TY - GEN A1 - Hempel, Sabrina A1 - Koseska, Aneta A1 - Nikoloski, Zoran A1 - Kurths, Jürgen T1 - Unraveling gene regulatory networks from time-resolved gene expression data BT - a measures comparison study N2 - Background: Inferring regulatory interactions between genes from transcriptomics time-resolved data, yielding reverse engineered gene regulatory networks, is of paramount importance to systems biology and bioinformatics studies. Accurate methods to address this problem can ultimately provide a deeper insight into the complexity, behavior, and functions of the underlying biological systems. However, the large number of interacting genes coupled with short and often noisy time-resolved read-outs of the system renders the reverse engineering a challenging task. Therefore, the development and assessment of methods which are computationally efficient, robust against noise, applicable to short time series data, and preferably capable of reconstructing the directionality of the regulatory interactions remains a pressing research problem with valuable applications. Results: Here we perform the largest systematic analysis of a set of similarity measures and scoring schemes within the scope of the relevance network approach which are commonly used for gene regulatory network reconstruction from time series data. In addition, we define and analyze several novel measures and schemes which are particularly suitable for short transcriptomics time series. We also compare the considered 21 measures and 6 scoring schemes according to their ability to correctly reconstruct such networks from short time series data by calculating summary statistics based on the corresponding specificity and sensitivity. Our results demonstrate that rank and symbol based measures have the highest performance in inferring regulatory interactions. In addition, the proposed scoring scheme by asymmetric weighting has shown to be valuable in reducing the number of false positive interactions. On the other hand, Granger causality as well as information-theoretic measures, frequently used in inference of regulatory networks, show low performance on the short time series analyzed in this study. Conclusions: Our study is intended to serve as a guide for choosing a particular combination of similarity measures and scoring schemes suitable for reconstruction of gene regulatory networks from short time series data. We show that further improvement of algorithms for reverse engineering can be obtained if one considers measures that are rooted in the study of symbolic dynamics or ranks, in contrast to the application of common similarity measures which do not consider the temporal character of the employed data. Moreover, we establish that the asymmetric weighting scoring scheme together with symbol based measures (for low noise level) and rank based measures (for high noise level) are the most suitable choices. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 371 KW - unferring cellular networks KW - mutual information KW - Escherichia-coli KW - cluster-analysis KW - series KW - algorithms KW - inference KW - models KW - recognition KW - variables Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400924 ER - TY - JOUR A1 - Arslan, Seçkin A1 - Bastiaanse, Roelien A1 - Felser, Claudia T1 - Looking at the evidence in visual world: eye-movements reveal how bilingual and monolingual Turkish speakers process grammatical evidentiality JF - Frontiers in psychology N2 - This study presents pioneering data on how adult early bilinguals (heritage speakers) and late bilingual speakers of Turkish and German process grammatical evidentiality in a visual world setting in comparison to monolingual speakers of Turkish. Turkish marks evidentiality, the linguistic reference to information source, through inflectional affixes signaling either direct (-DI) or indirect (-mls) evidentiality. We conducted an eyetracking-during-listening experiment where participants were given access to visual 'evidence' supporting the use of either a direct or indirect evidential form. The behavioral results indicate that the monolingual Turkish speakers comprehended direct and indirect evidential scenarios equally well. In contrast, both late and early bilinguals were less accurate and slower to respond to direct than to indirect evidentials. The behavioral results were also reflected in the proportions of looks data. That is, both late and early bilinguals fixated less frequently on the target picture in the direct than in the indirect evidential condition while the monolinguals showed no difference between these conditions. Taken together, our results indicate reduced sensitivity to the semantic and pragmatic function of direct evidential forms in both late and early bilingual speakers, suggesting a simplification of the Turkish evidentiality system in Turkish heritage grammars. We discuss our findings with regard to theories of incomplete acquisition and first language attrition. KW - evidentiality KW - information source KW - inference KW - witnessing KW - visual world paradigm KW - eye-movements KW - Turkish-German