Influence apart from Adoption: How Interaction between Programming and Scientific Practices Shapes Modes of Inquiry in Four Oceanography Teams

Thesis (Ph.D.)--University of Washington, 2016-06

Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences

Motivation: In any macromolecular polyprotic system - for example protein, DNA or RNA - the isoelectric point - commonly referred to as the pI - can be defined as the point of singularity in a titration curve, corresponding to the solution pH value at which the net overall surface charge - and thus the electrophoretic mobility - of the ampholyte sums to zero. Different modern analytical biochemistry and proteomics methods depend on the isoelectric point as a principal feature for protein and peptide characterization. Protein separation by isoelectric point is a critical part of 2-D gel electrophoresis, a key precursor of proteomics, where discrete spots can be digested in-gel, and proteins subsequently identified by analytical mass spectrometry. Peptide fractionation according to their pI is also widely used in current proteomics sample preparation procedures previous to the LC-MS/MS analysis. Therefore accurate theoretical prediction of pI would expedite such analysis. While such pI calculation is widely used, it remains largely untested, motivating our efforts to benchmark pI prediction methods. Results: Using data from the database PIP-DB and one publically available dataset as our reference gold standard, we have undertaken the benchmarking of pI calculation methods. We find that methods vary in their accuracy and are highly sensitive to the choice of basis set. The machine-learning algorithms, especially the SVM-based algorithm, showed a superior performance when studying peptide mixtures. In general, learning-based pI prediction methods (such as Cofactor, SVM and Branca) require a large training dataset and their resulting performance will strongly depend of the quality of that data. In contrast with Iterative methods, machine-learning algorithms have the advantage of being able to add new features to improve the accuracy of prediction. Contact: yperez@ebi.ac.uk Availability and Implementation: The software and data are freely available at https://github.com/ypriverol/pIR. Supplementary information: Supplementary data are available at Bioinformatics online.

Visualización de datos de comunidades colaborativas

Las comunidades colaborativas, donde grandes cantidades de personas colaboran para la producción de recursos compartidos (e.g. Github, Wikipedia, OpenStreetMap, Arduino, StackOverflow) están extendiéndose progresivamente a multitud de campos. No obstante, es complicado comprender cómo funcionan y evolucionan. ¿Qué tipos de usuarios son más activos en Wikia? ¿Cómo ha evolucionado el número de wikis activas en los últimos años? ¿Qué perfil de actividad presentan la mayor parte de colaboradores de Wikia? ¿Son más activos los hombres o las mujeres en la Wikipedia? En los proyectos de Github, ¿el esfuerzo de programación (y frecuencia de commits) se distribuye de forma homogénea a lo largo del tiempo o suele estar concentrado? Estas comunidades, típicamente online, dejan registrada su actividad en grandes bases de datos, muchas de ellas disponibles públicamente. Sin embargo, el ciudadano de a pie no tiene ni las herramientas ni el conocimiento necesario para sacar conclusiones de esos datos. En este TFG desarrollamos una herramienta de análisis exploratorio y visualización de datos de la plataforma Wikia, sitio web colaborativo que permite la creación, edición y modificación del contenido y estructura de miles de páginas web de tipo enciclopedia basadas en la tecnología wiki. Nuestro objetivo es que esta aplicación web sea usable por cualquiera y que no requiera que el usuario sea un experto en Big Data para poder visualizar las gráficas de evolución o distribuciones del comportamiento interno de la comunidad, pudiendo modificar algunos de sus parámetros y visualizando cómo cambian. Como resultado de este trabajo se ha desarrollado una primera versión de la aplicación disponible en GitHub1 y en http://chartsup.esy.es/

Hierarchical structures in Northern Hemispheric extratropical winter ocean-atmosphere interactions

Acknowledgements MW and RVD have been supported by the German Federal Ministry for Education and Research via the BMBF Young Investigators Group CoSy-CC2 (grant 18 Marc Wiedermann et al. no. 01LN1306A). JFD thanks the Stordalen Foundation and BMBF (project GLUES) for financial support. JK acknowledges the IRTG 1740 funded by DFG and FAPESP. Coupled climate network analysis has been performed using the Python package pyunicorn (Donges et al, 2015a) that is available at https://github.com/pik-copan/pyunicorn.

