Modelling Species Distributions with Deep Learning to Predict Plant Extinction Risk and Assess Climate Change Impacts

The post-2020 global biodiversity framework needs ambitious, research-based targets. Estimating the accelerated extinction risk due to climate change is critical. The International Union for Conservation of Nature (IUCN) measures the extinction risk of species. Automatic methods have been developed to provide information on the IUCN status of under-assessed taxa. However, these compensatory methods are based on current species characteristics, mainly geographical, which precludes their use in future projections. Here, we evaluate a novel method for classifying the IUCN status of species benefiting from the generalisation power of species distribution models based on deep learning. Our method matches state-of-the-art classification performance while relying on flexible SDM-based features that capture species' environmental preferences. Cross-validation yields average accuracies of 0.61 for status classification and 0.78 for binary classification. Climate change will reshape future species distributions. Under the species-environment equilibrium hypothesis, SDM projections approximate plausible future outcomes. Two extremes of species dispersal capacity are considered: unlimited or null. The projected species distributions are translated into features feeding our IUCN classification method. Finally, trends in threatened species are analysed over time and i) by continent and as a function of average ii) latitude or iii) altitude. The proportion of threatened species is increasing globally, with critical rates in Africa, Asia and South America. Furthermore, the proportion of threatened species is predicted to peak around the two Tropics, at the Equator, in the lowlands and at altitudes of 800-1,500 m.

AI-based Mapping of the Conservation Status of Orchid Assemblages at Global Scale

Although increasing threats on biodiversity are now widely recognised, there are no accurate global maps showing whether and where species assemblages are at risk. We hereby assess and map at kilometre resolution the conservation status of the iconic orchid family, and discuss the insights conveyed at multiple scales. We introduce a new Deep Species Distribution Model trained on 1M occurrences of 14K orchid species to predict their assemblages at global scale and at kilometre resolution. We propose two main indicators of the conservation status of the assemblages: (i) the proportion of threatened species, and (ii) the status of the most threatened species in the assemblage. We show and analyze the variation of these indicators at World scale and in relation to currently protected areas in Sumatra island. Global and interactive maps available online show the indicators of conservation status of orchid assemblages, with sharp spatial variations at all scales. The highest level of threat is found at Madagascar and the neighbouring islands. In Sumatra, we found good correspondence of protected areas with our indicators, but supplementing current IUCN assessments with status predictions results in alarming levels of species threat across the island. Recent advances in deep learning enable reliable mapping of the conservation status of species assemblages on a global scale. As an umbrella taxon, orchid family provides a reference for identifying vulnerable ecosystems worldwide, and prioritising conservation actions both at international and local levels.

A two-head loss function for deep Average-K classification

Average-K classification is an alternative to top-K classification in which the number of labels returned varies with the ambiguity of the input image but must average to K over all the samples. A simple method to solve this task is to threshold the softmax output of a model trained with the cross-entropy loss. This approach is theoretically proven to be asymptotically consistent, but it is not guaranteed to be optimal for a finite set of samples. In this paper, we propose a new loss function based on a multi-label classification head in addition to the classical softmax. This second head is trained using pseudo-labels generated by thresholding the softmax head while guaranteeing that K classes are returned on average. We show that this approach allows the model to better capture ambiguities between classes and, as a result, to return more consistent sets of possible classes. Experiments on two datasets from the literature demonstrate that our approach outperforms the softmax baseline, as well as several other loss functions more generally designed for weakly supervised multi-label classification. The gains are larger the higher the uncertainty, especially for classes with few samples.

Improve learning combining crowdsourced labels by weighting Areas Under the Margin

In supervised learning -- for instance in image classification -- modern massive datasets are commonly labeled by a crowd of workers. The obtained labels in this crowdsourcing setting are then aggregated for training. The aggregation step generally leverages a per worker trust score. Yet, such worker-centric approaches discard each task ambiguity. Some intrinsically ambiguous tasks might even fool expert workers, which could eventually be harmful for the learning step. In a standard supervised learning setting -- with one label per task and balanced classes -- the Area Under the Margin (AUM) statistic is tailored to identify mislabeled data. We adapt the AUM to identify ambiguous tasks in crowdsourced learning scenarios, introducing the Weighted AUM (WAUM). The WAUM is an average of AUMs weighted by worker and task dependent scores. We show that the WAUM can help discarding ambiguous tasks from the training set, leading to better generalization or calibration performance. We report improvements with respect to feature-blind aggregation strategies both for simulated settings and for the CIFAR-10H crowdsourced dataset.

How does the degree of novelty impacts semi-supervised representation learning for novel class retrieval?

Supervised representation learning with deep networks tends to overfit the training classes and the generalization to novel classes is a challenging question. It is common to evaluate a learned embedding on held-out images of the same training classes. In real applications however, data comes from new sources and novel classes are likely to arise. We hypothesize that incorporating unlabelled images of novel classes in the training set in a semi-supervised fashion would be beneficial for the efficient retrieval of novel-class images compared to a vanilla supervised representation. To verify this hypothesis in a comprehensive way, we propose an original evaluation methodology that varies the degree of novelty of novel classes by partitioning the dataset category-wise either randomly, or semantically, i.e. by minimizing the shared semantics between base and novel classes. This evaluation procedure allows to train a representation blindly to any novel-class labels and evaluate the frozen representation on the retrieval of base or novel classes. We find that a vanilla supervised representation falls short on the retrieval of novel classes even more so when the semantics gap is higher. Semi-supervised algorithms allow to partially bridge this performance gap but there is still much room for improvement.

