file sync

Fleeting Notes/Class/Bayesian Signal Processing/20260121.md

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+# BSP - Random Variables
+
+## Discrete Random Variables
+
+Imagine two sets, A and B. 
+
+There is A+B, which the set of elements in A or B,
+and $AB = A \union B$, which is the elements in A and B.
+
+Suppose our set S is {1, 2, 3, 4, 5, 6} where A is the evens,
+and B is less than 5. AB is {2, 4}, while A+B is {1, 2, 3,
+4, 6}.
+
+Sometimes  -A is known as NOT A, or $\bar A$.
+$\bar S = {}$.
+
+## Probability and Random Variables
+Set $\Omega$ is the set of all possible outcomes of an
+experiment.
+
+Events of some subset of outcomes are called 
+$\omega = {odd, even}$
+
+A trial is a single performance of an experiment (single
+sample).
+
+An experiment is to observe an single outcome $\zeta_i$.
+
+Experiment E means a set S of outcomes $\zeta$, certain
+subsets of S can be considered events.
+
+The space S is the certain event. Basically if it's in S, it
+happened. The null space is events that are impossible. E.g.
+can't get a 7 on a six-sided die.
+
+If event $\zeta_i$ consists of a single outcome then it is
+an elementary event. 
+
+Events A and B are mutually exclusive if they have no common
+elements (AB = null space)
+
+**Defining exactly what the events and outcomes are is super
+important**. It's very easy to get paradoxical results if
+careful choice of outcome and event is not chosen.
+
+### Example
+
+Assign each event a number $A \rightarrow P(A)$
+
+Axioms:
+1. $P(A) \geq 0$
+2. $P(S) = 1$
+3. if $AB = 0$ then $P(A+B) = P(A) + P(B)$
+
+Corollaries:
+1. $P(0) = 0$
+2. $P(A) = 1 - P(\bar A) \leq 1$
+*fundamentally the probability of an event is some number
+between 1 and 0*
+3. If $A$ and $B$ are not mutually exclusive, then 
+$P(A+B) = P(A) + P(B) - P(AB) \leq P(A) + P(B)$
+4. If $B \subset A \rightarrow P(A) = P(B) + P(\bar A B)
+   \geq P(B)$
+
+## Conditional Probability
+Given an event $B: P(B)\geq 0$, we define conditional
+probability as $P(A|B) = \frac{P(AB)}{P(B)}$.
+
+Sometimes people write *joint probability* as $P(A,B)$ which
+is exactly the same as $P(AB)$.
+
+Given $n$ mutually exclusive events $A_i,...,A_n$ where $A_1
++ A_2 + ... + A_n = S$. For an arbitrary event $B$, 
+
+$P(B) = \sum_i P(A_i, B)$
+$P(B) = \sum_i P(B | A_i) P(A_i)$
+
+We know $B = BS = B(A_1+...+A_n)$. With some rearranging
+knowing each of the A's are independent, $BA_i$ and $BA_j$
+are independent for all $i\neq j$. 
+
+Thus, $P(B) = P(BA_1) + ... + P(BA_n)$ but we showed earlier
+there's a different way to find $P(B)$.
+
+if $B = S$, $P(S|A_i) = 1$, then $P(S) = 1 = \sum_i P(A_i)$
+if $B = A_i$, $P(A_j|A_i) = 1$ when i = j, 0 otherwise
+
+
+> [!important] Development of Bayes' Theorem
+>
+> Bayesian statistics are a way of thinking about a **degree
+> of belief** in a probability, not an estimation of the
+> probability from a number of experiments.
+> 
+> We know:
+>
+> $P(AB) = P(A|B)P(B) = P(B|A)P(A)$
+>
+> Then Bayes Theorem becomes
+> $$P(A|B) = \frac{P(B|A) P(A)}{P(B)}$$
+>
+> and then when events $A_i$ are mutually exclusive...
+>
+> $$P(A_i|B) = \frac{P(B|A_i) P(A_i)}{\sum_i P(B|A_i) P(A_i)}$$
+> 

Fleeting Notes/Daily/2025-08-15.md

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+---
+id: 2025-08-15
+title: Daily — 2025-08-15
+type: daily
+created: 2025-08-15T21:38:18Z
+modified: 2025-08-15T21:41:25Z
+tags: [daily]
+---
+
+# Daily — 2025-08-15
+
+## Quick capture
+
+- Today I didn't really do anything! But I made a bit more
+progress on my Zettelkasten. It actually exists now and I
+made commands to use it.
+- I also made git pushing commands.
+
+## Tasks
+
+- [ ] 
+
+## Notes

Fleeting Notes/Daily/2025-08-18.md

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+---
+id: 2025-08-18
+title: Daily — 2025-08-18
+type: daily
+created: 2025-08-18T17:12:19Z
+modified: 2025-08-19T13:43:54Z
+tags: [daily]
+---
+
+# Daily — 2025-08-18
+
+## Quick capture
+
+- Installed VimTex and got latex working on my laptop with
+neovim
+
+- Zettled more about Strix and logic
+
+- Meeting with Babay's group in the INFSCI building.
+
+- Signed up for Strava. Considering doing a run club. Could
+  be coool!!!
+
+## Tasks
+
+- 
+
+## Notes
+
+Notes from Babay meeting:
+
+Emerson is going to upgrade the Ovation system in Cole's
+group. We're looking for controllers and things to use.
+Ideas from Babay's group:
+
+- Protocols: MODBUS and DNP3, HART protocol. Highway
+Addressable Remote something something. Similar to MODBUS
+and DNP3 in principal. 
+
+- Instrument light panel.
+
+- Testbed before Energy Innovation Center (EIC)? What tests can we do before going to
+EIC?

Fleeting Notes/Daily/2025-08-19.md

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+---
+id: 2025-08-19
+title: Daily — 2025-08-19
+type: daily
+created: 2025-08-19T14:31:15Z
+modified: 2025-08-19T19:06:40Z
+tags: [daily]
+---
+
+# Daily — 2025-08-19
+
+## Quick capture
+
+Goals for today:
+
+- Write powerpoint for Strix
+
+- Write heilmeir paragraphs for thesis idea
+
+- Tour new gym
+
+- Get details on dSPACE and speedgoat systems
+
+## Tasks
+
+- [ ] 
+
+## Notes
+
+Here is a list of I/O we can use in the PLC Cabinet:
+
+1. MODBUS compatibility (Babay / Cole)
+    - Over Ethernet is ideal, but other mediums would also
+    be nice to have.
+
+2. DNP3 (Babay)
+
+3. HART (Babay)
+
+4. Analog Inputs / Outputs
+    - +/- 10 V for dSPACE (Maximum range)
+    - +/- 10 V for TQ Equipment (Ball and Beam)
+    - 0-1.8V for BeagleBone Black
+    - IO101 from Speedgoat can use all of above (and +/- 5
+    V, +/- 3.3V)
+
+5. Digital Inputs / Outputs
+    - 10 V dSPACE and related
+    - 3.3 V for BeagleBone Black
+    - 5 V for Arduino
+    - IO101 can use all of above
+
+6. OPC UA, don't need right now but could be useful for
+   historians and working with data later.
+
+Obviously for digital signals we can use voltage regulators
+if required but it would definitely be nice to have 3.3V
+capability for the BeagleBone, and 5V for an Arduino.

Fleeting Notes/Daily/2025-08-20.md

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+---
+id: 2025-08-20
+title: Daily — 2025-08-20
+type: daily
+created: 2025-08-20T13:54:13Z
+modified: 2025-08-22T15:06:52Z
+tags: [daily]
+---
+
+# Daily — 2025-08-20
+
+## Quick capture
+
+- Workin in the morning on Strix presentaiton
+- Cole Group Meeting 10am - 11am
+- Write down weekly plan 11am+
+
+## Notes

Fleeting Notes/Daily/2025-08-22.md

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+---
+id: 2025-08-22
+title: Daily — 2025-08-22
+type: daily
+created: 2025-08-22T15:41:02Z
+modified: 2025-08-22T16:03:15Z
+tags: [daily]
+---
+
+# Daily — 2025-08-22
+
+## Quick capture
+
+- Got to work kind of late. Feeling sicky af. Probably no
+darts tonight with PSM.
+- Working on moving all my notes into zettels
+- Lunch w AS today
+- Okay i'm starting to feel a little better (12:03PM)
+
+## Tasks
+
+- [ ] 
+
+## Notes

Fleeting Notes/Daily/2025-08-25.md

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+---
+id: 2025-08-25
+title: Daily — 2025-08-25
+type: daily
+created: 2025-08-25T16:02:00Z
+modified: 2025-08-26T13:56:53Z
+tags: [daily]
+---
+
+# Daily — 2025-08-25
+
+## Quick capture
+
+- Got in a little later today, but the bike is here! Gotta
+text Alisa about it.
+
+- I have 2 classes today (grumble grumble grumble). 
+    - ME 3100 ERLM is Monday and Wednesday at 1PM-2:15PM
+    - NUCE 2101 - Nuclear Core Dynamics is tonight
+    6PM-8:30PM, like usual
+
+- I also enrolled in my health insurance.
+
+
+## Tasks
+
+- [ ] 
+
+## Notes

Fleeting Notes/Daily/2025-08-26.md

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+---
+id: 2025-08-26
+title: Daily — 2025-08-26
+type: daily
+created: 2025-08-26T15:05:38Z
+modified: 2025-08-26T15:06:58Z
+tags: [daily]
+---
+
+# Daily — 2025-08-26
+
+## Quick Capture
+
+- I started this morning doing some email
+- Now I'm hangin out in starbucks doing some work for the
+quad chart n'at
+- First, what the fuck is a quad chart??
+
+## Notes

Fleeting Notes/Daily/2025-08-27.md

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+---
+id: 2025-08-27
+title: Daily — 2025-08-27
+type: daily
+created: 2025-08-27T18:33:33Z
+modified: 2025-08-28T17:57:53Z
+tags: [daily]
+---
+
+# Daily — 2025-08-27
+
+## Quick capture
+
+COLE GROUP MEETING
+Accomplishments:
+- Quad chart
+- writing more about LTL and building out some notes from
+papers
+- Found resources about temporal logic
+- first nuce class has happened. Codes and standards were
+cancelled
+
+to do:
+- Write goals and outcomes
+- Write more about approach. This is squishtastic
+- Actually finalize some outcomes. How do i navigate the
+fact that within switching mechanisms there is dynamics
+happening
+- I didn't say anything about what a hybrid system is.
+That's kind of the whole point of the thing.
+
+## Notes

Fleeting Notes/Daily/2025-08-29.md

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+---
+id: 2025-08-29
+title: Daily — 2025-08-29
+type: daily
+created: 2025-08-29T14:23:06Z
+modified: 2025-08-29T15:44:16Z
+tags: [daily]
+---
+
+# Daily — 2025-08-29
+
+## Quick capture
+
+Yesterday I wrapped up a couple small things I needed to get
+done. First, I sold my bike to Alisa for 250! Pretty good
+deal for me, I made 30 on the sale. Then, I went to Harbor
+Freight and got some critical tools for working on the bike.
+It turns out, it's actually really hard to put a dirt bike
+on a stand. Heavy as all hell. But today, I'll get the sumo
+wheels on the bike!
+
+- [?] What tire pressure should I use for these new wheels?
+
+For work stuff, I've got to answer more Heilmeier questions
+and start writing a goals and outcomes section. The G&O
+should likely be a LaTeX document.
+
+The Emerson guys were here today too to fix up the ovation
+system. They told us they took the top off, affixed the
+power strip to the upper right side, and finally they told
+use we can totally take all the doors off if we wanted. They
+also said no 3.3V, they do all 24V stuff so they just don't
+carry the modules that go that low in power.
+
+## Tasks
+
+- [ ] 
+
+## Notes

Fleeting Notes/Daily/20250331_Should_I_Continue.md

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+# What should I do about my PhD?
+---
+
+The quick brown fox jumps over the lazy dog. The dog stays blissfully asleep. :)
+
+This time, I'm actually going to begin writing a journal. I feel like I have a 
+lot of thoughts that I let swim around, without doing much about them. To quote
+*the Happiness Lab* episode that I listened to today: 
+
+"Good intentions mean nothing if they don't translate into actions."
+
+So I'll take Dan's advice, and use writing to do thinking. I also think that 
+writing this journal can improve my writing skills. 
+
+So what's going on today?
+
+Well as I'm writing this, I'm on the 61D on my way into school listening to 
+*Spanish Pipedream* by John Prine. But what I really want to tell you about is
+the decision I'm trying to make about whether or not to finish my PhD here at 
+Pitt with Dan. Last Friday, I had a meeting with Dan about an idea I was 
+interested in pursuing that at the core involved working with a real, tangible
+system. That idea was politely dismissed, and I was 'nudged' back towards formal
+methods for critical infrastructure. My immediate impression is that formal
+methods for our lab is a crock of shit. 
+
+Dan means well and is genuinely looking out for my best interest, but that 
+doesn't translate into belief into his mission. Formal methods are an intense
+mathematical pursuit in order to prove 'correctness' of something to something 
+else. Formal methods experts may disagree with that characterization, but 
+ultimately that second 'something' can be a lot of things, such as a model of a
+plant, a written specification, or anything that can be logically defined. Dan
+wants to use formal methods to prove things about physical systems. His idea is
+aligned with what Manyu just finished up: can we use formal methods to prove that
+certain systems adhere to requirements using formal methods? This is connected
+in part to the HARDENS report, which tried to use formal methods tools at several 
+layers of abstraction to prove that a written requirement can be translated into 
+a proof for a determined plant design. There is certainly work to be done there.
+
+But is that work that I want to do? My brain says I could do it, but my gut 
+screams out a vehement no. This is the core issue--I know I could do it, but 
+once I would finish, where does that leave me? The answer: a formal methods 
+expert. Formal methods experts are highly sought after, but it is an intensely
+theoretical oriented field. When I think about what I want to do in my career 
+and what my values are, they are not only working through a computer (despite
+my aptitude for such). I want to build real things, works you can touch, and
+that interact with the world. A formal methods proof about a reactor that *might*
+get built is not in that alignment. 
+
+So what the hell do I do? As I write this, it seems pretty clear the relationship
+between myself and the Cole Lab's work is fractured. Going forward, I see three
+main options:
+
+1) Find another PhD advisor at Pitt. Bajaj is an obvious choice.
+2) Master out and go find a job.
+3) Go find another PhD opportunity somewhere else. Yichen did this.
+
+Pros and cons of each situation:
+
+1) Find another PhD advisor at Pitt
+    + I would be able to keep my NRC Fellowship
+    + I know people here already
+    + I've already passed the qualifying exam
+    - Money is garbage
+    - I don't think anyone is actually doing work that I really want to do
+    - Have to stay in Pittsburgh
+    - NRC debt keeps growing
+
+2) Master out and go find a job
+    + I would immediately make much more money
+    + Can move somewhere else (Boston?)
+    + NRC commitment is only a year
+    + Could find an interesting R&D job?
+    + Could get a second publication out for Bajaj's project
+    + Could pick up PhD again in a year or so. Work on projects to make 
+    myself super competitive 
+    - Dr. Sabo is on hold
+    - No thesis!
+
+3) Master out and start a PhD at another school
+    + Dr. Sabo is slightly delayed
+    + Could go work in Boston
+    + Could go work on something I feel passionate about
+    + Better degree diversity
+    + Teaching plan could still work out
+    - Slightly longer timeline
+    - Have to take another qualifying exam
+    - Still have the NRC commitment likely
+    - Would not make much money
+
+I think the smartest thing is to master out, find a job for a year that will
+satisfy the NRC requirement, and then if I want to, restart the PhD somewhere
+else. This would put me finishing sometime in 2030 or so. That's certainly a lot.
+If I went to find a PhD now, I would finish somewhere in 2029 or so, then have
+the 1-year NRC commitment. Hmmm. 
+
+I checked my current progress in my degree, and learned that I satisfy the controls
+track masters degree after this semester. I would need to negotiate two things:
+either ME 2046 or ME 2150 would need to count as a DSC elective, and NUCE 2100 
+would have to be accepted as a ME elective (it is cross listed as ME 2100, so 
+shouldn't be impossible to argue for). The next thing I need to do for this would
+to be to talk to Dan about it. 
+
+Thinking about stopping with the Master's feels good. I think I should seriously 
+pursue this, and maybe talk to Rachel and my family about it.
+
+## Chat w/ Pat
+Patrick and I got lunch today. He was generally pretty supportive and gave me 
+some sound advice that I can use. He asked me "have you read some literature 
+reviews?" And the answer to that is no, not really. He also advised to "just do
+something", which perhaps will help me feel like I'm actually getting something
+built. I think that is helpful. Going forward, I'm going to really try and do
+two things:
+
+1) Read at least 3 literature reviews by Friday
+2) Get ARCADE and I2C working by next Monday
+    [Could be interesting](https://www.adafruit.com/product/2264?gQT=0)
+
+I really don't know what I should do. This certainly is not a one day decision.
+Honestly, I may like the idea of option 3 the best, but I do need to do some work.
+I've got it in the works to:figure out how to get the MS along the way with Antoine,
+so we'll see how that happens. I think the earliest things would happen would be at
+the end of the summer.

