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By integrating heterogeneous functional genomic datasets, we have developed a new framework for detecting combinatorial control of gene expression, which includes estimating transcription factor activities using a singular value…

Considerable interest has recently been focused on studying multiple phenotypes simultaneously in both epidemiological and genomic studies, either to capture the multidimensionality of complex disorders or to understand shared etiology of…

We report on the possibilities of using the method of normal fundamental systems for solving some problems of oscillation theory. Large elastic dynamical systems with continuous and discrete parameters are considered, which have many…

Statistical models are often structurally unidentifiable, because different sets of parameters can lead to equal model outcomes. To be useful for prediction and parameter inference from data, stochastic population models need to be…

Variational inference is a popular method for estimating model parameters and conditional distributions in hierarchical and mixed models, which arise frequently in many settings in the health, social, and biological sciences. Variational…

A stochastic model is here introduced to investigate the molecular mechanisms which trigger the perception of pain. The action of analgesic drug compounds is discussed in a dynamical context, where the competition with inactive species is…

Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…

To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…

Scientists need to compare the support for models based on observed phenomena. The main goal of the evidential paradigm is to quantify the strength of evidence in the data for a reference model relative to an alternative model. This is done…

When describing images, humans tend not to talk about the obvious, but rather mention what they find interesting. We argue that abnormalities and deviations from typicalities are among the most important components that form what is worth…

Segregation of different cell types is a crucial process for the pattern formation in tissues, in particular during embryogenesis. Since the involved cell interactions are complex and difficult to measure individually in experiments,…

Machine learning models are essential tools in various domains, but their performance can degrade over time due to changes in data distribution or other factors. On one hand, detecting and addressing such degradations is crucial for…

Oscillatory activity is ubiquitous in natural and engineered network systems. The interaction scheme underlying interdependent oscillatory components governs the emergence of network-wide patterns of synchrony that regulate and enable…

We consider a model for substrate-depletion oscillations in genetic systems, based on a stochastic differential equation with a slowly evolving external signal. We show the existence of critical transitions in the system. We apply two…

This paper considers inference for a function of a parameter vector in a partially identified model with many moment inequalities. This framework allows the number of moment conditions to grow with the sample size, possibly at exponential…

When a founder cell and its progeny divide with incomplete cytokinesis, a network forms in which each intercellular bridge corresponds to a past mitotic event. Networks built in this manner are required for gamete production in many…

Hidden variable graphical models can sometimes imply constraints on the observable distribution that are more complex than simple conditional independence relations. These observable constraints can falsify assumptions of the model that…

Simulation models are an absolute necessity in the human and social sciences, which can only very exceptionally use experimental science methods to construct their knowledge. Models enable the simulation of social processes by replacing the…

As far as human perceptions and rational thinking are concerned, contradictions constitute a non negligible part of our reality. We often refer to these phenomena, in a more informal way, as the chicken or the egg causality dilemma.…

Synchronization is ubiquitous in nature, which is mathematically described by coupled oscillators. Synchronization strongly depends on the interaction network, and the network plays a crucial role in controlling the dynamics. To understand…