54,070 research outputs found
Computation of elementary modes: a unifying framework and the new binary approach
BACKGROUND: Metabolic pathway analysis has been recognized as a central approach to the structural analysis of metabolic networks. The concept of elementary (flux) modes provides a rigorous formalism to describe and assess pathways and has proven to be valuable for many applications. However, computing elementary modes is a hard computational task. In recent years we assisted in a multiplication of algorithms dedicated to it. We require a summarizing point of view and a continued improvement of the current methods. RESULTS: We show that computing the set of elementary modes is equivalent to computing the set of extreme rays of a convex cone. This standard mathematical representation provides a unified framework that encompasses the most prominent algorithmic methods that compute elementary modes and allows a clear comparison between them. Taking lessons from this benchmark, we here introduce a new method, the binary approach, which computes the elementary modes as binary patterns of participating reactions from which the respective stoichiometric coefficients can be computed in a post-processing step. We implemented the binary approach in FluxAnalyzer 5.1, a software that is free for academics. The binary approach decreases the memory demand up to 96% without loss of speed giving the most efficient method available for computing elementary modes to date. CONCLUSIONS: The equivalence between elementary modes and extreme ray computations offers opportunities for employing tools from polyhedral computation for metabolic pathway analysis. The new binary approach introduced herein was derived from this general theoretical framework and facilitates the computation of elementary modes in considerably larger networks
Robustness Verification of Support Vector Machines
We study the problem of formally verifying the robustness to adversarial
examples of support vector machines (SVMs), a major machine learning model for
classification and regression tasks. Following a recent stream of works on
formal robustness verification of (deep) neural networks, our approach relies
on a sound abstract version of a given SVM classifier to be used for checking
its robustness. This methodology is parametric on a given numerical abstraction
of real values and, analogously to the case of neural networks, needs neither
abstract least upper bounds nor widening operators on this abstraction. The
standard interval domain provides a simple instantiation of our abstraction
technique, which is enhanced with the domain of reduced affine forms, which is
an efficient abstraction of the zonotope abstract domain. This robustness
verification technique has been fully implemented and experimentally evaluated
on SVMs based on linear and nonlinear (polynomial and radial basis function)
kernels, which have been trained on the popular MNIST dataset of images and on
the recent and more challenging Fashion-MNIST dataset. The experimental results
of our prototype SVM robustness verifier appear to be encouraging: this
automated verification is fast, scalable and shows significantly high
percentages of provable robustness on the test set of MNIST, in particular
compared to the analogous provable robustness of neural networks
- …