PreprintPDF Available

DeepDoc: Natural Language Processing with Deep Neural Networks for the American Board of Internal Medicine Certification Exam

Authors:
Preprints and early-stage research may not have been peer reviewed yet.
Preprint

DeepDoc: Natural Language Processing with Deep Neural Networks for the American Board of Internal Medicine Certification Exam

Abstract and Figures

High quality practice and decision making is dependent on knowledge of a small team of physicians. With the growing amount of diagnoses, tests, and procedures, there is much room for improvement with clinical decision support technologies. We train a model to answer review questions for the American Board of Internal Medicine Certification Exam. We adapt approaches traditionally used for question answer tasks to our multiple choice exam, as well as experiment with the following enhancements: PubMed Embeddings, BiDAF, DrQA, SAR, GA, and RACE. Ultimately we find that GA models perform best (Accuracy: 0.38, AUROC: 0.64). Our work is an initial study towards the development of a intelligent medical QA system, demonstrating the capability of modern day machine learning to answer questions clinicians typically take many years to study for.
Content may be subject to copyright.
DeepDoc: Natural Language Processing with Deep
Neural Networks for the American Board of Internal
Medicine Certification Exam
Jonathan Wang
Biomedical Informatics
jonwang1@stanford.edu
Britni Chau
Computer Science
britnic@stanford.edu
Kinbert Chou
Computer Science
klchou@stanford.edu
Abstract
High quality practice and decision making is dependent on knowledge of a small
team of physicians. With the growing amount of diagnoses, tests, and procedures,
there is much room for improvement with clinical decision support technologies.
We train a model to answer review questions for the American Board of Internal
Medicine Certification Exam. We adapt approaches traditionally used for question
answer tasks to our multiple choice exam, as well as experiment with the following
enhancements: PubMed Embeddings, BiDAF, DrQA, SAR, GA, and RACE. Ul-
timately we find that GA models perform best (Accuracy: 0.38, AUROC: 0.64).
Our work is an initial study towards the development of a intelligent medical QA
system, demonstrating the capability of modern day machine learning to answer
questions clinicians typically take many years to study for.
1 Introduction
Despite the rapid and widely successful incorporation of artificial intelligence into a plethora of
different industries, when it comes to medicine, much of high quality practice and decision making is
dependent almost entirely upon a single physician. Providing high quality medical care consistently
involves a combination of clinical experience and knowledge derived from literature(
1
;
2
). However,
with the progressively growing number of possible medications, diagnoses, and procedures, applying
high quality care becomes more difficult to maintain, requiring larger amounts of time and resources
(
3
;
4
). Hence, physicians tend to rely on personal intuition, rather than data from robust scientific
studies, in clinical practice (5).
To our knowledge, no clinical information systems exist which query and answer natural language
questions in a way similar to Google search engine for medical professionals. The current study
proposes an initial foray into the development of an intelligent question and answer bot for medical
questions. This serves to save physicians valuable time through two functions 1) information retrieval
of protocols and facts 2) literature review to maintain clinical knowledge. Our interest is to take a
first pass at this through the development of an algorithm which answers American Internal Medicine
Board Examinations—a certification that all physicians must go through to practice general internal
medicine. Though a number of companies claim to have had success in developing these algorithms
(
6
;
7
;
8
), to our knowledge, none of them have reported these results or algorithms. Without published
findings, it is difficult to reproduce and further progress on the development of these algorithms (
9
).
Thus, this remains a potentially impactful problem to solve and would facilitate further development
of medical question answering algorithms.
1.1 Objective
First, we will gather data points by scraping board exam questions from a reputed question resource
(that we can not disclose due to privacy reasons). Then we will implement a variety of neural
1
network-based algorithms to demonstrate the capability of algorithms perform in the task of medical
question answering.
2 Related Work
Open-domain Question-Answering (QA) systems generally consist of two parts 1) a document
retriever that retrieves relevant information for answering a question, and 2) reading comprehension
to find answer within a smaller selection of text.
The first document retriever systems developed by Simmons in 1964 focused on matching dependency
parses of questions and answers to find relevant parts within a text corpus (
10
). Since then, a variety
of approaches have been pioneered namely Murax in 1993 (
11
) and NIST TREC QA in 1999 (
12
).
IBM"s DeepQA (
13
) brought much attention to this problem but ultimately, DrQA is widely known
as one of the first effective neural reading comprehension information retrievers (
14
). For this reason,
we choose to use DrQAs information retrieval in our analysis due to its demonstrated effectiveness
and readily available code.
Initial natural language processing (NLP) for reading comprehension focused on simpler reading
comprehension methods developed by Schank, Hirschman, and Burges (
15
;
16
;
17
). In 2016,
advances in computing power and data availability resulted in the first well-performing neural systems
for reading comprehension. The Stanford Question Answering Dataset (SqUAD) has facilitated
lots of advancement in the field especially through the public leaderboard (
18
). Namely two simple
networks have came out of these developments, Stanford Attentive Reader (SAR) and Gated Attention
Reader (GA) (
19
;
20
). We choose both of these due to their simplicity of implementation and high
performance.
