Refine
Year of publication
Document Type
- Conference Proceeding (41) (remove)
Has Fulltext
- yes (41)
Is part of the Bibliography
- no (41) (remove)
Keywords
Institute
- Informatik (41) (remove)
The Specialized Information Service Biodiversity Research (BIOfid) has been launched to mobilize valuable biological data from printed literature hidden in German libraries for over the past 250 years. In this project, we annotate German texts converted by OCR from historical scientific literature on the biodiversity of plants, birds, moths and butterflies. Our work enables the automatic extraction of biological information previously buried in the mass of papers and volumes. For this purpose, we generated training data for the tasks of Named Entity Recognition (NER) and Taxa Recognition (TR) in biological documents. We use this data to train a number of leading machine learning tools and create a gold standard for TR in biodiversity literature. More specifically, we perform a practical analysis of our newly generated BIOfid dataset through various downstream-task evaluations and establish a new state of the art for TR with 80.23% F-score. In this sense, our paper lays the foundations for future work in the field of information extraction in biology texts.
This paper proposes a new approach for the encoding of images by only a few important components. Classically, this is done by the Principal Component Analysis (PCA). Recently, the Independent Component Analysis (ICA) has found strong interest in the neural network community. Applied to images, we aim for the most important source patterns with the highest occurrence probability or highest information called principal independent components (PIC). For the example of a synthetic image composed by characters this idea selects the salient ones. For natural images it does not lead to an acceptable reproduction error since no a-priori probabilities can be computed. Combining the traditional principal component criteria of PCA with the independence property of ICA we obtain a better encoding. It turns out that this definition of PIC implements the classical demand of Shannon’s rate distortion theory.
The early prediction of mortality is one of the unresolved tasks in intensive care medicine. This contribution models medical symptoms as observations cased by transitions between hidden markov states. Learning the underlying state transition probabilities results in a prediction probability success of about 91%. The results are discussed and put in relation to the model used. Finally, the rationales for using the model are reflected: Are there states in the septic shock data?
In its first part, this contribution reviews shortly the application of neural network methods to medical problems and characterizes its advantages and problems in the context of the medical background. Successful application examples show that human diagnostic capabilities are significantly worse than the neural diagnostic systems. Then, paradigm of neural networks is shortly introduced and the main problems of medical data base and the basic approaches for training and testing a network by medical data are described. Additionally, the problem of interfacing the network and its result is given and the neuro-fuzzy approach is presented. Finally, as case study of neural rule based diagnosis septic shock diagnosis is described, on one hand by a growing neural network and on the other hand by a rule based system. Keywords: Statistical Classification, Adaptive Prediction, Neural Networks, Neurofuzzy, Medical Systems
Poster presentation: Calcium plays a pivotal role in relaying electrical signals of the cell to subcellular compartments, such as the nucleus. Since this one ion type is used by the cell for many processes a neuron needs to establish finely tuned calcium pathways in order to be able to differentiate multiple tasks, [1-3].
While it is known that neurons can actively change their shape upon neuronal activity, [4-7], we here present novel findings of activity-regulated nuclear morphology, [8,9]. With the help of an experimental and computational modeling approach, we show that hippocampal neurons can change the previously spherical shape of their nuclei to complex and infolded morphologies. This morphology regulation is demonstrated to be regulated by NMDA-receptor gated calcium, while synaptic and extra-synaptic NMDA-receptors elicit opposing effects on nuclear morphology, [8].
The structural alterations of the cell nucleus have significant effects on nuclear calcium dynamics. Compartmentalization of the nucleus, due to membrane infoldings, changes calcium frequencies, amplitudes and spatial distributions, [8,10]. Since these parameters have been shown to control downstream events towards gene transcription, [11,12], the results elucidate the cellular control of nuclear function with the help of morphology modulation. With respect to processes downstream of calcium, we show that histone H3 phosphorylation is closely linked to nuclear morphology. Investigating the nuclear morphologies of hippocampal neurons, two major classes were identified [9,10]. One class contains non-infolded nuclei that have the function of calcium signal integrators, while the other class contains highly infolded nuclei, which function as frequency detectors of nuclear calcium, [10].
