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Finding patterns in graphs is a fundamental problem in databases and data mining. In many applications, graphs are temporal and evolve over time, so we are interested in finding durable patterns, such as triangles and paths, which persist…
The sequential allocation protocol is a simple and popular mechanism to allocate indivisible goods, in which the agents take turns to pick the items according to a predefined sequence. While this protocol is not strategy-proof, it has been…
The Learnable Tree Filter presents a remarkable approach to model structure-preserving relations for semantic segmentation. Nevertheless, the intrinsic geometric constraint forces it to focus on the regions with close spatial distance,…
In this study we assessed the repeatability of the values of radiomics features for small prostate tumors using test-retest Multiparametric Magnetic Resonance Imaging (mpMRI) images. The premise of radiomics is that quantitative image…
A fundamental question in systems biology is what combinations of mean and variance of the species present in a stochastic biochemical reaction network are attainable by perturbing the system with an external signal. To address this…
Theoretical inverse problems are often studied in an ideal infinite-dimensional setting. The well-posedness theory provides a unique reconstruction of the parameter function, when an infinite amount of data is given. Through the lens of…
We study the parameterized complexity of a generalization of the coordinated motion planning problem on graphs, where the goal is to route a specified subset of a given set of $k$ robots to their destinations with the aim of minimizing the…
Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for…
This study addresses the predictive limitation of probabilistic circuits and introduces transformations as a remedy to overcome it. We demonstrate this limitation in robotic scenarios. We motivate that independent component analysis is a…
One of the most basic, longstanding open problems in the theory of dynamical systems is whether reachability is decidable for one-dimensional piecewise affine maps with two intervals. In this paper we prove that for injective maps, it is…
The basic (and traditional) crossing number problem is to determine the minimum number of crossings in a topological drawing of an input graph in the plane. We develop a unified framework yielding fixed-parameter tractable (FPT) algorithms…
Acquiring genomes at single-cell resolution has many applications such as in the study of microbiota. However, deep sequencing and assembly of all of millions of cells in a sample is prohibitively costly. A property that can come to rescue…
In this thesis, we present new techniques to deal with fundamental algorithmic graph problems where graphs are directed and partially dynamic, i.e. undergo either a sequence of edge insertions or deletions: - Single-Source Reachability…
Recently there has been much interest in graph-based learning, with applications in collaborative filtering for recommender networks, link prediction for social networks and fraud detection. These networks can consist of millions of…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…
We study the problem of change point localization in dynamic networks models. We assume that we observe a sequence of independent adjacency matrices of the same size, each corresponding to a realization of an unknown inhomogeneous Bernoulli…
Vertex deletion problems ask whether it is possible to delete at most $k$ vertices from a graph so that the resulting graph belongs to a specified graph class. Over the past years, the parameterized complexity of vertex deletion to a…
We consider the computational complexity of reconfiguration problems, in which one is given two combinatorial configurations satisfying some constraints, and is asked to transform one into the other using elementary transformations, while…
We study spreading processes in temporal graphs, i. e., graphs whose connections change over time. These processes naturally model real-world phenomena such as infectious diseases or information flows. More precisely, we investigate how…