Iain Marshall

Also published as: Iain J. Marshall


2021

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Paragraph-level Simplification of Medical Texts
Ashwin Devaraj | Iain Marshall | Byron Wallace | Junyi Jessy Li
Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

We consider the problem of learning to simplify medical texts. This is important because most reliable, up-to-date information in biomedicine is dense with jargon and thus practically inaccessible to the lay audience. Furthermore, manual simplification does not scale to the rapidly growing body of biomedical literature, motivating the need for automated approaches. Unfortunately, there are no large-scale resources available for this task. In this work we introduce a new corpus of parallel texts in English comprising technical and lay summaries of all published evidence pertaining to different clinical topics. We then propose a new metric based on likelihood scores from a masked language model pretrained on scientific texts. We show that this automated measure better differentiates between technical and lay summaries than existing heuristics. We introduce and evaluate baseline encoder-decoder Transformer models for simplification and propose a novel augmentation to these in which we explicitly penalize the decoder for producing “jargon” terms; we find that this yields improvements over baselines in terms of readability.

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What Would it Take to get Biomedical QA Systems into Practice?
Gregory Kell | Iain Marshall | Byron Wallace | Andre Jaun
Proceedings of the 3rd Workshop on Machine Reading for Question Answering

Medical question answering (QA) systems have the potential to answer clinicians’ uncertainties about treatment and diagnosis on-demand, informed by the latest evidence. However, despite the significant progress in general QA made by the NLP community, medical QA systems are still not widely used in clinical environments. One likely reason for this is that clinicians may not readily trust QA system outputs, in part because transparency, trustworthiness, and provenance have not been key considerations in the design of such models. In this paper we discuss a set of criteria that, if met, we argue would likely increase the utility of biomedical QA systems, which may in turn lead to adoption of such systems in practice. We assess existing models, tasks, and datasets with respect to these criteria, highlighting shortcomings of previously proposed approaches and pointing toward what might be more usable QA systems.

2020

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Trialstreamer: Mapping and Browsing Medical Evidence in Real-Time
Benjamin Nye | Ani Nenkova | Iain Marshall | Byron C. Wallace
Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics: System Demonstrations

We introduce Trialstreamer, a living database of clinical trial reports. Here we mainly describe the evidence extraction component; this extracts from biomedical abstracts key pieces of information that clinicians need when appraising the literature, and also the relations between these. Specifically, the system extracts descriptions of trial participants, the treatments compared in each arm (the interventions), and which outcomes were measured. The system then attempts to infer which interventions were reported to work best by determining their relationship with identified trial outcome measures. In addition to summarizing individual trials, these extracted data elements allow automatic synthesis of results across many trials on the same topic. We apply the system at scale to all reports of randomized controlled trials indexed in MEDLINE, powering the automatic generation of evidence maps, which provide a global view of the efficacy of different interventions combining data from all relevant clinical trials on a topic. We make all code and models freely available alongside a demonstration of the web interface.

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Evidence Inference 2.0: More Data, Better Models
Jay DeYoung | Eric Lehman | Benjamin Nye | Iain Marshall | Byron C. Wallace
Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

2019

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Browsing Health: Information Extraction to Support New Interfaces for Accessing Medical Evidence
Soham Parikh | Elizabeth Conrad | Oshin Agarwal | Iain Marshall | Byron Wallace | Ani Nenkova
Proceedings of the Workshop on Extracting Structured Knowledge from Scientific Publications

Standard paradigms for search do not work well in the medical context. Typical information needs, such as retrieving a full list of medical interventions for a given condition, or finding the reported efficacy of a particular treatment with respect to a specific outcome of interest cannot be straightforwardly posed in typical text-box search. Instead, we propose faceted-search in which a user specifies a condition and then can browse treatments and outcomes that have been evaluated. Choosing from these, they can access randomized control trials (RCTs) describing individual studies. Realizing such a view of the medical evidence requires information extraction techniques to identify the population, interventions, and outcome measures in an RCT. Patients, health practitioners, and biomedical librarians all stand to benefit from such innovation in search of medical evidence. We present an initial prototype of such an interface applied to pre-registered clinical studies. We also discuss pilot studies into the applicability of information extraction methods to allow for similar access to all published trial results.

2018

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Syntactic Patterns Improve Information Extraction for Medical Search
Roma Patel | Yinfei Yang | Iain Marshall | Ani Nenkova | Byron Wallace
Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 2 (Short Papers)

Medical professionals search the published literature by specifying the type of patients, the medical intervention(s) and the outcome measure(s) of interest. In this paper we demonstrate how features encoding syntactic patterns improve the performance of state-of-the-art sequence tagging models (both neural and linear) for information extraction of these medically relevant categories. We present an analysis of the type of patterns exploited and of the semantic space induced for these, i.e., the distributed representations learned for identified multi-token patterns. We show that these learned representations differ substantially from those of the constituent unigrams, suggesting that the patterns capture contextual information that is otherwise lost.

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A Corpus with Multi-Level Annotations of Patients, Interventions and Outcomes to Support Language Processing for Medical Literature
Benjamin Nye | Junyi Jessy Li | Roma Patel | Yinfei Yang | Iain Marshall | Ani Nenkova | Byron Wallace
Proceedings of the 56th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the ‘PICO’ elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

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Structured Multi-Label Biomedical Text Tagging via Attentive Neural Tree Decoding
Gaurav Singh | James Thomas | Iain Marshall | John Shawe-Taylor | Byron C. Wallace
Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing

We propose a model for tagging unstructured texts with an arbitrary number of terms drawn from a tree-structured vocabulary (i.e., an ontology). We treat this as a special case of sequence-to-sequence learning in which the decoder begins at the root node of an ontological tree and recursively elects to expand child nodes as a function of the input text, the current node, and the latent decoder state. We demonstrate that this method yields state-of-the-art results on the important task of assigning MeSH terms to biomedical abstracts.

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Learning Disentangled Representations of Texts with Application to Biomedical Abstracts
Sarthak Jain | Edward Banner | Jan-Willem van de Meent | Iain J. Marshall | Byron C. Wallace
Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing

We propose a method for learning disentangled representations of texts that code for distinct and complementary aspects, with the aim of affording efficient model transfer and interpretability. To induce disentangled embeddings, we propose an adversarial objective based on the (dis)similarity between triplets of documents with respect to specific aspects. Our motivating application is embedding biomedical abstracts describing clinical trials in a manner that disentangles the populations, interventions, and outcomes in a given trial. We show that our method learns representations that encode these clinically salient aspects, and that these can be effectively used to perform aspect-specific retrieval. We demonstrate that the approach generalizes beyond our motivating application in experiments on two multi-aspect review corpora.

2017

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Automating Biomedical Evidence Synthesis: RobotReviewer
Iain Marshall | Joël Kuiper | Edward Banner | Byron C. Wallace
Proceedings of ACL 2017, System Demonstrations

2016

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Leveraging coreference to identify arms in medical abstracts: An experimental study
Elisa Ferracane | Iain Marshall | Byron C. Wallace | Katrin Erk
Proceedings of the Seventh International Workshop on Health Text Mining and Information Analysis

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Rationale-Augmented Convolutional Neural Networks for Text Classification
Ye Zhang | Iain Marshall | Byron C. Wallace
Proceedings of the 2016 Conference on Empirical Methods in Natural Language Processing