=Paper=
{{Paper
|id=Vol-1609/16090428
|storemode=property
|title=Plant Identification in an Open-world (LifeCLEF 2016)
|pdfUrl=https://ceur-ws.org/Vol-1609/16090428.pdf
|volume=Vol-1609
|authors=Hervé Goëau,Pierre Bonnet,Alexis Joly
|dblpUrl=https://dblp.org/rec/conf/clef/GoeauBJ16
}}
==Plant Identification in an Open-world (LifeCLEF 2016)==
https://ceur-ws.org/Vol-1609/16090428.pdf
Plant identification in an open-world (LifeCLEF
2016)
Hervé Goëau1 , Pierre Bonnet4 , and Alexis Joly2,3
1
IRD, UMR AMAP, France, herve.goeau@cirad.fr
2
Inria ZENITH team, France, alexis.joly@inria.fr
3
LIRMM, Montpellier, France
4
CIRAD, UMR AMAP, France, pierre.bonnet@cirad.fr
Abstract. The LifeCLEF plant identification challenge aims at evaluat-
ing plant identification methods and systems at a very large scale, close
to the conditions of a real-world biodiversity monitoring scenario. The
2016-th edition was actually conducted on a set of more than 110K im-
ages illustrating 1000 plant species living in West Europe, built through
a large-scale participatory sensing platform initiated in 2011 and which
now involves tens of thousands of contributors. The main novelty over
the previous years is that the identification task was evaluated as an
open-set recognition problem, i.e. a problem in which the recognition
system has to be robust to unknown and never seen categories. Beyond
the brute-force classification across the known classes of the training set,
the big challenge was thus to automatically reject the false positive clas-
sification hits that are caused by the unknown classes. This overview
presents more precisely the resources and assessments of the challenge,
summarizes the approaches and systems employed by the participating
research groups, and provides an analysis of the main outcomes.
Keywords: LifeCLEF, plant, leaves, leaf, flower, fruit, bark, stem, branch,
species, retrieval, images, collection, species identification, citizen-science,
fine-grained classification, evaluation, benchmark
1 Introduction
Image-based plant identification is the most promising solution towards bridg-
ing the botanical taxonomic gap, as illustrated by the proliferation of research
work on the topic [7], [4], [13], [10], [1] as well as the emergence of dedicated
mobile applications such as LeafSnap [14] or Pl@ntNet [12]. As promising as
these applications are, their performance is still far from the requirements of a
fully automated ecological surveillance scenario. Allowing the mass of citizens to
produce accurate plant observations requires to equip them with much more ef-
fective identification tools. As an illustration, in 2015, 2,328,502 millions queries
have been submitted by the users of the Pl@ntNet mobile apps but only less
than 3% of them were finally shared and collaboratively validated. Allowing the
exploitation of the unvalidated observations could scale up the world-wide col-
lection of plant records by several orders of magnitude. Measuring and boosting
the performance of automated identification tools is therefore crucial. As a first
step towards evaluating the feasibility of such an automated biodiversity mon-
itoring paradigm, we created and shared a new testbed entirely composed of
image search logs of the Pl@ntNet mobile application (contrary to the previous
editions of the PlantCLEF benchmark that were based on explicitly shared and
validated plant observations).
As a concrete scenario, we focused on the monitoring of invasive exotic plant
species. These species represent today a major economic cost to our society
(estimated at nearly 12 billion euros a year in Europe) and one of the main
threats to biodiversity conservation [22]. This cost can even be more important
at the country level, such as in China where it is evaluated to be about 15 billion
US dollars annually [23], and more than 34 billion US dollars in the US [17]. The
early detection of the appearance of these species, as well as the monitoring of
changes in their distribution and phenology, are key elements to manage them,
and reduce the cost of their management. The analysis of Pl@ntNet search logs
can provide a highly valuable response to this problem because the presence of
these species is highly correlated with that of humans (and thus to the density
of data occurrences produced through the mobile application).
