Related papers: Power series method for solving TASEP-based models…
Tensor decomposition serves as a powerful primitive in statistics and machine learning, and has numerous applications in problems such as learning latent variable models or mixture of Gaussians. In this paper, we focus on using power…
We discuss non-reversible Markov-chain Monte Carlo algorithms that, for particle systems, rigorously sample the positional Boltzmann distribution and that have faster than physical dynamics. These algorithms all feature a non-thermal…
Motivated by recent experiments on an antibiotic resistance gene, we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation. We show that the range of possible interactions is…
RNA polymerase (RNAP) elongates RNA by walking along a DNA template and selectively incorporating ribonucleoside triphosphates (rNTPs). Rather than mechanically replicating the base sequence, RNAP conditions binding and chemistry on the…
In cells, most of cargos are transported by motor proteins along microtubule. Biophysically, unidirectional motion of large number of motor proteins along a single track can be described by totally asymmetric simple exclusion process…
From a multi-model compression perspective, model merging enables memory-efficient serving of multiple models fine-tuned from the same base, but suffers from degraded performance due to interference among their task-specific parameter…
We study a minimal lattice model which describes bidirectional transport of "particles" driven along a one dimensional track, as is observed in microtubule based, motor protein driven bidirectional transport of cargo vesicles, lipid bodies…
Despite their ubiquity in language generation, it remains unknown why truncation sampling heuristics like nucleus sampling are so effective. We provide a theoretical explanation for the effectiveness of the truncation sampling by proving…
We introduce the multispecies totally asymmetric simple exclusion process (mTASEP) with long-range swap, a new interacting particle system combining the backward-push rule with the forward-jump rule. Although governed by local dynamics, the…
In this paper we study an important global regulation mechanism of transcription of biological cells using specific macro-molecules, 6S RNAs. The functional property of 6S RNAs is of blocking the transcription of RNAs when the environment…
The generalized totally asymmetric exclusion process (TASEP) [J. Stat. Mech. P05014 (2012)] is an integrable generalization of the TASEP equipped with an interaction, which enhances the clustering of particles. The process interpolates…
In this paper we consider a model of particles jumping on a row of cells, called in physics the one dimensional totally asymmetric exclusion process (TASEP). More precisely we deal with the TASEP with open or periodic boundary conditions…
Consider the Totally Asymmetric Simple Exclusion Process (TASEP) on the integer lattice $ \mathbb{Z} $. We study the functional Large Deviations of the integrated current $ \mathsf{h}(t,x) $ under the hyperbolic scaling of space and time by…
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of…
The asymmetric simple exclusion process (ASEP) is a paradigm for non-equilibrium physics that appears as a building block to model various low-dimensional transport phenomena, ranging from intracellular traffic to quantum dots. We review…
We consider the totally asymmetric simple exclusion process (TASEP) starting with a shock discontinuity at the origin, with asymptotic densities $\lambda$ to the left of the origin and $\rho$ to the right of it and $\lambda<\rho$. We find…
Non-Autoregressive Neural Machine Translation (NAT) has achieved significant inference speedup by generating all tokens simultaneously. Despite its high efficiency, NAT usually suffers from two kinds of translation errors: over-translation…
Recent advances in machine translation (MT) have shown that Minimum Bayes Risk (MBR) decoding can be a powerful alternative to beam search decoding, especially when combined with neural-based utility functions. However, the performance of…
Recent whole genome polymerase binding assays have shown that a large proportion of unexpressed genes have pre-assembled RNA pol II transcription initiation complex stably bound to their promoters. Some such promoter proximally paused genes…
Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. In this work, we use the…