NLP Driven Models for Automatically Generating Survey Articles for Scientific Topics.

This thesis presents new methods that use natural language processing (NLP) driven models for summarizing research in scientific fields. Given a topic query in the form of a text string, we present methods for finding research articles relevant to the topic as well as summarization algorithms that use lexical and discourse information present in the text of these articles to generate coherent and readable extractive summaries of past research on the topic. In addition to summarizing prior research, good survey articles should also forecast future trends. With this motivation, we present work on forecasting future impact of scientific publications using NLP driven features.PhDComputer Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113407/1/rahuljha_1.pd

Smartcells : a Bio-Cloud theory towards intelligent cloud computing system

Cloud computing is the future of web technologies and the goal for all web companies as well. It reinforces some old concepts of building highly scalable Internet architectures and introduces some new concepts that entirely change the way applications are built and deployed. In the recent years, some technology companies adopted the cloud computing strategy. This adoption took place when these companies have predicted that cloud computing will be the solutions of Web problems such as availability. However, organizations find it almost impossible to launch the cloud idea without adopting previous approaches like that of Service-Oriented approach. As a result of this dependency, web service problems are transferred into the cloud. Indeed, the current cloud’s availability is too expensive due to service replication, some cloud services face performance problem, a majority of these services is weak regarding security, and cloud services are randomly discovered while it is difficult to precisely select the best ones in addition to being spontaneously fabricated in an ocean of services. Moreover, it is impossible to validate cloud services especially before runtime. Finally, according to the W3C standards, cloud services are not yet internationalized. Indeed, the predicted web is a smart service model while it lacks intelligence and autonomy. This is why the adoption of service-oriented model was not an ideal decision. In order to minimize the consequences of cloud problems and achieve more benefits, each cloud company builds its own cloud platform. Currently, cloud vendors are facing a big problem that can be summarized by the “Cloud Platform Battle”. The budget of this battle will cost about billions of dollars due to the absence of an agreement to reach a standard cloud platform. Why intelligent collaboration is not applied between distributed clouds to achieve better Cloud Computing results? The appropriate approach is to restructure the cloud model basis to recover its issues. Multiple intelligent techniques may be used to develop advanced intelligent Cloud systems. Classical examples of distributed intelligent systems include: human body, social insect colonies, flocks of vertebrates, multi-agent systems, transportation systems, multi-robot systems, and wireless sensor networks. However, the intelligent system that could be imitated is the human body system, in which billions of body cells work together to achieve accurate results. Inspired by Bio-Informatics strategy that benefits from technologies to solve biological facts (like our genes), this thesis research proposes a novel Bio-Cloud strategy which imitates biological facts (like brain and genes) in solving the Cloud Computing issues. Based on Bio-Cloud strategy, I have developed through this thesis project the “SmartCells” framework as a smart solution for Cloud problems. SmartCells framework covers: 1) Cloud problems which are inherited from the service paradigm (like issues of service reusability, security, etc.); 2) The intelligence insufficiency problem in Cloud Computing systems. SmartCells depends on collaborations between smart components (Cells) that take advantage of the variety of already built web service components to produce an intelligent Cloud system. Le « Cloud Computing » est certes le futur des technologies du web. Il renforce certains vieux concepts de construction d’architectures internet hautement évolutifs, et introduit de nouveaux concepts qui changent complètement la façon dont les applications sont développées et déployées. Au cours des dernières années, certaines entreprises technologiques ont adopté la stratégie du Cloud Computing. Cette adoption a eu lieu lorsque ces entreprises ont prédit que le Cloud Computing sera les solutions des plusieurs problèmes Web tels que la disponibilité. Toutefois, les organisations pensent qu'il est presque impossible de lancer l'idée du « Cloud » sans adopter les concepts et les normes antérieures comme celle du paradigme orienté service (Service-Oriented Paradigm). En raison de cette dépendance, les problèmes de l'approche orientée service et services web sont transférés au Cloud. En effet, la disponibilité du Cloud actuel s’avère trop chère à cause de la reproduction de services, certains services Cloud sont confrontés à des problèmes de performances, une majorité des services Cloud est faible en matière de sécurité, et ces services sont découverts d’une façon aléatoire, il est difficile de choisir le meilleur d’entre eux ainsi qu’ils sont composés d’un groupe de services web dans un monde de services. Egalement, il est impossible de valider les services Cloud en particulier, avant le temps d’exécution. Finalement, selon les normes du W3C, les services Cloud ne sont pas encore internationalisés. En effet, le web comme prévu, est un modèle de service intelligent bien qu’il manque d’intelligence et d’autonomie. Ainsi, l'adoption d'un modèle axé sur le service n’était pas une décision idéale. Afin de minimiser les conséquences des problèmes du Cloud et réaliser plus de profits, certaines entreprises de Cloud développent leurs propres plateformes de Cloud Computing. Actuellement, les fournisseurs du Cloud font face à un grand problème qui peut se résumer par la « Bataille de la plateforme Cloud ». Le budget de cette bataille coûte des milliards de dollars en l’absence d’un accord pour accéder à une plateforme Cloud standard. Pourquoi une collaboration intelligente n’est pas mise en place entre les nuages distribués pour obtenir de meilleurs résultats ? L’approche appropriée est de restructurer le modèle de cloud afin de couvrir ses problèmes. Des techniques intelligentes multiples peuvent être utilisées pour développer des systèmes Cloud intelligents avancés. Parmi les exemples classiques de systèmes intelligents distribués se trouvent : le corps humain, les colonies d’insectes sociaux, les troupeaux de vertébrés, les systèmes multi-agents, les systèmes de transport, les systèmes multi-robots, et les réseaux de capteurs sans fils. Toutefois, le système intelligent qui pourrait être imité est le système du corps humain dans lequel vivent des milliards de cellules du corps et travaillent ensemble pour atteindre des résultats précis. En s’inspirant de la stratégie Bio-Informatique qui bénéficie de technologies pour résoudre des faits biologiques (comme les gènes). Cette thèse propose une nouvelle stratégie Bio-Cloud qui imite des faits biologiques (comme le cerveau et les gènes) pour résoudre les problèmes du Cloud Computing mentionnés ci-haut. Ainsi, en me basant sur la stratégie Bio-Cloud, j’ai développé au cours de cette thèse la théorie « SmartCells » conçue comme une proposition (approche) cherchant à résoudre les problèmes du Cloud Computing. Cette approche couvre : 1) les problèmes hérités du paradigme services (comme les questions de réutilisation de services, les questions de sécurité, etc.); 2) le problème d’insuffisance d’intelligence dans les systèmes du Cloud Computing. SmartCells se base sur la collaboration entre les composants intelligents (les Cellules) qui profitent de la variété des composants des services web déjà construits afin de produire un système de Cloud intelligent

