49 citations · 132 across the 7 of their papers we have counts for
7 papers
Contrastive losses as generalized models of global epistasis
David H. Brookes, Jakub Otwinowski, Sam Sinai
Fitness functions map large combinatorial spaces of biological sequences to properties of interest. Inferring these multimodal functions from experimental data is a central task in…
Forecasting labels under distribution-shift for machine-guided sequence design
Lauren Berk Wheelock, Stephen Malina, Jeffrey Gerold +1
The ability to design and optimize biological sequences with specific functionalities would unlock enormous value in technology and healthcare. In recent years, machine learning-gu…
A primer on model-guided exploration of fitness landscapes for biological sequence design
Sam Sinai, Eric D Kelsic
Machine learning methods are increasingly employed to address challenges faced by biologists. One area that will greatly benefit from this cross-pollination is the problem of biolo…
AdaLead: A simple and robust adaptive greedy search algorithm for sequence design
Sam Sinai, Richard Wang, Alexander Whatley +3
Efficient design of biological sequences will have a great impact across many industrial and healthcare domains. However, discovering improved sequences requires solving a difficul…
Turbulent coherent structures and early life below the Kolmogorov scale
Madison S. Krieger, Sam Sinai, Martin A. Nowak
A great number of biological organisms live in aqueous environments. Major evolutionary transitions, including the emergence of life itself, likely occurred in such environments. W…
Variational auto-encoding of protein sequences
Sam Sinai, Eric Kelsic, George M. Church +1
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extr…
Primordial Sex Facilitates the Emergence of Evolution
Sam Sinai, Jason Olejarz, Iulia A. Neagu +1
Compartments are ubiquitous throughout biology, yet their importance stretches back to the origin of cells. In the context of origin of life, we assume that a protocell, a compartm…