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Posts tagged “science

Day #104: Experiment Prep

EEG headset

It looks like things are moving a little quicker than I thought for me. As you may or may not know, I’m getting ready to do an experiment. Well, we finally (finally!) finalized the protocol and just in time too. While I won’t make the deadline for my project update, I will have some data to show when we get to the conference, which is a good consolation prize.

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Day #103: A day off…

relaxing

I’ve got a lot going on, but today is a day off. It’s important to take time for yourself so when you need to do the work, you actually do the work. I’m sure we’ve all felt that way, where you force yourself to do something and spend 4+ hours doing something that you could do in less than an hour. Sometimes you need a break.

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Day #102: Finals ahead!

Warning sign

Well it’s that time of year again, finals! On one hand I’m excited at the prospect of being done with the term, on the other I’m a notoriously bad test taker. I deal with a lot of anxiety you see and even when I know how to solve the problem, come test day I end up drawing a blank or making very stupid mistakes. Standardized tests are the bane of my existence!!

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Day #101: Holiday

Well today is thanksgiving, not a holiday I celebrate, but I’m happy to have the day off at least. I’ll be taking the day to get some work done and relax some. Deadlines are coming so I can’t take the whole day to myself, but at least it’s a low stress day.

Until next time, don’t stop learning!


Day #100: Graduating lab members

Day 100 - PhD defense offense

Image from: xkcd.com

Wow, time flies, we’re already on day 100. Still not half way done, but it certainly doesn’t feel like 100 days of writing. Today has been a busy day, which is why I’m writing so late. With the end of the term comes other projects that need to be addressed, namely my qualifying exam, final exams, and other lab members having their Ph.D defense. Yep, we have not one, not two, but three people defending their Ph.D this term.

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Day #99: Data request, a update

letters vs email

Sometimes emails can still be exciting!

I’ve got news! In my last post on the subject I said that I wasn’t expecting a response from the lab I was requesting data from until Monday, if at all. Well would you believe I got a response! It wasn’t a “here’s the data response,” but it is progress. Let me explain why.

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Day #98: Laptop troubles

Well it finally happened. My laptop looks pretty dead. Right now I have it in pieces while I try to figure out what went wrong with it. Thankfully I have a desktop computer that I use for all my heavy computing as a back up. Just one more expense I guess, I should be grateful that it wasn’t something more serious like the hard drive going out.

So short post, I know, but I have to get this fixed or find some sort of resolution since my laptop is an important part of how I get work done. I’ll have a longer post tomorrow, but for now I think that is it.

Until next time, don’t stop learning!


Day #97: Neural network models

Neural net

Today should be an interesting day for me. I plan to do a deep dive into the world of neural networks to better understand how they work and the best type to apply to my data. There are a few, quite a few in fact that I could use and really it depends on how I want to frame my problem, so let’s look at what I’ve got planned.

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Day #96: The art of requesting data

Day 96 - mice

I have some data. This shouldn’t be news, I’ve been talking about how I’m trying to train a model to predict an output using this data and all the woes that have come from the training process. Turns out I have a problem, well more like questions that need answers and for that I need help.

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Day #95: Housework day

Pokemon procrastination

 

Pokemon procrastination

If only it was super effective!!!!!!

So far things have been non-stop and today is no exception. I have a lot of housework to do and balancing that work with my school work (all while still trying to find time to relax some) is difficult. Nevertheless today is housework day (mostly).

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Day #94: Paper formatting

submtting a paper

Ugh!! After over six weeks my paper was rejected becuase it didn’t fall in line with what the editor wanted. This is frustrating because each journal has different formatting requirements and you cannot submit to multiple journals at once so we need to sit and wait.

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Day #93: QE date is set… again!

5 tacks on a single date on a calendar

5 tacks on a single date on a calendar

Exciting news!!!!! Well as you can tell from the title, my qualifying exam date is set. After some time emailing back and forth I finally just sent out a doodle poll to get everyone to vote on what time would work best for them. Last night, my last committee member added their availability to the poll and with that, I have a new time and date!

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Day #92: Missed meetings…

65874759

As you may be aware, I am planning an experiment! Cue upbeat music Unfortunately record scratch I’m nowhere near ready. It’s been a process for sure and we are (maybe?) back on track to get started soon. Today I had a meeting scheduled with my PI to discuss the details, but…

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Day #91: Did that really just happen?

windows10 update screen

Screw you auto update

For those of you following along, I’ve been trying to crack a predictive model using some novel (read: super secret PhD work) neural data. It’s been a journey and I’ve trained and tested about a dozen or so models, with varying success. Things have been flying pretty smooth the past few weeks as I try to create the best model I could possibly create. Unfortunately, technology had other plans for me.

