Related papers: Phenotypic landscape inference reveals multiple ev…
We study the rank 4 linear matroid $M(H_4)$ associated with the 4-dimensional root system $H_4$. This root system coincides with the vertices of the 600-cell, a 4-dimensional regular solid. We determine the automorphism group of this…
In the field of image-based drug discovery, capturing the phenotypic response of cells to various drug treatments and perturbations is a crucial step. However, existing methods require computationally extensive and complex multi-step…
The fitness landscape encodes the mapping of genotypes to fitness and provides a succinct representation of possible trajectories followed by an evolving population. Evolutionary accessibility is quantified by the existence of…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
Do ecosystems primarily reflect evolutionary history or current environment? Predicting land-atmosphere exchange hinges on this unresolved question. Plant traits adapt to particular environments over evolutionary timescales, yet their…
It has previously been shown that the network of connected minima on a potential energy landscape is scale-free, and that this reflects a power-law distribution for the areas of the basins of attraction surrounding the minima. Here, we set…
Conventionally, convolutional neural networks (CNNs) process different images with the same set of filters. However, the variations in images pose a challenge to this fashion. In this paper, we propose to generate sample-specific filters…
Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long runs to deliver accurate posterior estimates. In this paper,…
We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape…
Recently, interest in crassulacean acid metabolism (CAM) photosynthesis has risen and new, physiologically based CAM models have emerged. These models show promise, yet unlike the more widely used physiological models of C3 and C4…
We propose a novel approach to image classification inspired by complex nonlinear biological visual processing, whereby classical convolutional neural networks (CNNs) are equipped with learnable higher-order convolutions. Our model…
Understanding how a diversity of plants in agroecosystems affects the adaptation of pathogens in a key issue in agroecology. We analyze PDE systems describing the dynamics of adaptation of two phenotypically structured populations, under…
Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to…
Our understanding of the evolutionary process has gone a long way since the publication, 150 years ago, of "On the origin of species" by Charles R. Darwin. The XXth Century witnessed great efforts to embrace replication, mutation, and…
Populations of widely distributed species often encounter and adapt to specific environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple…
We show that up to automorphisms of $\mathbb{P}^2_{\mathbb C}$ there are $5$ homogeneous convex foliations of degree four on $\mathbb{P}^2_{\mathbb C}.$ Using this result, we give a partial answer to a question posed in $2013$ by D.…
The epigenetic pathway of a cell as it differentiates from a stem cell state to a mature lineage-committed one has been historically understood in terms of Waddington's landscape, consisting of hills and valleys. The smooth top and…
The Weismann barrier, or the impossibility of inheritance of acquired traits, comprises a foundation of modern biology, and it has been a major obstacle in establishing the connection between evolution and ontogenesis. We propose the…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Cells can often choose among several stably heritable phenotypes. Examples are the expression of genes in eukaryotic cells where long chromosomal regions can adopt persistent and heritable silenced or active states, that may be associated…