Related papers: A (possible) mathematical model to describe biolog…
Materials in biology span all the scales from Angstroms to meters and typically consist of complex hierarchical assemblies of simple building blocks. Here we describe an application of category theory to describe structural and resulting…
The theme of the World Conference on Physics Education 2012 is "Context, Culture, and Representations." In this talk I present a brief outline of a theoretical framework that allows us to discuss these issues using a model based in…
Classical non-neural dependency parsers put considerable effort on the design of feature functions. Especially, they benefit from information coming from structural features, such as features drawn from neighboring tokens in the dependency…
Several approaches to cognition and intelligence research rely on statistics-based models testing, namely factor analysis. In the present work we exploit the emerging dynamical systems perspective putting the focus on the role of the…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
In biomedical applications of machine learning, relevant information often has a rich structure that is not easily encoded as real-valued predictors. Examples of such data include DNA or RNA sequences, gene sets or pathways, gene…
Predicting undesirable events during the execution of a business process instance provides the process participants with an opportunity to intervene and keep the process aligned with its goals. Few approaches for tackling this challenge…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
Ecosystems are commonly conceptualized as networks of interacting species. However, partitioning natural diversity of organisms into discrete units is notoriously problematic, and mounting experimental evidence raises the intriguing…
1. Theoretical models pertaining to feedbacks between ecological and evolutionary processes are prevalent in multiple biological fields. An integrative overview is currently lacking, due to little crosstalk between the fields and the use of…
Language model users often issue queries that lack specification, where the context under which a query was issued -- such as the user's identity, the query's intent, and the criteria for a response to be useful -- is not explicit. For…
In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing…
It is widely acknowledged by researchers and practitioners that software development methodologies are generally adapted to suit specific project contexts. Research into practices-as-implemented has been fragmented and has tended to focus…
Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…
Contextuality can be understood as the impossibility to construct a globally consistent description of a model even if there is local agreement. In particular, quantum models present this property. We can describe contextuality with the…
Understanding and quantifying causal relationships between variables is essential for reasoning about the physical world. In this work, we develop a resource-theoretic framework to do so. Here, we focus on the simplest nontrivial setting --…
We argue for a convergence of crystallography, materials science and biology, that will come about through asking materials questions about biology and biological questions about materials, illuminated by considerations of information. The…