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  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>EvalNE: A Framework for Evaluating Network Embeddings on Link Prediction</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Alexandru Maray</string-name>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Jefrey Lij jty</string-name>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Tijl De Biey</string-name>
        </contrib>
      </contrib-group>
      <abstract>
        <p>results. These methods map nodes in the network Network embedding (NE) methods aim to learn low- to d-dimensional vectors, typically in Euclidean space. dimensional representations of network nodes as vectors, The obtained representations are then used as features typically in Euclidean space. These representations are then for a variety of tasks such as visualization, multi-label validated on a variety of downstream prediction tasks. Link classi cation, clustering or link prediction. prediction is one of the most popular choices for assessing The challenges of evaluating NE methods for the performance of NE methods. However, the complex- link prediction Unfortunately, the practical perfority of link prediction requires a carefully designed evalu- mance of most NE methods is poorly understood and ation pipeline in order to provide consistent, reproducible not comparable due to inconsistent evaluation proceand comparable results. We argue this has not been con- dures. In this paper, we focus on a number of di culties sidered su ciently in many recent works. The main goal of speci c to the evaluation of NE methods for link predicthis paper is to overcome di culties associated with eval- tion. Link prediction is particularly challenging as the uation pipelines and reproducibility of results. We intro- evaluation involves a number of design choices that can duce EvalNE, an evaluation framework to transparently as- confound the results and are prone to errors. sess and compare the performance of NE methods on link For example, the implicit assumption is that the prediction. EvalNE provides automation and abstraction input graph is not complete and the purpose is to for tasks such as hyper-parameter tuning, model validation, predict the missing edges as accurately as possible. edge sampling, computation of edge embeddings and model To evaluate the performance of a NE method for link validation. The framework integrates e cient procedures for prediction, one thus needs an (incomplete) training edge and non-edge sampling and can be used to easily eval- graph along with a (more) complete version of that uate any o -the-shelf embedding method. The framework is graph for testing. freely available as a Python toolbox. Finally, demonstrating Much research has been devoted to determining the usefulness of EvalNE in practice, we conduct an empir- the best approach to generate these training graphs ical study in which we try to replicate and analyse experi- [8, 18, 29]. Theoretical and empirical evidence suggest mental sections of several in uential papers. that in order to fairly evaluate link prediction methods,</p>
      </abstract>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>-</title>
      <p>
        A related problem is the fact that, in addition 2
to the `positive' train and test edges, in most cases
also `negative' train and test edges (also called
nonedges) are required. Sometimes these are used also
to derive the embedding, while in other cases they are
used only to train a classi er that predicts links. These
sets of non-edges can be selected according to di erent
strategies [
        <xref ref-type="bibr" rid="ref14">14</xref>
        ] and can be of various sizes.
      </p>
      <p>
        Furthermore, many NE methods only provide node
embeddings. From these, edge embeddings need to
be derived prior to performing predictions. There are
several approaches for deriving edge embeddings [
        <xref ref-type="bibr" rid="ref4">4</xref>
        ],
and the selection of the edge embedding approach has
a strong impact on the performance [
        <xref ref-type="bibr" rid="ref10">10</xref>
        ].
      </p>
      <p>
        Also the metrics used to report the accuracy of
di erent methods vary wildly, from, e.g., AUC-ROC [
        <xref ref-type="bibr" rid="ref13">13</xref>
        ]
to precision-recall [
        <xref ref-type="bibr" rid="ref27">27</xref>
        ] to precision@k [
        <xref ref-type="bibr" rid="ref26">26</xref>
        ].