Hierarchical structures in Northern Hemispheric extratropical winter ocean-atmosphere interactions

Acknowledgements MW and RVD have been supported by the German Federal Ministry for Education and Research via the BMBF Young Investigators Group CoSy-CC2 (grant 18 Marc Wiedermann et al. no. 01LN1306A). JFD thanks the Stordalen Foundation and BMBF (project GLUES) for financial support. JK acknowledges the IRTG 1740 funded by DFG and FAPESP. Coupled climate network analysis has been performed using the Python package pyunicorn (Donges et al, 2015a) that is available at https://github.com/pik-copan/pyunicorn.

AGOCS – Accurate Google Cloud Simulator Framework

This paper presents the Accurate Google Cloud Simulator (AGOCS) – a novel high-fidelity Cloud workload simulator based on parsing real workload traces, which can be conveniently used on a desktop machine for day-to-day research. Our simulation is based on real-world workload traces from a Google Cluster with 12.5K nodes, over a period of a calendar month. The framework is able to reveal very precise and detailed parameters of the executed jobs, tasks and nodes as well as to provide actual resource usage statistics. The system has been implemented in Scala language with focus on parallel execution and an easy-to-extend design concept. The paper presents the detailed structural framework for AGOCS and discusses our main design decisions, whilst also suggesting alternative and possibly performance enhancing future approaches. The framework is available via the Open Source GitHub repository.

Decisions, decisions everywhere (in the open data era).

Abstract: Decision support systems have been widely used for years in companies to gain insights from internal data, thus making successful decisions. Lately, thanks to the increasing availability of open data, these systems are also integrating open data to enrich decision making process with external data. On the other hand, within an open-data scenario, decision support systems can be also useful to decide which data should be opened, not only by considering technical or legal constraints, but other requirements, such as "reusing potential" of data. In this talk, we focus on both issues: (i) open data for decision making, and (ii) decision making for opening data. We will first briefly comment some research problems regarding using open data for decision making. Then, we will give an outline of a novel decision-making approach (based on how open data is being actually used in open-source projects hosted in Github) for supporting open data publication. Bio of the speaker: Jose-Norberto Mazón holds a PhD from the University of Alicante (Spain). He is head of the "Cátedra Telefónica" on Big Data and coordinator of the Computing degree at the University of Alicante. He is also member of the WaKe research group at the University of Alicante. His research work focuses on open data management, data integration and business intelligence within "big data" scenarios, and their application to the tourism domain (smart tourism destinations). He has published his research in international journals, such as Decision Support Systems, Information Sciences, Data & Knowledge Engineering or ACM Transaction on the Web. Finally, he is involved in the open data project in the University of Alicante, including its open data portal at http://datos.ua.es

LiDom builder: Automatising the construction of multilingual domain modules

136 p.

The transformed-stationary approach: a generic and simplified methodology for non-stationary extreme value analysis

Statistical approaches to study extreme events require, by definition, long time series of data. In many scientific disciplines, these series are often subject to variations at different temporal scales that affect the frequency and intensity of their extremes. Therefore, the assumption of stationarity is violated and alternative methods to conventional stationary extreme value analysis (EVA) must be adopted. Using the example of environmental variables subject to climate change, in this study we introduce the transformed-stationary (TS) methodology for non-stationary EVA. This approach consists of (i) transforming a non-stationary time series into a stationary one, to which the stationary EVA theory can be applied, and (ii) reverse transforming the result into a non-stationary extreme value distribution. As a transformation, we propose and discuss a simple time-varying normalization of the signal and show that it enables a comprehensive formulation of non-stationary generalized extreme value (GEV) and generalized Pareto distribution (GPD) models with a constant shape parameter. A validation of the methodology is carried out on time series of significant wave height, residual water level, and river discharge, which show varying degrees of long-term and seasonal variability. The results from the proposed approach are comparable with the results from (a) a stationary EVA on quasi-stationary slices of non-stationary series and (b) the established method for non-stationary EVA. However, the proposed technique comes with advantages in both cases. For example, in contrast to (a), the proposed technique uses the whole time horizon of the series for the estimation of the extremes, allowing for a more accurate estimation of large return levels. Furthermore, with respect to (b), it decouples the detection of non-stationary patterns from the fitting of the extreme value distribution. As a result, the steps of the analysis are simplified and intermediate diagnostics are possible. In particular, the transformation can be carried out by means of simple statistical techniques such as low-pass filters based on the running mean and the standard deviation, and the fitting procedure is a stationary one with a few degrees of freedom and is easy to implement and control. An open-source MAT-LAB toolbox has been developed to cover this methodology, which is available at https://github.com/menta78/tsEva/(Mentaschi et al., 2016).

