An automatic approach to weighted subject indexing – An empirical study in the biomedical domain

Subject indexing is an intellectually intensive process that has many inherent uncertainties. Existing manual subject indexing systems generally produce binary outcomes for whether or not to assign an indexing term. This does not sufficiently reflect the extent to which the indexing terms are associated with the documents. On the other hand, the idea of probabilistic or weighted indexing was proposed a long time ago and has seen success in capturing uncertainties in the automatic indexing process. One hurdle to overcome in implementing weighted indexing in manual subject indexing systems is the practical burden that could be added to the already intensive indexing process. This study proposes a method to infer automatically the associations between subject terms and documents through text mining. By uncovering the connections between MeSH descriptors and document text, we are able to derive the weights of MeSH descriptors manually assigned to documents. Our initial results suggest that the inference method is feasible and promising. The study has practical implications for improving subject indexing practice and providing better support for information retrieval.Ye

Automatic indexing and retrieval of encounter-specific evidence for point-of-care support

Evidence-based medicine relies on repositories of empirical research evidence that can be used to support clinical decision making for improved patient care. However, retrieving evidence from such repositories at local sites presents many challenges. This paper describes a methodological framework for automatically indexing and retrieving empirical research evidence in the form of the systematic reviews and associated studies from The Cochrane Library, where retrieved documents are specific to a patient-physician encounter and thus can be used to support evidence-based decision making at the point of care. Such an encounter is defined by three pertinent groups of concepts - diagnosis, treatment, and patient, and the framework relies on these three groups to steer indexing and retrieval of reviews and associated studies. An evaluation of the indexing and retrieval components of the proposed framework was performed using documents relevant for the pediatric asthma domain. Precision and recall values for automatic indexing of systematic reviews and associated studies were 0.93 and 0.87, and 0.81 and 0.56, respectively. Moreover, precision and recall for the retrieval of relevant systematic reviews and associated studies were 0.89 and 0.81, and 0.92 and 0.89, respectively. With minor modifications, the proposed methodological framework can be customized for other evidence repositories

Combining global and local semantic contexts for improving biomedical information retrieval

Présenté lors de l'European Conference on Information Retrieval 2011International audienceIn the context of biomedical information retrieval (IR), this paper explores the relationship between the document's global context and the query's local context in an attempt to overcome the term mismatch problem between the user query and documents in the collection. Most solutions to this problem have been focused on expanding the query by discovering its context, either \textit{global} or \textit{local}. In a global strategy, all documents in the collection are used to examine word occurrences and relationships in the corpus as a whole, and use this information to expand the original query. In a local strategy, the top-ranked documents retrieved for a given query are examined to determine terms for query expansion. We propose to combine the document's global context and the query's local context in an attempt to increase the term overlap between the user query and documents in the collection via document expansion (DE) and query expansion (QE). The DE technique is based on a statistical method (IR-based) to extract the most appropriate concepts (global context) from each document. The QE technique is based on a blind feedback approach using the top-ranked documents (local context) obtained in the first retrieval stage. A comparative experiment on the TREC 2004 Genomics collection demonstrates that the combination of the document's global context and the query's local context shows a significant improvement over the baseline. The MAP is significantly raised from 0.4097 to 0.4532 with a significant improvement rate of +10.62\% over the baseline. The IR performance of the combined method in terms of MAP is also superior to official runs participated in TREC 2004 Genomics and is comparable to the performance of the best run (0.4075)

