Multidimensional Membership Mixture Models

We present the multidimensional membership mixture (M3) models where every dimension of the membership represents an independent mixture model and each data point is generated from the selected mixture components jointly. This is helpful when the data has a certain shared structure. For example, three unique means and three unique variances can effectively form a Gaussian mixture model with nine components, while requiring only six parameters to fully describe it. In this paper, we present three instantiations of M3 models (together with the learning and inference algorithms): infinite, finite, and hybrid, depending on whether the number of mixtures is fixed or not. They are built upon Dirichlet process mixture models, latent Dirichlet allocation, and a combination respectively. We then consider two applications: topic modeling and learning 3D object arrangements. Our experiments show that our M3 models achieve better performance using fewer topics than many classic topic models. We also observe that topics from the different dimensions of M3 models are meaningful and orthogonal to each other.Comment: 9 pages, 7 figure

Topic Uncovering and Image Annotation via Scalable Probit Normal Correlated Topic Models

Topic uncovering of the latent topics have become an active research area for more than a decade and continuous to receive contributions from all disciplines including computer science, information science and statistics. Since the introduction of Latent Dirichlet Allocation in 2003, many intriguing extension models have been proposed. One such extension model is the logistic normal correlated topic model, which not only uncovers hidden topic of a document, but also extract a meaningful topical relationship among a large number of topics. In this model, the Logistic normal distribution was adapted via the transformation of multivariate Gaussian variables to model the topical distribution of documents in the presence of correlations among topics. In this thesis, we propose a Probit normal alternative approach to modelling correlated topical structures. Our use of the Probit model in the context of topic discovery is novel, as many authors have so far concentrated solely of the logistic model partly due to the formidable inefficiency of the multinomial Probit model even in the case of very small topical spaces. We herein circumvent the inefficiency of multinomial Probit estimation by using an adaptation of the Diagonal Orthant Multinomial Probit (DO-Probit) in the topic models context, resulting in the ability of our topic modelling scheme to handle corpuses with a large number of latent topics. In addition, we extended our model and implement it into the context of image annotation by developing an efficient Collapsed Gibbs Sampling scheme. Furthermore, we employed various high performance computing techniques such as memory-aware Map Reduce, SpareseLDA implementation, vectorization and block sampling as well as some numerical efficiency strategy to allow fast and efficient sampling of our algorithm

Practical Natural Language Processing for Low-Resource Languages.

As the Internet and World Wide Web have continued to gain widespread adoption, the linguistic diversity represented has also been growing. Simultaneously the field of Linguistics is facing a crisis of the opposite sort. Languages are becoming extinct faster than ever before and linguists now estimate that the world could lose more than half of its linguistic diversity by the year 2100. This is a special time for Computational Linguistics; this field has unprecedented access to a great number of low-resource languages, readily available to be studied, but needs to act quickly before political, social, and economic pressures cause these languages to disappear from the Web. Most work in Computational Linguistics and Natural Language Processing (NLP) focuses on English or other languages that have text corpora of hundreds of millions of words. In this work, we present methods for automatically building NLP tools for low-resource languages with minimal need for human annotation in these languages. We start first with language identification, specifically focusing on word-level language identification, an understudied variant that is necessary for processing Web text and develop highly accurate machine learning methods for this problem. From there we move onto the problems of part-of-speech tagging and dependency parsing. With both of these problems we extend the current state of the art in projected learning to make use of multiple high-resource source languages instead of just a single language. In both tasks, we are able to improve on the best current methods. All of these tools are practically realized in the "Minority Language Server," an online tool that brings these techniques together with low-resource language text on the Web. The Minority Language Server, starting with only a few words in a language can automatically collect text in a language, identify its language and tag its parts of speech. We hope that this system is able to provide a convincing proof of concept for the automatic collection and processing of low-resource language text from the Web, and one that can hopefully be realized before it is too late.PhDComputer Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113373/1/benking_1.pd

