Stable Feature Selection for Biomarker Discovery

Feature selection techniques have been used as the workhorse in biomarker discovery applications for a long time. Surprisingly, the stability of feature selection with respect to sampling variations has long been under-considered. It is only until recently that this issue has received more and more attention. In this article, we review existing stable feature selection methods for biomarker discovery using a generic hierarchal framework. We have two objectives: (1) providing an overview on this new yet fast growing topic for a convenient reference; (2) categorizing existing methods under an expandable framework for future research and development

Authorship identification of translation algorithms.

Authorship analysis is a process of identifying a true writer of a given document and has been studied for decades. However, only a handful of studies of authorship analysis of translators are available despite the fact that online translations are widely available and also popularly employed in automatic translations of posts in social networking services. The identification of translation algorithms has potential to contribute to the investigation of cybercrimes, involving translation of scam messages by algorithmic translations to reach speakers of foreign languages. This study tested bag of words (BOW) approach in authorship attribution and the existing approaches to translator attribution. We also proposed a simple but accurate feature that extracts the combinations of lexical and syntactic information from texts. Our experiments show that the proposed feature is text size invariant

Graph-Based Fusion of Imaging, Genetic and Clinical Data for Degenerative Disease Diagnosis

Graph learning methods have achieved noteworthy performance in disease diagnosis due to their ability to represent unstructured information such as inter-subject relationships. While it has been shown that imaging, genetic and clinical data are crucial for degenerative disease diagnosis, existing methods rarely consider how best to use their relationships. How best to utilize information from imaging, genetic and clinical data remains a challenging problem. This study proposes a novel graph-based fusion (GBF) approach to meet this challenge. To extract effective imaging-genetic features, we propose an imaging-genetic fusion module which uses an attention mechanism to obtain modality-specific and joint representations within and between imaging and genetic data. Then, considering the effectiveness of clinical information for diagnosing degenerative diseases, we propose a multi-graph fusion module to further fuse imaging-genetic and clinical features, which adopts a learnable graph construction strategy and a graph ensemble method. Experimental results on two benchmarks for degenerative disease diagnosis (Alzheimer's Disease Neuroimaging Initiative and Parkinson's Progression Markers Initiative) demonstrate its effectiveness compared to state-of-the-art graph-based methods. Our findings should help guide further development of graph-based models for dealing with imaging, genetic and clinical data

Uncertainty-Aware Principal Component Analysis

We present a technique to perform dimensionality reduction on data that is subject to uncertainty. Our method is a generalization of traditional principal component analysis (PCA) to multivariate probability distributions. In comparison to non-linear methods, linear dimensionality reduction techniques have the advantage that the characteristics of such probability distributions remain intact after projection. We derive a representation of the PCA sample covariance matrix that respects potential uncertainty in each of the inputs, building the mathematical foundation of our new method: uncertainty-aware PCA. In addition to the accuracy and performance gained by our approach over sampling-based strategies, our formulation allows us to perform sensitivity analysis with regard to the uncertainty in the data. For this, we propose factor traces as a novel visualization that enables to better understand the influence of uncertainty on the chosen principal components. We provide multiple examples of our technique using real-world datasets. As a special case, we show how to propagate multivariate normal distributions through PCA in closed form. Furthermore, we discuss extensions and limitations of our approach

Using Ontology-Based Approaches to Representing Speech Transcripts for Automated Speech Scoring

