Hybrid methods for improving information access in clinical documents: concept,assertion, and relation identification

Objective

This paper describes the approaches the authors developed while participating in the i2b2/VA 2010 challenge to automatically extract medical concepts and annotate assertions on concepts and relations between concepts.

Design

The authors''approaches rely on both rule-based and machine-learning methods. Natural language processing is used to extract features from the input texts; these features are then used in the authors'' machine-learning approaches. The authors used Conditional Random Fields for concept extraction, and Support Vector Machines for assertion and relation annotation. Depending on the task, the authors tested various combinations of rule-based and machine-learning methods.

Results

The authors''assertion annotation system obtained an F-measure of 0.931, ranking fifth out of 21 participants at the i2b2/VA 2010 challenge. The authors'' relation annotation system ranked third out of 16 participants with a 0.709 F-measure. The 0.773 F-measure the authors obtained on concept extraction did not make it to the top 10.

Conclusion

On the one hand, the authors confirm that the use of only machine-learning methods is highly dependent on the annotated training data, and thus obtained better results for well-represented classes. On the other hand, the use of only a rule-based method was not sufficient to deal with new types of data. Finally, the use of hybrid approaches combining machine-learning and rule-based approaches yielded higher scores.     

Feature engineering combined with machine learning and rule-based methods for structured information extraction from narrative clinical discharge summaries

Objective

A system that translates narrative text in the medical domain into structured representation is in great demand. The system performs three sub-tasks: concept extraction, assertion classification, and relation identification.

Design

The overall system consists of five steps: (1) pre-processing sentences, (2) marking noun phrases (NPs) and adjective phrases (APs), (3) extracting concepts that use a dosage-unit dictionary to dynamically switch two models based on Conditional Random Fields (CRF), (4) classifying assertions based on voting of five classifiers, and (5) identifying relations using normalized sentences with a set of effective discriminating features.

Measurements

Macro-averaged and micro-averaged precision, recall and F-measure were used to evaluate results.

Results

The performance is competitive with the state-of-the-art systems with micro-averaged F-measure of 0.8489 for concept extraction, 0.9392 for assertion classification and 0.7326 for relation identification.

Conclusions

The system exploits an array of common features and achieves state-of-the-art performance. Prudent feature engineering sets the foundation of our systems. In concept extraction, we demonstrated that switching models, one of which is especially designed for telegraphic sentences, improved extraction of the treatment concept significantly. In assertion classification, a set of features derived from a rule-based classifier were proven to be effective for the classes such as conditional and possible. These classes would suffer from data scarcity in conventional machine-learning methods. In relation identification, we use two-staged architecture, the second of which applies pairwise classifiers to possible candidate classes. This architecture significantly improves performance.     

Automatic extraction of relations between medical concepts in clinical texts

Objective

A supervised machine learning approach to discover relations between medical problems, treatments, and tests mentioned in electronic medical records.

Materials and methods

A single support vector machine classifier was used to identify relations between concepts and to assign their semantic type. Several resources such as Wikipedia, WordNet, General Inquirer, and a relation similarity metric inform the classifier.

Results

The techniques reported in this paper were evaluated in the 2010 i2b2 Challenge and obtained the highest F1 score for the relation extraction task. When gold standard data for concepts and assertions were available, F1 was 73.7, precision was 72.0, and recall was 75.3. F1 is defined as 2*Precision*Recall/(Precision+Recall). Alternatively, when concepts and assertions were discovered automatically, F1 was 48.4, precision was 57.6, and recall was 41.7.

Discussion

Although a rich set of features was developed for the classifiers presented in this paper, little knowledge mining was performed from medical ontologies such as those found in UMLS. Future studies should incorporate features extracted from such knowledge sources, which we expect to further improve the results. Moreover, each relation discovery was treated independently. Joint classification of relations may further improve the quality of results. Also, joint learning of the discovery of concepts, assertions, and relations may also improve the results of automatic relation extraction.

Conclusion

Lexical and contextual features proved to be very important in relation extraction from medical texts. When they are not available to the classifier, the F1 score decreases by 3.7%. In addition, features based on similarity contribute to a decrease of 1.1% when they are not available.     

