Active learning: A step towards automating medical concept extraction

Objective This paper presents an automatic active learning-based system for the extraction of medical concepts from clinical free-text reports. Specifically, (1) the contribution of active learning in reducing the annotation effort, and (2) the robustness of incremental active learning framework across different selection criteria and datasets is determined. Materials and methods The comparative performance of an active learning framework and a fully supervised approach were investigated to study how active learning reduces the annotation effort while achieving the same effectiveness as a supervised approach. Conditional Random Fields as the supervised method, and least confidence and information density as two selection criteria for active learning framework were used. The effect of incremental learning vs. standard learning on the robustness of the models within the active learning framework with different selection criteria was also investigated. Two clinical datasets were used for evaluation: the i2b2/VA 2010 NLP challenge and the ShARe/CLEF 2013 eHealth Evaluation Lab. Results The annotation effort saved by active learning to achieve the same effectiveness as supervised learning is up to 77%, 57%, and 46% of the total number of sequences, tokens, and concepts, respectively. Compared to the Random sampling baseline, the saving is at least doubled. Discussion Incremental active learning guarantees robustness across all selection criteria and datasets. The reduction of annotation effort is always above random sampling and longest sequence baselines. Conclusion Incremental active learning is a promising approach for building effective and robust medical concept extraction models, while significantly reducing the burden of manual annotation.

Making sense of microposts (#MSM2013) concept extraction challenge

Microposts are small fragments of social media content that have been published using a lightweight paradigm (e.g. Tweets, Facebook likes, foursquare check-ins). Microposts have been used for a variety of applications (e.g., sentiment analysis, opinion mining, trend analysis), by gleaning useful information, often using third-party concept extraction tools. There has been very large uptake of such tools in the last few years, along with the creation and adoption of new methods for concept extraction. However, the evaluation of such efforts has been largely consigned to document corpora (e.g. news articles), questioning the suitability of concept extraction tools and methods for Micropost data. This report describes the Making Sense of Microposts Workshop (#MSM2013) Concept Extraction Challenge, hosted in conjunction with the 2013 World Wide Web conference (WWW'13). The Challenge dataset comprised a manually annotated training corpus of Microposts and an unlabelled test corpus. Participants were set the task of engineering a concept extraction system for a defined set of concepts. Out of a total of 22 complete submissions 13 were accepted for presentation at the workshop; the submissions covered methods ranging from sequence mining algorithms for attribute extraction to part-of-speech tagging for Micropost cleaning and rule-based and discriminative models for token classification. In this report we describe the evaluation process and explain the performance of different approaches in different contexts.

External knowledge and query strategies in active learning: A study in clinical information extraction

This paper presents a new active learning query strategy for information extraction, called Domain Knowledge Informativeness (DKI). Active learning is often used to reduce the amount of annotation effort required to obtain training data for machine learning algorithms. A key component of an active learning approach is the query strategy, which is used to iteratively select samples for annotation. Knowledge resources have been used in information extraction as a means to derive additional features for sample representation. DKI is, however, the first query strategy that exploits such resources to inform sample selection. To evaluate the merits of DKI, in particular with respect to the reduction in annotation effort that the new query strategy allows to achieve, we conduct a comprehensive empirical comparison of active learning query strategies for information extraction within the clinical domain. The clinical domain was chosen for this work because of the availability of extensive structured knowledge resources which have often been exploited for feature generation. In addition, the clinical domain offers a compelling use case for active learning because of the necessary high costs and hurdles associated with obtaining annotations in this domain. Our experimental findings demonstrated that 1) amongst existing query strategies, the ones based on the classification model’s confidence are a better choice for clinical data as they perform equally well with a much lighter computational load, and 2) significant reductions in annotation effort are achievable by exploiting knowledge resources within active learning query strategies, with up to 14% less tokens and concepts to manually annotate than with state-of-the-art query strategies.

Analysis of word embeddings and sequence features for clinical information extraction

This study investigates the use of unsupervised features derived from word embedding approaches and novel sequence representation approaches for improving clinical information extraction systems. Our results corroborate previous findings that indicate that the use of word embeddings significantly improve the effectiveness of concept extraction models; however, we further determine the influence that the corpora used to generate such features have. We also demonstrate the promise of sequence-based unsupervised features for further improving concept extraction.

Extraction automatique et visualisation des thèmes abordés dans des résumés de mémoires et de thèses en anthropologie au Québec, de 1985 à 2009

