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in Architecture & Planning
Periodicals

ImageJ2: ImageJ for the next generation of scientific image data

BACKGROUND: ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. RESULTS: We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. This next-generation ImageJ, called "ImageJ2" in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. CONCLUSIONS: Scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. ImageJ has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for ImageJ's development. The described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. Future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites.

Architecture & Planning• 2017• BioMed Central
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Periodicals

Deep Reinforcement Learning with Double Q-Learning

The popular Q-learning algorithm is known to overestimate action values under certain conditions. It was not previously known whether, in practice, such overestimations are common, whether they harm performance, and whether they can generally be prevented. In this paper, we answer all these questions affirmatively. In particular, we first show that the recent DQN algorithm, which combines Q-learning with a deep neural network, suffers from substantial overestimations in some games in the Atari 2600 domain. We then show that the idea behind the Double Q-learning algorithm, which was introduced in a tabular setting, can be generalized to work with large-scale function approximation. We propose a specific adaptation to the DQN algorithm and show that the resulting algorithm not only reduces the observed overestimations, as hypothesized, but that this also leads to much better performance on several games.

Architecture & Planning• 2016
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Periodicals

Whatever next? Predictive brains, situated agents, and the future of cognitive science

Brains, it has recently been argued, are essentially prediction machines. They are bundles of cells that support perception and action by constantly attempting to match incoming sensory inputs with top-down expectations or predictions. This is achieved using a hierarchical generative model that aims to minimize prediction error within a bidirectional cascade of cortical processing. Such accounts offer a unifying model of perception and action, illuminate the functional role of attention, and may neatly capture the special contribution of cortical processing to adaptive success. This target article critically examines this "hierarchical prediction machine" approach, concluding that it offers the best clue yet to the shape of a unified science of mind and action. Sections 1 and 2 lay out the key elements and implications of the approach. Section 3 explores a variety of pitfalls and challenges, spanning the evidential, the methodological, and the more properly conceptual. The paper ends (sections 4 and 5) by asking how such approaches might impact our more general vision of mind, experience, and agency.

Architecture & Planning• 2013• Cambridge University Press
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Periodicals

Internet of Things for Smart Cities

The Internet of Things (IoT) shall be able to incorporate transparently and seamlessly a large number of different and heterogeneous end systems, while providing open access to selected subsets of data for the development of a plethora of digital services. Building a general architecture for the IoT is hence a very complex task, mainly because of the extremely large variety of devices, link layer technologies, and services that may be involved in such a system. In this paper, we focus specifically to an urban IoT system that, while still being quite a broad category, are characterized by their specific application domain. Urban IoTs, in fact, are designed to support the Smart City vision, which aims at exploiting the most advanced communication technologies to support added-value services for the administration of the city and for the citizens. This paper hence provides a comprehensive survey of the enabling technologies, protocols, and architecture for an urban IoT. Furthermore, the paper will present and discuss the technical solutions and best-practice guidelines adopted in the Padova Smart City project, a proof-of-concept deployment of an IoT island in the city of Padova, Italy, performed in collaboration with the city municipality.

Architecture & Planning• 2014• Institute of Electrical and Electronics Engineers
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Periodicals

The<i>Gaia</i>mission

Gaia is a cornerstone mission in the science programme of the EuropeanSpace Agency (ESA). The spacecraft construction was approved in 2006, following a study in which the original interferometric concept was changed to a direct-imaging approach. Both the spacecraft and the payload were built by European industry. The involvement of the scientific community focusses on data processing for which the international Gaia Data Processing and Analysis Consortium (DPAC) was selected in 2007. Gaia was launched on 19 December 2013 and arrived at its operating point, the second Lagrange point of the Sun-Earth-Moon system, a few weeks later. The commissioning of the spacecraft and payload was completed on 19 July 2014. The nominal five-year mission started with four weeks of special, ecliptic-pole scanning and subsequently transferred into full-sky scanning mode. We recall the scientific goals of Gaia and give a description of the as-built spacecraft that is currently (mid-2016) being operated to achieve these goals. We pay special attention to the payload module, the performance of which is closely related to the scientific performance of the mission. We provide a summary of the commissioning activities and findings, followed by a description of the routine operational mode. We summarise scientific performance estimates on the basis of in-orbit operations. Several intermediate Gaia data releases are planned and the data can be retrieved from the Gaia Archive, which is available through the Gaia home page.