Text representation is a process of transforming text into some formats that computer systems can use for subsequent information-related tasks such as text classification. Representing text faces two main challenges: meaningfulness of representation and unknown terms. Research has shown evidence that these challenges can be resolved by using the rich semantics in ontologies. This study aims to address these challenges by using ontology-based representation and unknown term reasoning approaches in the context of content scoring of speech, which is a less explored area compared to some common ones such as categorizing text corpus (e.g. 20 newsgroups and Reuters). From the perspective of language assessment, the increasing amount of language learners taking second language tests makes automatic scoring an attractive alternative to human scoring for delivering rapid and objective scores of written and spoken test responses. This study focuses on the speaking section of second language tests and investigates ontology-based approaches to speech scoring. Most previous automated speech scoring systems for spontaneous responses of test takers assess speech by primarily using acoustic features such as fluency and pronunciation, while text features are less involved and exploited. As content is an integral part of speech, the study is motivated by the lack of rich text features in speech scoring and is designed to examine the effects of different text features on scoring performance. A central question to the study is how speech transcript content can be represented in an appropriate means for speech scoring. Previously used approaches from essay and speech scoring systems include bag-of-words and latent semantic analysis representations, which are adopted as baselines in this study; the experimental approaches are ontology-based, which can help improving meaningfulness of representation units and estimating importance of unknown terms. Two general domain ontologies, WordNet and Wikipedia, are used respectively for ontology-based representations. In addition to comparison between representation approaches, the author analyzes which parameter option leads to the best performance within a particular representation. The experimental results show that on average, ontology-based representations slightly enhances speech scoring performance on all measurements when combined with the bag-of-words representation; reasoning of unknown terms can increase performance on one measurement (cos.w4) but decrease others. Due to the small data size, the significance test (t-test) shows that the enhancement of ontology-based representations is inconclusive. The contributions of the study include: 1) it examines the effects of different representation approaches on speech scoring tasks; 2) it enhances the understanding of the mechanisms of representation approaches and their parameter options via in-depth analysis; 3) the representation methodology and framework can be applied to other tasks such as automatic essay scoring

An overview of clustering methods with guidelines for application in mental health research

Cluster analyzes have been widely used in mental health research to decompose inter-individual heterogeneity by identifying more homogeneous subgroups of individuals. However, despite advances in new algorithms and increasing popularity, there is little guidance on model choice, analytical framework and reporting requirements. In this paper, we aimed to address this gap by introducing the philosophy, design, advantages/disadvantages and implementation of major algorithms that are particularly relevant in mental health research. Extensions of basic models, such as kernel methods, deep learning, semi-supervised clustering, and clustering ensembles are subsequently introduced. How to choose algorithms to address common issues as well as methods for pre-clustering data processing, clustering evaluation and validation are then discussed. Importantly, we also provide general guidance on clustering workflow and reporting requirements. To facilitate the implementation of different algorithms, we provide information on R functions and librarie

Data- og ekspertdreven variabelseleksjon for prediktive modeller i helsevesenet : mot økt tolkbarhet i underbestemte maskinlæringsproblemer

