Georgiev Lab - User contributions [en]

Courses/Modelování a Simulace II - 2020/Final Project

2025-12-16T18:48:58Z

Georgiev:

Below you will find the PDF file describing the final project.

Due date: January 23

You are expected to provide not only the Monte Carlo estimate but also all supporting analysis that validates your MCMC algorithm.

----
Q&A

1. Question: I don't understand the purpose of the f array.

Answer: The f array gives you the frequencies of data points in a given block of the parameter space. And you use this in calculating your acceptance probability. So that probability of acceptance is equal to min(1,Fnew/Fold).

2. Question: I am getting the error message: Unable to perform assignment because the left and right sides have a different number of elements.

Error in updateFSA (line 13)
qc(j) = executeEvents(FSA{j},s(i),qc(j));

Error in NetworkSimRun (line 99)
qSupnew = updateFSA(FSAsup,enew,qSupc);

Answer: need to check your FSA files.

3. Question: How do we compute the error?

Answer: The data set alone will not give you an accurate estimate. You must generate more samples. Then you have three methods by which you can compute the error: z-score, t-score, boostrap. Which ever method you use, justify your answers. Recall the z-score assumes the sample standard deviation is the same as the actual standard deviation. The t-score and the z-score both depend on the central limit theorem.

----

Download the assignment description
[[File:2022-MS2_FinalProject.pdf]]

Please note that in problem 2, when comparing abnormal time estimated by MCMC to the abnormal time estimated from your simple Markov Chain model should only consider abnormal voltage at the second node (not the reactive power).

Assigned datasets (from the list below) will be mailed to you upon request (be email):
# DataSet100-01.mat
# DataSet100-02.mat
# DataSet100-03.mat
# DataSet100-04.mat
# DataSet100-05.mat
# DataSet100-06.mat
# DataSet100-07.mat
# DataSet100-08.mat
# DataSet100-09.mat
# DataSet100-10.mat
# DataSet100-11.mat
# DataSet100-12.mat
# DataSet100-13.mat
# DataSet100-14.mat
# DataSet100-15.mat

Courses

2025-10-03T03:08:00Z

Georgiev:

* [[Courses/Introduction to cellular system modeling - 2023|Introduction to cellular system modeling - 2024]]
* [[Courses/Modelování a Simulace II - 2020|Modelování a Simulace II - 2025]]

Courses

2025-02-14T14:58:27Z

Georgiev:

Courses/Modelování a Simulace II - 2020/Final Project

2024-12-07T02:05:36Z

Georgiev:

Below you will find the PDF file describing the final project.

Due date: 18.1.2025

You are expected to provide not only the Monte Carlo estimate but also all supporting analysis that validates your MCMC algorithm.

----
Q&A

1. Question: I don't understand the purpose of the f array.

Answer: The f array gives you the frequencies of data points in a given block of the parameter space. And you use this in calculating your acceptance probability. So that probability of acceptance is equal to min(1,Fnew/Fold).

2. Question: I am getting the error message: Unable to perform assignment because the left and right sides have a different number of elements.

Error in updateFSA (line 13)
qc(j) = executeEvents(FSA{j},s(i),qc(j));

Error in NetworkSimRun (line 99)
qSupnew = updateFSA(FSAsup,enew,qSupc);

Answer: need to check your FSA files.

3. Question: How do we compute the error?

Answer: The data set alone will not give you an accurate estimate. You must generate more samples. Then you have three methods by which you can compute the error: z-score, t-score, boostrap. Which ever method you use, justify your answers. Recall the z-score assumes the sample standard deviation is the same as the actual standard deviation. The t-score and the z-score both depend on the central limit theorem.

----

Download the assignment description
[[File:2022-MS2_FinalProject.pdf]]

Please note that in problem 2, when comparing abnormal time estimated by MCMC to the abnormal time estimated from your simple Markov Chain model should only consider abnormal voltage at the second node (not the reactive power).

Assigned datasets (from the list below) will be mailed to you upon request (be email):
# DataSet100-01.mat
# DataSet100-02.mat
# DataSet100-03.mat
# DataSet100-04.mat
# DataSet100-05.mat
# DataSet100-06.mat
# DataSet100-07.mat
# DataSet100-08.mat
# DataSet100-09.mat
# DataSet100-10.mat
# DataSet100-11.mat
# DataSet100-12.mat
# DataSet100-13.mat
# DataSet100-14.mat
# DataSet100-15.mat

File:MS2-2023 syllabus en.pdf

2024-09-20T02:05:36Z

Georgiev: Georgiev uploaded a new version of File:MS2-2023 syllabus en.pdf

File:MS2-2023 syllabus en.pdf

2024-09-20T02:04:54Z

Georgiev: Georgiev uploaded a new version of File:MS2-2023 syllabus en.pdf

File:MS2-2023 syllabus en.pdf

2024-09-20T02:04:13Z

Georgiev: Georgiev uploaded a new version of File:MS2-2023 syllabus en.pdf

Courses

2024-09-20T01:52:11Z

Georgiev:

