From SpaceStat to CyberGIS: Twenty Years of Spatial Data Analysis Software

This essay assesses the evolution of the way in which spatial data analytical methods have been incorporated into software tools over the past two decades. It is part retrospective and prospective, going beyond a historical review to outline some ideas about important factors that drove the software development, such as methodological advances, the open source movement and the advent of the internet and cyberinfrastructure. The review highlights activities carried out by the author and his collaborators and uses SpaceStat, GeoDa, PySAL and recent spatial analytical web services developed at the ASU GeoDa Center as illustrative examples. It outlines a vision for a spatial econometrics workbench as an example of the incorporation of spatial analytical functionality in a cyberGIS.

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

Data-driven modelling of biological multi-scale processes

Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript we review mathematical modelling approaches used to describe the individual spatial scales and how they are integrated into holistic models. We discuss the relation between spatial and temporal scales and the implication of that on multi-scale modelling. Based upon this overview over state-of-the-art modelling approaches, we formulate key challenges in mathematical and computational modelling of biological multi-scale and multi-physics processes. In particular, we considered the availability of analysis tools for multi-scale models and model-based multi-scale data integration. We provide a compact review of methods for model-based data integration and model-based hypothesis testing. Furthermore, novel approaches and recent trends are discussed, including computation time reduction using reduced order and surrogate models, which contribute to the solution of inference problems. We conclude the manuscript by providing a few ideas for the development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and Multiscale Dynamics (American Scientific Publishers

Construction of Hierarchical Neural Architecture Search Spaces based on Context-free Grammars

The discovery of neural architectures from simple building blocks is a long-standing goal of Neural Architecture Search (NAS). Hierarchical search spaces are a promising step towards this goal but lack a unifying search space design framework and typically only search over some limited aspect of architectures. In this work, we introduce a unifying search space design framework based on context-free grammars that can naturally and compactly generate expressive hierarchical search spaces that are 100s of orders of magnitude larger than common spaces from the literature. By enhancing and using their properties, we effectively enable search over the complete architecture and can foster regularity. Further, we propose an efficient hierarchical kernel design for a Bayesian Optimization search strategy to efficiently search over such huge spaces. We demonstrate the versatility of our search space design framework and show that our search strategy can be superior to existing NAS approaches. Code is available at https://github.com/automl/hierarchical_nas_construction

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