Machine-learning methods for structure prediction of β-barrel membrane proteins

Different types of proteins exist with diverse functions that are essential for living organisms. An important class of proteins is represented by transmembrane proteins which are specifically designed to be inserted into biological membranes and devised to perform very important functions in the cell such as cell communication and active transport across the membrane. Transmembrane β-barrels (TMBBs) are a sub-class of membrane proteins largely under-represented in structure databases because of the extreme difficulty in experimental structure determination. For this reason, computational tools that are able to predict the structure of TMBBs are needed. In this thesis, two computational problems related to TMBBs were addressed: the detection of TMBBs in large datasets of proteins and the prediction of the topology of TMBB proteins. Firstly, a method for TMBB detection was presented based on a novel neural network framework for variable-length sequence classification. The proposed approach was validated on a non-redundant dataset of proteins. Furthermore, we carried-out genome-wide detection using the entire Escherichia coli proteome. In both experiments, the method significantly outperformed other existing state-of-the-art approaches, reaching very high PPV (92%) and MCC (0.82). Secondly, a method was also introduced for TMBB topology prediction. The proposed approach is based on grammatical modelling and probabilistic discriminative models for sequence data labeling. The method was evaluated using a newly generated dataset of 38 TMBB proteins obtained from high-resolution data in the PDB. Results have shown that the model is able to correctly predict topologies of 25 out of 38 protein chains in the dataset. When tested on previously released datasets, the performances of the proposed approach were measured as comparable or superior to the current state-of-the-art of TMBB topology prediction.

Segmentazione e categorizzazione di oggetti mediante immagini depth e deep learning

Questo lavoro è iniziato con uno studio teorico delle principali tecniche di classificazione di immagini note in letteratura, con particolare attenzione ai più diffusi modelli di rappresentazione dell’immagine, quali il modello Bag of Visual Words, e ai principali strumenti di Apprendimento Automatico (Machine Learning). In seguito si è focalizzata l’attenzione sulla analisi di ciò che costituisce lo stato dell’arte per la classificazione delle immagini, ovvero il Deep Learning. Per sperimentare i vantaggi dell’insieme di metodologie di Image Classification, si è fatto uso di Torch7, un framework di calcolo numerico, utilizzabile mediante il linguaggio di scripting Lua, open source, con ampio supporto alle metodologie allo stato dell’arte di Deep Learning. Tramite Torch7 è stata implementata la vera e propria classificazione di immagini poiché questo framework, grazie anche al lavoro di analisi portato avanti da alcuni miei colleghi in precedenza, è risultato essere molto efficace nel categorizzare oggetti in immagini. Le immagini su cui si sono basati i test sperimentali, appartengono a un dataset creato ad hoc per il sistema di visione 3D con la finalità di sperimentare il sistema per individui ipovedenti e non vedenti; in esso sono presenti alcuni tra i principali ostacoli che un ipovedente può incontrare nella propria quotidianità. In particolare il dataset si compone di potenziali ostacoli relativi a una ipotetica situazione di utilizzo all’aperto. Dopo avere stabilito dunque che Torch7 fosse il supporto da usare per la classificazione, l’attenzione si è concentrata sulla possibilità di sfruttare la Visione Stereo per aumentare l’accuratezza della classificazione stessa. Infatti, le immagini appartenenti al dataset sopra citato sono state acquisite mediante una Stereo Camera con elaborazione su FPGA sviluppata dal gruppo di ricerca presso il quale è stato svolto questo lavoro. Ciò ha permesso di utilizzare informazioni di tipo 3D, quali il livello di depth (profondità) di ogni oggetto appartenente all’immagine, per segmentare, attraverso un algoritmo realizzato in C++, gli oggetti di interesse, escludendo il resto della scena. L’ultima fase del lavoro è stata quella di testare Torch7 sul dataset di immagini, preventivamente segmentate attraverso l’algoritmo di segmentazione appena delineato, al fine di eseguire il riconoscimento della tipologia di ostacolo individuato dal sistema.