Big Code Applications and Approaches

The availability of a huge amount of source code from code archives and open-source projects opens up the possibility to merge machine learning, programming languages, and software engineering research fields. This area is often referred to as Big Code where programming languages are treated instead of natural languages while different features and patterns of code can be exploited to perform many useful tasks and build supportive tools. Among all the possible applications which can be developed within the area of Big Code, the work presented in this research thesis mainly focuses on two particular tasks: the Programming Language Identification (PLI) and the Software Defect Prediction (SDP) for source codes. Programming language identification is commonly needed in program comprehension and it is usually performed directly by developers. However, when it comes at big scales, such as in widely used archives (GitHub, Software Heritage), automation of this task is desirable. To accomplish this aim, the problem is analyzed from different points of view (text and image-based learning approaches) and different models are created paying particular attention to their scalability. Software defect prediction is a fundamental step in software development for improving quality and assuring the reliability of software products. In the past, defects were searched by manual inspection or using automatic static and dynamic analyzers. Now, the automation of this task can be tackled using learning approaches that can speed up and improve related procedures. Here, two models have been built and analyzed to detect some of the commonest bugs and errors at different code granularity levels (file and method levels). Exploited data and models’ architectures are analyzed and described in detail. Quantitative and qualitative results are reported for both PLI and SDP tasks while differences and similarities concerning other related works are discussed.

Supporting requirement elicitation and ontology testing in knowledge graph engineering

Knowledge graphs and ontologies are closely related concepts in the field of knowledge representation. In recent years, knowledge graphs have gained increasing popularity and are serving as essential components in many knowledge engineering projects that view them as crucial to their success. The conceptual foundation of the knowledge graph is provided by ontologies. Ontology modeling is an iterative engineering process that consists of steps such as the elicitation and formalization of requirements, the development, testing, refactoring, and release of the ontology. The testing of the ontology is a crucial and occasionally overlooked step of the process due to the lack of integrated tools to support it. As a result of this gap in the state-of-the-art, the testing of the ontology is completed manually, which requires a considerable amount of time and effort from the ontology engineers. The lack of tool support is noticed in the requirement elicitation process as well. In this aspect, the rise in the adoption and accessibility of knowledge graphs allows for the development and use of automated tools to assist with the elicitation of requirements from such a complementary source of data. Therefore, this doctoral research is focused on developing methods and tools that support the requirement elicitation and testing steps of an ontology engineering process. To support the testing of the ontology, we have developed XDTesting, a web application that is integrated with the GitHub platform that serves as an ontology testing manager. Concurrently, to support the elicitation and documentation of competency questions, we have defined and implemented RevOnt, a method to extract competency questions from knowledge graphs. Both methods are evaluated through their implementation and the results are promising.

