arXiv subjects

Ani Nenkova

Publications and source records attributed to Ani Nenkova.

29 records · Page 2Linked to original sources

arXiv2022

Understanding Clinical Trial Reports: Extracting Medical Entities and Their Relations

The best evidence concerning comparative treatment effectiveness comes from clinical trials, the results of which are reported in unstructured articles. Medical experts must manually extract information from articles to inform decision-making, which is time-consuming and expensive. Here we consider the end-to-end task of both (a) extracting treatments and outcomes from full-text articles describing clinical trials (entity identification) and, (b) inferring the reported results for the former with respect to the latter (relation extraction). We introduce new data for this task, and evaluate models that have recently achieved state-of-the-art results on similar tasks in Natural Language Processing. We then propose a new method motivated by how trial results are typically presented that outperforms these purely data-driven baselines. Finally, we run a fielded evaluation of the model with a non-profit seeking to identify existing drugs that might be re-purposed for cancer, showing the potential utility of end-to-end evidence extraction systems.

cs.CL↗

arXiv2021

From Toxicity in Online Comments to Incivility in American News: Proceed with Caution

The ability to quantify incivility online, in news and in congressional debates, is of great interest to political scientists. Computational tools for detecting online incivility for English are now fairly accessible and potentially could be applied more broadly. We test the Jigsaw Perspective API for its ability to detect the degree of incivility on a corpus that we developed, consisting of manual annotations of civility in American news. We demonstrate that toxicity models, as exemplified by Perspective, are inadequate for the analysis of incivility in news. We carry out error analysis that points to the need to develop methods to remove spurious correlations between words often mentioned in the news, especially identity descriptors and incivility. Without such improvements, applying Perspective or similar models on news is likely to lead to wrong conclusions, that are not aligned with the human perception of incivility.

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arXiv2021

Entity-Switched Datasets: An Approach to Auditing the In-Domain Robustness of Named Entity Recognition Models

Named entity recognition systems perform well on standard datasets comprising English news. But given the paucity of data, it is difficult to draw conclusions about the robustness of systems with respect to recognizing a diverse set of entities. We propose a method for auditing the in-domain robustness of systems, focusing specifically on differences in performance due to the national origin of entities. We create entity-switched datasets, in which named entities in the original texts are replaced by plausible named entities of the same type but of different national origin. We find that state-of-the-art systems' performance vary widely even in-domain: In the same context, entities from certain origins are more reliably recognized than entities from elsewhere. Systems perform best on American and Indian entities, and worst on Vietnamese and Indonesian entities. This auditing approach can facilitate the development of more robust named entity recognition systems, and will allow research in this area to consider fairness criteria that have received heightened attention in other predictive technology work.

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arXiv2021

Interpretability Analysis for Named Entity Recognition to Understand System Predictions and How They Can Improve

Named Entity Recognition systems achieve remarkable performance on domains such as English news. It is natural to ask: What are these models actually learning to achieve this? Are they merely memorizing the names themselves? Or are they capable of interpreting the text and inferring the correct entity type from the linguistic context? We examine these questions by contrasting the performance of several variants of LSTM-CRF architectures for named entity recognition, with some provided only representations of the context as features. We also perform similar experiments for BERT. We find that context representations do contribute to system performance, but that the main factor driving high performance is learning the name tokens themselves. We enlist human annotators to evaluate the feasibility of inferring entity types from the context alone and find that, while people are not able to infer the entity type either for the majority of the errors made by the context-only system, there is some room for improvement. A system should be able to recognize any name in a predictive context correctly and our experiments indicate that current systems may be further improved by such capability.