Enhancing clinical concept extraction with distributional semantics

AbstractExtracting concepts (such as drugs, symptoms, and diagnoses) from clinical narratives constitutes a basic enabling technology to unlock the knowledge within and support more advanced reasoning applications such as diagnosis explanation, disease progression modeling, and intelligent analysis of the effectiveness of treatment. The recent release of annotated training sets of de-identified clinical narratives has contributed to the development and refinement of concept extraction methods. However, as the annotation process is labor-intensive, training data are necessarily limited in the concepts and concept patterns covered, which impacts the performance of supervised machine learning applications trained with these data. This paper proposes an approach to minimize this limitation by combining supervised machine learning with empirical learning of semantic relatedness from the distribution of the relevant words in additional unannotated text.The approach uses a sequential discriminative classifier (Conditional Random Fields) to extract the mentions of medical problems, treatments and tests from clinical narratives. It takes advantage of all Medline abstracts indexed as being of the publication type “clinical trials” to estimate the relatedness between words in the i2b2/VA training and testing corpora. In addition to the traditional features such as dictionary matching, pattern matching and part-of-speech tags, we also used as a feature words that appear in similar contexts to the word in question (that is, words that have a similar vector representation measured with the commonly used cosine metric, where vector representations are derived using methods of distributional semantics). To the best of our knowledge, this is the first effort exploring the use of distributional semantics, the semantics derived empirically from unannotated text often using vector space models, for a sequence classification task such as concept extraction. Therefore, we first experimented with different sliding window models and found the model with parameters that led to best performance in a preliminary sequence labeling task.The evaluation of this approach, performed against the i2b2/VA concept extraction corpus, showed that incorporating features based on the distribution of words across a large unannotated corpus significantly aids concept extraction. Compared to a supervised-only approach as a baseline, the micro-averaged F-score for exact match increased from 80.3% to 82.3% and the micro-averaged F-score based on inexact match increased from 89.7% to 91.3%. These improvements are highly significant according to the bootstrap resampling method and also considering the performance of other systems. Thus, distributional semantic features significantly improve the performance of concept extraction from clinical narratives by taking advantage of word distribution information obtained from unannotated data

Query expansion using medical information extraction for improving information retrieval in French medical domain

Many users’ queries contain references to named entities, and this is particularly true in the medical field. Doctors express their information needs using medical entities as they are elements rich with information that helps to better target the relevant documents. At the same time, many resources have been recognized as a large container of medical entities and relationships between them such as clinical reports; which are medical texts written by doctors. In this paper, we present a query expansion method that uses medical entities and their semantic relations in the query context based on an external resource in OWL. The goal of this method is to evaluate the effectiveness of an information retrieval system to support doctors in accessing easily relevant information. Experiments on a collection of real clinical reports show that our approach reveals interesting improvements in precision, recall and MAP in medical information retrieval

Integrating Medical Ontology and Pseudo Relevance Feedback For Medical Document Retrieval

The purpose of this thesis is to undertake and improve the accuracy of locating the relevant documents from a large amount of Electronic Medical Data (EMD). The unique goal of this research is to propose a new idea for using medical ontology to find an easy and more reliable approach for patients to have a better understanding of their diseases and also help doctors to find and further improve the possible methods of diagnosis and treatments. The empirical studies were based on the dataset provided by CLEF focused on health care data. In this research, I have used Information Retrieval to find and obtain relevant information within the large amount of data sets provided by CLEF. I then used ranking functionality on the Terrier platform to calculate and evaluate the matching documents in the collection of data sets. BM25 was used as the base normalization method to retrieve the results and Pseudo Relevance Feedback weighting model to retrieve the information regarding patients health history and medical records in order to find more accurate results. I then used Unified Medical Language System to develop indexing of the queries while searching on the Internet and looking for health related documents. UMLS software was actually used to link the computer system with the health and biomedical terms and vocabularies into classify tools; it works as a dictionary for the patients by translating the medical terms. Later I would like to work on using medical ontology to create a relationship between the documents regarding the medical data and my retrieved results

Hybrid image representation methods for automatic image annotation: a survey

In most automatic image annotation systems, images are represented with low level features using either global methods or local methods. In global methods, the entire image is used as a unit. Local methods divide images into blocks where fixed-size sub-image blocks are adopted as sub-units; or into regions by using segmented regions as sub-units in images. In contrast to typical automatic image annotation methods that use either global or local features exclusively, several recent methods have considered incorporating the two kinds of information, and believe that the combination of the two levels of features is beneficial in annotating images. In this paper, we provide a survey on automatic image annotation techniques according to one aspect: feature extraction, and, in order to complement existing surveys in literature, we focus on the emerging image annotation methods: hybrid methods that combine both global and local features for image representation