Knowledge Modelling and Learning through Cognitive Networks

One of the most promising developments in modelling knowledge is cognitive network science, which aims to investigate cognitive phenomena driven by the networked, associative organization of knowledge. For example, investigating the structure of semantic memory via semantic networks has illuminated how memory recall patterns influence phenomena such as creativity, memory search, learning, and more generally, knowledge acquisition, exploration, and exploitation. In parallel, neural network models for artificial intelligence (AI) are also becoming more widespread as inferential models for understanding which features drive language-related phenomena such as meaning reconstruction, stance detection, and emotional profiling. Whereas cognitive networks map explicitly which entities engage in associative relationships, neural networks perform an implicit mapping of correlations in cognitive data as weights, obtained after training over labelled data and whose interpretation is not immediately evident to the experimenter. This book aims to bring together quantitative, innovative research that focuses on modelling knowledge through cognitive and neural networks to gain insight into mechanisms driving cognitive processes related to knowledge structuring, exploration, and learning. The book comprises a variety of publication types, including reviews and theoretical papers, empirical research, computational modelling, and big data analysis. All papers here share a commonality: they demonstrate how the application of network science and AI can extend and broaden cognitive science in ways that traditional approaches cannot

Recent Advances in Social Data and Artificial Intelligence 2019

The importance and usefulness of subjects and topics involving social data and artificial intelligence are becoming widely recognized. This book contains invited review, expository, and original research articles dealing with, and presenting state-of-the-art accounts pf, the recent advances in the subjects of social data and artificial intelligence, and potentially their links to Cyberspace

End-to-end Learning for Mining Text and Network Data

A wealth of literature studies user behaviors in online communities, e.g., how users respond to information that are spreading over social networks. One way to study user responses is to analyze user-generated text, by identifying attitude towards target topics. Another way is to analyze the information diffusion networks over involved users. Conventional methods require manual encoding of world knowledge, which is ineffective in many cases. Therefore, to push research forward, we design end-to-end deep learning algorithms that learn high-level representations directly from data and optimize for particular tasks, relieving humans from hard coding features or rules, while achieving better performance. Specifically, I study attitude identification in the text mining domain, and important prediction tasks in the network domain. The key roles of text and networks in understanding user behaviors in online communities are not the only reason that we study them together. Compared with other types of data (e.g., image and speech), text and networks are both discrete and thus may share similar challenges and solutions. Attitude identification is conventionally decomposed into two separate subtasks: target detection that identifies whether a given target is mentioned in the text, and polarity classification that classifies the exact sentiment polarity. However, this decomposition fails to capture interactions between subtasks. To remedy the issue, we developed an end-to-end deep learning architecture, with the two subtasks interleaved by a memory network. Moreover, as the learned representations may share the same semantics for some targets, but vary for others, our model also incorporates the interactions among entities. For information networks, we aim to learn the representation of network structures in order to solve many valuable prediction tasks in the network community. An example of prediction tasks is network growth prediction, which assists decision makers in optimizing strategies. Instead of handcrafting features that could lead to severe loss of structural information, we propose to learn graph representations through a deep end-to-end prediction model. By finding "signatures" for graphs, we convert graphs into matrices, where convolutional neural networks could be applied. In additional to topology, information networks are often associated with different sources of information. We specifically consider the task of cascade prediction, where global context, text content on both nodes, and diffusion graphs play important roles for prediction. Conventional methods require manual specification of the interactions among different information sources, which is easy to miss key information. We present a novel, end-to-end deep learning architecture named DeepCas, which first represents a cascade graph as a set of cascade paths that are sampled through random walks. Such a representation not only allows incorporation of the global context, but also bounds the loss of structural information. After modeling the information of global context, we equip DeepCas with the ability to jointly model text and network in a unified framework. We present a gating mechanism to dynamically fuse the structural and textual representations of nodes based on their respective properties. To incorporate the text information associated with both diffusion items and nodes, attention mechanisms are employed over node text based on their interactions with item text.PHDInformationUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/140791/1/lichengz_1.pd

Computational approaches to discovering differentiation genes in the peripheral nervous system of drosophila melanogaster

