Guergana Savova


2021

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EntityBERT: Entity-centric Masking Strategy for Model Pretraining for the Clinical Domain
Chen Lin | Timothy Miller | Dmitriy Dligach | Steven Bethard | Guergana Savova
Proceedings of the 20th Workshop on Biomedical Language Processing

Transformer-based neural language models have led to breakthroughs for a variety of natural language processing (NLP) tasks. However, most models are pretrained on general domain data. We propose a methodology to produce a model focused on the clinical domain: continued pretraining of a model with a broad representation of biomedical terminology (PubMedBERT) on a clinical corpus along with a novel entity-centric masking strategy to infuse domain knowledge in the learning process. We show that such a model achieves superior results on clinical extraction tasks by comparing our entity-centric masking strategy with classic random masking on three clinical NLP tasks: cross-domain negation detection, document time relation (DocTimeRel) classification, and temporal relation extraction. We also evaluate our models on the PubMedQA dataset to measure the models’ performance on a non-entity-centric task in the biomedical domain. The language addressed in this work is English.

2020

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Extracting Relations between Radiotherapy Treatment Details
Danielle Bitterman | Timothy Miller | David Harris | Chen Lin | Sean Finan | Jeremy Warner | Raymond Mak | Guergana Savova
Proceedings of the 3rd Clinical Natural Language Processing Workshop

We present work on extraction of radiotherapy treatment information from the clinical narrative in the electronic medical records. Radiotherapy is a central component of the treatment of most solid cancers. Its details are described in non-standardized fashions using jargon not found in other medical specialties, complicating the already difficult task of manual data extraction. We examine the performance of several state-of-the-art neural methods for relation extraction of radiotherapy treatment details, with a goal of automating detailed information extraction. The neural systems perform at 0.82-0.88 macro-average F1, which approximates or in some cases exceeds the inter-annotator agreement. To the best of our knowledge, this is the first effort to develop models for radiotherapy relation extraction and one of the few efforts for relation extraction to describe cancer treatment in general.

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A BERT-based One-Pass Multi-Task Model for Clinical Temporal Relation Extraction
Chen Lin | Timothy Miller | Dmitriy Dligach | Farig Sadeque | Steven Bethard | Guergana Savova
Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing

Recently BERT has achieved a state-of-the-art performance in temporal relation extraction from clinical Electronic Medical Records text. However, the current approach is inefficient as it requires multiple passes through each input sequence. We extend a recently-proposed one-pass model for relation classification to a one-pass model for relation extraction. We augment this framework by introducing global embeddings to help with long-distance relation inference, and by multi-task learning to increase model performance and generalizability. Our proposed model produces results on par with the state-of-the-art in temporal relation extraction on the THYME corpus and is much “greener” in computational cost.

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Defining and Learning Refined Temporal Relations in the Clinical Narrative
Kristin Wright-Bettner | Chen Lin | Timothy Miller | Steven Bethard | Dmitriy Dligach | Martha Palmer | James H. Martin | Guergana Savova
Proceedings of the 11th International Workshop on Health Text Mining and Information Analysis

We present refinements over existing temporal relation annotations in the Electronic Medical Record clinical narrative. We refined the THYME corpus annotations to more faithfully represent nuanced temporality and nuanced temporal-coreferential relations. The main contributions are in re-defining CONTAINS and OVERLAP relations into CONTAINS, CONTAINS-SUBEVENT, OVERLAP and NOTED-ON. We demonstrate that these refinements lead to substantial gains in learnability for state-of-the-art transformer models as compared to previously reported results on the original THYME corpus. We thus establish a baseline for the automatic extraction of these refined temporal relations. Although our study is done on clinical narrative, we believe it addresses far-reaching challenges that are corpus- and domain- agnostic.

2019

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Cross-document coreference: An approach to capturing coreference without context
Kristin Wright-Bettner | Martha Palmer | Guergana Savova | Piet de Groen | Timothy Miller
Proceedings of the Tenth International Workshop on Health Text Mining and Information Analysis (LOUHI 2019)

This paper discusses a cross-document coreference annotation schema that was developed to further automatic extraction of timelines in the clinical domain. Lexical senses and coreference choices are determined largely by context, but cross-document work requires reasoning across contexts that are not necessarily coherent. We found that an annotation approach that relies less on context-guided annotator intuitions and more on schematic rules was most effective in creating meaningful and consistent cross-document relations.

