doi.bio/john_b_ingraham
John B Ingraham
John B Ingraham is a researcher in the field of machine learning and AI, with a focus on their applications in genomics and protein design. He is currently working at the startup FVL56, Inc.
Education and Career
John was a PhD student under the supervision of Debora Marks at Harvard Medical School. During his PhD, he focused on building probabilistic models of evolutionary variation in proteins and RNAs to understand how their structure, function, and physiological relevance are encoded in their genetic sequence.
Following his PhD, John worked as a postdoctoral researcher at the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL), collaborating with Tommi Jaakkola and Regina Barzilay as part of the MLPDS consortium. At CSAIL, he worked on accelerating the process of molecular and macromolecular design and discovery using structured machine learning models.
Publications
John has several notable publications in prestigious journals and conferences:
- "Deep generative models of genetic variation capture the effects of mutations" in Nature Methods (2018) with Adam Riesselman and Debora S Marks.
- "Learning protein structure with a differentiable simulator" in the International Conference on Learning Representations (2019) with Adam Riesselman, Chris Sander, and Debora S Marks.
- "Generative Models for Graph-Based Protein Design" in Neural Information Processing Systems (NeurIPS, 2019) with Vikas K. Garg, Regina Barzilay, and Tommi Jaakkola.
- "Mutation effects predicted from sequence co-variation" in Nature Biotechnology (2017) with Thomas A Hopf, Frank J Poelwijk, Charlotta PI Schärfe, Michael Springer, Chris Sander, and Debora S Marks.
- "Variational Inference for Sparse and Undirected Models" in the International Conference on Machine Learning (ICML, 2017) with Debora Marks.
John B Ingraham
John B Ingraham is a researcher in the field of AI, machine learning and genomics. He is currently working at the startup FVL56, Inc. Ingraham completed his postdoctoral research at the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL), working with Tommi Jaakkola and Regina Barzilay as part of the MLPDS consortium.
Education and Research
Prior to his work at MIT, Ingraham was a PhD student in Debora Marks' lab at Harvard Medical School. His research focused on building probabilistic models of evolutionary variation in proteins and RNAs to understand how their structure, function and physiological relevance are encoded in their genetic sequence.
Publications
Ingraham has published several papers in renowned journals and conferences, including:
- "Generative Models for Graph-Based Protein Design", NeurIPS 2019
- "Learning protein structure with a differentiable simulator", ICLR 2019
- "Deep generative models of genetic variation capture the effects of mutations", Nature Methods 2018
- "Mutation effects predicted from sequence co-variation", Nature Biotechnology 2017
- "Variational Inference for Sparse and Undirected Models", ICML 2017
Youtube Videos
Youtube Title: MIA: John Ingraham, Learning protein structure with a differentiable simulator
Youtube Link: link
Youtube Channel Name: Broad Institute
Youtube Channel Link: https://www.youtube.com/@broadinstitute
MIA: John Ingraham, Learning protein structure with a differentiable simulator
Youtube Title: L13a Generative Modeling for Science -- Guest Lecturer John Ingraham
Youtube Link: link
Youtube Channel Name: Pieter Abbeel
Youtube Channel Link: https://www.youtube.com/@PieterAbbeel
L13a Generative Modeling for Science -- Guest Lecturer John Ingraham
Youtube Title: MIA: Debora Marks, Structure & fitness from genomics sequences; John Ingraham & Adam Riesselman
Youtube Link: link
Youtube Channel Name: Broad Institute
Youtube Channel Link: https://www.youtube.com/@broadinstitute
MIA: Debora Marks, Structure & fitness from genomics sequences; John Ingraham & Adam Riesselman
Youtube Title: Jon Stewart Examines Biden’s Future Amidst Calls For Him to Drop Out | The Daily Show
Youtube Link: link
Youtube Channel Name: The Daily Show
Youtube Channel Link: https://www.youtube.com/@TheDailyShow
Jon Stewart Examines Biden’s Future Amidst Calls For Him to Drop Out | The Daily Show
