LSTM is dead. Long lives transformers.

 

LSTM is hard to training, and generally not transferable. So, LSTM typically require a new labeled training set for a new task. 

https://youtu.be/S27pHKBEp30

cpsc4180 data science programming, Python covid19 analysis

    == pre-class to do: 

calendar email invitation: including guests;  done. 

socrative questions (midterm exam, questions on contents from last lecture ).  done

update Canvas course materials, update learning objectives. assignments as needed.   done

* make sure grades are NOT shown on Canvas. 

Test-run code:  ipynb done

learning objectives:  updated on canvas, done

== In-class to do: 

clean up desktop space, calendars": 

ZOOM, live transcript (start video recording).  Turn the computer speaker on. 

Socrative sign in 

* go over python COVID19 data analysis

* start breakroom, ask students to explain their final projects to others. After the breakout room discussion, ask a student to explain other students topic, what are the interesting part of them. 

Mpro 3CL mutation structure and MD studies

 

https://pubs.acs.org/doi/10.1021/acs.jcim.0c00634

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7518256/

https://pubs.acs.org/doi/10.1021/acs.jcim.0c00634

https://www.biorxiv.org/content/10.1101/2021.07.17.452787v1.full

https://www.nature.com/articles/s41598-021-91585-6

3CL structure

 

It seems to me that 7JST is the apo form structure of the reference 3CL: https://www.rcsb.org/structure/7JST

A PubMed reference is https://pubmed.ncbi.nlm.nih.gov/33795671/

 

Spring 2022 courses, textbooks

 

CPSC 4900 CRN 20692 Software Engineering, Instructor Hong Qin

Title: Engineering Software Products: An Introduction to Modern Software Engineering
Year: 2020

Imprint: Pearson
Author: Ian Sommerville
Isbn10: 013521064X
Isbn13: 9780135210642
Item id: PGM2133348

CPSC 2100 CRN 20244 Software Design and Development

Textbook: 

Introduction to Computation and Programming Using Python, third edition: With Application to Computational Modeling and Understanding Data 3rd Edition

by John V. Guttag (Author)

• Publisher ‏ : ‎ The MIT Press; 3rd edition (January 5, 2021)
• Language ‏ : ‎ English
• Paperback ‏ : ‎ 496 pages
• ISBN-10 ‏ : ‎ 0262542366
• ISBN-13 ‏ : ‎ 978-0262542364
• 
  

CPSC 4180 data science, October 25, Pandas

   == pre-class to do: 

calendar email invitation: including guests;  done. 

socrative questions (midterm exam, questions on contents from last lecture ).  done

update Canvas course materials, update learning objectives. assignments as needed.   done

* make sure grades are NOT shown on Canvas. 

Test-run code:  ipynb done

learning objectives:  updated on canvas, done

== In-class to do: 

clean up desktop space, calendars": 

ZOOM, live transcript (start video recording).  Turn the computer speaker on. 

Socrative sign in 

* start breakroom, ask students to explain their final projects to others. After the breakout room discussion, ask a student to explain other students topic, what are the interesting part of them. 

* go over python pandas

* use Kindle textbook

Hadamard gate

 Hadamard gate puts a quantum bit (qubit) into superposition. 

E coli GWAS

 E. coli GWAS with additional data sets

output.gd seems to be files that HG used grep to extract SNP 

Hamiltonia operator

 https://en.wikipedia.org/wiki/Hamiltonian_(quantum_mechanics)

It refers to the total energy of a system (both kinetic and potential). Its energy spectrum or sets of energy eigenvalues is a set of possible outcomes of measurements. This is the foundation of quantum theory. 

probability 4 data science

 

https://probability4datascience.com/python01.html

Python, MATLAB, Julia, R

uniformed service university

 

https://www.usuhs.edu/research

4180 data science, final project, python numpy

  == pre-class to do: 

calendar email invitation: including guests;  done. 

socrative questions (midterm exam, questions on contents from last lecture ).  done

update Canvas course materials, update learning objectives. assignments as needed.   done

Test-run code:  ipynb done

learning objectives:  updated on canvas, done

== In-class to do: 

clean up desktop space, calendars": 

ZOOM, live transcript (start video recording).  Turn computer speaker on. 