Fleeting Notes/Daily/20250409_*horsenoises*.md

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+The quick brown fox jumps over the lazy dog. The dog stays blissfully asleep. :)
+
+Since last time, I have found a bit more resolve on what I'm going to do about 
+this whole PhD thing. I have decided I am going to earnestly try to find a topic
+that fits with the lab's formal methods bend--at least for the rest of the 
+spring and into the beginning of the summer. I am taking action to try and find
+a topic, like trying to read more surveys and actually doing things. This past 
+week was not necessarily super successful in that regard, but on the margins was
+an improvement. Oh, well.
+
+There is a couple reasons I think this is the right move. First, I am already 
+here. Any other route that ends with my PhD will add extra time before I am 
+finished. Any job search right now is also probably not a great idea, since 
+Trump and his merry men are starting a trade war, and consequently likely a 
+recession. I am in a good position right now, and there is value in taking stock
+of the opportunity that I have. 
+
+Robert also lended some helpful advice: certainly the topic of my PhD does not
+pigeon hole me into a field for the rest of my career. I think this is true in 
+a restricted sense, but not in the general sense. For my sake, this means if I 
+do something formal methods adjacent, it does not mean I need to be stuck in 
+formal methods forever, but also I should be careful that the work I do also
+lends itself to another field I find interesting. One such area is perhaps using
+formal methods with artificial intelligence to leverage these tools to create
+explainable AI based control. 
+
+I need to read more to really understand what that can be. Update to come.
+
+Now for a slight change of pace, some more personal details.
+
+The pursuit of an apartment for Amber and I continues to be a contentious topic.
+Amber was quite upset coming back from her trip that I 'did not take care of
+myself'--her accusation is that I did not eat balanced meals or in general act
+with personal motivation to do things that are good for me. This also compounded
+with my food habits with my night classes. I have eaten out a lot recently before
+class instead of cooking food at home the night before or so. Amber attributes 
+this to lazyness. This argument culminated in her saying that she feels more 
+like a mom than a girlfriend. That makes me really upset.
+
+Do I think she is right? Well, in terms of food, sure. She has a good point. I 
+could certainly eat better, and this past weekend I see what she is saying about
+balanced meals. Fair point and this is something I must correct. Something that
+does make me worried however is this idea that she is like my mom rather than 
+my girlfriend, and more broadly that she feels I make changes because she tells
+me so rather than because I want to on my own. This is a frustrating catch-22 in
+my opinion. If I do not learn what is upsetting her, I cannot change that 
+behavior. But, if she tells me and I do change that behavior, she takes credit 
+for it and gets upset anyways. Honestly, it makes me feel like damned in a way.
+I'll try and change nonetheless, but it is incredibly demotivating to think 
+she will believe it is just because 'she told me so'. 

Fleeting Notes/Daily/2025_07_30.md

@@ -0,0 +1,23 @@
+---
+---
+
+# 2025-07-30
+
+## Morning Brief
+Today's goal is to finish writing up some thesis ideas. I
+need to have 6 of them for a meeting with Dan. I used
+ChatGPT to help me brainstorm some ideas, but I need to go
+over them and format them in a way that is more
+approachable.
+
+On the other hand, I've been working on leaving my phone
+behind. I'm trying a new technique of just leaving it out of
+my reach. I can feel the itch in my brain that yearns for
+it... that's definitely an addiction I have to kick. 
+
+Anyways, here's the goals for today:
+
+- [ ] Write down 6 ideas for a thesis: [[thesis-ideas]]
+- [ ] Review literature notes, and organize my notes
+- [ ] Finish [[automation-levels-for-nuclear-reactor-operations-a-revised-perspective]]
+

Fleeting Notes/Daily/2025_07_31.md

@@ -0,0 +1,22 @@
+---
+---
+
+# 2025-07-31
+
+## Morning Brief
+Yesterday I wrote 2 thesis ideas and started a third. Today,
+we finish them! I'm struggling to write outcomes but we'll
+get there over time. I can do this.
+
+I started the morning with an hour of doomscrolling. I
+really have to sort that out.
+
+Tasks are the same from [[2025-07-30|yesterday]]. Maybe I
+should make a centralized page for tasks.
+
+- [ ] Make task page #admin
+
+## Lunch Brief
+
+
+## Note for tomorrow

Fleeting Notes/Daily/2025_08_01.md

@@ -0,0 +1,11 @@
+---
+---
+
+# 2025-08-01
+
+## Morning Brief
+Yesterday I finished two additional thesis ideas and got
+some more reading done 
+
+- [ ] Fill out health insurance enrollment
+

Fleeting Notes/Daily/2025_08_04.md

@@ -0,0 +1,17 @@
+---
+---
+
+# 2025-08-04
+
+## Morning Brief
+I didn't do shit. But I emailed Dan that I'd be OOO
+Wednesday and Thursday for the motorcycle course.
+
+I'm finishing those fucking thesis ideas today. ON GOD.
+[[thesis-ideas-2025-07-30]]
+
+I'm' also supposed to have a date with Miranda today, but
+she hasn't texted me back. Interesting. Jackie also
+complimented my socks and show combo. That was nice. I
+showed her and Natan [Angus](ourcowangus.com).
+

Fleeting Notes/Daily/2025_08_05.md

@@ -0,0 +1,22 @@
+---
+---
+
+# 2025-08-05
+
+## Morning Brief
+I didn't finish the thesis ideas from yesterday. Oopsie!
+Today is different though. Curently, I'm working from
+home^*, which really means I'm working in a coffee shop on
+Washington road. I'm at the Orbis Cafe, where I purchased a
+cinnamon roll and a cappucino. The caffeine has yet to hit,
+but when it does, I'll be cooking I'm sure. This is a nice
+spot and it's very relaxing to get things done while other
+people are around. I like this a lot, and perhaps I should
+do this more often while I'm at school too. 
+
+Anyways, Dan is OOO taking time off while he can before the
+fall semester. Who can blame him?
+
+Patrick and I discussed more PINN stuff yesterday. I should
+make a simple PINN demonstration.
+

Fleeting Notes/Daily/2025_08_06.md

@@ -0,0 +1,23 @@
+---
+---
+
+# 2025-08-06
+Today was the first day of the motorcycle safety course. It was
+good! I felt like I was honestly the best rider there. That being
+said, tomorrow is a new day and we'll see how it goes. Jackie
+looked like she had fun too.
+
+I had a great date yesterday. Miranda is very, very cool. She
+loves facebook marketplace, mac.bid, camping, and said her
+favorite book was *Dune*. My jaw just about fell open when I
+heard that. We're potentially going to go look at a van on
+Saturday. 
+
+I missed the Jumet Financial Open House. I slept right through
+that mf after getting back from the course. Whoops. I feel bad
+about it as Sam gave me a call right in the middle. No voicemail.
+Yikes. I'll see how that works out.
+
+Then, last thing today is getting some final writing done to say
+that I did any work today. No group meeting this week it looks
+like.

Fleeting Notes/Daily/2025_08_07.md

@@ -0,0 +1,11 @@
+---
+---
+
+# 2025-08-07
+Today I have not gotten too much done, but I did get here
+early today. Today, I'll sell the truck and work on Sam's
+car. I saw Patrick today too, which was nice. Robert's stuff
+is all gone.
+
+My main focus for today is to finish the thesis ideas and
+tune up the writing. That'll be enough.

Fleeting Notes/Daily/2025_08_11.md

@@ -0,0 +1,8 @@
+---
+---
+
+# 2025-08-11
+Today I'm finishing the thesis ideas, for real this time.
+
+I'm also going to get a model of a heat exchanger working.
+

Fleeting Notes/Daily/2025_08_12.md

@@ -0,0 +1,10 @@
+---
+---
+
+# 2025-08-12
+
+Yesterday I finished my thesis ideas! Hooray! It feels
+really good to actually have some writing finished. Today,
+I'm making a model for a simple heat exchanger in python.
+Then, I'm going to train a physics informed neural network
+on it and start fucking with parameters.

Fleeting Notes/Daily/2025_08_13.md

@@ -0,0 +1,67 @@
+---
+---
+
+# 2025-08-13
+
+Today is August 13th, 2025, otherwise known as judgment
+day. Just kidding, but today I have my meeting with Dan
+about my topic ideas. I feel anxious, but pretty good in
+general. I saw Dan this morning and he seems to be in good
+spirits. I can do this!
+
+My eye doctor appointment was also today. The results? My
+prescription is pretty much the same. I also do not have
+glaucoma it looks like. Doc was surprised I wear glasses at
+all, figuring the binocular detriment of glasses in my case.
+Honestly, he's right, I should wear contacts more often.
+I'll try to make a point to do that. Now that I have this
+new prescription, I can get on ordering more contacts from
+Costco. Dr. Clermont also recommend to try and stay around
+twelve hours of usage a day to minimize hydration issues. He
+said pushing 16 some times is okay. 12 hours would be 7-7
+(duh), while 16 would be 7-11pm. We also discussed LASIK,
+and he said honestly I'd be a great candidate. He gave me a
+note with a number to call.
+
+Today is also our group meeting. Apparently it's a
+'standup' now. 
+
+## Personal 
+
+Personally I'm doing pretty okay. I'm trying to focus on
+framing things in a more positive way. I think it is working
+somewhat; there's moments where things click in a way I
+don't feel as anxious about. 
+
+On the lady front, I finally hit app-burnout. I was reading
+a text and the typos just made me angry. Like, c'mon, read
+your message! This isn't rational, however, as any number of
+things can create a typo and it really isn't a big deal.
+There's no reason I should get so frustrated at something so
+small like that.
+
+Anyways, here's the roster and relevant updates:
+
+**Miranda**:
+Miranda is cool and I like her a good bit. She's funny,
+seems somewhat interested in me, and is a great time to be
+around. That being said, I need to be careful. I'm getting
+somewhat infatuated with her but there isn't really a super
+strong connection there yet. This is one that I need to
+really step off the brakes with and see how things develop.
+She is going on vacation with her family next Friday, and
+then going solo camping after that. Then, I'm really going
+to try and let her set something up.
+
+**Katarina**:
+Katarina is a recent match and is interesting as a prospect.
+She seems pretty nice and is a bioengineering PhD student in
+her 5th year. So almost done maybe? I'll get more details on
+Thursday night!
+
+**Abby:** 
+Abby is a nurse who I've had an interesting conversation
+with about religion. She has 'catholic' in her profile but
+is apparently not very religious actually. She has a dog
+named Goose! We're meeting up on Sunday to take Goosey-boy
+for a walk.