Youtube Title: LIVE: President Joe Biden press conference
Youtube Link: link
Youtube Channel Name: WFAA
Youtube Channel Link: https://www.youtube.com/@Wfaa8
LIVE: President Joe Biden press conference
Youtube Title: LIVE: President Joe Biden holds high-stakes solo press conference
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Youtube Channel Name: ABC News
Youtube Channel Link: https://www.youtube.com/@ABCNews
LIVE: President Joe Biden holds high-stakes solo press conference
Youtube Title: DAILY NEWS: Biden press conference news, analysis, quotes and highlights
Youtube Link: link
Youtube Channel Name: LiveNOW from FOX
Youtube Channel Link: https://www.youtube.com/@livenowfox
DAILY NEWS: Biden press conference news, analysis, quotes and highlights
Youtube Title: Supreme Court issues major ruling on Jan. 6
Youtube Link: link
Youtube Channel Name: Fox News
Youtube Channel Link: https://www.youtube.com/@FoxNews
Supreme Court issues major ruling on Jan. 6
Youtube Title: Laura Ingraham and Candace Owens REACT to SNL's Impressions of Them
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Youtube Channel Name: Entertainment Tonight
Youtube Channel Link: https://www.youtube.com/@EntertainmentTonight
Laura Ingraham and Candace Owens REACT to SNL's Impressions of Them
Youtube Title: Van Jones: Ingraham comments same as neo-Nazi's
Youtube Link: link
Youtube Channel Name: CNN
Youtube Channel Link: https://www.youtube.com/@CNN
Van Jones: Ingraham comments same as neo-Nazi's
Youtube Title: Sen. John Kennedy: Biden would be better suited selling catheters #shorts
Youtube Link: link
Youtube Channel Name: Fox News
Youtube Channel Link: https://www.youtube.com/@FoxNews
Sen. John Kennedy: Biden would be better suited selling catheters #shorts
Youtube Title: WATCH: NATO summit, Biden health concerns, Alec Baldwin trial & more | LiveNOW from FOX
Youtube Link: link
Youtube Channel Name: LiveNOW from FOX
Youtube Channel Link: https://www.youtube.com/@livenowfox
WATCH: NATO summit, Biden health concerns, Alec Baldwin trial & more | LiveNOW from FOX
Youtube Title: Watch how #Biden has aged from 1974 to 2022. #shorts #gerontocracy #presidents #insidernews
Youtube Link: link
Youtube Channel Name: Insider News
Youtube Channel Link: https://www.youtube.com/@InsiderNews
Watch how #Biden has aged from 1974 to 2022. #shorts #gerontocracy #presidents #insidernews
Youtube Title: Ingraham: Starve the virus, not the economy
Youtube Link: link
Youtube Channel Name: Fox News
Youtube Channel Link: https://www.youtube.com/@FoxNews
Ingraham: Starve the virus, not the economy
Youtube Title: Sen. Kennedy’s epic commentary on Biden: Economists ‘prostitute themselves to Democratic president’
Youtube Link: link
Youtube Channel Name: Fox News
Youtube Channel Link: https://www.youtube.com/@FoxNews
Sen. Kennedy’s epic commentary on Biden: Economists ‘prostitute themselves to Democratic president’
Youtube Title: Watch the first 2024 presidential debate in 3 minutes
Youtube Link: link
Youtube Channel Name: MSNBC
Youtube Channel Link: https://www.youtube.com/@msnbc
Watch the first 2024 presidential debate in 3 minutes
Youtube Title: Patti Blagojevich slams Mueller's 'unchecked power'
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Youtube Channel Name: Fox News
Youtube Channel Link: https://www.youtube.com/@FoxNews
Patti Blagojevich slams Mueller's 'unchecked power'
Youtube Title: Stephen Calls Bruce Willis A Liar… MISTAKE
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Youtube Channel Name: The Late Show with Stephen Colbert
Youtube Channel Link: https://www.youtube.com/@ColbertLateShow
Stephen Calls Bruce Willis A Liar... MISTAKE
Youtube Title: Weekend Update: Rep. Marjorie Taylor Greene on Science - SNL
Youtube Link: link
Youtube Channel Name: Saturday Night Live
Youtube Channel Link: https://www.youtube.com/@SaturdayNightLive
Weekend Update: Rep. Marjorie Taylor Greene on Science - SNL
Youtube Title: Jon Stewart Tackles The Trump Conviction Fallout & Puts The Media on Trial | The Daily Show
Youtube Link: link
Youtube Channel Name: The Daily Show
Youtube Channel Link: https://www.youtube.com/@TheDailyShow
Jon Stewart Tackles The Trump Conviction Fallout & Puts The Media on Trial | The Daily Show