Related papers: Computing the Inversion-Indel Distance

Supergranules are divergent 30-Mm sized cellular flows observed everywhere at the solar photosphere. Their place in the hierarchy of convective structures and their origin remain poorly understood (Rincon et al., 2018). Estimating…

Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a…

Graphs are versatile tools for representing structured data. As a result, a variety of machine learning methods have been studied for graph data analysis. Although many such learning methods depend on the measurement of differences between…

Starting with a similarity function between objects, it is possible to define a distance metric on pairs of objects, and more generally on probability distributions over them. These distance metrics have a deep basis in functional analysis,…

Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and protein. However, the DNA storage channel is prone to errors such as deletions, insertions, and substitutions. During the…

Semantic segmentation of medical images is an essential first step in computer-aided diagnosis systems for many applications. However, given many disparate imaging modalities and inherent variations in the patient data, it is difficult to…

In this work, we study linear error-correcting codes against adversarial insertion-deletion (indel) errors. While most constructions for the indel model are nonlinear, linear codes offer compact representations, efficient encoding, and…

Existing measures and representations for trajectories have two longstanding fundamental shortcomings, i.e., they are computationally expensive and they can not guarantee the `uniqueness' property of a distance function: dist(X,Y) = 0 if…

Although numerous improvements have been made in the field of image segmentation using convolutional neural networks, the majority of these improvements rely on training with larger datasets, model architecture modifications, novel loss…

We propose a new embedding method for a single vector and for a pair of vectors. This embedding method enables: a) efficient classification and regression of functions of single vectors; b) efficient approximation of distance functions; and…

We present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible…

We present the Inverse Drum Machine, a novel approach to Drum Source Separation that leverages an analysis-by-synthesis framework combined with deep learning. Unlike recent supervised methods that require isolated stem recordings for…

Deep learning has redefined the field of artificial intelligence (AI) thanks to the rise of artificial neural networks, which are architectures inspired by their neurological counterpart in the brain. Through the years, this dualism between…

In an oriented graph $\overrightarrow{G}$, the inversion of a subset $X$ of vertices is the operation that reverses the orientation of all arcs with both end-vertices in $X$. The inversion graph of a graph $G$, denoted by $\mathcal{I}(G)$,…

This Special Report summarizes the 2022 AAPM Grand Challenge on Deep-Learning spectral Computed Tomography (DL-spectral CT) image reconstruction. The purpose of the challenge is to develop the most accurate image reconstruction algorithm…

The clinical management of several cardiovascular conditions, such as pulmonary hypertension, require the assessment of the right ventricular (RV) function. This work addresses the fully automatic and robust access to one of the key RV…

Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations…

We propose a novel combination of methods that (i) portrays quantitative characteristics of a DNA sequence as an image, (ii) computes distances between these images, and (iii) uses these distances to output a map wherein each sequence is a…

Deep fully convolutional neural network (FCN) based architectures have shown great potential in medical image segmentation. However, such architectures usually have millions of parameters and inadequate number of training samples leading to…

Segmentation of the left ventricle (LV) from cardiac magnetic resonance imaging (MRI) datasets is an essential step for calculation of clinical indices such as ventricular volume and ejection fraction. In this work, we employ deep learning…