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Day #90: Memory

memorization

I have a lot of memorization to do these days. Things that are important , steps to set things up, new biology, new techniques, new, new, new… well you get the point. Memorization is the bain of my existence. It’s not even a matter of not wanting to memorize something, it’s just old war wounds, no really.

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Day #89: The stress of life

stress

Today I get to play catch up. I’m running on not a lot of sleep, but there is so much to be done it isn’t funny. Ironically enough, it’s not all school either. I have life things catching up with me, car repairs that I need to do, house things, you know the usual day to day things that pile up despite our best efforts.

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Day #88: Experimental Headaches

EEG

EEG cap

I’ve talked about my impending deadlines a lot lately. I also mentioned that I had an experiment that I needed to do to meet a deadline, well it looks like we may or may not meet this goal. Let’s talk about the latest headaches.

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Day #87: Classifier progress

Kernal function

Well it’s been an interesting experience. I’ve been working hard to train a binary classifier to predict the two classes in my data. There has been a lot of ups and downs and more importantly, there has been some progress. It isn’t perfect, but it’s a start, so let’s look at what I’ve got so far and where I’m headed.

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Day #86: Or maybe not…

vicous cat

Even my cat doesn’t like the news.

Last post I had triumphantly declared that I had scheduled my QE date…. wellllllll maybe not. I had a last minute email from one of my committee members saying they had another obligation that day that they had forgotten about. So today let’s talk about why that is okay, even though it isn’t really.

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Day #85: My QE date is set

Brain

Sometimes you need to get… a head. See what I did there?

Well it happened, the date for my qualifying exam has been set. I’m nervous, I’m excited, I’m mostly just anxious to get it done. Quite frankly I’m exhausted, so it will be nice to get one thing off my to-do list. Let’s look at how I need to get ready.

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Day #84: Model training progress

 

Day 84 - SVM hyperplane

Two dimensional data is easier to visualize than 202 dimensional data.

I don’t normally leave my computer on 24 hours a day, but it has been hard a work, so it hasn’t been off in days. Training a model can take some time, as I am finding out and while I’ve made progress on the resulting model, it’s still not where I want it. Let’s talk about what has been going on.

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Day #83: An unexpected gift

Day 83 - Gift

I’ll let you in on a secret, I’ve been doing science outreach on a regular basis for the past 3-4 years now. Specifically with Skype a scientist I’ve volunteered every term since it was pretty much first started. My secret, if not horribly kept, is this… I am ALWAYS nervous to give my talk. That doesn’t mean it isn’t worth it and let me explain why.

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Day #82: Congrats, it’s an overfit model

Day 82 - example overfit model

There I was patiently waiting for my data to finish being processed, an hour, two, time kept moving as did the little animation letting me know that the algorithm was still doing its thing. Then it was done, I had a new, more complete model and it was glorious… until it wasn’t.

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Day #81: Creating a Model

Day 81 - Classifier

Today is going to be a long day. I’m training a model using some data I’ve collected. Now, depending on your background that sentence either meant something to you or was complete gibberish. In either case, let’s talk about what I’m doing, even though I can’t get into specifics about my data.

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Day #80: Experimental Design

 

Day 80 - Experiment

I have funding for an experiment. Well let me rephrase, I’ve had funding for an experiment. It’s new, it’s exciting, it’s everything I wanted it to be… but there is a catch. My PI and I don’t see eye to eye regarding the experimental protocol. It’s not a matter of a fledgling PhD student thinking he knows better, he is well know for losing sight of the big picture in favor of collecting as much data as he possibly can.

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Day #79: QE update

day 79 - presentation

As promised from last post, I have an update regarding my QE. This will be brief, but there are a few final things I need to get done before I can do my presentation so let’s talk about that!

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Day #78: The Qualifying Exam

exam

It never occured to me that this was unique to the American higher education system. However, when I was having a conversation with an overseas collaborator at the Bristol Robotics Lab in the UK, I got a confused response when I mentioned I was getting ready to do my qualifier.

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Day #77: Sometimes life gets in the way

Well it looks like it’s another day without a post, don’t worry I’m not making it a habit, but I’ve had some personal issues come up today that I needed to deal with. Not to worry though, I’ll be back at it tomorrow.

