Related papers: A (possible) mathematical model to describe biolog…

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 work, we introduce the notion of Context-Based Prediction Models. A Context-Based Prediction Model determines the probability of a user's action (such as a click or a conversion) solely by relying on user and contextual features,…

One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…

Structural hierarchy, in which materials possess distinct features on multiple length scales, is ubiquitous in nature; diverse biological materials, such as bone, cellulose, and muscle, have as many as ten hierarchical levels. Structural…

Learning language of protein sequences, which captures non-local interactions between amino acids close in the spatial structure, is a long-standing bioinformatics challenge, which requires at least context-free grammars. However, complex…

Discrete temporal transitions occur in a variety of domains, but this work is mainly motivated by applications in molecular biology: explaining and analyzing observed transcriptome and proteome time series by literature and database…

Many biological systems regulate phenotypic heterogeneity as a fitness-maximising strategy in uncertain and dynamic environments. Analysis of such strategies is typically confined both to a discrete set of environmental conditions, and to a…

Defining the extent of epistasis - the non-independence of the effects of mutations - is essential for understanding the relationship of genotype, phenotype, and fitness in biological systems. The applications cover many areas of biological…

The lifetime of protein domains and ligand-receptor complexes under force is crucial for mechanosensitive functions, while many aspects of how force affects the lifetime still remain poorly understood. Here, we report a new analytical…

This is a non-technical introduction into theory of contextuality. More precisely, it presents the basics of a theory of contextuality called Contextuality-by-Default (CbD). One of the main tenets of CbD is that the identity of a random…

Hierarchy is one of the most conspicuous features of numerous natural, technological and social systems. The underlying structures are typically complex and their most relevant organizational principle is the ordering of the ties among the…

Context is a rich concept and is an elusive concept to define. The concept of context has been studied by philosophers, linguists, psychologists, and recently by computer scientists. Within each research community the term context was…

Context awareness is increasingly gaining applicability in interactive ubiquitous mobile computing systems. Each context-aware application has its own set of behaviors to react to context modifications. This paper is concerned with the…

A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…

We introduce a new notion, that of a contextuality profile of a system of random variables. Rather than characterizing a system's contextuality by a single number, its overall degree of contextuality, we show how it can be characterized by…

The mixed multinomial logit model assumes constant preference parameters of a decision-maker throughout different choice situations, which may be considered too strong for certain choice modelling applications. This paper proposes an…

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at…

The outcomes of elections, product sales, and the structure of social connections are all determined by the choices individuals make when presented with a set of options, so understanding the factors that contribute to choice is crucial. Of…

A class of models for large-scale evolution and mass extinctions is presented. These models incorporate environmental changes on all scales, from influences on a single species to global effects. This is a step towards a unified picture of…

In-context learning is a surprising and important phenomenon that emerged when modern language models were scaled to billions of learned parameters. Without modifying a large language model's weights, it can be tuned to perform various…