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Archive for April, 2020

Day 255: The impossibility of complete knowledge

Magic-spells

Have you ever tried to learn something and you just can’t seem to get it to stick in your brain? That would be my life, well most of my adult life since I left the Marines. There is just so much knowledge in the world and wrapping my brain around even a fraction of a fraction of a fraction of that knowledge seems to be an impossible task. So what is one to do?

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Day 254: Review – A Brain to Spine Interface for Transferring Artificial Sensory Information

Fig.1 of paper showing drawing of implanted electrodes and the two experimental setups for the rat.
Fig.1 of paper showing drawing of implanted electrodes and the two experimental setups for the rat.

Experimental setup for artificial sensory discrimination using DCS and brain-to-spine interface. (a) Rats were implanted with recording electrodes in motor cortex (M1), somatosensory cortex (S1) and striatum (STR) and dorsal column stimulating electrodes in the thoracic epidural space.  (b) Behavioral setup for artificial sensory discrimination using DCS (c) Setup for the brain-to-spine interface consisted of two modified aperture width tactile discrimination boxes.

If you ever were to read one of my review papers, this one’s for you. It’s so awesome and falls in line fairly closely to the things I want to accomplish, albeit going a different route to get there. I’m super excited to share this with all of you and I hope I did the study justice in my summation and while I admit, I had far too much enthusiasm with this one, it shouldn’t take away from just how amazing this is, see for yourself! The study is open access too, so if you want to know more details, you can go take a look!

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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.

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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.

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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.

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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.

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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.

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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.
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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!
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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.
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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

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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.

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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.

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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.

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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!

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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.

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Day 239: Review – Burst-modulated waveforms optimize electrical stimuli for charge efficiency and fiber selectivity

Example processed nerve responses during stimulation trials.
Example processed nerve responses during stimulation trials.

Example processed nerve responses during stimulation trials. The individual CNAP responses for each stimulus (thin traces) were averaged (thick trace, n=20 stimuli). All traces are shown from time 0 to 6ms. The top trace corresponds to an amplitude of 0, the bottom 1mA, and the traces in between are arranged in increments of 0.2mA. Peak latencies and heights (o’s) and widths at half peak height (x’s) were extracted from the averaged signal. The peaks labeled for the 0mA trial are due to noise and baseline activity. These peaks are not actual response peaks from the nerve and are ignored.

Another two weeks, another critical review and as always since my PI gets a copy, so do you. Technically this should’ve come yesterday, but I really wanted to follow up with the Roosevelt mess going on. In any case today we are looking at something not quite spinal cord stimulation, but has applications in the spinal cord stimulation field. Let’s take a look!

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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.

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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.

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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.

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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.

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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.

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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.

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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

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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.

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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.

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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.

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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.

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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.

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