A Personalized Privacy Management Framework for Android Applications

Ogni giorno, l'utente di smartphon e tablet, spesso senza rendersene conto, condivide, tramite varie applicazioni, un'enorme quantità di informazioni. Negli attuali sistemi operativi, l'assenza di meccanismi utili a garantire adeguatamente l'utente, ha spinto questo lavoro di ricerca verso lo sviluppo di un inedito framework.È stato necessario uno studio approfondito dello stato dell'arte di soluzioni con gli stessi obiettivi. Sono stati esaminati sia modelli teorici che pratici, con l'analisi accurata del relativo codice. Il lavoro, in stretto contatto con i colleghi dell'Università Centrale della Florida e la condivisione delle conoscenze con gli stessi, ha portato ad importanti risultati. Questo lavoro ha prodotto un framework personalizzato per gestire la privacy nelle applicazioni mobili che, nello specifico, è stato sviluppato per Android OS e necessita dei permessi di root per poter realizzare il suo funzionamento. Il framework in questione sfrutta le funzionalità offerte dal Xposed Framework, con il risultato di implementare modifiche al sistema operativo, senza dover cambiare il codice di Android o delle applicazioni che eseguono su quest’ultimo. Il framework sviluppato controlla l’accesso da parte delle varie applicazioni in esecuzione verso le informazioni sensibili dell’utente e stima l’importanza che queste informazioni hanno per l’utente medesimo. Le informazioni raccolte dal framework sulle preferenze e sulle valutazioni dell’utente vengono usate per costruire un modello decisionale che viene sfruttato da un algoritmo di machine-learning per migliorare l’interazione del sistema con l’utente e prevedere quelle che possono essere le decisioni dell'utente stesso, circa la propria privacy. Questo lavoro di tesi realizza gli obbiettivi sopra citati e pone un'attenzione particolare nel limitare la pervasività del sistema per la gestione della privacy, nella quotidiana esperienza dell'utente con i dispositivi mobili.

Moving from sustainable management to sustainable governance of natural resources: The role of social learning processes in rural India, Bolivia and Mali

The present paper discusses a conceptual, methodological and practical framework within which the limitations of the conventional notion of natural resource management (NRM) can be overcome. NRM is understood as the application of scientific ecological knowledge to resource management. By including a consideration of the normative imperatives that arise from scientific ecological knowledge and submitting them to public scrutiny, ‘sustainable management of natural resources’ can be recontextualised as ‘sustainable governance of natural resources’. This in turn makes it possible to place the politically neutralising discourse of ‘management’ in a space for wider societal debate, in which the different actors involved can deliberate and negotiate the norms, rules and power relations related to natural resource use and sustainable development. The transformation of sustainable management into sustainable governance of natural resources can be conceptualised as a social learning process involving scientists, experts, politicians and local actors, and their corresponding scientific and non-scientific knowledges. The social learning process is the result of what Habermas has described as ‘communicative action’, in contrast to ‘strategic action’. Sustainable governance of natural resources thus requires a new space for communicative action aiming at shared, intersubjectively validated definitions of actual situations and the goals and means required for transforming current norms, rules and power relations in order to achieve sustainable development. Case studies from rural India, Bolivia and Mali explore the potentials and limitations for broadening communicative action through an intensification of social learning processes at the interface of local and external knowledge. Key factors that enable or hinder the transformation of sustainable management into sustainable governance of natural resources through social learning processes and communicative action are discussed.

Accessible e-learning

People with disabilities often encounter difficulties while trying to learn something, because teaching material is for example not accessible to blind people or rooms, where courses take place, are not accessible to people using a wheelchair. E-learning provides an opportunity to disabled people. With the new German law on the equalisation of opportunities for people with disabilities for the first time access to information technology was explicitly taken up in German legislation. As a consequence of this law the framework law on universities (Hochschulrahmengesetz) was changed. The law now commit universities not to discriminate disabled students in their studies. For references on how universities can design accessible e-learning contents and provide accessible information online see http://wob11.de/links/anleitungen.html#elearning.

Pedagogical quality in e-learning

The article is concerned with design and use of e-learning technology to develop education qualitatively. The purpose is to develop a framework for a pedagogical evaluation of e-learning technology. The approach is that evaluation and design must be grounded in a learning theoretical approach, and it is argued that it is necessary to make a reflection of technology in relation to activities, learning principles, and a learning theory in order to qualitatively develop education. The article presents three frameworks developed on the basis of cognitivism, radical constructivism and activity theory. Finally, on the basis of the frameworks, the article discusses e-learning technology and, more specifically, design of virtual learning environments and learning objects. It is argued that e-learning technology is not pedagogically neutral, and that it is therefore necessary to focus on design of technology that explicitly supports a certain pedagogical approach. Further, it is argued that design should direct its focus away from organisation of content and towards design of activities.