bilingualism Y1 - 2015 U6 - https://doi.org/10.3389/fpsyg.2015.01387 SN - 1664-1078 VL - 6 PB - Frontiers Research Foundation CY - Lausanne ER - TY - GEN A1 - Arslan, Seçkin A1 - Bastiaanse, Roelien A1 - Felser, Claudia T1 - Looking at the evidence in visual world BT - eye-movements reveal how bilingual and monolingual Turkish speakers process grammatical evidentiality T2 - Postprints der Universität Potsdam : Humanwissenschaftliche Reihe N2 - This study presents pioneering data on how adult early bilinguals (heritage speakers) and late bilingual speakers of Turkish and German process grammatical evidentiality in a visual world setting in comparison to monolingual speakers of Turkish. Turkish marks evidentiality, the linguistic reference to information source, through inflectional affixes signaling either direct (-DI) or indirect (-mls) evidentiality. We conducted an eyetracking-during-listening experiment where participants were given access to visual 'evidence' supporting the use of either a direct or indirect evidential form. The behavioral results indicate that the monolingual Turkish speakers comprehended direct and indirect evidential scenarios equally well. In contrast, both late and early bilinguals were less accurate and slower to respond to direct than to indirect evidentials. The behavioral results were also reflected in the proportions of looks data. That is, both late and early bilinguals fixated less frequently on the target picture in the direct than in the indirect evidential condition while the monolinguals showed no difference between these conditions. Taken together, our results indicate reduced sensitivity to the semantic and pragmatic function of direct evidential forms in both late and early bilingual speakers, suggesting a simplification of the Turkish evidentiality system in Turkish heritage grammars. We discuss our findings with regard to theories of incomplete acquisition and first language attrition. T3 - Zweitveröffentlichungen der Universität Potsdam : Humanwissenschaftliche Reihe - 408 KW - evidentiality KW - information source KW - inference KW - witnessing KW - visual world paradigm KW - eye-movements KW - Turkish-German bilingualism Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-406307 IS - 408 ER - TY - THES A1 - Messi, Hugues Urbain Patrick T1 - Les sources du savoir - l’expression de l’inférence en Français T1 - The expression of inference in French T1 - Der Ausdruck der Inferenz auf Französisch BT - analyse sémantico-pragmatique et rhétorico-syntaxique Sur la base d’un corpus écrit de la langue écrite BT - a semantic-pragmatic and rhetoric-syntaxic Analyser based on a corpus of french written langage BT - eine semantisch-pragmatisch und rhetorisch-syntaktische Analyse basierend auf einem Korpus der geschriebenen Sprache N2 - 1. Unter Mediativität verstehen wir in dieser Dissertation die sprachliche Markierung der Informationsquelle. Ein Sprecher, der einen Sachverhalt vermittelt, hat die Möglichkeit durch sprachliche Mittel ausdrücklich zu markieren, wie er die übermittelte Information bekommen hat. Um diese Informationsquelle sprachlich zu deuten, werden im Französischen unter anderem einige Verben als mediative Marker (MM) verwendet. 2. Die untersuchten Elemente croire, imaginer, paraitre, penser, savoir, sembler, supposer, trouver sind „mediatiave Verben“. Jedes der untersuchten Verben weist besondere semantische und pragmatische Eigenschaften auf, die immer mit dem Ausdruck der Wissensquelle verbunden sind. Es handelt sich also um kognitive Verben (KV), die eine sprachliche Markierung der Informationsquelle vornehmen. Nach ihrem Verhalten in solchen Kontexten erfüllen sie die Funktion der „mediatiaven Markierung“. 3. Die epistemische Modalität ist der Meditivität untergeordnet. Die Erscheinungsform der Modalität (Modalitätstyp) bestimmt die Stärke der epistemischen Modalität. Keines der analysierten Verben drückt lediglich eine epistemische Leseart aus. Die Dichotomie zwischen der mediativen und epistemischen Modalität besteht darin, dass die erste die Wissensquelle ausdrückt und die zweite ausschließlich die Einstellung des Sprechers gegenüber dem Wahrheitsgrad der Äußerung widerspiegelt. 4. Für alle Konstruktionen der Form [V/øP] oder [V, P] ist P die Matrix des Satzes Unsere Ergebnisse zeigen, dass – obwohl diese Konstituenten verschiedene Stellen besetzen können – sie dennoch ihre Funktionen als Matrix behalten, indem sie die Propositionen, auf die sie sich beziehen, unter ihrer Rektion behalten. 5. Die Konstruktion [V/øP] und [V, P] stehen in freien Variation Da sich der Wechsel in einem vergleichbaren Kontext vollzieht, und da es in gleicher Umgebung eine freie Substitution gibt, handelt es sich bei den beiden Vorkommen [V/øP] und [V, P] um syntaktische Varianten. 