Concept graphs: Applications to biomedical text categorization and concept extraction

As science advances, the underlying literature grows rapidly providing valuable knowledge mines for researchers and practitioners. The text content that makes up these knowledge collections is often unstructured and, thus, extracting relevant or novel information could be nontrivial and costly. In addition, human knowledge and expertise are being transformed into structured digital information in the form of vocabulary databases and ontologies. These knowledge bases hold substantial hierarchical and semantic relationships of common domain concepts. Consequently, automating learning tasks could be reinforced with those knowledge bases through constructing human-like representations of knowledge. This allows developing algorithms that simulate the human reasoning tasks of content perception, concept identification, and classification. This study explores the representation of text documents using concept graphs that are constructed with the help of a domain ontology. In particular, the target data sets are collections of biomedical text documents, and the domain ontology is a collection of predefined biomedical concepts and relationships among them. The proposed representation preserves those relationships and allows using the structural features of graphs in text mining and learning algorithms. Those features emphasize the significance of the underlying relationship information that exists in the text content behind the interrelated topics and concepts of a text document. The experiments presented in this study include text categorization and concept extraction applied on biomedical data sets. The experimental results demonstrate how the relationships extracted from text and captured in graph structures can be used to improve the performance of the aforementioned applications. The discussed techniques can be used in creating and maintaining digital libraries through enhancing indexing, retrieval, and management of documents as well as in a broad range of domain-specific applications such as drug discovery, hypothesis generation, and the analysis of molecular structures in chemoinformatics

Augmenting Latent Dirichlet Allocation and Rank Threshold Detection with Ontologies

In an ever-increasing data rich environment, actionable information must be extracted, filtered, and correlated from massive amounts of disparate often free text sources. The usefulness of the retrieved information depends on how we accomplish these steps and present the most relevant information to the analyst. One method for extracting information from free text is Latent Dirichlet Allocation (LDA), a document categorization technique to classify documents into cohesive topics. Although LDA accounts for some implicit relationships such as synonymy (same meaning) it often ignores other semantic relationships such as polysemy (different meanings), hyponym (subordinate), meronym (part of), and troponomys (manner). To compensate for this deficiency, we incorporate explicit word ontologies, such as WordNet, into the LDA algorithm to account for various semantic relationships. Experiments over the 20 Newsgroups, NIPS, OHSUMED, and IED document collections demonstrate that incorporating such knowledge improves perplexity measure over LDA alone for given parameters. In addition, the same ontology augmentation improves recall and precision results for user queries

Committee-Based Sample Selection for Probabilistic Classifiers

In many real-world learning tasks, it is expensive to acquire a sufficient number of labeled examples for training. This paper investigates methods for reducing annotation cost by `sample selection'. In this approach, during training the learning program examines many unlabeled examples and selects for labeling only those that are most informative at each stage. This avoids redundantly labeling examples that contribute little new information. Our work follows on previous research on Query By Committee, extending the committee-based paradigm to the context of probabilistic classification. We describe a family of empirical methods for committee-based sample selection in probabilistic classification models, which evaluate the informativeness of an example by measuring the degree of disagreement between several model variants. These variants (the committee) are drawn randomly from a probability distribution conditioned by the training set labeled so far. The method was applied to the real-world natural language processing task of stochastic part-of-speech tagging. We find that all variants of the method achieve a significant reduction in annotation cost, although their computational efficiency differs. In particular, the simplest variant, a two member committee with no parameters to tune, gives excellent results. We also show that sample selection yields a significant reduction in the size of the model used by the tagger

A Comparison of Multi-instance Learning Algorithms

Motivated by various challenging real-world applications, such as drug activity prediction and image retrieval, multi-instance (MI) learning has attracted considerable interest in recent years. Compared with standard supervised learning, the MI learning task is more difficult as the label information of each training example is incomplete. Many MI algorithms have been proposed. Some of them are specifically designed for MI problems whereas others have been upgraded or adapted from standard single-instance learning algorithms. Most algorithms have been evaluated on only one or two benchmark datasets, and there is a lack of systematic comparisons of MI learning algorithms. This thesis presents a comprehensive study of MI learning algorithms that aims to compare their performance and find a suitable way to properly address different MI problems. First, it briefly reviews the history of research on MI learning. Then it discusses five general classes of MI approaches that cover a total of 16 MI algorithms. After that, it presents empirical results for these algorithms that were obtained from 15 datasets which involve five different real-world application domains. Finally, some conclusions are drawn from these results: (1) applying suitable standard single-instance learners to MI problems can often generate the best result on the datasets that were tested, (2) algorithms exploiting the standard asymmetric MI assumption do not show significant advantages over approaches using the so-called collective assumption, and (3) different MI approaches are suitable for different application domains, and no MI algorithm works best on all MI problems

Machine Learning in Automated Text Categorization

The automated categorization (or classification) of texts into predefined categories has witnessed a booming interest in the last ten years, due to the increased availability of documents in digital form and the ensuing need to organize them. In the research community the dominant approach to this problem is based on machine learning techniques: a general inductive process automatically builds a classifier by learning, from a set of preclassified documents, the characteristics of the categories. The advantages of this approach over the knowledge engineering approach (consisting in the manual definition of a classifier by domain experts) are a very good effectiveness, considerable savings in terms of expert manpower, and straightforward portability to different domains. This survey discusses the main approaches to text categorization that fall within the machine learning paradigm. We will discuss in detail issues pertaining to three different problems, namely document representation, classifier construction, and classifier evaluation.Comment: Accepted for publication on ACM Computing Survey

Evolving text classification rules with genetic programming

We describe a novel method for using genetic programming to create compact classification rules using combinations of N-grams (character strings). Genetic programs acquire fitness by producing rules that are effective classifiers in terms of precision and recall when evaluated against a set of training documents. We describe a set of functions and terminals and provide results from a classification task using the Reuters 21578 dataset. We also suggest that the rules may have a number of other uses beyond classification and provide a basis for text mining applications