Computational approaches for single-cell omics and multi-omics data

Single-cell omics and multi-omics technologies have enabled the study of cellular heterogeneity with unprecedented resolution and the discovery of new cell types. The core of identifying heterogeneous cell types, both existing and novel ones, relies on efficient computational approaches, including especially cluster analysis. Additionally, gene regulatory network analysis and various integrative approaches are needed to combine data across studies and different multi-omics layers. This thesis comprehensively compared Bayesian clustering models for single-cell RNAsequencing (scRNA-seq) data and selected integrative approaches were used to study the cell-type specific gene regulation of uterus. Additionally, single-cell multi-omics data integration approaches for cell heterogeneity analysis were investigated. Article I investigated analytical approaches for cluster analysis in scRNA-seq data, particularly, latent Dirichlet allocation (LDA) and hierarchical Dirichlet process (HDP) models. The comparison of LDA and HDP together with the existing state-of-art methods revealed that topic modeling-based models can be useful in scRNA-seq cluster analysis. Evaluation of the cluster qualities for LDA and HDP with intrinsic and extrinsic cluster quality metrics indicated that the clustering performance of these methods is dataset dependent. Article II and Article III focused on cell-type specific integrative analysis of uterine or decidual stromal (dS) and natural killer (dNK) cells that are important for successful pregnancy. Article II integrated the existing preeclampsia RNA-seq studies of the decidua together with recent scRNA-seq datasets in order to investigate cell-type-specific contributions of early onset preeclampsia (EOP) and late onset preeclampsia (LOP). It was discovered that the dS marker genes were enriched for LOP downregulated genes and the dNK marker genes were enriched for upregulated EOP genes. Article III presented a gene regulatory network analysis for the subpopulations of dS and dNK cells. This study identified novel subpopulation specific transcription factors that promote decidualization of stromal cells and dNK mediated maternal immunotolerance. In Article IV, different strategies and methodological frameworks for data integration in single-cell multi-omics data analysis were reviewed in detail. Data integration methods were grouped into early, late and intermediate data integration strategies. The specific stage and order of data integration can have substantial effect on the results of the integrative analysis. The central details of the approaches were presented, and potential future directions were discussed.  Laskennallisia menetelmiä yksisolusekvensointi- ja multiomiikkatulosten analyyseihin Yksisolusekvensointitekniikat mahdollistavat solujen heterogeenisyyden tutkimuksen ennennäkemättömällä resoluutiolla ja uusien solutyyppien löytämisen. Solutyyppien tunnistamisessa keskeisessä roolissa on ryhmittely eli klusterointianalyysi. Myös geenien säätelyverkostojen sekä eri molekyylidatatasojen yhdistäminen on keskeistä analyysissä. Väitöskirjassa verrataan bayesilaisia klusterointimenetelmiä ja yhdistetään eri menetelmillä kerättyjä tietoja kohdun solutyyppispesifisessä geeninsäätelyanalyysissä. Lisäksi yksisolutiedon integraatiomenetelmiä selvitetään kattavasti. Julkaisu I keskittyy analyyttisten menetelmien, erityisesti latenttiin Dirichletallokaatioon (LDA) ja hierarkkiseen Dirichlet-prosessiin (HDP) perustuvien mallien tutkimiseen yksisoludatan klusterianalyysissä. Kattava vertailu näiden kahden mallin sekä olemassa olevien menetelmien kanssa paljasti, että aihemallinnuspohjaiset menetelmät voivat olla hyödyllisiä yksisoludatan klusterianalyysissä. Menetelmien suorituskyky riippui myös kunkin analysoitavan datasetin ominaisuuksista. Julkaisuissa II ja III keskitytään naisen lisääntymisterveydelle tärkeiden kohdun stroomasolujen ja NK-immuunisolujen solutyyppispesifiseen analyysiin. Artikkelissa II yhdistettiin olemassa olevia tuloksia pre-eklampsiasta viimeisimpiin yksisolusekvensointituloksiin ja löydettiin varhain alkavan pre-eklampsian (EOP) ja myöhään alkavan pre-eklampsian (LOP) solutyyppispesifisiä vaikutuksia. Havaittiin, että erilaistuneen strooman markkerigeenien ilmentyminen vähentyi LOP:ssa ja NK-markkerigeenien ilmentyminen lisääntyi EOP:ssa. Julkaisu III analysoi strooman ja NK-solujen alapopulaatiospesifisiä geeninsäätelyverkostoja ja niiden transkriptiofaktoreita. Tutkimus tunnisti uusia alapopulaatiospesifisiä säätelijöitä, jotka edistävät strooman erilaistumista ja NK-soluvälitteistä immunotoleranssia Julkaisu IV tarkastelee yksityiskohtaisesti strategioita ja menetelmiä erilaisten yksisoludatatasojen (multi-omiikka) integroimiseksi. Integrointimenetelmät ryhmiteltiin varhaisen, myöhäisen ja välivaiheen strategioihin ja kunkin lähestymistavan menetelmiä esiteltiin tarkemmin. Lisäksi keskusteltiin mahdollisista tulevaisuuden suunnista

PERICLES Deliverable 4.3:Content Semantics and Use Context Analysis Techniques

The current deliverable summarises the work conducted within task T4.3 of WP4, focusing on the extraction and the subsequent analysis of semantic information from digital content, which is imperative for its preservability. More specifically, the deliverable defines content semantic information from a visual and textual perspective, explains how this information can be exploited in long-term digital preservation and proposes novel approaches for extracting this information in a scalable manner. Additionally, the deliverable discusses novel techniques for retrieving and analysing the context of use of digital objects. Although this topic has not been extensively studied by existing literature, we believe use context is vital in augmenting the semantic information and maintaining the usability and preservability of the digital objects, as well as their ability to be accurately interpreted as initially intended.PERICLE

Aligning Performance Management Systems for Lasting Outcomes in Humanitarian Operations

Logistics is dynamic, expansive, and critical to organizational success. While it is generally believed that effective logistics management is associated with positive performance outcomes, the links between organizational practice and performance are understudied. This dissertation leverages resource-based theory and organizational learning theory to examine organizational practice and performance in non-traditional logistics settings, with particular focus on military organizations and humanitarian operational settings. First, a meta-analytical study establishes generalizable associations between various operations management practices and performance outcomes. Then, this is applied to dynamic humanitarian logistics settings, exploring how practitioners perceive practice and performance, and how this is reported and documented for organizational performance improvement. A cumulative case study provides actionable recommendations for humanitarian practitioners and insights into an understudied area of performance management and organizational learning, which are then examined in-depth in a humanitarian field exercise. This dissertation demonstrates the importance of deliberate resource alignment, collaboration and learning for lasting logistics operations management success