Until next time, don’t stop learning!


Day #76: Organization

day 76 - organization

Today is going to be a busy one. Not for me exactly, but my computer will be busy cracking away at the code I wrote. Unfortunately it takes FOREVER to run, but it got me thinking about MATLAB and how we write code for everything.  More to the point, it got me thinking about how I organize my files.
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Day #75: Deadlines in Academia

5 tacks on a single date on a calendar

 

5 tacks on a single date on a calendar

Getting a PhD is a weird process. Sometimes it seems like everything is falling apart and somehow (hopefully) it comes together in the end. To that point, in an academic setting, deadlines tend to group together. For instance I have not one, not two, not three, not even four, but five deadlines coming up back to back. Today, let’s talk about why that is in my case.
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Day #74: Finding your motivation

day 74 - motivation

You don’t want to do it. I don’t blame you, I wouldn’t want to do it either. So what do you do when the work is piling up and the weight of things in your to do box is so massive that you feel like you can’t move? Well first, remember you’re not alone. Next, …well that depends on you.
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Day #73: Halloween!!

Today is Halloween, my favorite holiday! I don’t usually do anything too spectacular for the day, it’s more of an excuse to binge horror movies and enjoy the halloween candy I bought. In the spirit of halloween, I don’t plan on posting anything major today. We can get into it tomorrow, but as I’ve mentioned over the course of the last 72 days, taking a break can be a good thing.

If you are looking for a ghoulish reading treat, I recommend my yearly post on the REAL zombies of nature! Be warned, it’s not for the squeamish, that’s for sure! In lieu of my usual sign off, let’s just say

HAPPY HALLOWEEN!!!

halloween


Day #72: The dreaded email…

email

Fun fact, no one ever enjoyed sending an email. Least of all an email to someone you’ve never met, not just an email, a cold email. In the spirit of halloween, let’s talk about the scariest thing I can think of outside of the horror of finding no significance in your data.

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Day #71: Busy, busy, busy!

A quick update since I have a lot of work going on today.  Originally, I  has some outreach planned for the day, but that had to be rescheduled. I also had a very thorough review of my qualifying exam project with some very exciting results. Once I reschedule for the actual QE, I’ll talk more about that research, but I typically devote an hour or more to writing these posts and I cannot do that today. I anticipated this though and even included it in my original post, in any case, I have another Skype a scientist session scheduled for tomorrow, but I should have more time to devote to the blog after (or maybe before, who knows).

Until next time, don’t stop learning!


Day #70: The art of goal setting

day 70 - goals

Some days I feel zero motivation to do anything. Usually I indulge those feelings because if I don’t it won’t go away, more importantly if I don’t then I sit in front of a computer/book/etc. and get almost zero accomplished. Frankly, I think trying to power through the feeling and get work done just isn’t healthy and experience has shown it does absolutely nothing for me. This brings me to the topic of the day, goal setting!
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Day #69: The PERFECT daily routine

Day 69 - routine

This week we’ve taken a break from the math (well statistics if we want to be exact) and have looked at some of the other things that go on when doing your PhD. Tomorrow we (may) get back to the concepts, but today let’s talk about the perfect daily routine.

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Day #68: Hobbies are important!

hobbies

All work and no play… well you know how the saying goes. Here in the US we have this mindset where it’s work all day every day. That is probably one of the reasons we have such high rates of depression (we as in people pursuing a PhD). Sure one of my hobbies is blogging, I enjoy it and it is a great way to review the things I’ve been learning, but I have others and today I think we should talk about why that is important. (more…)


Day #67: On being a student coordinator

wiring

Look at my beautiful wiring job!!!!

I figure we can finish out the week by talking about yet another project that doesn’t involve my research. I’m a student chair for a workshop for neurotech entrepreneurs. Fun fact: I’ve never done this before. Yep, there has to be a first time for everything you do and this will be my first time attempting to run one of these things. Let’s talk about what that looks like. (more…)


Day #66: Sometimes we learn more from failure

BrokenLaser1

Not everything can be safely laser cut…

It has been a busy week, as you’ve seen I’ve had not one, but two Skype a scientist sessions in one day, then we did some outreach with some local 4th graders, yesterday I even posted photos of the event. Yesterday I also had a conference call to help set up an event that I’m helping run for neurotech entrepreneurs. If you follow me on twitter, you know I’ve pushed people to apply for it. So let’s talk about what I’ve got going on today!