2 Dataset
2.1 Training dataset
For the training set, we provided the PlantCLEF 2015 dataset enriched with
the ground truth annotations of the test images (that were kept secret during
the 2015 campaign). More precisely, PlantCLEF 2015 dataset is composed of
113,205 pictures belonging to 41,794 observations of 1000 species of trees, herbs
and ferns living in Western European regions. This data was collected by 8,960
distinct contributors. Each picture belongs to one and only one of the 7 types of
views reported in the meta-data (entire plant, fruit, leaf, flower, stem, branch,
leaf scan) and is associated with a single plant observation identifier allowing
to link it with the other pictures of the same individual plant (observed the
same day by the same person). An originality of the PlantCLEF dataset is that
its social nature makes it close to the conditions of a real-world identification
scenario: (i) images of the same species are coming from distinct plants living in
distinct areas, (ii) pictures are taken by different users that might not used the
same protocol of image acquisition, (iii) pictures are taken at different periods
in the year. Each image of the dataset is associated with contextual meta-data
(author, date, locality name, plant id) and social data (user ratings on image
quality, collaboratively validated taxon name, vernacular name) provided in a
structured xml file. The gps geo-localization and device settings are available
only for some of the images. More precisely, each image is associated with the
followings meta-data:
– ObservationId: the plant observation ID from which several pictures can
be associated
– FileName
– MediaId: id of the image
– View Content: Entire or Branch or Flower or Fruit or Leaf or LeafScan or
Stem
– ClassId: the class number ID that must be used as ground-truth. It is a
numerical taxonomical number used by Tela Botanica
– Species the species names (containing 3 parts: the Genus name, the specific
epithe, the author(s) who discovered or revised the name of the species)
– Genus: the name of the Genus, one level above the Species in the taxonom-
ical hierarchy used by Tela Botanica
– Family: the name of the Family, two levels above the Species in the taxo-
nomical hierarchy used by Tela Botanica
– Date: (if available) the date when the plant was observed
– Vote: the (round up) average of the user ratings of image quality
– Location: (if available) locality name, a town most of the time
– Latitude & Longitude: (if available) the GPS coordinates of the obser-
vation in the EXIF metadata, or if no GPS information were found in the
EXIF, the GPS coordinates of the locality where the plant was observed
(only for the towns of metropolitan France)
– Author: name of the author of the picture
– YearInCLEF: ImageCLEF2011, ImageCLEF2012, ImageCLEF2013, Plant-
CLEF2014, PlantCLEF2015 specifying when the image was integrated in the
challenge
– IndividualPlantId2014: the plant observation ID used last year during
the LifeCLEF2014 plant task
– ImageID2014: the image id.jpg used in 2014.
2.2 Test dataset
For the test set, we created a new annotated dataset based on the image queries
that were submitted by authenticated users of the Pl@ntNet mobile application
in 2015 (unauthenticated queries had to be removed for copyright issues). A
fraction of that queries were already associated to a valid species name because
they were explicitly shared by their authors and collaboratively revised. We
included in the test set the 4633 ones that were associated to a species belonging
to the 1000 species of the training set (populating the known classes). Remaining
pictures were distributed to a pool of botanists in charge of manually annotating
them either with a valid species name or with newly created tags of their choice
(and shared between them). In the period of time devoted to this process, they
were able to manually annotate 1821 pictures that were included in the test set.
