Uncertainty Detection as Approximate Max-Margin Sequence Labelling

This paper reports experiments for the CoNLL 2010 shared task on learning to detect hedges and their scope in natural language text. We have addressed the experimental tasks as supervised linear maximum margin prediction problems. For sentence level hedge detection in the biological domain we use an L1-regularised binary support vector machine, while for sentence level weasel detection in the Wikipedia domain, we use an L2-regularised approach. We model the in-sentence uncertainty cue and scope detection task as an L2-regularised approximate maximum margin sequence labelling problem, using the BIO-encoding. In addition to surface level features, we use a variety of linguistic features based on a functional dependency analysis. A greedy forward selection strategy is used in exploring the large set of potential features. Our official results for Task 1 for the biological domain are 85.2 F1-score, for the Wikipedia set 55.4 F1-score. For Task 2, our official results are 2.1 for the entire task with a score of 62.5 for cue detection. After resolving errors and final bugs, our final results are for Task 1, biological: 86.0, Wikipedia: 58.2; Task 2, scopes: 39.6 and cues: 78.5

Exploring Different Dimensions of Attention for Uncertainty Detection

Neural networks with attention have proven effective for many natural language processing tasks. In this paper, we develop attention mechanisms for uncertainty detection. In particular, we generalize standardly used attention mechanisms by introducing external attention and sequence-preserving attention. These novel architectures differ from standard approaches in that they use external resources to compute attention weights and preserve sequence information. We compare them to other configurations along different dimensions of attention. Our novel architectures set the new state of the art on a Wikipedia benchmark dataset and perform similar to the state-of-the-art model on a biomedical benchmark which uses a large set of linguistic features.Comment: accepted at EACL 201

Identifying Data Sharing in Biomedical Literature

Many policies and projects now encourage investigators to share their raw research data with other scientists. Unfortunately, it is difficult to measure the effectiveness of these initiatives because data can be shared in such a variety of mechanisms and locations. We propose a novel approach to finding shared datasets: using NLP techniques to identify declarations of dataset sharing within the full text of primary research articles. Using regular expression patterns and machine learning algorithms on open access biomedical literature, our system was able to identify 61% of articles with shared datasets with 80% precision. A simpler version of our classifier achieved higher recall (86%), though lower precision (49%). We believe our results demonstrate the feasibility of this approach and hope to inspire further study of dataset retrieval techniques and policy evaluation.
&#xa

An NLP Analysis of Health Advice Giving in the Medical Research Literature

Health advice – clinical and policy recommendations – plays a vital role in guiding medical practices and public health policies. Whether or not authors should give health advice in medical research publications is a controversial issue. The proponents of actionable research advocate for the more efficient and effective transmission of science evidence into practice. The opponents are concerned about the quality of health advice in individual research papers, especially that in observational studies. Arguments both for and against giving advice in individual studies indicate a strong need for identifying and accessing health advice, for either practical use or quality evaluation purposes. However, current information services do not support the direct retrieval of health advice. Compared to other natural language processing (NLP) applications, health advice has not been computationally modeled as a language construct either. A new information service for directly accessing health advice should be able to reduce information barriers and to provide external assessment in science communication. This dissertation work built an annotated corpus of scientific claims that distinguishes health advice according to its occurrence and strength. The study developed NLP-based prediction models to identify health advice in the PubMed literature. Using the annotated corpus and prediction models, the study answered research questions regarding the practice of advice giving in medical research literature. To test and demonstrate the potential use of the prediction model, it was used to retrieve health advice regarding the use of hydroxychloroquine (HCQ) as a treatment for COVID-19 from LitCovid, a large COVID-19 research literature database curated by the National Institutes of Health. An evaluation of sentences extracted from both abstracts and discussions showed that BERT-based pre-trained language models performed well at detecting health advice. The health advice prediction model may be combined with existing health information service systems to provide more convenient navigation of a large volume of health literature. Findings from the study also show researchers are careful not to give advice solely in abstracts. They also tend to give weaker and non-specific advice in abstracts than in discussions. In addition, the study found that health advice has appeared consistently in the abstracts of observational studies over the past 25 years. In the sample, 41.2% of the studies offered health advice in their conclusions, which is lower than earlier estimations based on analyses of much smaller samples processed manually. In the abstracts of observational studies, journals with a lower impact are more likely to give health advice than those with a higher impact, suggesting the significance of the role of journals as gatekeepers of science communication. For the communities of natural language processing, information science, and public health, this work advances knowledge of the automated recognition of health advice in scientific literature. The corpus and code developed for the study have been made publicly available to facilitate future efforts in health advice retrieval and analysis. Furthermore, this study discusses the ways in which researchers give health advice in medical research articles, knowledge of which could be an essential step towards curbing potential exaggeration in the current global science communication. It also contributes to ongoing discussions of the integrity of scientific output. This study calls for caution in advice-giving in medical research literature, especially in abstracts alone. It also calls for open access to medical research publications, so that health researchers and practitioners can fully review the advice in scientific outputs and its implications. More evaluative strategies that can increase the overall quality of health advice in research articles are needed by journal editors and reviewers, given their gatekeeping role in science communication

Recognizing speculative language in research texts

This thesis studies the use of sequential supervised learning methods on two tasks related to the detection of hedging in scientific articles: those of hedge cue identification and hedge cue scope detection. Both tasks are addressed using a learning methodology that proposes the use of an iterative, error-based approach to improve classification performance, suggesting the incorporation of expert knowledge into the learning process through the use of knowledge rules. Results are promising: for the first task, we improved baseline results by 2.5 points in terms of F-score by incorporating cue cooccurence information, while for scope detection, the incorporation of syntax information and rules for syntax scope pruning allowed us to improve classification performance from an F-score of 0.712 to a final number of 0.835. Compared with state-of-the-art methods, the results are very competitive, suggesting that the approach to improving classifiers based only on the errors commited on a held out corpus could be successfully used in other, similar tasks. Additionaly, this thesis presents a class schema for representing sentence analysis in a unique structure, including the results of different linguistic analysis. This allows us to better manage the iterative process of classifier improvement, where different attribute sets for learning are used in each iteration. We also propose to store attributes in a relational model, instead of the traditional text-based structures, to facilitate learning data analysis and manipulation

Categorising Modality in Biomedical Texts

The accurate recognition of modal information is vital for the correct interpretation of statements. In this paper, we report on the collection a list of words and phrases that express modal information in biomedical texts, and propose a categorisation scheme according to the type of information conveyed. We have performed a small pilot study through the annotation of 202 MEDLINE abstracts according to our proposed scheme. Our initial results suggest that modality in biomedical statements can be predicted fairly reliably though the presence of particular lexical items, together with a small amount of contextual information

Learning on the job: A Webinar Series for Early Career Librarians for Early Career Librarians

The Early Career Librarians Initiative (ECLI) aims to impart valuable professional information to Library Information Science (LIS) students and early career librarians. ECLI noticed a lack of content specific to the challenges and concerns often encountered by early career librarians. In an effort to address this gap, ECLI partnered with Region 3 of the Network of the National Library of Medicine (NNLM) and hosted a three-part webinar series on job searching, setting professional goals, and navigating promotion and tenure. ECLI members will share their experiences about this process, what skills they learned, and how these experiences impacted their professional growt