Approximation and inference methods for stochastic biochemical kinetics—a tutorial review

D Schnoerr, G Sanguinetti… - Journal of Physics A …, 2017 - iopscience.iop.org
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important
examples include gene expression and enzymatic processes in living cells. Such systems …

Quantum approximate optimization algorithm: Performance, mechanism, and implementation on near-term devices

L Zhou, ST Wang, S Choi, H Pichler, MD Lukin - Physical Review X, 2020 - APS
The quantum approximate optimization algorithm (QAOA) is a hybrid quantum-classical
variational algorithm designed to tackle combinatorial optimization problems. Despite its …

Dagma: Learning dags via m-matrices and a log-determinant acyclicity characterization

K Bello, B Aragam, P Ravikumar - Advances in Neural …, 2022 - proceedings.neurips.cc
The combinatorial problem of learning directed acyclic graphs (DAGs) from data was
recently framed as a purely continuous optimization problem by leveraging a differentiable …

Light emission from strongly driven many-body systems

A Pizzi, A Gorlach, N Rivera, A Nunnenkamp… - Nature Physics, 2023 - nature.com
Strongly driven systems of emitters offer an attractive source of light over broad spectral
ranges up to the X-ray region. A key limitation of these systems is that the light they emit is …

Coherent state based solutions of the time-dependent Schrödinger equation: hierarchy of approximations to the variational principle

M Werther, SL Choudhury… - International Reviews in …, 2021 - Taylor & Francis
In this review, we give a comprehensive comparison of the most widely used coherent state
(CS) based methods to solve the time-dependent Schrödinger equation (TDSE). Starting …

Heat kernel based community detection

K Kloster, DF Gleich - Proceedings of the 20th ACM SIGKDD …, 2014 - dl.acm.org
The heat kernel is a type of graph diffusion that, like the much-used personalized PageRank
diffusion, is useful in identifying a community nearby a starting seed node. We present the …

XTrace: Making the Most of Every Sample in Stochastic Trace Estimation

EN Epperly, JA Tropp, RJ Webber - SIAM Journal on Matrix Analysis and …, 2024 - SIAM
The implicit trace estimation problem asks for an approximation of the trace of a square
matrix, accessed via matrix-vector products (matvecs). This paper designs new randomized …

Prominent quantum many-body scars in a truncated Schwinger model

JY Desaules, A Hudomal, D Banerjee, A Sen, Z Papić… - Physical Review B, 2023 - APS
The high level of control and precision achievable in current synthetic quantum matter
setups has enabled first attempts at quantum-simulating various intriguing phenomena in …

Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations

JP Spence, YS Song - Science Advances, 2019 - science.org
Fine-scale rates of meiotic recombination vary by orders of magnitude across the genome
and differ between species and even populations. Studying cross-population differences …

Neural marching cubes

Z Chen, H Zhang - ACM Transactions on Graphics (TOG), 2021 - dl.acm.org
We introduce Neural Marching Cubes, a data-driven approach for extracting a triangle mesh
from a discretized implicit field. We base our meshing approach on Marching Cubes (MC) …