There is a growing interest in creating tools to assist in clinical note generation using the audio of provider-patient encounters. Motivated by this goal and with the help of providers and medical scribes, we developed an annotation scheme to extract relevant clinical concepts. We used this annotation scheme to label a corpus of about 6k clinical encounters. This was used to train a state-of-the-art tagging model. We report ontologies, labeling results, model performances, and detailed analyses of the results. Our results show that the entities related to medications can be extracted with a relatively high accuracy of 0.90 F-score, followed by symptoms at 0.72 F-score, and conditions at 0.57 F-score. In our task, we not only identify where the symptoms are mentioned but also map them to canonical forms as they appear in the clinical notes. Of the different types of errors, in about 19-38% of the cases, we find that the model output was correct, and about 17-32% of the errors do not impact the clinical note. Taken together, the models developed in this work are more useful than the F-scores reflect, making it a promising approach for practical applications.

Recently we proposed the Span Attribute Tagging (SAT) Model to infer clinical entities (e.g., symptoms) and their properties (e.g., duration). It tackles the challenge of large label space and limited training data using a hierarchical two-stage approach that identifies the span of interest in a tagging step and assigns labels to the span in a classification step. We extend the SAT model to jointly infer not only entities and their properties but also relations between them. Most relation extraction models restrict inferring relations between tokens within a few neighboring sentences, mainly to avoid high computational complexity. In contrast, our proposed Relation-SAT (R-SAT) model is computationally efficient and can infer relations over the entire conversation, spanning an average duration of 10 minutes. We evaluate our model on a corpus of clinical conversations. When the entities are given, the R-SAT outperforms baselines in identifying relations between symptoms and their properties by about 32% (0.82 vs 0.62 F-score) and by about 50% (0.60 vs 0.41 F-score) on medications and their properties. On the more difficult task of jointly inferring entities and relations, the R-SAT model achieves a performance of 0.34 and 0.45 for symptoms and medications respectively, which is significantly better than 0.18 and 0.35 for the baseline model. The contributions of different components of the model are quantified using ablation analysis.

This paper describes novel models tailored for a new application, that of extracting the symptoms mentioned in clinical conversations along with their status. Lack of any publicly available corpus in this privacy-sensitive domain led us to develop our own corpus, consisting of about 3K conversations annotated by professional medical scribes. We propose two novel deep learning approaches to infer the symptom names and their status: (1) a new hierarchical span-attribute tagging (SA-T) model, trained using curriculum learning, and (2) a variant of sequence-to-sequence model which decodes the symptoms and their status from a few speaker turns within a sliding window over the conversation. This task stems from a realistic application of assisting medical providers in capturing symptoms mentioned by patients from their clinical conversations. To reflect this application, we define multiple metrics. From inter-rater agreement, we find that the task is inherently difficult. We conduct comprehensive evaluations on several contrasting conditions and observe that the performance of the models range from an F-score of 0.5 to 0.8 depending on the condition. Our analysis not only reveals the inherent challenges of the task, but also provides useful directions to improve the models.

This paper presents a novel framework, MGNER, for Multi-Grained Named Entity Recognition where multiple entities or entity mentions in a sentence could be non-overlapping or totally nested. Different from traditional approaches regarding NER as a sequential labeling task and annotate entities consecutively, MGNER detects and recognizes entities on multiple granularities: it is able to recognize named entities without explicitly assuming non-overlapping or totally nested structures. MGNER consists of a Detector that examines all possible word segments and a Classifier that categorizes entities. In addition, contextual information and a self-attention mechanism are utilized throughout the framework to improve the NER performance. Experimental results show that MGNER outperforms current state-of-the-art baselines up to 4.4% in terms of the F1 score among nested/non-overlapping NER tasks.

Being able to recognize words as slots and detect the intent of an utterance has been a keen issue in natural language understanding. The existing works either treat slot filling and intent detection separately in a pipeline manner, or adopt joint models which sequentially label slots while summarizing the utterance-level intent without explicitly preserving the hierarchical relationship among words, slots, and intents. To exploit the semantic hierarchy for effective modeling, we propose a capsule-based neural network model which accomplishes slot filling and intent detection via a dynamic routing-by-agreement schema. A re-routing schema is proposed to further synergize the slot filling performance using the inferred intent representation. Experiments on two real-world datasets show the effectiveness of our model when compared with other alternative model architectures, as well as existing natural language understanding services.

Distantly supervised relation extraction greatly reduces human efforts in extracting relational facts from unstructured texts. However, it suffers from noisy labeling problem, which can degrade its performance. Meanwhile, the useful information expressed in knowledge graph is still underutilized in the state-of-the-art methods for distantly supervised relation extraction. In the light of these challenges, we propose CORD, a novelCOopeRativeDenoising framework, which consists two base networks leveraging text corpus and knowledge graph respectively, and a cooperative module involving their mutual learning by the adaptive bi-directional knowledge distillation and dynamic ensemble with noisy-varying instances. Experimental results on a real-world dataset demonstrate that the proposed method reduces the noisy labels and achieves substantial improvement over the state-of-the-art methods.

Answer selection is an important but challenging task. Significant progresses have been made in domains where a large amount of labeled training data is available. However, obtaining rich annotated data is a time-consuming and expensive process, creating a substantial barrier for applying answer selection models to a new domain which has limited labeled data. In this paper, we propose Knowledge-aware Attentive Network (KAN), a transfer learning framework for cross-domain answer selection, which uses the knowledge base as a bridge to enable knowledge transfer from the source domain to the target domains. Specifically, we design a knowledge module to integrate the knowledge-based representational learning into answer selection models. The learned knowledge-based representations are shared by source and target domains, which not only leverages large amounts of cross-domain data, but also benefits from a regularization effect that leads to more general representations to help tasks in new domains. To verify the effectiveness of our model, we use SQuAD-T dataset as the source domain and three other datasets (i.e., Yahoo QA, TREC QA and InsuranceQA) as the target domains. The experimental results demonstrate that KAN has remarkable applicability and generality, and consistently outperforms the strong competitors by a noticeable margin for cross-domain answer selection.