Generisches Framework Studi-App

Mit der Idee eines generischen, an vielfältige Hochschulanforderungen anpassbaren Studierenden-App-Frameworks haben sich innerhalb des Arbeitskreises Web der ZKI ca. 30 Hochschulen zu einem Entwicklungsverbund zusammengefunden. Ziel ist es, an den beteiligten Einrichtungen eine umfassende Zusammenstellung aller elektronischen Studienservices zu evaluieren, übergreifende Daten- und Metadatenmodelle für die Beschreibung dieser Dienste zu erstellen und Schnittstellen zu den gängigen Campusmanagementsystemen sowie zu Infrastrukturen der elektronischen Lehre (LMS, Druckdienste, elektronischen Katalogen usw.) zu entwickeln. In einem abschließenden Schritt werden auf dieser Middleware aufsetzende Studienmanagement-Apps für Studierende erstellt, die die verschiedenen Daten- und Kommunikationsströme der standardisierten Dienste und Kommunikationskanäle bündeln und in eine für den Studierenden leicht zu durchschauende, navigationsfreundliche Aufbereitung kanalisiert. Mit der Konzeption eines dezentralen, über eine Vielzahl von Hochschulen verteilten Entwicklungsprojektes unter einer zentralen Projektleitung wird sichergestellt, dass redundante Entwicklungen vermieden, bundesweit standardisierte Serviceangebote angeboten und Wissenstransferprozesse zwischen einer Vielzahl von Hochschulen zur Nutzung mobiler Devices (Smartphones, Tablets und entsprechende Apps) angeregt werden können. Die Unterstützung der Realisierung klarer Schnittstellenspezifikationen zu Campusmanagementsystemen durch deren Anbieter kann durch diese breite Interessensgemeinschaft ebenfalls gestärkt werden. Weiterhin zentraler Planungsinhalt ist ein Angebot für den App-Nutzer zum Aufbau eines datenschutzrechtlich integeren, persönlichen E-Portfolios. Details finden sich im Kapitel Projektziele weiter unten.

(Lifelong) learning in your pocket?

Der Beitrag fokussiert die Entwicklung, den Einsatz und die Nutzung von innovativen Technologien zur Unterstützung von Bildungsszenarien in Schule, Hochschule und Weiterbildung. Ausgehend von den verschiedenen Phasen des Corporate Learning, Social Learning, Mobile Learning und Intelligent Learning wird in einem ersten Abschnitt das Nutzungsverhalten von Technologien durch Kinder, Jugendliche und (junge) Erwachsene in Schule, Studium und Lehre betrachtet. Es folgt die Darstellung technologischer Entwicklungen auf Basis des Technology Life Cycle und die Konsequenzen von unterschiedlichen Entwicklungszuständen und Reifegraden von Technologien wie Content Learning Management, sozialen Netzwerken, mobilen Endgeräten, multidimensionalen und -modalen Räumen bis hin zu Anwendungen augmentierter Realität und des Internets der Dinge, Dienste und Daten für den Einsatz und die Nutzung in Bildungsszenarien. Nach der Darstellung von Anforderungen an digitale Technologien hinsichtlich Inhalte, Didaktik und Methodik wie etwa hinsichtlich der Erstellung von Inhalten, deren Wiederverwendung, Digitalisierung und Auffindbarkeit sowie Standards werden methodische Hinweise zur Nutzung digitaler Technologien zur Interaktion von Lernenden, von Lehrenden, sozialer Interaktion, kollaborativem Autorieren, Kommentierung, Evaluation und Begutachtung gegeben. Abschließend werden - differenziert für Schule und Hochschule - Erkenntnisse zu Rahmenbedingungen, Einflussgrößen, hemmenden und fördernden Faktoren sowie Herausförderungen bei der Einführung und nachhaltigen Implementation digitaler Technologien im schulischen Unterricht, in Lehre, Studium und Weiterbildung im Überblick zusammengefasst.

