Codelists play a crucial role in ensuring accurate and standardized communication within healthcare. However, preparation of high-quality codelists is a rigorous and time-consuming process. The literature focuses on transparency of clinical codelists and overlooks the utility of automation. Here we present a Codelist Generation Framework that can automate generation of codelists with minimal input from clinical experts. We demonstrate the process using a specific project, DynAIRx, producing appropriate codelists and a framework allowing future projects to take advantage of automated codelist generation. Both the framework and codelist are publicly available. DynAIRx is an NIHR-funded project aiming to develop AIs to help optimise prescribing of medicines in patients with multiple long-term conditions. DynAIRx requires complex codelists to describe the trajectory of each patient, and the interaction between their conditions. We promptly generated ≈ 214 codelists for DynAIRx using the proposed framework and validated them with a panel of experts, significantly reducing the amount of time required by making effective use of automation. The framework reduced the clinician time required to validate codes, automatically shrunk codelists using trusted sources and added new codes for review against existing codelists. In the DynAIRx case study, a codelist of ≈ 14000 codes required only 7-9 hours of clinician’s time in the end (while existing methods takes months), and application of the automation framework reduced the workload by >80

Adapting language models (LMs) to novel domains is often achieved through fine-tuning a pre-trained LM (PLM) on domain-specific data. Fine-tuning introduces new knowledge into an LM, enabling it to comprehend and efficiently perform a target domain task. Fine-tuning can however be inadvertently insensitive if it ignores the wide array of disparities (e.g in word meaning) between source and target domains. For instance, words such as chronic and pressure may be treated lightly in social conversations, however, clinically, these words are usually an expression of concern. To address insensitive fine-tuning, we propose Mask Specific Language Modeling (MSLM), an approach that efficiently acquires target domain knowledge by appropriately weighting the importance of domain-specific terms (DS-terms) during fine-tuning. MSLM jointly masks DS-terms and generic words, then learns mask-specific losses by ensuring LMs incur larger penalties for inaccurately predicting DS-terms compared to generic words. Results of our analysis show that MSLM improves LMs sensitivity and detection of DS-terms. We empirically show that an optimal masking rate not only depends on the LM, but also on the dataset and the length of sequences. Our proposed masking strategy outperforms advanced masking strategies such as span- and PMI-based masking.

Injecting textual information into knowledge graph (KG) entity representations has been a worthwhile expedition in terms of improving performance in KG oriented tasks within the NLP community. External knowledge often adopted to enhance KG embeddings ranges from semantically rich lexical dependency parsed features to a set of relevant key words to entire text descriptions supplied from an external corpus such as wikipedia and many more. Despite the gains this innovation (Text-enhanced KG embeddings) has made, the proposal in this work suggests that it can be improved even further. Instead of using a single text description (which would not sufficiently represent an entity because of the inherent lexical ambiguity of text), we propose a multi-task framework that jointly selects a set of text descriptions relevant to KG entities as well as align or augment KG embeddings with text descriptions. Different from prior work that plugs formal entity descriptions declared in knowledge bases, this framework leverages a retriever model to selectively identify richer or highly relevant text descriptions to use in augmenting entities. Furthermore, the framework treats the number of descriptions to use in augmentation process as a parameter, which allows the flexibility of enumerating across several numbers before identifying an appropriate number. Experiment results for Link Prediction demonstrate a 5.5% and 3.5% percentage increase in the Mean Reciprocal Rank (MRR) and Hits@10 scores respectively, in comparison to text-enhanced knowledge graph augmentation methods using traditional CNNs.

Automating the recognition of outcomes reported in clinical trials using machine learning has a huge potential of speeding up access to evidence necessary in healthcare decision-making. Prior research has however acknowledged inadequate training corpora as a challenge for the Outcome detection (OD) task. Additionally, several contextualized representations like BERT and ELMO have achieved unparalleled success in detecting various diseases, genes, proteins, and chemicals, however, the same cannot be emphatically stated for outcomes, because these models have been relatively under-tested and studied for the OD task. We introduce"EBM-COMET", a dataset in which 300 PubMed abstracts are expertly annotated for clinical outcomes. Unlike prior related datasets that use arbitrary outcome classifications, we use labels from a taxonomy recently published to standardize outcome classifications. To extract outcomes, we fine-tune a variety of pre-trained contextualized representations, additionally, we use frozen contextualized and context-independent representations in our custom neural model augmented with clinically informed Part-Of-Speech embeddings and a cost-sensitive loss function. We adopt strict evaluation for the trained models by rewarding them for correctly identifying full outcome phrases rather than words within the entities i.e. given an outcome"systolic blood pressure", the models are rewarded a classification score only when they predict all 3 words in sequence, otherwise, they are not rewarded. We observe our best model (BioBERT) achieve 81.5\% F1, 81.3\% sensitivity and 98.0\% specificity. We reach a consensus on which contextualized representations are best suited for detecting outcomes from clinical-trial abstracts. Furthermore, our best model outperforms scores published on the original EBM-NLP dataset leader-board scores.

Probing Pre-trained Language Models (PLMs) using prompts has indirectly implied that language models (LMs) can be treated as knowledge bases. To this end, this phenomena has been effective especially when these LMs are fine-tuned towards not just data of a specific domain, but also to the style or linguistic pattern of the prompts themselves. We observe that, satisfying a particular linguistic pattern in prompts is an unsustainable constraint that unnecessarily lengthens the probing task, especially because, they are often manually designed and the range of possible prompt template patterns can vary depending on the prompting objective and domain. We therefore explore an idea of using a position-attention mechanism to capture positional information of each word in a prompt relative to the mask to be filled, hence avoiding the need to re-construct prompts when the prompts linguistic pattern changes. Using our approach, we demonstrate the ability of eliciting answers to rare prompt templates (in a case study on health outcome generation) such as Postfix and Mixed patterns whose missing information is respectively at the start and in multiple random places of the prompt. More so, using various biomedical PLMs, our approach consistently outperforms a baseline in which the default mask language model (MLM) representation is used to predict masked tokens.

A health outcome is a measurement or an observation used to capture and assess the effect of a treatment. Automatic detection of health outcomes from text would undoubtedly speed up access to evidence necessary in healthcare decision making. Prior work on outcome detection has modelled this task as either (a) a sequence labelling task, where the goal is to detect which text spans describe health outcomes, or (b) a classification task, where the goal is to classify a text into a pre-defined set of categories depending on an outcome that is mentioned somewhere in that text. However, this decoupling of span detection and classification is problematic from a modelling perspective and ignores global structural correspondences between sentence-level and word-level information present in a given text. To address this, we propose a method that uses both word-level and sentence-level information to simultaneously perform outcome span detection and outcome type classification. In addition to injecting contextual information to hidden vectors, we use label attention to appropriately weight both word and sentence level information. Experimental results on several benchmark datasets for health outcome detection show that our proposed method consistently outperforms decoupled methods, reporting competitive results.

© 2019 for this paper by its authors. The validity and authenticity of annotations in datasets massively influences the performance of Natural Language Processing (NLP) systems. In other words, poorly annotated datasets are likely to produce fatal results in at-least most NLP problems hence misinforming consumers of these models, systems or applications. This is a bottleneck in most domains, especially in healthcare where crowdsourcing is a popular strategy in obtaining annotations. In this paper, we present a framework that automatically corrects incorrectly captured annotations of outcomes, thereby improving the quality of the crowdsourced annotations. We investigate a publicly available dataset called EBM-NLP, built to power NLP tasks in support of Evidence based Medicine (EBM) primarily focusing on health outcomes.