A flexible framework for deriving assertions from electronic medical records

Objective

This paper describes natural-language-processing techniques for two tasks: identification of medical concepts in clinical text, and classification of assertions, which indicate the existence, absence, or uncertainty of a medical problem. Because so many resources are available for processing clinical texts, there is interest in developing a framework in which features derived from these resources can be optimally selected for the two tasks of interest.

Materials and methods

The authors used two machine-learning (ML) classifiers: support vector machines (SVMs) and conditional random fields (CRFs). Because SVMs and CRFs can operate on a large set of features extracted from both clinical texts and external resources, the authors address the following research question: Which features need to be selected for obtaining optimal results? To this end, the authors devise feature-selection techniques which greatly reduce the amount of manual experimentation and improve performance.

Results

The authors evaluated their approaches on the 2010 i2b2/VA challenge data. Concept extraction achieves 79.59 micro F-measure. Assertion classification achieves 93.94 micro F-measure.

Discussion

Approaching medical concept extraction and assertion classification through ML-based techniques has the advantage of easily adapting to new data sets and new medical informatics tasks. However, ML-based techniques perform best when optimal features are selected. By devising promising feature-selection techniques, the authors obtain results that outperform the current state of the art.

Conclusion

This paper presents two ML-based approaches for processing language in the clinical texts evaluated in the 2010 i2b2/VA challenge. By using novel feature-selection methods, the techniques presented in this paper are unique among the i2b2 participants.     

Named entity recognition of follow-up and time information in 20 000 radiology reports

Objective

To develop a system to extract follow-up information from radiology reports. The method may be used as a component in a system which automatically generates follow-up information in a timely fashion.

Methods

A novel method of combining an LSP (labeled sequential pattern) classifier with a CRF (conditional random field) recognizer was devised. The LSP classifier filters out irrelevant sentences, while the CRF recognizer extracts follow-up and time phrases from candidate sentences presented by the LSP classifier.

Measurements

The standard performance metrics of precision (P), recall (R), and F measure (F) in the exact and inexact matching settings were used for evaluation.

Results

Four experiments conducted using 20 000 radiology reports showed that the CRF recognizer achieved high performance without time-consuming feature engineering and that the LSP classifier further improved the performance of the CRF recognizer. The performance of the current system is P=0.90, R=0.86, F=0.88 in the exact matching setting and P=0.98, R=0.93, F=0.95 in the inexact matching setting.

Conclusion

The experiments demonstrate that the system performs far better than a baseline rule-based system and is worth considering for deployment trials in an alert generation system. The LSP classifier successfully compensated for the inherent weakness of CRF, that is, its inability to use global information.     

à la Recherche du Temps Perdu: extracting temporal relations from medical text in the 2012 i2b2 NLP challenge

Objective

An analysis of the timing of events is critical for a deeper understanding of the course of events within a patient record. The 2012 i2b2 NLP challenge focused on the extraction of temporal relationships between concepts within textual hospital discharge summaries.

Materials and methods

The team from the National Research Council Canada (NRC) submitted three system runs to the second track of the challenge: typifying the time-relationship between pre-annotated entities. The NRC system was designed around four specialist modules containing statistical machine learning classifiers. Each specialist targeted distinct sets of relationships: local relationships, ‘sectime’-type relationships, non-local overlap-type relationships, and non-local causal relationships.

Results

The best NRC submission achieved a precision of 0.7499, a recall of 0.6431, and an F1 score of 0.6924, resulting in a statistical tie for first place. Post hoc improvements led to a precision of 0.7537, a recall of 0.6455, and an F1 score of 0.6954, giving the highest scores reported on this task to date.

Discussion and conclusions

Methods for general relation extraction extended well to temporal relations, and gave top-ranked state-of-the-art results. Careful ordering of predictions within result sets proved critical to this success.     

Automated concept-level information extraction to reduce the need for custom software and rules development

Objective

Despite at least 40 years of promising empirical performance, very few clinical natural language processing (NLP) or information extraction systems currently contribute to medical science or care. The authors address this gap by reducing the need for custom software and rules development with a graphical user interface-driven, highly generalizable approach to concept-level retrieval.

