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As one of the three main pillars of fine-grained complexity theory, the 3SUM problem explains the hardness of many diverse polynomial-time problems via fine-grained reductions. Many of these reductions are either directly based on or…
The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art algorithms, namely Convolutional Neural…
We give efficient algorithms for ranking Lyndon words of length $n$ over an alphabet of size $\sigma$. The rank of a Lyndon word is its position in the sequence of lexicographically ordered Lyndon words of the same length. The outputs are…
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
In spite of their superior performance, neural probabilistic language models (NPLMs) remain far less widely used than n-gram models due to their notoriously long training times, which are measured in weeks even for moderately-sized…
Low Diameter Decompositions (LDDs) are invaluable tools in the design of combinatorial graph algorithms. While historically they have been applied mainly to undirected graphs, in the recent breakthrough for the negative-length Single Source…
Symmetric submodular maximization is an important class of combinatorial optimization problems, including MAX-CUT on graphs and hyper-graphs. The state-of-the-art algorithm for the problem over general constraints has an approximation ratio…
We present the first dynamic algorithms for Dyck and tree edit distances with subpolynomial update times. Dyck edit distance measures how far a parenthesis string is from a well-parenthesized expression, while tree edit distance quantifies…
Algorithms for learning decision trees often include heuristic local-search operations such as (1) adjusting the threshold of a cut or (2) also exchanging the feature of that cut. We study minimizing the number of classification errors by…
The problem of finding a nontrivial factor of a polynomial f(x) over a finite field F_q has many known efficient, but randomized, algorithms. The deterministic complexity of this problem is a famous open question even assuming the…
A genetic algorithm is suitable for exploring large search spaces as it finds an approximate solution. Because of this advantage, genetic algorithm is effective in exploring vast and unknown space such as molecular search space. Though the…
In an undirected graph, a $k$-cut is a set of edges whose removal breaks the graph into at least $k$ connected components. The minimum weight $k$-cut can be computed in $O(n^{O(k)})$ time, but when $k$ is treated as part of the input,…
Randomization is a fundamental tool used in many theoretical and practical areas of computer science. We study here the role of randomization in the area of submodular function maximization. In this area most algorithms are randomized, and…
We give a deterministic algorithm for approximately counting satisfying assignments of a degree-$d$ polynomial threshold function (PTF). Given a degree-$d$ input polynomial $p(x_1,\dots,x_n)$ over $R^n$ and a parameter $\epsilon> 0$, our…
We study the online variant of the language distance problem for two classical formal languages, the language of palindromes and the language of squares, and for the two most fundamental distances, the Hamming distance and the edit…
Given a sequence composed of a limit number of characters, we try to "read" it as a "text". This involves to segment the sequence into "words". The difficulty is to distinguish good segmentation from enormous number of random ones.Aiming at…
We initiate a systematic study of pseudo-deterministic quantum algorithms. These are quantum algorithms that, for any input, output a canonical solution with high probability. Focusing on the query complexity model, our main contributions…
It was conjectured by \v{C}ern\'y in 1964, that a synchronizing DFA on $n$ states always has a synchronizing word of length at most $(n-1)^2$, and he gave a sequence of DFAs for which this bound is reached. Until now a full analysis of all…
The importance of classifying connections in large graphs has been the motivation for a rich line of work on distributed subgraph finding that has led to exciting recent breakthroughs. A crucial aspect that remained open was whether…
Motivated by the study of genome rearrangements, the NP-hard Minimum Common String Partition problems asks, given two strings, to split both strings into an identical set of blocks. We consider an extension of this problem to unbalanced…