A Representation Learning Approach to Animal Biodiversity Conservation (2020)

Abstract: Generating knowledge from natural language data has aided in solving many artificial intelligence problems. Vector representations of words have been the driving force behind the majority of natural language processing tasks. This paper develops a novel approach for predicting the conservation status of animal species using custom generated scientific name embeddings. We use two different vector embeddings generated using representation learning on Wikipedia text and animal taxonomy data. We generate name embeddings for all species in the animal kingdom using unsupervised learning and build a model on the IUCN Red List dataset to classify species into endangered or least-concern. To our knowledge, this is the first work that makes use of learnt features instead of handcrafted features for this task and achieves competitive results. Based on the high confidence results of our model, we also predict the conservation status of data deficient species whose conservation status is still unknown and thus steering more focus towards them for protection. These embeddings have also been made publicly available here. We believe this will greatly help in solving various downstream tasks and further advance research in the cross-domain involving natural language processing, conservation biology, and life sciences.

## introduction today, we are losing biodiversity at an unprecedented rate. animal species or "animalia" form one of the vital components of biodiversity and ensure the balance in our ecological system. hence, conservation of animals becomes an inherent part of biodiversity conservation and maintaining a functional ecological system. in this work, we try to address a particular aspect of global animal conservation that tries to identify species as endangered or least-concern. out of millions of different animal species on earth, only a few thousand have been studied and identified as endangered or not, to date. this points out at the time and resource constraints involved in studying each species individually and manually. international union for conservation of nature (iucn) maintains a list of all species 2 with their corresponding red list status. we base our work on two causes of extinction in animal species -because of either the habitat of the species being impacted due to various reasons or the loss of genetic variation. we present a data-driven tool that aims to steer the focus of researchers towards correct and possibly unexplored directions within animal conservation that helps prioritize species under study. we use reliable data sources for correctness and build a machine learning classification model to identify species as endangered or not. we use two sources of information to build our machine learning-based framework to predict animal species' red list status -wikipedia text of each species and the complete animal taxonomy structure. the labeled dataset provided by iucn for red list classification contains red list status of more than 38,000 species. we generate a hierarchical graph using the animal taxonomy data from which we generate node embeddings for each node in the graph representing a particular animal species and we also generate document embeddings from the wikipedia text. our work proposes the use of a non-linear combination of these embeddings learnt using a machine learning model to classify the species into endangered or least-concern. we believe that the information related to habitat is captured through wikipedia text as it contains descriptive details of the species' geography, traits, and other characteristic information. also, it is intuitive to use a graph representation learning method to capture the structural information of the taxonomy graph that depicts how different species are related to one another. we also train a probabilistic model to obtain a confidence score for our predictions since it is crucial to associate our predictions with a level of belief for this particular task. our results indicate that our method not only performs well on the binary classification task but is also able to classify more than half of the test data with a confidence c of 75 percent or more, with an accuracy of 87 percent. these promising results are highly motivating to propose the use of this model in a research or industrial setting as well as spark great research in this avenue. we demonstrate one such application by using the trained model on data-deficient species whose conservation status is unknown. we uncovered 1,040 out of 7,170 species as endangered showing how focus can be steered towards such species for more study to aid their conservation. ## related works there have been works related to the prediction of extinction status of animal and plant species where spatial and morphological traits data have been used with a number of machine learning classifiers like @xcite , eimear nic lughadha and rivers (2018), bolam (2018) and @xcite . in all these works, the latitude and longitude of where the species are found along with characteristic traits of these species like body mass, litter size, habitat breadth, trophic level have been explicitly used as features to build classifiers. also, these works have focused on global as well as specific regions and habitats where some of these species dwell. eimear nic lughadha and rivers (2018) is a review of several of such approaches to solving the same problem. @xcite proposed an approach to combine fasttext and node2vec to generate word embeddings for scientific names of drugs. they formulated a reasoning to encode morphology and hierarchical data in the vector representations of these drugs and evaluated their model on two bench-marking tasks for similarity measuring and two biomedical relation extraction tasks and have achieved competitive results on both. @xcite proposed a method to generate word embeddings for rare or unseen words by restricting morphologically similar words to have similar embeddings. gensim, proposed by @xcite , has an implementation of @xcite 's doc2vec that learns paragraph and document