      </p>
      <p>Finally, it appears to be common practice in recent
literature to use recommended default settings for
existing methods, while tuning the hyper-parameters for the
method being introduced. Especially when the
recommended default settings were informed by experiments
on other graphs than those used in the study at hand,
this can paint an unduly unfavorable picture.</p>
      <p>
        Contributions In this paper we propose EvalNE,
a framework that simpli es the complex and time
consuming process of evaluating NE methods for link
prediction. EvalNE automates many parts of the
evaluation process: hyper-parameter tuning, selection of
train and test edges, negative sampling, and more. The
framework: (1) Implements guidelines from research
in the area of link prediction evaluation and sampling
[
        <xref ref-type="bibr" rid="ref18 ref29 ref8">8, 18, 29</xref>
        ]. (2) Includes (novel) e cient edge and
nonedge sampling algorithms. (3) Provides the most widely
used edge embedding methods. (4) Evaluates the scala- 3
bility and accuracy of methods, through wall clock time
and a wide range of xed-threshold metrics and
threshold curves. (5) Integrates in a single operation the
evaluation of any set of NE methods coded in any language
on any number of networks. (6) Finally, EvalNE
ensures reproducibility and comparability of evaluations
and results through shareable con guration les.
      </p>
      <p>The remainder of this paper is organized as follows.
In Section 2 we give a brief overview of related work.
Section 3 presents the proposed evaluation framework.
Our experiments reproducing the experimental setups
of several papers and empirical analysis of the proposed
edge set selection strategy are reported in Section 4.
Finally Section 5 concludes this paper.</p>
      <p>The open-source toolbox is freely available at
https://github.com/Dru-Mara/EvalNE and the
documentation and examples at ReadTheDocs https://
evalne.readthedocs.io/en/latest/index.html.</p>
    </sec>
    <sec id="sec-2">
      <title>EvalNE Related Work</title>
      <p>
        Our work is related to the evaluation of link
prediction which has been studied in several recent works, i.e.,
[
        <xref ref-type="bibr" rid="ref18 ref20 ref29 ref8">8, 18, 20, 29</xref>
        ]. These studies focus on the impact of
different train set sampling strategies, negative sampling
and fair evaluations criteria.
      </p>
      <p>
        Link prediction as evaluation for the representations
learned by a NE algorithm was rst introduced in the
pioneering work of Grover et al. [
        <xref ref-type="bibr" rid="ref10">10</xref>
        ]. The survey work
of Zhang et al. [
        <xref ref-type="bibr" rid="ref31">31</xref>
        ] points out the importance of link
prediction as an application of network representation
learning. The authors also signal the inconsistencies in
the evaluation of di erent NE approaches and conduct
an empirical analysis of many of these methods on a
wide range of datasets. Their empirical study, however,
only focuses on vertex classi cation and clustering. The
importance of standard evaluation frameworks as tools
to bridge the gap between research and application of
NEs is discussed in Hamilton et al. [
        <xref ref-type="bibr" rid="ref12">12</xref>
        ].
      </p>
      <p>
        To the best of our knowledge only two
frameworks for the evaluation of NE methods currently exist.
OpenNE is a recently proposed toolbox for evaluating NE
methods on multi-label classi cation. The toolbox also
includes implementations of several state-of-the-art
embedding methods. GEM [
        <xref ref-type="bibr" rid="ref9">9</xref>
        ] is a similar framework which
also implements a variety of embedding methods and
includes basic evaluation on multi-label classi cation,
vizualization and link prediction tasks. These
frameworks, however, are focused on the implementations of
embedding methods rather than the evaluation pipeline.
Furthermore, these libraries are limited to the NE
methods provided by the authors or require new
implementations that comply with pre-de ned interfaces.
In this section we discuss the key aspects of EvalNE.
The framework has been designed as a pipeline of
interconnected and interchangeable building blocks, as
illustrated in Figure 1. These blocks have speci c
functions such as providing sets of train and test edges or
computing edge embeddings from given node
embeddings. The modular structure of our framework
simplies code maintenance and the addition of new features,
and allows for exible model evaluation. The framework
can be used to evaluate methods providing node
embeddings, edge embeddings, or similarity scores (we include
in this category the link prediction heuristics). Next,
we describe the core functions as well as other building
blocks that constitute EvalNE and provide some details
regarding the software design.
