Dataset Information

Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues.

ABSTRACT:

Background

Word sense disambiguation (WSD) is critical in the biomedical domain for improving the precision of natural language processing (NLP), text mining, and information retrieval systems because ambiguous words negatively impact accurate access to literature containing biomolecular entities, such as genes, proteins, cells, diseases, and other important entities. Automated techniques have been developed that address the WSD problem for a number of text processing situations, but the problem is still a challenging one. Supervised WSD machine learning (ML) methods have been applied in the biomedical domain and have shown promising results, but the results typically incorporate a number of confounding factors, and it is problematic to truly understand the effectiveness and generalizability of the methods because these factors interact with each other and affect the final results. Thus, there is a need to explicitly address the factors and to systematically quantify their effects on performance.

Results

Experiments were designed to measure the effect of "sample size" (i.e. size of the datasets), "sense distribution" (i.e. the distribution of the different meanings of the ambiguous word) and "degree of difficulty" (i.e. the measure of the distances between the meanings of the senses of an ambiguous word) on the performance of WSD classifiers. Support Vector Machine (SVM) classifiers were applied to an automatically generated data set containing four ambiguous biomedical abbreviations: BPD, BSA, PCA, and RSV, which were chosen because of varying degrees of differences in their respective senses. Results showed that: 1) increasing the sample size generally reduced the error rate, but this was limited mainly to well-separated senses (i.e. cases where the distances between the senses were large); in difficult cases an unusually large increase in sample size was needed to increase performance slightly, which was impractical, 2) the sense distribution did not have an effect on performance when the senses were separable, 3) when there was a majority sense of over 90%, the WSD classifier was not better than use of the simple majority sense, 4) error rates were proportional to the similarity of senses, and 5) there was no statistical difference between results when using a 5-fold or 10-fold cross-validation method. Other issues that impact performance are also enumerated.

Conclusion

Several different independent aspects affect performance when using ML techniques for WSD. We found that combining them into one single result obscures understanding of the underlying methods. Although we studied only four abbreviations, we utilized a well-established statistical method that guarantees the results are likely to be generalizable for abbreviations with similar characteristics. The results of our experiments show that in order to understand the performance of these ML methods it is critical that papers report on the baseline performance, the distribution and sample size of the senses in the datasets, and the standard deviation or confidence intervals. In addition, papers should also characterize the difficulty of the WSD task, the WSD situations addressed and not addressed, as well as the ML methods and features used. This should lead to an improved understanding of the generalizablility and the limitations of the methodology.

SUBMITTER: Xu H

PROVIDER: S-EPMC1550263 | biostudies-literature | 2006 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues.

Xu Hua H Markatou Marianthi M Dimova Rositsa R Liu Hongfang H Friedman Carol C

BMC bioinformatics 20060705

<h4>Background</h4>Word sense disambiguation (WSD) is critical in the biomedical domain for improving the precision of natural language processing (NLP), text mining, and information retrieval systems because ambiguous words negatively impact accurate access to literature containing biomolecular entities, such as genes, proteins, cells, diseases, and other important entities. Automated techniques have been developed that address the WSD problem for a number of text processing situations, but the ...[more]

PMID: 16822321

Similar Datasets

Project description:BACKGROUND: Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as simple terminologies, without making use of the ontology structure or the semantic similarity between terms. Another useful source of information for disambiguation are metadata. Here, we systematically compare three approaches to word sense disambiguation, which use ontologies and metadata, respectively. RESULTS: The 'Closest Sense' method assumes that the ontology defines multiple senses of the term. It computes the shortest path of co-occurring terms in the document to one of these senses. The 'Term Cooc' method defines a log-odds ratio for co-occurring terms including co-occurrences inferred from the ontology structure. The 'MetaData' approach trains a classifier on metadata. It does not require any ontology, but requires training data, which the other methods do not. To evaluate these approaches we defined a manually curated training corpus of 2600 documents for seven ambiguous terms from the Gene Ontology and MeSH. All approaches over all conditions achieve 80% success rate on average. The 'MetaData' approach performed best with 96%, when trained on high-quality data. Its performance deteriorates as quality of the training data decreases. The 'Term Cooc' approach performs better on Gene Ontology (92% success) than on MeSH (73% success) as MeSH is not a strict is-a/part-of, but rather a loose is-related-to hierarchy. The 'Closest Sense' approach achieves on average 80% success rate. CONCLUSION: Metadata is valuable for disambiguation, but requires high quality training data. Closest Sense requires no training, but a large, consistently modelled ontology, which are two opposing conditions. Term Cooc achieves greater 90% success given a consistently modelled ontology. Overall, the results show that well structured ontologies can play a very important role to improve disambiguation. AVAILABILITY: The three benchmark datasets created for the purpose of disambiguation are available in Additional file 1.

