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  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Not just about size - A Study on the Role of Distributed Word Representations in the Analysis of Scienti c Publications</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Andres Garcia-Silva</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Jose Manuel Gomez-Perez</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Expert System</institution>
          ,
          <addr-line>C/ Profesor Waksman 10, 28036 Madrid, Spain (agarcia</addr-line>
        </aff>
      </contrib-group>
      <abstract>
        <p>The emergence of knowledge graphs in the scholarly communication domain and recent advances in arti cial intelligence and natural language processing bring us closer to a scenario where intelligent systems can assist scientists over a range of knowledge-intensive tasks. In this paper we present experimental results about the generation of word embeddings from scholarly publications for the intelligent processing of scienti c texts extracted from SciGraph. We compare the performance of domain-speci c embeddings with existing pre-trained vectors generated from very large and general purpose corpora. Our results suggest that there is a trade-o between corpus speci city and volume. Embeddings from domain-speci c scienti c corpora e ectively capture the semantics of the domain. On the other hand, obtaining comparable results through general corpora can also be achieved, but only in the presence of very large corpora of well formed text. Furthermore, we also show that the degree of overlapping between knowledge areas is directly related to the performance of embeddings in domain evaluation tasks.</p>
      </abstract>
      <kwd-group>
        <kwd>Word Embeddings</kwd>
        <kwd>Knowledge Graphs</kwd>
        <kwd>Scholarly publications</kwd>
        <kwd>Convolutional Neural Networks</kwd>
      </kwd-group>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>-</title>
      <p>
        In 2017 Springer Nature released the rst version of SciGraph1, an open linked
data graph about publications from the editorial group and cooperating partners.
This graph connects funders, research projects, grants, conferences, a liations,
and publications, and in the future it is planned to add citations, patents, and
clinical trials. This initiative is a step forward to bring semantics to scholarly
publications that contributes to the vision where software agents assist
scientists in their research endeavors [
        <xref ref-type="bibr" rid="ref12 ref7">12, 7</xref>
        ]. Nevertheless, publication content is still
largely text-based, and hence the limitations for the automatic understanding of
content, reproducibility of experiments [
        <xref ref-type="bibr" rid="ref1">1</xref>
        ], and knowledge reuse [
        <xref ref-type="bibr" rid="ref6">6</xref>
        ] remain.
      </p>
      <p>We envision a scenario where knowledge graphs about Scholarly
communications contain semantic metadata about the content of the publication beyond the
1 SciGraph homepage: https://www.springernature.com/gp/researchers/scigraph
traditional descriptors used, including keywords and taxonomy categories where
articles are placed by authors or editors. This content-based metadata could
describe the work hypothesis, conclusions and the approach followed, among
others. Therefore, natural language processing (NLP) is a key enabler to extract
structured data from scholarly publications that can semantically enrich and
shed light on the publication content.</p>
      <p>
        Recently, distributed word representations in the form of dense vectors, known
as word embeddings, have been used with great success in NLP tasks such as
part-of-speech tagging, chunking, named entity recognition, semantic role
labeling and synonym detection [
        <xref ref-type="bibr" rid="ref3">3</xref>
        ]. Vectors can be learned from large corpora using
shallow neural networks [
        <xref ref-type="bibr" rid="ref18">18</xref>
        ] or following count-based approaches that perform
matrix factorization [
        <xref ref-type="bibr" rid="ref14 ref19 ref22">19, 14, 22</xref>
        ]. Mikolov et al. [
        <xref ref-type="bibr" rid="ref18">18</xref>
        ] showed that embeddings
capture semantic relations between words, for example between man and woman,
or cities and countries, and syntactic relations based on tenses, singular and
plurals, comparatives, superlatives, to name a few, that can be mapped to basic
vector operations.
