Proceedings - Boulder Peptide Foundation

BPS 2023

Zero shot (no training data) machine learning approaches for protein and peptide optimization.

Ewa Lis

CEO, Koliber Biosciences Inc.

ABSTRACT

The public release of DALL-E in 2021 and ChatGPT in 2023 has ushered in a new era in Artificial Intelligence enabling humans to work along AI to generate images and text. The use of these tools is fundamentally changing the way humans create by providing a variety of starting points, accelerating the process, and eliminating tedious tasks. The awe-inspiring success of ChatGPT is based on novel model architectures (transformers) as well as an unsupervised training approach with masked tokens that leverages vast unlabeled datasets. Similarly to natural language, transformers can be trained on amino acid sequence data enabling development of models that capture an evolutionary understanding of peptides and proteins.

This presentation demonstrates the progression of the Koliber AI peptide / protein platform towards minimizing dataset sizes required to train machine learning models. A suite of applications was explored including anti-microbial and immune-modulating peptides. The models were trained on a wide variety of peptide datasets including cyclic peptides and peptides with non-canonical amino acids. Examples are shown that demonstrate zero shot / de novo predictions of substitutions that enhance enzyme function via increase in activity and broadening of substrate specificity.

BIO

Ewa Lis Ph.D. is a Founder and CEO of Koliber Biosciences. Ewa specializes in building Artificial Intelligence systems to solve biological data problems. Her unique expertise spans both computer science including deep learning, data augmentation and graph networks as well as several areas of biological and chemical sciences. Prior to founding Koliber in 2014, Ewa held leadership positions at Life Technologies, Genomatica and Reveal Biosciences, where she developed innovative technologies from algorithms for pathology tissue classification to genome engineering research tools and microbially derived renewable chemicals. Ewa holds a BA in Chemistry from Cornell University and a Ph.D. in Biological Sciences from The Scripps Research Institute.

Oral Presentations in Scientific Sessions

The session topics for Scientific Program are Peptides in the Clinic, Drug Delivery, Chemistry of Complex Peptides, Spotlight on Discovery, and Peptide Showcase. Abstracts may be submitted via the Apply to Present page on the website. Submissions will be reviewed by the Scientific Advisory Board on a monthly basis and the speaker will be notified of a decision.

Presentation length: Format is 25-30 minutes slide presentation with 5-10 minutes for Q&A, with the exception of Peptide Showcase talks which are 10 minute slide presentations with 5 minutes for Q&A. Please confirm with your session chair to confirm the exact presentation length.

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Peptide Showcase Description

The Peptide Showcase is an opportunity for an individual or company to “showcase” new ideas, technology and pipeline assets. Priority shall be given to presentations from biotech and startup companies. Service providers and vendors are not eligible. Speakers in the session receive a complimentary event registration.

Posters

Posters can be presented on any topic relevant to peptides including original research, innovative products and technologies.

Eligibility- Any attendee (from academia, industry, biotech or vendor/sponsor) can present a poster. The presentation must contain original scientific thinking. To submit a poster go to the Submit a Poster link from the meeting menu. All submissions are reviewed on a rolling basis and will be notified of approval. September 1st is the last day to submit a poster abstract. Approved posters are published on the BPF website.

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