Paired Reading Program
Some topics of interest are here, and the list will get longer.
Mathematics, Physics, Biology, AI, Arts, Psychology, and Fun Activities.
Mathematics:
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The Mathematical Principles of Natural Philosophy - Sir Isaac Newton (1846)
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Mathematical Thought, from ancient to modern times, by Morris Kline, volumes I, II, III.
- 5 Greatest Mathematics Lectures Of All Time: free online lectures. The lectures that will make you fall in love with math.
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Infinite Powers, how calculus retreats the secrets of the Universe, by Steven Strogatz, New York Times Bestseller
- Mathematical History: The Story on Hamilton
- All the Mathematics You Missed, but need to know for graduate school, by Thomas A. Garrity
- How Not to Be Wrong, the power of mathematical thinking, by Jordan Ellenberg
- It must be Beautiful, great equations of modern science, edited by Graham Farmelo
- The Art of Statistics, how to learn from data, by David Spiegelhalter, New York Times Bestseller
- 300 Years of Optimal Control: From the Brachystochrone to the Maximum Principle
- The Moscow Puzzles: 359 Mathematical Recreations (Dover Recreational Math) , by Boris A. Kordemsky
- Problems in Mathematical Analysis by Deminovich (see PDF in D2L Content)
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YoutTube: The Riemann Hypothesis, Explained
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Understanding Fourier Transformation (graphs & animation):
English version with animation: https://www.jezzamon.com/fourier/index.html
Github: https://github.com/Jezzamonn/fourier
The Fourier Transform, explained in one sentence - Understanding Singular Value Decomposition (SVD) and its physics meaning
- From quadratic equations to Gauge Field Theory by Zexian Cao (use Google Translate to read)
Lecture: Article: - Why e, the Transcendental Math Constant, Is Just the Best
- Resources for Careers in Applied Mathematics
- Kevin Knudson - My Favorite Theorems (podcast on Theorems)
- Understanding Gradient, Divergence, and Curl:
Gradient 1,
Gradient 2,
Divergence,
Curl,
Three in All - Understanding Maxwell's Equations from different perspective:
Understanding Maxwell's Equations 1 (Source & Curl),
Understanding Maxwell's Equations 2 (Differential Form),
Understanding Maxwell's Equations 3 (Integral Form),
Fiber Bundle and Maxwell's Equations ,
Derive Magnetic Waves from Maxwell's Equations - ComplexNumbers and Complex Measurements
Help to Learn Differential Equations, Linear Algebra, Calculus, Precalculus/College Algebra Well: - Math Apps:
Differential Equations App: Slopes: A Differential Equations Graphing Environment
PPlane (Alun Lloyd: NCSU) dfield &pplane (UNM) XPPAUT (is a tool to solve
differential equations, difference equations, delay equations, functional equations, boundary value problems, and
stochastic equations) - Partial Differential Equations App: Waves: Partial Differential Equations
- SIMIODE (Systemic Initiative for Modeling Investigations & Opportunities with Differential
Equations)
Modeling Scenarios - Inquiry-Oriented Differential Equations
- Make Eigenvalues Resonate
- Linear Algebra: A Free text for a standard US undergraduate course
- Understanding Linear Algebra: An open-access linear algebra textbook, David Austin. 2022
- Matrix World: Drawn by Kenji Hiranabe with the help of Prof. Gilbert Strang Chinese version
- The Big Six Matrix Factorizations: by Nich Higham
- Celebrating the Cycloid by Ry Sullivan
- Desmos: Online Graphing Calculator.We're on a mission to help every student learn math and love learning math.
- Application of differentiations in neural networks
- How Infinite Series Reveal the Unity of Mathematics | Quanta Magazine
- Active Prelude to Calculus, Active Calculus, and Active Calculus Multivariable
- Representation theory
Optimization and Control - Physics-informed neural networks for PDE-constrained optimization and control
- Regularized Newton Method with Global O(1/k2) Convergence
- Convex Optimization: Algorithms and Complexity
- Optimization inequalities cheatsheet, By Fabian Pedregosa.
