Automatic document classification of biological literature

Background: Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. Results: We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. Conclusions: We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept

Concept Extraction and Clustering for Topic Digital Library Construction

This paper is to introduce a new approach to build topic digital library using concept extraction and document clustering. Firstly, documents in a special domain are automatically produced by document classification approach. Then, the keywords of each document are extracted using the machine learning approach. The keywords are used to cluster the documents subset. The clustered result is the taxonomy of the subset. Lastly, the taxonomy is modified to the hierarchical structure for user navigation by manual adjustments. The topic digital library is constructed after combining the full-text retrieval and hierarchical navigation function

The category proliferation problem in ART neural networks

This article describes the design of a new model IKMART, for classification of documents and their incorporation into categories based on the KMART architecture. The architecture consists of two networks that mutually cooperate through the interconnection of weights and the output matrix of the coded documents. The architecture retains required network features such as incremental learning without the need of descriptive and input/output fuzzy data, learning acceleration and classification of documents and a minimal number of user-defined parameters. The conducted experiments with real documents showed a more precise categorization of documents and higher classification performance in comparison to the classic KMART algorithm.Web of Science145634

Adaptive content mapping for internet navigation

The Internet as the biggest human library ever assembled keeps on growing. Although all kinds of information carriers (e.g. audio/video/hybrid file formats) are available, text based documents dominate. It is estimated that about 80% of all information worldwide stored electronically exists in (or can be converted into) text form. More and more, all kinds of documents are generated by means of a text processing system and are therefore available electronically. Nowadays, many printed journals are also published online and may even discontinue to appear in print form tomorrow. This development has many convincing advantages: the documents are both available faster (cf. prepress services) and cheaper, they can be searched more easily, the physical storage only needs a fraction of the space previously necessary and the medium will not age. For most people, fast and easy access is the most interesting feature of the new age; computer-aided search for specific documents or Web pages becomes the basic tool for information-oriented work. But this tool has problems. The current keyword based search machines available on the Internet are not really appropriate for such a task; either there are (way) too many documents matching the specified keywords are presented or none at all. The problem lies in the fact that it is often very difficult to choose appropriate terms describing the desired topic in the first place. This contribution discusses the current state-of-the-art techniques in content-based searching (along with common visualization/browsing approaches) and proposes a particular adaptive solution for intuitive Internet document navigation, which not only enables the user to provide full texts instead of manually selected keywords (if available), but also allows him/her to explore the whole database

Knowledge-rich Image Gist Understanding Beyond Literal Meaning

We investigate the problem of understanding the message (gist) conveyed by images and their captions as found, for instance, on websites or news articles. To this end, we propose a methodology to capture the meaning of image-caption pairs on the basis of large amounts of machine-readable knowledge that has previously been shown to be highly effective for text understanding. Our method identifies the connotation of objects beyond their denotation: where most approaches to image understanding focus on the denotation of objects, i.e., their literal meaning, our work addresses the identification of connotations, i.e., iconic meanings of objects, to understand the message of images. We view image understanding as the task of representing an image-caption pair on the basis of a wide-coverage vocabulary of concepts such as the one provided by Wikipedia, and cast gist detection as a concept-ranking problem with image-caption pairs as queries. To enable a thorough investigation of the problem of gist understanding, we produce a gold standard of over 300 image-caption pairs and over 8,000 gist annotations covering a wide variety of topics at different levels of abstraction. We use this dataset to experimentally benchmark the contribution of signals from heterogeneous sources, namely image and text. The best result with a Mean Average Precision (MAP) of 0.69 indicate that by combining both dimensions we are able to better understand the meaning of our image-caption pairs than when using language or vision information alone. We test the robustness of our gist detection approach when receiving automatically generated input, i.e., using automatically generated image tags or generated captions, and prove the feasibility of an end-to-end automated process