Progetto DERNetSoft: design e sviluppo di un'app mobile per un futuro più sostenibile

Da anni ormai siamo inconsapevolmente "in guerra" con la natura. Sfruttiamo e sprechiamo risorse naturali senza alcuna considerazione per le conseguenze. Le città sono considerate le principali fonti dei problemi ambientali e la regolamentazione del consumo energetico urbano è fondamentale per affrontare il cambiamento climatico globale. DERNetSoft Inc, start-up californiana, ha intravisto il problema come un’opportunità per creare un proprio business il cui scopo è quello di contribuire a costruire un futuro a basse emissioni di carbonio, fornendo un servizio tecnologico scalabile e conveniente per consentire la riduzione delle emissioni di gas a effetto serra a livello mondiale. Per farlo vengono utilizzati i concetti di DER Energy e Aggregation Energy. Nel volume di tesi si affrontano e descrivono la progettazione di un’applicazione mobile, multipiattaforma, sviluppata con il framework React Native. L’app sviluppata è supportata da un’architettura basata su dei micro servizi implementati tramite il cloud di Google. La principale funzionalità dell’applicazione sviluppata è quella di notificare gli utenti di un evento ELRP che, attraverso incentivi economici, promuove la riduzione del consumo energetico durante i periodi di forte stress o emergenza della rete elettrica.

Modelli di traffico per la formazione della congestione su una rete stradale

A partire dagli anni ’50 furono sviluppati numerosi modelli con l’intento di studiare i fenomeni connessi al traffico. Alcuni di essi riuscirono non solo a spiegare i fenomeni per i quali erano stati ideati ma misero in evidenza altre caratteristiche tipiche dei sistemi dinamici, come la presenza di cicli di isteresi e cambiamenti nella distribuzione dei tempi di percorrenza in situazioni di congestione. Questo lavoro si propone di verificare la validità di un modello semplificato ideato per mettere in luce i comportamenti tipici di un sistema di traffico, in particolare le congestioni che si vengono a creare sulla rete stradale. Tale modello è stato implementato per mezzo della libreria C++ Traffic Flow Dynamics Model, reperibile al link https://github.com/Grufoony/TrafficFlowDynamicsModel. Ai fini dello studio sono stati utilizzati i Diagrammi Fondamentali Macroscopici, particolari diagrammi che mettono in relazione gli osservabili principali di un network stradale quali velocità, densità e flusso. Variando il carico immesso nella rete stradale è stato possibile studiare il sistema in diversi regimi: carico costante, carico piccato e carico periodico. Mediante questi studi sono emerse diverse proprietà tipiche di ogni regime e, per alcuni di essi, è stata verificate e giustificate la presenza di uno o più cicli di isteresi. In ultimo è stata effettuata una breve analisi ad-hoc volta a evidenziare i cambiamenti nella distribuzione dei tempi di percorrenza in relazione al regime di traffico considerato.

Bio-QA-GNN: Reasoning with Language Models and Knowledge Graphs for Interpretable Biomedical Question Answering

Nowadays the idea of injecting world or domain-specific structured knowledge into pre-trained language models (PLMs) is becoming an increasingly popular approach for solving problems such as biases, hallucinations, huge architectural sizes, and explainability lack—critical for real-world natural language processing applications in sensitive fields like bioinformatics. One recent work that has garnered much attention in Neuro-symbolic AI is QA-GNN, an end-to-end model for multiple-choice open-domain question answering (MCOQA) tasks via interpretable text-graph reasoning. Unlike previous publications, QA-GNN mutually informs PLMs and graph neural networks (GNNs) on top of relevant facts retrieved from knowledge graphs (KGs). However, taking a more holistic view, existing PLM+KG contributions mainly consider commonsense benchmarks and ignore or shallowly analyze performances on biomedical datasets. This thesis start from a propose of a deep investigation of QA-GNN for biomedicine, comparing existing or brand-new PLMs, KGs, edge-aware GNNs, preprocessing techniques, and initialization strategies. By combining the insights emerged in DISI's research, we introduce Bio-QA-GNN that include a KG. Working with this part has led to an improvement in state-of-the-art of MCOQA model on biomedical/clinical text, largely outperforming the original one (+3.63\% accuracy on MedQA). Our findings also contribute to a better understanding of the explanation degree allowed by joint text-graph reasoning architectures and their effectiveness on different medical subjects and reasoning types. Codes, models, datasets, and demos to reproduce the results are freely available at: \url{https://github.com/disi-unibo-nlp/bio-qagnn}.