99 - Evaluating Protein Transfer Learning, With Roshan Rao And Neil Thomas

99 - Evaluating Protein Transfer Learning, With Roshan Rao And Neil Thomas

Author: Allen Institute for Artificial Intelligence December 16, 2019 Duration: 44:49
For this episode, we chatted with Neil Thomas and Roshan Rao about modeling protein sequences and evaluating transfer learning methods for a set of five protein modeling tasks. Learning representations using self-supervised pretaining objectives has shown promising results in transferring to downstream tasks in protein sequence modeling, just like it has in NLP. We started off by discussing the similarities and differences between language and protein sequence data, and how the contextual embedding techniques are applicable also to protein sequences. Neil and Roshan then described a set of five benchmark tasks to assess the quality of protein embeddings (TAPE), particularly in terms of how well they capture the structural, functional, and evolutionary aspects of proteins. The results from the experiments they ran with various model architectures indicated that there was not a single best performing model across all tasks, and that there is a lot of room for future work in protein sequence modeling. Neil Thomas and Roshan Rao are PhD students at UC Berkeley. Paper: https://www.biorxiv.org/content/10.1101/676825v1 Blog post: https://bair.berkeley.edu/blog/2019/11/04/proteins/

While NLP Highlights is currently on hiatus, its archive remains a compelling snapshot of conversations from the front lines of computational linguistics. Produced by the Allen Institute for Artificial Intelligence, this science podcast carved out a space for deep, researcher-led discussions about natural language processing. Each episode functions as an informal seminar, where the people actively designing algorithms and pushing the field forward explain their work in their own words. You'll hear about the nuanced challenges behind making machines understand, generate, and reason with human language, from foundational theories to unexpected applications. The dialogue in this podcast often delves into the "why" behind the research, not just the results, offering clarity on complex topics like machine translation, sentiment analysis, or large language models. It’s a chance to listen as experts articulate their thought processes, debates, and moments of insight, with all the candidness that comes from a conversation between peers. The views shared are personal perspectives from the hosts and their guests, independent of their affiliated institutions. For anyone curious about how machines learn to parse meaning, the archived episodes of NLP Highlights provide a thoughtful and accessible entry point.
Author: Language: English Episodes: 100

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