Fleeting Notes/Daily/2025_08_14.md

@@ -0,0 +1,78 @@
+---
+---
+
+# 2025-08-14
+
+## Work
+
+Yesterday Dan and I had our meeting about
+[[thesis-ideas-2025-07-30 | topic ideas]]. The results were
+as follows:
+
+5. Integrating Shielding in Nuclear Power
+3. Formally Verified NN CTRL of CRS
+1. Temporal Logic Specifications for Autonomous Control
+   Synthesis.
+1. Formally Verified Runtime Monitoring and Fallback
+6. High Assurance Fault Detection with Digital Twins
+4. Verified Adaptive Control.
+
+The final topic result? 
+
+*Hybrid Controller Synthesis from Temporal Logic
+Specifications* 
+
+The research will be basically a mix of the third and fourth
+idea. More work to come on this one.
+
+I also got roped into making a presentation about Strix for
+next week's meeting. So I must learn about that!
+
+## Reading
+
+Yesterday I read more of *The Power of Habit* and I learned
+about the **craving**. A craving is what actually makes the
+habit loop work. It was explained to me that the brain
+releases a spike in activity at first when it recognizes the
+reward. Once the cue and routine are associated with the
+reward, the brain over time will deliver the activity spike
+as an anticipation of the reward *earlier and earlier*. The
+result is that the brain gets the activity spike as soon as
+it sees the cue, anticipates the reward, and is thus
+motivated to do the routine. The craving is what makes
+habits easy. 
+
+
+## Personal 
+
+Finally my personal info. I feel pretty good today. I didn't
+get a lot done this morning but I'm steady cooking now that
+I'm working in a Starbucks on campus. I've been
+peoplewatching as people slowly move in for the fall
+semester. It's fun to see all the different kinds of people
+walking around and to see the connection between kids and
+parents. The kids definitely look more nervous on average
+than the parents. And I get it, the parents know what to
+expect, but for the kids, this is the transition to the deep
+end. They'll be fine.
+
+On the lady front, here's today's update:
+
+**Miranda:** 
+Honestly I'm getting a little bored. I think it might just
+be a texting issue, or perhaps the infatuation wearing off.
+That's okay though, she's really busy this week som maybe
+that has something to do with it.
+
+**Abby:** 
+No update!
+
+**Katarina:** 
+Also no update, but I'm excited for our date tonight. We'll
+see how it goes.
+
+I made some updates to my hinge profile to make things sound
+more serious and better indicate what I want / who I am.
+Maybe this'll stand out more. Honestly, I tried to write the
+profile like one I'd be looking for. 
+

Fleeting Notes/Daily/template.md

@@ -0,0 +1,10 @@
+---
+---
+
+# 2025-08-14
+
+## Work
+
+## Reading
+
+## Personal 

Fleeting Notes/Internship-spots.md

@@ -0,0 +1,42 @@
+# Internship Locations
+
+This is a short list of internship spots I am considering.
+The goal is to find an internship that starts next summer,
+and maybe can eventually be parlay'd into a job.
+
+## National Laboratories
+**Idaho National Laboratory**
+- Contacted Greg with research statement. 
+- He's talking about it with Wayne and Simon Pemblott.
+
+**Sandia National Laboratory**
+- Sent research statement to Lee. He liked it and offered
+comments.
+- There's a fellowship internship opportunity. I should
+check that out
+
+## Nuclear Companies
+**Westinghouse**
+- Is there any opportunities here? Maybe, maybe not. They
+seem pretty humdrummy
+
+**Oklo**
+- Do they have opportunities? Must find a recruiter.
+
+## Other Companies
+**Anduril**
+- Hehe cool robotics military tech
+- find a recruiter. They've got lots of jobs open
+
+**CIA**
+- Do they have internships?
+
+**Lockheed Martin**
+- Any cool advanced military gigs?
+
+**Applied Physics Lab**
+- We know Chris D'Angelo there
+
+**Loonwerks**
+- Spoke to Daren Cofer at NASA FM conference. Any
+opportunities there?

Fleeting Notes/Meetings/20260106-Meeting-With-INL.md

@@ -0,0 +1,37 @@
+# Meeting with Ginger and Benjamin about Summer Internship
+
+Also not directly an interview, but rather a check-in and
+conversation. Good conversation about the thrust they would
+be interested in me working on. CIE-group. They want to do a
+push about how we define resilliency, especially when it
+comes to cyber control systems. Probabilism and defense in
+depth is not enough, or perhaps not the right approach.
+
+Ginger also brought up good points. We want to be able to
+have evidence for autonomous control systems for things like
+liability courts. If something goes wrong, we want to be
+able to say why the control system made the right choice,
+based on formal methods approaches to justify control
+actions. Also talk about *graded* responses and saying
+whether or not we can justify operation of a degraded
+system.
+
+16-wk on-site internship. Relocation help included. Spoke
+highly of Dan and continued collaboration is an option.
+
+Two main deliverables:
+- a kind of state of the art on what 'resilience' is and how
+  it is determined
+- a thrust or way forward of what new metrics for resilience
+  could look like. Sounds like an advanced proposal
+- Conference paper?
+
+Team: Ginger, Benjamin, a gentleman named John, other
+individuals.
+
+Benjamin has a reachability manifesto he wants to send us.
+Dan as INL-vetted will probably get an email about it.
+
+More to come in the next couple of weeks. Need to evaluate
+against Emerson opportunity. This seems to have more
+direction.

Fleeting Notes/Meetings/CISA_training.md

@@ -0,0 +1,11 @@
+# CISA ICS Training Notes
+
+## Russ' Quiz
+% data breaches involving phishing --- 15%
+
+% of all breaches involving human error --- 68%
+
+% financially motivated incidents that involve ransomware or
+extrotion --- 92%
+
+Year the PLC was invented? --- 1968

Fleeting Notes/Meetings/INL.md

@@ -0,0 +1,7 @@
+# Notes from INL Internship Meeting
+
+**Attendees:** 
+- Dane
+- DGC
+- Greg Shannon
+- Wayne Austad

Fleeting Notes/Meetings/emerson.md

@@ -0,0 +1,17 @@
+# Meeting With Emerson about Internship 
+
+## Attendees
+Dan
+Myself
+Rick
+
+## 
+
+## Questions I have:
+- What does the day to day work you'd have me working on
+look like?
+- Size of the team?
+- On site in cranberry?
+- Next steps? When should I hear from you?
+
+

Fleeting Notes/Random things I found that I should look into.md

@@ -0,0 +1,2 @@
+[Vim for MATLAB](https://github.com/daeyun/vim-matlab)
+

Fleeting Notes/Weekly/2025_34.md

@@ -0,0 +1,32 @@
+---
+id: 2025-34
+title: Weekly — 2025-08-20
+type: Weekly
+created: 2025-08-20T13:54:13Z
+modified: 2025-08-20T19:10:24Z
+tags: [weekly]
+---
+
+# Weekly - 2025 CW 34 (Aug 18 - Aug 22)
+
+## Accomplishments
+1. Met with Babay's group and collected their needs for the
+   new ovation system stuff. The notes are in [[daily-2025-08-18]]
+
+2. Learned about logic. Started with propositional logic,
+   then did predicate logic, now am working on temporal
+logic.
+
+3. Made a presentation about Strix, and learned about parity
+   games. Strix uses determnistic parity games to do
+synthesis, and yields automata that are very small relative
+to competition. They're old though--2017 was the first Strix
+paper.
+
+## This week's plan
+
+1. Write heilmeir paragraphs for thesis topic
+
+2. Make Quad chart for ERLM
+
+3. Find and keep working on an LTL book

Fleeting Notes/Weekly/2025_35.md

@@ -0,0 +1,18 @@
+---
+id: 2025-35
+title: Weekly — 2025-08-20
+type: Weekly
+created: 2025-08-20T13:54:13Z
+modified: 2025-08-20T19:10:33Z
+tags: [weekly]
+---
+
+# Weekly - 2025 CW 35 (Aug 25 - Aug 30)
+
+## Last week's plan
+
+1. Write heilmeir paragraphs for thesis topic
+
+2. Make Quad chart for ERLM
+
+3. Find and keep working on an LTL book

Fleeting Notes/Weekly/2025_36.md

@@ -0,0 +1,27 @@
+---
+id: 2025-36
+title: Weekly — 2025-09-02
+type: Weekly
+created: 2025-08-20T13:54:13Z
+modified: 2025-09-03T18:59:44Z
+tags: [weekly]
+---
+
+# Weekly - 2025 CW 36 (Aug 25 - Aug 30)
+
+## Accomplishments
+- Wrote the goals and outcomes, went up to V4.
+- Goal was flubbed but have new content
+- started thinking about how continuous dynamics need to be
+  included. 
+- Tried to watch a video about hybrid system verification.
+Made fun of 'trajectories' nomenclature instead of
+executions and then shit really went off the rails fast.
+Lots of pretty figures but I have to be honest I have no
+idea what the fuck he was talking about.
+- Had crises about intellectual mert
+
+## To Do
+- Rewrite GO
+- SOTA. Start writing. 
+- look up cones for math

Fleeting Notes/Weekly/2025_46.md

@@ -0,0 +1,62 @@
+---
+id: 2025-46
+title: Weekly — 2025-11-12
+type: Weekly
+created: 2025-11-11T13:55:31-05:00
+modified: 2025-11-12T15:43:57-05:00
+tags: [weekly]
+---
+
+# Weekly - 2025 CW 46 (Wed 2025-11-12)
+
+## Accomplishments
+
+### Internship
+- ✓ Write cover letter for INL Application
+- ✓ Apply for INL Internship
+- ✓ Submit INL Application on Taleo
+
+### class.NUCE2-101.Exam2
+- ✓ Problem 1
+- ✓ Problem 2
+- ✓ Problem 3
+- ✓ Problem 4
+- ✓ Problem 5
+- ✓ Problem 6
+- ✓ Submit Exam 2
+
+### ERLM
+- ✓ Assertion-Evidence - do in lieu of class
+
+### General
+- ✓ Get Dan's approval for course
+- ✓ Create updated plan of study document
+
+## Pushed or Rescheduled
+
+### ERLM
+- Mock Peer Review Assignment (rescheduled)
+- Make data management plan (rescheduled)
+- Make biographical sketch (rescheduled)
+- Make facilities section (rescheduled)
+- Add more tasks for this week (rescheduled)
+- Draft Presentations (rescheduled)
+- Tune up state of the art for Proposal (rescheduled)
+- Final Presentations (rescheduled)
+
+## Cancelled or Deleted
+
+No tasks were cancelled or deleted this week.
+
+## To Do
+
+### Immediate (Due within 24 hours)
+None
+
+### Due Saturday, November 16 (4 days)
+- Submit enrollment form to Antoine
+- Mock Peer Review Assignment (ERLM)
+- Create ORCID account (ERLM)
+- Make data management plan (ERLM)
+- Make biographical sketch (ERLM)
+- Make facilities section (ERLM)

Fleeting Notes/Weekly/2025_47.md

@@ -0,0 +1,58 @@
+---
+id: 2025-47
+title: Weekly — 2025-11-19
+type: Weekly
+created: 2025-11-19T14:34:56-05:00
+modified: 2025-11-19T14:34:56-05:00
+tags: [weekly]
+---
+
+# Weekly - 2025 CW 47 (Wed 2025-11-19)
+
+## Accomplishments
+
+### ERLM
+- ✓ Assertion-Evidence --- do in lieu of class
+- ✓ Read Proposal 1
+- ✓ Read Proposal 2
+- ✓ Read Proposal 6
+- ✓ Create ORCID account
+- ✓ Make data management plan
+- ✓ Make biographical sketch
+- ✓ Make facilities section
+- ✓ Mock Peer Review Assignment
+- ✓ Add more tasks for this week
+
+### General
+- ✓ Get Dan's approval for course
+- ✓ Create updated plan of study document
+
+## Pushed or Rescheduled
+
+No tasks were rescheduled during this period.
+
+## Cancelled or Deleted
+
+No tasks were cancelled or deleted during this period.
+
+## To Do
+
+### Due This Week (Nov 19-26)
+
+**ERLM**
+- Draft Presentations (due 2025-11-21) [urgency: 8.75]
+
+### High Priority
+
+**ERLM**
+- Tune up state of the art for Proposal (due in 2 weeks) [urgency: 3.44]
+- Final Presentations (due in 2 weeks) [urgency: 3.44]
+
+**Zettelkasten (zk)**
+- Write zettels about Andre Platzer and differential dynamic logic [urgency: 3.19]
+- Write zettels about webofscience database [urgency: 3.19]
+- Deterministic Parity Automata [urgency: 2.95]
+- Mealy Machines [urgency: 2.95]
+- AIGER Circuits [urgency: 2.95]
+- Reactive Synthesis [urgency: 2.95]
+- Write about opp. chall. and res. needs for remote micro ope. [urgency: 2.92]

Fleeting Notes/Weekly/2025_49.md

@@ -0,0 +1,76 @@
+---
+id: 2025-49
+title: Weekly — 2025-12-03
+type: Weekly
+created: 2025-12-03T21:01:29-05:00
+modified: 2025-12-03T21:01:29-05:00
+tags: [weekly]
+---
+
+# Weekly - 2025 CW 49 (Wed 2025-12-03)
+
+## Accomplishments
+
+### ERLM
+- ✓ Draft Presentations
+
+### Chair-Search
+- ✓ Make list of tasks for contact about student groups
+
+## Pushed or Rescheduled
+
+The following tasks had their due dates modified during the past week:
+
+- Review and edit Goals and Outcomes section
+- Review and edit State of the Art section
+- Review and edit Research Approach section
+- Review and edit Metrics of Success section
+- Review and edit Risks and Contingencies section
+- Review and edit Broader Impacts section
+- Review and edit Budget section
+- Review and edit Schedule section
+- Verify RFP compliance for all sections
+- Final proofread and polish entire proposal
+- Review and edit Literature Review section
+- Review and edit Methodology Details section
+- Review and edit Expected Contributions section
+- Review and edit Timeline and Milestones section
+- Review and edit Team Qualifications section
+- Review and edit References section
+- Review and edit Appendices
+
+## Cancelled or Deleted
+
+No tasks were cancelled or deleted during this period.
+
+## To Do
+
+### Due This Week (Dec 4-10)
+
+**ERLM Project - Editing Tasks (Due Tomorrow: Dec 4)**
+
+All of the following editing tasks are due tomorrow and are high priority:
+
+- Review and edit Goals and Outcomes section (Urgency: 22.1) ⚡ ACTIVE
+- Review and edit State of the Art section (Urgency: 22.1) ⚡ ACTIVE
+- Review and edit Research Approach section (Urgency: 18.1)
+- Review and edit Metrics of Success section (Urgency: 18.1)
+- Review and edit Risks and Contingencies section (Urgency: 18.1)
+- Review and edit Broader Impacts section (Urgency: 18.1)
+- Review and edit Budget section (Urgency: 18.1)
+- Review and edit Schedule section (Urgency: 18.1)
+- Verify RFP compliance for all sections (Urgency: 18.1)
+- Final proofread and polish entire proposal (Urgency: 18.1)
+- Review and edit Literature Review section (Urgency: 18.1)
+- Review and edit Methodology Details section (Urgency: 18.1)
+- Review and edit Expected Contributions section (Urgency: 18.1)
+- Review and edit Timeline and Milestones section (Urgency: 18.1)
+- Review and edit Team Qualifications section (Urgency: 18.1)
+- Review and edit References section (Urgency: 18.1)
+- Review and edit Appendices (Urgency: 18.1)
+- Update abstract based on final content (Urgency: 18.1)
+- Compile final PDF submission (Urgency: 18.1)
+
+### High Priority
+
+All high-priority tasks are already listed above in the "Due This Week" section.

