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Health literacy is a prerequisite to informed health-related decision making. To facilitate understanding of information, text should be presented at an appropriate reading level for the reader. Cognitive studies suggest that the coherence of a text - the interconnectedness between the ideas it expresses - is especially important for low-knowledge readers, who lack the background knowledge to draw inferences from text that is implicitly connected only. Prior work in cognitive science has yielded automated methods to estimate coherence. These methods estimate the proximity between text representations in a semantic vector space, with the underlying idea that units of text that are poorly connected will be further apart in this space. In addition, recent work with large language models (LLMs) has produced probabilistic methodological analogues that have yet to be evaluated for this purpose. This work concerns the relationship between these automated measures and layperson comprehension of biomedical text. To characterize this relationship, we applied a range of automated measures of text coherence to a set of text snippets, some of which were deliberately modified to improve their accessibility in a series of reading comprehension experiments. Results indicate significant associations between reader comprehension - as estimated using multiple-choice questions - and LLM-derived coherence metrics. Interventions designed to improve the comprehensibility of passages also improved their coherence, as measured with the best-performing LLM-derived models and shown by improved reader understanding of the text. These findings support the utility of LLM-derived measures of text coherence as a means to identify gaps in connectedness that make biomedical text difficult for laypeople to understand, with the potential to inform both manual and automated methods to improve the accessibility of the biomedical literature., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Author TC serves on the editorial board for the Journal of Biomedical Informatics If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Inc.)

Many approaches in biomedical informatics (BMI) rely on the ability to define, gather, and manipulate biomedical data to support health through a cyclical research-practice lifecycle. Researchers within this field are often fortunate to work closely with healthcare and public health systems to influence data generation and capture and have access to a vast amount of biomedical data. Many informaticists also have the expertise to engage with stakeholders, develop new methods and applications, and influence policy. However, research and policy that explicitly seeks to address the systemic drivers of health would more effectively support health. Intersectionality is a theoretical framework that can facilitate such research. It holds that individual human experiences reflect larger socio-structural level systems of privilege and oppression, and cannot be truly understood if these systems are examined in isolation. Intersectionality explicitly accounts for the interrelated nature of systems of privilege and oppression, providing a lens through which to examine and challenge inequities. In this paper, we propose intersectionality as an intervention into how we conduct BMI research. We begin by discussing intersectionality's history and core principles as they apply to BMI. We then elaborate on the potential for intersectionality to stimulate BMI research. Specifically, we posit that our efforts in BMI to improve health should address intersectionality's five key considerations: (1) systems of privilege and oppression that shape health; (2) the interrelated nature of upstream health drivers; (3) the nuances of health outcomes within groups; (4) the problematic and power-laden nature of categories that we assign to people in research and in society; and (5) research to inform and support social change., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Objectives: We aimed to investigate how errors from automatic speech recognition (ASR) systems affect dementia classification accuracy, specifically in the "Cookie Theft" picture description task. We aimed to assess whether imperfect ASR-generated transcripts could provide valuable information for distinguishing between language samples from cognitively healthy individuals and those with Alzheimer's disease (AD)., Methods: We conducted experiments using various ASR models, refining their transcripts with post-editing techniques. Both these imperfect ASR transcripts and manually transcribed ones were used as inputs for the downstream dementia classification. We conducted comprehensive error analysis to compare model performance and assess ASR-generated transcript effectiveness in dementia classification., Results: Imperfect ASR-generated transcripts surprisingly outperformed manual transcription for distinguishing between individuals with AD and those without in the "Cookie Theft" task. These ASR-based models surpassed the previous state-of-the-art approach, indicating that ASR errors may contain valuable cues related to dementia. The synergy between ASR and classification models improved overall accuracy in dementia classification., Conclusion: Imperfect ASR transcripts effectively capture linguistic anomalies linked to dementia, improving accuracy in classification tasks. This synergy between ASR and classification models underscores ASR's potential as a valuable tool in assessing cognitive impairment and related clinical applications., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Changye Li reports financial support was provided by National Institute on Aging. Dr. Trevor Cohen is a member of the JBI Editorial Board. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The complex linguistic structures and specialized terminology of expert-authored content limit the accessibility of biomedical literature to the general public. Automated methods have the potential to render this literature more interpretable to readers with different educational backgrounds. Prior work has framed such lay language generation as a summarization or simplification task. However, adapting biomedical text for the lay public includes the additional and distinct task of background explanation: adding external content in the form of definitions, motivation, or examples to enhance comprehensibility. This task is especially challenging because the source document may not include the required background knowledge. Furthermore, background explanation capabilities have yet to be formally evaluated, and little is known about how best to enhance them. To address this problem, we introduce Retrieval-Augmented Lay Language (RALL) generation, which intuitively fits the need for external knowledge beyond that in expert-authored source documents. In addition, we introduce CELLS, the largest (63k pairs) and broadest-ranging (12 journals) parallel corpus for lay language generation. To evaluate RALL, we augmented state-of-the-art text generation models with information retrieval of either term definitions from the UMLS and Wikipedia, or embeddings of explanations from Wikipedia documents. Of these, embedding-based RALL models improved summary quality and simplicity while maintaining factual correctness, suggesting that Wikipedia is a helpful source for background explanation in this context. We also evaluated the ability of both an open-source Large Language Model (Llama 2) and a closed-source Large Language Model (GPT-4) in background explanation, with and without retrieval augmentation. Results indicate that these LLMs can generate simplified content, but that the summary quality is not ideal. Taken together, this work presents the first comprehensive study of background explanation for lay language generation, paving the path for disseminating scientific knowledge to a broader audience. Our code and data are publicly available at: https://github.com/LinguisticAnomalies/pls_retrieval., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Dr. Trevor Cohen is a member of the JBI Editorial Board., (Copyright © 2023. Published by Elsevier Inc.)

Background: Online health communities (OHCs) have emerged as prominent platforms for behavior modification, and the digitization of online peer interactions has afforded researchers with unique opportunities to model multilevel mechanisms that drive behavior change. Existing studies, however, have been limited by a lack of methods that allow the capture of conversational context and socio-behavioral dynamics at scale, as manifested in these digital platforms., Objective: We develop, evaluate, and apply a novel methodological framework, Pragmatics to Reveal Intent in Social Media (PRISM), to facilitate granular characterization of peer interactions by combining multidimensional facets of human communication., Methods: We developed and applied PRISM to analyze peer interactions (N = 2.23 million) in QuitNet, an OHC for tobacco cessation. First, we generated a labeled set of peer interactions (n = 2,005) through manual annotation along three dimensions: communication themes (CTs), behavior change techniques (BCTs), and speech acts (SAs). Second, we used deep learning models to apply our qualitative codes at scale. Third, we applied our validated model to perform a retrospective analysis. Finally, using social network analysis (SNA), we portrayed large-scale patterns and relationships among the aforementioned communication dimensions embedded in peer interactions in QuitNet., Results: Qualitative analysis showed that the themes of social support and behavioral progress were common. The most used BCTs were feedback and monitoring and comparison of behavior, and users most commonly expressed their intentions using SAs-expressive and emotion. With additional in-domain pre-training, bidirectional encoder representations from Transformers (BERT) outperformed other deep learning models on the classification tasks. Content-specific SNA revealed that users' engagement or abstinence status is associated with the prevalence of various categories of BCTs and SAs, which also was evident from the visualization of network structures., Conclusions: Our study describes the interplay of multilevel characteristics of online communication and their association with individual health behaviors., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Formal thought disorder (ThD) is a clinical sign of schizophrenia amongst other serious mental health conditions. ThD can be recognized by observing incoherent speech - speech in which it is difficult to perceive connections between successive utterances and lacks a clear global theme. Automated assessment of the coherence of speech in patients with schizophrenia has been an active area of research for over a decade, in an effort to develop an objective and reliable instrument through which to quantify ThD. However, this work has largely been conducted in controlled settings using structured interviews and depended upon manual transcription services to render audio