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Register a new userFast, Structured Clinical Documentation via Contextual Autocomplete
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Added by
Divya Gopinath
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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We present a system that uses a learned autocompletion mechanism to facilitate rapid creation of semi-structured clinical documentation. We dynamically suggest relevant clinical concepts as a doctor drafts a note by leveraging features from both unstructured and structured medical data. By constraining our architecture to shallow neural networks, we are able to make these suggestions in real time. Furthermore, as our algorithm is used to write a note, we can automatically annotate the documentation with clean labels of clinical concepts drawn from medical vocabularies, making notes more structured and readable for physicians, patients, and future algorithms. To our knowledge, this system is the only machine learning-based documentation utility for clinical notes deployed in a live hospital setting, and it reduces keystroke burden of clinical concepts by 67% in real environments.
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Autoregressive sequence models achieve state-of-the-art performance in domains like machine translation. However, due to the autoregressive factorization nature, these models suffer from heavy latency during inference. Recently, non-autoregressive sequence models were proposed to reduce the inference time. However, these models assume that the decoding process of each token is conditionally independent of others. Such a generation process sometimes makes the output sentence inconsistent, and thus the learned non-autoregressive models could only achieve inferior accuracy compared to their autoregressive counterparts. To improve then decoding consistency and reduce the inference cost at the same time, we propose to incorporate a structured inference module into the non-autoregressive models. Specifically, we design an efficient approximation for Conditional Random Fields (CRF) for non-autoregressive sequence models, and further propose a dynamic transition technique to model positional contexts in the CRF. Experiments in machine translation show that while increasing little latency (8~14ms), our model could achieve significantly better translation performance than previous non-autoregressive models on different translation datasets. In particular, for the WMT14 En-De dataset, our model obtains a BLEU score of 26.80, which largely outperforms the previous non-autoregressive baselines and is only 0.61 lower in BLEU than purely autoregressive models.
Knowledge is captured in the form of entities and their relationships and stored in knowledge graphs. Knowledge graphs enhance the capabilities of applications in many different areas including Web search, recommendation, and natural language understanding. This is mainly because, entities enable machines to understand things that go beyond simple tokens. Many modern algorithms use learned entity embeddings from these structured representations. However, building a knowledge graph takes time and effort, hence very costly and nontrivial. On the other hand, many Web sources describe entities in some structured format and therefore, finding ways to get them into useful entity knowledge is advantageous. We propose an approach that processes entity centric textual knowledge sources to learn entity embeddings and in turn avoids the need for a traditional knowledge graph. We first extract triples into the new representation format that does not use traditional complex triple extraction methods defined by pre-determined relationship labels. Then we learn entity embeddings through this new type of triples. We show that the embeddings learned from our approach are: (i) high quality and comparable to a known knowledge graph-based embeddings and can be used to improve them further, (ii) better than a contextual language model-based entity embeddings, and (iii) easy to compute and versatile in domain-specific applications where a knowledge graph is not readily available
Thanks to the increasing availability of drug-drug interactions (DDI) datasets and large biomedical knowledge graphs (KGs), accurate detection of adverse DDI using machine learning models becomes possible. However, it remains largely an open problem how to effectively utilize large and noisy biomedical KG for DDI detection. Due to its sheer size and amount of noise in KGs, it is often less beneficial to directly integrate KGs with other smaller but higher quality data (e.g., experimental data). Most of the existing approaches ignore KGs altogether. Some try to directly integrate KGs with other data via graph neural networks with limited success. Furthermore, most previous works focus on binary DDI prediction whereas the multi-typed DDI pharmacological effect prediction is a more meaningful but harder task. To fill the gaps, we propose a new method SumGNN: knowledge summarization graph neural network, which is enabled by a subgraph extraction module that can efficiently anchor on relevant subgraphs from a KG, a self-attention based subgraph summarization scheme to generate a reasoning path within the subgraph, and a multi-channel knowledge and data integration module that utilizes massive external biomedical knowledge for significantly improved multi-typed DDI predictions. SumGNN outperforms the best baseline by up to 5.54%, and the performance gain is particularly significant in low data relation types. In addition, SumGNN provides interpretable prediction via the generated reasoning paths for each prediction.
Millions of unsolicited medical inquiries are received by pharmaceutical companies every year. It has been hypothesized that these inquiries represent a treasure trove of information, potentially giving insight into matters regarding medicinal products and the associated medical treatments. However, due to the large volume and specialized nature of the inquiries, it is difficult to perform timely, recurrent, and comprehensive analyses. Here, we propose a machine learning approach based on natural language processing and unsupervised learning to automatically discover key topics in real-world medical inquiries from customers. This approach does not require ontologies nor annotations. The discovered topics are meaningful and medically relevant, as judged by medical information specialists, thus demonstrating that unsolicited medical inquiries are a source of valuable customer insights. Our work paves the way for the machine-learning-driven analysis of medical inquiries in the pharmaceutical industry, which ultimately aims at improving patient care.
The Clair library is intended to simplify a number of generic tasks in Natural Language Processing (NLP), Information Retrieval (IR), and Network Analysis. Its architecture also allows for external software to be plugged in with very little effort. Functionality native to Clairlib includes Tokenization, Summarization, LexRank, Biased LexRank, Document Clustering, Document Indexing, PageRank, Biased PageRank, Web Graph Analysis, Network Generation, Power Law Distribution Analysis, Network Analysis (clustering coefficient, degree distribution plotting, average shortest path, diameter, triangles, shortest path matrices, connected components), Cosine Similarity, Random Walks on Graphs, Statistics (distributions, tests), Tf, Idf, Community Finding.
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