Matlab Resources
- Quick Start Guide to Teaching with MATLAB
- Calculus-Integrals - Curriculum Module
- Cheat Sheets for Using MATLAB with Python
- Importing Models from TensorFlow, PyTorch, and ONNX to Matlab
- Workshop: Using MATLAB with Python
- Careers at MathWorks
Probablity and Statistics
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Probability Theory: The Logic of Science, by E.T. Jaynes
- A short history of equations
- 29 Statistical Concepts Explained in Simple English
- "Probabilistic Machine Learning" - a book series by Kevin Murphy, GitHub codes
- Introduction to Probability for Data Science by Stanley H. Chan 2021
- Free Textbook: Probability Course, Harvard University (Based on R)
- Introduction to Modern Statistics: by Mine Çetinkaya-Rundel and Johanna Hardin, 2022.
- 100 Free Tutorials for learning R: To view the tutorials: TOP 100 R TUTORIALS : STEP BY STEP GUIDE
- Statistics and Machine Learning in Python
- Baysian Method (Intro)
- 13 Probability Distribution with GitHub codes
- Linear regression in Python: Using numpy, scipy, and statsmodels
- Outlier Detection Techniques
- Two more books:
- Books from Clifford Pickover
- The Real Analysis Lifesaver: All the Tools You Need to Understand Proofs
MISC - Squaring the circle (Ah?!)
- Misconceptions about the Golden Ratio
- Power-law distributions in empirical data
- Triangular number patterns The powers of the multiplication table
- A stroke of genius: striving for greatness in all you do by R.W. Hamming (Turing Award winner)
- Incorporate the History of Mathematics in Teaching
- The Art of Teaching Math and Science: Series: PENCILS DOWN: EXPERIMENTS IN EDUCATION Quanta Magazine
- The Value of Science: by Richard P. Feynman, Format's Library
- Abubakar Abid Statement of Purpose PhD (MIT Biomedical Program)
- Order and Chaos: The Century Struggle of Set Theory
Math Bio: - The Brain Is a Dynamical System: SIAM 07-06-2022
- MatCont: ACM paper Tutorial by Hil Meijer 2016Intalling MatCont
- Estimating Time-Dependent Disease Transmission Intensity using Reported Data: An Application to Ebola and Selected Public Health Problems,
- The Mathematical Machinery That Makes Cells Move, SIAM News 09/01/2022.
- MAS377 Mathematical Biology by Dr. Alex Best 2021.
Physics:
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The Feynman Lectures on Physics
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Quantum Field Theory: As Simply as Possible, by A. Zee
- Introduction to Quantum Mechanics in pdf
- 5 Best Books To Study Quantum Mechanics | by Sunny Labh | Mar, 2022 | Medium
- 3 Books You Must Read As a Physics Enthusiast
- What is Quantum Mechanics (a great Intro)
- Check/Work on The Interactive Electromagnetism simulator App to provide feedback and users' experience to the developer
- Physics Review extra resources
BioPhysics: - Physics of Life: National Academie of Science, Engineering, Medicine
- Physical Biology of the Cell 2nd Edition
- Random Walks in Biology, by Howard C. Berg
- Stochastic Processes in Cell Biology, by Paul C. Bressholf
Biology:
- Immune: a journey into the mysterious system that keeps you alive, by Philipp Dettmer, creator of
@Kurz_Gesagt, New York Times bestseller, creator of Kurzgesagt - In a Nutshell, a famous YouTube channel with millions of viewers.Why Is Inflammation a Dangerous Necessity? Podcast with Steven Strogatz
- SARS-Cov-2: COVID-19 – A vascular disease, The Tangled History of mRNA Vaccines
- Cellular Cancer Biology Imaging Research(NCI)
- Books by Edward Wilson (1929-2021):
- Siciobiology: The new Synthesis, 1975.
