Archive - Nathan's Substack

Getting started in BioML Research & Engineering

How to break into BioML (biology + machine learning) or "TechBio"

May 19 •

March 2025

Hit the Vintage Store and Get Yourself Some CHEAP PLAID

Compressed Hourglass Embedding Adaptations of Proteins & Protein Latent Induced Diffusion: Two-stage latent diffusion for all-atom protein co-generation

Mar 19 •

and

December 2024

Building the brain of a biological foundation model

Concept-bottleneck protein language models for protein design

Dec 12, 2024 •

Aya Abdelsalam Ismail

and

October 2024

Peering into the Unseen Protein Universe

Blog summary of our ICLR 2024 Outstanding Paper Award Winner, "Protein Discovery with Discrete Walk-Jump Sampling"

Oct 17, 2024 •

and

August 2024

The Impact of AI/ML in Drug Discovery Isn't Where You Think It is

Two recent articles on the impact of AI/ML and computation in biology caught my attention, one by Andrew Dunn with the provocative title “In a reality…

Aug 26, 2024 •

and

June 2024

Open-Source Science in Machine Learning for Biology

I spend a good chunk of my time and effort at Prescient Design supporting open science and open sourcing our code.

Jun 11, 2024 •

February 2022

FastFlows: Flow-Based Models for Molecular Graph Generation

Deep learning invertible transformations for efficient generative modeling

Feb 14, 2022 •

May 2021

MoleculeNet Part 1: Datasets for Deep Learning in the Chemical and Life Sciences

Thoughts and Theory

May 17, 2021 •

April 2021

How and why to share scientific code

A simple guide to reproducible research without becoming a software engineer

Apr 15, 2021 •

March 2021

Modeling Protein-Ligand Interactions with Atomic Convolutional Neural Networks

Exploit local structure of three-dimensional molecular complexes to predict binding affinities

Mar 17, 2021 •

February 2021

What is Materials Science?

Why materials science is a mystery to most people and why it’s important

Feb 15, 2021 •

January 2021

Getting Started in Materials Informatics

How to get started doing research in materials informatics (data science + materials science).

Jan 20, 2021 •

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