      </p>
      <p>
        In this paper we explore the use of word embeddings in the scholarly
communications domain through an empirical study. Our goal was to understand
whether learning embeddings from a corpus of scienti c publications yields
better results than using public, pre-trained embeddings generated from very large
and general corpora. We learned word embeddings from the publications
described in SciGraph. Then, since intrinsic evaluation strategies like word
analogies were of limited utility in this case, we used the available metadata contained
in the knowledge graph to perform a task-based evaluation consisting of
classifying publications along SciGraph's categories. Classi ers were learned through
neural networks, including Convolutionals [
        <xref ref-type="bibr" rid="ref3">3</xref>
        ] (CNN), which have shown good
performance in text classi cation tasks [
        <xref ref-type="bibr" rid="ref11">11</xref>
        ]. In the paper, we also re ect on the
ability of CNNs to learn features for the task at hand, which has been proved in
computer vision [
        <xref ref-type="bibr" rid="ref24">24</xref>
        ] but still is a matter of debate in text understanding.
      </p>
      <p>
        Evaluation results show a trade o between the knowledge speci city of
the corpus used to train the word embeddings and its size. In our
evaluation task, embeddings from a scienti c publication corpus consistently generate
classi ers with a top performance that is only matched by classi ers learned
from embeddings from very large document corpora such as Common Crawl
(http://commoncrawl.org), with 42 billion tokens, or a mix of Wikipedia, news
and the UMBC web corpus [
        <xref ref-type="bibr" rid="ref10">10</xref>
        ], with 16 billions tokens. Nevertheless, corpus size
seems to lose relevance as the amount of short and informal language it contains
increases, e.g. as in Twitter. In addition, we found that embeddings from very
speci c knowledge elds that are conceptually close tend to perform better in
our evaluation task than embeddings from knowledge elds with less overlap.
      </p>
      <p>The rest of the paper is structured as follows. In section 2 we brie y
describe SciGraph content and ontologies. Next, section 3 presents an overview
of approaches to generate word embeddings, focusing on FastText and GloVe,
that we use in our experiments. In section 4 we introduce the text classi cation
problem and convolutional neural networks to cope with limitations of
traditional linear algorithms. In Section 5 we describe our experiments and discuss
the results, and nally, in section 6 we present our conclusions.
2</p>
    </sec>
    <sec id="sec-2">
      <title>A Knowledge Graph for Scholarly Publications</title>
      <p>
        SciGraph is a linked open data platform for the scienti c domain. It comprises
information from the complete research process: research projects, conferences,
authors and publications, among others. It contains metadata for millions of
entities stored in triples. Currently the knowledge graph contains 1 billion facts
(triples) about objects of interest to the scholarly domain, distributed over some
85 million entities described using 50 classes and more than 250 properties [
        <xref ref-type="bibr" rid="ref9">9</xref>
        ].
Currently, most of the knowledge graph is available under CC BY 4.0 License
(i.e., attribution) with the exception of abstracts and grant metadata, which are
available under CC BY-NC 4.0 License (i.e., attribution and non-comercial)
      </p>
      <p>A core ontology expressed in OWL encodes the semantics of the data in
the knowledge graph consisting of 47 classes and 253 properties. Nevertheless,
the semantic metadata regarding the publication content is scarce. According to
the ontology, just two predicates provide some information at a very high level
of abstraction about the article content: i) sg:hasFieldOfResearchCode
property relates an Australian and New Zealand Standard Research Classi cation
(ANZSRC) Field of Research (FOR) code to a publication, and ii) sg:hasSubject
property relates a publication to a subject term which describes one of the main
topics the publication is about. In addition, text content of publication is limited
to titles and abstracts of research articles and book chapters.