6. Der Konditional-Gebrauch dient hauptsächlich dazu, die Inferenztypen zu unterscheiden und gleichzeitig die zugrundeliegende Polyphonie zu verdeutlichen. Der Gebrauch des Konditionals drückt aus, dass es sich nicht um eine zuverlässig zutreffende Äußerung handelt. Der Ausdruck von Zweifeln kann im Französischen unter Verwendung spezifischer grammatischer Mittel erfolgen. Zu diesen gehört der Konditional zum Ausdruck der Mitigation (des Zweifels, der Reserviertheit usw.) und der Polyphonie. N2 - L’extériorisation de toute communication est assujettie à un mode d’accès du locuteur aux informations véhiculées. Les constatations faites de nos données prouvent que tous les huit verbes étudiés traduisent des mécanismes d’acquisition des connaissances que nous avons appelés en emprunt à (Vogeleer, 1995 :92) « l’accès cognitif au savoir ». C’est cette valeur intrinsèque qui vaut à ces termes la dénomination de verbes médiatifs. En d’autres mots, ce sont des éléments qui explicitent des processus d’accès du locuteur au savoir. Une source du savoir qui peut être directe (la vue, le touché, l’ouïe, l’odorat…) ou indirecte (ouï-dire) et surtout inférée. Nous entendons par inférence un processus d’analyse et de mise en relation d’éléments (prémisses), lesquelles permettent de tirer une conclusion par déduction, induction ou par abduction. Et selon que lesdites prémisses tendent à être plus ou moins fiables, ces processus inférentiels impliqueront des valeurs épistémiques à des degrés divers. Sur le plan rhétorico-syntaxique, nos analyses ont montré tous les verbes cognitifs (VC) de cette étude exigent l’occurrence d’autres constituants (actants) phrastiques qu’ils régissent. C’est grâce à cette valence verbale qu’ils gardent un pouvoir rectionnel dans les constructions asyndétiques. Ce sont donc les matrices des éléments sur lesquels ils se rapportent. Quant au cinétisme de ces verbes, il possède une fonction rhétorique et syntaxique. En effet, cet agencement particulier et souvent perturbant permet de traduire l’expression d’une figure de syntaxe à effet rhétorique : l’hyperbate. Une construction atypique qui, à travers les agencements anticonformistes, donne un sens de regressivité à l’énoncé et confère une saillance à des termes mis ce fait en exergue. KW - médiativité KW - marqueur médiatif KW - verbe cognitif KW - valence verbale KW - hyperbate  KW - inférence  KW - déduction  KW - induction  KW - abduction KW - matrice  KW - proposition principale KW - abduction KW - deduction KW - hyperbate KW - induction KW - inference KW - matrix KW - mediative marker KW - mediativity KW - main proposal KW - verbal valence KW - Abduktion KW - Deduktion KW - Induktion KW - Hyperbaton KW - Inferenz KW - Matrix-Satz KW - mediativer Marker KW - Mediativität KW - Hauptsatz KW - Verb-Valenz Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-469612 ER - TY - JOUR A1 - Vasishth, Shravan A1 - Gelman, Andrew T1 - How to embrace variation and accept uncertainty in linguistic and psycholinguistic data analysis JF - Linguistics : an interdisciplinary journal of the language sciences N2 - The use of statistical inference in linguistics and related areas like psychology typically involves a binary decision: either reject or accept some null hypothesis using statistical significance testing. When statistical power is low, this frequentist data-analytic approach breaks down: null results are uninformative, and effect size estimates associated with significant results are overestimated. Using an example from psycholinguistics, several alternative approaches are demonstrated for reporting inconsistencies between the data and a theoretical prediction. The key here is to focus on committing to a falsifiable prediction, on quantifying uncertainty statistically, and learning to accept the fact that - in almost all practical data analysis situations - we can only draw uncertain conclusions from data, regardless of whether we manage to obtain statistical significance or not. A focus on uncertainty quantification is likely to lead to fewer excessively bold claims that, on closer investigation, may turn out to be not supported by the data. KW - experimental linguistics KW - statistical data analysis KW - statistical KW - inference KW - uncertainty quantification Y1 - 2021 U6 - https://doi.org/10.1515/ling-2019-0051 SN - 0024-3949 SN - 1613-396X VL - 59 IS - 5 SP - 1311 EP - 1342 PB - De Gruyter Mouton CY - Berlin ER - TY - GEN A1 - Schmidt, Lennart A1 - Heße, Falk A1 - Attinger, Sabine A1 - Kumar, Rohini T1 - Challenges in applying machine learning models for hydrological inference: a case study for flooding events across Germany T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Machine learning (ML) algorithms are being increasingly used in Earth and Environmental modeling studies owing to the ever-increasing availability of diverse data sets and computational resources as well as advancement in ML algorithms. Despite advances in their predictive accuracy, the usefulness of ML algorithms for inference remains elusive. In this study, we employ two popular ML algorithms, artificial neural networks and random forest, to analyze a large data set of flood events across Germany with the goals to analyze their predictive accuracy and their usability to provide insights to hydrologic system functioning. The results of the ML algorithms are contrasted against a parametric approach based on multiple linear regression. For analysis, we