Related papers: BAUM: A DNA Assembler by Adaptive Unique Mapping a…
Tile assembly systems in the abstract Tile Assembly Model (aTAM) are computationally universal and capable of building complex shapes, but DNA-based implementations encounter formidable error rates that stifle this theoretical potential.…
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…
Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read…
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…
Optimization of high-dimensional black-box functions is an extremely challenging problem. While Bayesian optimization has emerged as a popular approach for optimizing black-box functions, its applicability has been limited to…
This paper is focused in designing an efficient on-line algorithm to reconstruct a DNA sequence and search the genes in it, we assume that the segment have no mutation or reading error, the algorithm is based on de Bruijn Graph for…
The rapid emergence of single-cell data has facilitated the study of many different biological conditions at the cellular level. Cluster analysis has been widely applied to identify cell types, capturing the essential patterns of the…
Mixed communities of organisms are found in many environments (from the human gut to marine ecosystems) and can have profound impact on human health and the environment. Metagenomics studies the genomic material of such communities through…
Motivation: As cancer researchers have come to appreciate the importance of intratumor heterogeneity, much attention has focused on the challenges of accurately profiling heterogeneity in individual patients. Experimental technologies for…
Computerized Tomography assembly and system configuration are optimized for enhanced invertibility in sparse data reconstruction. Assembly generating maximum principal components/condition number of weight matrix is designated as best…
Poor bucking decisions made by forest harvesters can have a negative effect on the products that are generated from the logs. Making the right bucking decisions is not an easy task because harvesters must rely on predictions of the stem…
Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -- called short reads -- that cause significant computational burden. To analyze the entire genome, each of the billions of…
Deep neural network learning can be formulated as a non-convex optimization problem. Existing optimization algorithms, e.g., Adam, can learn the models fast, but may get stuck in local optima easily. In this paper, we introduce a novel…
In this paper, we consider a class of nonconvex (not necessarily differentiable) optimization problems called generalized DC (Difference-of-Convex functions) programming, which is minimizing the sum of two separable DC parts and one…
To address the semantic inconsistency issue with SAM or other single-image segmentation models handling image sequences, we introduce BYOCL. This novel model outperforms SAM in extensive experiments, showcasing its Hierarchical prototype…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a…
Integrated sensing and communication (ISAC) has been envisioned to play a more important role in future wireless networks. However, the design of ISAC networks is challenging, especially when there are multiple communication and sensing…
A natural approach to software quality assurance consists in writing unit tests securing programmer-declared code invariants. Throughout the literature a great body of work has been devoted to tools and techniques automating this…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…