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Day #65: Lab Tour photos

As you may have seen, yesterday we had our lab tour group come through. So today I just wanted to share a few photos from the time they had with us, it was a lot of fun and hopefully we inspired a few kids!

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Day #64: Lab Tours!

 

20190405_101414

Just hanging out with some exoskeleton friends.

When doing your advanced degrees (Masters or PhD) you end up with a lot of different responsibilities that have nothing to do with your education. That isn’t to say that it isn’t an important thing or that I hate doing it, you just don’t learn anything with regard to your study subject. Today is one of those days, let’s talk about it.

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Day #63: The Importance of Science Outreach

skype a scientist

Today is Skype a Scientist day! Every term I volunteer my time and try to explain my journey, my research, and my pitfalls with students all over the US. Technically this is my second session (of six!) this term, but I wanted to talk about why I do what I do today. So if you’re interested in what it’s all about, keep reading.

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Day #54 : The Science Behind Real Zombies – 365 DoA

Zombies: Science Fiction vs. Fact

zombies ahead

Time for a break from stochastic processes, at least for the moment. Every year here we update and post our favorite Halloween tradition!  So today we bring you the science fact and fiction behind the undead. Zombies, those brain loving little things are everywhere. Sure, we are all familiar with the classic  zombie, but did you know that we aren’t the only zombie lovers out there? It turns out that nature has its own special types of zombies, but this isn’t a science fiction movie, this is science fact! Sometimes fact can be scarier than fiction, so let’s dive in. Let’s talk zombies.

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Day #22 : Parametric vs. NonParametric Statistics – 365 DoA

How Mean Meme

Technically we could call this parametric statistics part 2. However, since we are covering nonparametric statistics and more importantly the difference between parametric and nonparametric statistics, it would seem that this title makes more sense. As usual with a continuation, you probably want to start at the beginning where we define parametric statistics. Ready to get started?*

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Day #21 : Defining Parametric Statistics – 365 DoA

normal-distribution

It’s halloween time, we are talking about normally distributed data, so this fits, and I don’t want to hear otherwise!

Well my lovely readers, we’ve made it to the three week mark, 5.7% of the way through! Okay maybe that doesn’t seem like a big deal written like that, but hey it’s progress. So last post we had our independence day, or rather defined what it meant to have independent events vs. dependent events. We also said it was an important assumption in parametric statistics that our events are independent, but then we realized we never defined what parametric statistics even is, oops. So let’s stop dragging our feet and talk parametric statistics!*

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Day #20 : Independent Events – 365 DoA

correlation

By: xkcd

 

Because we introduced the central limit theorem last post, it’s time to introduce another important concept. The idea of independent events, while this may seem intuitive, it is one of the assumptions we make in parametric statistics, another concept we will define, but for now let’s jump into independence.*

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Day #19 : The Central Limit theorem – 365 DoA

 

 

CLT

Well here we are again, if you recall from our last post, we talked Bonferroni Correction. You may also recall that when the post concluded, there was no real topic for today. Well after some ruminating, before we jump into more statistics, we should talk about the central limit theorem. So let’s do a quick dive into what that is and why you should know it!*

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Day #18 : The Bonferroni Correction – 365 DoA

Keep calm and do the Bonferroni corrrection

Keep calm and do the Bonferroni corrrection

By now we are masters of statistics… right? Okay, not really, but we are getting there. So far we’ve covered two types of errors, type 1 which you can read about here, and type 2 which you can read about here. Armed with this new knowledge we can break into a way to correct for type 1 errors that come about from multiple comparisons. Sound confusing? Well, not for long, let’s break it down and talk Bonferroni.*

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Day #17 : Type 2 errors – 365 DoA

 

cat asleep

Last post we did a quick bit on type 1 errors. As with anything, there is more than one way to make an error. Today we are talking type 2 errors! They are related in the sense and we’ll go over what that means and compare the two right… now!*

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Day #16 : Type 1 errors – 365 DoA

tiny dog yawning

tiny dog yawning

We did it, we cracked the coin conundrum! We managed the money mystery! We checked the change charade! We … well you get the idea. Last post we (finally) determined if our coin was bias or not. Don’t worry, I won’t spoil it for you if you haven’t read it yet. I actually enjoyed working through a completely made up problem, so if you haven’t read it, you really should. Today we’re going to talk dogs, you’ll see what I mean, so let’s dive in.*

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