Agile in-litero experiments:how can semi-automated information extraction from neuroscientific literature help neuroscience model building?

In neuroscience, as in many other scientific domains, the primary form of knowledge dissemination is through published articles in peer-reviewed journals. One challenge for modern neuroinformatics is to design methods to make the knowledge from the tremendous backlog of publications accessible for search, analysis and its integration into computational models. In this thesis, we introduce novel natural language processing (NLP) models and systems to mine the neuroscientific literature. In addition to in vivo, in vitro or in silico experiments, we coin the NLP methods developed in this thesis as in litero experiments, aiming at analyzing and making accessible the extended body of neuroscientific literature. In particular, we focus on two important neuroscientific entities: brain regions and neural cells. An integrated NLP model is designed to automatically extract brain region connectivity statements from very large corpora. This system is applied to a large corpus of 25M PubMed abstracts and 600K full-text articles. Central to this system is the creation of a searchable database of brain region connectivity statements, allowing neuroscientists to gain an overview of all brain regions connected to a given region of interest. More importantly, the database enables researcher to provide feedback on connectivity results and links back to the original article sentence to provide the relevant context. The database is evaluated by neuroanatomists on real connectomics tasks (targets of Nucleus Accumbens) and results in significant effort reduction in comparison to previous manual methods (from 1 week to 2h). Subsequently, we introduce neuroNER to identify, normalize and compare instances of identify neuronsneurons in the scientific literature. Our method relies on identifying and analyzing each of the domain features used to annotate a specific neuron mention, like the morphological term 'basket' or brain region 'hippocampus'. We apply our method to the same corpus of 25M PubMed abstracts and 600K full-text articles and find over 500K unique neuron type mentions. To demonstrate the utility of our approach, we also apply our method towards cross-comparing the NeuroLex and Human Brain Project (HBP) cell type ontologies. By decoupling a neuron mention's identity into its specific compositional features, our method can successfully identify specific neuron types even if they are not explicitly listed within a predefined neuron type lexicon, thus greatly facilitating cross-laboratory studies. In order to build such large databases, several tools and infrastructureslarge-scale NLP were developed: a robust pipeline to preprocess full-text PDF articles, as well as bluima, an NLP processing pipeline specialized on neuroscience to perform text-mining at PubMed scale. During the development of those two NLP systems, we acknowledged the need for novel NLP approaches to rapidly develop custom text mining solutions. This led to the formalization of the agile text miningagile text-mining methodology to improve the communication and collaboration between subject matter experts and text miners. Agile text mining is characterized by short development cycles, frequent tasks redefinition and continuous performance monitoring through integration tests. To support our approach, we developed Sherlok, an NLP framework designed for the development of agile text mining applications

Multimodal interaction with mobile devices : fusing a broad spectrum of modality combinations

This dissertation presents a multimodal architecture for use in mobile scenarios such as shopping and navigation. It also analyses a wide range of feasible modality input combinations for these contexts. For this purpose, two interlinked demonstrators were designed for stand-alone use on mobile devices. Of particular importance was the design and implementation of a modality fusion module capable of combining input from a range of communication modes like speech, handwriting, and gesture. The implementation is able to account for confidence value biases arising within and between modalities and also provides a method for resolving semantically overlapped input. Tangible interaction with real-world objects and symmetric multimodality are two further themes addressed in this work. The work concludes with the results from two usability field studies that provide insight on user preference and modality intuition for different modality combinations, as well as user acceptance for anthropomorphized objects.Diese Dissertation präsentiert eine multimodale Architektur zum Gebrauch in mobilen Umständen wie z. B. Einkaufen und Navigation. Außerdem wird ein großes Gebiet von möglichen modalen Eingabekombinationen zu diesen Umständen analysiert. Um das in praktischer Weise zu demonstrieren, wurden zwei teilweise gekoppelte Vorführungsprogramme zum \u27stand-alone\u27; Gebrauch auf mobilen Geräten entworfen. Von spezieller Wichtigkeit war der Entwurf und die Ausführung eines Modalitäts-fusion Modul, das die Kombination einer Reihe von Kommunikationsarten wie Sprache, Handschrift und Gesten ermöglicht. Die Ausführung erlaubt die Veränderung von Zuverlässigkeitswerten innerhalb einzelner Modalitäten und außerdem ermöglicht eine Methode um die semantisch überlappten Eingaben auszuwerten. Wirklichkeitsnaher Dialog mit aktuellen Objekten und symmetrische Multimodalität sind zwei weitere Themen die in dieser Arbeit behandelt werden. Die Arbeit schließt mit Resultaten von zwei Feldstudien, die weitere Einsicht erlauben über die bevorzugte Art verschiedener Modalitätskombinationen, sowie auch über die Akzeptanz von anthropomorphisierten Objekten

