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Single cell segmentation is critical and challenging in live cell imaging data analysis. Traditional image processing methods and tools require time-consuming and labor-intensive efforts of manually fine-tuning parameters. Slight variations…
DNA methylation is a significant driver of cell-type heterogeneity and has been implicated in various regulatory processes ranging from cell differentiation to imprinting. As the methyl group is embedded in the DNA molecule, assessing DNA…
Landscape paradigm is ubiquitous in physics and other natural sciences, but it has to be supplemented with both quantitative and qualitatively meaningful tools for analyzing the topography of a given landscape. We here consider dynamic…
Finding meaningful distances between high-dimensional data samples is an important scientific task. To this end, we propose a new tree-Wasserstein distance (TWD) for high-dimensional data with two key aspects. First, our TWD is specifically…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
Temporal link prediction, aiming to predict future edges between paired nodes in a dynamic graph, is of vital importance in diverse applications. However, existing methods are mainly built upon uniform Euclidean space, which has been found…
Fitness landscapes are a useful concept to study the dynamics of meta-heuristics. In the last two decades, they have been applied with success to estimate the optimization power of several types of evolutionary algorithms, including genetic…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
This paper suggests that the fundamental haploid-diploid cycle of eukaryotic sex exploits a rudimentary form of the Baldwin effect. With this explanation for the basic cycle, the other associated phenomena can be explained as evolution…
Hierarchical data is common in many domains like life sciences and e-commerce, and its embeddings often play a critical role. While hyperbolic embeddings offer a theoretically grounded approach to representing hierarchies in low-dimensional…
We construct new substantive examples of non-autonomous vector fields on 3-dimensional sphere having a simple dynamics but non-trivial topology. The construction is based on two ideas: the theory of diffeomorpisms with wild separatrix…
Cancer cells can be described as an invasive species that is able to establish itself in a new environment. The concept of niche construction can be utilized to describe the process by which cancer cells terraform their environment, thereby…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Generative probabilistic models emerge as a new paradigm in data-driven, evolution-informed design of biomolecular sequences. This paper introduces a novel approach, called Edge Activation Direct Coupling Analysis (eaDCA), tailored to the…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
We define a model for random (abstract) cell complexes (CCs), similiar to the well-known Erd\H{o}s-R\'enyi model for graphs and its extensions for simplicial complexes. To build a random cell complex, we first draw from an Erd\H{o}s-R\'enyi…
The prevention of biodiversity loss in agricultural landscapes to protect ecosystem stability and functions is of major importance in itself and for the maintenance of associated ecosystem services. Intense agriculture leads to a loss in…
Heterogeneous graphs are present in various domains, such as social networks, recommendation systems, and biological networks. Unlike homogeneous graphs, heterogeneous graphs consist of multiple types of nodes and edges, each representing…
This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as…