Improved ESP-index: a practical self-index for highly repetitive texts

While several self-indexes for highly repetitive texts exist, developing a practical self-index applicable to real world repetitive texts remains a challenge. ESP-index is a grammar-based self-index on the notion of edit-sensitive parsing (ESP), an efficient parsing algorithm that guarantees upper bounds of parsing discrepancies between different appearances of the same subtexts in a text. Although ESP-index performs efficient top-down searches of query texts, it has a serious issue on binary searches for finding appearances of variables for a query text, which resulted in slowing down the query searches. We present an improved ESP-index (ESP-index-I) by leveraging the idea behind succinct data structures for large alphabets. While ESP-index-I keeps the same types of efficiencies as ESP-index about the top-down searches, it avoid the binary searches using fast rank/select operations. We experimentally test ESP-index-I on the ability to search query texts and extract subtexts from real world repetitive texts on a large-scale, and we show that ESP-index-I performs better that other possible approaches.Comment: This is the full version of a proceeding accepted to the 11th International Symposium on Experimental Algorithms (SEA2014

Event-based hyperspace analogue to language for query expansion

Bag-of-words approaches to information retrieval (IR) are effective but assume independence between words. The Hyperspace Analogue to Language (HAL) is a cognitively motivated and validated semantic space model that captures statistical dependencies between words by considering their co-occurrences in a surrounding window of text. HAL has been successfully applied to query expansion in IR, but has several limitations, including high processing cost and use of distributional statistics that do not exploit syntax. In this paper, we pursue two methods for incorporating syntactic-semantic information from textual ‘events’ into HAL. We build the HAL space directly from events to investigate whether processing costs can be reduced through more careful definition of word co-occurrence, and improve the quality of the pseudo-relevance feedback by applying event information as a constraint during HAL construction. Both methods significantly improve performance results in comparison with original HAL, and interpolation of HAL and relevance model expansion outperforms either method alone

Natural language processing

Beginning with the basic issues of NLP, this chapter aims to chart the major research activities in this area since the last ARIST Chapter in 1996 (Haas, 1996), including: (i) natural language text processing systems - text summarization, information extraction, information retrieval, etc., including domain-specific applications; (ii) natural language interfaces; (iii) NLP in the context of www and digital libraries ; and (iv) evaluation of NLP systems

DeepSig: Deep learning improves signal peptide detection in proteins

Motivation: The identification of signal peptides in protein sequences is an important step toward protein localization and function characterization. Results: Here, we present DeepSig, an improved approach for signal peptide detection and cleavage-site prediction based on deep learning methods. Comparative benchmarks performed on an updated independent dataset of proteins show that DeepSig is the current best performing method, scoring better than other available state-of-the-art approaches on both signal peptide detection and precise cleavage-site identification. Availability and implementation: DeepSig is available as both standalone program and web server at https://deepsig.biocomp.unibo.it. All datasets used in this study can be obtained from the same website

Building a Generation Knowledge Source using Internet-Accessible Newswire

In this paper, we describe a method for automatic creation of a knowledge source for text generation using information extraction over the Internet. We present a prototype system called PROFILE which uses a client-server architecture to extract noun-phrase descriptions of entities such as people, places, and organizations. The system serves two purposes: as an information extraction tool, it allows users to search for textual descriptions of entities; as a utility to generate functional descriptions (FD), it is used in a functional-unification based generation system. We present an evaluation of the approach and its applications to natural language generation and summarization.Comment: 8 pages, uses eps

Intelligent indexing of crime scene photographs

The Scene of Crime Information System's automatic image-indexing prototype goes beyond extracting keywords and syntactic relations from captions. The semantic information it gathers gives investigators an intuitive, accurate way to search a database of cases for specific photographic evidence. Intelligent, automatic indexing and retrieval of crime scene photographs is one of the main functions of SOCIS, our research prototype developed within the Scene of Crime Information System project. The prototype, now in its final development and evaluation phase, applies advanced natural language processing techniques to text-based image indexing and retrieval to tackle crime investigation needs effectively and efficiently

A Logic-based Approach for Recognizing Textual Entailment Supported by Ontological Background Knowledge

We present the architecture and the evaluation of a new system for recognizing textual entailment (RTE). In RTE we want to identify automatically the type of a logical relation between two input texts. In particular, we are interested in proving the existence of an entailment between them. We conceive our system as a modular environment allowing for a high-coverage syntactic and semantic text analysis combined with logical inference. For the syntactic and semantic analysis we combine a deep semantic analysis with a shallow one supported by statistical models in order to increase the quality and the accuracy of results. For RTE we use logical inference of first-order employing model-theoretic techniques and automated reasoning tools. The inference is supported with problem-relevant background knowledge extracted automatically and on demand from external sources like, e.g., WordNet, YAGO, and OpenCyc, or other, more experimental sources with, e.g., manually defined presupposition resolutions, or with axiomatized general and common sense knowledge. The results show that fine-grained and consistent knowledge coming from diverse sources is a necessary condition determining the correctness and traceability of results.Comment: 25 pages, 10 figure