3</p>
    </sec>
    <sec id="sec-3">
      <title>Word Embeddings</title>
      <p>
        Distributed word representations are based on the distributional hypothesis
where words that co-occurr in similar context are considered to have similar (or
related) meaning. Word embedding algorithms yield dense vectors so that words
with similar distributional context appear in the same region in the embedding
space [
        <xref ref-type="bibr" rid="ref22">22</xref>
        ]. Two main families of algorithms to generate embeddings have been
identi ed [
        <xref ref-type="bibr" rid="ref15 ref19">19, 15</xref>
        ]: global matrix factorization (count-based) [
        <xref ref-type="bibr" rid="ref14 ref19 ref22">14, 19, 22</xref>
        ], and local
context window methods (prediction) [
        <xref ref-type="bibr" rid="ref18">18</xref>
        ]. Nevertheless, Levy and Goldberg [
        <xref ref-type="bibr" rid="ref14">14</xref>
        ]
blurred that distinction, showing that local context window methods like the one
proposed by Mikolov et al. [
        <xref ref-type="bibr" rid="ref18">18</xref>
        ] are implicitly factorizing a word-context matrix,
whose cells are the pointwise mutual information (PMI) of the corresponding
word and context pairs, shifted by a global constant.
3.1
      </p>
      <sec id="sec-3-1">
        <title>Word2Vec: Distributed Word Representations</title>
        <p>
          The work by Mikolov et al. [
          <xref ref-type="bibr" rid="ref18">18</xref>
          ] brought back the research interest to word
embeddings in NLP since their approach reduced the computational
complexity required to generate word vectors, based on negative sampling and other
optimizations. This allowed training with much larger corpora than previous
architectures and their evaluation results showed that the vectors encoded
semantic and syntactic relations between words that could be calculated with
vector operations. They proposed two model architectures to compute
continuous word vectors from large datasets: Skip-gram and Continuous Bag-of-Words
Model (CBOW). The models were evaluated using semantic and syntactic
similarity test sets, with results showing that the Skip-gram model signi cantly
outperforms other architectures, specially in terms of semantic evaluation. On
the other hand, Levy et al. [
          <xref ref-type="bibr" rid="ref15">15</xref>
          ] showed that much of the performance gains
of word embeddings generated through these approaches are due to
hyperparameter optimizations and design choices, instead of the embedding algorithms
themselves. They also argued that these modi cations can be implemented in
matrix factorization approaches generating similar performance gains.
3.2
        </p>
      </sec>
      <sec id="sec-3-2">
        <title>FastText: Enriching Vectors with Subword Information</title>
        <p>
          Bojanowski et al. [
          <xref ref-type="bibr" rid="ref2">2</xref>
          ] proposed an evolution of the Skip-Gram model that takes
into account n-grams at the character level. The motivation behind it is
improving the representation of rare words and taking advantage of the words
structure, specially important in morphologically rich languages. This model combines
words and subwords in the form of character n-grams. They evaluate their model
with nine languages and di erent word similarity and analogies datasets. The
model outperforms Skip-gram and CBOW on almost every dataset. The results
also show that computing vectors for out-of-vocabulary words, by summing their
n-gram vectors, always obtains equal or better scores than not doing it.
3.3
        </p>
      </sec>
      <sec id="sec-3-3">
        <title>GloVe: Global Vectors for Word Representation</title>
        <p>
          Pennington et al. [
          <xref ref-type="bibr" rid="ref19">19</xref>
          ] proposed a model to generate word vectors by training
on the nonzero elements of a word coocurrence matrix, instead of training on
context windows for each word in the corpus. Their model performs more
efciently by grouping together coocurrence probabilities instead of training in
an online manner over the corpus. The model uses a weighted least squares
objective. The computational complexity is substantially reduced by training only
over the nonzero elements of the coocurrence matrix. Their experiments show
that GloVe outperforms Skip-gram and CBOW, among other approaches, while
substantially reducing the training time.
4
        </p>
      </sec>
    </sec>
    <sec id="sec-4">
      <title>Text Classi cation</title>
      <p>
        Classifying text documents in one or more classes is a main problem in NLP with
applications in e.g. sentiment analysis, spam detection, email sorting and
topicbased vertical search engines [
        <xref ref-type="bibr" rid="ref16">16</xref>
        ]. Naive Bayes (NB), their multinomial version
(MNB), and Support Vector Machines (SVM) models are frequently used for text
classi cation, depending on the problem to be addressed. For example, Wang et
al. [
        <xref ref-type="bibr" rid="ref23">23</xref>
        ] showed that NB performs better in sentiment analysis tasks with short
documents, while SVM obtains better results for longer texts. These algorithms
work in a highly dimensional space and therefore feature selection is required to
improve e ciency and accuracy. However, the choice of features is an empirical
task, often following a trial and error approach.
