DATA SCIENCE - MACHINE LEARNING - 2025

TABLE OF CONTENTS

• 00_Course_Intro
• 01_Python_Basic
• 02_Python_class_OOP
• 03_Vector_Matrix_Sparse

00_Course_Intro

• 00_Course_Intro_part_01: 1st/11/2025
  • bioinformatics and machine learning application
• 00_Course_Intro_part_02: 1st/11/2025
  • code demonstrations (1)
• 00_Course_Intro_part_03: 8th/11/2025
  • code demonstrations (2)
  • Bonus: Aristotle and De Anima
• 00_Course_Intro_part_04: 8th/11/2025
  • environment setup: conda, vscode, libraries installation
  • git & github

01_Python_Basic

• 01_Python_Basic_part_01: 15th/11/2025
  • print()
  • comments
  • format string
  • variables
  • type conversion
  • operators
  • git status/add/commit/push
  • Bonus: Immanuel Kant's Deontology, Jeremy Bentham utilitarism
• 01_Python_Basic_part_02: 22nd/11/2025
  • input() and eval()
  • import math; import random
  • dir()
  • string slicing, raw string, repr()
  • string methods
• 01_Python_Basic_part_03: 6th/12/2025
  • chr() and ord()
  • Regular Expression (re, regex)
• 01_Python_Basic_part_04: 13th/12/2025
  • datetime
  • date
  • timedelta
  • pytz (timezone handling)
  • Bonus: Schopenhauer will-representation, Sartre existentialism, Levi-Strauss structuralism
• 01_Python_Basic_part_05: 20th/12/2025
  • time module
  • calendar module
  • Bonus: the story of Wang Zhaojun
• 01_Python_Basic_part_06: 27th/12/2025
  • if-elif-else
  • match-case
  • try-except-assert-else
  • Bonus: Logic, Syllogism, Induction, Deduction, Abduction, Sophism, David Hume empiricism
• 01_Python_Basic_part_07: 3rd/01/2026
  • for loop, zip(), enumerate()
  • while loop
  • break-continue-pass
  • Bonus: Logic in cancer therapy, reasonable and true, black swan paradox
• 01_Python_Basic_part_08: 10th/01/2026
  • List
  • Tuple
  • Bonus: Francis 1 of France and Leonardo Da Vinci
• 01_Python_Basic_part_09: 17th/01/2026
  • Set - Frozenset
  • Dictionary
  • Bonus: Concept, Intension, Extension, Definition of a concept: What is brave? What is beauty? What is love?
• 01_Python_Basic_part_10: 24th/01/2026
  • Unpacking operators * and **
  • Progress Bar: alive_progress, tqdm
  • Bonus: Dialectic and GAN; Critical thinking: Equivocation, Does AI have conciousness? Why does God create Evil? How reincarnation works in Buddhism without a soul?
• 01_Python_Basic_part_11: 1st/02/2026
  • Progress Bar: tldm (upgraded version of tqdm)
  • TXT files handling
  • CSV and TSV files handling
  • JSON files handling
  • XML files handling
  • BeautifulSoup4: static web scrapping
• 01_Python_Basic_part_12: 8th/02/2026
  • os: operating-system dependent functionalities (os.getcwd(), os.chdir(), os.system(), etc.)
  • shutil: more shell utilities (shutil.copy(), shutil.move(), shutil.rmtree(), etc.)
  • Bonus: monitoring GPU usage (nvidia-smi, nvitop, amd-smi, amdgpu_top)
• 01_Python_Basic_part_13: 15th/02/2026
  • os.path: path handling with os.path submodule
  • pathlib.Path: path handling with Path object (OOP style)
• 01_Python_Basic_part_14: 01st/03/2026
  • PathObject.iterdir()
  • PathObject.glob(): pattern search
  • PathObject.rglob(): pattern search (recursive)
  • PathObject.walk()
  • (LEGACY) glob module
• 01_Python_Basic_part_15: 8th/03/2026
  • def, *args, **kwargs: User-defined function
  • Module and Package, __pycache__, __init__.py, if __name__ == "main"
  • lambda: Anonymous function
  • map() and starmap(): mapping iterables to a function
• 01_Python_Basic_part_16: 15th/03/2026
  • filter(): built-in function for boolean indexing in Python
  • counter(): built-in function for counting frequency (number of repeats) in Python
  • itertools: built-in module for handling discrete math and set like product(), permutations(), combinations()
  • Bonus: broadcasting-vectorization-parallel computing, reduction and scatter/gather, cartesian product and mendelian genetics, distance matrix and O(N^2)
• 01_Python_Basic_part_17: 22th/03/2026
  • multithreading: concurency computing
  • multiprocess: parallel computing with multiple CPU cores
  • Bonus: device-agnostic ML and DL libraries (tinygrad and Burn), GPU kernel, a glance at Rust programming language, probability and stochastic gradient descent
• 01_Python_Basic_part_18: 29th/03/2026
  • subprocess: running external commands and scripts in Python
  • plumbum: like subprocess but with more readable syntax
• 01_Python_Basic_part_19: 05th/04/2026
  • ArgumentParser, main() function: parsing inputs from terminal, make Python file a command line
  • logging, loguru, logger: manipulate log messages and create log files
  • warnings: handle warnings message in Python
  • VSCode debugging demonstration
  • Bonus: OpenCode and agentic AI workflow; A glance at Rust code; The story of Rust's creator

