Dictionary-based methods for information extraction

In this paper, we present a general method for information extraction that exploits the features of data compression techniques. We first define and focus our attention on the so-called dictionary of a sequence. Dictionaries are intrinsically interesting and a study of their features can be of great usefulness to investigate the properties of the sequences they have been extracted from e.g. DNA strings. We then describe a procedure of string comparison between dictionary-created sequences (or artificial texts) that gives very good results in several contexts. We finally present some results on self-consistent classification problems

Developing a Hybrid Dictionary-based Bio-entity Recognition Technique

Background: Bio-entity extraction is a pivotal component for information extraction from biomedical literature. The dictionary-based bio-entity extraction is the first generation of Named Entity Recognition (NER) techniques. Methods: This paper presents a hybrid dictionary-based bio-entity extraction technique. The approach expands the bio-entity dictionary by combining different data sources and improves the recall rate through the shortest path edit distance algorithm. In addition, the proposed technique adopts text mining techniques in the merging stage of similar entities such as Part of Speech (POS) expansion, stemming, and the exploitation of the contextual cues to further improve the performance. Results: The experimental results show that the proposed technique achieves the best or at least equivalent performance among compared techniques, GENIA, MESH, UMLS, and combinations of these three resources in F-measure. Conclusions: The results imply that the performance of dictionary-based extraction techniques is largely influenced by information resources used to build the dictionary. In addition, the edit distance algorithm shows steady performance with three different dictionaries in precision whereas the context-only technique achieves a high-end performance with three difference dictionaries in recall.X1133Ysciescopu

Artificial Sequences and Complexity Measures

In this paper we exploit concepts of information theory to address the fundamental problem of identifying and defining the most suitable tools to extract, in a automatic and agnostic way, information from a generic string of characters. We introduce in particular a class of methods which use in a crucial way data compression techniques in order to define a measure of remoteness and distance between pairs of sequences of characters (e.g. texts) based on their relative information content. We also discuss in detail how specific features of data compression techniques could be used to introduce the notion of dictionary of a given sequence and of Artificial Text and we show how these new tools can be used for information extraction purposes. We point out the versatility and generality of our method that applies to any kind of corpora of character strings independently of the type of coding behind them. We consider as a case study linguistic motivated problems and we present results for automatic language recognition, authorship attribution and self consistent-classification.Comment: Revised version, with major changes, of previous "Data Compression approach to Information Extraction and Classification" by A. Baronchelli and V. Loreto. 15 pages; 5 figure

Effectiveness of Word Extraction and Information Retrieval on Cancer from Thai Website

This article proposes word extraction and cancer information retrieval from the Thai website. For word extraction, TH-OnSeg is proposed as a words segmentation based on LexTo algorithm with cancer dictionary and cancer oncology. TH-Onseg is used to extract cancer related words to be used as document indexing for cancer websites. The experiments were conducted by comparing the word extraction with LexTo words segment algorithm based on Thai electronic dictionary. The results show that the TH-OnSeg technique has higher efficiency; it can extract more words than LexTo for unknown words, known words, and ambiguous words.  In addition, we propose a semantic web-based technique combined with n-grams for cancer information retrieval. The experiments were conducted by comparing the proposed technique with information retrieval methods in database.  The results show that the use of semantic web techniques combined with N-gram for cancer information retrieval yields the highest number of cancer websites. The highest recall is not less than 0.9 in all experimental cases of both misspellings and misspellings

An Approach for Chinese-Japanese Named Entity Equivalents Extraction Using Inductive Learning and Hanzi-Kanji Mapping Table

Named Entity Translation Equivalents extraction plays a critical role in machine translation (MT) and cross language information retrieval (CLIR). Traditional methods are often based on large-scale parallel or comparable corpora. However, the applicability of these studies is constrained, mainly because of the scarcity of parallel corpora of the required scale, especially for language pairs of Chinese and Japanese. In this paper, we propose a method considering the characteristics of Chinese and Japanese to automatically extract the Chinese-Japanese Named Entity (NE) translation equivalents based on inductive learning (IL) from monolingual corpora. The method adopts the Chinese Hanzi and Japanese Kanji Mapping Table (HKMT) to calculate the similarity of the NE instances between Japanese and Chinese. Then, we use IL to obtain partial translation rules for NEs by extracting the different parts from high similarity NE instances in Chinese and Japanese. In the end, the feedback processing updates the Chinese and Japanese NE entity similarity and rule sets. Experimental results show that our simple, efficient method, which overcomes the insufficiency of the traditional methods, which are severely dependent on bilingual resource. Compared with other methods, our method combines the language features of Chinese and Japanese with IL for automatically extracting NE pairs. Our use of a weak correlation bilingual text sets and minimal additional knowledge to extract NE pairs effectively reduces the cost of building the corpus and the need for additional knowledge. Our method may help to build a large-scale Chinese-Japanese NE translation dictionary using mono-lingual corpora

