I am currently reading Sun Tzu’s Art of War and, as cliche as it sounds, am finding much wisdom in it. I have been taking notes during my reading and I thought I’d share them in this post. Here I cover Books 1 and 2.| Matthew N. Bernstein
In a previous post, we discussed how RNA-seq provides measurements of relative expression between genes rather than measurements of absolute expression. In this post, we will discuss median-ratio normalization: a procedure that attempts to scale each sample’s read counts so that differences in the read counts between samples better reflects differences in absolute expression. We will start by describing the underlying assumption that must be met for median-ratio normalization to work and th...| Matthew N. Bernstein
THIS POST IS CURRENTLY UNDER CONSTRUCTION| Matthew N. Bernstein
If you’re a practitioner of machine learning, then there is little doubt you have seen or used an algorithm that falls into the general category of kernel methods. The premier example of such methods is the support vector machine. When introduced to these algorithms, one is taught that one must provide the algorithm with a kernel function that, intuitively, computes a degree of “similarity” between the objects you are classifying. In practice, one can get pretty far with only this under...| Matthew N. Bernstein
The dot product is a fundamental operation on two Euclidean vectors that captures a notion of similarity between the vectors. In this post, we’ll define the dot product and offer a number of angles for which to intuit the idea captured by this fundamental operation.| Matthew N. Bernstein
Cells are crowded spaces packed with biomolecules colliding and interacting with one another. Despite this chaotic environment, biologists routinely describe intracellular functions using the clean mathematical language of networks. In this post I will attempt to reconcile these two seemingly contradictory perspectives of the cell. This post will serve as a first part in a series of blog posts I hope to write where I will collect and connect some of the works that have helped me better “int...| Matthew N. Bernstein
I am currently reading Sun Tzu’s Art of War and, as cliche as it sounds, am finding much wisdom in it. I have been taking notes during my reading and I thought I’d share them in this post. Here I cover Books 1 and 2.| Matthew N. Bernstein
Diffusion models are a family of state-of-the-art probabilistic generative models that have achieved ground breaking results in a number of fields ranging from image generation to protein structure design. In Part 1 of this two-part series, I will walk through the denoising diffusion probabilistic model (DDPM) as presented by Ho, Jain, and Abbeel (2020). Specifically, we will walk through the model definition, the derivation of the objective function, and the training and sampling algorithms....| Matthew N. Bernstein
THIS POST IS CURRENTLY UNDER CONSTRUCTION| Matthew N. Bernstein
THIS POST IS CURRENTLY UNDER CONSTRUCTION| Matthew N. Bernstein
Throughout my blog posts on linear algebra, we have proven various properties about invertible matrices. In this post we bring, all of these statements into a single location and form a set of statements called the “invertible matrix theorem”. Each statement in the invertible matrix theorem proves that the matrix is invertible and implies all of the rest of the statements.| Matthew N. Bernstein
Variational autoencoders (VAEs) are a family of deep generative models with use cases that span many applications, from image processing to bioinformatics. There are two complimentary ways of viewing the VAE: as a probabilistic model that is fit using variational Bayesian inference, or as a type of autoencoding neural network. In this post, we present the mathematical theory behind VAEs, which is rooted in Bayesian inference, and how this theory leads to an emergent autoencoding algorithm. We...| Matthew N. Bernstein
Variational inference (VI) is a mathematical framework for doing Bayesian inference by approximating the posterior distribution over the latent variables in a latent variable model when the true posterior is intractable. In this post, we will discuss a flexible variational inference algorithm, called blackbox VI via the reparameterization gradient, that works “out of the box” for a wide variety of models with minimal need for the tedious mathematical derivations that deriving VI algorithm...| Matthew N. Bernstein