Reduction of dynamical biochemical reaction networks in computational biology

Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multi-scaleness is another property of these networks, that can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to simpler networks, in a way that depends only on the orders of magnitude and not on the exact values of the kinetic parameters. The main idea used for such robust simplifications of networks is the concept of dominance among model elements, allowing hierarchical organization of these elements according to their effects on the network dynamics. This concept finds a natural formulation in tropical geometry. We revisit, in the light of these new ideas, the main approaches to model reduction of reaction networks, such as quasi-steady state and quasi-equilibrium approximations, and provide practical recipes for model reduction of linear and nonlinear networks. We also discuss the application of model reduction to backward pruning machine learning techniques

Nature as a Network of Morphological Infocomputational Processes for Cognitive Agents

This paper presents a view of nature as a network of infocomputational agents organized in a dynamical hierarchy of levels. It provides a framework for unification of currently disparate understandings of natural, formal, technical, behavioral and social phenomena based on information as a structure, differences in one system that cause the differences in another system, and computation as its dynamics, i.e. physical process of morphological change in the informational structure. We address some of the frequent misunderstandings regarding the natural/morphological computational models and their relationships to physical systems, especially cognitive systems such as living beings. Natural morphological infocomputation as a conceptual framework necessitates generalization of models of computation beyond the traditional Turing machine model presenting symbol manipulation, and requires agent-based concurrent resource-sensitive models of computation in order to be able to cover the whole range of phenomena from physics to cognition. The central role of agency, particularly material vs. cognitive agency is highlighted

Bayesian models and algorithms for protein beta-sheet prediction

Prediction of the three-dimensional structure greatly benefits from the information related to secondary structure, solvent accessibility, and non-local contacts that stabilize a protein's structure. Prediction of such components is vital to our understanding of the structure and function of a protein. In this paper, we address the problem of beta-sheet prediction. We introduce a Bayesian approach for proteins with six or less beta-strands, in which we model the conformational features in a probabilistic framework. To select the optimum architecture, we analyze the space of possible conformations by efficient heuristics. Furthermore, we employ an algorithm that finds the optimum pairwise alignment between beta-strands using dynamic programming. Allowing any number of gaps in an alignment enables us to model beta-bulges more effectively. Though our main focus is proteins with six or less beta-strands, we are also able to perform predictions for proteins with more than six beta-strands by combining the predictions of BetaPro with the gapped alignment algorithm. We evaluated the accuracy of our method and BetaPro. We performed a 10-fold cross validation experiment on the BetaSheet916 set and we obtained significant improvements in the prediction accuracy

Bayesian models and algorithms for protein beta-sheet prediction

Prediction of the three-dimensional structure greatly benefits from the information related to secondary structure, solvent accessibility, and non-local contacts that stabilize a protein's structure. Prediction of such components is vital to our understanding of the structure and function of a protein. In this paper, we address the problem of beta-sheet prediction. We introduce a Bayesian approach for proteins with six or less beta-strands, in which we model the conformational features in a probabilistic framework. To select the optimum architecture, we analyze the space of possible conformations by efficient heuristics. Furthermore, we employ an algorithm that finds the optimum pairwise alignment between beta-strands using dynamic programming. Allowing any number of gaps in an alignment enables us to model beta-bulges more effectively. Though our main focus is proteins with six or less beta-strands, we are also able to perform predictions for proteins with more than six beta-strands by combining the predictions of BetaPro with the gapped alignment algorithm. We evaluated the accuracy of our method and BetaPro. We performed a 10-fold cross validation experiment on the BetaSheet916 set and we obtained significant improvements in the prediction accuracy

Modeling Life as Cognitive Info-Computation

This article presents a naturalist approach to cognition understood as a network of info-computational, autopoietic processes in living systems. It provides a conceptual framework for the unified view of cognition as evolved from the simplest to the most complex organisms, based on new empirical and theoretical results. It addresses three fundamental questions: what cognition is, how cognition works and what cognition does at different levels of complexity of living organisms. By explicating the info-computational character of cognition, its evolution, agent-dependency and generative mechanisms we can better understand its life-sustaining and life-propagating role. The info-computational approach contributes to rethinking cognition as a process of natural computation in living beings that can be applied for cognitive computation in artificial systems.Comment: Manuscript submitted to Computability in Europe CiE 201

Aerosol Data Sources and Their Roles within PARAGON

We briefly but systematically review major sources of aerosol data, emphasizing suites of measurements that seem most likely to contribute to assessments of global aerosol climate forcing. The strengths and limitations of existing satellite, surface, and aircraft remote sensing systems are described, along with those of direct sampling networks and ship-based stations. It is evident that an enormous number of aerosol-related observations have been made, on a wide range of spatial and temporal sampling scales, and that many of the key gaps in this collection of data could be filled by technologies that either exist or are expected to be available in the near future. Emphasis must be given to combining remote sensing and in situ active and passive observations and integrating them with aerosol chemical transport models, in order to create a more complete environmental picture, having sufficient detail to address current climate forcing questions. The Progressive Aerosol Retrieval and Assimilation Global Observing Network (PARAGON) initiative would provide an organizational framework to meet this goal

The Minimum Wiener Connector

The Wiener index of a graph is the sum of all pairwise shortest-path distances between its vertices. In this paper we study the novel problem of finding a minimum Wiener connector: given a connected graph $G=(V,E)$ and a set $Q\subseteq V$ of query vertices, find a subgraph of $G$ that connects all query vertices and has minimum Wiener index. We show that The Minimum Wiener Connector admits a polynomial-time (albeit impractical) exact algorithm for the special case where the number of query vertices is bounded. We show that in general the problem is NP-hard, and has no PTAS unless $\mathbf{P} = \mathbf{NP}$. Our main contribution is a constant-factor approximation algorithm running in time $\widetilde{O}(|Q||E|)$. A thorough experimentation on a large variety of real-world graphs confirms that our method returns smaller and denser solutions than other methods, and does so by adding to the query set $Q$ a small number of important vertices (i.e., vertices with high centrality).Comment: Published in Proceedings of the 2015 ACM SIGMOD International Conference on Management of Dat