Robust resource bounds with static analysis and Bayesian inference
There are two approaches to automatically deriving symbolic worst-case resource bounds
for programs: static analysis of the source code and data-driven analysis of cost …
for programs: static analysis of the source code and data-driven analysis of cost …
Efficient computation of the the volume of a polytope in high-dimensions using piecewise deterministic markov processes
A Chevallier, F Cazals… - … Conference on Artificial …, 2022 - proceedings.mlr.press
Computing the volume of a polytope in high dimensions is computationally challenging but
has wide applications. Current state-of-the-art algorithms to compute such volumes rely on …
has wide applications. Current state-of-the-art algorithms to compute such volumes rely on …
Geometric algorithms for sampling the flux space of metabolic networks
Systems Biology is a fundamental field and paradigm that introduces a new era in Biology.
The crux of its functionality and usefulness relies on metabolic networks that model the …
The crux of its functionality and usefulness relies on metabolic networks that model the …
Truncated log-concave sampling for convex bodies with Reflective Hamiltonian Monte Carlo
We introduce Reflective Hamiltonian Monte Carlo (ReHMC), an HMC-based algorithm to
sample from a log-concave distribution restricted to a convex body. The random walk is …
sample from a log-concave distribution restricted to a convex body. The random walk is …
Enhanced conformational exploration of protein loops using a global parameterization of the backbone geometry
T O'Donnell, F Cazals - Journal of Computational Chemistry, 2023 - Wiley Online Library
Flexible loops are paramount to protein functions, with action modes ranging from localized
dynamics contributing to the free energy of the system, to large amplitude conformational …
dynamics contributing to the free energy of the system, to large amplitude conformational …
[PDF][PDF] Analyses of Programs
L Pham - 2024 - cs.cmu.edu
Resource-bound analysis aims to infer symbolic bounds of worst-case resource usage (eg,
running time, memory, and energy) of programs as functions of program inputs. Resource …
running time, memory, and energy) of programs as functions of program inputs. Resource …
A kinematic view of protein loop flexibility, with applications to conformational exploration
T O'Donnell - 2022 - theses.hal.science
This thesis introduces the first global parametric model of protein loops amenable to
effective sampling strategies a-la Hit-and-Run, making four contributions. Starting with the …
effective sampling strategies a-la Hit-and-Run, making four contributions. Starting with the …