Anna Sappington | Searcharxiv

arXiv2024

Towards Probabilistically-Sound Beam Search with Masked Language Models

Beam search with masked language models (MLMs) is challenging in part because joint probability distributions over sequences are not readily available, unlike for autoregressive models. However, estimating such distributions has important domain-specific applications such as ancient text restoration and protein engineering. Here we present probabilistically-sound methods for beam search with MLMs. First, we clarify the conditions under which it is theoretically sound to perform text infilling with MLMs using standard beam search. When these conditions fail, we provide a probabilistically-sound inference time modification with no additional computational complexity and demonstrate that it is superior to the aforementioned beam search in the expected conditions. We then present empirical results comparing several infilling approaches with MLMs across several domains. Notably, our method probes the inductive biases of MLMs and explores the surprising contextual sensitivity of mask tokens for text infilling.

cs.LG↗

arXiv2023

Probabilistic Genotype-Phenotype Maps Reveal Mutational Robustness of RNA Folding, Spin Glasses, and Quantum Circuits

Recent studies of genotype-phenotype (GP) maps have reported universally enhanced phenotypic robustness to genotype mutations, a feature essential to evolution. Virtually all of these studies make a simplifying assumption that each genotype -- represented as a sequence -- maps deterministically to a single phenotype, such as a discrete structure. Here, we introduce probabilistic genotype-phenotype (PrGP) maps, where each genotype maps to a vector of phenotype probabilities, as a more realistic and universal language for investigating robustness in a variety of physical, biological, and computational systems. We study three model systems to show that PrGP maps offer a generalized framework which can handle uncertainty emerging from various physical sources: (1) thermal fluctuation in RNA folding, (2) external field disorder in spin glass ground state finding, and (3) superposition and entanglement in quantum circuits, which are realized experimentally on IBM quantum computers. In all three cases, we observe a novel biphasic robustness scaling which is enhanced relative to random expectation for more frequent phenotypes and approaches random expectation for less frequent phenotypes. We derive an analytical theory for the behavior of PrGP robustness, and we demonstrate that the theory is highly predictive of empirical robustness.

cond-mat.stat-mech↗