Related papers: Drawing a Waddington landscape to capture dynamic …
"Epigenetic Tracking" is the name of a model of cellular development that, coupled with an evolutionary technique, becomes an evo-devo (or "artificial embryology", or "computational development") method to generate 2d or 3d sets of…
We study a family of networks of autocatalytic reactions, which we call hyperchains, that are a generalization of hypercycles. Hyperchains, and the associated dynamical system called replicator equations, are a possible mechanism for…
Deep neural networks exhibit a fascinating spectrum of phenomena ranging from predictable scaling laws to the unpredictable emergence of new capabilities as a function of training time, dataset size and network size. Analysis of these…
Epigenetic Tracking (ET) is an Artificial Embryology system which allows for the evolution and development of large complex structures built from artificial cells. In terms of the number of cells, the complexity of the bodies generated with…
Energy landscape theory describes how a full-length protein can attain its native fold after sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the…
Learning on synthetic data and transferring the resulting properties to their real counterparts is an important challenge for reducing costs and increasing safety in machine learning. In this work, we focus on autoencoder architectures and…
How much information does a cell inherit from its ancestors beyond its genetic sequence? What are the epigenetic mechanisms that allow this? Despite the rise in available epigenetic data, how such information is inherited through the cell…
Functional brain connectivity changes dynamically over time, making its representation challenging for learning on non-Euclidean data. We present a framework that encodes dynamic functional connectivity as an image representation of…
Biomolecular networks have already found great utility in characterizing complex biological systems arising from pair-wise interactions amongst biomolecules. Here, we review how graph theoretical approaches can be applied not only for a…
Adaptation mechanism of cells on the basis of stochastic gene expression and epigenetic modification is proposed. From marginally stable states generated by epigenetic modification, a gene expression pattern that achieves greater cell…
The class of epistatic fitness landscapes is much more diverse than the class of non-epistatic landscapes, and so it stands to reason that there exist dynamical phenomena that can only be realized in the presence of epistasis. Here, we…
The primary objective of this thesis is to develop novel algorithmic approaches for Graph Representation Learning of static and single-event dynamic networks. In such a direction, we focus on the family of Latent Space Models, and more…
The study of dynamical systems defined on complex networks provides a natural framework with which to investigate myriad features of neural dynamics, and has been widely undertaken. Typically, however, networks employed in theoretical…
Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…
Epistatic interactions between mutations add substantial complexity to adaptive landscapes, and are often thought of as detrimental to our ability to predict evolution. Yet, patterns of global epistasis, in which the fitness effect of a…
Profiling cellular phenotypes from microscopic imaging can provide meaningful biological information resulting from various factors affecting the cells. One motivating application is drug development: morphological cell features can be…
Gradual transformation of the epidermal stem cells to corneocytes involves a chain of chronologically well-arranged events that mostly stimulated locally by their neighbors. Cell diversity that observed during the differentiation through…
In aiming to explain the establishment, maintenance and stability of methylation pattern in gene body of Arabidopsis we propose here a theoretical framework for understanding how the methylated and unmethylated states of cytosine residues…
An endogenous molecular-cellular network for both normal and abnormal functions is assumed to exist. This endogenous network forms a nonlinear stochastic dynamical system, with many stable attractors in its functional landscape. Normal or…
Evolution is a dynamic process. The two classical forces of evolution are mutation and selection. Assuming small mutation rates, evolution can be predicted based solely on the fitness differences between phenotypes. Predicting an…