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arXiv2020

Trialstreamer: Mapping and Browsing Medical Evidence in Real-Time

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.

cs.IR↗

arXiv2019

Predicting Annotation Difficulty to Improve Task Routing and Model Performance for Biomedical Information Extraction

Modern NLP systems require high-quality annotated data. In specialized domains, expert annotations may be prohibitively expensive. An alternative is to rely on crowdsourcing to reduce costs at the risk of introducing noise. In this paper we demonstrate that directly modeling instance difficulty can be used to improve model performance, and to route instances to appropriate annotators. Our difficulty prediction model combines two learned representations: a `universal' encoder trained on out-of-domain data, and a task-specific encoder. Experiments on a complex biomedical information extraction task using expert and lay annotators show that: (i) simply excluding from the training data instances predicted to be difficult yields a small boost in performance; (ii) using difficulty scores to weight instances during training provides further, consistent gains; (iii) assigning instances predicted to be difficult to domain experts is an effective strategy for task routing. Our experiments confirm the expectation that for specialized tasks expert annotations are higher quality than crowd labels, and hence preferable to obtain if practical. Moreover, augmenting small amounts of expert data with a larger set of lay annotations leads to further improvements in model performance.

cs.CL↗

arXiv2018

Named Person Coreference in English News

People are often entities of interest in tasks such as search and information extraction. In these tasks, the goal is to find as much information as possible about people specified by their name. However in text, some of the references to people are by pronouns (she, his) or generic descriptions (the professor, the German chancellor). It is therefore important that coreference resolution systems are able to link these different types of mentions to the correct person name. Here, we evaluate two state of the art coreference resolution systems on the subtask of Named Person Coreference, in which we are interested in identifying a person mentioned by name, along with all other mentions of the person, by pronoun or generic noun phrase. Our analysis reveals that standard coreference metrics do not reflect adequately the requirements in this task: they do not penalize systems for not identifying any mentions by name and they reward systems even if systems find correctly mentions to the same entity but fail to link these to a proper name (she--the student---no name). We introduce new metrics for evaluating named person coreference that address these discrepancies. We present a simple rule-based named entity recognition driven system, which outperforms the current state-of-the-art systems on these task-specific metrics and performs on par with them on traditional coreference evaluations. Finally, we present similar evaluation for coreference resolution of other named entities and show that the rule-based approach is effective only for person named coreference, not other named entity types.

cs.CL↗

arXiv2018

A Corpus with Multi-Level Annotations of Patients, Interventions and Outcomes to Support Language Processing for Medical Literature

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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arXiv2018

Syntactic Patterns Improve Information Extraction for Medical Search

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 linear and neural) for information extraction of these medically relevant categories. We present an analysis of the type of patterns exploited, and 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.

cs.CL↗

arXiv2017

Combining Lexical and Syntactic Features for Detecting Content-dense Texts in News

Content-dense news report important factual information about an event in direct, succinct manner. Information seeking applications such as information extraction, question answering and summarization normally assume all text they deal with is content-dense. Here we empirically test this assumption on news articles from the business, U.S. international relations, sports and science journalism domains. Our findings clearly indicate that about half of the news texts in our study are in fact not content-dense and motivate the development of a supervised content-density detector. We heuristically label a large training corpus for the task and train a two-layer classifying model based on lexical and unlexicalized syntactic features. On manually annotated data, we compare the performance of domain-specific classifiers, trained on data only from a given news domain and a general classifier in which data from all four domains is pooled together. Our annotation and prediction experiments demonstrate that the concept of content density varies depending on the domain and that naive annotators provide judgement biased toward the stereotypical domain label. Domain-specific classifiers are more accurate for domains in which content-dense texts are typically fewer. Domain independent classifiers reproduce better naive crowdsourced judgements. Classification prediction is high across all conditions, around 80%.

cs.CL↗

arXiv2017

Detecting (Un)Important Content for Single-Document News Summarization

We present a robust approach for detecting intrinsic sentence importance in news, by training on two corpora of document-summary pairs. When used for single-document summarization, our approach, combined with the "beginning of document" heuristic, outperforms a state-of-the-art summarizer and the beginning-of-article baseline in both automatic and manual evaluations. These results represent an important advance because in the absence of cross-document repetition, single document summarizers for news have not been able to consistently outperform the strong beginning-of-article baseline.

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