Joint Entity Extraction and Assertion Detection for Clinical Text

Negative medical findings are prevalent in clinical reports, yet discriminating them from positive findings remains a challenging task for information extraction. Most of the existing systems treat this task as a pipeline of two separate tasks, i.e., named entity recognition (NER) and rule-based negation detection. We consider this as a multi-task problem and present a novel end-to-end neural model to jointly extract entities and negations. We extend a standard hierarchical encoder-decoder NER model and first adopt a shared encoder followed by separate decoders for the two tasks. This architecture performs considerably better than the previous rule-based and machine learning-based systems. To overcome the problem of increased parameter size especially for low-resource settings, we propose the Conditional Softmax Shared Decoder architecture which achieves state-of-art results for NER and negation detection on the 2010 i2b2/VA challenge dataset and a proprietary de-identified clinical dataset.Comment: Accepted at the 57th Annual Meeting of the Association for Computational Linguistics (ACL 2019

Better Document-level Sentiment Analysis from RST Discourse Parsing

Discourse structure is the hidden link between surface features and document-level properties, such as sentiment polarity. We show that the discourse analyses produced by Rhetorical Structure Theory (RST) parsers can improve document-level sentiment analysis, via composition of local information up the discourse tree. First, we show that reweighting discourse units according to their position in a dependency representation of the rhetorical structure can yield substantial improvements on lexicon-based sentiment analysis. Next, we present a recursive neural network over the RST structure, which offers significant improvements over classification-based methods.Comment: Published at Empirical Methods in Natural Language Processing (EMNLP 2015

Morphological Priors for Probabilistic Neural Word Embeddings

Word embeddings allow natural language processing systems to share statistical information across related words. These embeddings are typically based on distributional statistics, making it difficult for them to generalize to rare or unseen words. We propose to improve word embeddings by incorporating morphological information, capturing shared sub-word features. Unlike previous work that constructs word embeddings directly from morphemes, we combine morphological and distributional information in a unified probabilistic framework, in which the word embedding is a latent variable. The morphological information provides a prior distribution on the latent word embeddings, which in turn condition a likelihood function over an observed corpus. This approach yields improvements on intrinsic word similarity evaluations, and also in the downstream task of part-of-speech tagging.Comment: Appeared at the Conference on Empirical Methods in Natural Language Processing (EMNLP 2016, Austin

Relation Extraction using Explicit Context Conditioning

Relation Extraction (RE) aims to label relations between groups of marked entities in raw text. Most current RE models learn context-aware representations of the target entities that are then used to establish relation between them. This works well for intra-sentence RE and we call them first-order relations. However, this methodology can sometimes fail to capture complex and long dependencies. To address this, we hypothesize that at times two target entities can be explicitly connected via a context token. We refer to such indirect relations as second-order relations and describe an efficient implementation for computing them. These second-order relation scores are then combined with first-order relation scores. Our empirical results show that the proposed method leads to state-of-the-art performance over two biomedical datasets.Comment: Accepted for Publication at NAACL 201

LATTE: Latent Type Modeling for Biomedical Entity Linking

Entity linking is the task of linking mentions of named entities in natural language text, to entities in a curated knowledge-base. This is of significant importance in the biomedical domain, where it could be used to semantically annotate a large volume of clinical records and biomedical literature, to standardized concepts described in an ontology such as Unified Medical Language System (UMLS). We observe that with precise type information, entity disambiguation becomes a straightforward task. However, fine-grained type information is usually not available in biomedical domain. Thus, we propose LATTE, a LATent Type Entity Linking model, that improves entity linking by modeling the latent fine-grained type information about mentions and entities. Unlike previous methods that perform entity linking directly between the mentions and the entities, LATTE jointly does entity disambiguation, and latent fine-grained type learning, without direct supervision. We evaluate our model on two biomedical datasets: MedMentions, a large scale public dataset annotated with UMLS concepts, and a de-identified corpus of dictated doctor's notes that has been annotated with ICD concepts. Extensive experimental evaluation shows our model achieves significant performance improvements over several state-of-the-art techniques.Comment: AAAI 2020 Conferenc