Related papers: A (possible) mathematical model to describe biolog…
Automation systems are increasingly being used in dynamic and various operating conditions. With higher flexibility demands, they need to promptly respond to surrounding dynamic changes by adapting their operation. Context information…
To make effective decisions, it is important to have a thorough understanding of the causal relationships among actions, environments, and outcomes. This review aims to surface three crucial aspects of decision-making through a causal lens:…
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…
Dependency syntax represents the structure of a sentence as a tree composed of dependencies, i.e., directed relations between lexical units. While in its more general form any such tree is allowed, in practice many are not plausible or are…
From critical infrastructure, to physiology and the human brain, complex systems rarely occur in isolation. Instead, the functioning of nodes in one system often promotes or suppresses the functioning of nodes in another. Despite advances…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
We propose to compose dynamic tree structures that place the objects in an image into a visual context, helping visual reasoning tasks such as scene graph generation and visual Q&A. Our visual context tree model, dubbed VCTree, has two key…
The implications of large-scale coherence in biological systems and possible links to quantum theory are only beginning to be explored. Whether quantum-like coherent phenomena are relevant, or even possible at all, at the high temperatures…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
In data analysis, latent variables play a central role because they help provide powerful insights into a wide variety of phenomena, ranging from biological to human sciences. The latent tree model, a particular type of probabilistic…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
The basic mechanics of evolution have been understood since Darwin. But debate continues over whether macroevolutionary phenomena are driven primary by the fitness structure of genotype space or by ecological interaction. In this paper we…
We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate…
We present a mathematical framework (referred to as Context-driven Actualization of Potential, or CAP) for describing how entities change over time under the influence of a context. The approach facilitates comparison of change of state of…
This paper is motivated by the desire to study package management using the toolkit of the semantics of functional languages. As it transpires, this is deeply related to the semantics of concurrent computation. The models we produce are not…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…
Object ranking is an important problem in the realm of preference learning. On the basis of training data in the form of a set of rankings of objects, which are typically represented as feature vectors, the goal is to learn a ranking…
The complex nature of organizational culture challenges our ability to infers its underlying dynamics from observational studies. Recent computational studies have adopted a distinct different view, where plausible mechanisms are proposed…
Interactions are ubiquitous across biological systems. These interactions can be abstracted as patterns of connections among distinct units such as genes, proteins, individual organisms, or species which form a hierarchy of biological…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…