Ontologies and Information Extraction

This report argues that, even in the simplest cases, IE is an ontology-driven process. It is not a mere text filtering method based on simple pattern matching and keywords, because the extracted pieces of texts are interpreted with respect to a predefined partial domain model. This report shows that depending on the nature and the depth of the interpretation to be done for extracting the information, more or less knowledge must be involved. This report is mainly illustrated in biology, a domain in which there are critical needs for content-based exploration of the scientific literature and which becomes a major application domain for IE

Clustering by compression

We present a new method for clustering based on compression. The method doesn't use subject-specific features or background knowledge, and works as follows: First, we determine a universal similarity distance, the normalized compression distance or NCD, computed from the lengths of compressed data files (singly and in pairwise concatenation). Second, we apply a hierarchical clustering method. The NCD is universal in that it is not restricted to a specific application area, and works across application area boundaries. A theoretical precursor, the normalized information distance, co-developed by one of the authors, is provably optimal but uses the non-computable notion of Kolmogorov complexity. We propose precise notions of similarity metric, normal compressor, and show that the NCD based on a normal compressor is a similarity metric that approximates universality. To extract a hierarchy of clusters from the distance matrix, we determine a dendrogram (binary tree) by a new quartet method and a fast heuristic to implement it. The method is implemented and available as public software, and is robust under choice of different compressors. To substantiate our claims of universality and robustness, we report evidence of successful application in areas as diverse as genomics, virology, languages, literature, music, handwritten digits, astronomy, and combinations of objects from completely different domains, using statistical, dictionary, and block sorting compressors. In genomics we presented new evidence for major questions in Mammalian evolution, based on whole-mitochondrial genomic analysis: the Eutherian orders and the Marsupionta hypothesis against the Theria hypothesis.Comment: LaTeX, 27 pages, 20 figure

Text Line Segmentation of Historical Documents: a Survey

There is a huge amount of historical documents in libraries and in various National Archives that have not been exploited electronically. Although automatic reading of complete pages remains, in most cases, a long-term objective, tasks such as word spotting, text/image alignment, authentication and extraction of specific fields are in use today. For all these tasks, a major step is document segmentation into text lines. Because of the low quality and the complexity of these documents (background noise, artifacts due to aging, interfering lines),automatic text line segmentation remains an open research field. The objective of this paper is to present a survey of existing methods, developed during the last decade, and dedicated to documents of historical interest.Comment: 25 pages, submitted version, To appear in International Journal on Document Analysis and Recognition, On line version available at http://www.springerlink.com/content/k2813176280456k3

Web and Semantic Web Query Languages

A number of techniques have been developed to facilitate powerful data retrieval on the Web and Semantic Web. Three categories of Web query languages can be distinguished, according to the format of the data they can retrieve: XML, RDF and Topic Maps. This article introduces the spectrum of languages falling into these categories and summarises their salient aspects. The languages are introduced using common sample data and query types. Key aspects of the query languages considered are stressed in a conclusion

Deepr: A Convolutional Net for Medical Records

Feature engineering remains a major bottleneck when creating predictive systems from electronic medical records. At present, an important missing element is detecting predictive regular clinical motifs from irregular episodic records. We present Deepr (short for Deep record), a new end-to-end deep learning system that learns to extract features from medical records and predicts future risk automatically. Deepr transforms a record into a sequence of discrete elements separated by coded time gaps and hospital transfers. On top of the sequence is a convolutional neural net that detects and combines predictive local clinical motifs to stratify the risk. Deepr permits transparent inspection and visualization of its inner working. We validate Deepr on hospital data to predict unplanned readmission after discharge. Deepr achieves superior accuracy compared to traditional techniques, detects meaningful clinical motifs, and uncovers the underlying structure of the disease and intervention space