- Naturalist, 1994
- Journey to the Ants, 1994; Tales From the Ant World, 2020
- Consilience: The Unity of Knowledge, 1998
- The Diversity of Life, 1999
- The Future of Life, 2002
- Letters to a Young Scientist, 2013
- The Meaning of Human Existence, 2014
- Half-earth, 2016 - Rosalind Franklin: The Dark Lady of DNA
- Cell Biology by the Numbers (free online book) BioNumbers database
- Janeway's Immunobiology Tenth Edition: 2022
- MIT Open Learning Library: Getting up to Speed in Biology
- edX: Introduction to Biology - The Secret of Life
- Modeling Life: The Mathematics of Biological Systems: Alan Garfinkel, Jane Shevtsov, Yina Guo, 2017. PDF
- A Calculus of Purpose: Arthur D Lander 2004. PDF
- Systems Biology:A New Biology for the 21st Century, 2009.National Research Council.
- The Nematode Game: was inspired by C. elegans locomotion, and built the “Nematode Game”! It’s like snake, but the nematode moves in a sinusoidal way and pirouettes off in a random direction every once in a while-so it can be harder than you think!
- Journal of Medical Entomology Special Collection: Genetic Control of Mosquitoes
- Exploring the mosquito-arbovirus network: a survey of vector competence experiments, bioRXiv, 2022.
- A weekly column, Setting it Straight, exclusive to the Doherty Institute website.
- A database of infectious disease transmission trees for public use. University of Georgia PDF
- MTSU Lab Directory 2022
- Gene Editing
AI:
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Stanford CS 229 Machine Learning: YouTube (Andrew Ng), Coursera: Machine Learning Specialization by Andrew Ng
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CS230 Deep Learning by Andrew Ng, Coursera: Deep Learning Specialization
- Deep Learning, by Goodfellow, Bengio, Courville
- Geoffrey Hinton Coursera Machine Learning Course
- Machine Learning Becomes a Mathematical Collaborator
- Advice on building a machine learning career and reading research papers by Prof. Andrew Ng
- Python 3.10.5 documentation
- CS197 Harvard: AI Research Experiences - Lecture 3 – “Shoulders of Giants” Reading AI Research Papers, 2022.
Pranav Rajpurkar. Website https://cs197.seas.harvard.edu/
Books: - INTRODUCTION TO MACHINE LEARNING (Cambridge University Press)
- Deep Learning, By Ian Goodfellow, Yoshua Bengio and Aaron Courville, MIT
- MIT 6.S191 Introduction to Deep Learning
- Free Book: A Comprehensive Guide to Machine Learning (Berkeley University): PDF
- Interactive deep learning book with multi-framework code, math, and discussions. Adopted at 300 universities from 55 countries including Stanford, MIT, Harvard, and Cambridge.
- Prof. Gilles Louppe's Deep Learning 2022 Lectures on GitHub
- Learning Python: Mark Lutz, O'Reilley 2009.
- Python for data analytics, 3rd edition, Wes McKinney, the creator of Pandas library, 2022
- Foundations of Machine Learning, Mehryar Mohri, Afshin Rostamizadeh, Ameet Talwarkar, MIT Press 2012
- Mathematics of Machine Learning book by Tivadar
- Probabilistic Machine Learning: An Introduction, by Kevin Patrick Murphy, MIT Press, March 2022. 2023 Version
- Understanding Machine Learning: From Theory to Algorithms: By Shai Shalev-Shwartz and Shai Ben-David, Cambridge University Press
- Neural Diffential Equations (A Chinese Intro here)
- Topology, Differential Calculus, and Optimization Theory For Computer Science and Machine Learning (U Penn)
- Mathematical Foundations of Artificial Intelligence: Statistics and Machine Learning in Python
- The Math of Machine Learning – Berkeley University Textbook PDF
- DataScience Concepts and Practice (2nd Edition): bit.ly/36OwKc9. Vijay Kotu and Bala Deshpande 2019
Free Book: Foundations of Data Science (from Microsoft Research Lab) - Python for data analytics: The creator of Pandas library, Wes McKinney, Book
- Free Book: Data-Science-Concepts-and-Practice-2019: by Vijay Kotu and Bala Deshpande, bit.ly/36OwKc9
- Computational Cognitive Neuroscience, 4th edition, O’Reilly, R. C., Munakata, Y., Frank, M. J., Hazy, T. E., and Contributors
(2012). Computational Cognitive Neuroscience. Wiki Book, 4th Edition (2020). GitHub
resources available in the link.
