arXiv subjects

Gasper Tkacik

Publications and source records attributed to Gasper Tkacik.

21 records · Page 2Linked to original sources

arXiv2005

Information based clustering: Supplementary material

This technical report provides the supplementary material for a paper entitled "Information based clustering", to appear shortly in Proceedings of the National Academy of Sciences (USA). In Section I we present in detail the iterative clustering algorithm used in our experiments and in Section II we describe the validation scheme used to determine the statistical significance of our results. Then in subsequent sections we provide all the experimental results for three very different applications: the response of gene expression in yeast to different forms of environmental stress, the dynamics of stock prices in the Standard and Poor's 500, and viewer ratings of popular movies. In particular, we highlight some of the results that seem to deserve special attention. All the experimental results and relevant code, including a freely available web application, can be found at http://www.genomics.princeton.edu/biophysics-theory .

q-bio.QM↗

arXiv2005

Estimating mutual information and multi--information in large networks

We address the practical problems of estimating the information relations that characterize large networks. Building on methods developed for analysis of the neural code, we show that reliable estimates of mutual information can be obtained with manageable computational effort. The same methods allow estimation of higher order, multi--information terms. These ideas are illustrated by analyses of gene expression, financial markets, and consumer preferences. In each case, information theoretic measures correlate with independent, intuitive measures of the underlying structures in the system.

cs.IT↗

arXiv2001

The Control System Modeling Language

The well-known Unified Modeling Language (UML) describes software entities, such as interfaces, classes, operations and attributes, as well as relationships among them, e.g. inheritance, containment and dependency. The power of UML lies in Computer Aided Software Engineering (CASE) tools such as Rational Rose, which are also capable of generating software structures from visual object definitions and relations. UML also allows add-ons that define specific structures and patterns in order to steer and automate the design process. We have developed an add-on called Control System Modeling Language (CSML). It introduces entities and relationships that we know from control systems, such as "property" representing a single controllable point/channel, or an "event" specifying that a device is capable of notifying its clients through events. Entities can also possess CSML-specific characteristics, such as physical units and valid ranges for input parameters. CSML is independent of any specific language or technology and generic such that any control system can be described with it. Simple transformation scripts map CSML defined structures to APIs and tools such as EPICS, CDEV, SCADA, Abeans, BACI and generate the appropriate database or source files. Advantages of control system development with CSML are discussed on a concrete example of a bending magnet's power supply in a synchrotron accelerator.

physics.acc-ph↗