Formal Model Engineering for Embedded Systems Using Real-Time Maude

This paper motivates why Real-Time Maude should be well suited to provide a formal semantics and formal analysis capabilities to modeling languages for embedded systems. One can then use the code generation facilities of the tools for the modeling languages to automatically synthesize Real-Time Maude verification models from design models, enabling a formal model engineering process that combines the convenience of modeling using an informal but intuitive modeling language with formal verification. We give a brief overview six fairly different modeling formalisms for which Real-Time Maude has provided the formal semantics and (possibly) formal analysis. These models include behavioral subsets of the avionics modeling standard AADL, Ptolemy II discrete-event models, two EMF-based timed model transformation systems, and a modeling language for handset software.Comment: In Proceedings AMMSE 2011, arXiv:1106.596

Interoperability between Multimedia Collections for Content and Metadata-Based Searching

Artiste is a European project developing a cross-collection search system for art galleries and museums. It combines image content retrieval with text based retrieval and uses RDF mappings in order to integrate diverse databases. The test sites of the Louvre, Victoria and Albert Museum, Uffizi Gallery and National Gallery London provide their own database schema for existing metadata, avoiding the need for migration to a common schema. The system will accept a query based on one museum’s fields and convert them, through an RDF mapping into a form suitable for querying the other collections. The nature of some of the image processing algorithms means that the system can be slow for some computations, so the system is session-based to allow the user to return to the results later. The system has been built within a J2EE/EJB framework, using the Jboss Enterprise Application Server

Novis: A notional machine implementation for teaching introductory programming

Comprehension of programming and programs is known to be a difficult task for many beginning students, with many computing courses showing significant drop out and failure rates. In this paper, we present a notional machine imple- mentation, Novis, to help with understanding of program- ming and its dynamics for beginning learners. The notional machine offers an abstraction of the physical machine de- signed for comprehension and learning purposes. Novis pro- vides a real-time visualisation of this notional machine, and is integrated into BlueJ

Concluding dialogue

This is a chapter in a book with the overall description: This is a critical time in design. Concepts and practices of design are changing in response to historical developments in the modes of industrial design production and consumption. Indeed, the imperative of more sustainable development requires profound reconsideration of design today. Theoretical foundations and professional definitions are at stake, with consequences for institutions such as museums and universities as well as for future practitioners. This is ‘critical’ on many levels, from the urgent need to address societal and environmental issues to the reflexivity required to think and do design differently

Introductions

This is the introduction to the book with the overall description: This is a critical time in design. Concepts and practices of design are changing in response to historical developments in the modes of industrial design production and consumption. Indeed, the imperative of more sustainable development requires profound reconsideration of design today. Theoretical foundations and professional definitions are at stake, with consequences for institutions such as museums and universities as well as for future practitioners. This is ‘critical’ on many levels, from the urgent need to address societal and environmental issues to the reflexivity required to think and do design differently

A signaling visualization toolkit to support rational design of combination therapies and biomarker discovery: SiViT

Targeted cancer therapy aims to disrupt aberrant cellular signalling pathways. Biomarkers are surrogates of pathway state, but there is limited success in translating candidate biomarkers to clinical practice due to the intrinsic complexity of pathway networks. Systems biology approaches afford better understanding of complex, dynamical interactions in signalling pathways targeted by anticancer drugs. However, adoption of dynamical modelling by clinicians and biologists is impeded by model inaccessibility. Drawing on computer games technology, we present a novel visualisation toolkit, SiViT, that converts systems biology models of cancer cell signalling into interactive simulations that can be used without specialist computational expertise. SiViT allows clinicians and biologists to directly introduce for example loss of function mutations and specific inhibitors. SiViT animates the effects of these introductions on pathway dynamics, suggesting further experiments and assessing candidate biomarker effectiveness. In a systems biology model of Her2 signalling we experimentally validated predictions using SiViT, revealing the dynamics of biomarkers of drug resistance and highlighting the role of pathway crosstalk. No model is ever complete: the iteration of real data and simulation facilitates continued evolution of more accurate, useful models. SiViT will make accessible libraries of models to support preclinical research, combinatorial strategy design and biomarker discovery

Attacking Visual Language Grounding with Adversarial Examples: A Case Study on Neural Image Captioning

Visual language grounding is widely studied in modern neural image captioning systems, which typically adopts an encoder-decoder framework consisting of two principal components: a convolutional neural network (CNN) for image feature extraction and a recurrent neural network (RNN) for language caption generation. To study the robustness of language grounding to adversarial perturbations in machine vision and perception, we propose Show-and-Fool, a novel algorithm for crafting adversarial examples in neural image captioning. The proposed algorithm provides two evaluation approaches, which check whether neural image captioning systems can be mislead to output some randomly chosen captions or keywords. Our extensive experiments show that our algorithm can successfully craft visually-similar adversarial examples with randomly targeted captions or keywords, and the adversarial examples can be made highly transferable to other image captioning systems. Consequently, our approach leads to new robustness implications of neural image captioning and novel insights in visual language grounding.Comment: Accepted by 56th Annual Meeting of the Association for Computational Linguistics (ACL 2018). Hongge Chen and Huan Zhang contribute equally to this wor

TinkerCell: Modular CAD Tool for Synthetic Biology

Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has been created in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various C and Python programs that are hosted by TinkerCell via an extensive C and Python API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. Because TinkerCell associates parameters and equations in a model with their respective part, parts can be loaded from databases along with their parameters and rate equations. The modular network design can be used to exchange modules as well as test the concept of modularity in biological systems. The flexible modeling framework along with the C and Python API allows TinkerCell to serve as a host to numerous third-party algorithms. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at www.tinkercell.com.Comment: 23 pages, 20 figure