S’insérant dans les domaines de la Lecture et de l’Analyse de Textes Assistées par Ordinateur (LATAO), de la Gestion Électronique des Documents (GÉD), de la visualisation de l’information et, en partie, de l’anthropologie, cette recherche exploratoire propose l’expérimentation d’une méthodologie descriptive en fouille de textes afin de cartographier thématiquement un corpus de textes anthropologiques. Plus précisément, nous souhaitons éprouver la méthode de classification hiérarchique ascendante (CHA) pour extraire et analyser les thèmes issus de résumés de mémoires et de thèses octroyés de 1985 à 2009 (1240 résumés), par les départements d’anthropologie de l’Université de Montréal et de l’Université Laval, ainsi que le département d’histoire de l’Université Laval (pour les résumés archéologiques et ethnologiques). En première partie de mémoire, nous présentons notre cadre théorique, c'est-à-dire que nous expliquons ce qu’est la fouille de textes, ses origines, ses applications, les étapes méthodologiques puis, nous complétons avec une revue des principales publications. La deuxième partie est consacrée au cadre méthodologique et ainsi, nous abordons les différentes étapes par lesquelles ce projet fut conduit; la collecte des données, le filtrage linguistique, la classification automatique, pour en nommer que quelques-unes. Finalement, en dernière partie, nous présentons les résultats de notre recherche, en nous attardant plus particulièrement sur deux expérimentations. Nous abordons également la navigation thématique et les approches conceptuelles en thématisation, par exemple, en anthropologie, la dichotomie culture ̸ biologie. Nous terminons avec les limites de ce projet et les pistes d’intérêts pour de futures recherches.

Towards concept identification using a knowledge-intensive approach

This paper presents a method for identifying concepts in microposts and classifying them into a predefined set of categories. The method relies on the DBpedia knowledge base to identify the types of the concepts detected in the messages. For those concepts that are not classified in the ontology we infer their types via the ontology properties which characterise the type.

Modelling users' contextual querying behaviour for web image searching

The rapid growth of visual information on Web has led to immense interest in multimedia information retrieval (MIR). While advancement in MIR systems has achieved some success in specific domains, particularly the content-based approaches, general Web users still struggle to find the images they want. Despite the success in content-based object recognition or concept extraction, the major problem in current Web image searching remains in the querying process. Since most online users only express their needs in semantic terms or objects, systems that utilize visual features (e.g., color or texture) to search images create a semantic gap which hinders general users from fully expressing their needs. In addition, query-by-example (QBE) retrieval imposes extra obstacles for exploratory search because users may not always have the representative image at hand or in mind when starting a search (i.e. the page zero problem). As a result, the majority of current online image search engines (e.g., Google, Yahoo, and Flickr) still primarily use textual queries to search. The problem with query-based retrieval systems is that they only capture users’ information need in terms of formal queries;; the implicit and abstract parts of users’ information needs are inevitably overlooked. Hence, users often struggle to formulate queries that best represent their needs, and some compromises have to be made. Studies of Web search logs suggest that multimedia searches are more difficult than textual Web searches, and Web image searching is the most difficult compared to video or audio searches. Hence, online users need to put in more effort when searching multimedia contents, especially for image searches. Most interactions in Web image searching occur during query reformulation. While log analysis provides intriguing views on how the majority of users search, their search needs or motivations are ultimately neglected. User studies on image searching have attempted to understand users’ search contexts in terms of users’ background (e.g., knowledge, profession, motivation for search and task types) and the search outcomes (e.g., use of retrieved images, search performance). However, these studies typically focused on particular domains with a selective group of professional users. General users’ Web image searching contexts and behaviors are little understood although they represent the majority of online image searching activities nowadays. We argue that only by understanding Web image users’ contexts can the current Web search engines further improve their usefulness and provide more efficient searches. In order to understand users’ search contexts, a user study was conducted based on university students’ Web image searching in News, Travel, and commercial Product domains. The three search domains were deliberately chosen to reflect image users’ interests in people, time, event, location, and objects. We investigated participants’ Web image searching behavior, with the focus on query reformulation and search strategies. Participants’ search contexts such as their search background, motivation for search, and search outcomes were gathered by questionnaires. The searching activity was recorded with participants’ think aloud data for analyzing significant search patterns. The relationships between participants’ search contexts and corresponding search strategies were discovered by Grounded Theory approach. Our key findings include the following aspects: - Effects of users' interactive intents on query reformulation patterns and search strategies - Effects of task domain on task specificity and task difficulty, as well as on some specific searching behaviors - Effects of searching experience on result expansion strategies A contextual image searching model was constructed based on these findings. The model helped us understand Web image searching from user perspective, and introduced a context-aware searching paradigm for current retrieval systems. A query recommendation tool was also developed to demonstrate how users’ query reformulation contexts can potentially contribute to more efficient searching.

Factors influencing robustness and effectiveness of conditional random fields in active learning frameworks

Active learning approaches reduce the annotation cost required by traditional supervised approaches to reach the same effectiveness by actively selecting informative instances during the learning phase. However, effectiveness and robustness of the learnt models are influenced by a number of factors. In this paper we investigate the factors that affect the effectiveness, more specifically in terms of stability and robustness, of active learning models built using conditional random fields (CRFs) for information extraction applications. Stability, defined as a small variation of performance when small variation of the training data or a small variation of the parameters occur, is a major issue for machine learning models, but even more so in the active learning framework which aims to minimise the amount of training data required. The factors we investigate are a) the choice of incremental vs. standard active learning, b) the feature set used as a representation of the text (i.e., morphological features, syntactic features, or semantic features) and c) Gaussian prior variance as one of the important CRFs parameters. Our empirical findings show that incremental learning and the Gaussian prior variance lead to more stable and robust models across iterations. Our study also demonstrates that orthographical, morphological and contextual features as a group of basic features play an important role in learning effective models across all iterations.

