Kai Chen
Kai Chen is a software engineer at Google. He received a Ph.D. in Computer Science from the University of Illinois at Urbana-Champaign in 2004. He is currently working on applied machine learning in healthcare and natural language processing. Previously he has worked on ML in online advertising. For a list of publications, please see his Google Scholar profile.
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Extracting Symptoms and their Status from Clinical Conversations
Nan Du
Linh Tran
Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics, Florence, Italy (2019), pp. 915-9125
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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 (SAT) 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.
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Automatically Charting Symptoms From Patient-Physician Conversations Using Machine Learning
Alvin Rishi Rajkomar
Kat Chou
Journal of the American Medical Association (2019)
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Introduction: Auto-charting -- creation structured sections of clinical notes generated directly from a patient-doctor encounter -- holds promise to lift documentation burden from physicians. However, clinicians exercise professional judgement in what and how to document, and it is unknown if a machine learning (ML) model could assist with these tasks.
Objective: Build a ML model to extract symptoms and status (i.e. experienced, not-experienced, not relevant for note) from transcripts of patient-doctor encounters and assess performance on common symptoms and conversations in which a human interpreterscribe is not used.
Methods: We generated a ML model to auto-generate a review of systems (ROS) from transcripts of 90,000 de-identified medical encounters. 2950 transcripts were labeled by medical scribes to identify 171 common symptoms. Model accuracy was stratified by how clearly a symptom was mentioned in conversation for 800 snippets, which was assessed by a formal rating system termed conversational clarity. The model was also qualitatively assessed in a variety of conversational motifs.
Results: Overall, the model had a sensitivity of 0.71 of matching the exact symptom labeled by a human with a positive predictive value of 0.69. Model sensitivity was associated with the clarity of a conversational (p<0.0001). 39.5% (316/800) snippets of common symptoms contained symptoms mentioned with high clarity, and in this group, the sensitivity of the model was 0.91. The model was robust to a variety of conversational motifs (e.g. detecting symptoms mentioned in colloquial ways).
Conclusions: Auto-generating a review of systems is feasible across a wide-range symptoms that are commonly discussed in doctor-patient encounter
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Current end-to-end Q&A models are primarily based on recurrent neural networks with attention. Despite their success, these models are often slow for both training and inference. We propose a novel Q&A model that does not require recurrent networks yet achieves equivalent or better performance than existing models. Our model is simple in that it consists exclusively of attention and convolutions. We present a thorough study of architectural choices that improve the accuracy of this simple model.
We also propose a novel data augmentation technique that not only enhances the training examples but also diversifies the phrasing of the sentences. It results in immediate improvement in the accuracy. This technique is of independent interest that it can be readily applied to other natural language processing tasks.
On the SQuAD dataset, our model is 3x faster in training and 10x faster in inference. The model achieves 82.2 F1 score on the development set, which is on par with best documented result of 81.8.
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Scalable and accurate deep learning for electronic health records
Alvin Rishi Rajkomar
Eyal Oren
Nissan Hajaj
Mila Hardt
Xiaobing Liu
Jake Marcus
Patrik Per Sundberg
Kun Zhang
Yi Zhang
Gerardo Flores
Gavin Duggan
Jamie Irvine
Kurt Litsch
Alex Mossin
Justin Jesada Tansuwan
De Wang
Dana Ludwig
Samuel Volchenboum
Kat Chou
Michael Pearson
Srinivasan Madabushi
Nigam Shah
Atul Butte
npj Digital Medicine (2018)
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Predictive modeling with electronic health record (EHR) data is anticipated to drive personalized medicine and improve healthcare quality. Constructing predictive statistical models typically requires extraction of curated predictor variables from normalized EHR data, a labor-intensive process that discards the vast majority of information in each patient’s record. We propose a representation of patients’ entire raw EHR records based on the Fast Healthcare Interoperability Resources (FHIR) format. We demonstrate that deep learning methods using this representation are capable of accurately predicting multiple medical events from multiple centers without site-specific data harmonization. We validated our approach using de-identified EHR data from two U.S. academic medical centers with 216,221 adult patients hospitalized for at least 24 hours. In the sequential format we propose, this volume of EHR data unrolled into a total of 46,864,534,945 data points, including clinical notes. Deep learning models achieved high accuracy for tasks such as predicting: in-hospital mortality (AUROC across sites 0.93-0.94), 30-day unplanned readmission (AUROC 0.75-0.76), prolonged length of stay (AUROC 0.85-0.86), and all of a patient’s final discharge diagnoses (frequency-weighted AUROC 0.90). These models outperformed state-of-the-art traditional predictive models in all cases. We also present a case-study of a neural-network attribution system, which illustrates how clinicians can gain some transparency into the predictions. We believe that this approach can be used to create accurate and scalable predictions for a variety of clinical scenarios, complete with explanations that directly highlight evidence in the patient’s chart.