Online Coureses - 70 Free Online Courses for Data Science to Advance Your Skills in 2022
- Open Machine Learning Collections
- Computer Science courses with video lectures (GitHub)
- Git ML YouTube Courses: A repository to index and organize the latest machine learning courses found on YouTube.
- Machine learning, in numpy: David Bourgin (Chinese version)
- 10 Best Udemy Courses for Machine Learning You Must Know in 2022
- Stanford <CS 25: Transformers United>, YouTube Reddit
- Michael Nilesen's page
Step-by-step Implementation - 100+ Machine Learning Projects in Python
- Gentle Dive into Math Behind Convolutional Neural Networks (CNN)
- Your First Deep Learning Project in Python with Keras Step-By-Step
- Complete Step-by-Step Gradient Descent Algorithm from Scratch
- One LEGO at a Time: Explaining the Math of how Neural Networks Learn with Implementation from Scratch
- Pen and Paper Exercises in Machine Learning, Michael U. Gutmann, 27 Jun 2022.
- Gradient Descent in Neural Network (small errors on independent and dependent variables, but still a good read)
- Nesterov’s Accelerated Gradient Descent
- An overview of gradient descent optimization algorithms
- Importing Models from TensorFlow, PyTorch, and ONNX to Matlab
- Cheat Sheets for Using MATLAB with Python
- Workshop: Using MATLAB with Python
- Nine Tool I Wish I Mastered before My PhD in Machine Learning, Aliaksei Mikhailiuk
Docker: Tutorial
Conda: Tutorial
Weights and biases: Tutorial
MLflow: Tutorial
GitHub: Tutorial
Screen: Tutorial
Inkscape: Tutorial
Streamlit: Tutorial
Lucidchart: Tutorial
Projects - Solved end-to-end Data Science projects, Get ready to use Data Science projects for solving real-world business problems
- Tiny Python Projects: by Ken Youens-Clark
- 140 Python Projects with Source Code by Priyesh Sinha
- 185 Python Projects with Source Code | by Aman Kharwal | Medium
- Fiji is an image processing package — a "batteries-included" distribution of ImageJ, bundling many plugins which facilitate scientific image analysis. YouTube on Fiji instructions
- Convolution
- Convolution Neural Networks (CNN) Optimization (in Chinese, with many good citations/sources in English)
- All the convolutions in Deep Learning (Chinese version)
A Comprehensive Introduction to Different Types of Convolutions in Deep Learning
GNN (Graph Neural Network)
Rediscovering orbital mechanics with machine learning: rediscover the Gravitational Law - Graph Neural Networks beyond Weisfeiler-Lehman and vanilla Message Passing
- How Graph Neural Networks (GNN) work: introduction to graph convolutions from scratch, Nikolas Adaloglou, 04-08-2021
Documentation - Jupyter Notebooks: Fundamentals of Machine Learning and Deep Learning
- Tensorflow 2.0 coding workshop notebooks
- Free 2,900-page Manual about Pandas - DataScienceCentral
- pandas documentation
- Python Data Science Handbook
- Python® Notes for Professionals book
- The Most Important Fundamentals of PyTorch you Should Know
- 100 Machine Learning Formulas
- 100+ Data Science, Deep Learning, AI & Machine Learning Cheat Sheet PDF
- Machine Learning with Applications in One Picture
- Neural Networks: The Backpropagation algorithm in a picture
- Machine Learning Technical Landscape
- The Black Magic of Deep Learning - Tips and Tricks for the practitioner
- 10 Popular Machine Learning Algorithms in a Nutshell
- 10 Commonly Used Activation Functions in Machine Learning
- 10 Machine Learning Algorithms In Python
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Supervised Clustering: How to Use SHAP Values for Better Cluster Analysis: Aidan Cooper 2022
Agent Based Modeling (ABM) - Mesa: Agent-based modeling in Python 3+
- AgentPy - Agent-based modeling in Python
- Git: /mesa
- Agent Based Models
- Understanding Agent Based Model with Python
- Introduction to Mesa: Agent-based Modeling in Python
