Related papers: Exact and Approximation Algorithms for DNA Tag Set…
We introduce the strongly NP-complete pagination problem, an extension of BIN PACKING where packing together two items may make them occupy less volume than the sum of their individual sizes. To achieve this property, an item is defined as…
We consider a problem that involves finding similar elements in a collection of sets. The problem is motivated by applications in machine learning and pattern recognition. We formulate the similar elements problem as an optimization and…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…
We present a novel approach for designing complex approximate arithmetic circuits that trade correctness for power consumption and play important role in many energy-aware applications. Our approach integrates in a unique way formal methods…
In large datasets, it is hard to discover and analyze structure. It is thus common to introduce tags or keywords for the items. In applications, such datasets are then filtered based on these tags. Still, even medium-sized datasets with a…
Given an edge-weighted (metric/general) complete graph with $n$ vertices, the maximum weight (metric/general) $k$-cycle/path packing problem is to find a set of $\frac{n}{k}$ vertex-disjoint $k$-cycles/paths such that the total weight is…
Pattern set mining, which is the task of finding a good set of patterns instead of all patterns, is a fundamental problem in data mining. Many different definitions of what constitutes a good set have been proposed in recent years. In this…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Obtaining high-quality labeled datasets is often costly, requiring either human annotation or expensive experiments. In theory, powerful pre-trained AI models provide an opportunity to automatically label datasets and save costs.…
Tagging has been recognized as a successful practice to boost relevance matching for information retrieval (IR), especially when items lack rich textual descriptions. A lot of research has been done for either multi-label text…
It is known that annotating named entities in unstructured and semi-structured data sets by their concepts improves the effectiveness of answering queries over these data sets. As every enterprise has a limited budget of time or…
Higher-dimensional orthogonal packing problems have a wide range of practical applications, including packing, cutting, and scheduling. Combining the use of our data structure for characterizing feasible packings with our new classes of…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
As transistor dimensions continue to shrink, binary devices are rapidly approaching their fundamental limits in power density. In response, multi-valued systems have attracted significant attention due to their enhanced information density.…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
Model structure and complexity selection remains a challenging problem in system identification, especially for parametric non-linear models. Many Evolutionary Algorithm (EA) based methods have been proposed in the literature for estimating…
Graphs provide a natural way to represent data by encoding information about objects and the relationships between them. With the ever-increasing amount of data collected and generated, locating specific patterns of relationships between…
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…