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A BERT-based Universal Model for Both Within- and Cross-sentence Clinical Temporal Relation Extraction
Chen Lin | Timothy Miller | Dmitriy Dligach | Steven Bethard | Guergana Savova
Proceedings of the 2nd Clinical Natural Language Processing Workshop

Classic methods for clinical temporal relation extraction focus on relational candidates within a sentence. On the other hand, break-through Bidirectional Encoder Representations from Transformers (BERT) are trained on large quantities of arbitrary spans of contiguous text instead of sentences. In this study, we aim to build a sentence-agnostic framework for the task of CONTAINS temporal relation extraction. We establish a new state-of-the-art result for the task, 0.684F for in-domain (0.055-point improvement) and 0.565F for cross-domain (0.018-point improvement), by fine-tuning BERT and pre-training domain-specific BERT models on sentence-agnostic temporal relation instances with WordPiece-compatible encodings, and augmenting the labeled data with automatically generated “silver” instances.

2018

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Self-training improves Recurrent Neural Networks performance for Temporal Relation Extraction
Chen Lin | Timothy Miller | Dmitriy Dligach | Hadi Amiri | Steven Bethard | Guergana Savova
Proceedings of the Ninth International Workshop on Health Text Mining and Information Analysis

Neural network models are oftentimes restricted by limited labeled instances and resort to advanced architectures and features for cutting edge performance. We propose to build a recurrent neural network with multiple semantically heterogeneous embeddings within a self-training framework. Our framework makes use of labeled, unlabeled, and social media data, operates on basic features, and is scalable and generalizable. With this method, we establish the state-of-the-art result for both in- and cross-domain for a clinical temporal relation extraction task.

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Spotting Spurious Data with Neural Networks
Hadi Amiri | Timothy Miller | Guergana Savova
Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers)

Automatic identification of spurious instances (those with potentially wrong labels in datasets) can improve the quality of existing language resources, especially when annotations are obtained through crowdsourcing or automatically generated based on coded rankings. In this paper, we present effective approaches inspired by queueing theory and psychology of learning to automatically identify spurious instances in datasets. Our approaches discriminate instances based on their “difficulty to learn,” determined by a downstream learner. Our methods can be applied to any dataset assuming the existence of a neural network model for the target task of the dataset. Our best approach outperforms competing state-of-the-art baselines and has a MAP of 0.85 and 0.22 in identifying spurious instances in synthetic and carefully-crowdsourced real-world datasets respectively.

2017

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Repeat before Forgetting: Spaced Repetition for Efficient and Effective Training of Neural Networks
Hadi Amiri | Timothy Miller | Guergana Savova
Proceedings of the 2017 Conference on Empirical Methods in Natural Language Processing

We present a novel approach for training artificial neural networks. Our approach is inspired by broad evidence in psychology that shows human learners can learn efficiently and effectively by increasing intervals of time between subsequent reviews of previously learned materials (spaced repetition). We investigate the analogy between training neural models and findings in psychology about human memory model and develop an efficient and effective algorithm to train neural models. The core part of our algorithm is a cognitively-motivated scheduler according to which training instances and their “reviews” are spaced over time. Our algorithm uses only 34-50% of data per epoch, is 2.9-4.8 times faster than standard training, and outperforms competing state-of-the-art baselines. Our code is available at scholar.harvard.edu/hadi/RbF/.

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Unsupervised Domain Adaptation for Clinical Negation Detection
Timothy Miller | Steven Bethard | Hadi Amiri | Guergana Savova
BioNLP 2017

Detecting negated concepts in clinical texts is an important part of NLP information extraction systems. However, generalizability of negation systems is lacking, as cross-domain experiments suffer dramatic performance losses. We examine the performance of multiple unsupervised domain adaptation algorithms on clinical negation detection, finding only modest gains that fall well short of in-domain performance.