employ a model-agnostic framework named Permuted Feature Importance to derive the influence of models' predictors. This allows us to compare the results of different algorithms for the first time in the context of hydrology. Our main findings are that (1) the ML models achieve higher prediction accuracy than linear regression, (2) the results reflect basic hydrological principles, but (3) further inference is hindered by the heterogeneity of results across algorithms. Thus, we conclude that the problem of equifinality as known from classical hydrological modeling also exists for ML and severely hampers its potential for inference. To account for the observed problems, we propose that when employing ML for inference, this should be made by using multiple algorithms and multiple methods, of which the latter should be embedded in a cross-validation routine. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1193 KW - machine learning KW - inference KW - floods Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523843 SN - 1866-8372 IS - 5 ER - TY - JOUR A1 - Schmidt, Lennart A1 - Heße, Falk A1 - Attinger, Sabine A1 - Kumar, Rohini T1 - Challenges in applying machine learning models for hydrological inference: a case study for flooding events across Germany JF - Water Resources Research N2 - Machine learning (ML) algorithms are being increasingly used in Earth and Environmental modeling studies owing to the ever-increasing availability of diverse data sets and computational resources as well as advancement in ML algorithms. Despite advances in their predictive accuracy, the usefulness of ML algorithms for inference remains elusive. In this study, we employ two popular ML algorithms, artificial neural networks and random forest, to analyze a large data set of flood events across Germany with the goals to analyze their predictive accuracy and their usability to provide insights to hydrologic system functioning. The results of the ML algorithms are contrasted against a parametric approach based on multiple linear regression. For analysis, we employ a model-agnostic framework named Permuted Feature Importance to derive the influence of models' predictors. This allows us to compare the results of different algorithms for the first time in the context of hydrology. Our main findings are that (1) the ML models achieve higher prediction accuracy than linear regression, (2) the results reflect basic hydrological principles, but (3) further inference is hindered by the heterogeneity of results across algorithms. Thus, we conclude that the problem of equifinality as known from classical hydrological modeling also exists for ML and severely hampers its potential for inference. To account for the observed problems, we propose that when employing ML for inference, this should be made by using multiple algorithms and multiple methods, of which the latter should be embedded in a cross-validation routine. KW - machine learning KW - inference KW - floods Y1 - 2019 VL - 56 IS - 5 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - JOUR A1 - Schmidt, Lennart A1 - Hesse, Falk A1 - Attinger, Sabine A1 - Kumar, Rohini T1 - Challenges in applying machine learning models for hydrological inference BT - a case study for flooding events across Germany JF - Water resources research N2 - Machine learning (ML) algorithms are being increasingly used in Earth and Environmental modeling studies owing to the ever-increasing availability of diverse data sets and computational resources as well as advancement in ML algorithms. Despite advances in their predictive accuracy, the usefulness of ML algorithms for inference remains elusive. In this study, we employ two popular ML algorithms, artificial neural networks and random forest, to analyze a large data set of flood events across Germany with the goals to analyze their predictive accuracy and their usability to provide insights to hydrologic system functioning. The results of the ML algorithms are contrasted against a parametric approach based on multiple linear regression. For analysis, we employ a model-agnostic framework named Permuted Feature Importance to derive the influence of models' predictors. This allows us to compare the results of different algorithms for the first time in the context of hydrology. Our main findings are that (1) the ML models achieve higher prediction accuracy than linear regression, (2) the results reflect basic hydrological principles, but (3) further inference is hindered by the heterogeneity of results across algorithms. Thus, we conclude that the problem of equifinality as known from classical hydrological modeling also exists for ML and severely hampers its potential for inference. To account for the observed problems, we propose that when employing ML for inference, this should be made by using multiple algorithms and multiple methods, of which the latter should be embedded in a cross-validation routine. KW - machine learning KW - inference KW - floods Y1 - 2020 U6 - https://doi.org/10.1029/2019WR025924 SN - 0043-1397 SN - 1944-7973 VL - 56 IS - 5 PB - American Geophysical Union CY - Washington ER -