Related papers: Large scale evaluation of differences between netw…
A multi-scale approach to the inverse reconstruction of a pattern's microstructure is reported. Instead of a correlation function, a pair of entropic descriptors (EDs) is proposed for stochastic optimization method. The first of them…
Networks represent relationships between entities in many complex systems, spanning from online social interactions to biological cell development and brain connectivity. In many cases, relationships between entities are unambiguously…
Ultrasound reflection tomography is widely used to image large complex specimens that are only accessible from a single side, such as well systems and nuclear power plant containment walls. Typical methods for inverting the measurement rely…
The relationship between the design and functionality of molecular networks is now a key issue in biology. Comparison of regulatory networks performing similar tasks can give insights into how network architecture is constrained by the…
Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…
Hierarchical graph clustering is a common technique to reveal the multi-scale structure of complex networks. We propose a novel metric for assessing the quality of a hierarchical clustering. This metric reflects the ability to reconstruct…
Gynandromorphs are creatures where at least two different body sections are a different sex. Bilateral gynandromorphs are half male and half female. Here we develop a theory of gynandromorph ontogeny based on developmental control networks.…
Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale…
In this report a systematic approach is used to determine the approximate genetic network and robust dependencies underlying differentiation. The data considered is in the form of a binary matrix and represent the expression of the nine…
Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use…
Pedigrees are directed acyclic graphs that represent ancestral relationships between individuals in a population. Based on a schematic recombination process, we describe two simple Markov models for sequences evolving on pedigrees - Model R…
While deep learning has revolutionized the prediction of rigid protein structures, modelling the conformational ensembles of Intrinsically Disordered Proteins (IDPs) remains a key frontier. Current AI paradigms present a trade-off: Protein…
The relations, rather than the elements, constitute the structure of networks. We therefore develop a systematic approach to the analysis of networks, modelled as graphs or hypergraphs, that is based on structural properties of…
Several approaches were proposed to describe the geomorphology of drainage networks and the abiotic/biotic factors determining their morphology. There is an intrinsic complexity of the explicit qualification of the morphological variations…
Identifying possible clusters in datasets and estimating their overall modularity are central tasks in pattern recognition. In the present work, concepts and methodologies are described for performing these tasks while considering only the…
Identifying unique characteristics in a network through comparison with another network is an essential network analysis task. For example, with networks of protein interactions obtained from normal and cancer tissues, we can discover…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
Deconvolution of cell mixtures in "bulk" transcriptomic samples from homogenate human tissue is important for understanding the pathologies of diseases. However, several experimental and computational challenges remain in developing and…
We propose an approach to 3D reconstruction via inverse procedural modeling and investigate two variants of this approach. The first option consists in the fitting set of input parameters using a genetic algorithm. We demonstrate the…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…