Modern data acquisition techniques in healthcare generate large collections of data from multiple sources, such as novel diagnosis and treatment methodologies. Some concrete examples are electronic healthcare record systems, genomics, and medical images. This leads to situations with often unstructured, high-dimensional heterogeneous patient cohort data where classical statistical methods may not be sufficient for optimal utilization of the data and informed decision-making. Instead, investigating such data structures with modern machine learning techniques promises to improve the understanding of patient health issues and may provide a better platform for informed decision-making by clinicians. Key requirements for this purpose include (a) sufficiently accurate predictions and (b) model interpretability. Achieving both aspects in parallel is difficult, particularly for datasets with few patients, which are common in the healthcare domain. In such cases, machine learning models encounter mathematically underdetermined systems and may overfit easily on the training data. An important approach to overcome this issue is feature selection, i.e., determining a subset of informative features from the original set of features with respect to the target variable. While potentially raising the predictive performance, feature selection fosters model interpretability by identifying a low number of relevant model parameters to better understand the underlying biological processes that lead to health issues. Interpretability requires that feature selection is stable, i.e., small changes in the dataset do not lead to changes in the selected feature set. A concept to address instability is ensemble feature selection, i.e. the process of repeating the feature selection multiple times on subsets of samples of the original dataset and aggregating results in a meta-model. This thesis presents two approaches for ensemble feature selection, which are tailored towards high-dimensional data in healthcare: the Repeated Elastic Net Technique for feature selection (RENT) and the User-Guided Bayesian Framework for feature selection (UBayFS). While RENT is purely data-driven and builds upon elastic net regularized models, UBayFS is a general framework for ensembles with the capabilities to include expert knowledge in the feature selection process via prior weights and side constraints. A case study modeling the overall survival of cancer patients compares these novel feature selectors and demonstrates their potential in clinical practice. Beyond the selection of single features, UBayFS also allows for selecting whole feature groups (feature blocks) that were acquired from multiple data sources, as those mentioned above. Importance quantification of such feature blocks plays a key role in tracing information about the target variable back to the acquisition modalities. Such information on feature block importance may lead to positive effects on the use of human, technical, and financial resources if systematically integrated into the planning of patient treatment by excluding the acquisition of non-informative features. Since a generalization of feature importance measures to block importance is not trivial, this thesis also investigates and compares approaches for feature block importance rankings. This thesis demonstrates that high-dimensional datasets from multiple data sources in the medical domain can be successfully tackled by the presented approaches for feature selection. Experimental evaluations demonstrate favorable properties of both predictive performance, stability, as well as interpretability of results, which carries a high potential for better data-driven decision support in clinical practice.Moderne datainnsamlingsteknikker i helsevesenet genererer store datamengder fra flere kilder, som for eksempel nye diagnose- og behandlingsmetoder. Noen konkrete eksempler er elektroniske helsejournalsystemer, genomikk og medisinske bilder. Slike pasientkohortdata er ofte ustrukturerte, høydimensjonale og heterogene og hvor klassiske statistiske metoder ikke er tilstrekkelige for optimal utnyttelse av dataene og god informasjonsbasert beslutningstaking. Derfor kan det være lovende å analysere slike datastrukturer ved bruk av moderne maskinlæringsteknikker for å øke forståelsen av pasientenes helseproblemer og for å gi klinikerne en bedre plattform for informasjonsbasert beslutningstaking. Sentrale krav til dette formålet inkluderer (a) tilstrekkelig nøyaktige prediksjoner og (b) modelltolkbarhet. Å oppnå begge aspektene samtidig er vanskelig, spesielt for datasett med få pasienter, noe som er vanlig for data i helsevesenet. I slike tilfeller må maskinlæringsmodeller håndtere matematisk underbestemte systemer og dette kan lett føre til at modellene overtilpasses treningsdataene. Variabelseleksjon er en viktig tilnærming for å håndtere dette ved å identifisere en undergruppe av informative variabler med hensyn til responsvariablen. Samtidig som variabelseleksjonsmetoder kan lede til økt prediktiv ytelse, fremmes modelltolkbarhet ved å identifisere et lavt antall relevante modellparametere. Dette kan gi bedre forståelse av de underliggende biologiske prosessene som fører til helseproblemer. Tolkbarhet krever at variabelseleksjonen er stabil, dvs. at små endringer i datasettet ikke fører til endringer i hvilke variabler som velges. Et konsept for å adressere ustabilitet er ensemblevariableseleksjon, dvs. prosessen med å gjenta variabelseleksjon flere ganger på en delmengde av prøvene i det originale datasett og aggregere resultater i en metamodell. Denne avhandlingen presenterer to tilnærminger for ensemblevariabelseleksjon, som er skreddersydd for høydimensjonale data i helsevesenet: "Repeated Elastic Net Technique for feature selection" (RENT) og "User-Guided Bayesian Framework for feature selection" (UBayFS). Mens RENT er datadrevet og bygger på elastic net-regulariserte modeller, er UBayFS et generelt rammeverk for ensembler som muliggjør inkludering av ekspertkunnskap i variabelseleksjonsprosessen gjennom forhåndsbestemte vekter og sidebegrensninger. En case-studie som modellerer overlevelsen av kreftpasienter sammenligner disse nye variabelseleksjonsmetodene og demonstrerer deres potensiale i klinisk praksis. Utover valg av enkelte variabler gjør UBayFS det også mulig å velge blokker eller grupper av variabler som representerer de ulike datakildene som ble nevnt over. Kvantifisering av viktigheten av variabelgrupper spiller en nøkkelrolle for forståelsen av hvorvidt datakildene er viktige for responsvariablen. Tilgang til slik informasjon kan føre til at bruken av menneskelige, tekniske og økonomiske ressurser kan forbedres dersom informasjonen integreres systematisk i planleggingen av pasientbehandlingen. Slik kan man redusere innsamling av ikke-informative variabler. Siden generaliseringen av viktighet av variabelgrupper ikke er triviell, undersøkes og sammenlignes også tilnærminger for rangering av viktigheten til disse variabelgruppene. Denne avhandlingen viser at høydimensjonale datasett fra flere datakilder fra det medisinske domenet effektivt kan håndteres ved bruk av variabelseleksjonmetodene som er presentert i avhandlingen. Eksperimentene viser at disse kan ha positiv en effekt på både prediktiv ytelse, stabilitet og tolkbarhet av resultatene. Bruken av disse variabelseleksjonsmetodene bærer et stort potensiale for bedre datadrevet beslutningsstøtte i klinisk praksis

