Variable expectations

Topic statement

Opening the quantitative toolbox for scientific discovery

Foundations of concentration and entropy

Where entropy comes from

Building graphs from gene sets

Gene-gene graphs and the Gene Ontology

Probability densities on embeddings

Tools for modeling distributions on data neighborhoods

Generating samples from kNN graphs

For “stationary” signals

The SVD and friends

Breaking down a (sparse) matrix quickly

Tree! I am no tree! I am an embedding!

Hierarchies on data

Detecting motifs in networks

Some linear algebra one-liners

Constructing data-driven neighborhood graphs

Building neighborhood graphs from datasets

SVD-based imputation methods

Using the SVD to perform ultra-efficient imputation

Laplacian regularization and trend filtering

Using graphs to regularize learning

Localized graph descriptions

Learning an interpretable coordinate system for a dataset

Looking up gene sets in databases

Some wrapper code for gProfiler

Interactive browser, part 3 - subset selection and scaling

Repurposing for single-cell data

Graph-based semi-supervised prediction

Harmonic analysis for learning on graphs

From local change to global order

Calculus on graphs as manifolds

Random projections and dimensionality reduction

Efficient, general applied tools

Graph sparsification

Removing edges while maintaining connectivity

Making animations and gifs

Stringing together plots into gifs

Interactive browser, part 2

cheminformatics

An interactively clustered heatmap

Building an interactive data browser

cheminformatics

Lightweight, performant exploration of chemical space

Measuring association between variables

A few new coefficients