recordings amenable to computational analysis. In this paper, we present an evaluation of such automated methods in the context of a fully automated system using Automated Speech Recognition (ASR) in place of a manual transcription service, with "audio diaries" collected in naturalistic settings from participants experiencing Auditory Verbal Hallucinations (AVH). We show that performance lost due to ASR errors can often be restored through the application of Time-Series Augmented Representations for Detection of Incoherent Speech (TARDIS), a novel approach that involves treating the sequence of coherence scores from a transcript as a time-series, providing features for machine learning. With ASR, TARDIS improves average AUC across coherence metrics for detection of severe ThD by 0.09; average correlation with human-labeled derailment scores by 0.10; and average correlation between coherence estimates from manual and ASR-derived transcripts by 0.29. In addition, TARDIS improves the agreement between coherence estimates from manual transcripts and human judgment and correlation with self-reported estimates of AVH symptom severity. As such, TARDIS eliminates a fundamental barrier to the deployment of automated methods to detect linguistic indicators of ThD to monitor and improve clinical care in serious mental illness., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Adverse Drug Events (ADEs) are prevalent, costly, and sometimes preventable. Post-marketing drug surveillance aims to monitor ADEs that occur after a drug is released to market. Reports of such ADEs are aggregated by reporting systems, such as the Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS). In this paper, we consider the topic of how best to represent data derived from reports in FAERS for the purpose of detecting post-marketing surveillance signals, in order to inform regulatory decision making. In our previous work, we developed aer2vec, a method for deriving distributed representations (concept embeddings) of drugs and side effects from ADE reports, establishing the utility of distributional information for pharmacovigilance signal detection. In this paper, we advance this line of research further by evaluating the utility of encoding orthographic and lexical information. We do so by adapting two Natural Language Processing methods, subword embedding and vector retrofitting, which were developed to encode such information into word embeddings. Models were compared for their ability to distinguish between positive and negative examples in a set of manually curated drug/ADE relationships, with both aer2vec enhancements offering advantages in performances over baseline models, and best performance obtained when retrofitting and subword embeddings were applied in concert. In addition, this work demonstrates that models leveraging distributed representations do not require extensive manual preprocessing to perform well on this pharmacovigilance signal detection task, and may even benefit from information that would otherwise be lost during the normalization and standardization process., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Introduction: Drug safety research asks causal questions but relies on observational data. Confounding bias threatens the reliability of studies using such data. The successful control of confounding requires knowledge of variables called confounders affecting both the exposure and outcome of interest. However, causal knowledge of dynamic biological systems is complex and challenging. Fortunately, computable knowledge mined from the literature may hold clues about confounders. In this paper, we tested the hypothesis that incorporating literature-derived confounders can improve causal inference from observational data., Methods: We introduce two methods (semantic vector-based and string-based confounder search) that query literature-derived information for confounder candidates to control, using SemMedDB, a database of computable knowledge mined from the biomedical literature. These methods search SemMedDB for confounders by applying semantic constraint search for indications treated by the drug (exposure) and that are also known to cause the adverse event (outcome). We then include the literature-derived confounder candidates in statistical and causal models derived from free-text clinical notes. For evaluation, we use a reference dataset widely used in drug safety containing labeled pairwise relationships between drugs and adverse events and attempt to rediscover these relationships from a corpus of 2.2 M NLP-processed free-text clinical notes. We employ standard adjustment and causal inference procedures to predict and estimate causal effects by informing the models with varying numbers of literature-derived confounders and instantiating the exposure, outcome, and confounder variables in the models with dichotomous EHR-derived data. Finally, we compare the results from applying these procedures with naive measures of association (χ 2 and reporting odds ratio) and with each other., Results and Conclusions: We found semantic vector-based search to be superior to string-based search at reducing confounding bias. However, the effect of including more rather than fewer literature-derived confounders was inconclusive. We recommend using targeted learning estimation methods that can address treatment-confounder feedback, where confounders also behave as intermediate variables, and engaging subject-matter experts to adjudicate the handling of problematic covariates., (Published by Elsevier Inc.)