02_Python_class_OOP

• 02_Python_class_OOP_part_01: 12th/04/2026
  • class, instance and object introduction
  • __init__, self, instance attribute
  • __dict__, __repr__, class attribute
  • magic methods: __new__, _len__, __getitem__, etc (and many more)
  • Bonus: RustPython, NuShell for data wrangling right in the terminal!!!
• 02_Python_class_OOP_part_02: 19th/04/2026
  • yield, next, iter
  • Iterator, Iterable, Generator
  • Use __next__ and __iter__ to create custom Iterable and Iterator
  • Example: create MiniLoader to load big 3D structures efficiently
  • The concept of DataLoader, shuffle and collate_fn
  • Bonus: ipython, bpython, setup alias linked to executable file, use conda without "conda activate"
• 02_Python_class_OOP_part_03: 26th/04/2026
  • More about DataLoader: collate_fn (flat style), indices shuffle
  • Diffusion model: complete input and incomplete input
  • Something about GaussianMixture model
  • Some plotly demonstrations
• 02_Python_class_OOP_part_04: 10th/05/2026
  • Some decorators in Python
  • @classmethod and @staticmethod
  • setter: @property
  • getter: @<property_name>.setter
  • Private attributes and methods (self._attribute````, _method(self), self.__attribute, __method(self)```)
  • Inhereitance, super().__init__()
  • Principles of Python OOP: Encapsulation, Abstraction, Inheritance, Polymorphism
  • rectangle_project: capstone project for 01_Python_Basic and 02_Python_class_OOP
  • Bonus 1: Zed - a blazing fast and clean editor written in Rust, disable all AI features with one button
  • Bonus 2: Positron - something like Rstudio but for Python
  • Bonus 3: starship and GruvboxRainbow, how to make the shell terminal look prettier

03_Vector_Matrix_Sparse

• 03_Vector_Matrix_Sparse_part_01: 24th/05/2026
  • create a vector: np.array(), np.arange(), np.random, np.choice(), np.choose()
  • read vector from npy, txt and csv files: np.load(), np.loadtxt(), np.genfromtxt()
  • attributes of a vector: ndim, shape, size, dtype, itemsize, nbytes
  • copy, type conversion
  • reshape, transpose, squeeze and expand_dims a vector
  • stack and concatenate multiple vectors
  • split a vector
  • repeat and unique
• 03_Vector_Matrix_Sparse_part_02: 31st/05/2026
  • indexing, fancy indexing, slicing, vector modification
  • mask array, boolean indexing (conditional filtering), ```np.isin()``
  • np.nditer()
  • sorting, argsort, searching
  • math methods
  • logical methods
• 03_Vector_Matrix_Sparse_part_03: 07th/06/2026
  • string handling with modules numpy.strings
  • np.apply_along_axis(), np.vectorize(), np.frompyfunc()
  • chaining methods
  • convert Numpy vector to other data structures
  • save numpy vector to files
• 03_Vector_Matrix_Sparse_part_04: 14th/06/2026
  • create a 2D matrix (and nD array): np.array(), np.arange(), np.random, np.choice(), np.choose()
  • read arrays from npy, txt and csv files: np.load(), np.loadtxt(), np.genfromtxt()
  • attributes of a 2D matrix: ndim, shape, size, dtype, itemsize, nbytes
  • copy, type conversion