In the common fruit fly, Drosophila melanogaster, neural cell fate specification is triggered by a group of conserved transcriptional regulators known as proneural factors. Proneural factors induce neural fate in uncommitted neuroectodermal progenitor cells, in a process that culminates in sensory neuron differentiation. While the role of proneural factors in early fate specification has been described, less is known about the transition between neural specification and neural differentiation. The aim of this thesis is to use computational methods to improve the understanding of terminal neural differentiation in the Peripheral Nervous System (PNS) of Drosophila. To provide an insight into how proneural factors coordinate the developmental programme leading to neural differentiation, expression profiling covering the first 3 hours of PNS development in Drosophila embryos had been previously carried out by Cachero et al. [2011]. The study revealed a time-course of gene expression changes from specification to differentiation and suggested a cascade model, whereby proneural factors regulate a group of intermediate transcriptional regulators which are in turn responsible for the activation of specific differentiation target genes. In this thesis, I propose to select potentially important differentiation genes from the transcriptional data in Cachero et al. [2011] using a novel approach centred on protein interaction network-driven prioritisation. This is based on the insight that biological hypotheses supported by diverse data sources can represent stronger candidates for follow-up studies. Specifically, I propose the usage of protein interaction network data because of documented transcriptome-interactome correlations, which suggest that differentially expressed genes encode products that tend to belong to functionally related protein interaction clusters. Experimental protein interaction data is, however, remarkably sparse. To increase the informative power of protein-level analyses, I develop a novel approach to augment publicly available protein interaction datasets using functional conservation between orthologous proteins across different genomes, to predict interologs (interacting orthologs). I implement this interolog retrieval methodology in a collection of open-source software modules called Bio:: Homology::InterologWalk, the first generalised framework using web-services for “on-the- fly” interolog projection. Bio::Homology::InterologWalk works with homology data for any of the hundreds of genomes in Ensembl and Ensembgenomes Metazoa, and with experimental protein interaction data curated by EBI Intact. It generates putative protein interactions and optionally collates meta-data into a prioritisation index that can be used to help select interologs with high experimental support. The methodology proposed represents a significant advance over existing interolog data sources, which are restricted to specific biological domains with fixed underlying data sources often only accessible through basic web-interfaces. Using Bio::Homology::InterologWalk, I build interolog models in Drosophila sensory neurons and, guided by the transcriptome data, find evidence implicating a small set of genes in a conserved sensory neuronal specialisation dynamic, the assembly of the ciliary dendrite in mechanosensory neurons. Using network community-finding algorithms I obtain functionally enriched communities, which I analyse using an array of novel computational techniques. The ensuing datasets lead to the elucidation of a cluster of interacting proteins encoded by the target genes of one of the intermediate transcriptional regulators of neurogenesis and ciliogenesis, fd3F. These targets are validated in vivo and result in improved knowledge of the important target genes activated by the transcriptional cascade, suggesting a scenario for the mechanisms orchestrating the ordered assembly of the cilium during differentiation

Natural Language Processing: Emerging Neural Approaches and Applications

This Special Issue highlights the most recent research being carried out in the NLP field to discuss relative open issues, with a particular focus on both emerging approaches for language learning, understanding, production, and grounding interactively or autonomously from data in cognitive and neural systems, as well as on their potential or real applications in different domains

Social Network Dynamics

This thesis focuses on the analysis of structural and topological network problems. In particular, in this work the privileged subjects of investigation will be both static and dynamic social networks. Nowadays, the constantly growing availability of Big Data describing human behaviors (i.e., the ones provided by online social networks, telco companies, insurances, airline companies. . . ) offers the chance to evaluate and validate, on large scale realities, the performances of algorithmic approaches and the soundness of sociological theories. In this scenario, exploiting data-driven methodologies enables for a more careful modeling and thorough understanding of observed phenomena. In the last decade, graph theory has lived a second youth: the scientific community has extensively adopted, and sharpened, its tools to shape the so called Network Science. Within this highly active field of research, it is recently emerged the need to extend classic network analytical methodologies in order to cope with a very important, previously underestimated, semantic information: time. Such awareness has been the linchpin for recent works that have started to redefine form scratch well known network problems in order to better understand the evolving nature of human interactions. Indeed, social networks are highly dynamic realities: nodes and edges appear and disappear as time goes by describing the natural lives of social ties: for this reason. it is mandatory to assess the impact that time-aware approaches have on the solution of network problems. Moving from the analysis of the strength of social ties, passing through node ranking and link prediction till reaching community discovery, this thesis aims to discuss data-driven methodologies specifically tailored to approach social network issues in semantic enriched scenarios. To this end, both static and dynamic analytical processes will be introduced and tested on real world data

Study on open science: The general state of the play in Open Science principles and practices at European life sciences institutes

Nowadays, open science is a hot topic on all levels and also is one of the priorities of the European Research Area. Components that are commonly associated with open science are open access, open data, open methodology, open source, open peer review, open science policies and citizen science. Open science may a great potential to connect and influence the practices of researchers, funding institutions and the public. In this paper, we evaluate the level of openness based on public surveys at four European life sciences institute