This study demonstrates the use of distributed vector representations and Pathfinder Network Scaling (PFNETS) to represent online vaccine content created by health experts and by laypeople. By analyzing a target audience's conceptualization of a topic, domain experts can develop targeted interventions to improve the basic health knowledge of consumers. The underlying assumption is that the content created by different groups reflects the mental organization of their knowledge. Applying automated text analysis to this content may elucidate differences between the knowledge structures of laypeople (heath consumers) and professionals (health experts). This paper utilizes vaccine information generated by laypeople and health experts to investigate the utility of this approach. We used an established technique from cognitive psychology, Pathfinder Network Scaling to infer the structure of the associational networks between concepts learned from online content using methods of distributional semantics. In doing so, we extend the original application of PFNETS to infer knowledge structures from individual participants, to infer the prevailing knowledge structures within communities of content authors. The resulting graphs reveal opportunities for public health and vaccination education experts to improve communication and intervention efforts directed towards health consumers. Our efforts demonstrate the feasibility of using an automated procedure to examine the manifestation of conceptual models within large bodies of free text, revealing evidence of conflicting understanding of vaccine concepts among health consumers as compared with health experts. Additionally, this study provides insight into the differences between consumer and expert abstraction of domain knowledge, revealing vaccine-related knowledge gaps that suggest opportunities to improve provider-patient communication., (Copyright © 2017 Elsevier Inc. All rights reserved.)

This paper concerns the generation of distributed vector representations of biomedical concepts from structured knowledge, in the form of subject-relation-object triplets known as semantic predications. Specifically, we evaluate the extent to which a representational approach we have developed for this purpose previously, known as Predication-based Semantic Indexing (PSI), might benefit from insights gleaned from neural-probabilistic language models, which have enjoyed a surge in popularity in recent years as a means to generate distributed vector representations of terms from free text. To do so, we develop a novel neural-probabilistic approach to encoding predications, called Embedding of Semantic Predications (ESP), by adapting aspects of the Skipgram with Negative Sampling (SGNS) algorithm to this purpose. We compare ESP and PSI across a number of tasks including recovery of encoded information, estimation of semantic similarity and relatedness, and identification of potentially therapeutic and harmful relationships using both analogical retrieval and supervised learning. We find advantages for ESP in some, but not all of these tasks, revealing the contexts in which the additional computational work of neural-probabilistic modeling is justified., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Objective: We develop and evaluate a methodological approach to measure the degree and nature of overlap in handoff communication content within and across clinical professions. This extensible, exploratory approach relies on combining techniques from conversational analysis and distributional semantics., Materials and Methods: We audio-recorded handoff communication of residents and nurses on the General Medicine floor of a large academic hospital (n=120 resident and n=120 nurse handoffs). We measured semantic similarity, a proxy for content overlap, between resident-resident and nurse-nurse communication using multiple steps: a qualitative conversational content analysis; an automated semantic similarity analysis using Reflective Random Indexing (RRI); and comparing semantic similarity generated by RRI analysis with human ratings of semantic similarity., Results: There was significant association between the semantic similarity as computed by the RRI method and human rating (ρ=0.88). Based on the semantic similarity scores, content overlap was relatively higher for content related to patient active problems, assessment of active problems, patient-identifying information, past medical history, and medications/treatments. In contrast, content overlap was limited on content related to allergies, family-related information, code status, and anticipatory guidance., Conclusions: Our approach using RRI analysis provides new opportunities for characterizing the nature and degree of overlap in handoff communication. Although exploratory, this method provides a basis for identifying content that can be used for determining shared understanding across clinical professions. Additionally, this approach can inform the development of flexibly standardized handoff tools that reflect clinical content that are most appropriate for fostering shared understanding during transitions of care., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Objective: To evaluate whether vector representations encoding latent topic proportions that capture similarities to MeSH terms can improve performance on biomedical document retrieval and classification tasks, compared to using MeSH terms., Materials and Methods: We developed the TopicalMeSH representation, which exploits the 'correspondence' between topics generated using latent Dirichlet allocation (LDA) and MeSH terms to create new document representations that combine MeSH terms and latent topic vectors. We used 15 systematic drug review corpora to evaluate performance on information retrieval and classification tasks using this TopicalMeSH representation, compared to using standard encodings that rely on either (1) the original MeSH terms, (2) the text, or (3) their combination. For the document retrieval task, we compared the precision and recall achieved by ranking citations using MeSH and TopicalMeSH representations, respectively. For the classification task, we considered three supervised machine learning approaches, Support Vector Machines (SVMs), logistic regression, and