Miscellaneous - Transformer models: an introduction and catalog — 2022 Edition
- How to Make Glowing Visualizations – Literally
- Great Plotting Tool: matplotlib: python plotting
- A Beginner’s Guide to Python for Cybersecurity
- Algorithms for decision making - MIT 2022
- Nine Tools I Wish I Mastered before My PhD in Machine Learning
- Asset2Vec: Turning 3D Objects into Vectors and Back
- Meta AI: Self-supervised learning
- Scraping Data from Google Search Using Python and Scrapy
- An open access book on scientific visualization using python and matplotlib
- Ten Signs of a Mature Data Science Capability
- Google AI Blog: Constrained Reweighting for Training Deep Neural Nets with Noisy Labels
- An elegant way to represent forward propagation and back propagation in a neural network
- Think Python
(online free version is available here) - Git:
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YouTube:
The Map ofQuantumComputing | Quantum Computers Explained,
Quantum Computers, Explained With Quantum Physics
Arts:
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Gardner's Art throught Ages: The Western Perspective, 16th edition
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Codex Atlanticus (Largest Existing Collection of Writings and Drawings of Leonardo Da Vinci)
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1001 Paintings You Must See Before You Die: revised and updated, by Stephen Farthing
- Algebraic Geometry in Architectural Design (use Google Translate to read, with 20 good references)
- Curiosa Mathematica: A COLLECTION OF BEAUTIFUL MATHEMATICS: ATTRACTIVE PICTURES AND FUN RESULTS
- Mathematical Art Galleries: Riemondrian Erick's Riemondrian Desmo Design
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Mathemalchemy: Cultural Programs of the National Academy of Sciences, Ingrid Daubechies and Dominique Ehrmann
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Calculus Art: Daily artwork created while teaching Integral Calculus. By Christopher Hanusa.
- Origami and the Structure of Materials
Philosophy:
Psychology:
- Depression: new treatments, new hope Nature Outlook
Biological factors that might contribute to clinical depression are coming into light. One increasingly supported theory is that depression is linked to a slowing of nerve growth — so measures that encourage neuron formation could help to stave off the condition. Obesity is both a cause and a consequence of depression, creating a vicious cycle. And the disruptions of ancient sleep patterns by electric lighting, smartphones and modern conveniences wreak havoc on mental health. Researchers around the world are finding links between depression and COVID-19, heart health, exercise and the use of social media.
Depression rates are rising fastest in young people. The condition is also disproportionately experienced by women, because the ebb and flow of hormones during menstruation, during pregnancy, after childbirth and during menopause can trigger biochemical cascades that result in the condition. These hormonal effects are very common around the time of menopause — yet the link is still ignored by many health-care professionals.
Antidepressant drugs are commonly prescribed as a treatment, but none is universally helpful. Other types of therapy are beginning to enter the scene, from psychedelic compounds such as psilocybin to implanted devices that zap the brain with pulses of electricity.
Others:
Fun Activities:
- Rubric Cubes,
- Metaverse Experiences
- Makers Space in the Library: 3D printing, Laser etching, Robots, AR
- Apps: Babble/Duolingo/Elloveo,
The Interactive Electromagnetism simulator App
Differential Equations App
Partial Differential Equations App - Gaming:
Kerbal Space Program: The Kerbal Math & Physics Lab (Christopher S. Vaughen)
The Nematode Game: a student designed game mimic Snake
