Related papers: DCJVis: visualization of genome rearrangements usi…
Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels,…
Aiming to obtain a high-resolution image, pansharpening involves the fusion of a multi-spectral image (MS) and a panchromatic image (PAN), the low-level vision task remaining significant and challenging in contemporary research. Most…
Far-UV circular dichroism (CD) spectroscopy provides a rapid, sensitive, nondestructive tool to analyze protein conformation by monitoring secondary structure composition. Originally intended for educational purposes, a spreadsheet-based…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…
In biomedical imaging analysis, the dichotomy between 2D and 3D data presents a significant challenge. While 3D volumes offer superior real-world applicability, they are less available for each modality and not easy to train in large scale,…
Data visualizations are created and shared on the web at an unprecedented speed, raising new needs and questions for processing and analyzing visualizations after they have been generated and digitized. However, existing formalisms focus on…
We introduce a hybrid metaphor for the visualization of the reconciliations of co-phylogenetic trees, that are mappings among the nodes of two trees. The typical application is the visualization of the co-evolution of hosts and parasites in…
As the availability of imagery data continues to swell, so do the demands on transmission, storage and processing power. Processing requirements to handle this plethora of data is quickly outpacing the utility of conventional processing…
GeneVis is a web-based tool to visualize complementary data sets of different disciplines within the field of genetics. It overlays gene-cluster information, gene-interaction data and gene-disease association data by means of web-based…
While convolutional neural networks (CNNs) and vision transformers (ViTs) have advanced medical image segmentation, they face inherent limitations such as local receptive fields in CNNs and high computational complexity in ViTs. This paper…
Program developers spend significant time on optimizing and tuning programs. During this iterative process, they apply optimizations, analyze the resulting code, and modify the compilation until they are satisfied. Understanding what the…
In this paper, we propose a cutting plane algorithm based on DC (Difference-of-Convex) programming and DC cut for globally solving Mixed-Binary Linear Program (MBLP). We first use a classical DC programming formulation via the exact…
Reconstructing ancestral gene orders is an important step towards understanding genome evolution. The Small Parsimony Problem (SPP) has been extensively studied in this regard. The problem aims at finding the gene orders at internal nodes…
A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation results. We manually drew a comprehensive map, ReconMap 2.0,…
Dynamic programming (DP) is a fundamental and powerful algorithmic paradigm taught in most undergraduate (and many graduate) algorithms classes. DP problems are challenging for many computer science students because they require identifying…
Analyzing CT scans, MRIs and X-rays is pivotal in diagnosing and treating diseases. However, detecting and identifying abnormalities from such medical images is a time-intensive process that requires expert analysis and is prone to…
In scientific visualization, scalar fields are often compared through edit distances between their merge trees. Typical tasks include ensemble analysis, feature tracking and symmetry or periodicity detection. Tree edit distances represent…
This master thesis introduces the idea of dynamic cutoffs in molecular dynamics simulations, based on the distance between particles and the interface, and presents a solution for detecting interfaces in real-time. Our dynamic cutoff method…
The BiCluster Editing problem aims at editing a given bipartite graph into a disjoint union of bicliques via a minimum number of edge deletion or addition operations. As a graph-based model for data clustering, the problem aims at a…