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Representations of Time Expressions for Temporal Relation Extraction with Convolutional Neural Networks
Chen Lin | Timothy Miller | Dmitriy Dligach | Steven Bethard | Guergana Savova
BioNLP 2017

Token sequences are often used as the input for Convolutional Neural Networks (CNNs) in natural language processing. However, they might not be an ideal representation for time expressions, which are long, highly varied, and semantically complex. We describe a method for representing time expressions with single pseudo-tokens for CNNs. With this method, we establish a new state-of-the-art result for a clinical temporal relation extraction task.

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Proceedings of the Biomedical NLP Workshop associated with RANLP 2017
Svetla Boytcheva | Kevin Bretonnel Cohen | Guergana Savova | Galia Angelova
Proceedings of the Biomedical NLP Workshop associated with RANLP 2017

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Neural Temporal Relation Extraction
Dmitriy Dligach | Timothy Miller | Chen Lin | Steven Bethard | Guergana Savova
Proceedings of the 15th Conference of the European Chapter of the Association for Computational Linguistics: Volume 2, Short Papers

We experiment with neural architectures for temporal relation extraction and establish a new state-of-the-art for several scenarios. We find that neural models with only tokens as input outperform state-of-the-art hand-engineered feature-based models, that convolutional neural networks outperform LSTM models, and that encoding relation arguments with XML tags outperforms a traditional position-based encoding.

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SemEval-2017 Task 12: Clinical TempEval
Steven Bethard | Guergana Savova | Martha Palmer | James Pustejovsky
Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval-2017)

Clinical TempEval 2017 aimed to answer the question: how well do systems trained on annotated timelines for one medical condition (colon cancer) perform in predicting timelines on another medical condition (brain cancer)? Nine sub-tasks were included, covering problems in time expression identification, event expression identification and temporal relation identification. Participant systems were evaluated on clinical and pathology notes from Mayo Clinic cancer patients, annotated with an extension of TimeML for the clinical domain. 11 teams participated in the tasks, with the best systems achieving F1 scores above 0.55 for time expressions, above 0.70 for event expressions, and above 0.40 for temporal relations. Most tasks observed about a 20 point drop over Clinical TempEval 2016, where systems were trained and evaluated on the same domain (colon cancer).

2016

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Unsupervised Document Classification with Informed Topic Models
Timothy Miller | Dmitriy Dligach | Guergana Savova
Proceedings of the 15th Workshop on Biomedical Natural Language Processing

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Improving Temporal Relation Extraction with Training Instance Augmentation
Chen Lin | Timothy Miller | Dmitriy Dligach | Steven Bethard | Guergana Savova
Proceedings of the 15th Workshop on Biomedical Natural Language Processing

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SemEval-2016 Task 12: Clinical TempEval
Steven Bethard | Guergana Savova | Wei-Te Chen | Leon Derczynski | James Pustejovsky | Marc Verhagen
Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval-2016)

2015

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SemEval-2015 Task 14: Analysis of Clinical Text
Noémie Elhadad | Sameer Pradhan | Sharon Gorman | Suresh Manandhar | Wendy Chapman | Guergana Savova
Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015)

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SemEval-2015 Task 6: Clinical TempEval
Steven Bethard | Leon Derczynski | Guergana Savova | James Pustejovsky | Marc Verhagen
Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015)

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Extracting Time Expressions from Clinical Text
Timothy Miller | Steven Bethard | Dmitriy Dligach | Chen Lin | Guergana Savova
Proceedings of BioNLP 15

2014

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SemEval-2014 Task 7: Analysis of Clinical Text
Sameer Pradhan | Noémie Elhadad | Wendy Chapman | Suresh Manandhar | Guergana Savova
Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014)

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Temporal Annotation in the Clinical Domain
William F. Styler IV | Steven Bethard | Sean Finan | Martha Palmer | Sameer Pradhan | Piet C de Groen | Brad Erickson | Timothy Miller | Chen Lin | Guergana Savova | James Pustejovsky
Transactions of the Association for Computational Linguistics, Volume 2

This article discusses the requirements of a formal specification for the annotation of temporal information in clinical narratives. We discuss the implementation and extension of ISO-TimeML for annotating a corpus of clinical notes, known as the THYME corpus. To reflect the information task and the heavily inference-based reasoning demands in the domain, a new annotation guideline has been developed, “the THYME Guidelines to ISO-TimeML (THYME-TimeML)”. To clarify what relations merit annotation, we distinguish between linguistically-derived and inferentially-derived temporal orderings in the text. We also apply a top performing TempEval 2013 system against this new resource to measure the difficulty of adapting systems to the clinical domain. The corpus is available to the community and has been proposed for use in a SemEval 2015 task.

