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  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Achieving Expert-Level Annotation Quality with CrowdTruth</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Anca Dumitrache</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Lora Aroyo</string-name>
          <email>lora.aroyog@vu.nl</email>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Chris Welty</string-name>
          <email>cawelty@gmail.com</email>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Google Research</institution>
          ,
          <addr-line>New York</addr-line>
          ,
          <country country="US">USA</country>
        </aff>
        <aff id="aff1">
          <label>1</label>
          <institution>IBM CAS</institution>
          ,
          <addr-line>Amsterdam</addr-line>
          ,
          <country country="NL">Netherlands</country>
        </aff>
        <aff id="aff2">
          <label>2</label>
          <institution>VU University Amsterdam</institution>
          ,
          <country country="NL">Netherlands</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>The lack of annotated datasets for training and benchmarking is one of the main challenges of Clinical Natural Language Processing. In addition, current methods for collecting annotation attempt to minimize disagreement between annotators, and therefore fail to model the ambiguity inherent in language. We propose the CrowdTruth method for collecting medical ground truth through crowdsourcing, based on the observation that disagreement between annotators can be used to capture ambiguity in text. In this work, we report on using this method to build a ground truth for medical relation extraction, and how it performed in training a classi cation model. Our results show that, with appropriate processing, the crowd performs just as well as medical experts in terms of the quality and e cacy of annotations. Furthermore, we show that the general practice of employing a small number of annotators for collecting ground truth is faulty, and that more annotators per sentence are needed to get the highest quality annotations.</p>
      </abstract>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>-</title>
      <p>
        Clinical Natural Language Processing (NLP) has become an invaluable tool for
navigating and processing medical data [
        <xref ref-type="bibr" rid="ref19">19</xref>
        ]. Clinical NLP relies on the
development of a set of gold standard annotations, or ground truth, for the purpose
of training, testing and evaluation. Ground truth is usually collected by humans
reading text and following a set of guidelines to ensure a uniform understanding
of the annotation task. In the medical domain, domain knowledge is usually
believed to be required from annotators, making the process for acquiring ground
truth more di cult. The lack of annotated datasets for training and
benchmarking is considered one of the big challenges of Clinical NLP [
        <xref ref-type="bibr" rid="ref8">8</xref>
        ].
      </p>
      <p>
        Furthermore, the process behind acquiring ground truth often presents aws [
        <xref ref-type="bibr" rid="ref5">5</xref>
        ].
It is assumed that the gold standard represents a universal and reliable model
for language. However, previous experiments we performed in medical relation
extraction [
        <xref ref-type="bibr" rid="ref2">2</xref>
        ] identi ed two issues with this assumption: (1) disagreement
between annotators is usually eliminated through overly prescriptive annotation
guidelines, thus creating arti cial data that is neither general nor re ects the
ambiguity inherent in natural language, and (2) the process of acquiring ground
truth by working exclusively with domain experts is costly and non-scalable,
both in terms of time and money.
      </p>
      <p>
        A possible solution to these issues is using crowdsourcing for collecting the
ground truth. Not only is this a much faster and cheaper procedure than expert
annotation, it also allows for collecting enough annotations per task in order to
represent the diversity inherent in language. Crowd workers, however, generally
lack medical expertise, which might impact the quality and reliability of their
work in more knowledge-intensive tasks. Previously, we studied medical relation
extraction in a relatively small set of 90 sentences [
        <xref ref-type="bibr" rid="ref3">3</xref>
        ], comparing the results from
the crowd with that of two expert medical annotators. We found that
disagreement within the crowd is consistent with expert inter-annotator disagreement.
Furthermore, sentences that registered high disagreement tended to be vague or
ambiguous when manually evaluated.
      </p>
      <p>Our approach, called CrowdTruth, can overcome the limitations of gathering
expert ground truth, by using disagreement analysis on crowd annotations to
model the ambiguity inherent in medical text. Furthermore, we claim that, even
for complex annotation tasks such as relation extraction, lack of medical
expertise of the crowd is compensated by collecting a large enough set of annotations.
We prove this in two ways, by manually judging the quality of the annotations
provided by experts and the crowd, and more importantly by training a model
for medical relation extraction with both CrowdTruth data and ground truth
from medical experts, and comparing them in a cross-validation experiment.</p>
      <p>In this paper, we make the following contributions: (1) a comparison of the
quality and e cacy of annotations for medical relation extraction provided by
both crowd and medical experts, showing that crowd annotations are equivalent
to those of experts, with appropriate processing; (2) an openly available dataset
of 900 English sentences for medical relation extraction, centering primarily on
the cause relation, that have been processed with disagreement analysis and
by experts; (3) an analysis of the optimal crowd settings for medical relation
extraction, showing that 10 workers per sentence yields the highest quality
annotations.
2</p>
    </sec>
    <sec id="sec-2">
      <title>Related Work</title>
      <p>
        There exists some research using crowdsourcing to collect semantic data for the
medical domain. [
        <xref ref-type="bibr" rid="ref18">18</xref>
        ] use crowdsourcing to verify relation hierarchies in
biomedical ontologies. On 14 relations from the SNOMED CT CORE Problem List
Subset, the authors report the crowd's accuracy at 85% for identifying whether
the relations were correct or not. In the eld of Biomedical NLP, [
        <xref ref-type="bibr" rid="ref7">7</xref>
        ] used
crowdsourcing to extract the gene-mutation relations in Medical Literature Analysis
and Retrieval System Online (MEDLINE) abstracts. Focusing on a very speci c
gene-mutation domain, the authors report a weighted accuracy of 82% over a
corpus of 250 MEDLINE abstracts. Both of these approaches present preliminary
results from experiments performed with small datasets.
      </p>
      <p>
        To our knowledge, the most extensive study of medical crowdsourcing was
performed by [
        <xref ref-type="bibr" rid="ref23">23</xref>
        ], who describe a method for crowdsourcing a ground truth for
medical named entity recognition and entity linking. In a dataset of over 1,000
clinical trials, the authors show no statistically signi cant di erence between the
crowd and expert-generated gold standard for the task of extracting medications
and their attributes. We extend these results by applying crowdsourcing to the
more complex task of medical relation extraction, that prima facie seems to
require more domain expertise than named entity recognition. Furthermore, we
test the viability of crowdsourced ground truth for relation extraction.
      </p>
      <p>
        Crowdsourcing ground truth has shown promising results in a variety of other
domains. [
        <xref ref-type="bibr" rid="ref13">13</xref>
        ] compared the crowd versus experts for the task of part-of-speech
tagging. The authors also show that models trained based on crowdsourced
annotation can perform just as well as expert-trained models. [
        <xref ref-type="bibr" rid="ref15">15</xref>
        ] studied
crowdsourcing for relation extraction in the general domain, comparing its e ciency to
that of fully automated information extraction approaches. Their results showed
the crowd was especially suited to identifying subtle formulations of relations
that do not appear frequently enough to be picked up by statistical methods.
      </p>
      <p>
        Other research for crowdsourcing ground truth includes: entity clustering
and disambiguation [
        <xref ref-type="bibr" rid="ref16">16</xref>
        ], Twitter entity extraction [
        <xref ref-type="bibr" rid="ref12">12</xref>
        ], multilingual entity
extraction and paraphrasing [
        <xref ref-type="bibr" rid="ref9">9</xref>
        ], and taxonomy creation [
        <xref ref-type="bibr" rid="ref10">10</xref>
        ]. However, all of these
approaches rely on the assumption that one black-and-white gold standard must
exist for every task. Disagreement between annotators is discarded by picking one
answer that re ects some consensus, usually through using majority vote. The
number of annotators per task is also kept low, between two and ve workers,
also in the interest of eliminating disagreement. The novelty in our approach is
to consider language ambiguity, and consequently inter-annotator disagreement,
as an inherent feature of the language. The metrics we employ for determining
the quality of crowd answers are speci cally tailored to quantify disagreement
between annotators, rather than eliminate it.
3
      </p>
    </sec>
    <sec id="sec-3">
      <title>Experimental Setup</title>
      <p>In order to perform the comparison between expert and crowdsourced gold
standards, we set up an experiment to train and evaluate a relation extraction model
for a sentence-level relation classi er. The classi er takes, as input, sentences and
two terms from the sentence, and returns a score re ecting the likelihood that a
speci c relation, in our case the cause relation between symptoms and disorders,
is expressed in the sentence between the terms. Starting from a set of 902
sentences that are likely to contain medical relations, we constructed a work ow for
collecting annotations through crowdsourcing. This output was analyzed with
CrowdTruth metrics for capturing disagreement, and then used to train a model
for relation extraction. In parallel, we also constructed a model based using a
traditional gold standard acquired from domain experts, that we then compare
to the crowd model.
3.1</p>
      <sec id="sec-3-1">
        <title>Data</title>
        <p>
          The dataset used in our experiments contains 902 medical sentences extracted
from PubMed article abstracts. The MetaMap parser [
          <xref ref-type="bibr" rid="ref1">1</xref>
          ] ran over the corpus to
identify medical terms from the UMLS vocabulary [
          <xref ref-type="bibr" rid="ref6">6</xref>
          ]. Distant supervision [
          <xref ref-type="bibr" rid="ref17">17</xref>
          ]
was used to select sentences with pairs of terms that are linked in UMLS by one
of our chosen seed medical relations. The intuition of distant supervision is that
since we know the terms are related, and they are in the same sentence, it is
more likely that the sentence expresses a relation between them (than just any
random sentence). The seed relations were restricted to a set of eleven UMLS
relations important for clinical decision making [
          <xref ref-type="bibr" rid="ref22">22</xref>
          ] (listed in Tab.1). Given a
relation, each sentence in the dataset can be either positive (i.e. the relation
is expressed between the two terms in the sentence), or negative (i.e. the
relation is not expressed). All of the data that we have used is available online at:
http://data.crowdtruth.org/medical-relex.
        </p>
        <p>For collecting annotations from medical experts, we employed medical
students, in their third year at American universities, that had just taken United
States Medical Licensing Examination (USMLE) and were waiting for their
results. Each sentence was annotated by exactly one person. The annotation task
consisted of deciding whether or not the UMLS seed relation discovered by
distant supervision is present in the sentence for the two selected terms.
3.2</p>
      </sec>
      <sec id="sec-3-2">
        <title>Crowdsourcing setup</title>
        <p>
          The crowdsourced annotation setup is based on our previous medical relation
extraction work [
          <xref ref-type="bibr" rid="ref4">4</xref>
          ], adapted into a work ow of three tasks (Fig.1). First, the
sentences were pre-processed using a named-entity recognition tool combining
the UMLS vocabulary with lexical parsing, to determine whether the terms
found with distant supervision are complete or not. The incomplete terms were
parsed through a crowdsourcing task (FactSpan) in order to get the full word
span of the medical terms. Next, the sentences with the corrected term spans
were sent to a relation extraction task (RelEx), where the crowd was asked to
decide which relation holds between the two extracted terms. To simplify the
task for the crowd, we combined the UMLS relations from distant supervision,
merging relations with similar meanings (e.g. disease has primary anatomic site
and has nding site). We also added four new relations (e.g. associated with),
to account for weaker, more general links between the terms. The full set of
the relations presented to the crowd is available in Tab.1. The workers were also
able to read the de nition of each relation. The task was multiple choice, workers
being able to choose more than one relation at the same time. There were also
options available for cases when the medical relation was other than the ones
we provided (other), and for when there was no relation between the terms
(none). Finally, the results from RelEx were passed to another crowdsourcing
        </p>
        <p>All three crowdsourcing tasks were run on the CrowdFlower platform 4 with
10-15 workers per sentence, to allow for a distribution of perspectives; the precise
settings for each task are available in Tab.2. Even with three tasks and 10-15
workers per sentence, compared to a single expert judgment per sentence, the
total cost of the crowd amounted to 2=3 of the sum paid for the experts. In
our case, cost was not the limiting factor for the experts, but their time and
availability.</p>
        <p>FactSpan RelEx RelDir
judgments (i.e. workers per sentence)
pay per sentence annotation (in $)
10
0.04
15
0.05
10
0.01</p>
        <p>
          http://CrowdFlower.com
crowdsourcing metrics [
          <xref ref-type="bibr" rid="ref14">14</xref>
          ], that have been successfully used to model relation
extraction [
          <xref ref-type="bibr" rid="ref4">4</xref>
          ]. These metrics attempt to model the crowdsourcing process based
on the triangle of reference [
          <xref ref-type="bibr" rid="ref20">20</xref>
          ], with the vertices being the input sentence, the
worker, and the seed relation. Ambiguity and disagreement at any of the vertices
(e.g. a sentence with unclear meaning, a poor quality worker, or an unclear
relation) will propagate in the system, in uencing the other components. For
example, a worker who annotates an unclear sentence is more likely to disagree
with the other workers, and this can impact that worker's quality. Therefore, the
CrowdTruth metrics model quality at each vertex in relation to all the others,
so that a high quality worker who annotates many low clarity sentences will
be recognized as high quality. In our work ow, these metrics are used both
to eliminate spammers [
          <xref ref-type="bibr" rid="ref21">21</xref>
          ], and to determine the clarity of the sentences and
relations. The main concepts are:
{ annotation vector: This construct is used to model the annotation of one
worker for one sentence. For each worker i submitting their solution to a task
on a sentence s, the vector Ws;i records their answers. If the worker selects
an answer, its corresponding component would be marked with `1', and `0'
otherwise. For instance, in the case of RelEx, the vector will have fourteen
components, one for each relation, as well as none and other.
{ sentence vector: This is the main component for modeling disagreement in
the crowdsourcing system. There is one such vector for every input sentence.
For every sentence s, it is computed by adding the annotation vectors for all
workers on the given task: Vs = Pi Ws;i .
{ sentence-annotation score: A core CrowdTruth concept, this metric computes
annotation ambiguity in a sentence with the use of cosine similarity. In the
case of RelEx, it becomes the sentence-relation score, and is computed as
the cosine similarity between the sentence vector and the unit vector for the
relation: srs(s; r) = cos(Vs; r^). The higher the value of this metric, the more
clearly the relation is expressed in the sentence.
3.4
        </p>
      </sec>
      <sec id="sec-3-3">
        <title>Training the model</title>
        <p>
          The sentences together with the relation annotations were then used to train a
manifold model for relation extraction [
          <xref ref-type="bibr" rid="ref22">22</xref>
          ]. This model was developed for the
medical domain, and tested for the relation set that we employ. It is trained
per individual relation, by feeding it both positive and negative data. It o ers
support for both discrete labels, and real values for weighting the con dence of
the training data entries, with positive values in (0; 1], and negative values in
[ 1; 0). Using this system, we train several models using ve-fold cross validation,
in order to compare performances of the crowd and expert dataset. In total, we
use four datasets:
1. baseline: Discrete (positive or negative) labels are given for each sentence
by the distant supervision method { for any relation, a positive example is
a sentence containing two terms related by cause in UMLS. This dataset
constitutes the baseline against which all other datasets are tested. Distant
supervision does not extract negative examples, so in order to generate a
negative set for one relation, we use positive examples for the other
(nonoverlapping) relations shown in Tab. 1.
2. expert: Discrete labels based on an expert's judgment as to whether the
baseline label is correct. The experts do not generate judgments for all
combinations of sentences and relations { for each sentence, the annotator decides on
the seed relation extracted with distant supervision. Similarly to the
baseline data, we reuse positive examples from the other relations to extend the
number of negative examples.
3. single: Discrete labels for every sentence are taken from one randomly selected
crowd worker who annotated the sentence. This data simulates the traditional
single annotator setting.
4. crowd: Weighted labels for every sentence are based on the CrowdTruth
sentence-relation score. The classi er expects positive scores for positive
examples, and negative scores for negative, so the sentence-relation scores must
be re-scaled. An important variable in the re-scaling is a threshold to
select positive and negative examples. The Results section compares the
performance of the crowd at di erent threshold values. Given a threshold, the
sentence-relation score is then linearly re-scaled into the [0:85; 1] interval for
the positive label weight, and the [ 1; 0:85] interval for negative. An
example of how the scores were processed is given in Tab.3.
3.5
        </p>
      </sec>
      <sec id="sec-3-4">
        <title>Evaluation setup</title>
        <p>In order for a meaningful comparison between the crowd and expert models,
the evaluation set needs to be carefully selected. The sentences in the test folds
were picked through the cross validation mechanism, but the scores were selected
from our test partition, which we veri ed to ensure correctness. To build the test
partition , we rst selected the positive/negative threshold for sentence-relation
score such that the crowd agrees the most with the experts. We assume that,
if both the expert and the crowd agree that a sentence is either a positive or
Sent.1: Renal osteodystrophy is a general complication of chronic renal failure and
end stage renal disease.</p>
        <p>Sent.2: If TB is a concern, a PPD is performed.
negative example, it can automatically be used as part of the test set. Such a
sentence was labeled with the crowd score. In the cases where the crowd and
experts disagree, we manually veri ed and assigned either a positive, negative,
or ambiguous value. The ambiguous cases were subsequently removed from the
test folds. In this way we created reliable, unbiased test scores, to be used in the
evaluation of the models.
4</p>
      </sec>
    </sec>
    <sec id="sec-4">
      <title>Results</title>
      <p>We compared each of the four datasets using the test partition as a gold standard,
to determine the quality of the cause relation annotations, as shown in Fig.2. As
expected, the baseline data performed the lowest, followed closely by the single
crowd worker. The expert annotations achieved an F1 score of 0.844. Since the
baseline, expert, and single sets are binary decisions, they appear as horizontal
lines. For the crowd annotations, we plotted the F1 against di erent
sentencerelation score thresholds for determining positive and negative sentences.
Between the thresholds of 0.6 and 0.8, the crowd out-performs the expert, reaching
the maximum of 0.907 F1 score at a threshold of 0.7. This di erence is signi cant
with p = 0:007, measured with McNemar's test. In Fig.3 we show the number
of sentences in which the crowd agrees with the expert (on both positive and
negative decisions), plotted against di erent positive/negative thresholds for the
sentence-relation score of cause. The maximum agreement with the expert set
is at the 0.7 threshold, the same as for the annotation quality F1 score (Fig.2),
with 755 sentences where crowd and expert agree.</p>
      <p>We next wanted to verify that this improvement in annotation quality has a
positive impact on the model that is trained with this data. In a cross-validation
experiment, we trained the model with each of the four datasets for
identifying the cause relation. The results of the evaluation (Fig.4) show the best
performance for the crowd model when the sentence-relation threshold for
deciding between negative/positive equals 0.5. Trained with this data, the classi er
model achieves an F1 score of 0.642, compared to the expert-trained model which
reaches 0.638. McNemar's test shows statistical signi cance with p = 0:016. This
result demonstrates that the crowd provides training data that is at least as good,
if not better than experts. In addition, the baseline scores an F1 of 0.575, and
the single annotator shows the worst performance, scoring at 0.483. The learning
curves (Fig.5) show that, above 400 sentences, the crowd consistently scores over
baseline and single in F1 score. After 600 sentences, the crowd also out-performs
the experts. The trend of the curve is still upward, indicating that more data is
necessary to get the best performance.</p>
      <p>Finally, we checked whether the number of workers per task was su cient
to produce a stable sentence-relation score. For the RelEx task, we ensured
that each sentence was checked by at least 10 workers, after spam removal.
The plot of the mean cosine distance between sentence vectors before and after
adding the latest worker shows that the sentence vector becomes stable after 10
workers (Fig. 6). Furthermore, the annotation quality F1 score per total number
of workers (Fig. 7) is also stable after 10 workers (the drop towards the end is
due to sparse data { only 54 sentences had 15 or more total workers).</p>
      <p>
        Our goal was to demonstrate that, like the crowdsourced medical entity
recognition work by Zhai et al. [
        <xref ref-type="bibr" rid="ref23">23</xref>
        ], the CrowdTruth approach of having multiple
annotators with precise quality scores can be harnessed to create gold standard
data with a quality that rivals annotated data created by medical experts. Our
results show this clearly, in fact with slight improvements, with a sizable dataset
(902 sentences) on a problem (relation extraction) that prima facie seems to
require more domain expertise. Tab.4 shows the results in more detail.
      </p>
      <p>
        The most curious aspect of the results is that the positive/negative
sentencerelation score threshold that gives the best quality annotations (Fig.2) is di erent
from the best threshold for training the model (Fig.4). It is the lower threshold
(equal to 0.5) that gives a better classi cation. This is most likely due to the
higher recall of the lower threshold, which exposes the classi er to more positive
examples. F-score is the harmonic mean between precision and recall, and does
not necessarily represent the best trade-o between them, as this experiment
shows. Indeed F-score may not be the best trade-o between precision and recall
for the classi er. In [
        <xref ref-type="bibr" rid="ref11">11</xref>
        ], we experimented with a weighted F-score, using the
CrowdTruth metrics to account for ambiguity in the sentences. Using this new
metric, we found an improved performance for both crowd and expert.
      </p>
      <p>It is also notable that the baseline out-performs the single annotator. This
could be an indicator that the crowd can only achieve quality when accounting
for the choices of multiple annotators. In addition, the recall score for baseline
is notably high. This could be a consequence of how the model performs its
training { one of the features it learns is the UMLS type of the terms. For cause,
term types are often enough to accurately qualify the relation.</p>
      <p>The learning curves (Fig.5) show we still have not reached the ideal amount
of training data, especially for the CrowdTruth approach, in which the weights
of sentences have less of a cumulative e ect, as opposed to datasets with binary
labels. In other words, when accounting for ambiguity in training, more data
points are needed to reach maximum performance. A bottleneck in this analysis
is the availability of expert annotations { we did not have the resources to collect
a larger expert dataset, and this indeed is the main reason to consider
crowdsourcing. It is also worth noting that, while the crowd annotations consistently
out-perform the distant-supervision baseline, we do not yet have a fair
comparison between a distant supervision approach and the CrowdTruth approach. The
real value of distant supervision is that large amounts of data can be gathered
rather easily and cheaply, since humans are not involved. We are working on
experiments to explore the trade-o between scale, quality, and cost, based on
the assumption that systems trained with either kind of data will eventually
reach a performance maximum.</p>
      <p>Finally, in Figs. 6 &amp; 7 we observe that we need at least 10 workers to get
a stable crowd score. This result goes against the general practice for building
a ground truth, where per task there usually are 2 to 5 annotators. Based on
our results, we believe that the general practice is wrong, and that outside of a
few clear cases, the input of more annotators is necessary to capture ambiguity.
Even with this added requirement, we found that crowdsourcing is still cheaper
than medical experts { the cost of the experts was 50% higher.
6</p>
    </sec>
    <sec id="sec-5">
      <title>Conclusion</title>
      <p>The lack of ground truth for training and benchmarking is one of the main
challenges of Clinical NLP. In addition, current methods for collecting annotation
attempt to minimize disagreement between annotators, but end up failing to
model the ambiguity inherent in language. We propose the CrowdTruth method
for crowdsourcing ground truth while also capturing and interpreting
disagreement. We used CrowdTruth to build a gold standard of 902 sentences for medical
relation extraction, which was employed in training a classi cation model. We
have shown that, with appropriate processing, the crowd performs just as well as
medical experts in terms of the quality and e cacy of annotations, while being
cheaper and more readily available. Our results indicate that at least 10 workers
per sentence are needed to get the highest quality annotations, in contrast to the
general practice of employing a small number of annotators for collecting ground
truth. We plan to continue our experiments by scaling out the crowdsourcing
approach, which has the possibility of performing better.</p>
    </sec>
    <sec id="sec-6">
      <title>Acknowledgments</title>
      <p>The authors would like to thank Chang Wang for support with using the medical
relation extraction classi er, and Anthony Levas for help with collecting the
expert annotations.</p>
    </sec>
  </body>
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