decision trees. We used these to classify documents as relevant or irrelevant using (independently) MeSH, TopicalMeSH, Words (i.e., n-grams extracted from citation titles and abstracts, encoded via bag-of-words representation), a combination of MeSH and Words, and a combination of TopicalMeSH and Words. We also used SVM to compare the classification performance of tf-idf weighted MeSH terms, LDA Topics, a combination of Topics and MeSH, and TopicalMeSH to supervised LDA's classification performance., Results: For the document retrieval task, using the TopicalMeSH representation resulted in higher precision than MeSH in 11 of 15 corpora while achieving the same recall. For the classification task, use of TopicalMeSH features realized a higher F1 score in 14 of 15 corpora when used by SVMs, 12 of 15 corpora using logistic regression, and 12 of 15 corpora using decision trees. TopicalMeSH also had better document classification performance on 12 of 15 corpora when compared to Topics, tf-idf weighted MeSH terms, and a combination of Topics and MeSH using SVMs. Supervised LDA achieved the worst performance in most of the corpora., Conclusion: The proposed TopicalMeSH representation (which combines MeSH terms with latent topics) consistently improved performance on document retrieval and classification tasks, compared to using alternative standard representations using MeSH terms alone, as well as, several standard alternative approaches., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Pharmacovigilance involves continually monitoring drug safety after drugs are put to market. To aid this process; algorithms for the identification of strongly correlated drug/adverse drug reaction (ADR) pairs from data sources such as adverse event reporting systems or Electronic Health Records have been developed. These methods are generally statistical in nature, and do not draw upon the large volumes of knowledge embedded in the biomedical literature. In this paper, we investigate the ability of scalable Literature Based Discovery (LBD) methods to identify side effects of pharmaceutical agents. The advantage of LBD methods is that they can provide evidence from the literature to support the plausibility of a drug/ADR association, thereby assisting human review to validate the signal, which is an essential component of pharmacovigilance. To do so, we draw upon vast repositories of knowledge that has been extracted from the biomedical literature by two Natural Language Processing tools, MetaMap and SemRep. We evaluate two LBD methods that scale comfortably to the volume of knowledge available in these repositories. Specifically, we evaluate Reflective Random Indexing (RRI), a model based on concept-level co-occurrence, and Predication-based Semantic Indexing (PSI), a model that encodes the nature of the relationship between concepts to support reasoning analogically about drug-effect relationships. An evaluation set was constructed from the Side Effect Resource 2 (SIDER2), which contains known drug/ADR relations, and models were evaluated for their ability to "rediscover" these relations. In this paper, we demonstrate that both RRI and PSI can recover known drug-adverse event associations. However, PSI performed better overall, and has the additional advantage of being able to recover the literature underlying the reasoning pathways it used to make its predictions., (Copyright © 2014 Elsevier Inc. All rights reserved.)

In this paper we utilize methods of hyperdimensional computing to mediate the identification of therapeutically useful connections for the purpose of literature-based discovery. Our approach, named Predication-based Semantic Indexing, is utilized to identify empirically sequences of relationships known as "discovery patterns", such as "drug x INHIBITS substance y, substance y CAUSES disease z" that link pharmaceutical substances to diseases they are known to treat. These sequences are derived from semantic predications extracted from the biomedical literature by the SemRep system, and subsequently utilized to direct the search for known treatments for a held out set of diseases. Rapid and efficient inference is accomplished through the application of geometric operators in PSI space, allowing for both the derivation of discovery patterns from a large set of known TREATS relationships, and the application of these discovered patterns to constrain search for therapeutic relationships at scale. Our results include the rediscovery of discovery patterns that have been constructed manually by other authors in previous research, as well as the discovery of a set of previously unrecognized patterns. The application of these patterns to direct search through PSI space results in better recovery of therapeutic relationships than is accomplished with models based on distributional statistics alone. These results demonstrate the utility of efficient approximate inference in geometric space as a means to identify therapeutic relationships, suggesting a role of these methods in drug repurposing efforts. In addition, the results provide strong support for the utility of the discovery pattern approach pioneered by Hristovski and his colleagues., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Major Depressive Disorder (MDD) and Posttraumatic Stress Disorder (PTSD) are highly prevalent illnesses, but the literature suggests they are under-detected and suboptimally managed by primary care practitioners (PCPs). In this paper, we propose and use an evaluation method, using digitally simulated patients (avatars) to evaluate the diagnostic and therapeutic reasoning of PCPs and compared it to the traditional use of paper-based cases. Verbal (think-aloud) protocols were captured in the context of a diagnostic and therapeutic reasoning task. Propositional and semantic representational analysis of simulation data during evaluation, showed specific deficiencies in PCP reasoning, suggesting a promise of this technology in training and evaluation in mental health. Avatars are flexible and easily modifiable and are also a cost-effective and easy-to-disseminate educational tool., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Extracting 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., (Copyright © 2011 Elsevier Inc. All rights reserved.)