Crowdsourcing for Engineering Design: Objective Evaluations and Subjective Preferences

Crowdsourcing enables designers to reach out to large numbers of people who may not have been previously considered when designing a new product, listen to their input by aggregating their preferences and evaluations over potential designs, aiming to improve ``good'' and catch ``bad'' design decisions during the early-stage design process. This approach puts human designers--be they industrial designers, engineers, marketers, or executives--at the forefront, with computational crowdsourcing systems on the backend to aggregate subjective preferences (e.g., which next-generation Brand A design best competes stylistically with next-generation Brand B designs?) or objective evaluations (e.g., which military vehicle design has the best situational awareness?). These crowdsourcing aggregation systems are built using probabilistic approaches that account for the irrationality of human behavior (i.e., violations of reflexivity, symmetry, and transitivity), approximated by modern machine learning algorithms and optimization techniques as necessitated by the scale of data (millions of data points, hundreds of thousands of dimensions). This dissertation presents research findings suggesting the unsuitability of current off-the-shelf crowdsourcing aggregation algorithms for real engineering design tasks due to the sparsity of expertise in the crowd, and methods that mitigate this limitation by incorporating appropriate information for expertise prediction. Next, we introduce and interpret a number of new probabilistic models for crowdsourced design to provide large-scale preference prediction and full design space generation, building on statistical and machine learning techniques such as sampling methods, variational inference, and deep representation learning. Finally, we show how these models and algorithms can advance crowdsourcing systems by abstracting away the underlying appropriate yet unwieldy mathematics, to easier-to-use visual interfaces practical for engineering design companies and governmental agencies engaged in complex engineering systems design.PhDDesign ScienceUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/133438/1/aburnap_1.pd