Therefore, 144 new tags were created to qualify the unknown classes such as for
instance non-plant objects, legs or hands, UVO (Unidentified Vegetal Object),
artificial plants, cactaceae, mushrooms, animals, food, vegetables or more precise
names of horticultural plants such as roses, geraniums, ficus, etc. For privacy
reasons, we had to remove all images tagged as people (about 1.1% of the tagged
queries). Finally, to complete the number of test images belonging to unknown
classes, we randomly selected a set of 1546 image queries that were associated to
a valid species name that do not belong to the Western European flora (and thus,
that do not belong to the 1000 species of the training set or to potentially highly
similar species). In the end, the test set was composed of 8,000 pictures, 4633
labeled with one of the 1000 known classes of the training set, and 3367 labeled as
new unknown classes. Among the 4633 images of known species, 366 were tagged
as invasive according to a selected list of 26 potentially invasive species. This
list was defined by aggregating several sources (such as the National Botanical
conservatory, and the Global Invasive Species Programme) and by computing
the intersection with the 1000 species of the training set.
3 Task Description
Based on the previously described testbed, we conducted a system-oriented eval-
uation involving different research groups who downloaded the data and ran their
system. To avoid participants tuning their algorithms on the invasive species sce-
nario and keep our evaluation generalizable to other ones, we did not provide the
list of species to be detected. Participants only knew that the targeted species
were included in a larger set of 1000 species for which we provided the training
set. Participants were also aware that (i) most of the test data does not belong
to the targeted list of species (ii) a large fraction of them does not belong to
the training set of the 1000 species, and (iii) a fraction of them might not even
be plants. In essence, the task to be addressed is related to what is sometimes
called open-set or open-world recognition problems [3,18], i.e. problems in which
the recognition system has to be robust to unknown and never seen categories.
Beyond the brute-force classification across the known classes of the training
set, a big challenge is thus to automatically reject the false positive classification
hits that are caused by the unknown classes (i.e. by the distractors). To measure
this ability of the evaluated systems, each prediction had to be associated with
a confidence score in p ∈ [0, 1] quantifying the probability that this prediction is
true (independently from the other predictions).
Each participating group was allowed to submit up to 4 runs built from dif-
ferent methods. Semi-supervised, interactive or crowdsourced approaches were
allowed but compared independently from fully automatic methods. Any human
assistance in the processing of the test queries had therefore to be signaled in
the submitted runs.
Participants to the challenge were allowed to use external training data at the
condition that the experiment is entirely re-producible, i.e. that the used exter-
nal resource is clearly referenced and accessible to any other research group in
the world, and, the additional resource does not contain any of the test obser-
vations. It was in particular strictly forbidden to crawl training data from the
following domain names:
http://ds.plantnet-project.org/
http://www.tela-botanica.org
http://identify.plantnet-project.org
http://publish.plantnet-project.org/
http://www.gbif.org/
4 Metric
The metric used to evaluate the performance of the systems is the classification
mean Average Precision, called hereinafter ”mAP-open”, considering each class
ci of the training set as a query. More concretely, for each class ci , we extract
from the run file all predictions with P redictedClassId = ci , rank them by
decreasing probability p ∈ [0, 1] and compute the Average Precision for that
class. The mean is then computed across all classes. Distractors associated to
high probability values (i.e. false alarms) are likely to highly degrade the mAP,
it is thus crucial to try rejecting them. To evaluate more specifically the targeted
usage scenario (i.e. invasive species), a secondary mAP (”mAP-open-invasive”)
was computed by considering as queries only a subset of the species that belong
to a black list of invasive species.
5 Participants and methods
94 research groups registered to LifeCLEF plant challenge 2016 and downloaded
the dataset. Among this large raw audience, 8 research groups succeeded in
submitting runs, i.e. files containing the predictions of the system(s) they ran.
Details of the methods and systems used in the runs are further developed in the
individual working notes of the participants (Bluefield [9], Sabanci [5], CMP [20],
LIIR, Floristic [6], UM [15], QUT [16], BME [2]). Table 1 provides the results
achieved by each run as well as a brief synthesis of the methods used in each of
them. Complementary, the following paragraphs give a few more details about
the methods and the overall strategy employed by each participant.
