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Nuclear Magnetic Resonance (NMR) spectroscopy is one of the major techniques in structural biology with over 11,800 protein structures deposited in the Protein Data Bank. NMR can elucidate structures and dynamics of small and medium size…
Learning on 3D structures of large biomolecules is emerging as a distinct area in machine learning, but there has yet to emerge a unifying network architecture that simultaneously leverages the graph-structured and geometric aspects of the…
We consider the problem of positioning a cloud of points in the Euclidean space $\mathbb{R}^d$, using noisy measurements of a subset of pairwise distances. This task has applications in various areas, such as sensor network localization and…
We present a non-parametric technique to infer the projected-mass distribution of a gravitational lens system with multiple strong-lensed images. The technique involves a dynamic grid in the lens plane on which the mass distribution of the…
The flawless functioning of a protein is essentially linked to its own three-dimensional structure. Therefore, the prediction of a protein structure from its amino acid sequence is a fundamental problem in many fields that draws researchers…
There are a number of ways to procedurally generate interesting three-dimensional shapes, and a method where a cellular neural network is combined with a mesh growth algorithm is presented here. The aim is to create a shape from a genetic…
When performing robot/vehicle localization using ground penetrating radar (GPR) to handle adverse weather and environmental conditions, existing techniques often struggle to accurately estimate distances when processing B-scan images with…
Diagnosis of breast cancer has been well studied in the past. Multiple linear programming models have been devised to approximate the relationship between cell features and tumour malignancy. However, these models are less capable in…
The interval Distance Geometry Problem (iDGP) consists in finding a realization in $\mathbb{R}^K$ of a simple undirected graph $G=(V,E)$ with nonnegative intervals assigned to the edges in such a way that, for each edge, the Euclidean…
We present a geometric formulation of the Multiple Kernel Learning (MKL) problem. To do so, we reinterpret the problem of learning kernel weights as searching for a kernel that maximizes the minimum (kernel) distance between two convex…
The fundamental inverse problem in distance geometry is the one of finding positions from inter-point distances. The Discretizable Molecular Distance Geometry Problem (DMDGP) is a subclass of the Distance Geometry Problem (DGP) whose search…
In real-time trajectory planning for unmanned vehicles, on-board sensors, radars and other instruments are used to collect information on possible obstacles to be avoided and pathways to be followed. Since, in practice, observations of the…
Nuclear Magnetic Resonance (NMR) spectrometry uses electro-frequency pulses to probe the resonance of a compound's nucleus, which is then analyzed to determine its structure. The acquisition time of high-resolution NMR spectra remains a…
Nuclear Magnetic Resonance (NMR) spectroscopy is one of the most powerful and widely used tools for molecular structure elucidation in organic chemistry. However, the interpretation of NMR spectra to determine unknown molecular structures…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…
Nuclear Magnetic Resonance (NMR) spectroscopy is a central characterization method for molecular structure elucidation, yet interpreting NMR spectra to deduce molecular structures remains challenging due to the complexity of spectral data…
Local learning of sparse image models has proven to be very effective to solve inverse problems in many computer vision applications. To learn such models, the data samples are often clustered using the K-means algorithm with the Euclidean…
The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on…
Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved residue-residue contact prediction, contact-based…