Architecture & Planning• 2016• EDP Sciences
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The magical number 4 in short-term memory: A reconsideration of mental storage capacity

Miller (1956) summarized evidence that people can remember about seven chunks in short-term memory (STM) tasks. However, that number was meant more as a rough estimate and a rhetorical device than as a real capacity limit. Others have since suggested that there is a more precise capacity limit, but that it is only three to five chunks. The present target article brings together a wide variety of data on capacity limits suggesting that the smaller capacity limit is real. Capacity limits will be useful in analyses of information processing only if the boundary conditions for observing them can be carefully described. Four basic conditions in which chunks can be identified and capacity limits can accordingly be observed are: (1) when information overload limits chunks to individual stimulus items, (2) when other steps are taken specifically to block the recording of stimulus items into larger chunks, (3) in performance discontinuities caused by the capacity limit, and (4) in various indirect effects of the capacity limit. Under these conditions, rehearsal and long-term memory cannot be used to combine stimulus items into chunks of an unknown size; nor can storage mechanisms that are not capacity-limited, such as sensory memory, allow the capacity-limited storage mechanism to be refilled during recall. A single, central capacity limit averaging about four chunks is implicated along with other, noncapacity-limited sources. The pure STM capacity limit expressed in chunks is distinguished from compound STM limits obtained when the number of separately held chunks is unclear. Reasons why pure capacity estimates fall within a narrow range are discussed and a capacity limit for the focus of attention is proposed.

Architecture & Planning• 2001• Cambridge University Press
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The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package<sup>*</sup>

Abstract The Astropy Project supports and fosters the development of open-source and openly developed Python packages that provide commonly needed functionality to the astronomical community. A key element of the Astropy Project is the core package astropy , which serves as the foundation for more specialized projects and packages. In this article, we provide an overview of the organization of the Astropy project and summarize key features in the core package, as of the recent major release, version 2.0. We then describe the project infrastructure designed to facilitate and support development for a broader ecosystem of interoperable packages. We conclude with a future outlook of planned new features and directions for the broader Astropy Project.

Architecture & Planning• 2018• Institute of Physics
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Accelerated Profile HMM Searches

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the "multiple segment Viterbi" (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call "sparse rescaling". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.

Architecture & Planning• 2011• Public Library of Science
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Internet of Things: A Survey on Enabling Technologies, Protocols, and Applications

This paper provides an overview of the Internet of Things (IoT) with emphasis on enabling technologies, protocols, and application issues. The IoT is enabled by the latest developments in RFID, smart sensors, communication technologies, and Internet protocols. The basic premise is to have smart sensors collaborate directly without human involvement to deliver a new class of applications. The current revolution in Internet, mobile, and machine-to-machine (M2M) technologies can be seen as the first phase of the IoT. In the coming years, the IoT is expected to bridge diverse technologies to enable new applications by connecting physical objects together in support of intelligent decision making. This paper starts by providing a horizontal overview of the IoT. Then, we give an overview of some technical details that pertain to the IoT enabling technologies, protocols, and applications. Compared to other survey papers in the field, our objective is to provide a more thorough summary of the most relevant protocols and application issues to enable researchers and application developers to get up to speed quickly on how the different protocols fit together to deliver desired functionalities without having to go through RFCs and the standards specifications. We also provide an overview of some of the key IoT challenges presented in the recent literature and provide a summary of related research work. Moreover, we explore the relation between the IoT and other emerging technologies including big data analytics and cloud and fog computing. We also present the need for better horizontal integration among IoT services. Finally, we present detailed service use-cases to illustrate how the different protocols presented in the paper fit together to deliver desired IoT services.

Architecture & Planning• 2015• Institute of Electrical and Electronics Engineers
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Reinforcement Learning: A Survey

This paper surveys the field of reinforcement learning from a computer-science perspective. It is written to be accessible to researchers familiar with machine learning. Both the historical basis of the field and a broad selection of current work are summarized. Reinforcement learning is the problem faced by an agent that learns behavior through trial-and-error interactions with a dynamic environment. The work described here has a resemblance to work in psychology, but differs considerably in the details and in the use of the word ``reinforcement.'' The paper discusses central issues of reinforcement learning, including trading off exploration and exploitation, establishing the foundations of the field via Markov decision theory, learning from delayed reinforcement, constructing empirical models to accelerate learning, making use of generalization and hierarchy, and coping with hidden state. It concludes with a survey of some implemented systems and an assessment of the practical utility of current methods for reinforcement learning.

Architecture & Planning• 1996• AI Access Foundation
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