Refine
Year of publication
Document Type
- Preprint (26)
- Article (2)
- Part of a Book (2)
- Conference Proceeding (2)
- Book (1)
Has Fulltext
- yes (33)
Is part of the Bibliography
- no (33)
Keywords
- Deutsch (5)
- Satzanalyse (4)
- speech tagging (2)
- Acquisition (1)
- Arabisch (1)
- Automatische Sprachanalyse (1)
- Englisch (1)
- Fehlererkennung (1)
- Fehlertoleranz (1)
- German (1)
Pseudomonas aeruginosa is a human pathogen that causes health-care associated blood stream infections (BSI). Although P. aeruginosa BSI are associated with high mortality rates, the clinical relevance of pathogen-derived prognostic biomarker to identify patients at risk for unfavorable outcome remains largely unexplored. We found novel pathogen-derived prognostic biomarker candidates by applying a multi-omics approach on a multicenter sepsis patient cohort. Multi-level Cox regression was used to investigate the relation between patient characteristics and pathogen features (2298 accessory genes, 1078 core protein levels, 107 parsimony-informative variations in reported virulence factors) with 30-day mortality. Our analysis revealed that presence of the helP gene encoding a putative DEAD-box helicase was independently associated with a fatal outcome (hazard ratio 2.01, p = 0.05). helP is located within a region related to the pathogenicity island PAPI-1 in close proximity to a pil gene cluster, which has been associated with horizontal gene transfer. Besides helP, elevated protein levels of the bacterial flagellum protein FliL (hazard ratio 3.44, p < 0.001) and of a bacterioferritin-like protein (hazard ratio 1.74, p = 0.003) increased the risk of death, while high protein levels of a putative aminotransferase were associated with an improved outcome (hazard ratio 0.12, p < 0.001). The prognostic potential of biomarker candidates and clinical factors was confirmed with different machine learning approaches using training and hold-out datasets. The helP genotype appeared the most attractive biomarker for clinical risk stratification due to its relevant predictive power and ease of detection.
Traditionally, parsers are evaluated against gold standard test data. This can cause problems if there is a mismatch between the data structures and representations used by the parser and the gold standard. A particular case in point is German, for which two treebanks (TiGer and TüBa-D/Z) are available with highly different annotation schemes for the acquisition of (e.g.) PCFG parsers. The differences between the TiGer and TüBa-D/Z annotation schemes make fair and unbiased parser evaluation difficult [7, 9, 12]. The resource (TEPACOC) presented in this paper takes a different approach to parser evaluation: instead of providing evaluation data in a single annotation scheme, TEPACOC uses comparable sentences and their annotations for 5 selected key grammatical phenomena (with 20 sentences each per phenomena) from both TiGer and TüBa-D/Z resources. This provides a 2 times 100 sentence comparable testsuite which allows us to evaluate TiGer-trained parsers against the TiGer part of TEPACOC, and TüBa-D/Z-trained parsers against the TüBa-D/Z part of TEPACOC for key phenomena, instead of comparing them against a single (and potentially biased) gold standard. To overcome the problem of inconsistency in human evaluation and to bridge the gap between the two different annotation schemes, we provide an extensive error classification, which enables us to compare parser output across the two different treebanks. In the remaining part of the paper we present the testsuite and describe the grammatical phenomena covered in the data. We discuss the different annotation strategies used in the two treebanks to encode these phenomena and present our error classification of potential parser errors.
Parsing coordinations
(2009)
The present paper is concerned with statistical parsing of constituent structures in German. The paper presents four experiments that aim at improving parsing performance of coordinate structure: 1) reranking the n-best parses of a PCFG parser, 2) enriching the input to a PCFG parser by gold scopes for any conjunct, 3) reranking the parser output for all possible scopes for conjuncts that are permissible with regard to clause structure. Experiment 4 reranks a combination of parses from experiments 1 and 3. The experiments presented show that n- best parsing combined with reranking improves results by a large margin. Providing the parser with different scope possibilities and reranking the resulting parses results in an increase in F-score from 69.76 for the baseline to 74.69. While the F-score is similar to the one of the first experiment (n-best parsing and reranking), the first experiment results in higher recall (75.48% vs. 73.69%) and the third one in higher precision (75.43% vs. 73.26%). Combining the two methods results in the best result with an F-score of 76.69.
The ACL 2008 Workshop on Parsing German features a shared task on parsing German. The goal of the shared task was to find reasons for the radically different behavior of parsers on the different treebanks and between constituent and dependency representations. In this paper, we describe the task and the data sets. In addition, we provide an overview of the test results and a first analysis.
The problem of vocalization, or diacritization, is essential to many tasks in Arabic NLP. Arabic is generally written without the short vowels, which leads to one written form having several pronunciations with each pronunciation carrying its own meaning(s). In the experiments reported here, we define vocalization as a classification problem in which we decide for each character in the unvocalized word whether it is followed by a short vowel. We investigate the importance of different types of context. Our results show that the combination of using memory-based learning with only a word internal context leads to a word error rate of 6.64%. If a lexical context is added, the results deteriorate slowly.
How to compare treebanks
(2008)
Recent years have seen an increasing interest in developing standards for linguistic annotation, with a focus on the interoperability of the resources. This effort, however, requires a profound knowledge of the advantages and disadvantages of linguistic annotation schemes in order to avoid importing the flaws and weaknesses of existing encoding schemes into the new standards. This paper addresses the question how to compare syntactically annotated corpora and gain insights into the usefulness of specific design decisions. We present an exhaustive evaluation of two German treebanks with crucially different encoding schemes. We evaluate three different parsers trained on the two treebanks and compare results using EVALB, the Leaf-Ancestor metric, and a dependency-based evaluation. Furthermore, we present TePaCoC, a new testsuite for the evaluation of parsers on complex German grammatical constructions. The testsuite provides a well thought-out error classification, which enables us to compare parser output for parsers trained on treebanks with different encoding schemes and provides interesting insights into the impact of treebank annotation schemes on specific constructions like PP attachment or non-constituent coordination.
Part-of-Speech tagging is generally performed by Markov models, based on bigram or trigram models. While Markov models have a strong concentration on the left context of a word, many languages require the inclusion of right context for correct disambiguation. We show for German that the best results are reached by a combination of left and right context. If only left context is available, then changing the direction of analysis and going from right to left improves the results. In a version of MBT (Daelemans et al., 1996) with default parameter settings, the inclusion of the right context improved POS tagging accuracy from 94.00% to 96.08%, thus corroborating our hypothesis. The version with optimized parameters reaches 96.73%.
The Conference on Computational Natural Language Learning features a shared task, in which participants train and test their learning systems on the same data sets. In 2007, as in 2006, the shared task has been devoted to dependency parsing, this year with both a multilingual track and a domain adaptation track. In this paper, we define the tasks of the different tracks and describe how the data sets were created from existing treebanks for ten languages. In addition, we characterize the different approaches of the participating systems, report the test results, and provide a first analysis of these results.
Recent approaches to Word Sense Disambiguation (WSD) generally fall into two classes: (1) information-intensive approaches and (2) information-poor approaches. Our hypothesis is that for memory-based learning (MBL), a reduced amount of data is more beneficial than the full range of features used in the past. Our experiments show that MBL combined with a restricted set of features and a feature selection method that minimizes the feature set leads to competitive results, outperforming all systems that participated in the SENSEVAL-3 competition on the Romanian data. Thus, with this specific method, a tightly controlled feature set improves the accuracy of the classifier, reaching 74.0% in the fine-grained and 78.7% in the coarse-grained evaluation.