Information Extraction from Text for Improving Research on Small Molecules and Histone Modifications

The cumulative number of publications, in particular in the life sciences, requires efficient methods for the automated extraction of information and semantic information retrieval. The recognition and identification of information-carrying units in text – concept denominations and named entities – relevant to a certain domain is a fundamental step. The focus of this thesis lies on the recognition of chemical entities and the new biological named entity type histone modifications, which are both important in the field of drug discovery. As the emergence of new research fields as well as the discovery and generation of novel entities goes along with the coinage of new terms, the perpetual adaptation of respective named entity recognition approaches to new domains is an important step for information extraction. Two methodologies have been investigated in this concern: the state-of-the-art machine learning method, Conditional Random Fields (CRF), and an approximate string search method based on dictionaries. Recognition methods that rely on dictionaries are strongly dependent on the availability of entity terminology collections as well as on its quality. In the case of chemical entities the terminology is distributed over more than 7 publicly available data sources. The join of entries and accompanied terminology from selected resources enables the generation of a new dictionary comprising chemical named entities. Combined with the automatic processing of respective terminology – the dictionary curation – the recognition performance reached an F1 measure of 0.54. That is an improvement by 29 % in comparison to the raw dictionary. The highest recall was achieved for the class of TRIVIAL-names with 0.79. The recognition and identification of chemical named entities provides a prerequisite for the extraction of related pharmacological relevant information from literature data. Therefore, lexico-syntactic patterns were defined that support the automated extraction of hypernymic phrases comprising pharmacological function terminology related to chemical compounds. It was shown that 29-50 % of the automatically extracted terms can be proposed for novel functional annotation of chemical entities provided by the reference database DrugBank. Furthermore, they are a basis for building up concept hierarchies and ontologies or for extending existing ones. Successively, the pharmacological function and biological activity concepts obtained from text were included into a novel descriptor for chemical compounds. Its successful application for the prediction of pharmacological function of molecules and the extension of chemical classification schemes, such as the the Anatomical Therapeutic Chemical (ATC), is demonstrated. In contrast to chemical entities, no comprehensive terminology resource has been available for histone modifications. Thus, histone modification concept terminology was primary recognized in text via CRFs with a F1 measure of 0.86. Subsequent, linguistic variants of extracted histone modification terms were mapped to standard representations that were organized into a newly assembled histone modification hierarchy. The mapping was accomplished by a novel developed term mapping approach described in the thesis. The combination of term recognition and term variant resolution builds up a new procedure for the assembly of novel terminology collections. It supports the generation of a term list that is applicable in dictionary-based methods. For the recognition of histone modification in text it could be shown that the named entity recognition method based on dictionaries is superior to the used machine learning approach. In conclusion, the present thesis provides techniques which enable an enhanced utilization of textual data, hence, supporting research in epigenomics and drug discovery

Automated Recognition of Brain Region Mentions in Neuroscience Literature

The ability to computationally extract mentions of neuroanatomical regions from the literature would assist linking to other entities within and outside of an article. Examples include extracting reports of connectivity or region-specific gene expression. To facilitate text mining of neuroscience literature we have created a corpus of manually annotated brain region mentions. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. The corpus is freely available at http://www.chibi.ubc.ca/WhiteText/

Pooling-Invariant Image Feature Learning

Unsupervised dictionary learning has been a key component in state-of-the-art computer vision recognition architectures. While highly effective methods exist for patch-based dictionary learning, these methods may learn redundant features after the pooling stage in a given early vision architecture. In this paper, we offer a novel dictionary learning scheme to efficiently take into account the invariance of learned features after the spatial pooling stage. The algorithm is built on simple clustering, and thus enjoys efficiency and scalability. We discuss the underlying mechanism that justifies the use of clustering algorithms, and empirically show that the algorithm finds better dictionaries than patch-based methods with the same dictionary size