Materials and methods

A ‘learn by example’ approach combines features derived from open-source NLP pipelines with open-source machine learning classifiers to automatically and iteratively evaluate top-performing configurations. The Fourth i2b2/VA Shared Task Challenge''s concept extraction task provided the data sets and metrics used to evaluate performance.

Results

Top F-measure scores for each of the tasks were medical problems (0.83), treatments (0.82), and tests (0.83). Recall lagged precision in all experiments. Precision was near or above 0.90 in all tasks.

Discussion

With no customization for the tasks and less than 5 min of end-user time to configure and launch each experiment, the average F-measure was 0.83, one point behind the mean F-measure of the 22 entrants in the competition. Strong precision scores indicate the potential of applying the approach for more specific clinical information extraction tasks. There was not one best configuration, supporting an iterative approach to model creation.

Conclusion

Acceptable levels of performance can be achieved using fully automated and generalizable approaches to concept-level information extraction. The described implementation and related documentation is available for download.     

A sequence labeling approach to link medications and their attributes in clinical notes and clinical trial announcements for information extraction

Objective

The goal of this work was to evaluate machine learning methods, binary classification and sequence labeling, for medication–attribute linkage detection in two clinical corpora.

Data and methods

We double annotated 3000 clinical trial announcements (CTA) and 1655 clinical notes (CN) for medication named entities and their attributes. A binary support vector machine (SVM) classification method with parsimonious feature sets, and a conditional random fields (CRF)-based multi-layered sequence labeling (MLSL) model were proposed to identify the linkages between the entities and their corresponding attributes. We evaluated the system''s performance against the human-generated gold standard.

Results

The experiments showed that the two machine learning approaches performed statistically significantly better than the baseline rule-based approach. The binary SVM classification achieved 0.94 F-measure with individual tokens as features. The SVM model trained on a parsimonious feature set achieved 0.81 F-measure for CN and 0.87 for CTA. The CRF MLSL method achieved 0.80 F-measure on both corpora.

Discussion and conclusions

We compared the novel MLSL method with a binary classification and a rule-based method. The MLSL method performed statistically significantly better than the rule-based method. However, the SVM-based binary classification method was statistically significantly better than the MLSL method for both the CTA and CN corpora. Using parsimonious feature sets both the SVM-based binary classification and CRF-based MLSL methods achieved high performance in detecting medication name and attribute linkages in CTA and CN.     

A knowledge discovery and reuse pipeline for information extraction in clinical notes

Objective

Information extraction and classification of clinical data are current challenges in natural language processing. This paper presents a cascaded method to deal with three different extractions and classifications in clinical data: concept annotation, assertion classification and relation classification.

Materials and Methods

A pipeline system was developed for clinical natural language processing that includes a proofreading process, with gold-standard reflexive validation and correction. The information extraction system is a combination of a machine learning approach and a rule-based approach. The outputs of this system are used for evaluation in all three tiers of the fourth i2b2/VA shared-task and workshop challenge.

Results

Overall concept classification attained an F-score of 83.3% against a baseline of 77.0%, the optimal F-score for assertions about the concepts was 92.4% and relation classifier attained 72.6% for relationships between clinical concepts against a baseline of 71.0%. Micro-average results for the challenge test set were 81.79%, 91.90% and 70.18%, respectively.

Discussion

The challenge in the multi-task test requires a distribution of time and work load for each individual task so that the overall performance evaluation on all three tasks would be more informative rather than treating each task assessment as independent. The simplicity of the model developed in this work should be contrasted with the very large feature space of other participants in the challenge who only achieved slightly better performance. There is a need to charge a penalty against the complexity of a model as defined in message minimalisation theory when comparing results.

Conclusion

A complete pipeline system for constructing language processing models that can be used to process multiple practical detection tasks of language structures of clinical records is presented.     

Automatically extracting sentences from Medline citations to support clinicians’ information needs

Objective

Online health knowledge resources contain answers to most of the information needs raised by clinicians in the course of care. However, significant barriers limit the use of these resources for decision-making, especially clinicians’ lack of time. In this study we assessed the feasibility of automatically generating knowledge summaries for a particular clinical topic composed of relevant sentences extracted from Medline citations.

