Fast Parallel Cheminformatics Workflows With Dask

 This is just a pointer to my new fastpages blog site. 

Comments

Post a Comment

Popular posts from this blog

Generative Molecular Design Isn't As Easy As People Make It Look

Image
I was taken aback by a recent CNBC article entitled “ Generative AI will be designing new drugs all on its own in the near future ”.  I should know better than to pay attention to AI articles in the popular press, but I feel that even scientists working in drug discovery may have a skewed perception of what generative AI can and can’t do.  To understand exactly what’s involved, it might be instructive to walk through a typical generative molecular design workflow and point out a few things.  First, these programs are far from autonomous.  Even when presented with a well-defined problem, generative algorithms produce a tremendous amount of nonsense.  Second, domain expertise is essential when sifting through the molecules produced by a generative algorithm.  Without a significant medicinal chemistry background, one can’t make sense of the results.  Third, while a few nuggets exist in the generative modeling output, a lot of work and good old-fashioned c...
Read more

We Need Better Benchmarks for Machine Learning in Drug Discovery

Image
Most papers describing new methods for machine learning (ML) in drug discovery report some sort of benchmark comparing their algorithm and/or molecular representation with the current state of the art.  In the past, I’ve written extensively about statistics and how methods should be compared .  In this post, I’d like to focus instead on the datasets we use to benchmark and compare methods.  Many papers I’ve read recently use the MoleculeNet dataset, released by the Pande group at Stanford in 2017, as the “standard” benchmark.   This is a mistake.  In this post, I’d like to use the MoleculeNet dataset to point out flaws in several widely used benchmarks.  Beyond this, I’d like to propose some alternate strategies that could be used to improve benchmarking efforts and help the field to move forward.   To begin, let’s examine the MoleculeNet benchmark, which to date, has been cited more than 1,800 times.   The MoleculeNet collection consis...
Read more

AI in Drug Discovery 2023 - A Highly Opinionated Literature Review (Part I)

Image
Here’s the first part of my review of some interesting machine learning (ML) papers I read in 2023.  As with the previous editions , this shouldn’t be considered a comprehensive review.  The papers covered here reflect my research interests and biases, and I’ve certainly overlooked areas that others consider vital.  This post is pretty long, so I've split it into three parts, with parts II and III to be posted in the next couple of weeks.    I. Docking, protein structure prediction, and benchmarking II. Large Language Models, active learning, federated learning, generative models, and explainable AI III. Review articles 2023 was a bit of a mixed bag for AI in drug discovery.  Several groups reported that the deep learning methods for protein-ligand docking weren’t quite what they were initially cracked up to be.  AlphaFold2 became pervasive, and people started to investigate, with mixed success, the utility of predicted protein structures.  There...
Read more