the bug that taught me more about PyTorch than years of using it
a loss plateau that looked like my mistake turned out to be a PyTorch bug. tracking it down meant peeling back every layer of abstraction, from optimizer internals to GPU kernels.
Elana Simon
(matrices & molecules) a collection of deep-dives into ML x bio
Latest posts
The Illustrated AlphaFold
A visual walkthrough of the AlphaFold3 architecture, with more details and diagrams than you were probably looking for.
Mapping Chemical Space with UMAP
Note: this was originally written for the Reverie Labs blog which got taken down after acquisition so now it’s re-posted here This blog post discusses why it is important to visualize the latent space of chemical datasets, what makes UMAP a useful tool for this purpose, and how we use UMAP at Reverie Labs. As an example, we use the Blood Brain Barrier Permeability (BBBP) dataset from MoleculeNet…