* [[Courses/Introduction to cellular system modeling - 2021|Introduction to cellular system modeling - 2021]]
* [[Courses/Introduction to cellular system modeling - 2022|Introduction to cellular system modeling - 2022]]
* [[Courses/Introduction to cellular system modeling - 2023|Introduction to cellular system modeling - 2023]]
* [[Courses/Modelování a Simulace II - 2020|Modelování a Simulace II - 2024]]

Courses/Introduction to cellular system modeling - 2023

2024-04-05T00:22:14Z

Georgiev:

*[http://ccy.zcu.cz/files/ZMB_2016/Lectures/Lecture1.pdf LECTURE 1 (Overview of Synthetic Biology)]
*[[:File:ZMB-Lecture-2-GeneticSyntax.pdf|LECTURE 2 (DNA Syntax)]]
*[[:File:ZMB-Lecture-3-PolypeptideSyntax.pdf|LECTURE 3 (Protein Syntax)]]
*[[:File:ZMB-Lecture-4-DNAsynthesis.pdf|LECTURE 4 (DNA Synthesis)]]

Courses/Introduction to cellular system modeling - 2023

2024-03-18T20:43:43Z

Georgiev: Created page with "*[http://ccy.zcu.cz/files/ZMB_2016/Lectures/Lecture1.pdf LECTURE 1 (Overview of Synthetic Biology)] *LECTURE 2 (DNA Syntax)"

*[http://ccy.zcu.cz/files/ZMB_2016/Lectures/Lecture1.pdf LECTURE 1 (Overview of Synthetic Biology)]
*[[:File:ZMB-Lecture-2-GeneticSyntax.pdf|LECTURE 2 (DNA Syntax)]]

Courses

2024-03-18T20:39:28Z

Georgiev:

Courses/Modelování a Simulace II - 2014/EXERCISE 1 - 2014

2023-10-05T02:22:26Z

Georgiev:

The purpose of this exercise is to
1) install the UMDES FSA library,
2) create the component FSA models for our case study,
3) run some simple test to make sure no syntax errors were made,
4) import the models into Matlab,
5) simulate the automata for a given string of events.

Step 1: Installation
The executables, including a user guide, are located here: [https://gitlab.eecs.umich.edu/wikis/desuma/-/wikis/UMDES-Software-Library University of Michigan DES Group]. Scroll down to the download section a select executables. You will be asked to fill in some information. Place the executable files in a separate directory where you can easily access them.

Step 2: create the component FSA models
* Download The Case study component graphs - [http://ccy.zcu.cz/files/MS2_2014/MS2_RS_automata_components_2.pdf FSA schematics].
* Build the finite state machines by following the file format here: [https://gitlab.eecs.umich.edu/wikis/desuma/-/wikis/Input-File-Formats FSM file format]
* note 1: the file extension is not important
* note 2: place the files in a separate directory

Step 3: test the accessibility of the constructed FSA
* copy and paste the UMDES executables "acc" and "co_acc", which compute the accessible and co-accessible parts of your FSAs, into the FSA folder
* execute the commands
* the acc and co_acc operations must work and must not delete any states
* note that you may have to change the file permissions to executable ([https://macpaw.com/how-to/permission-denied-terminal see here for instructions on mac])

step 4: download the following Matlab files and import some FSMs into Matlab
* [http://ccy.zcu.cz/files/MS2_2014/MATLAB2UMDES.m MATLAB2UMDES.m]
* [http://ccy.zcu.cz/files/MS2_2014/UMDES2MATLAB.m UMDES2MATLAB.m]
* [http://ccy.zcu.cz/files/MS2_2014/setEvents.m setEvents.m]
* [http://ccy.zcu.cz/files/MS2_2014/executeEvents.m executeEvents.m]
* follow the instructions in UMDES2MATLAB.m to import an automata into Matlab

step 5: test whether your automata accept the following strings, verify the final states are correct
* T_sensor: s1 = {'vm' 'vn' 'vp' 'vm' 'vp'}, s2 = {'vm' 'vn' 'vm' 'vp' 'vp'}
* T_switch: s1 = {'tp' 'tf' 'tm' 'tf' 'tm' 'tf' 'tm'}, s2 = {'tm' 'tf' 'tm' 'tp' 'tf' 'tp' 'tf'}

Courses/Modelování a Simulace II - 2014/EXERCISE 1 - 2014

2023-10-05T02:19:11Z

Georgiev:

The purpose of this exercise is to
1) install the UMDES FSA library,
2) create the component FSA models for our case study,
3) run some simple test to make sure no syntax errors were made,
4) import the models into Matlab,
5) simulate the automata for a given string of events.