A recent trend in the literature has been to characterize healthcare activities in terms of complex systems theory. Complexity has often been loosely and variously defined, with meanings ranging from "not simple" to "complicated" to "intractable." In this paper, we consider various aspects of complexity and how they relate to modern healthcare practice, with the aim of developing research approaches for studying complex healthcare environments. We propose a theoretical lens for understanding and studying complexity in healthcare systems based on degrees of interrelatedness of system components. We also describe, with relevant caveats, how complex healthcare systems are generally decomposable, rendering them more tractable for further study. The ideas of interrelatedness among the components of a system as a measure of complexity and functional decomposition as a mechanism for studying meaningful subcomponents of a complex system can be used as a framework for understanding complex healthcare systems. Using examples drawn from current literature and our own research, we explain the feasibility of this approach for understanding, studying, and managing complex healthcare systems., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Lapses in patient safety have been linked to unexpected perturbations in clinical workflow. The effectiveness of workflow analysis becomes critical to understanding the impact of these perturbations on patient outcome. The typical methods used for workflow analysis, such as ethnographic observations and interviewing, are limited in their ability to capture activities from different perspectives simultaneously. This limitation, coupled with the complexity and dynamic nature of clinical environments makes understanding the nuances of clinical workflow difficult. The methods proposed in this research aim to provide a quantitative means of capturing and analyzing workflow. The approach taken utilizes recordings of motion and location of clinical teams that are gathered using radio identification tags and observations. This data is used to model activities in critical care environments. The detected activities can then be replayed in 3D virtual reality environments for further analysis and training. Using this approach, the proposed system augments existing methods of workflow analysis, allowing for capture of workflow in complex and dynamic environments. The system was tested with a set of 15 simulated clinical activities that when combined represent workflow in trauma units. A mean recognition rate of 87.5% was obtained in automatically recognizing the activities., (Copyright © 2010 Elsevier Inc. All rights reserved.)

The notion that human error should not be tolerated is prevalent in both the public and personal perception of the performance of clinicians. However, researchers in other safety-critical domains have long since abandoned the quest for zero defects as an impractical goal, choosing to focus instead on the development of strategies to enhance the ability to recover from error. This paper presents a cognitive framework for the study of error recovery, and the results of our empirical research into error detection and recovery in the critical care domain, using both laboratory-based and naturalistic approaches. Both attending physicians and residents were prone to commit, detect and recover from errors, but the nature of these errors was different. Experts corrected the errors as soon as they detected them and were better able to detect errors requiring integration of multiple elements in the case. Residents were more cautious in making decisions showing a slower error recovery pattern, and the detected errors were more procedural in nature with specific patient outcomes. Error detection and correction are shown to be dependent on expertise, and on the nature of the everyday tasks of the clinicians concerned. Understanding the limits and failures of human decision-making is important if we are to build robust decision-support systems to manage the boundaries of risk of error in decision-making. Detection and correction of potential error is an integral part of cognitive work in the complex, critical care workplace., (Copyright © 2010 Elsevier Inc. All rights reserved.)