Extending this interdisciplinary approach of investigating structure/function relationships in neurons, the effects of cellular morphology – as well as the morphology of the endoplasmic reticulum and other organelles – on neuronal calcium signals is currently being investigated. This endeavor makes use of highly detailed, three-dimensional models of neuronal calcium dynamics, including the three-dimensional morphology of the cell and its organelles.
We empirically investigate algorithms for solving Connected Components in the external memory model. In particular, we study whether the randomized O(Sort(E)) algorithm by Karger, Klein, and Tarjan can be implemented to compete with practically promising and simpler algorithms having only slightly worse theoretical cost, namely Borůvka’s algorithm and the algorithm by Sibeyn and collaborators. For all algorithms, we develop and test a number of tuning options. Our experiments are executed on a large set of different graph classes including random graphs, grids, geometric graphs, and hyperbolic graphs. Among our findings are: The Sibeyn algorithm is a very strong contender due to its simplicity and due to an added degree of freedom in its internal workings when used in the Connected Components setting. With the right tunings, the Karger-Klein-Tarjan algorithm can be implemented to be competitive in many cases. Higher graph density seems to benefit Karger-Klein-Tarjan relative to Sibeyn. Borůvka’s algorithm is not competitive with the two others.
From 12.12.2010 to 17.12.2010, the Dagstuhl Seminar 10501 "Advances and Applications of Automata on Words and Trees" was held in Schloss Dagstuhl - Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
Seminar: 10501 - Advances and Applications of Automata on Words and Trees. The aim of the seminar was to discuss and systematize the recent fast progress in automata theory and to identify important directions for future research. For this, the seminar brought together more than 40 researchers from automata theory and related fields of applications. We had 19 talks of 30 minutes and 5 one-hour lectures leaving ample room for discussions. In the following we describe the topics in more detail.
This paper describes the ongoing efforts of the authors to present ancient Greek and Roman numismatic data on the public internet, with an emphasis on efforts to integrate information from multiple sources using Linked Data and Semantic Web techniques. By way of very modern metaphor, it is useful to think of coins as intentionally created packages of 'named entities'. Each coin was struck by a particular authority, often at a known site, and coins often make reference to familiar concepts such as deities, historical events, or symbols that were widely recognized in the ancient world. The institutions represented among the authors have deployed search interfaces that allow users to take advantage of this aspect of numismatic databases. The American Numismatic Society's database provides faceted search to its collection of over 550,000 objects. The Portable Antiquities Scheme (PAS) in the UK presents individual finds (and hoards) recorded throughout the country. The Römisch-Germanische Kommission and the University of Frankfurt (DBIS) are developing a prototype metaportal (INTERFACE) that accesses national databases of coin finds held in in Frankfurt, Vienna and Utrecht. Each of these resources is beginning to explore Semantic Web/Linked data approaches so that the role of numismatic standards is immediately coming to the fore. DBIS and INTERFACE are developing a numismatic ontology. At the ANS and PAS, the public database already presents RDF serializations based on Dublin Core. Together, the authors have begun to explore standardization of conceptual names on the basis of the vocabulary presented at the site http://nomisma.org . Nomisma.org is a collaborative effort to provide stable digital representations of numismatic concepts and entities. It provides URIs for such basic concepts as 'coin', 'mint', 'axis'. All of these are defined within the scope of numismatics but are already being linked to other stable resources where available. This is particularly the case for mints. For example, the URI http://nomisma.org/id/corinth is intended to represent that ancient city in its role as a minter/issuer of coins. The URI is linked via the SKOS ontology to the Pleiades Gazetteer of ancient places. This allows Nomisma to be the basis for a common representation of the concept that an object is a coin minted at Corinth. The ANS has already deployed such relationships in its public database. The work of all these projects is very much in progress so that this paper hopes to generate discussion on how multiple large projects can move forward in their own work while encouraging sufficient commonality to support large scale research questions undertaken by diverse audiences.