Step 1: Installation
The executables, including a user guide, are located here: [https://gitlab.eecs.umich.edu/wikis/desuma/-/wikis/UMDES-Software-Library University of Michigan DES Group]. Scroll down to the download section a select executables. You will be asked to fill in some information. Place the executable files in a separate directory where you can easily access them.

Step 2: create the component FSA models
* Download The Case study component graphs - [http://ccy.zcu.cz/files/MS2_2014/MS2_RS_automata_components_2.pdf FSA schematics].
* Build the finite state machines by following the file format here: [https://gitlab.eecs.umich.edu/wikis/desuma/-/wikis/Input-File-Formats FSM file format]
* note 1: the file extension is not important
* note 2: place the files in a separate directory

Step 3: test the accessibility of the constructed FSA
* copy and paste the UMDES executables "acc" and "co_acc", which compute the accessible and co-accessible parts of your FSAs, into the FSA folder
* execute the commands
* the acc and co_acc operations must work and must not delete any states

step 4: download the following Matlab files and import some FSMs into Matlab
* [http://ccy.zcu.cz/files/MS2_2014/MATLAB2UMDES.m MATLAB2UMDES.m]
* [http://ccy.zcu.cz/files/MS2_2014/UMDES2MATLAB.m UMDES2MATLAB.m]
* [http://ccy.zcu.cz/files/MS2_2014/setEvents.m setEvents.m]
* [http://ccy.zcu.cz/files/MS2_2014/executeEvents.m executeEvents.m]
* follow the instructions in UMDES2MATLAB.m to import an automata into Matlab

step 5: test whether your automata accept the following strings, verify the final states are correct
* T_sensor: s1 = {'vm' 'vn' 'vp' 'vm' 'vp'}, s2 = {'vm' 'vn' 'vm' 'vp' 'vp'}
* T_switch: s1 = {'tp' 'tf' 'tm' 'tf' 'tm' 'tf' 'tm'}, s2 = {'tm' 'tf' 'tm' 'tp' 'tf' 'tp' 'tf'}

Courses/Modelování a Simulace II - 2014/EXERCISE 1 - 2014

2023-10-05T02:18:02Z

Georgiev:

The purpose of this exercise is to
1) install the UMDES FSA library,
2) create the component FSA models for our case study,
3) run some simple test to make sure no syntax errors were made,
4) import the models into Matlab,
5) simulate the automata for a given string of events.

Step 1: Installation
The executables, including a user guide, are located here: [https://gitlab.eecs.umich.edu/wikis/desuma/-/wikis/UMDES-Software-Library University of Michigan DES Group]. Scroll down to the download section a select executables. You will be asked to fill in some information. Place the executable files in a separate directory where you can easily access them.

Step 2: create the component FSA models
* Download The Case study component graphs - [http://ccy.zcu.cz/files/MS2_2014/MS2_RS_automata_components_2.pdf FSA schematics].
* Build the finite state machines by following the file format here: [https://www.eecs.umich.edu/umdes/projects/lib/formats.html#fsm FSM file format]
* note 1: the file extension is not important
* note 2: place the files in a separate directory

Step 3: test the accessibility of the constructed FSA
* copy and paste the UMDES executables "acc" and "co_acc", which compute the accessible and co-accessible parts of your FSAs, into the FSA folder
* execute the commands
* the acc and co_acc operations must work and must not delete any states

step 4: download the following Matlab files and import some FSMs into Matlab
* [http://ccy.zcu.cz/files/MS2_2014/MATLAB2UMDES.m MATLAB2UMDES.m]
* [http://ccy.zcu.cz/files/MS2_2014/UMDES2MATLAB.m UMDES2MATLAB.m]
* [http://ccy.zcu.cz/files/MS2_2014/setEvents.m setEvents.m]
* [http://ccy.zcu.cz/files/MS2_2014/executeEvents.m executeEvents.m]
* follow the instructions in UMDES2MATLAB.m to import an automata into Matlab

step 5: test whether your automata accept the following strings, verify the final states are correct
* T_sensor: s1 = {'vm' 'vn' 'vp' 'vm' 'vp'}, s2 = {'vm' 'vn' 'vm' 'vp' 'vp'}
* T_switch: s1 = {'tp' 'tf' 'tm' 'tf' 'tm' 'tf' 'tm'}, s2 = {'tm' 'tf' 'tm' 'tp' 'tf' 'tp' 'tf'}

Courses/Modelování a Simulace II - 2020

2023-09-22T04:18:06Z

Georgiev:

*[[:File:MS2-2023_syllabus_en.pdf |Syllabus]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture1_NetworkDescription.pdf Network Description]
*[http://ccy.zcu.cz/files/MS2_2015/Lectures/Lecture2b_2015.pdf LECTURE 1 (DES intro)]
*[http://ccy.zcu.cz/files/MS2_2014/Lectures/Lecture3_2014.pdf LECTURE 2 (DES observers, composition, and control)]
*[[Courses/Modelování a Simulace II - 2014/EXERCISE 1 - 2014|EXERCISE 1]]
*[[Courses/Modelování a Simulace II - 2014/EXERCISE 2 - 2014|EXERCISE 2]]
*[http://ccy.zcu.cz/files/MS2_2014/Lectures/Lecture4_2014.pdf LECTURE 3 (Discrete state Markov Chains)]
*[[Media: MarkovChains_supplement.pdf|LECTURE 3 (supplement)]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture6_MonteCarlo.pdf LECTURE 4 (Monte Carlo Method)]
*[[Courses/Modelování a Simulace II - 2014/EXERCISE 3 - 2020|EXERCISE 3]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture7_MCMC.pdf LECTURE 5 (MCMC)]
*[[Courses/Modelování a Simulace II - 2017/EXERCISE 4|EXERCISE 4]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture8_Validation.pdf LECTURE 6 (Validation)]
*[[Courses/Modelování a Simulace II - 2017/EXERCISE 3|EXERCISE 5]]
*[[Courses/Modelování a Simulace II - 2020/Final Project|FINAL PROJECT]]

File:MS2-2023 syllabus en.pdf

2023-09-22T04:17:28Z

Georgiev:

Courses

2023-09-22T04:14:41Z

Georgiev:

* [[Courses/Introduction to cellular system modeling - 2021|Introduction to cellular system modeling - 2021]]
* [[Courses/Introduction to cellular system modeling - 2022|Introduction to cellular system modeling - 2022]]
* [[Courses/Modelování a Simulace II - 2020|Modelování a Simulace II - 2023]]

Courses/Introduction to cellular system modeling - 2022

2023-05-16T04:09:51Z

Georgiev:

Lectures
*[http://ccy.zcu.cz/files/ZMB_2016/Lectures/Lecture1.pdf LECTURE 1 (Overview of Synthetic Biology)]
*[[:File:ZMB-Lecture-2-GeneticSyntax.pdf|LECTURE 2 (DNA Syntax)]]
*[[:File:ZMB-Lecture-3-PolypeptideSyntax.pdf|LECTURE 3 (Protein Syntax)]]
*[[:File:ZMB-Lecture-4-DNAsynthesis.pdf|LECTURE 4 (DNA Synthesis)]]
*[[:File:ZMB2023-FinalProject-links.pdf|Final Project (Oscillator design)]]

File:ZMB2023-FinalProject-links.pdf

2023-05-16T04:09:26Z

Georgiev:

Courses/Introduction to cellular system modeling - 2022

2023-05-16T03:57:37Z

Georgiev:

File:ZMB2023-FinalProject.pdf

2023-05-16T03:56:33Z

Georgiev:

Courses/Introduction to cellular system modeling - 2022

2023-04-11T06:17:15Z

Georgiev:

Courses/Introduction to cellular system modeling - 2022

2023-04-11T06:16:53Z

Georgiev:

File:ZMB-Lecture-4-DNAsynthesis.pdf

2023-04-11T06:16:14Z

Georgiev:

File:ZMB-Lecture-2-GeneticSyntax.pdf

2023-03-07T22:21:59Z

Georgiev: Georgiev uploaded a new version of File:ZMB-Lecture-2-GeneticSyntax.pdf

File:ZMB-Lecture-2-GeneticSyntax.pdf

2023-03-07T22:21:50Z

Georgiev: Georgiev uploaded a new version of File:ZMB-Lecture-2-GeneticSyntax.pdf

Courses/Introduction to cellular system modeling - 2022

2023-03-07T22:17:36Z

Georgiev: Created page with "Lectures *[http://ccy.zcu.cz/files/ZMB_2016/Lectures/Lecture1.pdf LECTURE 1 (Overview of Synthetic Biology)] *LECTURE 2 (DNA Syntax)"

Lectures
*[http://ccy.zcu.cz/files/ZMB_2016/Lectures/Lecture1.pdf LECTURE 1 (Overview of Synthetic Biology)]
*[[:File:ZMB-Lecture-2-GeneticSyntax.pdf|LECTURE 2 (DNA Syntax)]]

Courses

2023-03-07T18:09:12Z

Georgiev:

* [[Courses/Introduction to cellular system modeling - 2021|Introduction to cellular system modeling - 2021]]
* [[Courses/Modelování a Simulace II - 2020|Modelování a Simulace II - 2022]]
* [[Courses/Introduction to cellular system modeling - 2022|Introduction to cellular system modeling - 2022]]

Courses

2023-03-07T18:09:00Z

Georgiev:

* [[Courses/Introduction to cellular system modeling - 2021|Introduction to cellular system modeling - 2021]]
* [[Courses/Modelování a Simulace II - 2020|Modelování a Simulace II - 2022]] 
* [[Courses/Introduction to cellular system modeling - 2022|Introduction to cellular system modeling - 2022]]

Courses

2023-03-07T18:08:48Z

Georgiev:

* [[Courses/Introduction to cellular system modeling - 2021|Introduction to cellular system modeling - 2021]]
* [[Courses/Modelování a Simulace II - 2020|Modelování a Simulace II - 2022]] 
 
* [[Courses/Introduction to cellular system modeling - 2022|Introduction to cellular system modeling - 2022]]

File:2022-MS2 FinalProject.pdf

2022-12-08T19:17:28Z

Georgiev:

Courses/Modelování a Simulace II - 2020/Final Project

2022-12-08T19:17:01Z

Georgiev:

Below you will find the PDF file describing the final project.