4.1
      </p>
      <sec id="sec-4-1">
        <title>Convolutional Neural Networks</title>
        <p>
          Convolutional neural networks (CNN) were originally proposed for image
recognition following a connectionist approach inspired on the visual cortex of the
brain. A rst layer of simple cells activates with simple elements, like edges or
corners, and subsequent layers contain more and more complex cells, which
combine simple cells outputs to detect certain shapes, regardless of their position.
CNNs are based on convolutional layers [
          <xref ref-type="bibr" rid="ref13">13</xref>
          ] that slide lters (or kernels) across
the input data and return the dot products of the elements of the lter and each
fragment of the input. In doing so, CNNs automatically learn features from the
data, alleviating the manual selection required in traditional approaches.
Stacking several convolutional layers allows feature composition, increasing the level
of abstraction as we go from the initial layers to the output.
        </p>
        <p>
          Single layer CNNs, consisting of a single convolutional layer, pooling, and
fully connected neural layers, have been proposed for natural language
processing applications. Collobert and Weston [
          <xref ref-type="bibr" rid="ref3">3</xref>
          ] used a single layer CNN in various
NLP-related tasks such as part of speech tagging, named entity recognition, and
chuncking, and reached state of the art performance without the need of
handcrafted features. Similarly Kim [
          <xref ref-type="bibr" rid="ref11">11</xref>
          ] used this architecture for text classi cation
and his results improved over the state of the art according to existing
benchmarks for sentiment analysis at di erent granularity levels, detecting subjective
and objective sentences, and question classi cation.
        </p>
        <p>
          Multi layer CNN, with more than one convolutional layer, pooling and fully
connected neural layers, have been proposed to include information at the
character level as a complement to word level information. Dos Santos et al. [
          <xref ref-type="bibr" rid="ref20">20</xref>
          ]
proposed a multi layer CNN with two convolutional layers to analyse sentiments in
short texts. Similarly, Zhang et al. [
          <xref ref-type="bibr" rid="ref25">25</xref>
          ] presented a multi layer convolutional
neural network with up to six convolutional layers. Their experiments showed that
character-level CNN is an e ective method, however its performance depends on
many factors, such as dataset size and texts quality among other variables.
Convolutional neural networks applied to text classi cation use word embeddings as
input. In some approaches, the CNN architecture learns the embeddings as part
of the neural network training [
          <xref ref-type="bibr" rid="ref3">3</xref>
          ], while others use pre-trained embeddings [
          <xref ref-type="bibr" rid="ref20">20</xref>
          ].
5
        </p>
      </sec>
    </sec>
    <sec id="sec-5">
      <title>Experiments</title>
      <p>
        So as to produce word embeddings from SciGraph publications we need to gather
publication text from the knowledge graph. To this purpose, we query SciGraph
for nodes of type sg:Article and sg:BookChapter, identify research articles and
book chapters, and lter them according to publication date in the range 2001 to
2017. For each node, we query its title (rdfs:label ) and abstract (sg:abstract ) and
keep only publications written in English. In total our dataset consists roughly
of 3.2 million publications, 1 million distinct words, and 886 million tokens. In
terms of size, it is similar to the United Nations corpus [
        <xref ref-type="bibr" rid="ref26">26</xref>
        ] (around 600 million
tokens), which on the other hand is very general.