In many respects, the critical care workplace resembles a paradigmatic complex system: on account of the dynamic and interactive nature of collaborative clinical work, these settings are characterized by non-linear, inter-dependent and emergent activities. Developing a comprehensive understanding of the work activities in critical care settings enables the development of streamlined work practices, better clinician workflow and most importantly, helps in the avoidance of and recovery from potential errors. Sensor-based technology provides a flexible and viable way to complement human observations by providing a mechanism to capture the nuances of certain activities with greater precision and timing. In this paper, we use sensor-based technology to capture the movement and interactions of clinicians in the Trauma Center of an Emergency Department (ED). Remarkable consistency was found between sensor data and human observations in terms of clinician locations and interactions. With this validation and greater precision with sensors, ED environment was characterized in terms of (a) the degree of randomness or entropy in the environment, (b) the movement patterns of clinicians, (c) interactions with other clinicians and finally, (d) patterns of collaborative organization with team aggregation and dispersion. Based on our results, we propose three opportunities for the use of sensor technologies in critical care settings: as a mechanism for real-time monitoring and analysis for ED activities, education and training of clinicians, and perhaps most importantly, investigating the root-causes, origins and progression of errors in the ED. Lessons learned and the challenges encountered in designing and implementing the sensor technology sensor data are discussed., (Copyright © 2011 Elsevier Inc. All rights reserved.)

The rapid growth of biomedical literature is evident in the increasing size of the MEDLINE research database. Medical Subject Headings (MeSH), a controlled set of keywords, are used to index all the citations contained in the database to facilitate search and retrieval. This volume of citations calls for efficient tools to assist indexers at the US National Library of Medicine (NLM). Currently, the Medical Text Indexer (MTI) system provides assistance by recommending MeSH terms based on the title and abstract of an article using a combination of distributional and vocabulary-based methods. In this paper, we evaluate a novel approach toward indexer assistance by using nearest neighbor classification in combination with Reflective Random Indexing (RRI), a scalable alternative to the established methods of distributional semantics. On a test set provided by the NLM, our approach significantly outperforms the MTI system, suggesting that the RRI approach would make a useful addition to the current methodologies.

The discovery of implicit connections between terms that do not occur together in any scientific document underlies the model of literature-based knowledge discovery first proposed by Swanson. Corpus-derived statistical models of semantic distance such as Latent Semantic Analysis (LSA) have been evaluated previously as methods for the discovery of such implicit connections. However, LSA in particular is dependent on a computationally demanding method of dimension reduction as a means to obtain meaningful indirect inference, limiting its ability to scale to large text corpora. In this paper, we evaluate the ability of Random Indexing (RI), a scalable distributional model of word associations, to draw meaningful implicit relationships between terms in general and biomedical language. Proponents of this method have achieved comparable performance to LSA on several cognitive tasks while using a simpler and less computationally demanding method of dimension reduction than LSA employs. In this paper, we demonstrate that the original implementation of RI is ineffective at inferring meaningful indirect connections, and evaluate Reflective Random Indexing (RRI), an iterative variant of the method that is better able to perform indirect inference. RRI is shown to lead to more clearly related indirect connections and to outperform existing RI implementations in the prediction of future direct co-occurrence in the MEDLINE corpus., (2009 Elsevier Inc. All rights reserved.)

Over the past 15 years, a range of methods have been developed that are able to learn human-like estimates of the semantic relatedness between terms from the way in which these terms are distributed in a corpus of unannotated natural language text. These methods have also been evaluated in a number of applications in the cognitive science, computational linguistics and the information retrieval literatures. In this paper, we review the available methodologies for derivation of semantic relatedness from free text, as well as their evaluation in a variety of biomedical and other applications. Recent methodological developments, and their applicability to several existing applications are also discussed.

Cognitive studies reveal that less-than-expert clinicians are less able to recognize meaningful patterns of data in clinical narratives. Accordingly, psychiatric residents early in training fail to attend to information that is relevant to diagnosis and the assessment of dangerousness. This manuscript presents cognitively motivated methodology for the simulation of expert ability to organize relevant findings supporting intermediate diagnostic hypotheses. Latent Semantic Analysis is used to generate a semantic space from which meaningful associations between psychiatric terms are derived. Diagnostically meaningful clusters are modeled as geometric structures within this space and compared to elements of psychiatric narrative text using semantic distance measures. A learning algorithm is defined that alters components of these geometric structures in response to labeled training data. Extraction and classification of relevant text segments is evaluated against expert annotation, with system-rater agreement approximating rater-rater agreement. A range of biomedical informatics applications for these methods are suggested.