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We present a new distributed model of probabilistically checkable proofs (PCP). A satisfying assignment $x \in \{0,1\}^n$ to a CNF formula $\varphi$ is shared between two parties, where Alice knows $x_1, \dots, x_{n/2}$, Bob knows…
Nowadays, equivalence problems are widely used in cryptography, most notably to establish cryptosystems such as digital signatures, with MEDS, LESS, PERK as the most recent ones. However, in the context of matrix codes, only the code…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose order and/or…
We study the hardness of the problem of finding the distance of quantum error-correcting codes. The analogous problem for classical codes is known to be NP-hard, even in approximate form. For quantum codes, various problems related to…
DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited…
The knapsack problem (KP) is a very famous NP-hard problem in combinatorial optimization. Also its generalization to multiple dimensions named d-dimensional knapsack problem (d-KP) and to multiple knapsacks named multiple knapsack problem…
Nowadays, Cellular Neural Networks (CNN) are practically implemented in parallel, analog computers, showing a fast developing trend. Physicist must be aware that such computers are appropriate for solving in an elegant manner practically…
The {\em shortest common superstring} and the {\em shortest common supersequence} are two well studied problems having a wide range of applications. In this paper we consider both problems with resource constraints, denoted as the…
This paper discusses scalability of standard genetic programming (GP) and the probabilistic incremental program evolution (PIPE). To investigate the need for both effective mixing and linkage learning, two test problems are considered:…
The problem of computing distances of error-correcting codes is fundamental in both the classical and quantum settings. While hardness for the classical version of these problems has been known for some time (in both the exact and…
Image instance retrieval is the problem of retrieving images from a database which contain the same object. Convolutional Neural Network (CNN) based descriptors are becoming the dominant approach for generating {\it global image…
In the pinwheel problem, one is given an $m$-tuple of positive integers $(a_1, \ldots, a_m)$ and asked whether the integers can be partitioned into $m$ color classes $C_1,\ldots,C_m$ such that every interval of length $a_i$ has non-empty…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
Conformal prediction (CP) is a powerful framework for uncertainty quantification, generating prediction sets with coverage guarantees. Split conformal prediction relies on labeled data in the calibration procedure. However, the labeled data…
Convolutional Neural Networks (CNNs) work very well for supervised learning problems when the training dataset is representative of the variations expected to be encountered at test time. In medical image segmentation, this premise is…
We present two results about using allele-count (AC) burdens of rare SNPs discovered in a case-control sequencing study for prediction or validation in an external prospective study. When genotyping only the SNPs polymorphic in the sequence…
In this work, we study the parallel complexity of the Euclidean minimum-weight perfect matching (EWPM) problem. Here our graph is the complete bipartite graph $G$ on two sets of points $A$ and $B$ in $\mathbb{R}^2$ and the weight of each…
Persistent cycles, especially the minimal ones, are useful geometric features functioning as augmentations for the intervals in a purely topological persistence diagram (also termed as barcode). In our earlier work, we showed that computing…
We consider the hardness of approximation of optimization problems from the point of view of definability. For many NP-hard optimization problems it is known that, unless P = NP, no polynomial-time algorithm can give an approximate solution…