      </p>
    </sec>
    <sec id="sec-3">
      <title>3.1 Evaluation framework The core building</title>
      <p>blocks of our framework are the data split and model
evaluation. These blocks constitute the most basic 2. Initialize the set of training edges Etrain to all edges
pipeline for assessing the quality of link predictions. Be- in ST
fore describing these, we introduce some notation.</p>
      <p>
        We represent a directed weighted network as G = 3. Select edges uniformly at random without
replace(V; E; W ) with vertex set V = f1; : : : ; N g, edge set ment from the remaining edges E n Etrain.
E V V and weight matrix W 2 IRN N. Edges are We select a spanning tree uniformly at random from
represented as ordered pairs e = (u; v) 2 E with weights the set of all possible ones using Broder's algorithm [
        <xref ref-type="bibr" rid="ref2">2</xref>
        ]:
we 2 [0; 1). Etrain and Etest denote the training
and testing edge sets. We represent the embedding
of network nodes into a d-dimensional space as X =
(x1; x2; : : : ; xN ) where X 2 IRN d.
1. Select a random vertex s of G and start a random
walk on the graph until every vertex is visited. For
each vertex i 2 V n fsg collect the edge e = (j; i)
that corresponds to the rst entrance to vertex i.
      </p>
      <p>Let T be this collection of edges.
3.1.1 Data split As pointed out in Section 1, in
order to perform link prediction on a given input graph 2. Output the set T.</p>
      <p>
        G, sets of train and test edges are required. The
set of train edges is generally required to span all The complexity of the uniform spanning tree
gennodes in G and induce a training graph Gtrain with eration methods is O(n log n) on expectation [
        <xref ref-type="bibr" rid="ref2">2</xref>
        ]. The
a single connected component, because embeddings of same bound applies for the proposed train-test split
alindependent components will be far away from and gorithm as the addition of random edges to the train
unrelated to each other. set can be e ciently done in O(jEtrainj) time. A more
      </p>
      <p>
        Most studies resort to a naive algorithm to derive e cient algorithm for constructing a uniform spanning
a connected Gtrain. The procedure removes edges from tree of a given graph exists. This method, named
Wilan input graph iteratively until the required number of son's algorithm [
        <xref ref-type="bibr" rid="ref28">28</xref>
        ], will be included in future versions
train edges remain. The removed edges are used as test of EvalNE.
samples. In each iteration, the connectedness of the For directed graphs G we rst construct an
equivgraph needs to be checked and only remove an edge if alent undirected version G by adding reciprocals for
it does not cause the graph to become disconnected. every edge in E. We then run the same algorithm
deThis requirement is generally satis ed by running a scribed above on G and include in the train set only
Breadth First Search (BFS) on the graph after each edge those edges present in the initial directed graph G. This
removal, which is a costly operation (O(jV j + jEj)). method results in a weakly connected training graph
      </p>
      <p>Integrated in our evaluation framework, we include spanning the same nodes as the original G.
a novel algorithm to perform the train-test splits which, In addition to train and test edges, sets of train
as we will show in Section 4, is orders of magnitude and test non-edges (also referred to as negative samples )
faster yet equally simple. Our algorithm, also accounts are required in order to evaluate link prediction. These
for the fact that the training graph Gtrain must span all are edges between pairs of vertices u; v such that e =
nodes in G and contain a single connected component. (u; v) 2= E. The proposed toolbox can compute these</p>
      <p>Given as input an undirected graph G = (V; E; W ) non-edges according to either the open world or the
and a target number of train edges jEtrainj, the pro- closed world assumption. The two strategies only di er
posed algorithm to split the train and test edges pro- in the selection of the train non-edges. Under the open