Due date: 18.1.2023

You are expected to provide not only the Monte Carlo estimate but also all supporting analysis that validates your MCMC algorithm.

----
Q&A

1. Question: I don't understand the purpose of the f array.

Answer: The f array gives you the frequencies of data points in a given block of the parameter space. And you use this in calculating your acceptance probability. So that probability of acceptance is equal to min(1,Fnew/Fold).

2. Question: I am getting the error message: Unable to perform assignment because the left and right sides have a different number of elements.

Error in updateFSA (line 13)
qc(j) = executeEvents(FSA{j},s(i),qc(j));

Error in NetworkSimRun (line 99)
qSupnew = updateFSA(FSAsup,enew,qSupc);

Answer: need to check your FSA files.

3. Question: How do we compute the error?

Answer: The data set alone will not give you an accurate estimate. You must generate more samples. Then you have three methods by which you can compute the error: z-score, t-score, boostrap. Which ever method you use, justify your answers. Recall the z-score assumes the sample standard deviation is the same as the actual standard deviation. The t-score and the z-score both depend on the central limit theorem.

----

Download the assignment description
[[File:2022-MS2_FinalProject.pdf]]

Please note that in problem 2, when comparing abnormal time estimated by MCMC to the abnormal time estimated from your simple Markov Chain model should only consider abnormal voltage at the second node (not the reactive power).

Assigned datasets (from the list below) will be mailed to you upon request (be email):
# DataSet100-01.mat
# DataSet100-02.mat
# DataSet100-03.mat
# DataSet100-04.mat
# DataSet100-05.mat
# DataSet100-06.mat
# DataSet100-07.mat
# DataSet100-08.mat
# DataSet100-09.mat
# DataSet100-10.mat
# DataSet100-11.mat
# DataSet100-12.mat
# DataSet100-13.mat
# DataSet100-14.mat
# DataSet100-15.mat

Courses/Modelování a Simulace II - 2020/Final Project

2022-12-08T19:14:54Z

Georgiev:

Below you will find the PDF file describing the final project.

Due date: 18.1.2023

You are expected to provide not only the Monte Carlo estimate but also all supporting analysis that validates your MCMC algorithm.

----
Q&A

1. Question: I don't understand the purpose of the f array.

Answer: The f array gives you the frequencies of data points in a given block of the parameter space. And you use this in calculating your acceptance probability. So that probability of acceptance is equal to min(1,Fnew/Fold).

2. Question: I am getting the error message: Unable to perform assignment because the left and right sides have a different number of elements.

Error in updateFSA (line 13)
qc(j) = executeEvents(FSA{j},s(i),qc(j));

Error in NetworkSimRun (line 99)
qSupnew = updateFSA(FSAsup,enew,qSupc);

Answer: need to check your FSA files.

3. Question: How do we compute the error?

Answer: The data set alone will not give you an accurate estimate. You must generate more samples. Then you have three methods by which you can compute the error: z-score, t-score, boostrap. Which ever method you use, justify your answers. Recall the z-score assumes the sample standard deviation is the same as the actual standard deviation. The t-score and the z-score both depend on the central limit theorem.

----

Download the assignment description
[[File:2022_MS2_FinalProject.pdf]]

Please note that in problem 2, when comparing abnormal time estimated by MCMC to the abnormal time estimated from your simple Markov Chain model should only consider abnormal voltage at the second node (not the reactive power).

Assigned datasets (from the list below) will be mailed to you upon request (be email):
# DataSet100-01.mat
# DataSet100-02.mat
# DataSet100-03.mat
# DataSet100-04.mat
# DataSet100-05.mat
# DataSet100-06.mat
# DataSet100-07.mat
# DataSet100-08.mat
# DataSet100-09.mat
# DataSet100-10.mat
# DataSet100-11.mat
# DataSet100-12.mat
# DataSet100-13.mat
# DataSet100-14.mat
# DataSet100-15.mat

File:2020 MS2 FinalProject.pdf

2022-12-08T19:14:12Z

Georgiev: Georgiev uploaded a new version of File:2020 MS2 FinalProject.pdf

Courses/Modelování a Simulace II - 2020/Final Project

2022-12-08T18:34:17Z

Georgiev:

Below you will find the PDF file describing the final project.

