Related papers: Partial DNA Assembly: A Rate-Distortion Perspectiv…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
A new family of compound Poisson distribution functions from statistical linguistic is used to study the n-tuples and nucleotide composition features of DNA sequences. The relative frequency distribution of the 6-tuples and 7- tuples…
Substances such as chemical compounds are invisible to human eyes, they are usually captured by sensing equipments with their spectral fingerprints. Though spectra of pure chemicals can be identified by visual inspection, the spectra of…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
Complex structures are typical in machine learning. Tailoring learning algorithms for every structure requires an effort that may be saved by defining a generic learning procedure adaptive to any complex structure. In this paper, we propose…
Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons…
Rate distortion theory was developed for optimizing lossy compression of data, but it also has a lot of applications in statistics. In this paper we will see how rate distortion theory can be used to analyze a complicated data set involving…
In a multicellular organism different cell types express a gene in different amounts. Samples from which gene expression levels can be measured typically contain a mixture of different cell types, the resulting measurements thus give only…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
Assembly planning is the core of automating product assembly, maintenance, and recycling for modern industrial manufacturing. Despite its importance and long history of research, planning for mechanical assemblies when given the final…
A tame filtration of an algebra is defined by the growth of its terms, which has to be majorated by an exponential function. A particular case is the degree filtration used in the definition of the growth of finitely generated algebras. The…
Next-generation sequencing (NGS) technologies allow new methodologies for alternative splicing (AS) analysis. Current computational methods for AS from NGS data are mainly focused on predicting splice site junctions or de novo assembly of…
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
Directed acyclic graphs are the basic representation of the structure underlying Bayesian networks, which represent multivariate probability distributions. In many practical applications, such as the reverse engineering of gene regulatory…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
In recent years, the advancement of AI technologies has accelerated the development of smart factories. In particular, the automatic monitoring of product assembly progress is crucial for improving operational efficiency, minimizing the…
Autonomous part assembly is a challenging yet crucial task in 3D computer vision and robotics. Analogous to buying an IKEA furniture, given a set of 3D parts that can assemble a single shape, an intelligent agent needs to perceive the 3D…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…