interesting to share anyway.

(more…)


Day #227: Coronavirus and the military response – Part 2

USS Theodore Roosevelt

USS Theodore Roosevelt

Sometimes I hate it when I’m right. The military is as consistent as ever and we have some unfortunate updates today regarding the crew of the U.S.S. Theodore Roosevelt. It is about what I expected, even with the public looking in and I think we can break down the response and I’ll go ahead and make my prediction for what’s going to happen next, spoiler, it won’t be pretty.

(more…)


Day #226: Coronavirus and the military response

U.S.S. Theodore Roosevelt

U.S.S. Theodore Roosevelt

Well I got word yesterday that the coronavirus found its way onto an aircraft carrier. For anyone who’s never seen one in person, because the pictures don’t do it justice, these things are huge. Think floating cities with the crew size to match. Inside an aircraft carrier, there are roughly 3,000+ people who work, live, and maintain the ship. The one in question, the U.S.S. Theodore Roosevelt has over 4,000 crew members and those are just the ones that need to be quarantined. This is bad for a lot of reasons. For those of you who haven’t served in the military, I’ll explain.

(more…)


Day #223: Hell is other people

From Dante's Inferno, a drawing of Lucifer in hell
From Dante's Inferno, a drawing of Lucifer in hell

15th century art impression of Dante’s Lucifer from Inferno

Sure, Sartre didn’t mean that hell is literally other people, that is a common misconception and therefore the quote is often misused. However, I’m misusing it on purpose because right now in my situation, hell really is other people. Did I mention that I hate group work? I really do and as a change of pace I’m going to try to explain without the tangents I tend to take because it’s going to be a fairly long story.

(more…)


Day #222: We’re still experimenting…?

Uncertainty

Yesterday we did science. It’s a weird feeling to be doing science when there is a pandemic going on, but I actually enjoyed it. There is something about being in a small(ish) windowless room and getting to tune out the rest of the world for a few hours. Yes, I said a few hours, experimenting takes time. Things are in flux though, even for me when I seem to have the most consistent schedule out of our lab.

(more…)


Day #221: Doing my part

My first print from way back when I got the 3D printer (a Lulzbot Taz 6).
My first print from way back when I got the 3D printer (a Lulzbot Taz 6).

My first print from way back when I got the 3D printer (a Lulzbot Taz 6).

Another day another update. I have to admit while the situation is fast changing it gives me something new to write about at least. Small victories maybe, I don’t know. The point is I was never one to sit around and let things happen. I’m a fairly busy person, between school and my fellowship I don’t get a lot of time to do things. Thankfully someone else with more time and/or resources has set up a way to help with the coronavirus supply shortage. (more…)


Day #220: Modeling the spread of COVID-19

covid19 map

Here’s the situation. We still have classes despite the county shuttering for a few weeks. I mean they are online classes, don’t panic, we’re using zoom like a lot of schools. However, it means that we still have class work and what not going on. For our last assignment we had to come up with our own problem to solve, then solve it. It wasn’t as easy as it sounds, but that is how I got this request (see the title of the post). Don’t worry I’ll explain. (more…)


Day #219: The county is on lockdown now

stay home limit travel save lives

stay home limit travel save lives

Finally. The county has asked that everyone shelter in place basically. Only go out if you need to go out. Everything is shut down and people seem to be taking this seriously (somewhat). While I am still pissed off about yesterday’s statements by the GOP, this is a good thing and I’ll take a win when we can get it. Unfortunately, there are some caveats to the lockdown and of course it affects me… (more…)


Day #218: You too are expendable

herd immunity

Well after yesterday’s post there has been a huge shift in rhetoric, so either the GOP reads my blog and thought it would be great to apply the same principle to America in general, or I just happened to guess right. I have to say, being okay with mass murdering a large portion of Americans seems like a bad idea, but clearly we have only the “smartest” people working in our government and not just the wealthiest… right?  For posterity’s sake let me explain since (I hope) 10 years from now someone reading this will have no clue what I’m referring to.

(more…)


The VA wants me dead, do you?

I swear I didn't kill anyone by the incredibly talented Lora Zombie.
I swear I didn't kill anyone by the incredibly talented Lora Zombie.

I swear I didn’t kill anyone by the incredibly talented Lora Zombie.

I hate writing about the VA, I really do. Unfortunately because I live here in the US where we think it’s our right to die from disease and have ludicrous amounts of medical debt for a sprained ankle, it’s a conversation we should have. Hello America, I served my country and now my country wants me dead. I sincerely wish I was exaggerating. Please hold your, “thank you for your service” for the end that way I can tell you to go fuck yourself. Let me explain…

(more…)


Day #216: So I’m “essential” now…

pandemic

Fun fact, I love pandemic movies. Movies, not so much living through one. As humans we are selfish, greedy, prone to panic, and for being “evolved” we are so very, very stupid. Basically every dumb choice you see the characters in those movies make while screaming, “you idiot, that would never happen in real life!” Well, it’s happening and wow does it do a number on a persons mental health. But hey guess what? I’m essential, so let’s figure out what that means in a time where the world is practically on fire.

(more…)