Due date: 18.1.2023

You are expected to provide not only the Monte Carlo estimate but also all supporting analysis that validates your MCMC algorithm.

----
Q&A

1. Question: I don't understand the purpose of the f array.

Answer: The f array gives you the frequencies of data points in a given block of the parameter space. And you use this in calculating your acceptance probability. So that probability of acceptance is equal to min(1,Fnew/Fold).

2. Question: I am getting the error message: Unable to perform assignment because the left and right sides have a different number of elements.

Error in updateFSA (line 13)
qc(j) = executeEvents(FSA{j},s(i),qc(j));

Error in NetworkSimRun (line 99)
qSupnew = updateFSA(FSAsup,enew,qSupc);

Answer: need to check your FSA files.

3. Question: How do we compute the error?

Answer: The data set alone will not give you an accurate estimate. You must generate more samples. Then you have three methods by which you can compute the error: z-score, t-score, boostrap. Which ever method you use, justify your answers. Recall the z-score assumes the sample standard deviation is the same as the actual standard deviation. The t-score and the z-score both depend on the central limit theorem.

----

Download the assignment description
[[File:2020_MS2_FinalProject.pdf]]

Please note that in problem 2, when comparing abnormal time estimated by MCMC to the abnormal time estimated from your simple Markov Chain model should only consider abnormal voltage at the second node (not the reactive power).

Assigned datasets (from the list below) will be mailed to you upon request (be email):
# DataSet100-01.mat
# DataSet100-02.mat
# DataSet100-03.mat
# DataSet100-04.mat
# DataSet100-05.mat
# DataSet100-06.mat
# DataSet100-07.mat
# DataSet100-08.mat
# DataSet100-09.mat
# DataSet100-10.mat
# DataSet100-11.mat
# DataSet100-12.mat
# DataSet100-13.mat
# DataSet100-14.mat
# DataSet100-15.mat

Courses/Modelování a Simulace II - 2020

2022-11-18T08:06:38Z

Georgiev:

*[[:File:MS2-2022_syllabus_en.pdf|Syllabus]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture1_NetworkDescription.pdf Network Description]
*[http://ccy.zcu.cz/files/MS2_2015/Lectures/Lecture2b_2015.pdf LECTURE 1 (DES intro)]
*[http://ccy.zcu.cz/files/MS2_2014/Lectures/Lecture3_2014.pdf LECTURE 2 (DES observers, composition, and control)]
*[[Courses/Modelování a Simulace II - 2014/EXERCISE 1 - 2014|EXERCISE 1]]
*[[Courses/Modelování a Simulace II - 2014/EXERCISE 2 - 2014|EXERCISE 2]]
*[http://ccy.zcu.cz/files/MS2_2014/Lectures/Lecture4_2014.pdf LECTURE 3 (Discrete state Markov Chains)]
*[[Media: MarkovChains_supplement.pdf|LECTURE 3 (supplement)]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture6_MonteCarlo.pdf LECTURE 4 (Monte Carlo Method)]
*[[Courses/Modelování a Simulace II - 2014/EXERCISE 3 - 2020|EXERCISE 3]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture7_MCMC.pdf LECTURE 5 (MCMC)]
*[[Courses/Modelování a Simulace II - 2017/EXERCISE 4|EXERCISE 4]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture8_Validation.pdf LECTURE 6 (Validation)]
*[[Courses/Modelování a Simulace II - 2017/EXERCISE 3|EXERCISE 5]]
*[[Courses/Modelování a Simulace II - 2020/Final Project|FINAL PROJECT]]

Courses/Modelování a Simulace II - 2020

2022-09-29T09:45:47Z

Georgiev:

*[[:File:MS2-2022_syllabus_en.pdf|Syllabus]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture1_NetworkDescription.pdf Network Description]
*[http://ccy.zcu.cz/files/MS2_2015/Lectures/Lecture2b_2015.pdf LECTURE 1 (DES intro)]
*[http://ccy.zcu.cz/files/MS2_2014/Lectures/Lecture3_2014.pdf LECTURE 2 (DES observers, composition, and control)]
*[[Courses/Modelování a Simulace II - 2014/EXERCISE 1 - 2014|EXERCISE 1]]
*[[Courses/Modelování a Simulace II - 2014/EXERCISE 2 - 2014|EXERCISE 2]]
*[[Courses/Modelování a Simulace II - 2018/Assignment 1|ASSIGNMENT 1]]
*[http://ccy.zcu.cz/files/MS2_2014/Lectures/Lecture4_2014.pdf LECTURE 3 (Discrete state Markov Chains)]
*[[Media: MarkovChains_supplement.pdf|LECTURE 3 (supplement)]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture6_MonteCarlo.pdf LECTURE 4 (Monte Carlo Method)]
*[[Courses/Modelování a Simulace II - 2014/EXERCISE 3 - 2020|EXERCISE 3]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture7_MCMC.pdf LECTURE 5 (MCMC)]
*[[Courses/Modelování a Simulace II - 2017/EXERCISE 4|EXERCISE 4]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture8_Validation.pdf LECTURE 6 (Validation)]
*[[Courses/Modelování a Simulace II - 2017/EXERCISE 3|EXERCISE 5]]
*[[Courses/Modelování a Simulace II - 2020/Final Project|FINAL PROJECT]]