A Fast Platform for Interactive E-Learning Systems

Modern e-learning systems represent a special type of web information systems. By definition, information systems are special computerized systems used to perform data operations by multiple users simultaneously. Each active user consumes an amount of hardware resources. A shortage of hardware resources can be caused by growing number of simultaneous users. Such situation can result in overall malfunctioning or slowed-down system. In order to avoid this problem, the underlying hardware system gets usually continuously upgraded. These upgrades, typically accompanied with various software updates, usually result in a temporarily increased amount of available resources. This work deals with the problem in a different way by proposing an implementation of a web e-learning system with a modified software architecture reducing resource usage of the server part to the bare minimum. In order to implement a full-scale e-learning system that could be used as a substitute to a conventional web e-learning system, a Rich Internet Application framework was used as basis. The technology allowed implementation of advanced interactivity features and provided an easy transfer of a substantial part of the application logic from server to clients. In combination with a special server application, the server part of the new system is able to run with a reasonable performance on a hardware with very limited computing resources.

Rahmenwerk für zielgruppenorientiertes Blended E-Learning im MINT-Bereich im Kontext des Lebenslangen Lernens

Das heutige Leben der Menschen ist vom Internet durchdrungen, kaum etwas ist nicht „vernetzt“ oder „elektronisch verfügbar“. Die Welt befindet sich im Wandel, die „Informationsgesellschaft“ konsumiert in Echtzeit Informationen auf mobilen Endgeräten, unabhängig von Zeit und Ort. Dies gilt teilweise auch für den Aus- und Weiterbildungssektor: Unter „E-Learning“ versteht man die elektronische Unterstützung des Lernens. Gelernt wird „online“; Inhalte sind digital verfügbar. Zudem hat sich die Lebenssituation der sogenannten „Digital Natives“, der jungen Individuen in der Informationsgesellschaft, verändert. Sie fordern zeitlich und räumlich flexible Ausbildungssysteme, erwarten von Bildungsinstitutionen umfassende digitale Verfügbarkeit von Informationen und möchten ihr Leben nicht mehr Lehr- und Zeitplänen unterordnen – das Lernen soll zum eigenen Leben passen, lebensbegleitend stattfinden. Neue „Lernszenarien“, z.B. für alleinerziehende Teilzeitstudierende oder Berufstätige, sollen problemlos möglich werden. Dies soll ein von der europäischen Union erarbeitetes Paradigma leisten, das unter dem Terminus „Lebenslanges Lernen“ zusammengefasst ist. Sowohl E-Learning, als auch Lebenslanges Lernen gewinnen an Bedeutung, denn die (deutsche) Wirtschaft thematisiert den „Fachkräftemangel“. Die Nachfrage nach speziell ausgebildeten Ingenieuren im MINT-Bereich soll schnellstmöglich befriedigt, die „Mitarbeiterlücke“ geschlossen werden, um so weiterhin das Wachstum und den Wohlstand zu sichern. Spezielle E-Learning-Lösungen für den MINT-Bereich haben das Potential, eine schnelle sowie flexible Aus- und Weiterbildung für Ingenieure zu bieten, in der Fachwissen bezogen auf konkrete Anforderungen der Industrie vermittelt wird. Momentan gibt es solche Systeme allerdings noch nicht. Wie sehen die Anforderungen im MINT-Bereich an eine solche E-Learning-Anwendung aus? Sie muss neben neuen Technologien vor allem den funktionalen Anforderungen des MINTBereichs, den verschiedenen Zielgruppen (wie z.B. Bildungsinstitutionen, Lerner oder „Digital Natives“, Industrie) und dem Paradigma des Lebenslangen Lernens gerecht werden, d.h. technische und konzeptuelle Anforderungen zusammenführen. Vor diesem Hintergrund legt die vorliegende Arbeit ein Rahmenwerk für die Erstellung einer solchen Lösung vor. Die praktischen Ergebnisse beruhen auf dem Blended E-Learning-System des Projekts „Technische Informatik Online“ (VHN-TIO).

Implicit task sequence learning

Implicit task sequence learning (TSL) can be considered as an extension of implicit sequence learning which is typically tested with the classical serial reaction time task (SRTT). By design, in the SRTT there is a correlation between the sequence of stimuli to which participants must attend and the sequence of motor movements/key presses with which participants must respond. The TSL paradigm allows to disentangle this correlation and to separately manipulate the presences/absence of a sequence of tasks, a sequence of responses, and even other streams of information such as stimulus locations or stimulus-response mappings. Here I review the state of TSL research which seems to point at the critical role of the presence of correlated streams of information in implicit sequence learning. On a more general level, I propose that beyond correlated streams of information, a simple statistical learning mechanism may also be involved in implicit sequence learning, and that the relative contribution of these two explanations differ according to task requirements. With this differentiation, conflicting results can be integrated into a coherent framework.

