相关论文: Presence-absence reasoning for evolutionary phenot…

Three steps aid in the analysis of selection. First, describe phenotypes by their component causes. Components include genes, maternal effects, symbionts, and any other predictors of phenotype that are of interest. Second, describe fitness…

A rigorous understanding of how multicellular behaviors arise from the actions of single cells requires quantitative frameworks that bridge the gap between genetic circuits, the arrangement of cells in space, and population-level behaviors.…

Deep-learning models can extract a rich assortment of features from data. Which features a model uses depends not only on \emph{predictivity} -- how reliably a feature indicates training-set labels -- but also on \emph{availability} -- how…

Biological genotypes do not code directly for phenotypes; developmental physiology is the control layer that separates genomes from capacities ascertained by selection. A key aspect is competency, as cells are not a passive material but…

Small-molecule drug discovery requires simultaneous optimization of numerous properties of candidate molecules. These properties can be investigated through the analysis of high-dimensional biological signatures, such as cell morphology and…

Motivations: People are generating an enormous amount of social data to describe their health care experiences, and continuously search information about diseases, symptoms, diagnoses, doctors, treatment options and medicines. The…

An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability relies on the existence of sufficiently large genotype networks, that is ensembles of sequences with the same phenotype that…

Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside of the range of conditions to…

An approach to amputation, the process of introducing missing values to a complete dataset, is presented. It allows to construct missingness indicators in a flexible and principled way via copulas and Bernoulli margins and to incorporate…

Computational phenotyping is essential for biomedical research but often requires significant time and resources, especially since traditional methods typically involve extensive manual data review. While machine learning and natural…

The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…

Abundance data are used in ecology for species monitoring and conservation. These count data often display several specific characteristics like numerous missing data, high variance, and a high proportion of zeros, particularly when…

Establishing the emergence of evolutionary behavior as a defining characteristic of 'life' is a major step in the Artificial life (ALife) studies. We present here an abstract formal framework for this aim based upon the notion of high-level…

This study investigates the use of unsupervised word embeddings and sequence features for sample representation in an active learning framework built to extract clinical concepts from clinical free text. The objective is to further reduce…

Evolutionary dynamics can be studied in well-mixed or structured populations. Population structure typically arises from the heterogeneous distribution of individuals in physical space or on social networks. Here we introduce a new type of…

Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…

Automated phenotyping of plants for breeding and plant studies promises to provide quantitative metrics on plant traits at a previously unattainable observation frequency. Developers of tools for performing high-throughput phenotyping are,…

Evolutionary success depends on the capacity to adapt: organisms must respond to environmental challenges through both genetic innovation and lifetime learning. The gene-centric paradigm attributes evolutionary causality exclusively to…

It is commonly argued that an undesirable feature of a theoretical or phenomenological model is that salient observables are sensitive to values of parameters in the model. But in what sense is it undesirable to have such 'fine-tuning' of…

A macroscopic theory for describing cellular states during steady-growth is presented, which is based on the consistency between cellular growth and molecular replication, as well as the robustness of phenotypes against perturbations.…