Reading Notes
Personal reading notes for academic books, organized by [Year]-[Book Title]-[Author] folder naming convention.
Books
2017 - The Mathematics and Mechanics of Biological Growth - Goriely
Author: Alain Goriely (University of Oxford) | Publisher: Springer, Interdisciplinary Applied Mathematics Vol. 45
Mathematical theory of biological growth and morphoelasticity. Covers 1D (rods/fibers), 2D (shells/membranes), and 3D (general theory) approaches to growth kinematics and mechanics.
Status: 17 chapters
2002 - Mathematical Biology I - Murray
Author: J.D. Murray, FRS (University of Oxford) | Publisher: Springer, 3rd edition, 2002 | Series: Interdisciplinary Applied Mathematics Vol. 17
Classic introduction to mathematical biology. Focuses on deterministic models: population dynamics, predator-prey systems, epidemiology, enzyme kinetics, chemical oscillations, reaction-diffusion waves, and fractals.
Status: 14 chapters + book summary
Also see:
2002-Mathematical-Biology-Murray/Murray - Mathematical Biology/— same book, alternative folder structure with 14 chapters + summary
2002 - Mathematical Biology II - Murray
Author: J.D. Murray, FRS (University of Oxford) | Publisher: Springer, 3rd edition, 2003 | Series: Interdisciplinary Applied Mathematics Vol. 18
Second volume focusing on spatial models and pattern formation. Explores how biological patterns — from leopard spots to vascular networks to epidemic wave fronts — emerge from reaction-diffusion and mechanochemical theory.
Status: 14 chapters + book summary
2009 - Mathematical Physiology - Keener
Author: James Keener (University of Utah) | Publisher: Springer, 3rd edition, 2009 | Series: Interdisciplinary Applied Mathematics Vol. 29
Systems physiology approached through dynamical systems and nonlinear dynamics. Covers membrane dynamics, cardiac physiology, neural excitability, calcium dynamics, blood flow regulation, and stroke physiology. Emphasizes the interplay between structure and function at multiple scales.
Status: 20 chapters + book summary
2009 - Causality - Pearl
Author: Judea Pearl (UCLA) | Publisher: Cambridge University Press, 2nd edition, 2009
Foundational text on causal inference. Establishes the mathematical framework linking probability theory and graph theory to causal reasoning. Covers Bayesian networks, d-separation, causal discovery algorithms (IC, IC*), and the do-calculus.
Status: 12 chapters + cross-reference indexes
2013 - Multi-Modality Atherosclerosis Imaging - Saba
Author: Luca Saba (University of Cagliari) | Publisher: Academic Press, 2013
Comprehensive survey of imaging modalities for atherosclerosis — ultrasound (US), computed tomography (CT), magnetic resonance (MR), positron emission tomography (PET), and hybrid fusion systems (PET/CT, PET/MR). Covers plaque characterization, stenosis quantification, vulnerable plaque detection, and clinical workflow integration.
Status: 29 chapters + book summary
2016 - Deep Learning - Goodfellow
Authors: Ian Goodfellow, Yoshua Bengio, Aaron Courville | Publisher: MIT Press, 2016 | ISBN: 978-0262035613
Comprehensive textbook in three parts: (I) Applied math & ML foundations, (II) modern deep networks, (III) deep learning research. Covers linear algebra, probability, optimization, regularization, CNNs, RNNs, autoencoders, VAEs, GANs, and more.
Status: 20 chapters + book summary
2018 - The Book of Why - Pearl
Author: Judea Pearl (UCLA) | Publisher: Basic Books, 2018
Accessible introduction to causal inference for a general audience. Introduces the Ladder of Causation (Association → Intervention → Counterfactual), the do-calculus, and the Causal Revolution. Draws on historical examples from Galton to modern machine learning.
Status: 10 chapters
2019 - Statistical Learning Methods - LiHang
Author: Li Hang | Publisher: 2019
Systematic introduction to statistical learning methods. Covers supervised learning (perceptron, SVM, decision trees, boosting) and unsupervised learning (clustering, dimensionality reduction). Establishes the unified framework of model + strategy + algorithm.
Status: 22 chapters
2015 - Decision Making Under Uncertainty - Kochenderfer
Author: Mykel J. Kochenderfer (MIT) | Publisher: MIT Press, 2015 | ISBN: 978-0262029254
Decision theory meets engineering: a rigorous introduction to sequential decision-making under uncertainty. Part I (ch.1-7) covers probabilistic models, decision theory, MDP/POMDP frameworks, model uncertainty and reinforcement learning, and cooperative agents. Part II (ch.8-12) applies these methods to video surveillance, speech processing, aircraft collision avoidance (ACAS X), unmanned aerial vehicles, and human-machine systems.
Status: 12 chapters + book summary
2022 - Vascular Biomechanics: Concepts, Models, and Applications - Gasser
Author: T. Christian Gasser (KTH Solid Mechanics, Department of Engineering Mechanics) | Publisher: Springer, 2022 | Pages: 622
Comprehensive introduction to vascular biomechanics spanning the full range from modeling philosophy to clinical applications. Chapters cover: (1) modeling in bioengineering (bottom-up/top-down, white/black/gray-box, sensitivity analysis, verification, validation, statistics, AI); (2) circulatory system (macro/microcirculation, WindKessel models, vessel networks, transcapillary exchange); (3) continuum mechanics (kinematics, stress, constitutive modeling, governing laws, damage/failure); (4) finite element method (shape functions, variational principles, FE equations, constraints, Newton-Raphson, arc-length); (5) conduit vessels (histology, anisotropic hyperelasticity, Yeoh/Fung/GOH models, residual stress, visco-hyperelasticity, damage); (6) hemodynamics (blood composition, rheology, viscosity models, hemolysis, Navier-Stokes, Womersley flow); (7) vascular wall as active entity (vasoreactivity, SMC contraction, arteriogenesis, growth & remodeling).
Status: 7 chapters + book summary + 35-term glossary
2026 - Transcriptomics in Atherosclerosis - Devaux
Author: (Ed.) | Publisher: 2026
Frontiers in transcriptomics applied to atherosclerosis: single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, bulk RNA-seq analysis, cell-type deconvolution, gene regulatory networks, and endothelial-to-mesenchymal transition. Bridges molecular biology and systems pathophysiology of vascular disease.
Status: 18 chapters + book summary
Backup / Archive
Pearl_2009_Causality_bak
Earlier draft of notes for Pearl's Causality (2009), prior to reorganization. Contains 12 chapters of notes.