Social skills as predictors of communication, performance and quality of collaboration in project-based learning

The assumption that social skills are necessary ingredients of collaborative learning is well established but rarely empirically tested. In addition, most theories on collaborative learning focus on social skills only at the personal level, while the social skill configurations within a learning group might be of equal importance. Using the integrative framework, this study investigates which social skills at the personal level and at the group level are predictive of task-related e-mail communication, satisfaction with performance and perceived quality of collaboration. Data collection took place in a technology-enhanced long-term project-based learning setting for pre-service teachers. For data collection, two questionnaires were used, one at the beginning and one at the end of the learning cycle which lasted 3 months. During the project phase, the e-mail communication between group members was captured as well. The investigation of 60 project groups (N = 155 for the questionnaires; group size: two or three students) and 33 groups for the e-mail communication (N = 83) revealed that personal social skills played only a minor role compared to group level configurations of social skills in predicting satisfaction with performance, perceived quality of collaboration and communication behaviour. Members from groups that showed a high and/or homogeneous configuration of specific social skills (e.g., cooperation/compromising, leadership) usually were more satisfied and saw their group as more efficient than members from groups with a low and/or heterogeneous configuration of skills.

Learning reward timing in cortex through reward dependent expression of synaptic plasticity.

The ability to represent time is an essential component of cognition but its neural basis is unknown. Although extensively studied both behaviorally and electrophysiologically, a general theoretical framework describing the elementary neural mechanisms used by the brain to learn temporal representations is lacking. It is commonly believed that the underlying cellular mechanisms reside in high order cortical regions but recent studies show sustained neural activity in primary sensory cortices that can represent the timing of expected reward. Here, we show that local cortical networks can learn temporal representations through a simple framework predicated on reward dependent expression of synaptic plasticity. We assert that temporal representations are stored in the lateral synaptic connections between neurons and demonstrate that reward-modulated plasticity is sufficient to learn these representations. We implement our model numerically to explain reward-time learning in the primary visual cortex (V1), demonstrate experimental support, and suggest additional experimentally verifiable predictions.

Spike timing dependent plasticity: a consequence of more fundamental learning rules.

Spike timing dependent plasticity (STDP) is a phenomenon in which the precise timing of spikes affects the sign and magnitude of changes in synaptic strength. STDP is often interpreted as the comprehensive learning rule for a synapse - the "first law" of synaptic plasticity. This interpretation is made explicit in theoretical models in which the total plasticity produced by complex spike patterns results from a superposition of the effects of all spike pairs. Although such models are appealing for their simplicity, they can fail dramatically. For example, the measured single-spike learning rule between hippocampal CA3 and CA1 pyramidal neurons does not predict the existence of long-term potentiation one of the best-known forms of synaptic plasticity. Layers of complexity have been added to the basic STDP model to repair predictive failures, but they have been outstripped by experimental data. We propose an alternate first law: neural activity triggers changes in key biochemical intermediates, which act as a more direct trigger of plasticity mechanisms. One particularly successful model uses intracellular calcium as the intermediate and can account for many observed properties of bidirectional plasticity. In this formulation, STDP is not itself the basis for explaining other forms of plasticity, but is instead a consequence of changes in the biochemical intermediate, calcium. Eventually a mechanism-based framework for learning rules should include other messengers, discrete change at individual synapses, spread of plasticity among neighboring synapses, and priming of hidden processes that change a synapse's susceptibility to future change. Mechanism-based models provide a rich framework for the computational representation of synaptic plasticity.

Learning and emotion - perspectives for theory and research

There is growing interest in and knowledge about the interplay of learning and emotion. However, the different approaches and empirical studies correspond to each other only to a low extent. To prevent this research field from increasing fragmentation, a shared basis of theory and research is needed. The presentation aims at giving an overview of the state of the art, developing a general framework for theory and research, and outlining crucial topics for future theory and research. The presentation focuses on the influence of emotions on learning. First, theories about the impact of emotions on learning are introduced. Second, the importance of these theories for school learning are discussed. Third, empirical evidence resulting from school-based research about the role of emotions for learning is presented. Finally, further research demands are stressed.