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International audience; Building accurate knowledge of the identity, the geographic distribution and the evolution of species is essential for the sustainable development of humanity, as well as for biodiversity conservation. However, the difficulty of identifying plants, animals and fungi is hindering the aggregation of new data and knowledge. Identifying and naming living organisms is almost impossible for the general public and is often difficult even for professionals and naturalists. Bridging this gap is a key step towards enabling effective biodiversity monitoring systems. The LifeCLEF campaign, presented in this paper, has been promoting and evaluating advances in this domain since 2011. The 2022 edition proposes five data-oriented challenges related to the identification and prediction of biodiversity: (i) PlantCLEF: very large-scale plant identification, (ii) BirdCLEF: bird species recognition in audio soundscapes, (iii) GeoLifeCLEF: remote sensing based prediction of species, (iv) SnakeCLEF: snake species identification on a global scale, and (v) FungiCLEF: fungi recognition as an open set classification problem. This paper overviews the motivation, methodology and main outcomes of that five challenges.

International audience; Building accurate knowledge of the identity, the geographic distribution and the evolution of species is essential for the sustainable development of humanity, as well as for biodiversity conservation. However, the difficulty of identifying plants, animals and fungi is hindering the aggregation of new data and knowledge. Identifying and naming living organisms is almost impossible for the general public and is often difficult even for professionals and naturalists. Bridging this gap is a key step towards enabling effective biodiversity monitoring systems. The LifeCLEF campaign, presented in this paper, has been promoting and evaluating advances in this domain since 2011. The 2022 edition proposes five data-oriented challenges related to the identification and prediction of biodiversity: (i) PlantCLEF: very large-scale plant identification, (ii) BirdCLEF: bird species recognition in audio soundscapes, (iii) GeoLifeCLEF: remote sensing based prediction of species, (iv) SnakeCLEF: Snake Species Identification in Medically Important scenarios, and (v) FungiCLEF: Fungi recognition from images and metadata.

Recent progress in self-supervised learning has resulted in models that are capable of extracting rich representations from image collections without requiring any explicit label supervision. However, to date the vast majority of these approaches have restricted themselves to training on standard benchmark datasets such as ImageNet. We argue that fine-grained visual categorization problems, such as plant and animal species classification, provide an informative testbed for self-supervised learning. In order to facilitate progress in this area we present two new natural world visual classification datasets, iNat2021 and NeWT. The former consists of 2.7M images from 10k different species uploaded by users of the citizen science application iNaturalist. We designed the latter, NeWT, in collaboration with domain experts with the aim of benchmarking the performance of representation learning algorithms on a suite of challenging natural world binary classification tasks that go beyond standard species classification. These two new datasets allow us to explore questions related to large-scale representation and transfer learning in the context of fine-grained categories. We provide a comprehensive analysis of feature extractors trained with and without supervision on ImageNet and iNat2021, shedding light on the strengths and weaknesses of different learned features across a diverse set of tasks. We find that features produced by standard supervised methods still outperform those produced by self-supervised approaches such as SimCLR. However, improved self-supervised learning methods are constantly being released and the iNat2021 and NeWT datasets are a valuable resource for tracking their progress., Comment: CVPR 2021

Conservation science depends on an accurate understanding of what's happening in a given ecosystem. How many species live there? What is the makeup of the population? How is that changing over time? Species Distribution Modeling (SDM) seeks to predict the spatial (and sometimes temporal) patterns of species occurrence, i.e. where a species is likely to be found. The last few years have seen a surge of interest in applying powerful machine learning tools to challenging problems in ecology. Despite its considerable importance, SDM has received relatively little attention from the computer science community. Our goal in this work is to provide computer scientists with the necessary background to read the SDM literature and develop ecologically useful ML-based SDM algorithms. In particular, we introduce key SDM concepts and terminology, review standard models, discuss data availability, and highlight technical challenges and pitfalls., Comment: ACM COMPASS 2021

Predicting all applicable labels for a given image is known as multi-label classification. Compared to the standard multi-class case (where each image has only one label), it is considerably more challenging to annotate training data for multi-label classification. When the number of potential labels is large, human annotators find it difficult to mention all applicable labels for each training image. Furthermore, in some settings detection is intrinsically difficult e.g. finding small object instances in high resolution images. As a result, multi-label training data is often plagued by false negatives. We consider the hardest version of this problem, where annotators provide only one relevant label for each image. As a result, training sets will have only one positive label per image and no confirmed negatives. We explore this special case of learning from missing labels across four different multi-label image classification datasets for both linear classifiers and end-to-end fine-tuned deep networks. We extend existing multi-label losses to this setting and propose novel variants that constrain the number of expected positive labels during training. Surprisingly, we show that in some cases it is possible to approach the performance of fully labeled classifiers despite training with significantly fewer confirmed labels., CVPR 2021. Supplementary material included