Methods

The proposed approach combines information retrieval and semantic information extraction techniques to identify relevant sentences from Medline abstracts. We assessed this approach in two case studies on the treatment alternatives for depression and Alzheimer''s disease.

Results

A total of 515 of 564 (91.3%) sentences retrieved in the two case studies were relevant to the topic of interest. About one-third of the relevant sentences described factual knowledge or a study conclusion that can be used for supporting information needs at the point of care.

Conclusions

The high rate of relevant sentences is desirable, given that clinicians’ lack of time is one of the main barriers to using knowledge resources at the point of care. Sentence rank was not significantly associated with relevancy, possibly due to most sentences being highly relevant. Sentences located closer to the end of the abstract and sentences with treatment and comparative predications were likely to be conclusive sentences. Our proposed technical approach to helping clinicians meet their information needs is promising. The approach can be extended for other knowledge resources and information need types.     

MCORES: a system for noun phrase coreference resolution for clinical records

Objective

Narratives of electronic medical records contain information that can be useful for clinical practice and multi-purpose research. This information needs to be put into a structured form before it can be used by automated systems. Coreference resolution is a step in the transformation of narratives into a structured form.

Methods

This study presents a medical coreference resolution system (MCORES) for noun phrases in four frequently used clinical semantic categories: persons, problems, treatments, and tests. MCORES treats coreference resolution as a binary classification task. Given a pair of concepts from a semantic category, it determines coreferent pairs and clusters them into chains. MCORES uses an enhanced set of lexical, syntactic, and semantic features. Some MCORES features measure the distance between various representations of the concepts in a pair and can be asymmetric.

Results and Conclusion

MCORES was compared with an in-house baseline that uses only single-perspective ‘token overlap’ and ‘number agreement’ features. MCORES was shown to outperform the baseline; its enhanced features contribute significantly to performance. In addition to the baseline, MCORES was compared against two available third-party, open-domain systems, RECONCILE_ACL09 and the Beautiful Anaphora Resolution Toolkit (BART). MCORES was shown to outperform both of these systems on clinical records.     

Machine learning-based coreference resolution of concepts in clinical documents

Objective

Coreference resolution of concepts, although a very active area in the natural language processing community, has not yet been widely applied to clinical documents. Accordingly, the 2011 i2b2 competition focusing on this area is a timely and useful challenge. The objective of this research was to collate coreferent chains of concepts from a corpus of clinical documents. These concepts are in the categories of person, problems, treatments, and tests.

Design

A machine learning approach based on graphical models was employed to cluster coreferent concepts. Features selected were divided into domain independent and domain specific sets. Training was done with the i2b2 provided training set of 489 documents with 6949 chains. Testing was done on 322 documents.

Results

The learning engine, using the un-weighted average of three different measurement schemes, resulted in an F measure of 0.8423 where no domain specific features were included and 0.8483 where the feature set included both domain independent and domain specific features.

Conclusion

Our machine learning approach is a promising solution for recognizing coreferent concepts, which in turn is useful for practical applications such as the assembly of problem and medication lists from clinical documents.     

Application of statistical machine translation to public health information: a feasibility study

Objective

Accurate, understandable public health information is important for ensuring the health of the nation. The large portion of the US population with Limited English Proficiency is best served by translations of public-health information into other languages. However, a large number of health departments and primary care clinics face significant barriers to fulfilling federal mandates to provide multilingual materials to Limited English Proficiency individuals. This article presents a pilot study on the feasibility of using freely available statistical machine translation technology to translate health promotion materials.

Design

The authors gathered health-promotion materials in English from local and national public-health websites. Spanish versions were created by translating the documents using a freely available machine-translation website. Translations were rated for adequacy and fluency, analyzed for errors, manually corrected by a human posteditor, and compared with exclusively manual translations.

Results

Machine translation plus postediting took 15–53 min per document, compared to the reported days or even weeks for the standard translation process. A blind comparison of machine-assisted and human translations of six documents revealed overall equivalency between machine-translated and manually translated materials. The analysis of translation errors indicated that the most important errors were word-sense errors.

Conclusion

The results indicate that machine translation plus postediting may be an effective method of producing multilingual health materials with equivalent quality but lower cost compared to manual translations.     

Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010

Objective

As clinical text mining continues to mature, its potential as an enabling technology for innovations in patient care and clinical research is becoming a reality. A critical part of that process is rigid benchmark testing of natural language processing methods on realistic clinical narrative. In this paper, the authors describe the design and performance of three state-of-the-art text-mining applications from the National Research Council of Canada on evaluations within the 2010 i2b2 challenge.

Design

The three systems perform three key steps in clinical information extraction: (1) extraction of medical problems, tests, and treatments, from discharge summaries and progress notes; (2) classification of assertions made on the medical problems; (3) classification of relations between medical concepts. Machine learning systems performed these tasks using large-dimensional bags of features, as derived from both the text itself and from external sources: UMLS, cTAKES, and Medline.

Measurements

Performance was measured per subtask, using micro-averaged F-scores, as calculated by comparing system annotations with ground-truth annotations on a test set.

Results

The systems ranked high among all submitted systems in the competition, with the following F-scores: concept extraction 0.8523 (ranked first); assertion detection 0.9362 (ranked first); relationship detection 0.7313 (ranked second).

Conclusion

For all tasks, we found that the introduction of a wide range of features was crucial to success. Importantly, our choice of machine learning algorithms allowed us to be versatile in our feature design, and to introduce a large number of features without overfitting and without encountering computing-resource bottlenecks.     

Coreference resolution of medical concepts in discharge summaries by exploiting contextual information

Objective

Patient discharge summaries provide detailed medical information about hospitalized patients and are a rich resource of data for clinical record text mining. The textual expressions of this information are highly variable. In order to acquire a precise understanding of the patient, it is important to uncover the relationship between all instances in the text. In natural language processing (NLP), this task falls under the category of coreference resolution.

Design

A key contribution of this paper is the application of contextual-dependent rules that describe relationships between coreference pairs. To resolve phrases that refer to the same entity, the authors use these rules in three representative NLP systems: one rule-based, another based on the maximum entropy model, and the last a system built on the Markov logic network (MLN) model.

Results

The experimental results show that the proposed MLN-based system outperforms the baseline system (exact match) by average F-scores of 4.3% and 5.7% on the Beth and Partners datasets, respectively. Finally, the three systems were integrated into an ensemble system, further improving performance to 87.21%, which is 4.5% more than the official i2b2 Track 1C average (82.7%).

Conclusion

In this paper, the main challenges in the resolution of coreference relations in patient discharge summaries are described. Several rules are proposed to exploit contextual information, and three approaches presented. While single systems provided promising results, an ensemble approach combining the three systems produced a better performance than even the best single system.     

Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules

Objective

This paper describes the coreference resolution system submitted by Mayo Clinic for the 2011 i2b2/VA/Cincinnati shared task Track 1C. The goal of the task was to construct a system that links the markables corresponding to the same entity.

Materials and methods

The task organizers provided progress notes and discharge summaries that were annotated with the markables of treatment, problem, test, person, and pronoun. We used a multi-pass sieve algorithm that applies deterministic rules in the order of preciseness and simultaneously gathers information about the entities in the documents. Our system, MedCoref, also uses a state-of-the-art machine learning framework as an alternative to the final, rule-based pronoun resolution sieve.

Results

The best system that uses a multi-pass sieve has an overall score of 0.836 (average of B³, MUC, Blanc, and CEAF F score) for the training set and 0.843 for the test set.

Discussion

A supervised machine learning system that typically uses a single function to find coreferents cannot accommodate irregularities encountered in data especially given the insufficient number of examples. On the other hand, a completely deterministic system could lead to a decrease in recall (sensitivity) when the rules are not exhaustive. The sieve-based framework allows one to combine reliable machine learning components with rules designed by experts.

Conclusion

Using relatively simple rules, part-of-speech information, and semantic type properties, an effective coreference resolution system could be designed. The source code of the system described is available at https://sourceforge.net/projects/ohnlp/files/MedCoref.     

Temporal reasoning over clinical text: the state of the art

Objectives

To provide an overview of the problem of temporal reasoning over clinical text and to summarize the state of the art in clinical natural language processing for this task.

Target audience

This overview targets medical informatics researchers who are unfamiliar with the problems and applications of temporal reasoning over clinical text.

