Search Results for author: Sam Sinai

Found 5 papers, 2 papers with code

Forecasting labels under distribution-shift for machine-guided sequence design

no code implementations18 Nov 2022 Lauren Berk Wheelock, Stephen Malina, Jeffrey Gerold, Sam Sinai

The ability to design and optimize biological sequences with specific functionalities would unlock enormous value in technology and healthcare.

Decision Making

AdaLead: A simple and robust adaptive greedy search algorithm for sequence design

1 code implementation5 Oct 2020 Sam Sinai, Richard Wang, Alexander Whatley, Stewart Slocum, Elina Locane, Eric D. Kelsic

In this work, we implement an open-source Fitness Landscape EXploration Sandbox (FLEXS: github. com/samsinai/FLEXS) environment to test and evaluate these algorithms based on their optimality, consistency, and robustness.

A primer on model-guided exploration of fitness landscapes for biological sequence design

no code implementations4 Oct 2020 Sam Sinai, Eric D Kelsic

This primer can serve as a starting point for researchers from different domains that are interested in the problem of searching a sequence space with a model, but are perhaps unaware of approaches that originate outside their field.

BIG-bench Machine Learning Experimental Design

Variational auto-encoding of protein sequences

2 code implementations9 Dec 2017 Sam Sinai, Eric Kelsic, George M. Church, Martin A. Nowak

Here we present an embedding of natural protein sequences using a Variational Auto-Encoder and use it to predict how mutations affect protein function.

Primordial Sex Facilitates the Emergence of Evolution

no code implementations2 Dec 2016 Sam Sinai, Jason Olejarz, Iulia A. Neagu, Martin A. Nowak

Compartments are ubiquitous throughout biology, yet their importance stretches back to the origin of cells.

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