ceeds as follows: world assumption, train non-edges are selected such
that they are not in Etrain. Thus, this strategy allows
1. Obtain a uniform spanning tree ST of G overlapping between train non-edges and test real edges.
Under the closed world assumption, we consider the 3.2.2 Link prediction heuristics A training graph
non-edges to be known a priori and therefore select Gtrain = (V; Etrain; W ) spanning the same set of
them so that they are neither in Etrain nor in Etest. vertices as the initial graph G but containing only</p>
      <p>
        The number of train and test edges and non-edges the edges in the train set is provided as input to the
are user-controlled parameters. The minimum number link prediction heuristics. Depending on the input
of train edges is determined by the size of the spanning graph type we use one of the following de nitions. For
tree and the combined sets of non-edges have a trivial undirected graphs we use the ones presented below,
upper limit of (N N ) jEj. However, for the train set where (u) denotes the neighbourhood of a node u. For
size, fractions between 50% and 90% of total edges E directed graphs we restrict our analysis to either the
are recommended. For values below 50%, the resulting in-neighbourhood ( i(u)) or the out-neighbourhood
training graph will often not preserve the properties of ( o(u)) of the nodes.
the original graph G as shown in [
        <xref ref-type="bibr" rid="ref16">16</xref>
        ].
3.1.2 Evaluation The proposed framework can
evaluate the scalability, parameter sensitivity and accuracy
of embedding methods. We assess the scalability
directly by measuring the wall clock time. The
performance of the methods can be easily reported for
different values of embedding dimensionality and
hyperparameter values. Finally, the link prediction accuracy
is reported using two types of metrics: xed-threshold
metrics and threshold curves. Fixed-threshold metrics
summarize the performance of the methods to single
values. The framework provides the following measures:
confusion matrix (TP, FN, FP, TN), precision, recall,
fallout, miss, accuracy, F-score and AUC-ROC.
Threshold curves present the performance of the methods for
a range of threshold values between 0 and 1. EvalNE
includes precision-recall curves [
        <xref ref-type="bibr" rid="ref18">18</xref>
        ] and receiver
operating curves [
        <xref ref-type="bibr" rid="ref6">6</xref>
        ]. The framework also recommends the
most suitable metrics based on the evaluation setup.
      </p>
    </sec>
    <sec id="sec-4">
      <title>3.2 Baselines and building blocks In addition to</title>
      <p>
        the core building blocks, and in order to extend the
evaluation process to di erent types of embedding methods,
our framework also provides data preprocessing, data
manipulation, and node to edge embedding functions.
Moreover, EvalNE integrates a standard binary
classication technique which can be used, for example, to
obtain link predictions from edge embeddings.
Furthermore, the toolbox contains a series of built-in link
prediction heuristics which can be used as baselines.
3.2.1 Preprocessing The toolbox o ers a variety
of functions to load, store, and manipulate networks.
These include methods to prune nodes based on degree,
remove self-loops, relabel nodes, obtain sets of speci c
types of edges, restrict networks to their main connected
components and obtain common network statistics. The
preprocessing functions of EvalNE build on top of and
can be used in combination with those provided by other
mainstream software packages (e.g. NetworkX [
        <xref ref-type="bibr" rid="ref11">11</xref>
        ]).