Fleeting Notes/Weekly/2025_50.md

@@ -0,0 +1,58 @@
+---
+id: 2025-50
+title: Weekly — 2025-12-17
+type: Weekly
+created: 2025-12-17T20:56:30Z
+modified: 2025-12-17T20:56:30Z
+tags: [weekly]
+---
+
+# Weekly - 2025 CW 50 (Wed 2025-12-17)
+
+## Accomplishments
+
+### Chair-Search
+- ✓ Review Zbeeb, Khaled application
+- ✓ Review Christopher, Gordon application
+- ✓ Review Robles Hernandez, Francisco Carlos application
+- ✓ Review Asmatulu, Ramazan application
+- ✓ Review Gupta, Sanju application
+- ✓ Review Yang, Xiaodong application
+- ✓ Review Kim, Harrison application
+- ✓ Review Makhlouf, Abdelsalam application
+- ✓ Review Gouma, Pelagia application
+- ✓ Review Akkus, Ozan application
+- ✓ Review Narayan, Roger application
+
+### Internship
+- ✓ Tune up presentation for Emerson... digital twins
+
+## Pushed or Rescheduled
+
+No tasks were rescheduled during this period.
+
+## Cancelled or Deleted
+
+No tasks were cancelled or deleted during this period.
+
+## To Do
+
+### Due This Week
+
+**Due within 24 hours:**
+- **Union** — Talk to Jessica about getting a room for an event (Due: 1d, Urgency: 9.23)
+
+### High Priority
+
+**Zettelkasten (zk):**
+- Write zettels about Andre Platzer and differential dynamic logic (Urgency: 3.34)
+- Write zettels about webofscience database (Urgency: 3.34)
+- Deterministic Parity Automata (Urgency: 3.1)
+- Mealy Machines (Urgency: 3.1)
+- AIGER Circuits (Urgency: 3.1)
+- Reactive Synthesis (Urgency: 3.1)
+- Write about opp. chall. and res. needs for remote micro ope. (Urgency: 3.07)
+
+**Other Projects:**
+- **ERLM** — Add research tasks to research approach section (Urgency: 2.36)
+- **Thesis** — The Algorithmic Analysis of Hybrid Systems (1995) [reading] (Urgency: 2.3)

Fleeting Notes/Weekly/2026_02.md

@@ -0,0 +1,61 @@
+---
+id: 2026-02
+title: Weekly — 2026-01-07
+type: Weekly
+created: 2026-01-07T18:49:47Z
+modified: 2026-01-07T18:49:47Z
+tags: [weekly]
+---
+
+# Weekly - 2026 CW 02 (Wed 2026-01-07)
+
+## Accomplishments
+
+### Union
+- ✓ Talk to Jessica about getting a room for an event
+
+### Thesis
+- ✓ Find out what 10 CFR is. Specifically, 10 CFR 50.34 and 10 CFR 55.59. Emergency Operating Procedures?
+
+### Internship
+- INL internship meeting yesterday. Went very well. 
+
+## Pushed or Rescheduled
+
+- (Union) Follow up with Jessica about room booking
+- (Chair-Search) Read Clarks application and provide review scores
+- (Chair-Search) Read remaining two applicants and provide scores
+
+## Cancelled or Deleted
+
+No tasks were cancelled or deleted in the past 7 days.
+
+## To Do
+
+### Due This Week
+
+**Due in 10 hours:**
+- (Chair-Search) Read additional applican and provide scords
+
+**Due 2026-01-08:**
+- (Thesis) The Algorithmic Analysis of Hybrid Systems (1995) [Urgency: 14.6]
+- (Thesis) Hybrid Automata: An Algorithmic Approach to the Specification and Verification of Hybrid Systems (1993) [Urgency: 10.6]
+- (Thesis) Hamilton-Jacobi Reachability: A Brief Overview and Recent Advances (2017) [Urgency: 10.6]
+- (Chair-Search) Read Clarks application and provide review scores [Urgency: 9.15]
+- (Chair-Search) Read remaining two applicants and provide scores [Urgency: 9.15]
+- (ENGR1933) Complete RAMP training [Urgency: 9.15]
+
+**Due 2026-01-13:**
+- Fill out graduate student evaluation form [Urgency: 5.86]
+
+### High Priority
+
+- (Union) Follow up with Jessica about room booking [Urgency: 16.8]
+- (Thesis) Do FRET tutorials [Urgency: 13.1]
+- (zk) AIGER Circuits [Urgency: 3.22]
+- (zk) Reactive Synthesis [Urgency: 3.22]
+- (zk) Write about opp. chall. and res. needs for remote micro ope. [Urgency: 3.18]
+- (ERLM) Add research tasks to research approach section [Urgency: 2.48]
+- (Thesis) Hybrid Systems: Review and Recent Progress (2003) [Urgency: 2.41]
+- Have meeting with Dan about performance review
+- Internship items: Follow up with Emerson next week about paperwork

Fleeting Notes/Weekly/2026_03.md

@@ -0,0 +1,82 @@
+---
+id: 2026-03
+title: Weekly — 2026-01-14
+type: Weekly
+created: 2026-01-14T18:46:24Z
+modified: 2026-01-14T19:21:41Z
+tags: [weekly]
+---
+
+# Weekly - 2026 CW 03 (Wed 2026-01-14)
+
+## Accomplishments
+- Finished FRET tutorial I was working on. I've still got
+weird dependency things I need to figure out. Moving to a
+mac has caused some interesting quirks but I'm working them
+out.
+- Read Hybrid Automata: An Algorithmic Approach to
+Specification and Verification of Hybrid Systems
+- Did 2 interviews for chair search and read additional
+applicants stuff. 
+- Bob asked me for help for ENGR 1933. I completed my RAMP
+training to get recertified. 
+- Completed the review form.
+- Did maneuvering with Emerson to get them moving on an
+offer. INL sent me a formal offer letter.
+
+### Chair-Search
+- ✓ Read additional applican and provide scords
+- ✓ Read Clarks application and provide review scores
+- ✓ Read remaining two applicants and provide scores
+
+### Thesis
+- ✓ Do FRET tutorials
+
+## Pushed or Rescheduled
+
+### Thesis
+- The Algorithmic Analysis of Hybrid Systems (1995) — rescheduled
+- Hybrid Automata: An Algorithmic Approach to the Specification and Verification of Hybrid Systems (1993) — rescheduled
+- Hamilton-Jacobi Reachability: A Brief Overview and Recent Advances (2017) — rescheduled
+
+### Other
+- Investigate DICE conference — rescheduled
+
+## Cancelled or Deleted
+
+No tasks were cancelled or deleted this week.
+
+## To Do
+- Decide on an internship
+- Additional interviews this week
+- Review meeting is this week.
+- Re-outline research approach. Identify the holes
+- Plan out a prelim problem. Maybe a simple version of what
+  HARDENS did. Just initiating scram?
+- Follow up with IT about what the hell is sending packets
+from the ARCADE puter.
+
+
+### Due This Week
+
+No tasks are due in the next 7 days.
+
+### High Priority
+
+**Thesis (reading)**
+- The Algorithmic Analysis of Hybrid Systems (1995) — Urgency: 17.8 (overdue by 5 days)
+- Hybrid Automata: An Algorithmic Approach to the Specification and Verification of Hybrid Systems (1993) — Urgency: 13.8 (overdue by 5 days)
+- Hamilton-Jacobi Reachability: A Brief Overview and Recent Advances (2017) — Urgency: 13.8 (overdue by 5 days)
+- Hybrid Systems: Review and Recent Progress (2003) — Urgency: 2.45
+- Multiple Lyapunov Functions and Other Analysis Tools for Switched and Hybrid Systems (1998) — Urgency: 2.45
+
+**Other**
+- Investigate DICE conference — Urgency: 15.8
+
+**ERLM (editing/writing)**
+- Add research tasks to research approach section — Urgency: 2.51
+
+**Zettelkasten**
+- AIGER Circuits — Urgency: 3.25
+- Reactive Synthesis — Urgency: 3.25
+- Write about opp. chall. and res. needs for remote micro ope. — Urgency: 3.22

Fleeting Notes/Weekly/2026_05.md

@@ -0,0 +1,78 @@
+---
+id: 2026-05
+title: Weekly — 2026-01-28
+type: Weekly
+created: 2026-01-28T18:38:10Z
+modified: 2026-01-28T18:45:48Z
+tags: [weekly]
+---
+
+# Weekly - 2026 CW 05 (Wed 2026-01-28)
+
+## Accomplishments
+
+**Thesis**
+- ✓ Edit research approach some
+- ✓ The Algorithmic Analysis of Hybrid Systems (1995) (reading, overdue from 2026-01-09)
+- ✓ Edit research approach
+- Set up the ARCADE computer and got the undergrads an
+account
+- Couple of the last interviews for the chair search. Things
+  are looking really good and should wind down in intensity
+  for a bit
+
+**General**
+- ✓ Write email to INL about rejecting offer
+- ✓ Make groupchat for Sam's bachelor party
+
+## Pushed or Rescheduled
+
+**Poker**
+- Make development plan (overdue by 3 days)
+- Make plan about table layout (overdue by 3 days)
+
+**Thesis**
+- Write: Define hybrid systems and requirements (tablesetting intro) (overdue by 13 hours)
+- Write: Requirements mapping to system components (operational vs strategic) (overdue by 13 hours)
+- Write: Requirements extraction and discrete abstraction (overdue by 13 hours)
+- Write: Reactive synthesis implementation and tools (LTL, FRET) (overdue by 13 hours)
+- Write: Continuous components intro and mode types overview (overdue by 13 hours)
+- Write: Transitory modes (entry/exit, reachability verification) (overdue by 13 hours)
+- Write: Stabilizing modes (barrier certificates) (overdue by 13 hours)
+- Write: Expulsory modes (failure detection, ...) (overdue by 13 hours)
+
+## Cancelled or Deleted
+
+No tasks were cancelled or deleted in the past week.
+
+## To Do
+
+Finish writing about research approach. Redo risks and
+contingencies section based on research approach. For
+example, risk of continuous discrete abstraction being not
+good, risk of how much system variation is needed? Can only
+really do parametric uncertainty. Unless?
+
+**Due This Week**
+
+No tasks with explicit due dates in the next 7 days.
+
+**High Priority**
+
+These tasks are overdue and require immediate attention:
+
+**Thesis (urgency 14.5)**
+- Hybrid Automata: An Algorithmic Approach to the Specification and Verification of Hybrid Systems (1993) (reading, overdue by 2 weeks)
+- Hamilton-Jacobi Reachability: A Brief Overview and Recent Advances (2017) (reading, overdue by 2 weeks)
+
+**Poker (urgency 11.4)**
+- Make development plan (overdue by 3 days)
+- Make plan about table layout (overdue by 3 days)
+
+**Thesis Writing (urgency 10.9)**
+- Write: Define hybrid systems and requirements (tablesetting intro) (overdue by 13 hours)
+- Write: Requirements mapping to system components (operational vs strategic) (overdue by 13 hours)
+- Write: Requirements extraction and discrete abstraction (overdue by 13 hours)
+- Write: Reactive synthesis implementation and tools (LTL, FRET) (overdue by 13 hours)
+- Write: Continuous components intro and mode types overview (overdue by 13 hours)
+- Write: Transitory modes (entry/exit, reachability verification) (overdue by 13 hours)

Hub Notes/HUB-20250818131731-logics.md

@@ -0,0 +1,38 @@
+---
+id: HUB-20250818131731
+title: Logics
+type: hub
+created: 2025-08-18T17:17:31Z
+modified: 2025-08-18T19:44:30Z
+tags: [hub]
+aliases: []
+---
+
+# Logics
+
+> Logic is a way of transforming ideas in a plain language
+> into precise mathematical statements. There are a bunch of
+> different types of logic, as linked below, but in all of
+> them there's an emphasis on precision.
+
+## Contents (map of notes)
+
+- [[Propositional Logic]]  
+- [[Predicate Logic]]  
+- [[Temporal Logic]]  
+
+## Permanent seeds (key ideas)
+
+- [[ ]]  
+
+## Related hubs
+
+- [[]]  
+
+## Sources / Literature
+
+- 
+
+## Open questions / Next actions
+
+- [ ] 

Hub Notes/HUB-20250822135454-formal-methods.md

@@ -0,0 +1,38 @@
+---
+id: HUB-20250822135454
+title: Formal Methods
+type: hub
+created: 2025-08-22T17:54:54Z
+modified: 2025-08-22T17:57:39Z
+tags: [hub]
+aliases: []
+---
+
+# Formal Methods
+
+> The purpose of this hub is to make a high level hub of
+> everything formal methods related (which is a lot!!!)
+
+## Related hubs
+
+- [[formal-methods-in-machine-learning]]  
+
+## Related Zettels
+### Topics
+
+[[Abstract Interpretation for Formal Methods]]
+[[Satisfiability Modulo Theory]]
+[[Mixed Integer Linear Programming]]
+[[Complete vs. Incomplete Formal Methods]]
+
+### Tools
+[[Strix]]
+
+
+## Sources / Literature
+
+- [[a-review-of-formal-methods-applied-to-machine-learning]]
+
+## Open questions / Next actions
+
+- [ ] 

Permanent Notes/20250815170942-zettelkasten.md

@@ -0,0 +1,20 @@
+---
+id: 20250815170942
+title: Zettelkasten
+type: permanent
+created: 2025-08-15T21:09:42Z
+modified: 2025-08-15T21:18:21Z
+tags: []
+---
+
+# Zettelkasten
+
+Zettelkasten is a note taking system that uses a series of
+single idea notes to build connections between notes. There
+are different kinds of zettelkasten notes:
+
+1. [[permanent-notes]]
+2. [[literature-notes]]
+3. [[hub-notes]]
+and 
+4. [[fleeting-notes]]

Permanent Notes/20250815171141-permanent-notes.md

@@ -0,0 +1,10 @@
+---
+id: 20250815171141
+title: Permanent Notes
+type: permanent
+created: 2025-08-15T21:11:41Z
+modified: 2025-08-15T21:11:56Z
+tags: []
+---
+
+# Permanent Notes

Permanent Notes/20250815171436-literature-notes.md

@@ -0,0 +1,22 @@
+---
+id: 20250815171436
+title: Literature Notes
+type: permanent
+created: 2025-08-15T21:14:36Z
+modified: 2025-08-15T21:20:37Z
+tags: []
+---
+
+# Literature Notes
+
+Literature notes are notes that reference research. They
+should be like fleeting notes almost, where they only have
+one real connection--the resource used to derive the notes.
+From that point, the individual thoughts should be moved
+into permanent notes that are focused on each idea rather
+than the resource itself.
+
+I've created two folders in my literature notes: Processed
+and the root folder. This is pretty self explanatory, but
+for thoroughness, once lit notes are processed into
+zettels they move into the processed folder.

Permanent Notes/20250815171449-hub-notes.md

@@ -0,0 +1,21 @@
+---
+id: 20250815171449
+title: Hub Notes
+type: permanent
+created: 2025-08-15T21:14:49Z
+modified: 2025-08-15T21:22:59Z
+tags: []
+---
+
+# Hub Notes
+
+Hub notes are a way to systemitize knowledge. They include
+mostly links to other things that are derivatives or subsets
+of the hub note topic. Here's an example:
+
+A hub note might contain 'Functional Programming Languages'
+and link to several language topics 'Haskell', 'F*', etc.
+where each of those might also be a hub note.
+
+Hub notes are supposed to be a map in a sense of all the
+notes they contain.

