Many Roads to Synchrony: Natural Time Scales and Their Algorithms

We consider two important time scales---the Markov and cryptic orders---that monitor how an observer synchronizes to a finitary stochastic process. We show how to compute these orders exactly and that they are most efficiently calculated from the epsilon-machine, a process's minimal unifilar model. Surprisingly, though the Markov order is a basic concept from stochastic process theory, it is not a probabilistic property of a process. Rather, it is a topological property and, moreover, it is not computable from any finite-state model other than the epsilon-machine. Via an exhaustive survey, we close by demonstrating that infinite Markov and infinite cryptic orders are a dominant feature in the space of finite-memory processes. We draw out the roles played in statistical mechanical spin systems by these two complementary length scales.Comment: 17 pages, 16 figures: http://cse.ucdavis.edu/~cmg/compmech/pubs/kro.htm. Santa Fe Institute Working Paper 10-11-02

WikiPathways: building research communities on biological pathways.

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further

Model Checking of Software Defined Networks using Header Space Analysis

This thesis investigates the topic of verifying network status validity with a Cyber Security perspective. The fields of interest are dynamic networks like OpenFlow and Software Defined Networks, where these problems may have larger attack surface and greater impact. The framework under study is called Header Space Analysis, a formal model and protocol-agnostic framework that allows to perform static policy checking both in classical TCP/IP networks and modern dynamic SDN. The goal is to analyse some classes of network failure, declaring valid network states and recognizing invalid ones. HSA has evolved in NetPlumber, to face problems caused by high dynamics of SDN networks. The main difference between HSA and NetPlumber is the incremental way that the latter performs checks and keeps state updated, verifying the actual state compliance with the expected state defined in its model, but the concept is the same: declare what's allowed and recognize states violating that model. The second and main contribute of this thesis is to expand existing vision with the purpose of increasing the network security degree, introducing model-checking-based networks through the definition of an abstraction layer that provides a security-focused model-checking service to SDN. The developed system is called MCS (Model Checking Service) and is implemented for an existing SDN solution called ONOS, using NetPlumber as underlying model-checking technology, but it's validity is general, uncoupled with any kind of SDN implementation. Finally, the demo shows how some cases of well-known security attacks in modern networks can be prevented or mitigated using the reactive behavior of MCS

Connected Information Management

Society is currently inundated with more information than ever, making efficient management a necessity. Alas, most of current information management suffers from several levels of disconnectedness: Applications partition data into segregated islands, small notes don’t fit into traditional application categories, navigating the data is different for each kind of data; data is either available at a certain computer or only online, but rarely both. Connected information management (CoIM) is an approach to information management that avoids these ways of disconnectedness. The core idea of CoIM is to keep all information in a central repository, with generic means for organization such as tagging. The heterogeneity of data is taken into account by offering specialized editors. The central repository eliminates the islands of application-specific data and is formally grounded by a CoIM model. The foundation for structured data is an RDF repository. The RDF editing meta-model (REMM) enables form-based editing of this data, similar to database applications such as MS access. Further kinds of data are supported by extending RDF, as follows. Wiki text is stored as RDF and can both contain structured text and be combined with structured data. Files are also supported by the CoIM model and are kept externally. Notes can be quickly captured and annotated with meta-data. Generic means for organization and navigation apply to all kinds of data. Ubiquitous availability of data is ensured via two CoIM implementations, the web application HYENA/Web and the desktop application HYENA/Eclipse. All data can be synchronized between these applications. The applications were used to validate the CoIM ideas

Bifurcations and synchronization using an integrated programmable chaotic circuit

This paper presents a CMOS chip which can act as an autonomous stand-alone unit to generate different real-time chaotic behaviors by changing a few external bias currents. In particular, by changing one of these bias currents, the chip provides different examples of a period-doubling route to chaos. We present experimental orbits and attractors, time waveforms and power spectra measured from the chip. By using two chip units, experiments on synchronization can be carried out as well in real-time. Measurements are presented for the following synchronization schemes: linear coupling, drive-response and inverse system. Experimental statistical characterizations associated to these schemes are also presented. We also outline the possible use of the chip for chaotic encryption of audio signals. Finally, for completeness, the paper includes also a brief description of the chip design procedure and its internal circuitry

Towards multiple interactions of inner and outer sensations in corporeal awareness

Under normal circumstances, different inner- and outer-body sources are integrated to form coherent and accurate mental experiences of the state of the body, leading to the phenomenon of corporeal awareness. How these processes are affected by changes in inner and outer inputs to the body, remains unclear. Here, we aim to present empirical evidence in which people experiencing a massive sensory disconnect may continue to experience feelings of their body state, suggesting that misperceptions of body awareness are determined by incomplete inner and outer signals. In these clinical populations, despite a long period of massive deafferentation, the activity of the neural structures subserving inner and outer body processing can be manipulated and tuned by means of body illusions that are usually based on multisensory stimulation. We suggest that a multisensory therapeutic approach could be adopted in the context of therapies for patients suffering from deafferentation. In this way, these individuals could regain a more complete feeling of their body state and the sensations they experience, which vary widely depending on their neurological condition

Are Product Owners communicators? A multi-method research approach to provide a more comprehensive picture of Product Owners in practice

Product Owners have an important role in the agile and hybrid software development process. While this role is supposed to maximize the value of a product, there seem to be several scattered results on how they achieve this, as well as what actually constitutes this role in practice. To consolidate current research results and to further analyze the key attribute of Product Owners, we conducted a multi-method research approach spanning a systematic mapping study and a consecutive case study in a hybrid development environment. The results of the mapping study states that Product Owners are communicators. We further investigated on this and used the shadowing technique to observe three Product Owners' communication activities. The results support that statement, as the gained data reveal that Product Owners spend 65% of their time in meetings. But rather than just providing the team with the necessary requirements for the product under development, Product Owners need this time to synchronize and align their work, streamline the agile process of large-scale Scrum, discuss team-based topics, and to solve upcoming issues addressed by the team. These results contribute to draw a more comprehensive picture of the important but yet complex role of Product Owners in practice. © 2020 John Wiley & Sons, Ltd

Using Information Systems in Innovation Networks: Uncovering Network Resources

In order to innovate, firms progressively combine complementary abilities through forming networks. Such innovation networks represent temporary assemblages of partners that, in collaboration, pursue new product developments. Existing theories suggest that successful participation in such networks depends on firms’ having certain firm-level dynamic capabilities (i.e., skill in sensing the network and its environment, learning about the network, and coordinating and integrating individual resources across the network). In this paper, we argue that firms also have to develop particular networking capabilities (i.e., they have to understand who they are partnering with, what each partner can contribute, and how exactly each partner can cooperate with others across the network). We show that inter-organizational information systems (IS) are vital for facilitating the development of these networking capabilities. IS are also vital in developing unique constellations of resources (i.e., physical, human, and organizational resources) that we term IS-embedded network resources. These resources are manifested in the IS and are unique to the innovation network because they go beyond resources at the firm level. Using three innovation networks as case studies, we provide empiric evidence on how IS support networking capabilities to arrive at unique resource constellations embedded in IS and how the set of IS-embedded network resources is a determining factor for competitive advantage in innovation networks