      </p>
    </sec>
    <sec id="sec-5">
      <title>Common neighbours (CN):</title>
    </sec>
    <sec id="sec-6">
      <title>Jaccard coe cient (JC):</title>
      <p>CN(u; v) = j (u) \ (v)j
JC(u; v) = j (u) \ (v)j
j (u) [ (v)j</p>
    </sec>
    <sec id="sec-7">
      <title>Adamic-Adar index (AA):</title>
      <p>AA(u; v) =
X
w2 (u)\ (v)
1
log j (w)j</p>
    </sec>
    <sec id="sec-8">
      <title>Resource allocation index (RAI):</title>
      <p>RAI(u; v) =
X</p>
      <p>1
w2 (u)\ (v) j (w)j
PA(u; v) = j (u)j j (v)j
1
Katz(u; v) = X l j (u; vjl)j
l=1</p>
    </sec>
    <sec id="sec-9">
      <title>Preferential attachment (PA):</title>
    </sec>
    <sec id="sec-10">
      <title>Katz:</title>
      <p>For Katz, the parameter 2 [0; 1] is a damping
factor and j (u; vjl)j represents the number of paths of
length l from node u to node v.</p>
      <p>In addition to these methods, a random prediction
model is provided for reference. This method simply
outputs a uniform random value in [0; 1] as the
likelihood of a link between any pair of given vertices (u; v).</p>
    </sec>
    <sec id="sec-11">
      <title>3.2.3 Node to edge embeddings Unlike for the</title>
      <p>abovementioned LP heuristics where the output can
be directly used for link prediction, for NE methods
this is generally not the case. Most implementations of
NE methods produce only node embeddings. Thus, an
additional step of learning edge embeddings is required
in order to predict links via binary classi cation.</p>
      <p>The edge representations are typically derived in an
unsupervised fashion. For example, to derive the edge
embedding y(u;v) for edge e = (u; v), we apply a binary
operator over the embeddings of nodes u and v, i.e.
xu and xv respectively:
y(u;v) = xu
xv:</p>
      <p>
        In [
        <xref ref-type="bibr" rid="ref10">10</xref>
        ] the authors propose the following
alternatives for the operator which we include in our
evaluation framework. Any other user-de ned
operators can be also easily integrated.
      </p>
    </sec>
    <sec id="sec-12">
      <title>Average (Avg.):</title>
      <p>Hadamard (Had.):
xu
xv
xu;i + xv;i
2
xu
xv
xu;i xv;i</p>
    </sec>
    <sec id="sec-13">
      <title>Weighted L1:</title>
      <p>Weighted L2:
jjxu xvjj1
jxu;i
xv;ij
new les de ning their own evaluations (e.g. by adding
new methods or di erent networks) and share them in
order to ensure the reproducibility of results.</p>
      <p>When used as an API, the framework exposes
a modular design with blocks providing independent
and self contained functionalities which can be easily
exploited. The user interacts with the library trough an
evaluator object which integrates all the building blocks
and orchestrates the evaluation pipelines. As an API
EvalNE provides users with access to more advanced
capabilities and more exible evaluation work ows.
4</p>
    </sec>
    <sec id="sec-14">
      <title>Experiments</title>
      <p>
        In this section we seek to prove the simplicity and
usefulness of our evaluation framework. To this end
we have selected four papers from the NE literature,
i.e. Node2vec, PRUNE, CNE and SDNE and replicated
their experimental setups. We have also conducted a
series of experiments in which we compare our edge
set selection algorithm to the naive approach. We
performed these comparisons in terms of both scalability
and link prediction accuracy. All experiments were run
on a single machine equiped with a Intel R CoreTM i5
processor and 16GB of RAM.
jjxu xvjj2 jxu;i xv;ij2 4.1 Experimental setups Next, we present the
main characteristics of the experimental settings we
3.2.4 Binary classi cation Most NE methods have replicated and some important remarks:
(e.g., [
        <xref ref-type="bibr" rid="ref10 ref13 ref15 ref7">7, 10, 13, 15</xref>
        ]) rely on a logistic regression classi- Node2vec [
        <xref ref-type="bibr" rid="ref10">10</xref>
        ]: In this work the authors
evaluer to predict link probabilities from edge embeddings. ate the following embedding methods and link
predicIn EvalNE we include logistic regression with 10-fold tion heuristics: Node2vec, DeepWalk [
        <xref ref-type="bibr" rid="ref22">22</xref>
        ], LINE [
        <xref ref-type="bibr" rid="ref23">23</xref>
        ],
cross validation. The framework, however, is exible Spectral Clustering [
        <xref ref-type="bibr" rid="ref24">24</xref>
        ], CN, JC, AA, and PA.
