Related papers: Building maximal green sequences via component pre…
A new variant of the GMRES method is presented for solving linear systems with the same matrix and subsequently obtained multiple right-hand sides. The new method keeps such properties of the classical GMRES algorithm as follows. Both bases…
We propose a new way of looking at global optimization of off-lattice protein models. We present a dual optimization concept of predicting optimal sequences as well as optimal folds. We validate the utility of the recently introduced…
The forest of mutations associated to a multitype branching forest is obtained by merging together all vertices of its clusters and by preserving connections between them. We first show that the forest of mutations of any mulitype branching…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
We present an adaptive-order positivity-preserving conservative finite-difference scheme that allows a high-order solution away from shocks and discontinuities while guaranteeing positivity and robustness at discontinuities. This is…
In this paper we use a splitting technique to develop new multiscale basis functions for the multiscale finite element method (MsFEM). The multiscale basis functions are iteratively generated using a Green's kernel. The Green's kernel is…
We introduce a new numerical method to compute resonances induced by localized defects in crystals. This method solves an integral equation in the defect region to compute analytic continuations of resolvents. Such an approach enables one…
We study maximum antichains in two posets related to quiver representations. Firstly, we consider the set of isomorphism classes of indecomposable representations ordered by inclusion. For various orientations of the Dynkin diagram of type…
This work is concerned with constructing a second-order, invariant-domain preserving approximation of the compressible multi-species Euler equations where each species is modeled by an ideal gas equation of state. We give the full solution…
Conserved quantities increasingly underpin the inference of physical models. Recently new conserved quantities have been found in this context, that currently lack an interpretation. Here, we show that irreversible reactions in CRNs and…
This paper extends the semiconservative quasispecies equations to account for arbitrary post-replication lesion repair efficiency. Such an extension could be an important tool for understanding processes such as cancer development and stem…
We give a self-contained treatment of the theory of persistence modules indexed over the real line. We give new proofs of the standard results. Persistence diagrams are constructed using measure theory. Linear algebra lemmas are simplified…
Current discrete randomness and information conservation inequalities are over total recursive functions, i.e. restricted to deterministic processing. This restriction implies that an algorithm can break algorithmic randomness conservation…
Exceptional sequences are certain ordered sequences of quiver representations. We use noncrossing edge-labeled trees in a disk with boundary vertices (expanding on T. Araya's work) to classify exceptional sequences of representations of Q,…
We provide an example of a distribution preserving source separation method, which aims at addressing perceptual shortcomings of state-of-the-art methods. Our approach uses unconditioned generative models of signal sources. Reconstruction…
The ancestral sequence reconstruction problem is the inference, back in time, of the properties of common sequence ancestors from measured properties of contemporary populations. Standard algorithms for this problem assume independent…
The irreducible components of varieties parametrizing the finite dimensional representations of a finite dimensional algebra $\Lambda$ are explored, with regard to both their geometry and the structure of the modules they encode. Provided…
Machine-learning generative methods for material design are constructed by representing a given chemical structure, either a solid or a molecule, over appropriate atomic features, generally called structural descriptors. These must be fully…
The problem of robustly reconstructing a large number from its erroneous remainders with respect to several moduli, namely the robust remaindering problem, may occur in many applications including phase unwrapping, frequency detection from…
We give strong bounds for the rate of convergence of the regenerative process distribution to the stationary distribution in the total variation metric. These bounds are obtained by using coupling method. We propose this method for…