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The verification of reductions, representative subsets of interleavings, simplifies correctness proofs of parameterized concurrent programs. We introduce an expressive class of syntactic reductions, which we call natural reductions. Natural…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
We study the problem of computing the minimum adversarial perturbation of the Nearest Neighbor (NN) classifiers. Previous attempts either conduct attacks on continuous approximations of NN models or search for the perturbation by some…
Let $M$ be a non-zero binary matrix with distinct rows where the rows are closed under certain logical operators. In this article, we investigate the existence of columns containing an equal or greater number of ones than zeros.…
Finding a maximum cardinality common independent set in two matroids (also known as \textsc{Matroid Intersection}) is a classical combinatorial optimization problem, which generalizes several well-known problems, such as finding a maximum…
For a complexity class $C$ and language $L$, a constructive separation of $L \notin C$ gives an efficient algorithm (also called a refuter) to find counterexamples (bad inputs) for every $C$-algorithm attempting to decide $L$. We study the…
Matrix completion aims to reconstruct a data matrix based on observations of a small number of its entries. Usually in matrix completion a single matrix is considered, which can be, for example, a rating matrix in recommendation system.…
Recent studies on frequent itemset mining algorithms resulted in significant performance improvements. However, if the minimal support threshold is set too low, or the data is highly correlated, the number of frequent itemsets itself can be…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…
The multinomial model is one of the simplest statistical models. When constraints are placed on the possible values for the probabilities, however, it becomes much more difficult to deal with. Model checking and checking for prior-data…
In the biclustering problem, we seek to simultaneously group observations and features. While biclustering has applications in a wide array of domains, ranging from text mining to collaborative filtering, the problem of identifying…
A natural strengthening of an algorithm for the (promise) constraint satisfaction problem is its singleton version: we first fix a variable to an element from its domain, then run the algorithm, and remove the element from the domain if the…
Given an initial family of sets, we may take unions, intersections and complements of the sets contained in this family in order to form a new collection of sets; our construction process is done recursively until we obtain the last family.…
Contrastive learning produces coherent semantic feature embeddings by encouraging positive samples to cluster closely while separating negative samples. However, existing contrastive learning methods lack principled guarantees on coverage…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
Symmetric submodular function minimization admits purely combinatorial algorithms using special orderings of the ground set. Extending the minimum-cut algorithm of Nagamochi and Ibaraki (1992), Queyranne (1998) showed that the maximum…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
Representing a proof tree by a combinator term that reduces to the tree lets subtle forms of duplication within the tree materialize as duplicated subterms of the combinator term. In a DAG representation of the combinator term these…
A coreset (or core-set) of an input set is its small summation, such that solving a problem on the coreset as its input, provably yields the same result as solving the same problem on the original (full) set, for a given family of problems…