Experiand allows for any binary classi er to be used. ments are performed on the Facebook [
        <xref ref-type="bibr" rid="ref17">17</xref>
        ], PPI [
        <xref ref-type="bibr" rid="ref10">10</xref>
        ], and
AstroPh[
        <xref ref-type="bibr" rid="ref17">17</xref>
        ] datasets with 50-50 train-test splits. The
3.3 Software design The EvalNE framework is pro- same number of edges and non-edges are used
throughvided as a Python toolbox compatible with Python2 and out the experiment. The results are reported in terms of
Python3 and which can be easily installed and used on AUC-ROC and the edge embedding methods used are
Linux, MacOS, and Microsoft Windows. The toolbox average, Hadamard, weighted L1 and weighted L2.
depends only on a small number of popular open-source PRUNE [
        <xref ref-type="bibr" rid="ref15">15</xref>
        ]: This experimental setup includes
Python packages and the coding style and code docu- Node2vec, DeepWalk, LINE, SDNE, PRUNE and
mentation comply with the PEP8 and numpy docstring NRCL [
        <xref ref-type="bibr" rid="ref27">27</xref>
        ]. The networks used are HepPH [
        <xref ref-type="bibr" rid="ref17">17</xref>
        ],
FBstandards, respectively. The documentation provided wallpost [
        <xref ref-type="bibr" rid="ref25">25</xref>
        ] and Webspam and the train-test fraction
includes instructions on the installation and use as well is 0.8 with similar sizes of the non-edge sets. The node
as examples of high-level and low-level use and integra- to edge embedding operator used is not reported by the
tion with existing code. authors and the results are presented in terms of
AUC
      </p>
      <p>
        EvalNE can be used both as a command line tool ROC. In this setting, the network used are directed.
and an API. As a command line tool, the framework CNE [
        <xref ref-type="bibr" rid="ref13">13</xref>
        ]: The evaluation setup in this case is
simrequires as input a con guration le de ning a com- ilar to that of Node2vec with the following di erences:
plete experimental setup, from methods to evaluate to CNE and Metapath2vec [
        <xref ref-type="bibr" rid="ref5">5</xref>
        ] methods are also evaluated;
networks, edge splits and parameters to be tuned. For BlogCatalog [
        <xref ref-type="bibr" rid="ref30">30</xref>
        ], Wikipedia [
        <xref ref-type="bibr" rid="ref17">17</xref>
        ] and StudentDB are
inconvenience, several pre- lled con guration les which cluded in the list of evaluated networks and the results
reproduce the experimental sections of in uential pa- are only reported for the Hadamard operator. It should
pers on NE are provided as examples. Users can create be noted that two authors of this paper are also authors
      </p>
      <p>4.2 Evaluation results For each of the
experimenTable 1: All the datasets used for evaluation. tal settings reproduced we present a table containing
the original values reported in the paper, and in
parentheses the di erence between our result and these values
of CNE, and to some degree the development of CNE in- (Tables 3{6). Positive values in parentheses, thus,
indispired this work. However, the code used for evaluation cate that our results are higher than the ones reported
in that paper was completely separate. in the original papers by that margin, while negative</p>
      <p>
        SDNE [
        <xref ref-type="bibr" rid="ref26">26</xref>
        ]: The authors report in this case exper- values indicate the opposite.
iments using the following methods: DeepWalk, LINE, The results obtained show that our experiments
SDNE, GraRep [
        <xref ref-type="bibr" rid="ref3">3</xref>
        ], LapEig [
        <xref ref-type="bibr" rid="ref1">1</xref>
        ] and CN. The link predic- align fairly well with those reported in the CNE and
tion experiments are performed on the GR-QC dataset PRUNE papers. The only exception is the result of
[
        <xref ref-type="bibr" rid="ref17">17</xref>
        ] with a 0.85 train-test fraction. The results are re- Metapath2vec on the Facebook dataset, which
substanported only for the Hadamard operator and in terms tially di ers from the CNE paper. For Node2vec and
of precision@k for a collection of values between 2 and SDNE, the di erences are larger and occasionally severe
