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Deep neural networks proved to be a very useful and powerful tool with many practical applications. They especially excel at learning from large data sets with labeled samples. However, in order to achieve good learning results, the network…
Perfect adaptation in a dynamical system is the phenomenon that one or more variables have an initial transient response to a persistent change in an external stimulus but revert to their original value as the system converges to…
Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary…
The Dynamic-Mode Decomposition (DMD) is a well established data-driven method of finding temporally evolving linear-mode decompositions of nonlinear time series. Traditionally, this method presumes that all relevant dimensions are sampled…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
We give new deterministic bounds for fully-dynamic graph connectivity. Our data structure supports updates (edge insertions/deletions) in $O(\log^2n/\log\log n)$ amortized time and connectivity queries in $O(\log n/\log\log n)$ worst-case…
We consider problems that can be formulated as a task of finding an optimal triangulation of a graph w.r.t. some notion of optimality. We present algorithms parameterized by the size of a minimum edge clique cover ($cc$) to such problems.…
The process of evolutionary diversification unfolds in a vast genotypic space of potential outcomes. During the past century there have been remarkable advances in the development of theory for this diversification, and the theory's success…
We study the D-optimal Data Fusion (DDF) problem, which aims to select new data points, given an existing Fisher information matrix, so as to maximize the logarithm of the determinant of the overall Fisher information matrix. We show that…
Reconstruction of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. The problem is known to be NP-hard even for datasets known to only contain siblings. Some recent methods have been…
The convolution between a text string $S$ of length $N$ and a pattern string $P$ of length $m$ can be computed in $O(N \log m)$ time by FFT. It is known that various types of approximate string matching problems are reducible to…
The temporal dynamics of a complex system such as a social network or a communication network can be studied by understanding the patterns of link appearance and disappearance over time. A critical task along this understanding is to…
In the Directed Feedback Vertex Set (DFVS) problem, the input is a directed graph $D$ on $n$ vertices and $m$ edges, and an integer $k$. The objective is to determine whether there exists a set of at most $k$ vertices intersecting every…
In this paper, we propose a new distributed algorithm, called Directed Transmission Method (DTM). DTM is a fully asynchronous and continuous-time iterative algorithm to solve SPD sparse linear system. As an architecture-aware algorithm, DTM…
We study the problem of recovering an incomplete $m\times n$ matrix of rank $r$ with columns arriving online over time. This is known as the problem of life-long matrix completion, and is widely applied to recommendation system, computer…
For the last thirty years, several Dynamic Memory Managers (DMMs) have been proposed. Such DMMs include first fit, best fit, segregated fit and buddy systems. Since the performance, memory usage and energy consumption of each DMM differs,…
In the paper, we propose an adaptive data-driven model-based approach for filling the gaps in time series. The approach is based on the automated evolutionary identification of the optimal structure for a composite data-driven model. It…
The classic algorithm [Papadimitriou, J.ACM '81] for IPs has a running time $n^{O(m)}(m\cdot\max\{\Delta,\|\textbf{b}\|_{\infty}\})^{O(m^2)}$, where $m$ is the number of constraints, $n$ is the number of variables, and $\Delta$ and…
We first design an $\mathcal{O}(n^2)$ solution for finding a maximum induced matching in permutation graphs given their permutation models, based on a dynamic programming algorithm with the aid of the sweep line technique. With the support…
We present Propulate, an evolutionary optimization algorithm and software package for global optimization and in particular hyperparameter search. For efficient use of HPC resources, Propulate omits the synchronization after each generation…