Related papers: Phenotypic landscape inference reveals multiple ev…
Recent attempts for unsupervised landmark learning leverage synthesized image pairs that are similar in appearance but different in poses. These methods learn landmarks by encouraging the consistency between the original images and the…
Understanding the evolutionary relationship among species is of fundamental importance to the biological sciences. The location of the root in any phylogenetic tree is critical as it gives an order to evolutionary events. None of the…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
In this paper we suggest that, under suitable conditions, supervised learning can provide the basis to formulate at the microscopic level quantitative questions on the phenotype structure of multicellular organisms. The problem of…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Computational Phenotype Discovery research has taken various pragmatic approaches to disentangling phenotypes from the episodic observations in Electronic Health Records. In this work, we use transformation into continuous, longitudinal…
A mechanism of sympatric speciation is presented based on the interaction-induced developmental plasticity of phenotypes. First, phenotypes of individuals with identical genotypes split into a few groups, according to instability in the…
Motivation: Driver (epi)genomic alterations underlie the positive selection of cancer subpopulations, which promotes drug resistance and relapse. Even though substantial heterogeneity is witnessed in most cancer types, mutation accumulation…
The Rosids is one of the largest groups of flowering plants, with 140 families and ~70,000 species. Previous phylogenetic studies of the rosids have primarily utilized organelle genes that likely differ in evolutionary histories from…
A technique named Feature Learning from Image Markers (FLIM) was recently proposed to estimate convolutional filters, with no backpropagation, from strokes drawn by a user on very few images (e.g., 1-3) per class, and demonstrated for…
This paper describes a method for inferring three-dimensional (3D) plant branch structures that are hidden under leaves from multi-view observations. Unlike previous geometric approaches that heavily rely on the visibility of the branches…
Deep phenotyping is an emerging conceptual paradigm and experimental approach that seeks to measure many aspects of phenotypes and link them to understand the underlying biology. Successful deep phenotyping has mostly been applied in…
The unwelcome evolution of malignancy during cancer progression emerges through a selection process in a complex heterogeneous population structure. In the present work, we investigate evolutionary dynamics in a phenotypically heterogeneous…
The relationship between microscopic observations and macroscopic behavior is a fundamental open question in biophysical systems. Here, we develop a unified approach that---in contrast with existing methods---predicts cell type from…
Spatial patterns are widely observed in numerous nonequilibrium natural systems, often undergoing complex transitions and bifurcations, thereby exhibiting significant importance in many physical and biological systems such as embryonic…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
Motivation. Cancer heterogeneity is observed at multiple biological levels. To improve our understanding of these differences and their relevance in medicine, approaches to link organ- and tissue-level information from diagnostic images and…
Medicines and agricultural biocides are often discovered using large phenotypic screens across hundreds of compounds, where visible effects of whole organisms are compared to gauge efficacy and possible modes of action. However, such…
This paper proposes a novel heterogeneous grid convolution that builds a graph-based image representation by exploiting heterogeneity in the image content, enabling adaptive, efficient, and controllable computations in a convolutional…
Existing studies comparing individual-based models of growing cell populations and their continuum counterparts have mainly focused on homogeneous populations, in which all cells have the same phenotypic characteristics. However,…