Contributions to reasoning on imprecise data

This thesis contains four contributions which advocate cautious statistical modelling and inference. They achieve it by taking sets of models into account, either directly or indirectly by looking at compatible data situations. Special care is taken to avoid assumptions which are technically convenient, but reduce the uncertainty involved in an unjustified manner. This thesis provides methods for cautious statistical modelling and inference, which are able to exhaust the potential of precise and vague data, motivated by different fields of application, ranging from political science to official statistics. At first, the inherently imprecise Nonparametric Predictive Inference model is involved in the cautious selection of splitting variables in the construction of imprecise classification trees, which are able to describe a structure and allow for a reasonably high predictive power. Dependent on the interpretation of vagueness, different strategies for vague data are then discussed in terms of finite random closed sets: On the one hand, the data to be analysed are regarded as set-valued answers of an item in a questionnaire, where each possible answer corresponding to a subset of the sample space is interpreted as a separate entity. By this the finite random set is reduced to an (ordinary) random variable on a transformed sample space. The context of application is the analysis of voting intentions, where it is shown that the presented approach is able to characterise the undecided in a more detailed way, which common approaches are not able to. Altough the presented analysis, regarded as a first step, is carried out on set-valued data, which are suitably self-constructed with respect to the scientific research question, it still clearly demonstrates that the full potential of this quite general framework is not exhausted. It is capable of dealing with more complex applications. On the other hand, the vague data are produced by set-valued single imputation (imprecise imputation) where the finite random sets are interpreted as being the result of some (unspecified) coarsening. The approach is presented within the context of statistical matching, which is used to gain joint knowledge on features that were not jointly collected in the initial data production. This is especially relevant in data production, e.g. in official statistics, as it allows to fuse the information of already accessible data sets into a new one, without the requirement of actual data collection in the field. Finally, in order to share data, they need to be suitably anonymised. For the specific class of anonymisation techniques of microaggregation, its ability to infer on generalised linear regression models is evaluated. Therefore, the microaggregated data are regarded as a set of compatible, unobserved underlying data situations. Two strategies to follow are proposed. At first, a maximax-like optimisation strategy is pursued, in which the underlying unobserved data are incorporated into the regression model as nuisance parameters, providing a concise yet over-optimistic estimation of the regression coefficients. Secondly, an approach in terms of partial identification, which is inherently more cautious than the previous one, is applied to estimate the set of all regression coefficients that are obtained by performing the estimation on each compatible data situation. Vague data are deemed favourable to precise data as they additionally encompass the uncertainty of the individual observation, and therefore they have a higher informational value. However, to the present day, there are few (credible) statistical models that are able to deal with vague or set-valued data. For this reason, the collection of such data is neglected in data production, disallowing such models to exhaust their full potential. This in turn prevents a throughout evaluation, negatively affecting the (further) development of such models. This situation is a variant of the chicken or egg dilemma. The ambition of this thesis is to break this cycle by providing actual methods for dealing with vague data in relevant situations in practice, to stimulate the required data production.Diese Schrift setzt sich in vier Beiträgen für eine vorsichtige statistische Modellierung und Inferenz ein. Dieses wird erreicht, indem man Mengen von Modellen betrachtet, entweder direkt oder indirekt über die Interpretation der Daten als Menge zugrunde liegender Datensituationen. Besonderer Wert wird dabei darauf gelegt, Annahmen zu vermeiden, die zwar