Zero-shot Medical Entity Retrieval without Annotation: Learning From Rich Knowledge Graph Semantics

Medical entity retrieval is an integral component for understanding and communicating information across various health systems. Current approaches tend to work well on specific medical domains but generalize poorly to unseen sub-specialties. This is of increasing concern under a public health crisis as new medical conditions and drug treatments come to light frequently. Zero-shot retrieval is challenging due to the high degree of ambiguity and variability in medical corpora, making it difficult to build an accurate similarity measure between mentions and concepts. Medical knowledge graphs (KG), however, contain rich semantics including large numbers of synonyms as well as its curated graphical structures. To take advantage of this valuable information, we propose a suite of learning tasks designed for training efficient zero-shot entity retrieval models. Without requiring any human annotation, our knowledge graph enriched architecture significantly outperforms common zero-shot benchmarks including BM25 and Clinical BERT with 7% to 30% higher recall across multiple major medical ontologies, such as UMLS, SNOMED, and ICD-10.

Towards Clinical Encounter Summarization: Learning to Compose Discharge Summaries from Prior Notes

The records of a clinical encounter can be extensive and complex, thus placing a premium on tools that can extract and summarize relevant information. This paper introduces the task of generating discharge summaries for a clinical encounter. Summaries in this setting need to be faithful, traceable, and scale to multiple long documents, motivating the use of extract-then-abstract summarization cascades. We introduce two new measures, faithfulness and hallucination rate for evaluation in this task, which complement existing measures for fluency and informativeness. Results across seven medical sections and five models show that a summarization architecture that supports traceability yields promising results, and that a sentence-rewriting approach performs consistently on the measure used for faithfulness (faithfulness-adjusted $F_3$) over a diverse range of generated sections.

An Empirical Investigation Towards Efficient Multi-Domain Language Model Pre-training

Pre-training large language models has become a standard in the natural language processing community. Such models are pre-trained on generic data (e.g. BookCorpus and English Wikipedia) and often fine-tuned on tasks in the same domain. However, in order to achieve state-of-the-art performance on out of domain tasks such as clinical named entity recognition and relation extraction, additional in domain pre-training is required. In practice, staged multi-domain pre-training presents performance deterioration in the form of catastrophic forgetting (CF) when evaluated on a generic benchmark such as GLUE. In this paper we conduct an empirical investigation into known methods to mitigate CF. We find that elastic weight consolidation provides best overall scores yielding only a 0.33% drop in performance across seven generic tasks while remaining competitive in bio-medical tasks. Furthermore, we explore gradient and latent clustering based data selection techniques to improve coverage when using elastic weight consolidation and experience replay methods.

Improve black-box sequential anomaly detector relevancy with limited user feedback

Anomaly detectors are often designed to catch statistical anomalies. End-users typically do not have interest in all of the detected outliers, but only those relevant to their application. Given an existing black-box sequential anomaly detector, this paper proposes a method to improve its user relevancy using a small number of human feedback. As our first contribution, the method is agnostic to the detector: it only assumes access to its anomaly scores, without requirement on any additional information inside it. Inspired by a fact that anomalies are of different types, our approach identifies these types and utilizes user feedback to assign relevancy to types. This relevancy score, as our second contribution, is used to adjust the subsequent anomaly selection process. Empirical results on synthetic and real-world datasets show that our approach yields significant improvements on precision and recall over a range of anomaly detectors.

COVID-19 Knowledge Graph: Accelerating Information Retrieval and Discovery for Scientific Literature

The coronavirus disease (COVID-19) has claimed the lives of over 350,000 people and infected more than 6 million people worldwide. Several search engines have surfaced to provide researchers with additional tools to find and retrieve information from the rapidly growing corpora on COVID-19. These engines lack extraction and visualization tools necessary to retrieve and interpret complex relations inherent to scientific literature. Moreover, because these engines mainly rely upon semantic information, their ability to capture complex global relationships across documents is limited, which reduces the quality of similarity-based article recommendations for users. In this work, we present the COVID-19 Knowledge Graph (CKG), a heterogeneous graph for extracting and visualizing complex relationships between COVID-19 scientific articles. The CKG combines semantic information with document topological information for the application of similar document retrieval. The CKG is constructed using the latent schema of the data, and then enriched with biomedical entity information extracted from the unstructured text of articles using scalable AWS technologies to form relations in the graph. Finally, we propose a document similarity engine that leverages low-dimensional graph embeddings from the CKG with semantic embeddings for similar article retrieval. Analysis demonstrates the quality of relationships in the CKG and shows that it can be used to uncover meaningful information in COVID-19 scientific articles. The CKG helps power www.cord19.aws and is publicly available.

Towards User Friendly Medication Mapping Using Entity-Boosted Two-Tower Neural Network

Recent advancements in medical entity linking have been applied in the area of scientific literature and social media data. However, with the adoption of telemedicine and conversational agents such as Alexa in healthcare settings, medical name inference has become an important task. Medication name inference is the task of mapping user friendly medication names from a free-form text to a concept in a normalized medication list. This is challenging due to the differences in the use of medical terminology from health care professionals and user conversations coming from the lay public. We begin with mapping descriptive medication phrases (DMP) to standard medication names (SMN). Given the prescriptions of each patient, we want to provide them with the flexibility of referring to the medication in their preferred ways. We approach this as a ranking problem which maps SMN to DMP by ordering the list of medications in the patient's prescription list obtained from pharmacies. Furthermore, we leveraged the output of intermediate layers and performed medication clustering. We present the Medication Inference Model (MIM) achieving state-of-the-art results. By incorporating medical entities based attention, we have obtained further improvement for ranking models.

Severing the Edge Between Before and After: Neural Architectures for Temporal Ordering of Events

In this paper, we propose a neural architecture and a set of training methods for ordering events by predicting temporal relations. Our proposed models receive a pair of events within a span of text as input and they identify temporal relations (Before, After, Equal, Vague) between them. Given that a key challenge with this task is the scarcity of annotated data, our models rely on either pretrained representations (i.e. RoBERTa, BERT or ELMo), transfer and multi-task learning (by leveraging complementary datasets), and self-training techniques. Experiments on the MATRES dataset of English documents establish a new state-of-the-art on this task.

CALM: Continuous Adaptive Learning for Language Modeling

Training large language representation models has become a standard in the natural language processing community. This allows for fine tuning on any number of specific tasks, however, these large high capacity models can continue to train on domain specific unlabeled data to make initialization even more robust for supervised tasks. We demonstrate that in practice these pre-trained models present performance deterioration in the form of catastrophic forgetting when evaluated on tasks from a general domain such as GLUE. In this work we propose CALM, Continuous Adaptive Learning for Language Modeling: techniques to render models which retain knowledge across multiple domains. With these methods, we are able to reduce the performance gap across supervised tasks introduced by task specific models which we demonstrate using a continual learning setting in biomedical and clinical domains.

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.

Towards Annotating and Creating Sub-Sentence Summary Highlights

Highlighting is a powerful tool to pick out important content and emphasize. Creating summary highlights at the sub-sentence level is particularly desirable, because sub-sentences are more concise than whole sentences. They are also better suited than individual words and phrases that can potentially lead to disfluent, fragmented summaries. In this paper we seek to generate summary highlights by annotating summary-worthy sub-sentences and teaching classifiers to do the same. We frame the task as jointly selecting important sentences and identifying a single most informative textual unit from each sentence. This formulation dramatically reduces the task complexity involved in sentence compression. Our study provides new benchmarks and baselines for generating highlights at the sub-sentence level.