10000. In this setup, the number of train non-edges is (di erences over 0:15 are marked in bold in all tables).
the same as that of train edges while all the remaining Possible explanations for these inconsistencies are the
non-endges in the graph are used for testing. use of di erent implementations of NE methods, di
er
      </p>
      <p>In our experiments we have replicated these setting ent not reported default parameters or the use of
parwith the following exceptions (1) for node2vec we did allelization. In addition, we have also observed
impornot include spectral clustering and (2) for PRUNE we tant di erences when computing the AUC-ROC directly
could not obtain NRCL and lacked the computational from class labels or from class probabilities. In order to
resources to evaluate the NE methods on the Webspam reproduce the CNE experiments we used class
probabildataset. In all cases we report the same metrics as the ities, while for Node2vec we used class labels as seem to
original authors and average the results over ve inde- have been done by the original authors.
pendent executions. We used the open-world assump- These results illustrate the need to: (a) create
retion for the non-edges, logistic regression for binary clas- producible pipelines for experiments, and (b) report
si cation and tuned the same hyper-parameters. All speci cs about the parameter settings and precise
imexperiments were run using speci c con guration les plementations used in the evaluation.
created for each setting which will be made public.</p>
      <p>Regarding the implementations, we evaluated the
LP heuristics included in EvalNE; original code by the
authors for Deepwalk1 , Node2vec2, LINE3, PRUNE4,
CNE5, and Metapath2vec6, and for the remaining ones,
the implementations in the OpenNE7 library. Table 1
contains the main characteristics of all the networks
used. Network sizes are those corresponding to the main
(weakly) connected components of each graph.
4.3 Edge sampling We compared the proposed edge
and non-edge sampling strategy in terms of accuracy
and scalability to the naive approach. For the accuracy
experiment we selected the Facebook, PPI, and AstroPh
datasets, and performed link predictions with the CN,
JC, AA, and PA heuristics. We collected all the metrics
available in EvalNE and computed for each the absolute
di erence between the naive and proposed approach.</p>
      <p>The recall presents the highest deviation, so we show
these results in Table 2. Although recall di ers up to
0.0393, in this case it is traded o with precision. The
accuracy in this case di ers only by 0.0154. For the
AUC-ROC, one of the most widely used metrics, the
maximum deviation is of 0:015 reached on the AstroPh
dataset by the PA heuristic. Across methods and
1https://github.com/phanein/deepwalk
2https://github.com/aditya-grover/node2vec
3https://github.com/tangjianpku/LINE
4https://github.com/ntumslab/PRUNE
5https://bitbucket.org/ghentdatascience/cne/
6https://ericdongyx.github.io/metapath2vec/m2v.html
7https://github.com/thunlp/OpenNE</p>
      <p>Avg.</p>
      <p>Had.</p>
      <p>W L1
W L2</p>
      <p>CN
JC
AA
PA
DeepWalk
LINE
node2vec
DeepWalk
LINE
node2vec
DeepWalk
LINE
node2vec
DeepWalk
LINE
node2vec</p>
      <p>Facebook
0:81 (+0:14)
0:88 (+0:04)
0:83 (+0:13)
0:71 (+0:04)
0:72 ( 0:01)
0:70 ( 0:03)
0:73 ( 0:01)
0:97 ( 0:03)
0:95 ( 0:06)</p>
      <p>0:97 (0:0)
0:96 ( 0:01)
0:95 ( 0:33)
0:96 ( 0:01)
0:96 ( 0:01)
0:95 ( 0:33)
0:96 (0:0)</p>
      <p>PPI
0:71 (+0:06)
0:70 (+0:04)
0:71 (+0:06)
0:67 (+0:13)
0:69 (+0:08)
0:63 (+0:12)
0:75 ( 0:01)
0:74 ( 0:2)
0:72 ( 0:01)
0:77 ( 0:17)
0:60 (+0:14)
0:70 ( 0:01)
0:63 ( 0:03)
0:61 (+0:14)
0:71 ( 0:02)
0:62 ( 0:02)</p>
      <p>AstroPh
0:82 (+0:13)
0:81 (+0:12)
0:83 (+0:12)
0:70 (+0:08)
0:71 (+0:01)
0:65 (+0:14)
0:72 ( 0:02)
0:93 ( 0:12)
0:89 (+0:05)
0:94 ( 0:05)
0:83 (+0:09)
0:88 ( 0:28)
0:85 (+0:03)
0:83 (+0:09)
0:89 ( 0:27)
0:85 (+0:03)
