Denis Newman-Griffis


2020

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Development of Natural Language Processing Tools to Support Determination of Federal Disability Benefits in the U.S.
Bart Desmet | Julia Porcino | Ayah Zirikly | Denis Newman-Griffis | Guy Divita | Elizabeth Rasch
Proceedings of the 1st Workshop on Language Technologies for Government and Public Administration (LT4Gov)

The disability benefits programs administered by the US Social Security Administration (SSA) receive between 2 and 3 million new applications each year. Adjudicators manually review hundreds of evidence pages per case to determine eligibility based on financial, medical, and functional criteria. Natural Language Processing (NLP) technology is uniquely suited to support this adjudication work and is a critical component of an ongoing inter-agency collaboration between SSA and the National Institutes of Health. This NLP work provides resources and models for document ranking, named entity recognition, and terminology extraction in order to automatically identify documents and reports pertinent to a case, and to allow adjudicators to search for and locate desired information quickly. In this paper, we describe our vision for how NLP can impact SSA’s adjudication process, present the resources and models that have been developed, and discuss some of the benefits and challenges in working with large-scale government data, and its specific properties in the functional domain.

2019

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HARE: a Flexible Highlighting Annotator for Ranking and Exploration
Denis Newman-Griffis | Eric Fosler-Lussier
Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP): System Demonstrations

Exploration and analysis of potential data sources is a significant challenge in the application of NLP techniques to novel information domains. We describe HARE, a system for highlighting relevant information in document collections to support ranking and triage, which provides tools for post-processing and qualitative analysis for model development and tuning. We apply HARE to the use case of narrative descriptions of mobility information in clinical data, and demonstrate its utility in comparing candidate embedding features. We provide a web-based interface for annotation visualization and document ranking, with a modular backend to support interoperability with existing annotation tools. Our system is available online at https://github.com/OSU-slatelab/HARE.

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Writing habits and telltale neighbors: analyzing clinical concept usage patterns with sublanguage embeddings
Denis Newman-Griffis | Eric Fosler-Lussier
Proceedings of the Tenth International Workshop on Health Text Mining and Information Analysis (LOUHI 2019)

Natural language processing techniques are being applied to increasingly diverse types of electronic health records, and can benefit from in-depth understanding of the distinguishing characteristics of medical document types. We present a method for characterizing the usage patterns of clinical concepts among different document types, in order to capture semantic differences beyond the lexical level. By training concept embeddings on clinical documents of different types and measuring the differences in their nearest neighborhood structures, we are able to measure divergences in concept usage while correcting for noise in embedding learning. Experiments on the MIMIC-III corpus demonstrate that our approach captures clinically-relevant differences in concept usage and provides an intuitive way to explore semantic characteristics of clinical document collections.

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Characterizing the Impact of Geometric Properties of Word Embeddings on Task Performance
Brendan Whitaker | Denis Newman-Griffis | Aparajita Haldar | Hakan Ferhatosmanoglu | Eric Fosler-Lussier
Proceedings of the 3rd Workshop on Evaluating Vector Space Representations for NLP

Analysis of word embedding properties to inform their use in downstream NLP tasks has largely been studied by assessing nearest neighbors. However, geometric properties of the continuous feature space contribute directly to the use of embedding features in downstream models, and are largely unexplored. We consider four properties of word embedding geometry, namely: position relative to the origin, distribution of features in the vector space, global pairwise distances, and local pairwise distances. We define a sequence of transformations to generate new embeddings that expose subsets of these properties to downstream models and evaluate change in task performance to understand the contribution of each property to NLP models. We transform publicly available pretrained embeddings from three popular toolkits (word2vec, GloVe, and FastText) and evaluate on a variety of intrinsic tasks, which model linguistic information in the vector space, and extrinsic tasks, which use vectors as input to machine learning models. We find that intrinsic evaluations are highly sensitive to absolute position, while extrinsic tasks rely primarily on local similarity. Our findings suggest that future embedding models and post-processing techniques should focus primarily on similarity to nearby points in vector space.

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Classifying the reported ability in clinical mobility descriptions
Denis Newman-Griffis | Ayah Zirikly | Guy Divita | Bart Desmet
Proceedings of the 18th BioNLP Workshop and Shared Task

Assessing how individuals perform different activities is key information for modeling health states of individuals and populations. Descriptions of activity performance in clinical free text are complex, including syntactic negation and similarities to textual entailment tasks. We explore a variety of methods for the novel task of classifying four types of assertions about activity performance: Able, Unable, Unclear, and None (no information). We find that ensembling an SVM trained with lexical features and a CNN achieves 77.9% macro F1 score on our task, and yields nearly 80% recall on the rare Unclear and Unable samples. Finally, we highlight several challenges in classifying performance assertions, including capturing information about sources of assistance, incorporating syntactic structure and negation scope, and handling new modalities at test time. Our findings establish a strong baseline for this novel task, and identify intriguing areas for further research.

2018

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Embedding Transfer for Low-Resource Medical Named Entity Recognition: A Case Study on Patient Mobility
Denis Newman-Griffis | Ayah Zirikly
Proceedings of the BioNLP 2018 workshop

Functioning is gaining recognition as an important indicator of global health, but remains under-studied in medical natural language processing research. We present the first analysis of automatically extracting descriptions of patient mobility, using a recently-developed dataset of free text electronic health records. We frame the task as a named entity recognition (NER) problem, and investigate the applicability of NER techniques to mobility extraction. As text corpora focused on patient functioning are scarce, we explore domain adaptation of word embeddings for use in a recurrent neural network NER system. We find that embeddings trained on a small in-domain corpus perform nearly as well as those learned from large out-of-domain corpora, and that domain adaptation techniques yield additional improvements in both precision and recall. Our analysis identifies several significant challenges in extracting descriptions of patient mobility, including the length and complexity of annotated entities and high linguistic variability in mobility descriptions.

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Jointly Embedding Entities and Text with Distant Supervision
Denis Newman-Griffis | Albert M Lai | Eric Fosler-Lussier
Proceedings of The Third Workshop on Representation Learning for NLP

Learning representations for knowledge base entities and concepts is becoming increasingly important for NLP applications. However, recent entity embedding methods have relied on structured resources that are expensive to create for new domains and corpora. We present a distantly-supervised method for jointly learning embeddings of entities and text from an unnanotated corpus, using only a list of mappings between entities and surface forms. We learn embeddings from open-domain and biomedical corpora, and compare against prior methods that rely on human-annotated text or large knowledge graph structure. Our embeddings capture entity similarity and relatedness better than prior work, both in existing biomedical datasets and a new Wikipedia-based dataset that we release to the community. Results on analogy completion and entity sense disambiguation indicate that entities and words capture complementary information that can be effectively combined for downstream use.

2017

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Insights into Analogy Completion from the Biomedical Domain
Denis Newman-Griffis | Albert Lai | Eric Fosler-Lussier
BioNLP 2017

Analogy completion has been a popular task in recent years for evaluating the semantic properties of word embeddings, but the standard methodology makes a number of assumptions about analogies that do not always hold, either in recent benchmark datasets or when expanding into other domains. Through an analysis of analogies in the biomedical domain, we identify three assumptions: that of a Single Answer for any given analogy, that the pairs involved describe the Same Relationship, and that each pair is Informative with respect to the other. We propose modifying the standard methodology to relax these assumptions by allowing for multiple correct answers, reporting MAP and MRR in addition to accuracy, and using multiple example pairs. We further present BMASS, a novel dataset for evaluating linguistic regularities in biomedical embeddings, and demonstrate that the relationships described in the dataset pose significant semantic challenges to current word embedding methods.