Related papers: Genomic Problems Involving Copy Number Profiles: C…
The decoding problem is a ubiquitous algorithmic task in fault-tolerant quantum computing, and solving it efficiently is essential for scalable quantum computing. Here, we prove that minimum-weight decoding is NP-hard in three…
Learning scientific document representations can be substantially improved through contrastive learning objectives, where the challenge lies in creating positive and negative training samples that encode the desired similarity semantics.…
Molecular sequence analysis is crucial for comprehending several biological processes, including protein-protein interactions, functional annotation, and disease classification. The large number of sequences and the inherently complicated…
Array-Based Comparative Genomic Hybridization (aCGH) is a method used to search for genomic regions with copy numbers variations. For a given aCGH profile, one challenge is to accurately segment it into regions of constant copy number.…
Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid…
The computation of genomic distances has been a very active field of computational comparative genomics over the last 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and…
Inspired by number series tests to measure human intelligence, we suggest number sequence prediction tasks to assess neural network models' computational powers for solving algorithmic problems. We define the complexity and difficulty of a…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
Recent advances in genomics have underscored the surprising ubiquity of DNA copy number variation (CNV). Fortunately, modern genotyping platforms also detect CNVs with fairly high reliability. Hidden Markov models and algorithms have played…
The problem of clustering fingerprint vectors is an interesting problem in Computational Biology that has been proposed in (Figureroa et al. 2004). In this paper we show some improvements in closing the gaps between the known lower bounds…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…
The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
A binary matrix has the Consecutive Ones Property (C1P) if its columns can be ordered in such a way that all 1's on each row are consecutive. A Minimal Conflicting Set is a set of rows that does not have the C1P, but every proper subset has…
We introduce a binary embedding framework, called Proximity Preserving Code (PPC), which learns similarity and dissimilarity between data points to create a compact and affinity-preserving binary code. This code can be used to apply fast…
This paper surveys results on complexity of the optimal recombination problem (ORP), which consists in finding the best possible offspring as a result of a recombination operator in a genetic algorithm, given two parent solutions. We…
We give simple deterministic reductions demonstrating the NP-hardness of approximating the nearest codeword problem and minimum distance problem within arbitrary constant factors (and almost-polynomial factors assuming NP cannot be solved…
Recent studies demonstrated the eligibility of convolutional neural networks (CNNs) for solving the image registration problem. CNNs enable faster transformation estimation and greater generalization capability needed for better support…
Copy Number Variations (CNVs) of regions of the human genome are important in disease association studies.The digital array is a nanofluidic biochip which utilizes integrated channels and valves that partition mixtures of sample and…