Bluefield system, Japan, 4 runs, [9]: A VGGNet [19] based system with
the addition of Spatial Pyramid Pooling, Parametric ReLU and unknown class
rejection based on the minimal prediction score of training data (Run 1). Run 2
is the same as run 1 but with a slightly different rejection making use of a vali-
dation set. Run 3 and 4 are respectively the same as Run 1 and 2 but the scores
of the images belonging to the same observation were summed and normalised.
BME TMIT system, Hungary, 4 runs, [2]: This team attempted to com-
bine three classification methods: (i) one based on dense SIFT features, fisher
vectors and SVM (Run 2), (ii) the second one based on AlexNet CNN (Run 1)
and (iii), the last one based on a SVM trained on the meta-data. Run 3 cor-
responds to the combination of three classifiers (using a weighted average) and
Run 4 added two rejection mechanisms to Run3 (a distance-based rejection for
Table 1: Results of the LifeCLEF 2016 Plant Identification Task. Column ”Key-
words” & ”Rejection” attempt to give the main idea of the method used.
mAP-
mAP- mAP-
Run Key-words Rejection open-
open closed
invasive
VGGNet, combine outputs thresholds by class
Bluefield Run4 0.742 0.717 0.827
from a same observation (train+validation)
2x(VGGNet,GoogleNet) GoogleNet
SabanciU
tuned with resp. 70k, 115k 70k/70k 0.738 0.704 0.806
GebzeTU Run1
training images Plant/ImageNet
Manually removed
SabanciU...Run3 SabanciUGebzeTU Run1 0.737 0.703 0.807
90 test images
Bluefield Run3 Bluefield Run 4 thresholds by class 0.736 0.718 0.82
SabanciU...Run2 SabanciUGebzeTU Run1 - 0.736 0.683 0.807
SabanciU...Run4 SabanciUGebzeTU Run1 - 0.735 0.695 0.802
CMP Run1 Bagging of 3xResNet-152 - 0.71 0.653 0.79
CaffeNet, VGGNet16,
LIIR KUL Run3 3xGoogleNet, adding 12k threshold 0.703 0.674 0.761
external plant images
LIIR KUL Run2 LIIR KUL Run 3 threshold 0.692 0.667 0.744
LIIR KUL Run1 LIIR KUL Run 3 threshold 0.669 0.652 0.708
UM Run4 VGGNet16 - 0.669 0.598 0.742
CMP Run2 ResNet-152 - 0.644 0.564 0.729
CMP Run3 ResNet-152 (2015training) - 0.639 0.59 0.723
1 ”general” GoogleNet, 6
QUT Run3 ”organ” GoogleNets, - 0.629 0.61 0.696
observation combination
Floristic Run3 GoogleNet, metadata - 0.627 0.533 0.693
UM Run1 VGGNet16 - 0.627 0.537 0.7
Floristic Run1 GoogleNet - 0.619 0.541 0.694
Bluefield Run1 VGGNet thresholds by class 0.611 0.6 0.692
Bluefield Run2 VGGNet thresholds by class 0.611 0.6 0.693
Floristic Run2 GoogleNet thresholds by class 0.611 0.538 0.681
QUT Run1 GoogleNet - 0.601 0.563 0.672
VGGNet16 with dedicated
UM Run3 and combined organ & - 0.589 0.509 0.652
species layers
6 ”organ” GoogleNets,
QUT Run2 0.564 0.562 0.641
observation combination
VGGNet16 from scratch
UM Run2 - 0.481 0.446 0.552
(without ImageNet2012)
QUT Run4 QUT Run3 threshold 0.367 0.359 0.378
AlexNet & BVWs &
BMETMITRun4 - 0.174 0.144 0.213
metadata
AlexNet & BVWs & threshold by
BMETMITRun3 0.17 0.125 0.197
metadata classifier
BMETMITRun1 AlexNet - 0.169 0.125 0.196
BMETMITRun2 BVWs (fisher vectors) - 0.066 0.128 0.101
the fisher vectors and the minimal prediction score of training data for the CNN).