Our NLP task is multiple choice, thus it strays away from open-domain Question-Answering because
we have one more input, the set of answers, and a different output, the probability of each answer.
RACE is the largest dataset to our knowledge that uses modern day machine learning to answer
multiple choice questions (21). We adapt code for their SAR and GA, and use it for our own task.
Finally, we looked at QA systems currently being implemented in medical contexts. The main
clinical decision support system used today is UpToDate which simply retrieves articles of relevant
information (
22
). MedQA and MEANS attempt to answer questions through ontologies and semantic
web technologies, but neither leverage neural networks for reading comprehension (
23
;
24
). We
could not find any literature citing the use of neural networks to answer questions for the American
Medical Board Examinations.
3 Methods and Experiments
3.1 Data
3.1.1 Collection
Our data is pulled from 3,600 American Board of Internal Medicine Certification Exam review
questions. Due to privacy concerns, we are unable to disclose the source. Each question is comprised
of a question, accompanying context passage, and 4 or 5 answer choice selections. Once an answer
choice is selected, the correct answer, explanation passage, key point, and learning objective are
revealed. There may be images or tables in the question and/or explanation. The exam website
dynamically loads questions using Javascript, thus downloading and parsing HTML files directly
did not provide the information we desired. We use Charles Web Debugging Proxy to identify the
location the of the API that the Javascript calls to request the information (
25
). We then use a Python
script adapted from StackOverflow to scrape these examples from the API to obtain raw text data
(
26
;
27
). Ultimately, 3564 examples were scraped from 2012, 2015, and 2018 exams, where 36 were
removed due to missing information.
3.2 Preprocessing
We used Regex and BeautifulSoup to parse the following fields for each question (
28
). An example
of a passage, question, explanation, and answer choices can be found in Appendix A.
2
Question ID (str): UUID of example
Question (str): Question
Passage (str): Contextual information
for question
Answer Choices (dict): key is answer
choice (char), value is answer choice de-
scriptor (str)
Learning Objective (str): Learning ob-
jective of the question
Key Point (str): Key idea needed to an-
swer the question properly
Distribution of Answer Selections
(list[float]): the percent distribution of
answer selections made my human test
takers
Question Type (str): Category of ques-
tion (cardiovascular, neurology, etc)
Year (str): Year question was published
Table in Explanation (bool)
Image in Explanation (bool)
Table in Passage (bool)
Image in Passage (bool)
The resulting splits are: Train: 2364 examples (2012, 2016 data), Dev: 600 examples (half of 2018
data), Test: 600 examples (half of 2018 data).
3.3 Prediction Task
Our question answering task is defined as the following. Given a passage
p
, question
q
, and a list of
4-5 candidate answers ai, our system will select the the correct answer.
We also adapt the task such that the question answering system has access to a corpus of text to help
it answer the question (Fig 1). In this case, we use explanations from the training set as this corpus of
text, with the intuition that similar question’s explanations may contain useful information. In this
case, the true explanation
e
is used for the training set, and an explanation retrieved from the training
set via an information retriever
ˆe
is used for the dev and test set. This is explained in more detail
within the DrQA section.
Figure 1: High-level architecture of our system. DrQA retrieves top three relevant explanations.
The retrieved explanations, passage, question, and answer options are fed as inputs into a reading
comprehension algorithm to output a prediction.
3.4 Architectures
For this project, our focus was on the adaption of existing work for a new problem. Additional
experiments and architectures are described in detail. Diagrams for each of the different architectures
can be found in Appendix B.
3.4.1 BiDAF Baseline
The Bidirectional Attention Flow model (BiDAF) is a machine comprehension question answering
model (
29
). The BiDAF model takes as input a context and a question answerable by a span of that
context. This input is transformed into pre-trained word embedding vectors, which are further refined
through another embedding layer that learns to adjust the word vectors based on context of the input.
Finally, a bidirectional attention layer that models the similarity of words between the context and
answer conditions an LSTM layer to generate the predicted spans.
3
For our baseline, we adapted the default BiDAF model provided to suit multiple choice question
answering. Instead of using the SQuAD dataset, we use our passage, question, and answer choices
from the medical exam.
To adjust the model for multiple choice question answering, we model each example as follows:
P A ={p;< sep >;a1;...;< sep >;a5}
Q={q}
P A
consists of the question passage pre-pended to each answer choice descriptor. Each answer
choice descriptor is pre-pended by a separation token token as shown above.
Q
consists of the
corresponding question. The max tokenized length of
P A
is 461 and
Q
is 37. We pad all inputs to
this corresponding length.
