Kevin K. Yang: Engineering Proteins with ML

Kevin K. Yang: Engineering Proteins with ML

Author: Daniel Bashir September 28, 2023 Duration: 1:00:00

In episode 92 of The Gradient Podcast, Daniel Bashir speaks to Kevin K. Yang.

Kevin is a senior researcher at Microsoft Research (MSR) who works on problems at the intersection of machine learning and biology, with an emphasis on protein engineering. He completed his PhD at Caltech with Frances Arnold on applying machine learning to protein engineering. Before joining MSR, he was a machine learning scientist at Generate Biomedicines, where he used machine learning to optimize proteins.

Have suggestions for future podcast guests (or other feedback)? Let us know here or reach us at editor@thegradient.pub

Subscribe to The Gradient Podcast:  Apple Podcasts  | Spotify | Pocket Casts | RSSFollow The Gradient on Twitter

Outline:

* (00:00) Intro

* (02:40) Kevin’s background

* (06:00) Protein engineering early in Kevin’s career

* (12:10) From research to real-world proteins: the process

* (17:40) Generative models + pretraining for proteins

* (22:47) Folding diffusion for protein structure generation

* (30:45) Protein evolutionary dynamics and generative models of protein sequences

* (40:03) Analogies and disanalogies between protein modeling and language models

* (41:45) In representation learning

* (45:50) Convolutions vs. transformers and inductive biases

* (49:25) Pretraining tasks for protein structure

* (51:45) More on representation learning for protein structure

* (54:06) Kevin’s thoughts on interpretability in deep learning for protein engineering

* (56:50) Multimodality in protein engineering and future directions

* (59:14) Outro

Links:

* Kevin’s Twitter and homepage

* Research

* Generative models + pre-training for proteins and chemistry

* Broad intro to techniques in the space

* Protein structure generation via folding diffusion

* Protein sequence design with deep generative models (review)

* Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins

* Protein generation with evolutionary diffusion: sequence is all you need

* ML for protein engineering

* ML-guided directed evolution for protein engineering (review)

* Learned protein embeddings for ML

* Adaptive machine learning for protein engineering (review)

* Multimodal deep learning for protein engineering



Get full access to The Gradient at thegradientpub.substack.com/subscribe

Hosted by Daniel Bashir, The Gradient: Perspectives on AI moves beyond surface-level headlines to explore the intricate machinery and human ideas shaping artificial intelligence. Each episode is built on a foundation of deep research, leading to conversations that are both technically substantive and broadly accessible. You'll hear from researchers, engineers, and philosophers who are actively building and critiquing our technological future, discussing not just how AI systems work, but the larger implications of their integration into society. This isn't about speculative hype; it's a grounded examination of real progress, persistent challenges, and ethical considerations from those on the front lines. The discussions peel back layers on topics like model architecture, policy, and the fundamental science behind the algorithms becoming part of our daily lives. For anyone curious about the substance behind the buzz-whether you have a technical background or are simply keen to understand a defining technology of our age-this podcast offers a crucial and thoughtful resource. Tune in for a consistently detailed and nuanced take that treats artificial intelligence with the complexity it deserves.
Author: Language: English Episodes: 100

The Gradient: Perspectives on AI
Podcast Episodes
Ted Gibson: The Structure and Purpose of Language [not-audio_url] [/not-audio_url]

Duration: 2:13:24
In episode 107 of The Gradient Podcast, Daniel Bashir speaks to Professor Ted Gibson.Ted is a Professor of Cognitive Science at MIT. He leads the TedLab, which investigates why languages look the way they do; the relatio…
Eric Jang: AI is Good For You [not-audio_url] [/not-audio_url]

Duration: 1:29:57
In episode 105 of The Gradient Podcast, Daniel Bashir speaks to Eric Jang.Have suggestions for future podcast guests (or other feedback)? Let us know here or reach us at editor@thegradient.pubSubscribe to The Gradient Po…
2023 in AI, with Nathan Benaich [not-audio_url] [/not-audio_url]

Duration: 1:35:37
In episode 104 of The Gradient Podcast, Daniel Bashir speaks to Nathan Benaich.Nathan is Founder and General Partner at Air Street Capital, a VC firm focused on investing in AI-first technology and life sciences companie…
Kathleen Fisher: DARPA and AI for National Security [not-audio_url] [/not-audio_url]

Duration: 46:16
In episode 103 of The Gradient Podcast, Daniel Bashir speaks to Dr. Kathleen Fisher.As the director of DARPA’s Information Innovation Office (I2O), Dr. Kathleen Fisher oversees a portfolio that includes most of the agenc…
Peter Tse: The Neuroscience of Consciousness and Free Will [not-audio_url] [/not-audio_url]

Duration: 2:24:04
In episode 102 of The Gradient Podcast, Daniel Bashir speaks to Peter Tse.Professor Tse is a Professor of Cognitive Neuroscience and chair of the department of Psychological and Brain Sciences at Dartmouth College. His r…
Vera Liao: AI Explainability and Transparency [not-audio_url] [/not-audio_url]

Duration: 1:37:03
In episode 101 of The Gradient Podcast, Daniel Bashir speaks to Vera Liao.Vera is a Principal Researcher at Microsoft Research (MSR) Montréal where she is part of the FATE (Fairness, Accountability, Transparency, and Eth…
Thomas Dietterich: From the Foundations [not-audio_url] [/not-audio_url]

Duration: 2:01:57
In episode 100 of The Gradient Podcast, Daniel Bashir speaks to Professor Thomas Dietterich.Professor Dietterich is Distinguished Professor Emeritus in the School of Electrical Engineering and Computer Science at Oregon…
Martin Wattenberg: ML Visualization and Interpretability [not-audio_url] [/not-audio_url]

Duration: 1:42:05
In episode 99 of The Gradient Podcast, Daniel Bashir speaks to Professor Martin Wattenberg.Professor Wattenberg is a professor at Harvard and part-time member of Google Research’s People + AI Research (PAIR) initiative,…