      </p>
      <p>We use FastText with the Skip-gram algorithm and GloVe to generate
embeddings from our dataset. In both cases we generate embeddings with 300
dimensions, truncate the vocabulary at a minimum count of 5 (word frequency),
and set the context window size equal to 10. We have faced some issues with the
implementation of GloVe when we use the default number of iterations, since
some embeddings where produced with null values. In order to address these
issues, we decreased the iteration number from 15 to 12. Bear in mind that a lower
number of iterations may in uence the evaluation of the resulting embeddings.</p>
      <p>
        On the other hand, to compare SciGraph embeddings we use pre-trained
embeddings generated with GloVe and FastText learned from very large and
general corpora. FastText embeddings where generated from Common Crawl
and Wikipedia [
        <xref ref-type="bibr" rid="ref8">8</xref>
        ], and from Wikipedia exclusively [
        <xref ref-type="bibr" rid="ref2">2</xref>
        ], while GloVe embeddings
were learned from Wikipedia, Gigaword, Common Crawl, and Twitter [
        <xref ref-type="bibr" rid="ref19">19</xref>
        ].
5.1
      </p>
      <sec id="sec-5-1">
        <title>Analogical Reasoning and Word Similarity</title>
        <p>
          We initially evaluate our word embeddings through intrinsic evaluation methods
[
          <xref ref-type="bibr" rid="ref21">21</xref>
          ], such as the analogy task [
          <xref ref-type="bibr" rid="ref17">17</xref>
          ] and word similarity. The goal of the
analogy task is to nd x such that the relation x:y resembles a sample relation a:b
by operating on the corresponding word vectors. The analogy dataset2 contains
19,544 question pairs (8,869 semantic and 10,675 syntactic questions) and 14
types of relations (9 syntactic and 5 semantic). The word similarity evaluation
is based on the WordSim353 dataset3, which contains 353 word pairs with
similarity scores assigned by humans that we compare with similarity based on the
word embeddings.
        </p>
        <p>Table 1 reports the accuracy values for SciGraph and pre-trained embeddings
in the analogy task and Spearmans's rank correlation coe cient in word
similarity. As expected, given the rather small size of the SciGraph corpus (886M
tokens) compared to the other sources (number of tokens between 3B and 42B)
and the fact that SciGraph focuses on the scienti c domain, the performance
obtained was signi cantly lower. A quick look at those benchmarks clearly shows
that the SciGraph corpus does not cover all the vocabulary and semantic and
syntactic relations that are evaluated in such tasks. However, as we will see
below, the fact that SciGraph embeddings do not perform well in this task does
not mean that they are not suitable for other tasks focused on the domain from
which they were learned. Since word analogies and similarity are not t, with the
existing benchmarks, to evaluate SciGraph embeddings, we propose an extrinsic
evaluation method in the form of a classi cation task.
2 https://aclweb.org/aclwiki/Google analogy test set (State of the art)
3 https://aclweb.org/aclwiki/WordSimilarity-353 Test Collection (State of the art)
Algorithm Dimensions Corpus
Analogy</p>
        <p>Word Sim.</p>
        <p>
          Sem. Synt. Total Spearman's rho
GloVe
FastText
GloVe
FastText
300 Wiki+Giga (6B) 77.4 67.0 71.7
300 Common Crawl (42B) 81.9 69.3 75.0
300 Wikipedia (3B*) 77.8 74.9 76.2
300 SciGraph (886M) 8.1 1.7 4.6
300 SciGraph (886M) 17.1 48.5 34.3
Table 1. Results from the word analogy and similarity tasks
In SciGraph, each publication has one or more eld of research codes that
classify the documents in 22 categories such as Mathematical Sciences, Engineering
or Medical and Health Sciences. Based on this classi cation scheme, we de ne a
multi-label classi cation problem to predict one or more categories for each
publication through neural networks. The design and con guration of a particular
neural network architecture is a complex task that falls out of the scope of this
paper. Several approaches try to assist [
          <xref ref-type="bibr" rid="ref5">5</xref>
          ] data scientist in this task, simplifying
the process and helping to select the optimal [
          <xref ref-type="bibr" rid="ref27">27</xref>
          ] con guration. In our case,
we use two types of neural networks: a regular, fully connected network and a
convolutional one. The neural network is composed of an input layer, a fully
connected 50-unit neural layer with a ReLU activation function, and an output
sigmoid layer. The convolutional network was an out-of-the-box implementation
available in Keras with 3 convolutional layers with 128 lters and a 5-element
window size, each followed by a max pooling layer, a fully-connected 128-unit
ReLU layer and a sigmoid output.
