Petti Group

Publications

Fitness landscapes

1. 2026

   On learning functions over biological sequence space: relating Gaussian process priors, regularization, and gauge fixing

   S. Petti, C. Martí-Gómez, J. B. Kinney, J. Zhou, D. M. McCandlish

   Journal of Mathematical Biology arXiv

2. 2026

   Inferring genotype–phenotype maps using attention models

   K. Rijal, C. M. Holmes, S. Petti, G. Reddy, M. M. Desai, P. Mehta

   PNAS Nexus

3. 2025

   Learning sequence-function relationships with scalable, interpretable Gaussian processes

   J. Zhou, C. Martí-Gómez, S. Petti, D. M. McCandlish

   bioRxiv preprint

4. 2023

   Inferring sparse structure in genotype–phenotype maps

   S. Petti*, G. Reddy*, M. M. Desai

   Genetics

* Equal contribution.

Protein structure search and alignment

1. 2025

   An interpretable alphabet for local protein structure search based on amino acid neighborhoods

   S. Zerefa, J. Cool, P. Singh, S. Petti

   Bioinformatics Code

2. 2025

   SoftAlign: End-to-end protein structures alignment

   J. Trinquier, S. Petti, S. Park, K. Herath, M. van Kempen, S. Feng, J. Söding, M. Steinegger, S. Ovchinnikov

   bioRxiv preprint

3. 2022

   End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman

   S. Petti, N. Bhattacharya, R. Rao, J. Dauparas, N. Thomas, J. Zhou, A. Rush, P. Koo, S. Ovchinnikov

   Bioinformatics Code

4. 2022

   Constructing benchmark test sets for biological sequence analysis using independent set algorithms

   S. Petti, S. R. Eddy

   PLOS Computational Biology Code

Stochastic processes

1. 2025

   A large deviation principle for block models

   C. Borgs, J. Chayes, J. Gaudio, S. Petti, S. Sen

   Combinatorics, Probability and Computing arXiv

2. 2022

   Correlation decay for hard spheres via Markov chains

   T. Helmuth, W. Perkins, S. Petti

   Annals of Applied Probability arXiv

3. 2022

   Approximating sparse graphs: the random overlapping communities model

   S. Petti, S. S. Vempala

   Random Structures & Algorithms

4. 2019

   Thresholds in random motif graphs

   M. Anastos, P. Michaeli, S. Petti

   RANDOM

5. 2018

   Balanced allocation through random walk

   A. Frieze, S. Petti

   Information Processing Letters

6. 2018

   The cover time of a biased random walk on G(n, p)

   C. Cooper, A. Frieze, S. Petti

   ANALCO

7. 2016

   Cortical computation via iterative constructions

   C. Papadimitriou, S. Petti, S. Vempala

   COLT

Other

1. 2026

   Agnosiophobia in a virtual agent: behavioral and dynamical architecture in Lenia

   J. Cool, B. Hartl, M. Levin, S. Petti

   arXiv preprint

2. 2020

   Differential privacy in the 2020 US census: what will it do? Quantifying the accuracy/privacy tradeoff

   S. Petti, A. D. Flaxman

   Gates Open Research

3. 2017

   A space of phylogenetic networks

   S. L. Devadoss, S. Petti

   SIAM Journal on Applied Algebra and Geometry