Related papers: Exact and Approximation Algorithms for DNA Tag Set…

We study optimal decision policies for integer linear programs with a fixed feasible set and varying cost vectors, represented as linear decision trees. Once synthesized for a given feasible set, they return an optimal solution for any…

Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA…

We study the Short Path Packing problem which asks, given a graph $G$, integers $k$ and $\ell$, and vertices $s$ and $t$, whether there exist $k$ pairwise internally vertex-disjoint $s$-$t$ paths of length at most $\ell$. The problem has…

The last decade has seen a flurry of research on all-pairs-similarity-search (or, self-join) for text, DNA, and a handful of other datatypes, and these systems have been applied to many diverse data mining problems. Surprisingly, however,…

Suffix trees are an important data structure at the core of optimal solutions to many fundamental string problems, such as exact pattern matching, longest common substring, matching statistics, and longest repeated substring. Recent lines…

Data Augmentation (DA) is known to improve the generalizability of deep neural networks. Most existing DA techniques naively add a certain number of augmented samples without considering the quality and the added computational cost of these…

Finding an optimal assignment between two sets of objects is a fundamental problem arising in many applications, including the matching of `bag-of-words' representations in natural language processing and computer vision. Solving the…

Annotating images with tags is useful for indexing and retrieving images. However, many available annotation data include missing or inaccurate annotations. In this paper, we propose an image annotation framework which sequentially performs…

To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…

Retrieval-Augmented Generation enhances language models by retrieving external knowledge to support informed and grounded responses. However, traditional RAG methods rely on fragment-level retrieval, limiting their ability to address…

An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…

Several real problems ranging from text classification to computational biology are characterized by hierarchical multi-label classification tasks. Most of the methods presented in literature focused on tree-structured taxonomies, but only…

Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the given pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation…

Pairwise comparison labels are more informative and less variable than class labels, but generating them poses a challenge: their number grows quadratically in the dataset size. We study a natural experimental design objective, namely,…

We propose a linear-time, single-pass, top-down algorithm for multiple testing on directed acyclic graphs (DAGs), where nodes represent hypotheses and edges specify a partial ordering in which hypotheses must be tested. The procedure is…

A search engine's ability to retrieve desirable datasets is important for data sharing and reuse. Existing dataset search engines typically rely on matching queries to dataset descriptions. However, a user may not have enough prior…

This study aims to optimize the existing retrieval-augmented generation model (RAG) by introducing a graph structure to improve the performance of the model in dealing with complex knowledge reasoning tasks. The traditional RAG model has…

Causal structure learning, also known as causal discovery, aims to estimate causal relationships between variables as a form of a causal directed acyclic graph (DAG) from observational data. One of the major frameworks is the order-based…

In this paper, we address a class of specially structured problems that include speed planning, for mobile robots and robotic manipulators, and dynamic programming. We develop two new numerical procedures, that apply to the general case and…

To equip DNA-based data storage with random-access capabilities, Yazdi et al. (2018) prepended DNA strands with specially chosen address sequences called primers and provided certain design criteria for these primers. We provide explicit…