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A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
As a fundamental problem in many different fields, link prediction aims to estimate the likelihood of an existing link between two nodes based on the observed information. Since this problem is related to many applications ranging from…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
Image matching, which establishes correspondences between two-view images to recover 3D structure and camera geometry, serves as a cornerstone in computer vision and underpins a wide range of applications, including visual localization, 3D…
In change-point analysis, one aims at finding the locations of abrupt distributional changes (if any) in a sequence of multivariate observations. In this article, we propose some nonparametric methods based on averages of pairwise distances…
The numerical properties of algorithms for finding the intersection of sets depend to some extent on the regularity of the sets, but even more importantly on the regularity of the intersection. The alternating projection algorithm of von…
We propose a method to match anatomical locations between pairs of medical images in longitudinal comparisons. The matching is made possible by computing a descriptor of the query point in a source image based on a hierarchical sparse…
Persistent (co)homology is a central construction in topological data analysis, where it is used to quantify prominence of features in data to produce stable descriptors suitable for downstream analysis. Persistence is challenging to…
A protein contact map is a binary symmetric adjacency matrix capturing the distance relationship between atoms of a protein. Each cell (i, j) of a protein contact map states whether the atoms (nodes) i and j are within some Euclidean…
Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and…
This paper addresses the problem of correlation estimation in sets of compressed images. We consider a framework where images are represented under the form of linear measurements due to low complexity sensing or security requirements. We…
Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the…
We address the problem of distributed matching of features in networks with vision systems. Every camera in the network has limited communication capabilities and can only exchange local matches with its neighbors. We propose a distributed…
The structure of a protein is crucial in determining its functionality, and is much more conserved than sequence during evolution. A key task in structural biology is to compare protein structures in order to determine evolutionary…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
Contact-assisted protein folding has made very good progress, but two challenges remain. One is accurate contact prediction for proteins lack of many sequence homologs and the other is that time-consuming folding simulation is often needed…
We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in…
Time series exploration and mining has many applications across several industrial and scientific domains. In this paper, we consider the problem of detecting locally similar pairs and groups, called bundles, over co-evolving time series.…
Dynamic graphs are rife with higher-order interactions, such as co-authorship relationships and protein-protein interactions in biological networks, that naturally arise between more than two nodes at once. In spite of the ubiquitous…