technisch bequem sind, aber die zugrunde liegende Unsicherheit der Daten in ungerechtfertigter Weise reduzieren. In dieser Schrift werden verschiedene Methoden der vorsichtigen Modellierung und Inferenz vorgeschlagen, die das Potential von präzisen und unscharfen Daten ausschöpfen können, angeregt von unterschiedlichen Anwendungsbereichen, die von Politikwissenschaften bis zur amtlichen Statistik reichen. Zuerst wird das Modell der Nonparametrischen Prädiktiven Inferenz, welches per se unscharf ist, in der vorsichtigen Auswahl von Split-Variablen bei der Erstellung von Klassifikationsbäumen verwendet, die auf Methoden der Imprecise Probabilities fußen. Diese Bäume zeichnen sich dadurch aus, dass sie sowohl eine Struktur beschreiben, als auch eine annehmbar hohe Prädiktionsgüte aufweisen. In Abhängigkeit von der Interpretation der Unschärfe, werden dann verschiedene Strategien für den Umgang mit unscharfen Daten im Rahmen von finiten Random Sets erörtert. Einerseits werden die zu analysierenden Daten als mengenwertige Antwort auf eine Frage in einer Fragebogen aufgefasst. Hierbei wird jede mögliche (multiple) Antwort, die eine Teilmenge des Stichprobenraumes darstellt, als eigenständige Entität betrachtet. Somit werden die finiten Random Sets auf (gewöhnliche) Zufallsvariablen reduziert, die nun in einen transformierten Raum abbilden. Im Rahmen einer Analyse von Wahlabsichten hat der vorgeschlagene Ansatz gezeigt, dass die Unentschlossenen mit ihm genauer charakterisiert werden können, als es mit den gängigen Methoden möglich ist. Obwohl die vorgestellte Analyse, betrachtet als ein erster Schritt, auf mengenwertige Daten angewendet wird, die vor dem Hintergrund der wissenschaftlichen Forschungsfrage in geeigneter Weise selbst konstruiert worden sind, zeigt diese dennoch klar, dass die Möglichkeiten dieses generellen Ansatzes nicht ausgeschöpft sind, so dass er auch in komplexeren Situationen angewendet werden kann. Andererseits werden unscharfe Daten durch eine mengenwertige Einfachimputation (imprecise imputation) erzeugt. Hier werden die finiten Random Sets als Ergebnis einer (unspezifizierten) Vergröberung interpretiert. Der Ansatz wird im Rahmen des Statistischen Matchings vorgeschlagen, das verwendet wird, um gemeinsame Informationen über ursprünglich nicht zusammen erhobene Merkmale zur erhalten. Dieses ist insbesondere relevant bei der Datenproduktion, beispielsweise in der amtlichen Statistik, weil es erlaubt, die verschiedenartigen Informationen aus unterschiedlichen bereits vorhandenen Datensätzen zu einen neuen Datensatz zu verschmelzen, ohne dass dafür tatsächlich Daten neu erhoben werden müssen. Zudem müssen die Daten für den Datenaustausch in geeigneter Weise anonymisiert sein. Für die spezielle Klasse der Anonymisierungstechnik der Mikroaggregation wird ihre Eignung im Hinblick auf die Verwendbarkeit in generalisierten linearen Regressionsmodellen geprüft. Hierfür werden die mikroaggregierten Daten als eine Menge von möglichen, unbeobachtbaren zu Grunde liegenden Datensituationen aufgefasst. Es werden zwei Herangehensweisen präsentiert: Als Erstes wird eine maximax-ähnliche Optimisierungsstrategie verfolgt, dabei werden die zu Grunde liegenden unbeobachtbaren Daten als Nuisance Parameter in das Regressionsmodell aufgenommen, was eine enge, aber auch über-optimistische Schätzung der Regressionskoeffizienten liefert. Zweitens wird ein Ansatz im Sinne der partiellen Identifikation angewendet, der per se schon vorsichtiger ist (als der vorherige), indem er nur die Menge aller möglichen Regressionskoeffizienten schätzt, die erhalten werden können, wenn die Schätzung auf jeder zu Grunde liegenden Datensituation durchgeführt wird. Unscharfe Daten haben gegenüber präzisen Daten den Vorteil, dass sie zusätzlich die Unsicherheit der einzelnen Beobachtungseinheit umfassen. Damit besitzen sie einen höheren Informationsgehalt. Allerdings gibt es zur Zeit nur wenige glaubwürdige statistische Modelle, die mit unscharfen Daten umgehen können. Von daher wird die Erhebung solcher Daten bei der Datenproduktion vernachlässigt, was dazu führt, dass entsprechende statistische Modelle ihr volles Potential nicht ausschöpfen können. Dies verhindert eine vollumfängliche Bewertung, wodurch wiederum die (Weiter-)Entwicklung jener Modelle gehemmt wird. Dies ist eine Variante des Henne-Ei-Problems. Diese Schrift will durch Vorschlag konkreter Methoden hinsichtlich des Umgangs mit unscharfen Daten in relevanten Anwendungssituationen Lösungswege aus der beschriebenen Situation aufzeigen und damit die entsprechende Datenproduktion anregen