datasets, the results obtained with the naive approach
were slightly higher than those using our method.</p>
      <p>Regarding the scalability experiments, in Figure 2
we summarize the execution time in seconds of both
methods on four di erent datasets. This experiment
shows that the proposed method is several order of
magnitude faster than the naive approach and independent
on the number of train and test edges required. The
execution time of the naive approach decreases, as
expected, as the number of test edges requested becomes
StudentDb</p>
      <p>Facebook</p>
      <p>GrQc</p>
      <p>Proposed edge split</p>
      <p>Naive edge split
10 2</p>
      <p>0.6 0.7
Proportion or train edges
0.8
0.9
0
2000</p>
      <p>4000 6000
Number of graph nodes
8000
10000
0:0016 and maximum di erence 0:2429. This indicate
that, in general, the train-test split size has indeed a
strong impact on the method results.
smaller. In Figure 3 we select the BlogCatalog dataset
and restrict it to sub-graphs of di erent number of nodes
ranging from 400 up to 10000. The execution times
using both sampling strategies are reported in Figure 3. 5 Conclusions</p>
      <p>For our proposed strategy we have also evaluated The recent surge of research in the area of network
emthe variance observed in the performance metrics for beddings has resulted in a wide variety of data sets,
di erent number of repetitions of the experiments (or metrics, and setups for evaluating and comparing the
equivalently, the e ect of averaging the results over utility of embedding methods. Comparability across
di erent number of edge splits). In this case we used studies is lacking and not all evaluations are equally
the same datasets, NE methods and LP heuristics as sound. This highlights the need for speci c tools and
in the node2vec experiment and 50-50 and 90-10 train- pipelines to ensure the correct evaluation of these
methtest splits. We compared the results obtained in a ods. Particularly, the use of representation learning for
single run with those averaged over ve independent link prediction tasks requires train and test sampling,
runs for both split fractions. For the 50-50 split the non-edge sampling, and in many cases selection of edge
average di erence observed over all methods, datasets embedding methods and binary classi ers. The
evaland metrics is 3:4 10 3 with a variance of 1:8 10 5 uation procedure, thus, becomes an ensemble of tasks
and a maximum di erence of 0:0293. For the 90-10 which allow for many errors or inconsistencies.
split, the average di erence is 3:0 10 3 the variance of In this work we have proposed EvalNE, a novel
1:0 10 5 and maximum di erence 0:0186. These results framework that can be used to evaluate any network
indicate that a single train and test split already gives a embedding method for link prediction. Our pipeline
su ciently good estimate of the generalization error of automates the selection of train and test edge sets,
the models. Thus, experiment repeats are not necessary simpli es the process of tuning model parameters and
for networks of similar sizes. These observations seem reports the accuracy of the methods according to many
to hold for di erent train-test split fractions. criteria. Our experiments highlight the importance</p>
      <p>Finally, we study the e ect of the train-test split of the edge sampling strategy and parameter tuning
sizes on the method results. We use an indentical setting for evaluating NE methods. We have also introduced
as described above and compare the absolute di erence a scalable procedure to sample edge sets from given
of the results obtained using a 50-50 split with those networks and showed empirically that is orders or
obtained using a 90-10. The average di erence across magnitude faster than the naive approach that has been
all methods, datasets and metrics is 0:038, the variance used in recent literature.</p>
    </sec>
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