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Single-cell RNA sequencing (scRNA-seq) data analysis is pivotal for understanding cellular heterogeneity. However, the high sparsity and complex noise patterns inherent in scRNA-seq data present significant challenges for traditional…

Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…

Semantic change detection (SCD) extends the binary change detection task to provide not only the change locations but also the detailed "from-to" categories in multi-temporal remote sensing data. Such detailed semantic insights into changes…

The edit distance under the DCJ model can be computed in linear time for genomes with equal content or with Indels. But it becomes NP-Hard in the presence of duplications, a problem largely unsolved especially when Indels are considered. In…

While most current high-throughput DNA sequencing technologies generate short reads with low error rates, emerging sequencing technologies generate long reads with high error rates. A basic question of interest is the tradeoff between read…

While deep learning approaches have shown remarkable performance in many imaging tasks, most of these methods rely on availability of large quantities of data. Medical image data, however, is scarce and fragmented. Generative Adversarial…

Aiming to generate easy-to-handle assembly sequences for robotic assembly, this study tackles assembly sequence generation by considering two tradeoff objectives: (1) insertion conditions and (2) degrees of constraints among assembled…

In just the last decade, a multitude of bio-technologies and software pipelines have emerged to revolutionize genomics. To further their central goal, they aim to accelerate and improve the quality of de novo whole-genome assembly starting…

Despite their effectiveness, current deep learning models face challenges with images coming from different domains with varying appearance and content. We introduce SegCLR, a versatile framework designed to segment images across different…

The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…

The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…

Large-scale medical segmentation datasets often combine manual and pseudo-labels of uneven quality, which can compromise training and evaluation. Low-quality labels may hamper performance and make the model training less robust. To address…

Automatic defect detection for 3D printing processes, which shares many characteristics with change detection problems, is a vital step for quality control of 3D printed products. However, there are some critical challenges in the current…

The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic…

Single-Cell RNA sequencing (scRNA-seq) measurements have facilitated genome-scale transcriptomic profiling of individual cells, with the hope of deconvolving cellular dynamic changes in corresponding cell sub-populations to better…

We introduce an approach to integrate segmentation information within a convolutional neural network (CNN). This counter-acts the tendency of CNNs to smooth information across regions and increases their spatial precision. To obtain…

Accurately segmenting structural cracks at the pixel level remains a major hurdle, as existing methods fail to integrate local textures with pixel dependencies, often leading to fragmented and incomplete predictions. Moreover, their high…

Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…

The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…

At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…