Giulia Bernardini

Giulia Bernardini, Alexander Lindermayr, Alberto Marchetti-Spaccamela et al.

We introduce a novel measure for quantifying the error in input predictions. The error is based on a minimum-cost hyperedge cover in a suitably defined hypergraph and provides a general template which we apply to online graph problems. The measure captures errors due to absent predicted requests as well as unpredicted actual requests; hence, predicted and actual inputs can be of arbitrary size. We achieve refined performance guarantees for previously studied network design problems in the online-list model, such as Steiner tree and facility location. Further, we initiate the study of learning-augmented algorithms for online routing problems, such as the online traveling salesperson problem and the online dial-a-ride problem, where (transportation) requests arrive over time (online-time model). We provide a general algorithmic framework and we give error-dependent performance bounds that improve upon known worst-case barriers, when given accurate predictions, at the cost of slightly increased worst-case bounds when given predictions of arbitrary quality.

Giulia Bernardini, Leo van Iersel, Esther Julien et al.

Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers of phylogenetic trees or are limited to severely restricted classes of networks. In this paper, we apply the recently-introduced theoretical framework of cherry picking to design a class of efficient heuristics that are guaranteed to produce a network containing each of the input trees, for datasets consisting of binary trees. Some of the heuristics in this framework are based on the design and training of a machine learning model that captures essential information on the structure of the input trees and guides the algorithms towards better solutions. We also propose simple and fast randomised heuristics that prove to be very effective when run multiple times. Unlike the existing exact methods, our heuristics are applicable to datasets of practical size, and the experimental study we conducted on both simulated and real data shows that these solutions are qualitatively good, always within some small constant factor from the optimum. Moreover, our machine-learned heuristics are one of the first applications of machine learning to phylogenetics and show its promise.

Giulia Bernardini, Philip Bille, Inge Li Gørtz et al.

For databases consisting of many text documents, one of the most fundamental data analysis tasks is counting (i) how often a pattern appears as a substring in the database (substring counting) and (ii) how many documents in the collection contain the pattern as a substring (document counting). If such a database contains sensitive data, it is crucial to protect the privacy of individuals in the database. Differential privacy is the gold standard for privacy in data analysis. It gives rigorous privacy guarantees, but comes at the cost of yielding less accurate results. In this paper, we carry out a theoretical study of substring and document counting under differential privacy. We propose a data structure storing $ε$-differentially private counts for all possible query patterns with a maximum additive error of $O(\ell\cdot\mathrm{polylog}(n\ell|Σ|))$, where $\ell$ is the maximum length of a document in the database, $n$ is the number of documents, and $|Σ|$ is the size of the alphabet. We also improve the error bound for document counting with $(ε, δ)$-differential privacy to $O(\sqrt{\ell}\cdot\mathrm{polylog}(n\ell|Σ|))$. We show that our additive errors for substring counting and document counting are optimal up to an $O(\mathrm{polylog}(n\ell))$ factor both for $ε$-differential privacy and $(ε, δ)$-differential privacy. Our data structures immediately lead to improved algorithms for related problems, such as privately mining frequent substrings and q-grams. Additionally, we develop a new technique of independent interest for differentially privately computing a general class of counting functions on trees.