CMP system, Czech Republic, 3 runs: This team built their system with the
very deep residual CNN approach ResNet with 152 layers [11] which achieved the
best results in both ILSVRC 2015 and COCO 2015 (Common Objects in Con-
text) challenges last year. They added a fully-connected layer with 512 neurons
on top of the network, right before softmax classifier with an maxout activation
function [8]. They obtained thus a first run (run 2) by using all the 2016 training
dataset while they used only the 2015 training dataset in run 3. Run 1 achieved
the best performances by using a bagging approach of 3 ResNet-152: the training
dataset was divided into three folds, and each CNN was using a different fold
for validation and the remaining two folds for fine tuning.
Floristic system, France, 3 runs, [6]: This participant used a modified
GoogleNet architecture by adding batch normalisation and ReLU activation
function instead of the PReLU ones (run 1). In Run 2, adaptive thresholds
(one for each class) based on the prediction of the training images in the fine
tuned CNN were estimated for removing too low prediction on test images. Run
3 used a visual similarity search for scaling down the initial CNN prediction
when a test image gives inhomogeneous knns according to the metadata (organ
tags, GPS, genus and family levels).
LIIR KUL system, Belgium, 3 runs: This team used a ensemble classifier
of 5 fine-tuned models: one CaffeNet, one VGGNet16 and 3 GoogLeNet. They
added 12k external training data from Oxford flowers set, LeafSnap and trunk12
and attempted to exploit information in the metadata, mostly range maps from
GPS coordinates comparing predictions with content tags. As a rejection criteria,
they used a threshold on confidence of best prediction, one different threshold
for each run (run 1: 0.25, run 2: 0.2, run 3: 0.15).
QUT system, Australia, 4 runs, [16]: This participant compared a stan-
dard CNN fine tuned approach based on GoogleNet (run 1) with a bagging
approach ”mixDCNN” (run 2) built on the top of 6 fine tuned GoogleNet on the
6 training subsets corresponding to the 6 distinct organs (”leaf” and ”leafscan”
training images are actually merged into one subset). Outputs are weighted by
”occupation probabilities” which give for each CNN a confidence about their
prediction. Run 3 merged the two approaches, run 4 too but with a threshold
attempting to remove false positives.
Sabanci system, Turkey, 4 runs, [5]: This team used a CNN-based sys-
tem with 2 main configurations. Run 1: an ensemble of GoogleLeNet [21] and
VGGNet [19] fine-tuned on LifeCLEF 2015 data (for recognizing the targeted
species), as well as a second GoogleNet fine-tuned on the binary rejection prob-
lem (using 70k images of PlantCLEF2016 training set for the known class label
and 70K external images from the ILSCVR dataset for the unknown class label).
Run 2 is the same than Run 1 but without rejection. Run 3 is the same than
Run 1 but with manual rejection of 90 obviously non plant images.
UM system, Malaysia & UK, 4 runs: This team used a CNN system based
on a VGGNet 16 layers. They modified the higher convolutional level in order
to learn at the same time combinations of species and organs. VGGNet16 with
dedicated and combined organ & species layers with seven organ labels: branch,
entire, flower, fruit, leaf, leafscan and stem.