Stir bar sorptive extraction of diclofenac from liquid formulations: A proof of concept study

A new stir bar sorptive extraction (SBSE) technique coupled with HPLC-UV method for quantification of diclofenac in pharmaceutical formulations has been developed and validated as a proof of concept study. Commercially available polydimethylsiloxane stir bars (Twister (TM)) were used for method development and SBSE extraction (pH, phase ratio, stirring speed, temperature, ionic strength and time) and liquid desorption (solvents, desorption method, stirring time etc) procedures were optimised. The method was validated as per ICH guidelines and was successfully applied for the estimation of diclofenac from three liquid formulations viz. Voltarol (R) Optha single dose eye drops, Voltarol (R) Ophtha multidose eye drops and Voltarol (R) ampoules. The developed method was found to be linear (r=0.9999) over 100-2000 ng/ml concentration range with acceptable accuracy and precision (tested over three QC concentrations). The SBSE extraction recovery of the diclofenac was found to be 70% and the LOD and LOQ of the validated method were found to be 16.06 and 48.68 ng/ml, respectively. Furthermore, a forced degradation study of a diclofenac formulation leading to the formation of structurally similar cyclic impurity (indolinone) was carried out. The developed extraction method showed comparable results to that of the reference method, i.e. method was capable of selectively extracting the indolinone and diclofenac from the liquid matrix. Data on inter and intra stir bar accuracy and precision further confirmed robustness of the method, supporting the multiple re-use of the stir bars. (C) 2010 Elsevier B.V. All rights reserved.

A Concept of Semantics Extraction from Web Data by Induction of Fuzzy Ontologies

Traditionally, ontologies describe knowledge representation in a denotational, formalized, and deductive way. In addition, in this paper, we propose a semiotic, inductive, and approximate approach to ontology creation. We define a conceptual framework, a semantics extraction algorithm, and a first proof of concept applying the algorithm to a small set of Wikipedia documents. Intended as an extension to the prevailing top-down ontologies, we introduce an inductive fuzzy grassroots ontology, which organizes itself organically from existing natural language Web content. Using inductive and approximate reasoning to reflect the natural way in which knowledge is processed, the ontology’s bottom-up build process creates emergent semantics learned from the Web. By this means, the ontology acts as a hub for computing with words described in natural language. For Web users, the structural semantics are visualized as inductive fuzzy cognitive maps, allowing an initial form of intelligence amplification. Eventually, we present an implementation of our inductive fuzzy grassroots ontology Thus,this paper contributes an algorithm for the extraction of fuzzy grassroots ontologies from Web data by inductive fuzzy classification.

Toward a fuzzy domain ontology extraction method for adaptive e-learning

With the widespread applications of electronic learning (e-Learning) technologies to education at all levels, increasing number of online educational resources and messages are generated from the corresponding e-Learning environments. Nevertheless, it is quite difficult, if not totally impossible, for instructors to read through and analyze the online messages to predict the progress of their students on the fly. The main contribution of this paper is the illustration of a novel concept map generation mechanism which is underpinned by a fuzzy domain ontology extraction algorithm. The proposed mechanism can automatically construct concept maps based on the messages posted to online discussion forums. By browsing the concept maps, instructors can quickly identify the progress of their students and adjust the pedagogical sequence on the fly. Our initial experimental results reveal that the accuracy and the quality of the automatically generated concept maps are promising. Our research work opens the door to the development and application of intelligent software tools to enhance e-Learning.

Medical free-text to concept mapping as an information retrieval problem

Concept mapping involves determining relevant concepts from a free-text input, where concepts are defined in an external reference ontology. This is an important process that underpins many applications for clinical information reporting, derivation of phenotypic descriptions, and a number of state-of-the-art medical information retrieval methods. Concept mapping can be cast into an information retrieval (IR) problem: free-text mentions are treated as queries and concepts from a reference ontology as the documents to be indexed and retrieved. This paper presents an empirical investigation applying general-purpose IR techniques for concept mapping in the medical domain. A dataset used for evaluating medical information extraction is adapted to measure the effectiveness of the considered IR approaches. Standard IR approaches used here are contrasted with the effectiveness of two established benchmark methods specifically developed for medical concept mapping. The empirical findings show that the IR approaches are comparable with one benchmark method but well below the best benchmark.

A coarse grid extraction of sound signals for computational aeroacoustics

Sound waves are propagating pressure fluctuations, which are typically several orders of magnitude smaller than the pressure variations in the flow field that account for flow acceleration. On the other hand, these fluctuations travel at the speed of sound in the medium, not as a transported fluid quantity. Due to the above two properties, the Reynolds averaged Navier–Stokes equations do not resolve the acoustic fluctuations. This paper discusses a defect correction method for this type of multi-scale problems in aeroacoustics. Numerical examples in one dimensional and two dimensional are used to illustrate the concept. Copyright (C) 2002 John Wiley & Sons, Ltd.