Permanent Notes/20250815171459-fleeting-notes.md

@@ -0,0 +1,19 @@
+---
+id: 20250815171459
+title: Fleeting Notes
+type: permanent
+created: 2025-08-15T21:14:59Z
+modified: 2025-08-15T21:24:24Z
+tags: []
+---
+
+# Fleeting Notes
+
+Fleeting Notes are notes that are similar to unprocessed
+notes in [[literature-notes]], but they are not connected to
+a resource like a literature note is. They are notes that
+won't often get revisited (if at all). Daily notes are
+pretty much the quintessential example of a fleeting note,
+but also random ideas are a thing for fleeting notes too. I
+have a processed folder in my fleeting notes to do a similar
+process as lit notes.

Permanent Notes/20250818132007-propositional-logic.md

@@ -0,0 +1,38 @@
+---
+id: 20250818132007
+title: Propositional Logic
+type: permanent
+created: 2025-08-18T17:20:07Z
+modified: 2025-08-18T19:52:42Z
+tags: []
+---
+
+# Propositional Logic
+
+Propositional logic makes statements saying things like 'if
+x, then y'. They are statements that are either **true or
+false**, and have binary variables (P, Q, R, X, Y, etc...)
+
+Here's some examples:
+
+*If x, then y.* 
+
+$$x\rightarrow y$$
+
+*If x and y, then z.* 
+
+$ (x \wedge y) \rightarrow z $
+
+*Either the pump is on or the power is out.*
+
+$ Pump \oplus \neg Power $ 
+
+The pump is on and water is flowing if and only if the power
+is on.
+
+$( Pump \wedge Water) \leftrightarrow Power$
+
+
+Propositional logic is expanded upon by 
+[[predicate-logic]].
+

Permanent Notes/20250818132018-predicate-logic.md

@@ -0,0 +1,63 @@
+---
+id: 20250818132018
+title: Predicate Logic
+type: permanent
+created: 2025-08-18T17:20:18Z
+modified: 2025-08-18T20:20:03Z
+tags: []
+---
+
+# Predicate Logic
+
+Predicate logic extends propositional logic by using
+predicates and quantifiers. 
+
+- **Predicates** express properties or relations (e.g., 
+$Pump(x)$ or $Connected(v,c)$).
+
+- **Quantifiers** let us say something about *all* or *some*
+in the domain.
+    - $\forall$ = for all 
+    - $\exists$ = exists, at least one
+    - $\exists!$ = there exists exactly one
+
+Predicates kind of look like functions: $Pump(x)$ means $x$ is
+a pump.
+
+**Relational Predicates** have two inputs:
+$Connected(x,y)$ means pump $x$ is connected to valve $y$
+
+## Examples
+
+Predicate logic requires you to *introduce the
+variable first*. This feels weird at first, but is
+mathematically explicit. The predicate does not define the
+input, it only defines the property! 
+
+Here's an example:
+
+$\forall x (Pump(x) \rightarrow Working(x))$
+
+Means that 'every pump works'. But, we define first a set x,
+then specify it is a pump for all x, and that they all of x,
+which are all pumps, work.
+
+What if we have one pump that doesn't work?
+
+$\exists x(Pump(x) \wedge \neg Working(x))$
+
+## Nested Qualifiers
+
+We can stack qualifiers and do some nifty things. 
+How do we say: There exists one controller that stabilizes
+every plant?
+
+$ \exists k \forall G (Plant(G) \rightarrow Stabilizes(k,G))$
+
+This is obviously not possible. So how do we say the
+opposite, that for any plant there exists at least one
+stabilizing controller:
+
+$ \forall G \exists k (Plant(G) \rightarrow (Controller(k)
+\wedge Stabilizes(k,G)))$
+

Permanent Notes/20250818132022-temporal-logic.md

@@ -0,0 +1,63 @@
+---
+id: 20250818132022
+title: Temporal Logic
+type: permanent
+created: 2025-08-18T17:20:22Z
+modified: 2025-08-21T16:42:25Z
+tags: []
+---
+
+# Temporal Logic
+
+## What is Temporal Logic?
+
+An extension of **predicate logic** that allows reasoning
+about how statements evolve over **time**.  
+- Used heavily in **formal verification**, **model
+checking**, and **control systems safety**.  
+- Reasoning is over **infinite traces** (sequences of
+states).  
+
+---
+
+## Core Temporal Operators
+
+| Symbol | LaTeX | Name | Meaning |
+|--------|-------|------|---------|
+| X φ | `X \varphi` | Next | φ holds in the **next** state |
+| F φ | `\Diamond \varphi` | Eventually | φ will hold at some time in the **future** |
+| G φ | `\Box \varphi` | Globally (Always) | φ holds at **all future times** |
+| φ U ψ | `\varphi \, U \, \psi` | Until | φ must hold until ψ holds |
+
+---
+
+## Example Specifications
+
+1. **Safety:**  
+   *“The reactor temperature never exceeds 600°C.”*  
+   $G\,(temp < 600)$
+
+2. **Liveness:**  
+   *“The pump will eventually turn on.”*  
+
+    $F(PumpOn)$
+
+3. **Response:**  
+   *“Whenever a request occurs, it will eventually be granted.”*  
+   $G\,(request \rightarrow F\,grant)$
+
+4. **Stability:**  
+   *“If the valve opens, it stays open until pressure is safe.”*  
+    $G\,(ValveOpen\rightarrow (ValveOpen\;U\;PressureSafe))$
+
+## Why It Matters
+- **Formal Methods:** Express constraints on **system behaviors over time**.  
+- **Model Checking:** Tools like SPIN, NuSMV, Spot verify LTL specs.  
+- **Engineering Applications:**  
+  - Ensure control systems obey safety invariants.  
+  - Specify liveness goals for controllers (e.g., “eventually stabilize temperature”).  
+  - Used in **TLA+**, runtime monitoring, and shield synthesis.
+
+## Related Notes
+[[strix]] - a reactive synthesis tool using temporal logic
+specs

Permanent Notes/20250818164800-safety-properties.md

@@ -0,0 +1,22 @@
+---
+id: 20250818164800
+title: Safety Properties
+type: permanent
+created: 2025-08-18T20:48:00Z
+modified: 2025-08-18T20:54:35Z
+tags: []
+---
+
+# Safety Properties
+
+Safety properites say that nothing bad ever happens. They
+often are specified as such using some formal requirement. 
+
+In [[Temporal Logic | LTL]], they can look like this:
+
+*The traffic light will never been red and green at the same
+time.* 
+
+$G \neg (green \wedge red)$
+
+A sort of opposite of safety proprerties is [[liveness-properties]].

Permanent Notes/20250818165010-liveness-properties.md

@@ -0,0 +1,22 @@
+---
+id: 20250818165010
+title: Liveness Properties
+type: permanent
+created: 2025-08-18T20:50:10Z
+modified: 2025-08-18T20:54:38Z
+tags: []
+---
+
+# Liveness Properties
+
+Liveness properties are kinda the dual of
+[[safety-properties]], but instead they say that something
+good will eventually happen.
+
+Here's an example:
+
+*If there's someone waiting, the light will eventually turn
+green:* 
+
+$ G(request \rightarrow F\, green)$
+

Permanent Notes/20250819103208-strix.md

@@ -0,0 +1,31 @@
+---
+id: 20250819103208
+title: Strix
+type: permanent
+created: 2025-08-19T14:32:08Z
+modified: 2025-08-21T16:42:39Z
+tags: []
+---
+
+# Strix
+
+Strix is a reactive synthesis tool that takes linear
+temporal logic specifications and turns them into
+implementations using Mealy machines or AIGER circuits.
+Strix does this using deterministic parity automata (DPA).
+With these, they can use much more efficient parity game
+algorithms as opposed to using symbolic methods.
+
+Strix was debuted after SYNTCOMP2017, to great success.
+Their automata at the time were much smaller than
+competitive models, and their solve times were on average
+much faster. They also solved some benchmarks that other
+tools previously had been unable to solve.
+
+## Related Notes
+[[Temporal Logic]]
+[[SYNTCOMP]]
+[[Deterministic Parity Automata]]
+[[Mealy Machines]]
+[[AIGER Circuits]]
+[[Reactive Synthesis]]

Permanent Notes/20250821123741-syntcomp.md

@@ -0,0 +1,21 @@
+---
+id: 20250821123741
+title: SYNTCOMP
+type: permanent
+created: 2025-08-21T16:37:41Z
+modified: 2025-08-21T16:42:25Z
+tags: []
+---
+
+# SYNTCOMP
+
+SYNTCOMP, otherwise known as the Reactive Synthesis
+Competition, is a yearly competition for reactive synthesis
+tools to compete against one another to try and solve
+synthesis benchmarks.
+
+SYNTCOMP has been around since 2014. Usually, they run all
+the code on their own machines to ensure fairness. 
+
+SYNTCOMP is a satelite event of CAV, the International
+Conference on Computer-Aided Verification.

Permanent Notes/20250822134355-formal-methods-in-machine-learning.md

@@ -0,0 +1,10 @@
+---
+id: 20250822134355
+title: Formal Methods in Machine Learning
+type: permanent
+created: 2025-08-22T17:43:55Z
+modified: 2025-08-22T17:43:55Z
+tags: []
+---
+
+# Formal Methods in Machine Learning

Permanent Notes/20250822135802-abstract-interpretation-for-formal-methods.md

@@ -0,0 +1,15 @@
+---
+id: 20250822135802
+title: Abstract Interpretation for Formal Methods
+type: permanent
+created: 2025-08-22T17:58:02Z
+modified: 2025-08-25T16:01:46Z
+tags: []
+---
+
+# Abstract Interpretation for Formal Methods
+
+Abstract interpretation in a formal methods context takes
+something about a system and makes an approximation of it in
+order to make reasoning about it easier.
+

Permanent Notes/20250826111220-quad-charts.md

@@ -0,0 +1,58 @@
+---
+id: 20250826111220
+title: Quad Charts
+type: permanent
+created: 2025-08-26T15:12:20Z
+modified: 2025-08-26T15:20:50Z
+tags: []
+---
+
+# Quad Charts
+
+Quad charts are the briefest of research proposals, and are
+a way of conveying a research idea in just one
+slide. 
+
+The audience for a quad chart is usually non-technical. The
+content should reflect this.
+
+Quad charts consist of quadrants:
+
+## Quadrant 1 (Upper Left): Goals and Objectives
+
+This quadrant states the goal of the research in a single
+sentence, and lists the outcomes underneath it. Often you
+can start with "The goal of this research is to..."
+
+Then, the outcomes follow: "If this research is
+successful, we should be able to do the following:
+
+1. ...
+2. ...
+3. ...
+(4.?)
+
+It is critical that no jargon is used here. It is very
+tempting to do so.
+
+## Quadrant 2 (Bottom Left): Research Approach
+
+This quadrant answers the question: "What's new in your
+approach?"
+
+## Quadrant 3 (Top Right): Pretty Picture
+
+This is a break for the reader, and likely the first thing
+they'll actually look at on the chart. This figure should
+illustrate a key idea about the work that you want the
+reader to take away.
+
+No personal information should be included.
+
+## Quadrant 4 (Bottom Right): Impact and Contact Info
+
+This quadrant answers the question of "Who cares? What
+difference will it make if you're successful?"
+
+This quadrant should also contain contact info of the
+principal investigator, and if applicable, their advisor.

Permanent Notes/20250826114550-heilmeier-catechism.md

@@ -0,0 +1,40 @@
+---
+id: 20250826114550
+title: Heilmeier Catechism
+type: permanent
+created: 2025-08-26T15:45:50Z
+modified: 2025-08-26T16:02:59Z
+tags: []
+---
+
+# Heilmeier Catechism
+
+George Heilmeier was a program manager at the Defense
+Advanced Research Projects Administration (DARPA) who was
+flummoxed with research proposals for artificial
+intelligence. In order to quickly sort through the
+proposals, he developed an 8 question system to quickly cut
+through the muck.
+
+This is the Heilmeier Catechism:
+
+1. What are you trying to do? Articulate your research with
+   absolutely no jargon.
+
+2. How is it done today and what are the limits of current
+   practice?
+
+3. What's new in your approach and why will you be
+   successful?
+
+4. Who cares? If you're successful, what difference will it
+   make?
+
+5. What are the risks?
+
+6. How long will it take?
+
+7. How much will it cost?
+
+8. What are the midterm and final exams? How will you
+   measure success?

Permanent Notes/20250829114522-hybrid-systems.md

@@ -0,0 +1,57 @@
+---
+id: 20250829114522
+title: Hybrid Systems
+type: permanent
+created: 2025-08-29T15:45:22Z
+modified: 2025-09-11T21:46:53Z
+tags: []
+---
+
+# Hybrid Systems
+
+I'm borrowing a lot from
+[[multiple-lyapunov-functions-and-other-analysis-tools-for-swtiched-and-hybrid-systems]].
+
+Hybrid systems are those that combine continuous and
+discrete dynamics together. This is usually some sort of
+finite automata + differential equations.
+
+Hybrid systems can be written like:
+
+$$\dot{x}(t) = \xi(t), \quad t\geq 0$$
+
+where $x(t)$ is the continuous component of the state.
+$\xi(t)$ is a vector field that depends on $x(t)$ and the
+hybrid dynamics.
+
+Switching between modes (aka discontinuities in $\xi(\cdot)$)
+can happen in one of two ways:
+
+1. **Autonomous Switching** - Autonomous switches happen
+   depending on state values of $x(t)$.
+
+2. **Controlled Switching** - $\xi(\cdot)$ changes abruptly
+   in response to a control command.
+
+One may write a continuous time autonomous hybrid system
+like this:
+
+$$\dot{x}(t) = f(x(t), q(t))$$
+$$q(t) = \nu(x(t), q(t^-))$$
+
+where:
+- $x(t) \in R^n$
+- $q(t) \in Q \simeq {1,...,N}$
+- $f(\cdot,q): R^n \rightarrow R^n,q \in Q$, with each
+[[lipschitz-continuous]]. These are the *continuous
+dynamics*.
+- $\nu: R^n \times Q \rightarrow Q$ is the *finite dynamics*
+
+A controlled system might be written as:
+$$\dot{x}(t) = f(x(t), q(t), u(t))$$
+$$q(t) = \nu(x(t), q(t^-), u(t))$$
+
+where:
+- $u(t) \in R^m$
+
+

Permanent Notes/20250911165736-switched-systems.md

@@ -0,0 +1,35 @@
+---
+id: 20250911165736
+title: Switched Systems
+type: permanent
+created: 2025-09-11T20:57:36Z
+modified: 2025-09-11T21:09:55Z
+tags: []
+---
+
+# Switched Systems
+
+Switched systems are those that mix continuous and discrete
+dynamics. They are systems that are 'multimodal'. This means
+that they can have different continuous dynamic modes.
+
+I'm borrowing form
+[[multiple-lyapunov-functions-and-other-analysis-tools-for-swtiched-and-hybrid-systems]],
+but here's a short description of how they work.
+
+A prototypical switched system is as follows:
+$$\dot{x}(t)=f_i ( x(t)), \quad i \in Q \simeq {1,...,N}$$
+
+with two conditions:
+1. Each $f_i$ is globally [[Lipschitz Continuous]]
+2. The i's are picked in a way that there are finite
+   switches in finite time.
+
+
+There's also this thing called a *continuous switched
+system*. A continuous switched system is one that does not
+change continuous states when a switch occurs. That is to
+say when switching from $i$ to $i'$:
+
+$$f_i(x(t_i),t_i) = f_{i'}(x(t_{i'}),t_{i'})$$
+

Permanent Notes/20250911170650-lipschitz-continuous.md

@@ -0,0 +1,24 @@
+---
+id: 20250911170650
+title: Lipschitz Continuous
+type: permanent
+created: 2025-09-11T21:06:50Z
+modified: 2025-09-16T16:32:37Z
+tags: []
+---
+
+# Lipschitz Continuous
+
+Lipschitz continuous functions are a special case of
+continuous functions. Lipschitz continuity means that a cone
+can be created with slope less than some real number
+$K$. 
+
+Fora a real valued function in one dimension, Lipschitz
+continuity is defined as:
+
+$$| f(x_1) - f(x_2)| \leq K|x_1 - x_2|$$
+
+Lipschitz continuity can be expanded to vector fields. From
+here, we can say that ODE trajectories do NOT intersect, and
+that every trajectory is unique. 