        </p>
        <p>To evaluate the classi ers we select articles published in 2011 and use ten-fold
cross-validation. As baseline, we train a classi er that learns from embeddings
generated randomly following a normal distribution. As upper bound we learn
a classi er model that learns a new set of word embeddings during training
of either the neural and the convolutional networks. The performance of the
classi ers is shown in table 2.</p>
        <p>The results of the regular neural network show that for this architecture the
best classi er is produced from FastText SciGraph embeddings and FastText
Wiki+Web+News, although the f-score is far from the upper bound, meaning
that there is still room to get better embeddings for this learning algorithm.
Looking at the results produced by the convolutional network, we see that all
the classi ers have increased their performance to a similar level and the
fmeasure variation is very close to the upper-bound of 0.79. Also note that the
baseline classi er learned from random embeddings has risen its performance to
0.72 and now is closer to the upper bound.</p>
        <p>The fact that, regardless of the corpora used to generate the word
embeddings, the convolutional network systematically obtains a performance similar
Dim.</p>
        <p>F-Score</p>
        <p>NN CNN
300 0.13 0.72
300 0.78 0.79
Algorithm</p>
        <p>Dataset
Random Normal Dist.</p>
        <p>Classi er
GloVe
FastText
GloVe
FastText</p>
        <p>Wiki+Giga (6B) 300 0.67 0.77
Common Crawl (42B) 300 0.67 0.77
Twitter (27B) 200 0.61 0.75
Wiki+Web+News (16B) 300 0.69 0.78
Wiki (3B) 300 0.68 0.77
Scigraph (886M)
Scigraph (886M)
300 0.67 0.76
300 0.69 0.78
to the best results produced by the upper bound is interesting and shows
evidence of the bene ts derived from automatic feature selection and composition
in text classi cation. The convolutional network trained on Twitter embeddings
is the only case that achieved lower results. This is partially due to the informal
language, both vocabulary and grammar, as well as the shorter text found in
Twitter, which does not have a signi cant overlap with the rather formal and
speci c scienti c vocabulary presented in our dataset.
5.3</p>
      </sec>
      <sec id="sec-5-2">
        <title>Fine-Grained Classi cation</title>
        <p>We further the evaluation of SciGraph embeddings through a ne-grained
classi cation task where we aim at predicting second-level categories in three elds
of knowledge: Computer Science, Mathematics, and Chemistry. In addition to
the previous embeddings, we generate embeddings for each speci c eld. We
widen the dataset and include publications between 2011 and 2012 so that each
second-level category counts on more samples. Finally, we evaluate the
multilabel classi ers using ten-fold cross validation and focus on CNNs due to the
superior performance showed in the previous experiment.</p>
        <p>Evaluation results (table 3) show that embeddings generated from the
document corpora of each knowledge eld in SciGraph consistently lead to the
best classi ers and their performance is very similar to the upper bound.
FastText (Wiki+Web+News) embeddings and GloVe (Wiki+Giga) achieve similar
f-scores. In this ne-grained classi cation, we observe that embeddings from the
SciGraph general corpus produce average results and do not completely
discriminate second-level categories across knowledge elds. This is partially due to
di erences in corpora size between the general and eld-speci c cases but also in
the semantics captured for each speci c word in their corresponding vectors. In
the case of the general corpus, the latter is in uenced by all the di erent contexts
where a particular word can appear across elds of knowledge. As a consequence,
Algorithm</p>
        <p>Dataset
Random Normal
Classi er
GloVe
FastText</p>
        <p>Wiki+Giga (6B)
Common Crawl (42B)
Twitter (27B)
Wiki+Web+News (16B)
Wiki</p>
        <p>Dim.</p>
        <p>300
300
300
300
200
300
300
the location in the vector space of the point associated to a particular word is
shifted compared to embeddings generated locally to each eld.</p>
        <p>Table 4 compares the performance of the classi ers learned, using only
embeddings generated from each knowledge eld. In general, embeddings generated
from a eld produce the best classi er for such eld. In addition, we observe that
the conceptual proximity between knowledge elds also in uences the results.