Courses/Modelování a Simulace II - 2020

2022-09-29T09:45:34Z

Georgiev:

**[[:File:MS2-2022_syllabus_en.pdf|Syllabus]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture1_NetworkDescription.pdf Network Description]
*[http://ccy.zcu.cz/files/MS2_2015/Lectures/Lecture2b_2015.pdf LECTURE 1 (DES intro)]
*[http://ccy.zcu.cz/files/MS2_2014/Lectures/Lecture3_2014.pdf LECTURE 2 (DES observers, composition, and control)]
*[[Courses/Modelování a Simulace II - 2014/EXERCISE 1 - 2014|EXERCISE 1]]
*[[Courses/Modelování a Simulace II - 2014/EXERCISE 2 - 2014|EXERCISE 2]]
*[[Courses/Modelování a Simulace II - 2018/Assignment 1|ASSIGNMENT 1]]
*[http://ccy.zcu.cz/files/MS2_2014/Lectures/Lecture4_2014.pdf LECTURE 3 (Discrete state Markov Chains)]
*[[Media: MarkovChains_supplement.pdf|LECTURE 3 (supplement)]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture6_MonteCarlo.pdf LECTURE 4 (Monte Carlo Method)]
*[[Courses/Modelování a Simulace II - 2014/EXERCISE 3 - 2020|EXERCISE 3]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture7_MCMC.pdf LECTURE 5 (MCMC)]
*[[Courses/Modelování a Simulace II - 2017/EXERCISE 4|EXERCISE 4]]
*[http://ccy.zcu.cz/files/MS2_permanent/Lectures/Lecture8_Validation.pdf LECTURE 6 (Validation)]
*[[Courses/Modelování a Simulace II - 2017/EXERCISE 3|EXERCISE 5]]
*[[Courses/Modelování a Simulace II - 2020/Final Project|FINAL PROJECT]]

File:MS2-2022 syllabus en.pdf

2022-09-29T09:43:59Z

Georgiev:

Courses/Modelování a Simulace II - 2020/Final Project

2022-09-29T09:41:34Z

Georgiev:

Below you will find the PDF file describing the final project.

Due date: 18.1.2022

You are expected to provide not only the Monte Carlo estimate but also all supporting analysis that validates your MCMC algorithm.

----
Q&A

1. Question: I don't understand the purpose of the f array.

Answer: The f array gives you the frequencies of data points in a given block of the parameter space. And you use this in calculating your acceptance probability. So that probability of acceptance is equal to min(1,Fnew/Fold).

2. Question: I am getting the error message: Unable to perform assignment because the left and right sides have a different number of elements.

Error in updateFSA (line 13)
qc(j) = executeEvents(FSA{j},s(i),qc(j));

Error in NetworkSimRun (line 99)
qSupnew = updateFSA(FSAsup,enew,qSupc);

Answer: need to check your FSA files.

3. Question: How do we compute the error?

Answer: The data set alone will not give you an accurate estimate. You must generate more samples. Then you have three methods by which you can compute the error: z-score, t-score, boostrap. Which ever method you use, justify your answers. Recall the z-score assumes the sample standard deviation is the same as the actual standard deviation. The t-score and the z-score both depend on the central limit theorem.

----

Download the assignment description
[[File:2020_MS2_FinalProject.pdf]]

Please note that in problem 2, when comparing abnormal time estimated by MCMC to the abnormal time estimated from your simple Markov Chain model should only consider abnormal voltage at the second node (not the reactive power).

Assigned datasets (from the list below) will be mailed to you upon request (be email):
# DataSet100-01.mat
# DataSet100-02.mat
# DataSet100-03.mat
# DataSet100-04.mat
# DataSet100-05.mat
# DataSet100-06.mat
# DataSet100-07.mat
# DataSet100-08.mat
# DataSet100-09.mat
# DataSet100-10.mat
# DataSet100-11.mat
# DataSet100-12.mat
# DataSet100-13.mat
# DataSet100-14.mat
# DataSet100-15.mat

Courses

2022-09-29T09:30:18Z

Georgiev:

Courses

2022-09-29T09:29:25Z

Georgiev:

* Modelování a Simulace II - 2012 
* Modelování a Simulace II - 2013 
* Courses/Modelování a Simulace II - 2014|Modelování a Simulace II - 2014 
* Introduction to cellular system modeling - 2014 
* Introduction to cellular system modeling - 2015 
* [[Courses/Introduction to biocybernetics - 2015|Introduction to biocybernetics - 2015]] 
* [[Courses/Modelování a Simulace II - 2015|Modelování a Simulace II - 2015]] 
* [[Courses/Introduction to cellular system modeling - 2016|Introduction to cellular system modeling - 2016]] 
* [[Courses/Modelování a Simulace II - 2016|Modelování a Simulace II - 2016]] 
* [[Courses/Introduction to cellular system modeling - 2017|Introduction to cellular system modeling - 2017]] 
* [[Courses/Modelování a Simulace II - 2017|Modelování a Simulace II - 2017]] 
* [[Courses/Introduction to cellular system modeling - 2018|Introduction to cellular system modeling - 2018]] 
* [[Courses/Modelování a Simulace II - 2018|Modelování a Simulace II - 2018]] 
* [[Courses/Introduction to cellular system modeling - 2019|Introduction to cellular system modeling - 2019]] 
* [[Courses/Modelování a Simulace II - 2020|Modelování a Simulace II - 2020]] 
* [[Courses/Introduction to cellular system modeling - 2019|Introduction to cellular system modeling - 2020]] 
* [[Courses/Introduction to cellular system modeling - 2021|Introduction to cellular system modeling - 2021]]
* [[Courses/Modelování a Simulace II - 2020|Modelování a Simulace II - 2022]]

Courses

2022-09-29T09:29:12Z

Georgiev:

* Modelování a Simulace II - 2012 
* Modelování a Simulace II - 2013 
* Courses/Modelování a Simulace II - 2014|Modelování a Simulace II - 2014 
* Introduction to cellular system modeling - 2014 
* Introduction to cellular system modeling - 2015 
* [[Courses/Introduction to biocybernetics - 2015|Introduction to biocybernetics - 2015]] 
* [[Courses/Modelování a Simulace II - 2015|Modelování a Simulace II - 2015]] 
* [[Courses/Introduction to cellular system modeling - 2016|Introduction to cellular system modeling - 2016]] 
* [[Courses/Modelování a Simulace II - 2016|Modelování a Simulace II - 2016]] 
* [[Courses/Introduction to cellular system modeling - 2017|Introduction to cellular system modeling - 2017]] 
* [[Courses/Modelování a Simulace II - 2017|Modelování a Simulace II - 2017]] 
* [[Courses/Introduction to cellular system modeling - 2018|Introduction to cellular system modeling - 2018]] 
* [[Courses/Modelování a Simulace II - 2018|Modelování a Simulace II - 2018]] 
* [[Courses/Introduction to cellular system modeling - 2019|Introduction to cellular system modeling - 2019]] 
* [[Courses/Modelování a Simulace II - 2020|Modelování a Simulace II - 2020]] 
* [[Courses/Introduction to cellular system modeling - 2019|Introduction to cellular system modeling - 2020]] 
* [[Courses/Introduction to cellular system modeling - 2021|Introduction to cellular system modeling - 2021]]
 
* [[Courses/Modelování a Simulace II - 2020|Modelování a Simulace II - 2020]]

Courses

2022-09-29T09:28:38Z

Georgiev:

* Modelování a Simulace II - 2012 
* Modelování a Simulace II - 2013 
* Courses/Modelování a Simulace II - 2014|Modelování a Simulace II - 2014 
* Introduction to cellular system modeling - 2014 
* Introduction to cellular system modeling - 2015 
* [[Courses/Introduction to biocybernetics - 2015|Introduction to biocybernetics - 2015]] 
* [[Courses/Modelování a Simulace II - 2015|Modelování a Simulace II - 2015]] 
* [[Courses/Introduction to cellular system modeling - 2016|Introduction to cellular system modeling - 2016]] 
* [[Courses/Modelování a Simulace II - 2016|Modelování a Simulace II - 2016]] 
* [[Courses/Introduction to cellular system modeling - 2017|Introduction to cellular system modeling - 2017]] 
* [[Courses/Modelování a Simulace II - 2017|Modelování a Simulace II - 2017]] 
* [[Courses/Introduction to cellular system modeling - 2018|Introduction to cellular system modeling - 2018]] 
* [[Courses/Modelování a Simulace II - 2018|Modelování a Simulace II - 2018]] 
* [[Courses/Introduction to cellular system modeling - 2019|Introduction to cellular system modeling - 2019]] 
* [[Courses/Modelování a Simulace II - 2020|Modelování a Simulace II - 2020]] 
* [[Courses/Introduction to cellular system modeling - 2019|Introduction to cellular system modeling - 2020]] 
* [[Courses/Introduction to cellular system modeling - 2021|Introduction to cellular system modeling - 2021]]
* [[Courses/Introduction to cellular system modeling - 2019|Introduction to cellular system modeling - 2022]]

File:ZMB-Lecture-3-PolypeptideSyntax.pdf

2022-04-07T10:54:46Z