Permanent Notes/20251030141457-nuclear-operating-procedures.md

@@ -0,0 +1,20 @@
+---
+id: 20251030141457
+title: Nuclear Operating Procedures
+type: permanent
+created: 2025-10-30T18:14:57Z
+modified: 2025-10-30T18:19:21Z
+tags: []
+---
+
+# Nuclear Operating Procedures
+Nuclear operating procedures are big books of procedures
+that reactor operators use to perform control of reactors.
+Operating procedures are built on a per-plant basis, but are
+also designed with the general plant architecture in mind
+[[nureg899]]. 
+
+Operating procedures have different categories:
+1. Regular operating procedures
+2. [[Emergency Operating Procedures]]
+3. Theres ones about severe accidents too.

Permanent Notes/20251030141936-emergency-operating-procedures.md

@@ -0,0 +1,40 @@
+---
+id: 20251030141936
+title: Emergency Operating Procedures
+type: permanent
+created: 2025-10-30T18:19:36Z
+modified: 2025-10-30T19:30:12Z
+tags: []
+---
+
+# Emergency Operating Procedures
+Emergency operating procedures for nuclear power are special
+procedures that are used when off-normal conditions are
+present. They are for when 'shit hits the fan'. 
+
+EOPs have defining regulations. Most notably [[nureg899]].
+NUREG899 is a writers guide to emergency operating
+procedures.
+
+EOPs should be 'function-oriented'. This means operators
+should not need to know a root cause to start performing
+control operations in an emergency. Critical functions in an
+emergency are usually:
+
+1. [[Containment Integrity]]
+2. [[Reactivity Control]]
+3. [[Heat Removal]]
+4. [[Reactor Coolant Inventory Control]]
+
+If each of these are maintained, the reactor can be 'safe',
+and the risk of environmental release is minimized. [[nureg899]]
+
+EOPs should minimize cross referencing because it increases
+decision time and is disruptive changing between documents
+[[nureg899]].
+
+EOPs today are reveiwed with simulation exercises,
+control-room walkthroughs, seminars, and numerical analysis
+[[nureg899]].
+
+

Permanent Notes/20251223161108-andre-platzer.md

@@ -0,0 +1,22 @@
+---
+id: 20251223161108
+title: Andre Platzer
+type: permanent
+created: 2025-12-23T21:11:08Z
+modified: 2025-12-23T21:53:21Z
+tags: []
+---
+
+# Andre Platzer
+
+Andre Platzer is a computer scientist who is a professor at
+both Carnegie Mellon and the Karlsruhe Institute of
+Technology. Platzer is a leading researcher in 
+[[differential dynamic logic]] and [[cyber-physical
+systems]]. He has helped to create
+software like [[KeYmaera X]]. 
+
+He has also written a book, called "Logical Foundations of
+Cyber-Physical Systems." Manyu worked with KeYmaera X some
+and was inspired by his work.
+

Permanent Notes/20251223162450-web-of-science.md

@@ -0,0 +1,17 @@
+---
+id: 20251223162450
+title: Web of Science
+type: permanent
+created: 2025-12-23T21:24:50Z
+modified: 2025-12-23T21:29:48Z
+tags: []
+---
+
+# Web of Science
+
+Web of Science is a citation aggregator and database. Web of
+Science has both forward and backward citation sources, and
+other tools for doing source analysis. It is good to find
+resources, but also to connect resources to one another.
+
+This is useful in [[snowballing]]. 

Permanent Notes/20251223162954-snowballing.md

@@ -0,0 +1,21 @@
+---
+id: 20251223162954
+title: Snowballing
+type: permanent
+created: 2025-12-23T21:29:54Z
+modified: 2025-12-23T21:31:23Z
+tags: []
+---
+
+# Snowballing
+
+Snowballing is a form of source discovery. Snowballing means
+to start with a source, and travel forwards and backwards
+in time with respect to citations. From this, one can find
+closely related papers to an original source without too
+much effort. 
+
+Snowballing has been found in the literature to be an
+efficient source of collecting relevant sources given a
+certain topic. One needs to find the first bit of snow (a
+good first resource), to start the snowball. 

Permanent Notes/20251223163648-deterministic-parity-automata.md

@@ -0,0 +1,27 @@
+---
+id: 20251223163648
+title: Deterministic Parity Automata
+type: permanent
+created: 2025-12-23T21:36:48Z
+modified: 2025-12-23T21:40:09Z
+tags: []
+---
+
+# Deterministic Parity Automata
+
+Deterministic parity automata are a type of automata where
+the environment and the system play against one another, and
+describes the interactions therein. DPA are exhaustive, and
+end up with a result determining which player 'wins'. 
+
+DPA's have a scoring mechanism that results in an even or
+odd final score. An even final score indicates that the
+'controller' wins the game. There is no input from the
+environment that can't be controlled by the controller. All
+traces end up in a favorable state, with no infinite loops.
+An odd score means the opposite. There exists some limit
+cycle where the controller can't reach a desired mode and
+stay there. 
+
+DPA's are used in [[strix]]. They're how Strix does it's
+generation from temporal logics to a final automaton.

Permanent Notes/20251223165340-mealy-machines.md

@@ -0,0 +1,49 @@
+---
+id: 20251223165340
+title: Mealy Machines
+type: permanent
+created: 2025-12-23T21:53:40Z
+modified: 2025-12-23T22:38:18Z
+tags: []
+---
+
+# Mealy Machines
+
+Mealy machines are a formalization of a system that has
+states drawn as nodes and transitions drawn from state to
+state. 
+
+From Wikipedia:
+```
+    A mealy machine is a finite state machine whose
+output values are determined by both its current state, and
+the current inputs.
+```
+
+Mealy machines can also be defined as a six-tuple:
+
+$$(S, S_0, \Sigma, \Lambda, T, G)$$
+
+where 
+- S is the finite set of states
+- S_0 is the start state
+- $\Sigma$ is the input alphabet
+- $\Lambda$ is the output alphabet
+- $T : S \times \Sigma \rightarrow S$ is the state
+transition function
+- $G : S \times \Sigma \rightarrow \Lambda$ is the output
+function
+
+Mealy machines have the advantage that they generally can
+produce smaller sized automata (aka less states). This is
+because transitions themselves in a Mealy machine are states
+in a Moore machine. The state of 'opening' in a Moore
+machine is the transition itself in a Mealy machine. Outputs
+aren't just based on state, so it isn't necesary to create a
+state to produce an output like a Moore machine. An output
+action can be created with the current state AND the input
+together.
+
+## Related
+[[Finite State Machines]]
+

Permanent Notes/20251223170627-finite-state-machines.md

@@ -0,0 +1,49 @@
+---
+id: 20251223170627
+title: Finite State Machines
+type: permanent
+created: 2025-12-23T22:06:27Z
+modified: 2025-12-23T22:39:00Z
+tags: []
+---
+
+# Finite State Machines
+
+Finite State Machines are a computer science term for
+machines that have a finite number of states, with clearly
+defined transitions between them. Sometimes, FSM are
+referred to simply as *state machines*. 
+
+FSM are an abstraction of a computational system. FSM are
+heavily used in systems that have clearly defined discrete
+states. Examples include traffic lights, elevators,
+combination locks, or others.
+
+FSM have **actions**. Actions are the unabstractified
+version of whatever the execution is. For physical systems,
+it might be something like turning a motor on.
+
+FSM can be categorized into two main categories:
+
+## Acceptors (or 'detectors' or 'recognizers') Acceptors are
+a type of FSM that produce binary output, recognizing
+whether or not a given input is accepted. Examples of
+systems that are acceptors include things like ready-commit
+systems, or a password checker. These systems have an input,
+and reach a state that determines the input is acceptable,
+or incorrect. 
+
+## Transducers
+Transducers are a set of finite state machines that produce
+an output based on input or state using *actions*. Actions
+in this case represent a transition between state that
+also has some external change. A finite state machine of an
+elevator would have actions of the elevator changing between
+floors, for example.
+
+Transducers with respect to control have two different
+types:
+[[mealy-machines]] -- these have output depend on state and input
+[[moore-machines]] -- these have output depend on state ONLY
+
+

Permanent Notes/20251223171835-moore-machines.md

@@ -0,0 +1,39 @@
+---
+id: 20251223171835
+title: Moore Machines
+type: permanent
+created: 2025-12-23T22:18:35Z
+modified: 2025-12-23T22:52:38Z
+tags: []
+---
+
+# Moore Machines
+Moore machines are a type of finite state machine whose
+output only depends on output state. Moore machines are
+useful because they simplify the behavior of a system to the
+simplest behaviours possible. They can be defined as a
+six-tuple:
+
+
+$$(S, S_0, \Sigma, \Lambda, T, G)$$
+
+where 
+- S is the finite set of states
+- S_0 is the start state
+- $\Sigma$ is the input alphabet
+- $\Lambda$ is the output alphabet
+- $T : S \times \Sigma \rightarrow S$ is the state
+transition function
+- $G : S \rightarrow \Lambda$ is the output
+function
+
+Moore machines do not have exit actions. They can only
+change their output based on a change of state. This means
+for systems with physical characteristics, such as a door
+opening or closing system, the intermediate states of
+opening and closing have to exist in a Moore machine. It is
+not possible to go from Open to Closed directly, because
+Open can't generate the output Closed. Instead, Open + the
+input 'open_door' or similar goes to the state 'closing',
+which can then create an action of 'motor_on' or similar,
+and then finally get to the final state Closed.

Permanent Notes/20260109155358-hybrid-automata.md

@@ -0,0 +1,17 @@
+---
+id: 20260109155358
+title: Hybrid Automata
+type: permanent
+created: 2026-01-09T20:53:58Z
+modified: 2026-01-09T21:08:30Z
+tags: []
+---
+
+# Hybrid Automata
+Hybrid automata are a framework for the formal modeling of
+computed systems. Hybrid automata are a generalization of
+[[timed automata]], where all states are governed by
+differential equations.
+
+## Relevant Sources
+[[hybrid-automata-an-algorithmic-approach-to-the-specification-and-verification-of-hybrid-systems]]

Permanent Notes/20260109155410-linear-hybrid-automata.md

@@ -0,0 +1,16 @@
+---
+id: 20260109155410
+title: Linear Hybrid Automata
+type: permanent
+created: 2026-01-09T20:54:10Z
+modified: 2026-01-09T21:11:18Z
+tags: []
+---
+
+# Linear Hybrid Automata
+Linear hybrid automata are [[hybrid-automata]] systems where
+'the rate of change with time is constant' for each
+variable, and the 'terms involved in the invariants, guards,
+and assignments are required to be linear'.
+
+A special case of linear hybrid automata are [[timed-automata]].