We first use the embedding layer to derive glove word embeddings from our padded inputs. The
embeddings are then passed through an adapted highway, encoding, and modeling layer from the
default BiDAF baseline. For our output layer, we used linear transformations to combine the attention
and LSTM outputs. However, since the question is multiple choice, we modify the architecture to
identify the SEP token for the corresponding answer. To do this, we remove the second LSTM and
linear layer used find the ending of the span. To find the appropriate SEP token, we use a mask at all
indices except those occupied by SEP tokens prior to applying the final softmax. Thus, this gives us
a probability distribution over our 4 or 5 answer choices. In prediction, we take the argmax of the
resulting probabilities as our predicted answer selection.
The modeling of the multiple choice question structure has, to our knowledge, never been tried before.
The intuition is that SEP token hidden states will learn to highlight whether or not the answer follows
it. The bidirectional flow will help identify what portions of question and the context/answer that
matter when looking for the SEP token of interest.
3.4.2 Stanford Attentive Reader Baseline
We adapt the implementation of the Stanford Attentive Reader (SAR) baseline for RACE, a multiple
choice question answering dataset (
19
;
21
). The input to SAR is a tuple of query,
u
, composed of
question passage prepended to question, the correct answer explanation passage,
e
, and answers:
{u, e, a1, ...a5}
. Instead of bidirectional LSTMs, RACE uses bidirectional Gated Recurrent Units
(GRU) to encode the embedding representation of
u
to
hu
,
e
to
he
1...he
n
, and
ai
to
hai
. GRUs are used
because they are easy to modify and do not require memory units; they perform similarly to LSTMs
and train more quickly. RACE then uses a bilinear attention defined by
αi=softmaxi((he
i)TW1hu)
,
se= Σialphaihe
i
between each explanation passage position and the question to summarize the most
relevant part of the explanation with respect to the question (
se
). Next, once more using the bilinear
attention a similarity score is determined between summarized explanation and each option. We alter
the model such that if the question originally had four options, the dummy coded fifth option has a
score that is masked to 0. The argmax of the softmax of the scores is returned as the model’s answer
prediction: predi=sof tmaxi(haiW2se).
3.4.3 Gated Attention Reader Baseline
We adapt the implementation of the Gated Attention Reader (GA) baseline for RACE as well (
20
;
21
).
The input to Gated Attention Reader (GA) is a tuple of query,
u
composed of question passage
prepended to question, the correct answer explanation passage,
e
, and answers:
{u, e, a1, ...a5}
. GA
reader derives a multi-hop representation of the query and explanation by fine tuning the query and
explanation’s embedding representations iteratively across hops. The idea is that its learning mimics
the comprehension processing pattern of humans, in that the semantic understanding of the words
of the passage are developed over multiple passes of the passage in relation to having understood
the query. This is the benefit of multiple hop architecture in contrast to previous models that are
restricted to token or sentence level attention. The passage is read over
k
hops, where the input
x
to the
k
th layer is the bidirectional GRU encoding of the embedding of the explanation from the
k1
layer:
ek=
GRU
k
e(x(k1))
. Over
k
hops, the query is is refined in tangent using a separate
bidirectional GRU:
uk=
GRU
k
u(y)
. Per hop, a multiplicative attention mechanism of the form
4
αi=softmax(uTei)
,
˜ui=i
,
xi=ei˜ui
is applied to extract the most relevant parts of the
explanation in relation to query. Multiplicative attention is used because it has been found to be more
effective as a fine-grained sentiment filter than additive attention. Once all
k
hops have been made
and the final representation of the explanation,
se
, has been attained, RACE’s implementation of
GA applies a bilinear attention between option and summarized explanation to derive a similarity
score. We alter the model such that if the question originally had four options, the dummy coded fifth
option has a score that is masked to 0. The argmax of the softmax of the scores is returned as the
model’s answer prediction:
predi=sof tmaxi(haiW se)
. Note that RACE’s implementation of GA
disregards character level word embeddings.
3.5 Modifications and Experiments
3.5.1 Varying Options Lengths
We altered the BiDAF Baseline to answer multiple choice questions, as described in 3.4.1. Addition-
ally, we alter the SAR and GA baselines to answer 4-5 multiple choice questions through a mask
applied to the dummy coded fifth option prior to the final softmax.
3.5.2 Bio-NLP Embeddings
Bio-NLP 2016 is a neural word embedding trained on scientific literature from PubMed (
30
). In
place of GloVe embeddings, we use Bio-NLP embeddings to encode
p
,
q
,
a1...a5
. Our initial GLoVE
embeddings yielded embeddings for 74% of tokenized words in our vocabulary. The implemented
PubMed embeddings yielded embeddings for 90% of words, suggesting vocabulary within our
examples contain rarer medical nomenclature. Additionally, the PubMed embeddings demonstrate
a slight increase in performance in comparison to the raw baselines (Table 1). Note that we used
default embeddings for our baselines, this meant that the GLoVE embeddings used in SQuAD
were dimension 300, while in SAR and GA they were dimension 100. Meanwhile, the PubMed
embeddings were dimension 200. Thus, this improvement in accuracy may be due to the differing
embedding sizes rather than the embeddings themselves.
3.5.3 DrQA
DrQA is a question answering system characterized by its unique breakdown of the question an-
swering task. Unlike rote KB QA methods which typically uses a non-sophisticated search function
to extract documents from a domain, DrQA applies state of the art methods to extract the most
relevant documents in its knowledge domain (Document Retriever), then predict the answer from
those documents (Document Reader).
This differs from search and Knowledge-Based (KB) QA systems such as IBM Watson (
13
) whose
performance heavily relies on repetitively seeing accurate information, or SQuAD which assumes no
prior knowledge in its answers and whose answers can be found in the short accompanying text to its
questions (
18
). Due to our limited data we can’t rely on breadth of knowledge domain to answer our
questions. Furthermore, unlike SQuAD, the exam requires prior knowledge to solve its questions.
Thus we try to implement a document retriever method to improve performance for our task.
We adapt DrQA’s document retriever to our task as follows: First, each explanation provided in
the training set serves as a document. In total, there are 2364 documents. TF-IDF weighting using
bigram feature vectors determine the similarity between document and a query represented by the
concatenation of passage, question, and the four-five answer options
{p;q;a1;...a5}
. Due to the
additional complexity added from the use of bigram instead of bag-of-words feature vectors, Murmur3
hashing is used to preserve time and space efficiency. We then feed the top three retrieved documents
along with the original inputs {p;q},{a1...a5}into SAR and GA for the dev and test set (described
in more deetail below). Thus, instead of having the inputs of
{p}
,
{q},{a1...a5}
, the DrQA model
will have inputs of
{ˆe}
,
{p;q},{a1...a5}
. In the training set, we use the true explanations
e
instead
of DrQA retrieved explanations
hate
so the model learns on documents that actually contain signal.
The intuition here is that similar explanations from previous iterations of the test may have useful
information for answering a given question in the dev/test set.
To retrieve documents from DrQA, we query using passage, question, and answers concatenated into
a single string
{p;q},{a1...a5}
. To determine what to query with, we performed a brief analysis of
5
what queries would yield the true explanation most frequently. We found that question, passage, and
answer yielded over 87% accuracy within the top 3 documents. However, dropping answers yielded
only around 46% accuracy within the top 3 documents, which suggests there is a highly correlated
mapping between answers and explanations. When we tried answers alone, this yielded an even
higher accuracy of around 93% in the top three. Using such a small amount of text to query would not
yield robust matches when looking for relevant explanations that don’t directly match the question,
so we choose to use the top 3 documents from a {p;q},{a1...a5}query.
To make use of the three retrieved articles in the dev/test set, we run the model three times on each of
the articles separately before ensembling using a 0.5, 0.3, 0.2 weighting scheme on the probability
outputs. This weighted scheme is based on the percentage of times the first, second, or third document
retrieved was the true explanation as decribed above.
3.5.4 Hyperparamater Tuning
To improve the performance of the final models, we perform hyperparameter tuning using random
search over a hyperparameter space. Appendix C contains information on the default hyperparameters
used for the models, as well as the search space used in our hyperparameter search.
Out of 138 sets of parameters, the set
{
learning rate 0.570811, dropout rate 0.80538, gradient clipping
10.730696, epochs 50, hidden size 6
}
resulted in the best performance for GA with a dev accuracy
of 38.6%. Out of 153 sets of parameters, the set
{
learning rate 0.079253, dropout rate 0.605804,
gradient clipping 5.93294, epochs 67, hidden size 58
}
resulted in the best performance for SAR with
a dev accuracy of 38.1%.
We tuned each model for 32 hours, totaling 64 GPU hours.
Our results show that tuning improved performance for SAR, but decreased performance on GA
(Table 1). We suspect that this is likely due having too large of a search space and not enough GPU
computing hours.
3.5.5 Ensembling
We ensemble the two tuned models by averaging their probability outputs. This gave a very slight
improvement in model performance (0.2% accuracy) (Table 1).
4 Evaluation
4.1 Evaluation Metrics
We only report multi-class accuracy in lieu of f1, precision, and recall. This is because our questions
have between four and five answer choices. Thus, when we reconstructed the analysis into a one vs
all format (essentially flatenning the predicted probabilities in the nx5 array and removing the fifth
column for rows without a fifth question), micro-averaged f1, precision, and recall are mathematically
equivalent to accuracy.
Our scraped review questions also contain the percentage of people who answered the question
correctly. We create a weighted score metric that weights each question by (1-percentage answered
correctly). This captures how well the algorithm does on questions people are not generally good at
answering. For example, if 90% of people answer a question correctly, it will have a 0.1 weight.
Finally we report micro-averaged AUROC, which represents the ability of the model to distinguish
between correct and incorrect answers.
4.2 Results
Overall, our results demonstrate that GA w/ DrQA appears to be the best model for this problem
with an accuracy of 0.37, weighted score of 0.36, and AUROC of 0.64. (Table 1). This is actually
reasonable performance, as passing the exam generally requires around 50-60% accuracy, with a
top performers scoring around 85%. Additionally, on the RACE dataset, these same state of the
art algorithms only perform with an accuracy of 43% (with a human ceiling performance of 93%).
6
Figure 2: Precision-Recall curve for top per-
forming models and baselines.
Figure 3: ROC curve for top performing mod-
els and baselines.
Table 1: Evaluation metrics show outperformance of GA over SAR models. Here, the ensembled
model represents averaged probability outputs from the two tuned models. BiDAF = Bidirectional
Attention Flow model; SAR = Stanford Attnetive Reader model; GA = Gated Attention Model;
BioEmbeddings = embeddings extracted from Bio-NLP group; *= includes BioEmbeddings; bold
indicates highest score in each category.
Model Accuracy Weighted Score AUROC
Random 0.222 0.234 0.500
BiDAF Baseline 0.273 0.255 0.571
SAR Baseline 0.310 0.304 0.588
GA Baseline 0.360 0.341 0.626
SAR w/ BioEmbeddings 0.322 0.301 0.605
GA w/ BioEmbeddings 0.377 0.344 0.638
SAR w/ DrQA* 0.325 0.299 0.616
GA w/ DrQA* 0.373 0.357 0.640
SAR w/ DrQA and tuning* 0.335 0.309 0.634
GA w/ DrQA and tuning* 0.335 0.302 0.628
Ensembled Model 0.337 0.308 0.633
We speculate this may be due to the ability of GA to capture long-term dependencies through its
multi-hop architecture.
We plot Precision-Recall Curve to demonstrate the tradeoff between true positive rate and positive
predictive value for our top performing SAR and GA models compared to baselines 2. We also plot
an ROC curve to demonstrate the tradeoff between sensitivity and specificity for these same models
3. These are generated using a flattened version of the array of scores, with a removed fifth column
for questions without a fifth answer to account for varying number of options. This is also known as
micro averaging.
Additionally, we evaluate the ensembled model (average of the two tuned SAR and GA models) with
true explanations
e
in comparison to using drQA to find relevant explanations from the training set
ˆe
(Table 2). Surprisingly, we perform only slightly better with correct explanations, despite training
on data with correct explanations. This strongly suggests that our reading comprehension model
is not performing well for this task as it is unable to find relevant information from even the true
explanations. We believe this may be due to the longer lengths that our inputs now contain, as GRUs
perform better at understanding shorter spans of text, and these longer spans of text may not work
well with the neural network architectures employed.
5 Qualitative analysis
It is hard to diagnose whether errors are a result of information retrieval or reading comprehension
due to the blackbox nature of neural network architectures. Thus, we looked at the top 5 examples (15
explanations) that had the highest probability score for the correct answer. Additionally, we looked at
the bottom 5 examples (15 explanations) that had the lowest probability score for the correct answer
7
Table 2: Ensembled model with correct explanations shows little improvement over predictions using
DrQA retrieved explanations. Bold indicates highest score in each category.
Model Accuracy Weighted Score AUROC
Correct Explanations 0.340 0.304 0.639
DrQA Explanations 0.337 0.308 0.633
from our ensembled model. These examples were then randomized, and we had a team member
label whether the retrieved explanations were relevant to the question or whether the explanation was
helpful in answering the question or not (Table 3).
As shown, in only very few cases the returned explanation appears to be helpful (7-13%). Thus, when
we retrieve the top three explanations, only about 30% of the questions contain useful information
in the retrieved explanations. Many times the retrieved explanation appears to contain information
relevant to only one answer choice rather than all four or five answer choices. Ultimately this reveals
that our information retrieval system does not seem to be grabbing documents with information as
useful as the explanations from . In light of the results from Table 2, it appears that both reading
comprehension and our document retriever could benefit from additional modifications.
Table 3: Qualitative analysis reveals our information retrieval system only retrieves helpful explana-
tions 6-13% of the time.
Examples Relevant Explanation (%) Helpful Explanation (%)
Top 5 26.6 13.3
Bottom 5 20.0 6.6
We additionally performed an analysis of the model performance on questions with images and with
tables within the passage. We found there was little difference (within 2% accuracy) in performance
on these questions.
6 Conclusions, Limitations, Future Work
This study is the first to our knowledge to tackle the problem of answering questions to the American
Internal Medical Board physician certification examination. Within the span of 5 weeks, we are able
to adapt existing state of the art network architectures used for the RACE dataset to answer questions
with an accuracy of 38%. This is surprisingly good performance, considering a passing score on the
exam is around 50-60% and initial models trained on the RACE dataset were around 43%. Upon
making the leaderboard public, scores on the RACE dataset improved to 75%, we hope a similar
dataset and effort can be made for medical questions in the future. This could rapidly progress the
field in a way that could save physicians time and improve the standard of care.
As noted in our discussion, there is great room for improvement in both our neural reading compre-
hension algorithms as well as our document retriever. We are limited by the amount of data publicly
available for these exams, as well as time to tune our hyperparameters. Additionally, as with many
neural network architectures, diagnosing errors in the model is difficult to the black box nature of the
algorithms. Having access to past explanations for questions in a model is also a relatively unrealistic
way to represent information gathered from outside sources, however, in theory, physicians should
have access to this information as well prior to taking an exam.
Future work in this area would include more creative ways of leveraging outside information with
DrQA, for example, through Wikipedia or PubMed. Additionally, we are interested in experimenting
with other network architectures including character level-embeddings or Bio-BERT (
31
). Finally, it
would be compelling to externally validate our model on a real-world exam made publicly available.
7 Additional Information
Mentor: Suvadip Paul
8
External Collaborators:
We have two advisors for the project: Yuhao Zhang, a graduate
student with Christopher Manning, and Jonathan Chen, an assistant professor in the division
of Biomedical Informatics Research in the Department of Medicine
Sharing Project:
Jonathan Wang is sharing the data with CS270 class, where they are
working on the same dataset for a different prediction task.
References
[1]
D. L. Sackett, W. M. C. Rosenberg, J. A. M. Gray, R. B. Haynes, and W. S. Richardson,
“Evidence based medicine: what it is and what it isn’t,” 1996.
[2]
G. H. Guyatt, D. L. Sackett, J. C. Sinclair, R. Hayward, D. J. Cook, R. J. Cook, E. Bass,
H. Gerstein, B. Haynes, A. Holbrook, and Others, “Users’ guides to the medical literature: IX.
A method for grading health care recommendations,” Jama, vol. 274, no. 22, pp. 1800–1804,
1995.
[3]
S. Timmermans and A. Mauck, “The promises and pitfalls of evidence-based medicine,Health
Affairs, vol. 24, no. 1, pp. 18–28, 2005.
[4]
D. T. Durack, “The weight of medical knowledge.,” The New England journal of medicine,
vol. 298, no. 14, pp. 773–5, 1978.
[5]
R. Madhok, “Crossing the Quality Chasm: Lessons from Health Care Quality Improvement
Efforts in England,Baylor University Medical Center Proceedings, vol. 15, no. 1, pp. 77–83,
2017.
[6]
Dom Galeon, “This robot has passed a medical licensing exam with flying colours | World
Economic Forum.
[7] “CloudMedx Clinical AI outperforms human doctors on a US medical exam.”
[8] “This AI Just Beat Human Doctors On A Clinical Exam.”
[9]
Sam Finnikin, “Babylon’s ‘chatbot’ claims were no more than clever PR | Article | Pulse Today.”
[10]
R. F. Simmons, “Natural language question-answering systems: 1969,” Communications of the
ACM, vol. 13, no. 1, pp. 15–30, 1970.
[11]
J. Kupiec, “Murax: A robust linguistic approach for question answering using an on-line
encyclopedia,” in Proceedings of the 16th annual international ACM SIGIR conference on
Research and development in information retrieval, pp. 181–190, ACM, 1993.
[12]
E. M. Voorhees and D. M. Tice, “The trec-8 question answering track evaluation,” in TREC,
vol. 1999, p. 82, Citeseer, 1999.
[13]
D. Ferrucci, A. Levas, S. Bagchi, D. Gondek, and E. T. Mueller, “Watson: beyond jeopardy!,
Artificial Intelligence, vol. 199, pp. 93–105, 2013.
[14]
D. Chen, A. Fisch, J. Weston, and A. Bordes, “Reading Wikipedia to Answer Open-Domain
Questions,” mar 2017.
[15] R. C. Schank, “The yale ai project,” SAM–A story understander, Research Rept, vol. 43, 1975.
[16]
L. Hirschman, M. Light, E. Breck, and J. D. Burger, “Deep read: A reading comprehension
system,” in Proceedings of the 37th annual meeting of the Association for Computational Lin-
guistics on Computational Linguistics, pp. 325–332, Association for Computational Linguistics,
1999.
[17]
M. Richardson, C. J. Burges, and E. Renshaw, “Mctest: A challenge dataset for the open-domain
machine comprehension of text,” in Proceedings of the 2013 Conference on Empirical Methods
in Natural Language Processing, pp. 193–203, 2013.
[18]
P. Rajpurkar, R. Jia, and P. Liang, “Know what you don’t know: Unanswerable questions for
squad,” CoRR, vol. abs/1806.03822, 2018.
9
[19]
D. Chen, J. Bolton, and C. D. Manning, “A Thorough Examination of the CNN/Daily Mail
Reading Comprehension Task,” jun 2016.
[20]
B. Dhingra, H. Liu, Z. Yang, W. W. Cohen, and R. Salakhutdinov, “Gated-Attention Readers
for Text Comprehension,” jun 2016.
[21]
G. Lai, Q. Xie, H. Liu, Y. Yang, and E. Hovy, “RACE: Large-scale ReAding Comprehension
Dataset From Examinations,” apr 2017.
[22]
T. Isaac, J. Zheng, and A. Jha, “Use of uptodate and outcomes in us hospitals,Journal of
hospital medicine, vol. 7, no. 2, pp. 85–90, 2012.
[23]
M. Lee, J. Cimino, H. R. Zhu, C. Sable, V. Shanker, J. Ely, and H. Yu, “Beyond information
retrieval—medical question answering,” in AMIA annual symposium proceedings, vol. 2006,
p. 469, American Medical Informatics Association, 2006.
[24]
A. B. Abacha and P. Zweigenbaum, “Means: A medical question-answering system combining
nlp techniques and semantic web technologies,” Information processing & management, vol. 51,
no. 5, pp. 570–594, 2015.
[25]
“Charles Web Debugging Proxy
HTTP Monitor / HTTP Proxy / HTTPS & SSL Proxy /
Reverse Proxy.
[26] G. v. . C. v. W. e. I. C. Rossum, “Python tutorial,” Python, 1995.
[27] “How to scrape a website that requires login first with Python - Stack Overflow.”
[28] “Beautiful Soup Documentation — Beautiful Soup 4.4.0 documentation.”
[29]
M. Seo, A. Kembhavi, A. Farhadi, and H. Hajishirzi, “Bidirectional Attention Flow for Machine
Comprehension,” nov 2016.
[30]
B. Chiu, G. Crichton, A. Korhonen, and S. Pyysalo, “How to Train good Word Embeddings for
Biomedical NLP,” pp. 166–174, 2016.
[31]
J. Lee, W. Yoon, S. Kim, D. Kim, S. Kim, C. H. So, and J. Kang, “BioBERT: a pre-trained
biomedical language representation model for biomedical text mining,” jan 2019.
8 Appendix
8.1 Appendix A: Example of a Review Question
Passage:
A 76-year-old woman is evaluated in the emergency department for dizziness, shortness of
breath, and palpitations that began acutely one hour ago. She has a history of hypertension and heart
failure with preserved ejection fraction. Medications are hydrochlorothiazide, lisinopril, and aspirin.
On physical examination, she is afebrile, blood pressure is 80/60 mm Hg, pulse rate is 155/min,
and respiration rate is 30/min. Oxygen saturation is 80% with 40% oxygen by face mask. Cardiac
auscultation reveals an irregularly irregular rhythm, tachycardia, and some variability in S1 intensity.
Crackles are heard bilaterally one-third up in the lower lung fields.
Electrocardiogram demonstrates atrial fibrillation with a rapid ventricular rate.
Question: Which of the following is the most appropriate acute treatment?
Answer Options: A. Adenosine B. Amiodarone C. Cardioversion D. Diltiazem E. Metoprolol
Correct answer: C. Cardioversion.
Explanation:
This patient with atrial fibrillation is hemodynamically unstable and should undergo
immediate cardioversion. She has hypotension and pulmonary edema in the setting of rapid atrial
fibrillation. In patients with heart failure with preserved systolic function, usually due to hypertension,
the loss of the atrial “kick” with atrial fibrillation can sometimes lead to severe symptoms. The best
treatment in this situation is immediate cardioversion to convert the patient to normal sinus rhythm.
Although there is a risk of a thromboembolic event since she is not anticoagulated, she is currently in
10
extremis and is at risk of imminent demise if not aggressively treated. In addition, she acutely became
symptomatic 1 hour ago, and while this is not proof that she developed atrial fibrillation very recently,
her risk of thromboembolism is low if the atrial fibrillation developed within the previous 48 hours.
Adenosine can be useful for diagnosing a supraventricular tachycardia and can treat atrioventricular
node-dependent tachycardias such as atrioventricular nodal reentrant tachycardia, but it is not useful
in the treatment of atrial fibrillation.
Amiodarone can convert atrial fibrillation to normal sinus rhythm as well as provide rate control, but
immediate treatment is needed and amiodarone may take several hours to work. Oral amiodarone
may be a reasonable option for long-term atrial fibrillation prevention in this patient given the severity
of her symptoms, especially if she has significant left ventricular hypertrophy.
Metoprolol or diltiazem would slow her heart rate; however, she is hypotensive and these medications
could make her blood pressure lower. In addition, she is in active heart failure, and metoprolol or
diltiazem could worsen the pulmonary edema.
Key Point:
Patients with atrial fibrillation who are hemodynamically unstable should undergo
immediate cardioversion.
8.2 Appendix B: Neural Network Architecture Diagrams
Images taken from their respective papers.
Figure 4: BiDAF Model (29)
11
Figure 5: Stanford Attentive Reader Model (19)
Figure 6: Gated Attention Reader Model (20)
8.3 Appendix C: Hyperparameter tuning details
For the BiDAF baseline, we use the default tuning parameters provided. The initial SAR parameters
are: dropout rate 0.5, batch size 64, num epochs 100, sgd optimizer, learning rate 0.01, gradient
clipping 10, hidden size 100.
The initial GA parameters are: dropout 0.5, batch size 64, num epochs 100, sgd optimizer, learning
rate 0.3, gradient clipping 10, hidden size 125. These are based on best parameters found in the
RACE paper.
Since both models appear to be overfitting (by greater than 10% difference between training and dev
set accuracy), we increased dropout rate. We tuned parameters in the following ranges: learning rate
with logarithmic distribution (0.01,1), number of epochs with uniform distribution (50,80), dropout
rate with uniform distribution (0.4,1), gradient clipping with uniform distribution (4,14), and hidden
size with uniform distribution (SAR: (50,125), GA: (60,130)). All other parameters maintained their
default values.
12
ResearchGate has not been able to resolve any citations for this publication.
Conference Paper
Full-text available
Article
Full-text available
This paper presents a vision for applying the Watson technology to health care and describes the steps needed to adapt and improve performance in a new domain. Specifically, it elaborates upon a vision for an evidence-based clinical decision support system, based on the DeepQA technology, that affords exploration of a broad range of hypotheses and their associated evidence, as well as uncovers missing information that can be used in mixed-initiative dialog. It describe the research challenges, the adaptation approach, and finally reports results on the first steps we have taken toward this goal.
Article
Machine Comprehension (MC), answering questions about a given context, re-quires modeling complex interactions between the context and the query. Recently, attention mechanisms have been successfully extended to MC. Typically these mechanisms use attention to summarize the query and context into a single vectors, couple attentions temporally, and often form a unidirectional attention. In this paper we introduce the Bidirectional Attention Flow (BIDAF) Model, a multi-stage hierarchical process that represents the context at different levels of granularity and uses a bi-directional attention flow mechanism to achieve a query-aware context representation without early summarization. Our experimental evaluations show that our model achieves the state-of-the-art results in Stanford QA(SQuAD) and CNN/DailyMail Cloze Test datasets.
Conference Paper
Enabling a computer to understand a document so that it can answer comprehension questions is a central, yet unsolved goal of NLP. A key factor impeding its solution by machine learned systems is the limited availability of human-annotated data. Hermann et al. (2015) seek to solve this problem by creating over a million training examples by pairing CNN and Daily Mail news articles with their summarized bullet points, and show that a neural network can then be trained to give good performance on this task. In this paper, we conduct a thorough examination of this new reading comprehension task. Our primary aim is to understand what depth of language understanding is required to do well on this task. We approach this from one side by doing a careful hand-analysis of a small subset of the problems and from the other by showing that simple, carefully designed systems can obtain accuracies of 72.4% and 75.8% on these two datasets, exceeding current state-of-the-art results by over 5% and approaching what we believe is the ceiling for performance on this task.
Article
In this paper we study the problem of answering cloze-style questions over short documents. We introduce a new attention mechanism which uses multiplicative interactions between the query embedding and intermediate states of a recurrent neural network reader. This enables the reader to build query-specific representations of tokens in the document which are further used for answer selection. Our model, the Gated-Attention Reader, outperforms all state-of-the-art models on several large-scale benchmark datasets for this task---the CNN \& Dailymail news stories and Children's Book Test. We also provide a detailed analysis of the performance of our model and several baselines over a subset of questions manually annotated with certain linguistic features. The analysis sheds light on the strengths and weaknesses of several existing models.
Article
THE ULTIMATE PURPOSE of applied health research is to improve health care. Summarizing the literature to adduce recommendations for clinical practice is an important part of the process. Recently, the health sciences community has reduced the bias and imprecision of traditional literature summaries and their associated recommendations through the development of rigorous criteria for both literature overviews1-3 and practice guidelines.4,5 Even when recommendations come from such rigorous approaches, however, it is important to differentiate between those based on weak vs strong evidence. Recommendations based on inadequate evidence often require reversal when sufficient data become available,6 while timely implementation of recommendations based on strong evidence can save lives.6 In this article, we suggest an approach to classifying strength of recommendations. We direct our discussion primarily at clinicians who make treatment recommendations that they hope their colleagues will follow. However, we believe that any clinician who attends to