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Asymmetric distributed constraint optimization problems (ADCOPs) are an emerging model for coordinating agents with personal preferences. However, the existing inference-based complete algorithms which use local eliminations cannot be…
Today when many practitioners run basic NLP on the entire web and large-volume traffic, faster methods are paramount to saving time and energy costs. Recent advances in GPU hardware have led to the emergence of bi-directional LSTMs as a…
In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary `Tree of Life'. This approach recognises that extinction not only removes species but…
We revisit the problem of finding optimal strategies for deterministic Markov Decision Processes (DMDPs), and a closely related problem of testing feasibility of systems of $m$ linear inequalities on $n$ real variables with at most two…
Recent years have seen deep neural networks (DNNs) becoming wider and deeper to achieve better performance in many applications of AI. Such DNNs however require huge amounts of memory to store weights and intermediate results (e.g.,…
Optimization for deep networks is currently a very active area of research. As neural networks become deeper, the ability in manually optimizing the network becomes harder. Mini-batch normalization, identification of effective respective…
Given a clique-width $k$-expression of a graph $G$, we provide $2^{O(k)}\cdot n$ time algorithms for connectivity constraints on locally checkable properties such as Node-Weighted Steiner Tree, Connected Dominating Set, or Connected Vertex…
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community…
Evolutionary optimisation algorithm is employed to design networks of phase-repulsive oscillators that achieve an anti-phase synchronised state. By introducing the link frustration, the evolutionary process is implemented by rewiring the…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
A breakthrough result of Cygan et al. (FOCS 2011) showed that connectivity problems parameterized by treewidth can be solved much faster than the previously best known time $\mathcal{O}^*(2^{\mathcal{O}(tw \log(tw))})$. Using their inspired…
Optimal control problems driven by evolutionary partial differential equations arise in many industrial applications and their numerical solution is known to be a challenging problem. One approach to obtain an optimal feedback control is…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
In the last couple of decades, there has been major advancements in the domain of missing data imputation. The techniques in the domain include amongst others: Expectation Maximization, Neural Networks with Evolutionary Algorithms or…
This work addresses inverse linear optimization where the goal is to infer the unknown cost vector of a linear program. Specifically, we consider the data-driven setting in which the available data are noisy observations of optimal…
In this study, we investigate the application of Semidefinite Programming (SDP) to phylogenetics. SDP is a powerful optimization framework that seeks to optimize a linear objective function over the cone of positive semidefinite matrices.…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the given pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
This paper characterizes and discusses devolutionary genetic algorithms and evaluates their performances in solving the minimum labeling Steiner tree (MLST) problem. We define devolutionary algorithms as the process of reaching a feasible…
We introduce an extension of Stochastic Dual Dynamic Programming (SDDP) to solve stochastic convex dynamic programming equations. This extension applies when some or all primal and dual subproblems to be solved along the forward and…