Related papers: Drawing a Waddington landscape to capture dynamic …

We propose a simple model for genetic adaptation to a changing environment, describing a fitness landscape characterized by two maxima. One is associated with "specialist" individuals that are adapted to the environment; this maximum moves…

Adaptive landscape has been a fundamental concept in many branches of modern biology since Wright's first proposition in 1932. Meanwhile, the general existence of landscape remains controversial. The causes include the mixed uses of…

Learning graph representations is a fundamental task aimed at capturing various properties of graphs in vector space. The most recent methods learn such representations for static networks. However, real world networks evolve over time and…

Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…

The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…

We discuss the population dynamics with selection and random diffusion, keeping the total population constant, in a fitness landscape associated with Constraint Satisfaction, a paradigm for difficult optimization problems. We obtain a phase…

Epigenetics is a driving force of important and ubiquitous phenomena in nature such as cell differentiation or even metamorphosis. Oppositely to its widespread role, understanding the biophysical principles that allow epigenetics to control…

We are facing a real challenge when coping with the continuous acceleration of scientific production and the increasingly changing nature of science. In this article, we extend the classical framework of co-word analysis to the study of…

Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence,…

Despite the significant recent progress in deep generative models, the underlying structure of their latent spaces is still poorly understood, thereby making the task of performing semantically meaningful latent traversals an open research…

Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…

Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map.…

Embedding static graphs in low-dimensional vector spaces plays a key role in network analytics and inference, supporting applications like node classification, link prediction, and graph visualization. However, many real-world networks…

Nature features a plethora of extraordinary photonic architectures that have been optimized through natural evolution. While numerical optimization is increasingly and successfully used in photonics, it has yet to replicate any of these…

In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…

Zooplankton images, like many other real world data types, have intrinsic properties that make the design of effective classification systems difficult. For instance, the number of classes encountered in practical settings is potentially…

We propose a novel ECGAN for the challenging semantic image synthesis task. Although considerable improvements have been achieved by the community in the recent period, the quality of synthesized images is far from satisfactory due to three…

Neoteny, also spelled Paedomorphosis, can be defined in biological terms as the retention by an organism of juvenile or even larval traits into later life. In some species, all morphological development is retarded; the organism is…

The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks…

Despite the prevalence of recent success in learning from static graphs, learning from time-evolving graphs remains an open challenge. In this work, we design new, more stringent evaluation procedures for link prediction specific to dynamic…