Stochastic smoothing of the top-K calibrated hinge loss for deep imbalanced classification

In modern classification tasks, the number of labels is getting larger and larger, as is the size of the datasets encountered in practice. As the number of classes increases, class ambiguity and class imbalance become more and more problematic to achieve high top-1 accuracy. Meanwhile, Top-K metrics (metrics allowing K guesses) have become popular, especially for performance reporting. Yet, proposing top-K losses tailored for deep learning remains a challenge, both theoretically and practically. In this paper we introduce a stochastic top-K hinge loss inspired by recent developments on top-K calibrated losses. Our proposal is based on the smoothing of the top-K operator building on the flexible "perturbed optimizer" framework. We show that our loss function performs very well in the case of balanced datasets, while benefiting from a significantly lower computational time than the state-of-the-art top-K loss function. In addition, we propose a simple variant of our loss for the imbalanced case. Experiments on a heavy-tailed dataset show that our loss function significantly outperforms other baseline loss functions.

Classification Under Ambiguity: When Is Average-K Better Than Top-K?

When many labels are possible, choosing a single one can lead to low precision. A common alternative, referred to as top-$K$ classification, is to choose some number $K$ (commonly around 5) and to return the $K$ labels with the highest scores. Unfortunately, for unambiguous cases, $K>1$ is too many and, for very ambiguous cases, $K \leq 5$ (for example) can be too small. An alternative sensible strategy is to use an adaptive approach in which the number of labels returned varies as a function of the computed ambiguity, but must average to some particular $K$ over all the samples. We denote this alternative average-$K$ classification. This paper formally characterizes the ambiguity profile when average-$K$ classification can achieve a lower error rate than a fixed top-$K$ classification. Moreover, it provides natural estimation procedures for both the fixed-size and the adaptive classifier and proves their consistency. Finally, it reports experiments on real-world image data sets revealing the benefit of average-$K$ classification over top-$K$ in practice. Overall, when the ambiguity is known precisely, average-$K$ is never worse than top-$K$, and, in our experiments, when it is estimated, this also holds.

Reproducible Performance Optimization of Complex Applications on the Edge-to-Cloud Continuum

In more and more application areas, we are witnessing the emergence of complex workflows that combine computing, analytics and learning. They often require a hybrid execution infrastructure with IoT devices interconnected to cloud/HPC systems (aka Computing Continuum). Such workflows are subject to complex constraints and requirements in terms of performance, resource usage, energy consumption and financial costs. This makes it challenging to optimize their configuration and deployment. We propose a methodology to support the optimization of real-life applications on the Edge-to-Cloud Continuum. We implement it as an extension of E2Clab, a previously proposed framework supporting the complete experimental cycle across the Edge-to-Cloud Continuum. Our approach relies on a rigorous analysis of possible configurations in a controlled testbed environment to understand their behaviour and related performance trade-offs. We illustrate our methodology by optimizing Pl@ntNet, a world-wide plant identification application. Our methodology can be generalized to other applications in the Edge-to-Cloud Continuum.

Hyperspherical embedding for novel class classification

Deep learning models have become increasingly useful in many different industries. On the domain of image classification, convolutional neural networks proved the ability to learn robust features for the closed set problem, as shown in many different datasets, such as MNIST FASHIONMNIST, CIFAR10, CIFAR100, and IMAGENET. These approaches use deep neural networks with dense layers with softmax activation functions in order to learn features that can separate classes in a latent space. However, this traditional approach is not useful for identifying classes unseen on the training set, known as the open set problem. A similar problem occurs in scenarios involving learning on small data. To tackle both problems, few-shot learning has been proposed. In particular, metric learning learns features that obey constraints of a metric distance in the latent space in order to perform classification. However, while this approach proves to be useful for the open set problem, current implementation requires pair-wise training, where both positive and negative examples of similar images are presented during the training phase, which limits the applicability of these approaches in large data or large class scenarios given the combinatorial nature of the possible inputs.In this paper, we present a constraint-based approach applied to the representations in the latent space under the normalized softmax loss, proposed by[18]. We experimentally validate the proposed approach for the classification of unseen classes on different datasets using both metric learning and the normalized softmax loss, on disjoint and joint scenarios. Our results show that not only our proposed strategy can be efficiently trained on larger set of classes, as it does not require pairwise learning, but also present better classification results than the metric learning strategies surpassing its accuracy by a significant margin.

The GeoLifeCLEF 2020 Dataset

Understanding the geographic distribution of species is a key concern in conservation. By pairing species occurrences with environmental features, researchers can model the relationship between an environment and the species which may be found there. To facilitate research in this area, we present the GeoLifeCLEF 2020 dataset, which consists of 1.9 million species observations paired with high-resolution remote sensing imagery, land cover data, and altitude, in addition to traditional low-resolution climate and soil variables. We also discuss the GeoLifeCLEF 2020 competition, which aims to use this dataset to advance the state-of-the-art in location-based species recommendation.