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Descending-Path Convolution Kernel for Syntactic Structures
Chen Lin | Timothy Miller | Alvin Kho | Steven Bethard | Dmitriy Dligach | Sameer Pradhan | Guergana Savova
Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers)

2013

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Discovering Temporal Narrative Containers in Clinical Text
Timothy Miller | Steven Bethard | Dmitriy Dligach | Sameer Pradhan | Chen Lin | Guergana Savova
Proceedings of the 2013 Workshop on Biomedical Natural Language Processing

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Proceedings of the Workshop on NLP for Medicine and Biology associated with RANLP 2013
Guergana Savova | Kevin Bretonnel Cohen | Galia Angelova
Proceedings of the Workshop on NLP for Medicine and Biology associated with RANLP 2013

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Active Learning for Phenotyping Tasks
Dmitriy Dligach | Timothy Miller | Guergana Savova
Proceedings of the Workshop on NLP for Medicine and Biology associated with RANLP 2013

2012

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Active Learning for Coreference Resolution
Timothy Miller | Dmitriy Dligach | Guergana Savova
BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing

2011

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Proceedings of the Second Workshop on Biomedical Natural Language Processing
Guergana Savova | Kevin Bretonnel Cohen | Galia Angelova
Proceedings of the Second Workshop on Biomedical Natural Language Processing

2009

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Proceedings of the Workshop on Biomedical Information Extraction
Guergana Savova | Vangelis Karkaletsis | Galia Angelova
Proceedings of the Workshop on Biomedical Information Extraction

2008

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System Evaluation on a Named Entity Corpus from Clinical Notes
Karin Schuler | Vinod Kaggal | James Masanz | Philip Ogren | Guergana Savova
Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC'08)

This paper presents the evaluation of the dictionary look-up component of Mayo Clinic’s Information Extraction system. The component was tested on a corpus of 160 free-text clinical notes which were manually annotated with the named entity disease. This kind of clinical text presents many language challenges such as fragmented sentences and heavy use of abbreviations and acronyms. The dictionary used for this evaluation was a subset of SNOMED-CT with semantic types corresponding to diseases/disorders without any augmentation. The algorithm achieves an F-score of 0.56 for exact matches and F-scores of 0.76 and 0.62 for right and left-partial matches respectively. Machine learning techniques are currently under investigation to improve this task.

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Constructing Evaluation Corpora for Automated Clinical Named Entity Recognition
Philip Ogren | Guergana Savova | Christopher Chute
Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC'08)

We report on the construction of a gold-standard dataset consisting of annotated clinical notes suitable for evaluating our biomedical named entity recognition system. The dataset is the result of consensus between four human annotators and contains 1,556 annotations on 160 clinical notes using 658 unique concept codes from SNOMED-CT corresponding to human disorders. Inter-annotator agreement was calculated on annotations from 100 of the documents for span (90.9%), concept code (81.7%), context (84.8%), and status (86.0%) agreement. Complete agreement for span, concept code, context, and status was 74.6%. We found that creating a consensus set based on annotations from two independently-created annotation sets can reduce inter-annotator disagreement by 32.3%. We found little benefit to pre-annotating the corpus with a third-party named entity recognizer.

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Conditional Random Fields and Support Vector Machines for Disorder Named Entity Recognition in Clinical Texts
Dingcheng Li | Guergana Savova | Karin Kipper-Schuler
Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing

2006

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Cluster Stopping Rules for Word Sense Discrimination
Guergana Savova | Terry Therneau | Christopher Chute
Proceedings of the Workshop on Making Sense of Sense: Bringing Psycholinguistics and Computational Linguistics Together