Permanent Notes/20260109155415-timed-automata.md

@@ -0,0 +1,27 @@
+---
+id: 20260109155415
+title: Timed Automata
+type: permanent
+created: 2026-01-09T20:54:15Z
+modified: 2026-01-09T21:13:51Z
+tags: []
+---
+
+# Timed Automata
+Timed automata are linear hybrid automata with the
+special condition that every continuously changing variable
+is a *clock*. That means that every variable varies one to
+one with time, just counting time.
+
+Timed automata have invariants and guards that compare time
+only with constants. There are no other continuous dynamics
+here. 
+
+An example of a timed automata is something like an alarm.
+Easy peasy, is time greater or less than a value. If it is,
+trigger the alarm! One might also have a constant setting
+whether or not an alarm is 'enabled'. But, there's no other
+dynamics than time itself.
+
+## Relevant Sources
+[[hybrid-automata-an-algorithmic-approach-to-the-specification-and-verification-of-hybrid-systems]]

Permanent Notes/20260109155838-reactive-programs.md

@@ -0,0 +1,23 @@
+---
+id: 20260109155838
+title: Reactive Programs
+type: permanent
+created: 2026-01-09T20:58:38Z
+modified: 2026-01-09T21:08:01Z
+tags: []
+---
+
+# Reactive Programs
+Reactive programs, or reactive systems, are those that have
+an output or state change controlled by the current state
+and input. These programs react to environmental changes in
+real time. Basically every relevant control system is a
+'reactive' system, but in computer science, reactive
+programs have a unique meaning. Reactive computer programs
+are those that have computation depending on external
+inputs, a.k.a. stuff from OUTSIDE of the computer's world.
+
+
+## Relevant Sources
+[[strix-explicit-reactive-synthesis-strikes-back]]
+[[hybrid-automata-an-algorithmic-approach-to-the-specification-and-verification-of-hybrid-systems]]

Permanent Notes/20260114132351-bayes-theorem.md

@@ -0,0 +1,49 @@
+---
+id: 20260114132351
+title: Bayes' Theorem
+type: permanent
+created: 2026-01-14T18:23:51Z
+modified: 2026-01-14T18:43:20Z
+tags: []
+---
+
+# Bayes' Theorem
+
+Suppose we know $P(x)$, *the prior*, and we get some data
+$Y$, and we want to know the probability $P(X|Y)$, which in
+English is *the probability of our model being correct given
+the data we've collected*.
+
+We can use Bayes' Theorem to find it!
+
+$$ P(X|Y) = \frac{P(Y|X) P(X)}{P(Y)} $$
+
+Where:
+- $P(X|Y)$ is called the *posterior*
+- $P(Y|X)$ is called the *likelihood*
+- $P(X)$ is called the *prior*
+- $P(Y)$ is called the *evidence*
+
+We can usually find the evidence by the following formula:
+
+$$ P(Y) = \sum P(Y|x_i) P(x_i) $$
+
+We can apply Bayes' Theorem to states in time too.
+
+$$ P(X_t|Y_t) = \frac{P(Y_t|X_t) P(X_t)}{P(Y_t)} $$
+
+where:
+- $X_{t+1} = f(x_t, w_t)$
+- $Y_{t} = f(x_t) + v_t$
+
+$w_t$ is process noise, while $v_t$ is measurement noise.
+
+Bayes' Rule is great for simulation and data-based
+approaches.
+
+## Related Ideas
+[[Expected Value]]
+
+## Sources
+Bayesian Signal Processing w/ Dan (1/12)
+

Permanent Notes/20260114133159-expected-value.md

@@ -0,0 +1,21 @@
+---
+id: 20260114133159
+title: Expected Value
+type: permanent
+created: 2026-01-14T18:31:59Z
+modified: 2026-01-14T18:41:57Z
+tags: []
+---
+
+# Expected Value
+Expected value is pretty much the mean of a function, but
+more specifically, it's the weighted average of all possible
+outcomes of a function:
+
+$$ \hat X = E{X} $$
+
+If we have an estimate of a posterior using [[Bayes'
+Theorem]], we can get the following result:
+
+$$ \hat X = \sum_i X^i \hat{Pr}(X^i|Y) $$
+

Permanent Notes/20260114153529-random-number-generation.md

@@ -0,0 +1,39 @@
+---
+id: 20260114153529
+title: Random Number Generation
+type: permanent
+created: 2026-01-14T20:35:29Z
+modified: 2026-01-14T20:46:35Z
+tags: []
+---
+
+# Random Number Generation (RNG)
+Random number generation is all about getting random
+numbers, and is easily defined as picking a number from a
+uniform distribution. Generally, there's two types:
+
+## True RNG
+True RNG is systems that are truly random. Random systems
+are almost always derived from [[chaotic systems]], which
+technically are deterministic, but as so final state
+sensitive they're basically intractable and 'random' values
+can be extracted. Sometimes lava lamps (turbulence) is used,
+sometimes isotope decay is the thing.
+
+## Pseudo RNG
+Computers can't really do true RNG. They just can't handle
+non-deterministic outcomes. In addition, true RNG is *slow*. 
+
+As such computers build PRNG. 
+
+>[!definition] Pseudo Random Number Generator
+> 
+> $\text{Struct}(S, \mu, f, U, g)$
+>
+> Where:
+> - $S$ is a finite set of states 
+> - $\mu$ is a distribution on S for the initial state (seed!)
+> - $f:S \rightarrow S$, the state transition function
+> - $U$ is the output space [0,1), or perhaps {0,...,m-1}
+> - $g:S \rightarrow U$, the output function
+> 

Permanent Notes/Literature Notes/LIT-20250819112550-strix-explicit-reactive-synthesis-strikes-back.md

@@ -0,0 +1,60 @@
+---
+id: LIT-20250819112550
+title: Strix Explicit Reactive Synthesis Strikes Back!
+type: literature
+created: 2025-08-19T15:25:50Z
+modified: 2026-01-09T21:08:06Z
+citekey: meyerStrixExplicitReactive2018
+---
+
+# Strix: Explicit Reactive Synthesis Strikes Back!
+
+Authors:
+1. [[Phillipp Meyer]]
+2. [[Salomon Sickert]]
+3. [[Michael Luttenberger]]
+
+## First Pass
+**Category:** Design paper. They made a new LTL synthesizer
+
+**Context:** 
+Strix is a response to other reative LTL syntehsizer
+competition entries.
+
+**Correctness:** 
+Seems good to me! They have data to back up their stuff.
+
+**Contributions:** 
+They contribute Strix, a tool that uses Determinstic Parity
+Automata (DPA) to simplify synthesis. DPA helps Strix solve
+problems faster by using parity game solvers as opposed to
+symbolic or bounded methods currently used.
+
+**Clarity:** 
+Easy to read!
+
+## Second Pass
+**What is the main thrust?**
+The main thrust is their new tool, Strix.
+
+**What is the supporting evidence?**
+They make a testing suite that is supposed to be similar to
+the SYNTCOMP2017 testing setup, and run their solver
+through the same trials that the competition included. They
+achieve pretty good results: much much faster solve times
+while also keeping automata size small.
+
+**What are the key findings?**
+Strix is pretty good. The use of DBAs seems effective. Their
+'quality', a measure of automata size vs specification size,
+is also pretty good compared to other synthesizers.
+
+## Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+
+**Weak Points? Strong Points?**
+
+## Spawned Zettels
+[[Reactive Programs]]

Permanent Notes/Literature Notes/LIT-20250822120822-a-review-of-formal-methods-applied-to-machine-learning.md

@@ -0,0 +1,97 @@
+---
+id: LIT-20250822120822
+title: A Review of Formal Methods applied to Machine Learning
+type: literature
+created: 2025-08-22T16:08:22Z
+modified: 2025-08-22T16:11:25Z
+citekey: 
+---
+
+# A Review of Formal Methods applied to Machine Learning
+
+**Category:** This is a review paper. 
+
+**Context:** This paper tries to keep up with where formal
+methods are for machine learning based systems. It is not
+necessarily a controls paper, but a broader machine learning
+paper in general.
+
+**Correctness:** Really well written on the first pass. Easy
+to understand and things seem well cited.
+
+**Contributions:** Great citations showing links to
+different papers and also provides nice spots for forward
+research. Talks about how verification needs to be done
+along the whole pipeline: from data prep to training to
+implementation. There needs to be more work on proving
+things about model behavior, but in general this review has
+a positive outlook on the field. 
+
+**Clarity:** Very well written, easy to understand. Except,
+what is abstractification of a network?
+
+## Second Pass
+This review gives an overview of formal
+methods applied to machine learning. Formal methods has been
+used for ML to test for robustness for various perturbations
+on inputs. They start by talking about several types of
+formal methods, including deductive verification, design by
+refinement, proof assistants, model checking, and semantic
+static analysis, and then finally, abstract interpretation
+of semantic static analysis. The last one has been used the
+most in FM of ML.
+
+A large part of the paper focuses on formal methods for
+neural network perturbation robustness. They split up the
+methods into two types: complete and incomplete formal
+methods. Complete formal methods are *sound* and *complete*.
+This means they do not have false positives or false
+negatives. These methods generally do not apply well to
+large networks (beyond hundreds gets rough), but give the
+highest level of assurance. Here, there are two more
+subcategories: SMT based solvers and MILP-based solvers.
+
+SMT solvers are Satisfiability Modulo Theory solvers. These
+solvers a set of constraints and check to see whether or not
+all of the constraints can be satisfied. Safety conditions
+are encoded as the *nA Review of Formal Methods applied to Machine Learningegation* of the safety constraint. That
+way, if a safety condition is violated, the SMT solver will
+pick it up as a counter example. 
+
+MILP based solvers are Mixed Integer Linear Programming
+solvers. MILPs use linear programming where certain
+constraints are integers to reduce the solving space.
+Instead of having an explicity satisffiability condition on
+safety or not, MILPs instead can use a minimizing function
+to generate counter examples. For example, a MILP saftey
+condition might be formalized as: $$ \text{min}\space
+\bf{x}_n$$ where a negative value of $\bf{x}_n$ is 'a valid
+counter example'.
+
+There are also 'incomplete formal methods'. These incomplete
+methods are sound, meaning they will not produce false
+negatives, but they may not be complete, meaning they may
+produce false positives. They scale better, but the false
+positives can be pretty annoying.
+
+One of the main incomplete methods is abstract
+interpretation. Things get very weird very fast--this is all
+about zonotopes and using over approximation of sets to say
+things about stability. There is weird stuff going on with
+cell splitting and merging that seems like a to grasp. But,
+apparently it works. 
+
+Next, they spend some time talking about other machine
+learning methods and the formal methods that have been
+applied to them. Of particular interest to me is the formal
+method application to support vector machines and decision
+trees. There are some useful methods for detecting
+robustness to adversarial inputs, and knowing what the
+nearest misclassification adversarial case is.
+
+## Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+
+**Weak Points? Strong Points?**

Permanent Notes/Literature Notes/LIT-202509012125-how-to-choose-a-good-scientific-problem.md

@@ -0,0 +1,42 @@
+---
+id: LIT-20250819112550
+title: How To Choose a Good Scientific Problem
+type: literature
+created: 2025-08-19T15:25:50Z
+modified: 2025-09-02T01:41:17Z
+citekey: 
+---
+
+# How to Choose a Good Scientific Problem
+
+## Authors
+[[Uri Alon]]
+
+## Notes
+Uri is all about the 'nuturing lab', which means a lab's
+goal is not just to advance knowledge, but to nurture future
+scientists. 
+
+He describes problems on two axes: interest and difficulty.
+Interest here means how much knowledge we gain from solving
+the problem. He says grad students should choose easy
+problems, with ideally low interest, then postdocs move to
+high interest and easy (to save time), and finally new
+professors move towards the hard problems with high impact,
+as they have time to do so. 
+
+Uri also argues that taking time to find a good topic is
+time well spent. It can save a lot of time down the line.
+
+The inner and outer voices can lead to different ideas.
+Outer voices are those of peers, the department, or speakers
+at a conference-- but the inner voice is the more valuable
+voice. That is your own voice. Uri descirbes the inner voice
+is often something that needs nurtured, but can lead to
+less laborious science, and more self expression.
+
+Finally Uri talks about the schema that should be considered
+during research. It is not useful to think students will go
+from A->B taking the shortest path. There must be room to
+wander, as that is where new problems can be best found.
+This is what really lets students grow.

Permanent Notes/Literature Notes/LIT-20250911143337-multiple-lyapunov-functions-and-other-analysis-tools-for-swtiched-and-hybrid-systems.md

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+---
+id: LIT-20250911143337
+title: Multiple Lyapunov Functions and Other Analysis Tools for Swtiched and Hybrid Systems
+type: literature
+created: 2025-09-11T18:33:37Z
+modified: 2025-09-16T17:23:17Z
+citekey: 
+---
+
+# Multiple Lyapunov Functions and Other Analysis Tools for Swtiched and Hybrid Systems
+
+## First Pass
+**Category:** 
+Theoretical methods paper. This paper introduces a couple of
+new ways to work with hybrid systems and also does
+introduction of a lot of terms.
+
+**Context:** 
+Branicky is doing a lot of work with hybrid systems. He
+defines what a switched system is, what a hybrid system is,
+what a continuous switched system is and also included
+definitions of autonomy in there too
+
+**Correctness:** 
+Been cited like 2000 times.
+
+**Contributions:** 
+Multiple Lyapunov theory and Stability via Iterated Function
+Systems.
+
+**Clarity:** 
+Complex ideas written simply. Easy to read.
+
+## Second Pass
+**What is the main thrust?**
+
+**What is the supporting evidence?**
+
+**What are the key findings?**
+
+## Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+ 
+**Weak Points? Strong Points?**
+
+## Zettels Created
+[[Switched Systems]]
+[[hybrid-systems]]
+[[lipschitz-continuous]]
+

Permanent Notes/Literature Notes/LIT-20251023125758-nureg899.md

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+---
+id: LIT-20251023125758
+title: NUREG899
+type: literature
+created: 2025-10-23T16:57:58Z
+modified: 2025-10-30T18:20:30Z
+citekey: 
+---
+
+# NUREG899
+
+Emergency operating procedures should be
+*function-oriented*. That means that operators 'do not have
+to immediately diagnose an event... to maintain the plant in
+a safe configuration." Critical functions are cited as:
+
+1. Containment integrity
+2. Reactivity Control
+3. Heat Removal
+4. Reactor coolant inventory control
+
+Functions  are maintained by 'tasks'. Tasks are specific
+actions that are taken to maintain or achieve a function.
+
+This doc says EOPs are verified and validated by:
+1. Excercising EOPs on simulators
+2. Control room walk-throughs
+3. Desk top reviews
+4. Seminars
+5. Computer modeling and analysis
+
+OPs should minimize the use of cross referencing because it
+increases decision times and increases the chance of human
+error. It's 'disruptive'.
+
+Operator Aids are things like flowcharts or graphs that can
+help an operator learn things more quickly and clearly than
+text alone can provide. They should be easily learned and
+retained, while being precise and not cluttered.
+Interpretability is paramount.
+
+EOPs have segments:
+1. Cover page
+2. Table of contents if applicable
+3. Scope
+4. A set of entry conditions
+5. Automatic actions that happen by automated systems
+6. What the operator should do immediately
+7. Things the operator should do afterwards based on
+   reference to written procedures
+8. Relevant supporting material.
+
+Control rooms should have a sufficient number of EOP
+handbooks such that everyone can use one, they're easy to
+get to, and also be located such that they don't interfere
+with workstations or cover up controls. If there's multiple
+control rooms that share a common area, each control room
+should have it's own set of EOPs. They should not be sharing
+copies, essentially.
+
+Appendix B talks about logical statements. They're written
+strangely like program control flow, underlined, and
+capitalized:
+
+IF RPS scram has not initiated,
+THEN initiate SLC and isolate RWCU

Permanent Notes/Literature Notes/LIT-20260109152249-hybrid-automata-an-algorithmic-approach-to-the-specification-and-verification-of-hybrid-systems.md

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+---
+id: LIT-20260109152249
+title: Hybrid automata: An algorithmic approach to the specification and verification of hybrid systems
+type: literature
+created: 2026-01-09T20:22:49Z
+modified: 2026-01-09T21:14:05Z
+citekey: 
+---
+
+# Hybrid automata: An algorithmic approach to the specification and verification of hybrid systems
+
+## First Pass
+**Category:** 
+New methods paper
+
+**Context:** 
+This paper was released in the early 1990's when formal
+methods was gaining some steam for proving algorithms. This
+paper talks about the challenges of hybrid systems, where
+there are discrete changes on top of continuous dynamics.
+
+**Correctness:** 
+It's an extremely well cited paper.
+
+**Contributions:** 
+The [[Hybrid Automata]]
+
+**Clarity:** 
+4/5. Dense. Mathematical.
+
+## Second Pass
+**What is the main thrust?**
+
+**What is the supporting evidence?**
+
+**What are the key findings?**
+
+## Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+
+**Weak Points? Strong Points?**
+
+## Spawned Zettels
+[[Hybrid Automata]]
+[[Linear Hybrid Automata]]
+[[Timed Automata]]
+[[reactive-programs]]