Multimodal interaction with mobile devices : fusing a broad spectrum of modality combinations

This dissertation presents a multimodal architecture for use in mobile scenarios such as shopping and navigation. It also analyses a wide range of feasible modality input combinations for these contexts. For this purpose, two interlinked demonstrators were designed for stand-alone use on mobile devices. Of particular importance was the design and implementation of a modality fusion module capable of combining input from a range of communication modes like speech, handwriting, and gesture. The implementation is able to account for confidence value biases arising within and between modalities and also provides a method for resolving semantically overlapped input. Tangible interaction with real-world objects and symmetric multimodality are two further themes addressed in this work. The work concludes with the results from two usability field studies that provide insight on user preference and modality intuition for different modality combinations, as well as user acceptance for anthropomorphized objects.Diese Dissertation präsentiert eine multimodale Architektur zum Gebrauch in mobilen Umständen wie z. B. Einkaufen und Navigation. Außerdem wird ein großes Gebiet von möglichen modalen Eingabekombinationen zu diesen Umständen analysiert. Um das in praktischer Weise zu demonstrieren, wurden zwei teilweise gekoppelte Vorführungsprogramme zum 'stand-alone'; Gebrauch auf mobilen Geräten entworfen. Von spezieller Wichtigkeit war der Entwurf und die Ausführung eines Modalitäts-fusion Modul, das die Kombination einer Reihe von Kommunikationsarten wie Sprache, Handschrift und Gesten ermöglicht. Die Ausführung erlaubt die Veränderung von Zuverlässigkeitswerten innerhalb einzelner Modalitäten und außerdem ermöglicht eine Methode um die semantisch überlappten Eingaben auszuwerten. Wirklichkeitsnaher Dialog mit aktuellen Objekten und symmetrische Multimodalität sind zwei weitere Themen die in dieser Arbeit behandelt werden. Die Arbeit schließt mit Resultaten von zwei Feldstudien, die weitere Einsicht erlauben über die bevorzugte Art verschiedener Modalitätskombinationen, sowie auch über die Akzeptanz von anthropomorphisierten Objekten

Combining SOA and BPM Technologies for Cross-System Process Automation

This paper summarizes the results of an industry case study that introduced a cross-system business process automation solution based on a combination of SOA and BPM standard technologies (i.e., BPMN, BPEL, WSDL). Besides discussing major weaknesses of the existing, custom-built, solution and comparing them against experiences with the developed prototype, the paper presents a course of action for transforming the current solution into the proposed solution. This includes a general approach, consisting of four distinct steps, as well as specific action items that are to be performed for every step. The discussion also covers language and tool support and challenges arising from the transformation

Excellentia Eminentia Effectio

"In these pages you will learn about the fascinating research endeavors that each of our faculty members is undertaking. We have divided their research into the broad categories of health, sustainability, information, and systems. While we recognize the imperfect nature of categorizing research that, by its very nature may be interdisciplinary or transdisciplinary, we nonetheless believe it will be helpful as a way to see the depth and breadth of our research endeavors within each grouping. As you read the profiles on these pages, I know you will begin to appreciate that, taken as a whole, the research spectrum at Columbia Engineering is exceptional and that, as our professors go about their work, they are at the cusp of making breakthroughs that will have a major impact on the way we live our lives today and tomorrow.

Proceedings of the NASA Conference on Space Telerobotics, volume 1

The theme of the Conference was man-machine collaboration in space. Topics addressed include: redundant manipulators; man-machine systems; telerobot architecture; remote sensing and planning; navigation; neural networks; fundamental AI research; and reasoning under uncertainty