Disease modeling for public health
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Outbreak Simulation [in progress]

We:
Oct 13, 2025
50 min

Simulating Correlated Outbreak Parameters Using Copulas

I wanted to simulate synthetic outbreaks based on realistic distributions for the following three parameters:
Jul 25, 2025
7 min

Outbreak Simulation: Pre-emptive vs. Reactive Vaccination

When managing infectious disease risks such as cholera, limited vaccine supply often forces decision-makers to choose between pre-emptive and reactive vaccination campaigns. This post explores a cost-benefit model comparing the two strategies using analytical expressions…
Jun 28, 2025
4 min

Optimizing Vaccination Strategies: Pre-emptive vs. Reactive Vaccination

When managing infectious disease risks such as cholera, limited vaccine supply often forces decision-makers to choose between pre-emptive and reactive vaccination campaigns. This post explores a cost-benefit model comparing the two strategies using analytical expressions…
Jun 27, 2025
19 min

다니엘 베르누이의 천연두 연구: 최초의 감염병 수리모형

감염병
수리모형
역학
역사
18세기 유럽은 천연두(smallpox)의 그림자 아래 살고 있었다. 이 무서운 질병은 매년 수십만 명의 목숨을 앗아갔으며, 생존자들에게는 평생 지울 수 없는 흉터를 남겼다 (Razzell, 1977). 이런 상황에서 한 수학자가 수학적 사고를…
May 6, 2025
6 min

왜 수학으로 감염병을 설명하는가?

수학은 세상을 설명하는 언어다. [전통적인 text. 혹은 유클리드, 아르케메데스, ] 바이러스는 숫자를 모른다. 바이러스 어떤 수식을 계산해서 다음 날 환자수를 결정하지는 않을 것이다. 그런데 우리는 바이러스의 전파 과정을 숫자로 설명한다. 왜 그럴까?
Apr 18, 2025
4 min

The Ross-Macdonald Framework: Foundational Mathematical Models in Vector-Borne Disease Epidemiology

The mathematical modeling of infectious diseases has become an indispensable tool in modern epidemiology, guiding intervention strategies and policy decisions. While…
Apr 17, 2025
10 min

The Birth of Epidemic Modeling: Daniel Bernoulli and the Smallpox Inoculation Controversy

Mathematical modeling of infectious diseases is now a cornerstone of public health decision-making. During COVID-19, we all became familiar with concepts like “flattening…
Apr 14, 2025
7 min

Regularization in statistical models

Regularization is a fundamental technique in statistical modeling that helps prevent overfitting and improves model generalization. This blog post explores different…
Feb 2, 2025
4 min

Understanding correlation, covariation, and least squares regression

Understanding relationships between variables is a fundamental aspect of statistical analysis. Three key concepts in this domain are correlation, covariation, and least…
Jan 30, 2025
3 min

Distribution Matching Methods: From Theory to Practice

When working with data from different sources or distributions, we often need to…
Oct 31, 2024
7 min

Bayesian workflow: fake social contact data example

Bayesian workflow
negative binomial
social contact
This post is my attempt to follow along a Bayesian Workflow by Gelman et al and create examples for better understanding. While my ultimate goal is to study infectious disease transmission using a dynamic model following…
Jul 21, 2024
12 min

Modeling human behavior: Infectious disease transmission modeling perspective

Bayesian workflow
negative binomial
social contact
감염병의 전파 양상을 연구하는 감염병 역학…
Jul 21, 2024
1 min

Kalman filter to estimate R using the FKF package

kalman filter
Arroyo-Marioli et al used a Kalman filter approach to estimate. I tried to reproduce in R. Let’s use a SIR model as was used in my previous post to…
Jul 11, 2024
5 min

Learning ChatGPT 4: Universal Approximation Theorem

Universal Approximation Theorem
Neural network
Arbitrary-Width
Arbitrary-Depth
Neural networks can approximate any function according to the Universal Approximation Theorem. A more precise statement of the theorem is that neural networks with a single hidden layer…
Jun 24, 2024
3 min

Parallel simulation in R

parallelism
foreach
doParallel
I find that parallel, doParallel and foreach packages provide the easiest approach for parallel computing in R. The doParallel vignette provides a great overview. librar…
Jun 14, 2024
2 min

Basic reproduction number: An algorithmic approach

Basic reproduction number
Mathematica
algorithmic approach
next generation matrix
A recent article published in Mathematics discusses an approach to calculating R0. Since I have previously written a post about calculating R0 using Sympy, I wanted to explore a new approach proposed by the…
Jun 2, 2024
5 min

Claude 3

LLM
Claude
Testing Claude 3 with R
May 30, 2024
2 min

Learning ChatGPT 2: Approximating a tower function using a neural net

Neural network
Adam
matrix
The blog post by Stephen Wolfram discusses a neural network for approximating some sort of a step function. This post is my attempt to reproduce it. A YouTube video and a book…
May 28, 2024
3 min

A very basic implementation of a neural network

GPT-2
ChatGPT
Wolfram
I am documenting my learning of a neural network. The contents are mostly based on the e-book.
May 27, 2024
3 min

Variables selection in statistical models

R
variable selection
generalized linear model
When building statistical models, one of the most critical steps is variable selection. This process involves choosing the appropriate predictors or features that will be…
May 18, 2024
5 min

Learning ChatGPT 1: Probabilities for the next word

GPT-2
ChatGPT
Wolfram
Inspired by the blog post by Stephen Wolfram about the workings of the GPT-2 system, I decided to learn a bit about ChatGPT myself. Luckily, GPT-2 is now available for R. My first task is simply to learn to run the model and generate the probability table for the words that can follow the text, “The best thing about…
May 1, 2024
3 min

Logistic function in R

Logistic function
indirect vaccine effectiveness
oral cholera vaccine
The logistic function, represented as: f(x)=L1+e−k(x−x0) , where x0,L, and k represent tht value of the function’s midpoint, the supremum of the values of the function…
Apr 19, 2024
6 min

Waning vaccine efficacy on susceptibility

Vaccine
waning
SEIR
Erlang distribution
In this article, I examined the process of modifying the disease transmission model (for instance, the SEIR model) to include vaccination and the waning of vaccine-induced immunity as it might happen in a clinical trial. A straightforward method to represent this…
Apr 8, 2024
11 min

SEIR model with varying number of compartments

SEIR
Erlang distribution
The SEIR …
Apr 5, 2024
6 min
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