148,751 research outputs found
Engineering simulations for cancer systems biology
Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions
Applying Formal Methods to Networking: Theory, Techniques and Applications
Despite its great importance, modern network infrastructure is remarkable for
the lack of rigor in its engineering. The Internet which began as a research
experiment was never designed to handle the users and applications it hosts
today. The lack of formalization of the Internet architecture meant limited
abstractions and modularity, especially for the control and management planes,
thus requiring for every new need a new protocol built from scratch. This led
to an unwieldy ossified Internet architecture resistant to any attempts at
formal verification, and an Internet culture where expediency and pragmatism
are favored over formal correctness. Fortunately, recent work in the space of
clean slate Internet design---especially, the software defined networking (SDN)
paradigm---offers the Internet community another chance to develop the right
kind of architecture and abstractions. This has also led to a great resurgence
in interest of applying formal methods to specification, verification, and
synthesis of networking protocols and applications. In this paper, we present a
self-contained tutorial of the formidable amount of work that has been done in
formal methods, and present a survey of its applications to networking.Comment: 30 pages, submitted to IEEE Communications Surveys and Tutorial
Thirty Years of Machine Learning: The Road to Pareto-Optimal Wireless Networks
Future wireless networks have a substantial potential in terms of supporting
a broad range of complex compelling applications both in military and civilian
fields, where the users are able to enjoy high-rate, low-latency, low-cost and
reliable information services. Achieving this ambitious goal requires new radio
techniques for adaptive learning and intelligent decision making because of the
complex heterogeneous nature of the network structures and wireless services.
Machine learning (ML) algorithms have great success in supporting big data
analytics, efficient parameter estimation and interactive decision making.
Hence, in this article, we review the thirty-year history of ML by elaborating
on supervised learning, unsupervised learning, reinforcement learning and deep
learning. Furthermore, we investigate their employment in the compelling
applications of wireless networks, including heterogeneous networks (HetNets),
cognitive radios (CR), Internet of things (IoT), machine to machine networks
(M2M), and so on. This article aims for assisting the readers in clarifying the
motivation and methodology of the various ML algorithms, so as to invoke them
for hitherto unexplored services as well as scenarios of future wireless
networks.Comment: 46 pages, 22 fig
Many-Task Computing and Blue Waters
This report discusses many-task computing (MTC) generically and in the
context of the proposed Blue Waters systems, which is planned to be the largest
NSF-funded supercomputer when it begins production use in 2012. The aim of this
report is to inform the BW project about MTC, including understanding aspects
of MTC applications that can be used to characterize the domain and
understanding the implications of these aspects to middleware and policies.
Many MTC applications do not neatly fit the stereotypes of high-performance
computing (HPC) or high-throughput computing (HTC) applications. Like HTC
applications, by definition MTC applications are structured as graphs of
discrete tasks, with explicit input and output dependencies forming the graph
edges. However, MTC applications have significant features that distinguish
them from typical HTC applications. In particular, different engineering
constraints for hardware and software must be met in order to support these
applications. HTC applications have traditionally run on platforms such as
grids and clusters, through either workflow systems or parallel programming
systems. MTC applications, in contrast, will often demand a short time to
solution, may be communication intensive or data intensive, and may comprise
very short tasks. Therefore, hardware and software for MTC must be engineered
to support the additional communication and I/O and must minimize task dispatch
overheads. The hardware of large-scale HPC systems, with its high degree of
parallelism and support for intensive communication, is well suited for MTC
applications. However, HPC systems often lack a dynamic resource-provisioning
feature, are not ideal for task communication via the file system, and have an
I/O system that is not optimized for MTC-style applications. Hence, additional
software support is likely to be required to gain full benefit from the HPC
hardware
Technology assessment of advanced automation for space missions
Six general classes of technology requirements derived during the mission definition phase of the study were identified as having maximum importance and urgency, including autonomous world model based information systems, learning and hypothesis formation, natural language and other man-machine communication, space manufacturing, teleoperators and robot systems, and computer science and technology
Towards formal models and languages for verifiable Multi-Robot Systems
Incorrect operations of a Multi-Robot System (MRS) may not only lead to
unsatisfactory results, but can also cause economic losses and threats to
safety. These threats may not always be apparent, since they may arise as
unforeseen consequences of the interactions between elements of the system.
This call for tools and techniques that can help in providing guarantees about
MRSs behaviour. We think that, whenever possible, these guarantees should be
backed up by formal proofs to complement traditional approaches based on
testing and simulation.
We believe that tailored linguistic support to specify MRSs is a major step
towards this goal. In particular, reducing the gap between typical features of
an MRS and the level of abstraction of the linguistic primitives would simplify
both the specification of these systems and the verification of their
properties. In this work, we review different agent-oriented languages and
their features; we then consider a selection of case studies of interest and
implement them useing the surveyed languages. We also evaluate and compare
effectiveness of the proposed solution, considering, in particular, easiness of
expressing non-trivial behaviour.Comment: Changed formattin
Overview on agent-based social modelling and the use of formal languages
Transdisciplinary Models and Applications investigates a variety of programming languages used in validating and verifying models in order to assist in their eventual implementation. This book will explore different methods of evaluating and formalizing simulation models, enabling computer and industrial engineers, mathematicians, and students working with computer simulations to thoroughly understand the progression from simulation to product, improving the overall effectiveness of modeling systems.Postprint (author's final draft
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