Project description:BackgroundEvaluation of Word Sense Disambiguation (WSD) methods in the biomedical domain is difficult because the available resources are either too small or too focused on specific types of entities (e.g. diseases or genes). We present a method that can be used to automatically develop a WSD test collection using the Unified Medical Language System (UMLS) Metathesaurus and the manual MeSH indexing of MEDLINE. We demonstrate the use of this method by developing such a data set, called MSH WSD.MethodsIn our method, the Metathesaurus is first screened to identify ambiguous terms whose possible senses consist of two or more MeSH headings. We then use each ambiguous term and its corresponding MeSH heading to extract MEDLINE citations where the term and only one of the MeSH headings co-occur. The term found in the MEDLINE citation is automatically assigned the UMLS CUI linked to the MeSH heading. Each instance has been assigned a UMLS Concept Unique Identifier (CUI). We compare the characteristics of the MSH WSD data set to the previously existing NLM WSD data set.ResultsThe resulting MSH WSD data set consists of 106 ambiguous abbreviations, 88 ambiguous terms and 9 which are a combination of both, for a total of 203 ambiguous entities. For each ambiguous term/abbreviation, the data set contains a maximum of 100 instances per sense obtained from MEDLINE.We evaluated the reliability of the MSH WSD data set using existing knowledge-based methods and compared their performance to that of the results previously obtained by these algorithms on the pre-existing data set, NLM WSD. We show that the knowledge-based methods achieve different results but keep their relative performance except for the Journal Descriptor Indexing (JDI) method, whose performance is below the other methods.ConclusionsThe MSH WSD data set allows the evaluation of WSD algorithms in the biomedical domain. Compared to previously existing data sets, MSH WSD contains a larger number of biomedical terms/abbreviations and covers the largest set of UMLS Semantic Types. Furthermore, the MSH WSD data set has been generated automatically reusing already existing annotations and, therefore, can be regenerated from subsequent UMLS versions.

Project description:Biomedical and life science literature is an essential way to publish experimental results. With the rapid growth of the number of new publications, the amount of scientific knowledge represented in free text is increasing remarkably. There has been much interest in developing techniques that can extract this knowledge and make it accessible to aid scientists in discovering new relationships between biological entities and answering biological questions. Making use of the word2vec approach, we generated word vector representations based on a corpus consisting of over 16 million PubMed abstracts. We developed a text mining pipeline to produce word2vec embeddings with different properties and performed validation experiments to assess their utility for biomedical analysis. An important pre-processing step consisted in the substitution of synonymous terms by their preferred terms in biomedical databases. Furthermore, we extracted gene-gene networks from two embedding versions and used them as prior knowledge to train Graph-Convolutional Neural Networks (CNNs) on large breast cancer gene expression data and on other cancer datasets. Performances of resulting models were compared to Graph-CNNs trained with protein-protein interaction (PPI) networks or with networks derived using other word embedding algorithms. We also assessed the effect of corpus size on the variability of word representations. Finally, we created a web service with a graphical and a RESTful interface to extract and explore relations between biomedical terms using annotated embeddings. Comparisons to biological databases showed that relations between entities such as known PPIs, signaling pathways and cellular functions, or narrower disease ontology groups correlated with higher cosine similarity. Graph-CNNs trained with word2vec-embedding-derived networks performed sufficiently good for the metastatic event prediction tasks compared to other networks. Such performance was good enough to validate the utility of our generated word embeddings in constructing biological networks. Word representations as produced by text mining algorithms like word2vec, therefore are able to capture biologically meaningful relations between entities. Our generated embeddings are publicly available at https://github.com/genexplain/Word2vec-based-Networks/blob/main/README.md.

Dataset Information

Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues.

Background

Results

Conclusion

Publications

Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets