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Generalized Additive Models (GAMs) are commonly considered *interpretable* within the ML community, as their structure makes the relationship between inputs and outputs relatively understandable. Therefore, it may seem natural to…
In this article we highlight chemotaxis (cellular movement) as a rich source of potential engineering applications and computational models, highlighting current research and possible future work. We first give a brief description of the…
This paper concerns applications of genetic algorithms and genetic programming to tasks for which it is difficult to find a representation that does not map to a highly complex and discontinuous fitness landscape. In such cases the standard…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the…
We axiomatize the molecular-biology reasoning style, show compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to help infer phenotypes and to predict life cycles from genotypes. The…
The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it…
The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…
In this introductory review, we give an overview of the computational chemistry methods commonly used in the field of metal-organic frameworks (MOFs), to describe or predict the structures themselves and characterize their various…
For the first time, the crystal structure of the Kob-Andersen mixture has been probed by genetic algorithms calculations. The stable structures of the system with different molar fractions of the components have been identified and their…
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…
Due to the subtle balance of intermolecular interactions that govern structure-property relations, predicting the stability of crystal structures formed from molecular building blocks is a highly non-trivial scientific problem. A…
Colorectal cancers are the third most common type of cancer. They originate from intestinal crypts, glands that descend from the intestinal lumen into the underlying connective tissue. Normal crypts are thought to exist in a dynamic…
How thousands of microtubules and molecular motors self-organize into spindles remains poorly understood. By combining static, nanometer-resolution, large-scale electron tomography reconstructions and dynamic, optical-resolution, polarized…
Stem cell heterogeneity is essential for the homeostasis in tissue development. This paper established a general formulation for understanding the dynamics of stem cell regeneration with cell heterogeneity and random transitions of…
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…
This paper explains genetic algorithm for novice in this field. Basic philosophy of genetic algorithm and its flowchart are described. Step by step numerical computation of genetic algorithm for solving simple mathematical equality problem…
A fundamental question in biology is how cell populations evolve into different subtypes based on homogeneous processes at the single cell level. Here we show that population bimodality can emerge even when biological processes are…
A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…