6 Official Results
We report in Figure 1 the scores achieved by the 29 collected runs for the two
official evaluation metrics (mAP-open and mAP-open-invasive). To better assess
the impact of the distractors (i.e. the images in the test set belonging to unknown
classes), we also report the mAP obtained when removing them (and denoted
as mAP-closed). As a first noticeable remark, the top-26 runs which performed
the best were based on Convolutional Neural Networks (CNN). This definitely
confirms the supremacy of deep learning approaches over previous methods, in
particular the one bases on hand-crafted features (such as BME TMIT Run
2). The different CNN-based systems mainly differed in (i) the architecture of
the used CNN, (ii) the way in which the rejection of the unknown classes was
managed and (iii), various system design improvements such as classifier ensem-
bles, bagging or observation-level pooling. An impressive mAP of 0.718 (for the
targeted invasive species monitoring scenario) was achieved by the best system
configuration of Bluefield (run 3). The gain achieved by this run is however more
related to the use of the observation-level pooling (looking at Bluefield run 1 for
comparison) than to a good rejection of the distractors. Comparing the metric
mAP-open with mAP-closed, the figure actually shows that the presence of the
unknown classes degrades the performance of all systems in a roughly similar
way. This difficulty of rejecting the unknown classes is confirmed by the very low
difference between the runs of the participants who experimented their system
with or without rejection (e.g. Sabanci Run 1 vs. Run 2 or FlorisTic Run 1 vs.
Run 2). On the other side, one can remark that all systems are quite robust to
the presence of unknown classes since the drop in performance is not too high.
Actually, as all the used CNNs were pre-trained on a large generalist data set
beforehand (ImageNet), it is likely that they have learned a diverse enough set
of visual patterns to avoid underfiting.
7 Complementary Analysis: Impact of the degree of
novelty
Within the conducted evaluation, the proportion of unknown classes in the test
set was still reasonable (actually only 42%) because of the procedure used to
Fig. 1. Scores achieved by all systems evaluated within the plant identification task
of LifeCLEF 2016, mAP-open: mean Average Precision on the 1000 species of the
training set and distractors in the test set, mAP-open-invasive: mean Average Pre-
cision with distractors but restricted to 26 invasive species only, mAP-closed: mean
Average Precision on the 1000 species but without distractors in the test set
create it. In a real mobile search data stream, the proportion of images belonging
to unknown classes could actually be much higher. To simulate such a higher
degree of novelty, we progressively down sampled the test images belonging to
known classes and recomputed the mAP-open evaluation metric. Results of this
experiment are provided in Figure. For clarity, we only reported the curves of
the best systems (for various degrees of novelty). As a first conclusion, the chart
clearly shows that the degree of novelty in the test set has a strong influence
on the performance of all systems. Even when 25% of the queries still belong
to a known class, none of the evaluated systems reach a mean average precision
greater than 0.45 (to be compared to 0.83 in a closed world). Some systems do
however better resist to the novelty than others. The performance of the best run
of Bluefield on the official test set does for instance quickly degrade with higher
novelty rates (despite the use of a rejection strategy). Looking at the best run
of Sabanci, one can see that the use of a supervised rejection class is the most
beneficial strategy for moderate novelty rates but then the performance also
degrades for high rates. Interestingly, the comparison of LIIR KUL Run1 and
LIIR KUL Run3 show that simply using a higher rejection threshold applied
to the CNN probabilities is more beneficial in the context of high unknown
class rates. Thus, we believe there is still rooms of improvements in the design of
adaptive rejection methods that would allow to automatically adapt the strength
of the rejection to the degree of novelty.
Fig. 2. Impact of the degree of novelty: Mean Average Precision vs. proportion of test
images belonging to known classes
8 Conclusion
This paper presented the overview and the results of the LifeCLEF 2016 plant
identification challenge following the five previous ones conducted within CLEF
evaluation forum. The main novelty compared to the previous year was that
the identification task was evaluated as an open-set recognition problem, i.e. a
problem in which the recognition system has to be robust to unknown and never
seen categories. The main conclusion was that CNNs appeared to be naturally
quite robust to the presence of unknown classes in the test set but that none
of the rejection methods additionally employed by the participants improved
that robustness. Also, the proportion of novelty in the test was still moderate.
We therefore conducted additional experiments showing that the preformance of
CNNs is strongly affected by higher rates of images belonging to unknown classes
and that the problem is clearly still open. In the end, our study shows that
there is still some room of improvement before being able to share automatically
identified plant observations within international biodiversity platforms. The
proportion of false positives would actually be too high for being acceptable for
biologists.
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