embeddings via the distributed cbow and skip-gram models. this work has been successfully applied to various tasks such as sentiment classification, text classification, and language understanding. several methods have been proposed for generating vector representations using graph neural networks for graphical data like social networks, communication networks, and word co-occurrence networks. @xcite proposed a method based on random walks to encode graphical representations of social networks and protein sequences and achieved state-of-the-art results on benchmark multi-class classification tasks for both. further, they also assessed the quality of vector embeddings generated using node2vec on a pos-tagger task on a large wikipedia corpus. @xcite show the performance of various machine learning methods on predicting the conservation status of over 150,000 plant species using open-source geographic, environmental, and morphological trait data. another similar work in this area is done by @xcite . they show the performance of six statistical machine learning models on predicting the red list status of mammals achieving classification accuracy up to 92%. they also reported that the area under roc for their best models ranged between 0.873 and 0.961. this work is the closest to ours, however, it uses handcrafted features as opposed to our learned features and only works with the mammal subset of animalia. we consider this as a benchmark for our work, although it is not a completely fair comparison since the dataset is not the same. also, our work revolves exactly around the limitations of their work. to the best of our knowledge, our work is the first to predict the conservation status using contextual data in the form of wikipedia text coupled with taxonomic information using learned features on the entire animal kingdom. ## main contribution some of the works we have seen carefully collate a dataset of species information that includes various parameters related to geographical information and physical characteristics. our work mainly focuses on potentially eliminating the need for manually building handcrafted features by providing implicit features to our model through learned vector representations. the contribution of this paper is as follows - ## experiment figure 1 shows the entire experiment pipeline starting with data collection and preprocessing to generating embeddings for animal species and finally using this as input for models used for classification of red list status of animal species. we discuss three different classifiers because there is not much prior research in this field, especially using automated feature engineering and machine learning. we explore various models that attempt to capture different patterns in the data and try to gain various insights from them. the dataset we have is relatively small, so we chose a random forest model since it generally performs well on smaller datasets. the nature of this problem demands a degree of belief against the predictions we are making, in the sense that we would like to know if the system predicts a particular animal species to be endangered, how confidently it makes that prediction. so we implemented a bayesian neural network model as well, using a multi-layer perceptron model as a baseline, which gives us a confidence score associated with the prediction it makes. this is highly intuitive and it can be directly used in correlation with prioritizing research. ## results as described above, seven different classifiers were run on the dataset. the results are summarized in the bnn model, along with predicting the class, also outputs a confidence score corresponding to the classification. our model was run with two confidence thresholds (c), 0.75 and 0.9 as shown in the table on the same test data of 3,521 animal species. for @xmath0.75, the model predicted for 52% of the test species and for @xmath1.9, it predicted for 20% of the test species. the corresponding performance metrics are shown in the mlp and bnn models were run for data-deficient species using the same 400-dimensional input and out of 7,170 species, 1,040 species were classified as endangered by the model and figure 3 shows two of them. the embeddings for all these 7,170 data deficient animal species along with the training and test embeddings for the scientific names used in this work have been made publicly available for further research in this domain. model f1 score mcc roc-auc rf w/ node2vec 0.862 0.421 0.784 rf w/ doc2vec 0.869 0.440 0.820 rf w/ node2vec + doc2vec 0.860 0.378 0.827 mlp w/ node2vec 0.843 0.331 0.729 mlp w/ doc2vec 0.886 0.568 0.864 mlp w/ node2vec + doc2vec 0.885 0.583 0.873 bnn w/ node2vec + doc2vec + @xmath2.75 0.856 0.736 0.868 bnn w/ node2vec + doc2vec + @xmath3.9 0.889 0.845 0.911 ## conclusions and future work this work presents a novel approach of using custom embeddings for predicting red list status with an intuition of capturing geographical as well as genetic information for all species of the animal kingdom using a contextual training corpus and hierarchical taxonomy graph data. we propose to use a combination of document embeddings and graph vector representations that enables the classification of animal species as being endangered or not with a definite sense of belief. we show that our model performs well with significant confidence levels which makes it useful in real-world settings. in the future, we plan to obtain a more scientific text corpus to enhance the quality of the document embeddings, along with using a hybrid model of learnt features and explicit species metadata. we also plan to implement attention-based models for both text and graph inputs for better representations and to capture parts of inputs that are of more importance, making the system more explainable @xcite . we believe that our framework can assist environmental researchers to further advance the study of animal conservation in the right direction. this work brings a different approach to research in the cross-domain of natural language and biology and opens up new paths to involve machine learning in the most interesting and impactful tasks.