Socrative sign in 

* start breakroom, ask students to explain their final projects to others. After the breakout room discussion, ask a student to explain other students topic, what are the interesting part of them. 

* go over python lecture 3. Numpy. 

cpsc 4180 project, python lecture 2, data types etc

  == pre-class to do: 

calendar email invitation: including guests;  done. 

socrative questions (midterm exam, questions on contents from last lecture ).  done

update Canvas course materials, update learning objectives. assignments as needed.   done

Test-run code:  ipynb done

learning objectives:  updated on canvas, done

== In-class to do: 

clean up desktop space, calendars": 

ZOOM, live transcript (start video recording).  Turn computer speaker on. 

Socrative sign in 

* start breakroom, ask students to explain their final projects to others. After the breakout room discussion, ask a student to explain other students topic, what are the interesting part of them. 

* go over python lecture 2. 

COVID19 mutation websites

 

https://covidcg.org/?tab=group

cpsc 4180, python day 1, final project topics

 == pre-class to do: 

calendar email invitation: including guests;  done. 

socrative questions (midterm exam, questions on contents from last lecture ).  done

update Canvas course materials, update learning objectives. assignments as needed.   done

Test-run code:  ipynb done. 

learning objectives:  updated on canvas, done

== In-class to do: 

clean up desktop space, calendars": 

ZOOM, live transcript (start video recording).  Turn computer speaker on. 

Socrative sign in 

* Remind student to submit topics for final project

* install Anaconda; Jupyter-Notebook; 

student coding project

 

phone: put a ring on finger

satellite image of a house -> estimate area

Redesign a known software from Android store/ Apple store, website

The Top 10 Programming Project Ideas for Beginners

• 1) Build a Multi-Page Responsive Website.
• 2) Redesign an Existing Website Template.
• 3) Design a Small JavaScript Game.
• 4) Create a Simple Application.
• 5) Random Number Generator.
• 6) Web Scraping Using Python.
• 7) Build a Working Chess Game.

4180 midterm project review

 

breakout rooms, 

each group do a group presentation with one student leader. 

go over student videos

collect sample student videos and codes. 

midterm grade report, fall 2021, deadline Oct 13 10am

 

 

Midterm grading is open for Fall 2021 Full Term (202140)  and will remain open until Wednesday, October 13th at 10am. It is important to your students that the mid-term grade is entered on time because the last day for an official withdrawal from any class with a W for the Full Term is Monday October 25^th.    

 

To enter grades go to our main webpage https://www.utc.edu/, select “Tools” in the upper right hand corner then select “MyMocsNet”. Enter your UTCID and Password and hit enter, then click on Login to My MocsNet.

• ­Choose the “Self-Service Banner” tab at the top of webpage (Listed under My Sites and your name)
• Under Faculty Services – select “Midterm and Faculty Grade Submission” 
• This will take you directly into the grading area of Self Service Banner
• Select “Midterm Grades”

 

Access to a tutorial on how to download grades from Canvas and import them into Banner, can be found here.

 

Click on the arrow next to the search box for grading guidelines and a link to the training. Please note you do not have to enter a last date of attendance for midtermgrades.  

  

PH term2 course plans

 

PH term2 course plans

Individual study: 

 AlphaFold; recent research in object segmentation and tracking; recent trends in deep learning; 

Doctoral Research: MG's project, understand the codes, data sets (training data sets), help draft and revise manuscripts. 

ncbi third party login

 

https://ncbiinsights.ncbi.nlm.nih.gov/my-ncbi-login-transition-tips/

cpsc4180 data science, midterm , Q&A

midterm discussion 1

files submission issues: size limit? 

python part: required for computer science students. bonus points for biology students. 

Coding #2 pie chart, my example has only 9 clades.