Scope

We review the major applications of text-based temporal reasoning, describe the challenges for software systems handling temporal information in clinical text, and give an overview of the state of the art. Finally, we present some perspectives on future research directions that emerged during the recent community-wide challenge on text-based temporal reasoning in the clinical domain.     

Research and applications: Imaging informatics for consumer health: towards a radiology patient portal

Objective

With the increased routine use of advanced imaging in clinical diagnosis and treatment, it has become imperative to provide patients with a means to view and understand their imaging studies. We illustrate the feasibility of a patient portal that automatically structures and integrates radiology reports with corresponding imaging studies according to several information orientations tailored for the layperson.

Methods

The imaging patient portal is composed of an image processing module for the creation of a timeline that illustrates the progression of disease, a natural language processing module to extract salient concepts from radiology reports (73% accuracy, F₁ score of 0.67), and an interactive user interface navigable by an imaging findings list. The portal was developed as a Java-based web application and is demonstrated for patients with brain cancer.

Results and discussion

The system was exhibited at an international radiology conference to solicit feedback from a diverse group of healthcare professionals. There was wide support for educating patients about their imaging studies, and an appreciation for the informatics tools used to simplify images and reports for consumer interpretation. Primary concerns included the possibility of patients misunderstanding their results, as well as worries regarding accidental improper disclosure of medical information.

Conclusions

Radiologic imaging composes a significant amount of the evidence used to make diagnostic and treatment decisions, yet there are few tools for explaining this information to patients. The proposed radiology patient portal provides a framework for organizing radiologic results into several information orientations to support patient education.     

Use of a support vector machine for categorizing free-text notes: assessment of accuracy across two institutions

Background

Electronic health record (EHR) users must regularly review large amounts of data in order to make informed clinical decisions, and such review is time-consuming and often overwhelming. Technologies like automated summarization tools, EHR search engines and natural language processing have been shown to help clinicians manage this information.

Objective

To develop a support vector machine (SVM)-based system for identifying EHR progress notes pertaining to diabetes, and to validate it at two institutions.

Materials and methods

We retrieved 2000 EHR progress notes from patients with diabetes at the Brigham and Women''s Hospital (1000 for training and 1000 for testing) and another 1000 notes from the University of Texas Physicians (for validation). We manually annotated all notes and trained a SVM using a bag of words approach. We then used the SVM on the testing and validation sets and evaluated its performance with the area under the curve (AUC) and F statistics.

Results

The model accurately identified diabetes-related notes in both the Brigham and Women''s Hospital testing set (AUC=0.956, F=0.934) and the external University of Texas Faculty Physicians validation set (AUC=0.947, F=0.935).

Discussion

Overall, the model we developed was quite accurate. Furthermore, it generalized, without loss of accuracy, to another institution with a different EHR and a distinct patient and provider population.

Conclusions

It is possible to use a SVM-based classifier to identify EHR progress notes pertaining to diabetes, and the model generalizes well.     

Comprehensive temporal information detection from clinical text: medical events,time, and TLINK identification

Background

Temporal information detection systems have been developed by the Mayo Clinic for the 2012 i2b2 Natural Language Processing Challenge.

Objective

To construct automated systems for EVENT/TIMEX3 extraction and temporal link (TLINK) identification from clinical text.

Materials and methods

The i2b2 organizers provided 190 annotated discharge summaries as the training set and 120 discharge summaries as the test set. Our Event system used a conditional random field classifier with a variety of features including lexical information, natural language elements, and medical ontology. The TIMEX3 system employed a rule-based method using regular expression pattern match and systematic reasoning to determine normalized values. The TLINK system employed both rule-based reasoning and machine learning. All three systems were built in an Apache Unstructured Information Management Architecture framework.

Results

Our TIMEX3 system performed the best (F-measure of 0.900, value accuracy 0.731) among the challenge teams. The Event system produced an F-measure of 0.870, and the TLINK system an F-measure of 0.537.

Conclusions

Our TIMEX3 system demonstrated good capability of regular expression rules to extract and normalize time information. Event and TLINK machine learning systems required well-defined feature sets to perform well. We could also leverage expert knowledge as part of the machine learning features to further improve TLINK identification performance.