For example, embeddings obtained from Mathematics perform well in
Computer Science and Chemistry, which are both related to Mathematics. The other
way around also holds: embeddings from Computer Science and Chemistry
perform well in Mathematics. However, Chemistry embeddings obtain worse results
in Computer Science and Computer Science embeddings perform worse in the
Chemistry category. This could be related to the fact that these knowledge areas
have less similarities with each other than with Mathematics. Curiously,
Computer Science and Chemistry embeddings seem to work even better for
Mathematics than for their originating elds, which will need to be further researched.</p>
        <p>Embeddings</p>
        <p>F-Score</p>
        <p>Computer Science Mathematics Chemistry</p>
      </sec>
    </sec>
    <sec id="sec-6">
      <title>Conclusions and Future Work</title>
      <p>This paper presents experimental results related to the generation and evaluation
of word embeddings from scholarly communications in the scienti c domain,
leveraging SciGraph content and metadata. We compare the resulting,
domainspeci c embeddings with pre-trained vectors generated from large and general
purpose corpora over a selection of intrinsic and extrinsic tasks.</p>
      <p>We show that intrinsic evaluation methods like word analogy and word
similarity are not a reliable benchmark for embeddings learned from scienti c
corpora, the reason being the mismatch in terms of vocabulary and domain
coverage between the scienti c corpus and the evaluation dataset. Our ndings should
raise community awareness about the need for larger (or domain-speci c)
intrinsic evaluation benchmarks for word embeddings. We followed on to conduct an
extrinsic evaluation in the form of a domain-speci c classi cation task for
scienti c publications at di erent granularity levels. The evaluation shows that our
classi ers make the most of embeddings generated through FastText both from
a corpus of scienti c publications (886 million tokens) and from a much larger
mix of Wikipedia, Web content, and News (16 billions tokens).</p>
      <p>Our results raise an interesting discussion about corpus size vs. speci city
for domain-dependent tasks. For scholarly communications and in the optimal
con gurations of the evaluation systems, the embeddings learned from focused
corpora produce similar results to those generated from much larger and
general corpora with many billions tokens. We also observed that all the classi ers
learned through convolutional neural networks were closer to the upper bound,
indicating that the features learned by the convolutional network are more
expressive than pre-trained word embeddings. In both cases, the features learned
during the training of the convolutional nets seem to improve over the knowledge
captured in the input word vectors, making the overall system more resilient to
the quality of such vectors for the task at hand. In addition, we showed that
embeddings generated from speci c knowledge elds perform well in classi cation
tasks over related knowledge elds, such as Computer Science and Mathematics,
and not so well where the knowledge elds are not so close, such as Computer
Science and Chemistry.</p>
      <p>
        We expect that this work lays a foundation for the future use of word
embeddings in NLP tasks applied to scienti c publications. Applications include, e.g.
the curation of existing knowledge graphs, such as SciGraph itself, with metadata
about the publication content so that not only accessory, but also content-wise
structured metadata is available for software applications. Related work in this
direction involves merging embeddings and Expert System's Cogito knowledge
graph 4 in a joint word-concept vector space [
        <xref ref-type="bibr" rid="ref4">4</xref>
        ], which showed improvements
in word similarity evaluations with respect to traditional word embeddings and
other NLP downstream tasks. Finally, interesting work lays ahead in trying to
better understand the features learnt by convolutional neural networks in NLP
and their representation for human inspection.
4 http://www.expertsystem.com/products/cogito-cognitive-technology/
      </p>
    </sec>
    <sec id="sec-7">
      <title>Acknowledgments</title>
      <p>We gratefully acknowledge the EU Horizon 2020 program for research and
innovation under grant EVER-EST-674907. We also thank Constantino Roman for
his contributions to the experimental evaluation of this work.</p>
    </sec>
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