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In this work we present a method for semi-supervised learning
from transcripts of dialogue between humans. We consider
the scenario in which a large amount of transcripts are available,
and we would like to extract some semantic information from
them; however, only a small number of transcripts have been
labeled with this information. We present a method for leveraging
the unlabeled data to learn a better model than could be
learned from the labeled data alone. First, a recurrent neural
network (RNN) encoder-decoder is trained on the task of predicting
nearby turns on the full dialogue corpus; next, the RNN
encoder is reused as a feature representation for the supervised
learning problem. While previous work has explored the use of
pre-training for non-dialogue corpora, our method is specifically
geared toward the dialogue use case. We demonstrate an improvement
on a clinical documentation task, particularly in the
regime of small amounts of labeled data. We compare several
types of encoders, both in the context of a classification task and
in a human-evaluation of their learned representations. We show
that our method significantly improves the classification task in
the case where only a small amount of labeled data is available.
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Efficient Estimation of Word Representations in Vector Space
Tomas Mikolov
International Conference on Learning Representations (2013)
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We propose two novel model architectures for computing continuous vector representations of words from very large data sets. The quality of these representations is measured in a word similarity task, and the results are compared to the previously best performing techniques based on different types of neural networks. We observe large improvements in accuracy at much lower computational cost, i.e. it takes less than a day to learn high quality word vectors from a 1.6 billion words data set. Furthermore, we show that these vectors provide state-of-the-art performance on our test set for measuring syntactic and semantic word similarities.
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Distributed Representations of Words and Phrases and their Compositionality
Tomas Mikolov
Ilya Sutskever
Neural and Information Processing System (NIPS) (2013)
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The recently introduced continuous Skip-gram model is an efficient method for
learning high-quality distributed vector representations that capture a large number
of precise syntactic and semantic word relationships. In this paper we present
several extensions that improve both the quality of the vectors and the training
speed. By subsampling of the frequent words we obtain significant speedup and
also learn more regular word representations. We also describe a simple alternative
to the hierarchical softmax called negative sampling.
An inherent limitation of word representations is their indifference to word order
and their inability to represent idiomatic phrases. For example, the meanings of
“Canada” and “Air” cannot be easily combined to obtain “Air Canada”. Motivated
by this example, we present a simple method for finding phrases in text, and show
that learning good vector representations for millions of phrases is possible.
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Building high-level features using large scale unsupervised learning
Marc'Aurelio Ranzato
Rajat Monga
Matthieu Devin
Andrew Ng
International Conference in Machine Learning (2012)
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We consider the problem of building highlevel, class-specific feature detectors from only unlabeled data. For example, is it possible to learn a face detector using only unlabeled images?
To answer this, we train a 9-layered locally connected sparse autoencoder with pooling and local contrast normalization on a large dataset of images (the model has 1 billion connections, the dataset has 10 million 200x200 pixel images downloaded from the Internet). We train this network using model parallelism and asynchronous SGD on a cluster with 1,000 machines (16,000 cores) for three days. Contrary to what appears to be a widely-held intuition, our experimental results reveal that it is possible to train a face detector without having to label images as containing a face or not. Control experiments show that this feature detector is robust not only to translation but also to scaling and out-of-plane rotation. We also find that the same network is sensitive to other high-level concepts such as cat faces and human bodies. Starting with these learned features, we trained our network to obtain 15.8% accuracy in recognizing 20,000 object categories from ImageNet, a leap of 70% relative improvement over the previous state-of-the-art.
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Large Scale Distributed Deep Networks
Rajat Monga
Matthieu Devin
Mark Z. Mao
Marc’Aurelio Ranzato
Paul Tucker
Ke Yang
Andrew Y. Ng
NIPS (2012)
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Recent work in unsupervised feature learning and deep learning has shown that being able to train large models can dramatically improve performance. In this paper, we consider the problem of training a deep network with billions of parameters using tens of thousands of CPU cores. We have developed a software framework called DistBelief that can utilize computing clusters with thousands of machines to train large models. Within this framework, we have developed two algorithms for large-scale distributed training: (i) Downpour SGD, an asynchronous stochastic gradient descent procedure supporting a large number of model replicas, and (ii) Sandblaster, a framework that supports a variety of distributed batch optimization procedures, including a distributed implementation of L-BFGS. Downpour SGD and Sandblaster L-BFGS both increase the scale and speed of deep network training. We have successfully used our system to train a deep network 30x larger than previously reported in the literature, and achieves state-of-the-art performance on ImageNet, a visual object recognition task with 16 million images and 21k categories. We show that these same techniques dramatically accelerate the training of a more modestly- sized deep network for a commercial speech recognition service. Although we focus on and report performance of these methods as applied to training large neural networks, the underlying algorithms are applicable to any gradient-based machine learning algorithm.
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