Permanent Notes/Literature Notes/to_process/A Review of Formal Methods applied to Machine Learning-Note.md

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+# First Pass
+**Category:** 
+This is a review paper. 
+
+**Context:** 
+This paper tries to keep up with where formal methods are for machine 
+learning based systems. It is not necessarily a controls paper, but a broader
+machine learning paper in general.
+
+**Correctness:** 
+Really well written on the first pass. Easy to understand and things seem 
+well cited.
+
+**Contributions:** 
+Great citations showing links to different papers and also provides nice spots
+for forward research. Talks about how verification needs to be done along the
+whole pipeline: from data prep to training to implementation. There needs to 
+be more work on proving things about model behavior, but in general this
+review has a positive outlook on the field. 
+
+**Clarity:** 
+Very well written, easy to understand. Except, what is abstractification of a 
+network?
+
+# Second Pass
+This review gives an overview of formal methods applied to machine learning.
+Formal methods has been used for ML to test for robustness for various 
+perturbations on inputs. They start by talking about several types of formal 
+methods, including deductive verification, design by refinement, proof 
+assistants, model checking, and semantic static analysis, and then finally, 
+abstract interpretation of semantic static analysis. The last one has been 
+used the most in FM of ML.
+
+A large part of the paper focuses on formal methods for neural network 
+perturbation robustness. They split up the methods into two types: complete
+and incomplete formal methods. Complete formal methods are *sound* and 
+*complete*. This means they do not have false positives or false negatives. 
+These methods generally do not apply well to large networks (beyond 
+hundreds gets rough), but give the highest level of assurance. Here, there
+are two more subcategories: SMT based solvers and MILP-based solvers.
+
+SMT solvers are Satisfiability Modulo Theory solvers. These solvers a set
+of constraints and check to see whether or not all of the constraints can be 
+satisfied. Safety conditions are encoded as the *negation* of the safety constraint.
+That way, if a safety condition is violated, the SMT solver will pick it up as a 
+counter example. 
+
+MILP based solvers are Mixed Integer Linear Programming solvers. MILPs use
+linear programming where certain constraints are integers to reduce the
+solving space. Instead of having an explicity satisffiability condition on safety
+or not, MILPs instead can use a minimizing function to generate counter
+examples. For example, a MILP saftey condition might be formalized as:
+$$ \text{min}\space \bf{x}_n$$
+where a negative value of $\bf{x}_n$ is 'a valid counter example'.
+
+There are also 'incomplete formal methods'. These incomplete methods are
+sound, meaning they will not produce false negatives, but they may not be
+complete, meaning they may produce false positives. They scale better, but
+the false positives can be pretty annoying.
+
+One of the main incomplete methods is abstract interpretation. Things get very
+weird very fast--this is all about zonotopes and using over approximation of sets
+to say things about stability. There is weird stuff going on with cell splitting 
+and merging that seems like a to grasp. But, apparently it works. 
+
+Next, they spend some time talking about other machine learning methods and
+the formal methods that have been applied to them. Of particular interest to me
+is the formal method application to support vector machines and decision 
+trees. There are some useful methods for detecting robustness to adversarial 
+inputs, and knowing what the nearest misclassification adversarial case is.
+
+# Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+
+**Weak Points? Strong Points?**

Permanent Notes/Literature Notes/to_process/A systematic classification of neural-network-based control-Note.md

@@ -0,0 +1,32 @@
+# First Pass
+**Category:**
+This paper is a literature review
+
+**Context:** 
+Mukul says that there are a whole bunch of thrusts out there about neural 
+network based controllers, and that there needs to be a better way to 
+parse what research is what
+
+**Correctness:** 
+Looks good to me I suppose.
+
+**Contributions:** 
+Here's the most important figure in the whole thing:
+![[Pasted image 20250721095146.png]]
+
+**Clarity:** 
+Well written.
+
+# Second Pass
+**What is the main thrust?**
+
+**What is the supporting evidence?**
+
+**What are the key findings?**
+
+# Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+
+**Weak Points? Strong Points?**

Permanent Notes/Literature Notes/to_process/An autonomous control framework for advanced reactors-notes.md

@@ -0,0 +1,59 @@
+---
+alias: tee-hee-hee
+---
+
+# An autonomous control framework for advanced reactors notes
+
+## First Pass
+**Category:** 
+This is a vision-like paper.
+
+**Context:** 
+Dr. Wood is a professor of nuclear engineering at the University of Tennesse.
+He started working at UT after working at ORNL for 20+ years where he was
+a senior researcher. He works on common cause failures.
+
+**Correctness:** 
+There are not many citations, and a lot of the paper seems like it is off-the-cuff. 
+This was an invited article though in the *Nuclear Engineering and Technology* 
+journal. He's also got quite the resume.
+
+**Contributions:** 
+Dr. Wood gives a good overview of where we are (automated control), and
+where we need to go (autonomous control). Comparisons are made to other 
+industries, and how they've addressed these challenges. Clarifications are made
+with respect to how the nuclear industry is unique.
+
+**Clarity:** 
+Well written and clear, but a bit wordy at times. Examples are used but 
+sometimes it just feels like a mouthful.
+
+## Second Pass
+**What is the main thrust?**
+Wood talks a lot about what it means for a system to be autonomous. He 
+actually starts with a etymological argument- "*automatos* means self-acting,
+whereas *autonomos* means independent." The point of an autonomous system 
+is that it must be able to make intelligent decisions that a human would 
+otherwise make. Knowing how to handle degraded or faulty sensors or 
+actuators, switching controller trains, and knowing when scramming is
+necessary are all decisions that an autonomous system would make, that
+a simple automated system could not. The key is in the decision making.
+
+**What is the supporting evidence?**
+Dr. Wood compares a lot to NASA control systems for the Mars rovers. These
+systems use two tiers of controllers: a decision layer and a functionality layer. 
+The functionality layer does what you think--it manages the physical 
+functioning. The decision layer is different. It decides on controller modes and 
+works instead with operational level goals.
+
+**What are the key findings?**
+The biggest findings are that an autonomous control system for a nuclear
+power plant is possible, but by far the biggest roadblock is a high assurance 
+decision making system. 
+
+## Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+
+**Weak Points? Strong Points?**

Permanent Notes/Literature Notes/to_process/Automation levels for nuclear reactor operations- A revised perspective - Note.md

@@ -0,0 +1,36 @@
+# First Pass
+**Category:** 
+This is a paper following a workshop. It is kind of a big picture / idea 
+type paper.
+
+**Context:** 
+This paper was written after a workshop took place to talk about recent NRC
+regulations. They talk about how different industries categorize the level
+of autonomy in systems, and create autonomous levels of reactor control.
+
+**Correctness:** 
+Vivek Agarwal chaired ANS in Chicago this past year. He's the real deal
+
+**Contributions:** 
+They contribute a first thought on how to go about creating milestones for
+autonomous systems, and give us a language to use when describing what level
+of autonomy a system is gunning for.
+
+**Clarity:** 
+Clearly written. Very nice!
+
+# Second Pass
+**What is the main thrust?**
+
+**What is the supporting evidence?**
+
+**What are the key findings?**
+
+# Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+
+**Weak Points? Strong Points?**
+
+<!The quick brown fox jumps over the lazy dog. The dog takes a nice nap. :)>

Permanent Notes/Literature Notes/to_process/Economics and finance of Small Modular Reactors- A systematic review and research agenda-Note.md

@@ -0,0 +1,32 @@
+# First Pass
+**Category:** 
+Systematic Review
+
+**Context:** 
+This paper is from the civil engineering school at the University of Leeds. 
+They are doing an overview of economics and finance research of small
+modular reactors.
+
+**Correctness:** 
+Can not say. Is a review!
+
+**Contributions:** 
+They do a good break down of the research we have done ('what we know') and
+what needs done ('what we do not know'). They point out a big discrepancy that we do not have a lot of research on operations and maintenance costs. 
+
+**Clarity:** 
+Nicely written. Easy to understand.
+
+# Second Pass
+**What is the main thrust?**
+
+**What is the supporting evidence?**
+
+**What are the key findings?**
+
+# Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+
+**Weak Points? Strong Points?**

Permanent Notes/Literature Notes/to_process/Enhancing Cyber-Physical System Dependability via Synthesis- Challenges and Future Directions-Note.md

@@ -0,0 +1,33 @@
+# First Pass
+**Category:** This paper is an experimental paper. 
+
+**Context:** The context of this paper is using a couple different techniques 
+synthesize control programs using different formal methods tools.
+
+**Correctness:** I trust Max's integrity. Some of the citations were funky and
+the intro was fluffy though.
+
+**Contributions:** 
+This paper shows that using LTL and other formal methods still struggles to 
+generate controllers for significantly challenging systems. The high bay 
+warehouse used to create this paper had to be simplified. Then, they introduce
+an SMT solver based method to try to generate code.
+
+**Clarity:** 
+The intro and conclusion do not provide very strong clarity on what they 
+actually did other than "high assurance is high difficulty", and that we're not 
+really there yet on HACPS.
+
+# Second Pass
+**What is the main thrust?**
+
+**What is the supporting evidence?**
+
+**What are the key findings?**
+
+# Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+
+**Weak Points? Strong Points?**

Permanent Notes/Literature Notes/to_process/Evaluating Robustness of Neural Networks with Mixed Integer Programming-Note.md

@@ -0,0 +1,42 @@
+# First Pass
+**Category:** 
+This is a methods paper. 
+
+**Context:** 
+This paper proposes a way of using mixed integer linear programming (MILP)
+to  evaluate properties of neural networks.
+
+**Correctness:** 
+Formal
+
+**Contributions:** 
+They do nifty things with bounds tightening and presolving that makes their
+solver very fast compared to the state of the art or Reluplex. They also talk 
+about stable and unstable neurons.
+
+**Clarity:** 
+They have a really good explanation of what a MILP problem is and how one
+might encode a neural network as one.
+
+# Second Pass
+**What is the main thrust?**
+The main thrust is their new solving method of MILPs for neural networks.
+With their method, neural networks can have their neurons analyzed to 
+prove whether or not the network is robust to input perturbations. This is 
+especially important for classifiers, who need to know if there are sneaky
+nonlinearities that can be harmful to a built system (like a glitch). This 
+method of bounds tightening and MILP usage makes their solver much faster
+and therein more capable to handle large networks.
+
+**What is the supporting evidence?**
+They have a whole bunch of experimental results.
+
+**What are the key findings?**
+MILPs and bound tightening is very good!
+
+# Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+
+**Weak Points? Strong Points?**

Permanent Notes/Literature Notes/to_process/Formal requirements elicitation with FRET-Note.md

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+# First Pass
+**Category:** 
+This is a weird one. This paper is essentially just a 'state-of-the-FRET' paper
+
+**Context:** 
+FRET comes from NASA and is a tool to line up requirements in a temporal
+language.
+
+**Correctness:** 
+Formal. But they don't really go into details.
+
+**Contributions:** 
+Really I don't think they contribute much here than an explanation of what's
+going on.
+
+**Clarity:** 
+Easy to read. 
+
+# Second Pass
+**What is the main thrust?**
+
+**What is the supporting evidence?**
+
+**What are the key findings?**
+
+# Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+
+**Weak Points? Strong Points?**

Permanent Notes/Literature Notes/to_process/Formal verification of neural network controlled autonomous systems-Note.md

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+# First Pass
+**Category:** 
+Methods paper
+
+**Context:** 
+Using NN w/ LiDAR to say safety reliability claims using FM
+
+**Correctness:** 
+Assumptions seem good, other than anticipating LiDAR as a 
+continuous data stream. 
+
+**Contributions:** 
+1. Framewok for formally proving safety properties of autonomous robots using LiDAR and NNs
+2. Something something imaging-adapted partitions. A 'notion'
+
+**Clarity:** 
+Very well written and clear.
+
+# Second Pass
+**What is the main thrust?**
+
+**What is the supporting evidence?**
+
+**What are the key findings?**
+
+# Third Pass
+**Recreation Notes:**
+
+**Hidden Findings:**
+
+**Weak Points? Strong Points?**

Permanent Notes/Literature Notes/to_process/Hardware In The Loop Papers-Note.md

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+---
+creation date: 2024-08-08
+modification date: Thursday 8th August 2024 09:57:16
+tags:
+  - Research
+  - "#Survey"
+---
+# Preamble
+### Notable Links
+[[ARCADE Implementation at the University of Pittsburgh]]
+[[1. A shortlist of ARCADE Experiments]]
+## What are we doing?
+Collecting and organizing papers about HiTL testing. Making notes about 'em. Stuff like that.
+## Why are we doing it?
+08-08-2024: I'm writing a paper for [[2. (SR-CIST) Workshop on Security and Resiliency of Critical Infrastructure and Space Technologies]] and really need to know about hardware in the loop testing. 
+## Who cares?
+Me. Andrew, probably. Dan, a lot.
+# Papers
+## Summary Table
+```dataview
+table without id
+link(file.path, title) as "Title", year as "Year", authors as "Authors", readstatus as "Read Status"
+from outgoing([[]])
+where readstatus or readstatus=False 
+sort readstatus desc, year desc
+```
+## Papers about ARCADE
+[[maccaroneADVANCEDREACTORCYBER]]
+[[chenFullscopeHighfidelitySimulatorbased2024]]
+
+## Hardware In The Loop Papers
+[[mihalicHardwareintheLoopSimulationsHistorical2022]]
+[[bullockHardwareintheloopSimulation2004]]
+[[puysHardwareInTheLoopLabsSCADA2021]]
+[[choiRealTimeHardwareintheLoopHIL2021]]
+
+## Cybersecurity of OT Papers
+[[sunSoKAttacksIndustrial2021]]
+[[mclaughlinControllerawareFalseData2014]]
+[[chekoleEnforcingMemorySafety2018]]
+[[kushnerRealStoryStuxnet2013]]
+[[CyberAttackGerman2015]]
+[[sguegliaFederalOfficialsInvestigating2023]]
+## Formal Methods and PLCs
+[[fernandezadiegoApplyingModelChecking2015]]
+[[lopez-miguelPLCverifStatusFormal2022]]
+[[kleinFormallyVerifiedSoftware2018]] -- Littlebird paper
+
+## Kry10
+[[Kry10TechnicalOverview]]