Building accurate knowledge of the identity, the geographic distribution and the evolution of species is essential for the sustainable development of humanity, as well as for biodiversity conservation. However, the difficulty of identifying plants and animals in the field is hindering the aggregation of new data and knowledge. Identifying and naming living plants or animals is almost impossible for the general public and is often difficult even for professionals and naturalists. Bridging this gap is a key step towards enabling effective biodiversity monitoring systems. The LifeCLEF campaign, presented in this paper, has been promoting and evaluating advances in this domain since 2011. The 2021 edition proposes four data-oriented challenges related to the identification and prediction of biodiversity: (i) PlantCLEF: cross-domain plant identification based on herbarium sheets, (ii) BirdCLEF: bird species recognition in audio soundscapes, (iii) GeoLifeCLEF: location-based prediction of species based on environmental and occurrence data and (iv) SnakeCLEF: image-based snake identification.

International audience; Building accurate knowledge of the identity, the geographic distribution and the evolution of species is essential for the sustainable development of humanity, as well as for biodiversity conservation. However, the difficulty of identifying plants and animals is hindering the aggregation of new data and knowledge. Identifying and naming living plants or animals is almost impossible for the general public and is often difficult even for professionals and naturalists. Bridging this gap is a key step towards enabling effective biodiversity monitoring systems. The LifeCLEF campaign, presented in this paper, has been promoting and evaluating advances in this domain since 2011. The 2021 edition proposes four data-oriented challenges related to the identification and prediction of biodiversity: (i) PlantCLEF: cross-domain plant identification based on herbarium sheets, (ii) BirdCLEF: bird species recognition in audio soundscapes, (iii) GeoLifeCLEF: remote sensing based prediction of species, and (iv) SnakeCLEF: Automatic Snake Species Identification with Country-Level Focus.

International audience; Building accurate knowledge of the identity, the geographic distribution and the evolution of species is essential for the sustainable development of humanity, as well as for biodiversity conservation. However, the difficulty of identifying plants and animals in the field is hindering the aggregation of new data and knowledge. Identifying and naming living plants or animals is almost impossible for the general public and is often difficult even for professionals and naturalists. Bridging this gap is a key step towards enabling effective biodiversity monitoring systems. The LifeCLEF campaign, presented in this paper, has been promoting and evaluating advances in this domain since 2011. The 2020 edition proposes four data-oriented challenges related to the identification and prediction of biodiversity: (i) PlantCLEF: cross-domain plant identification based on herbarium sheets (ii) BirdCLEF: bird species recognition in audio soundscapes, (iii) GeoLifeCLEF: location-based prediction of species based on environmental and occurrence data, and (iv) SnakeCLEF: snake identification based on image and geographic location

International audience; Building accurate knowledge of the identity, the geographic distribution and the evolution of species is essential for the sustainable development of humanity, as well as for biodiversity conservation. However, the difficulty of identifying plants and animals in the field is hindering the aggregation of new data and knowledge. Identifying and naming living plants or animals is almost impossible for the general public and is often difficult even for professionals and naturalists. Bridging this gap is a key step towards enabling effective biodiversity monitoring systems. The LifeCLEF campaign, presented in this paper, has been promoting and evaluating advances in this domain since 2011. The 2020 edition proposes four data-oriented challenges related to the identification and prediction of biodiversity: (i) PlantCLEF: cross-domain plant identification based on herbarium sheets, (ii) BirdCLEF: bird species recognition in audio soundscapes, (iii) GeoLifeCLEF: location-based prediction of species based on environmental and occurrence data, and (iv) SnakeCLEF: image-based snake identification.

Marine seismic surveying discerns subsurface seafloor geology, indicative of, for example, petroleum deposits, by emitting high-intensity, low-frequency impulsive sounds. Impacts on fish are uncertain. Opportunistic monitoring of acoustic signatures from a seismic survey on the inner continental shelf of North Carolina, USA, revealed noise exceeding 170 dB re 1 μ Pa peak on two temperate reefs federally designated as Essential Fish Habitat 0.7 and 6.5 km from the survey ship path. Videos recorded fish abundance and behavior on a nearby third reef 7.9 km from the seismic track. During seismic surveying, reef-fish abundance declined by 78% during evening hours when fish habitat use was highest on the previous three days without seismic noise. Despite absence of videos documenting fish returns after seismic surveying, the significant reduction in fish occupation of the reef represents disruption to daily pattern. This numerical response confirms that conservation concerns associated with seismic surveying are realistic.

Appearance information alone is often not sufficient to accurately differentiate between fine-grained visual categories. Human experts make use of additional cues such as where, and when, a given image was taken in order to inform their final decision. This contextual information is readily available in many online image collections but has been underutilized by existing image classifiers that focus solely on making predictions based on the image contents. We propose an efficient spatio-temporal prior, that when conditioned on a geographical location and time, estimates the probability that a given object category occurs at that location. Our prior is trained from presence-only observation data and jointly models object categories, their spatio-temporal distributions, and photographer biases. Experiments performed on multiple challenging image classification datasets show that combining our prior with the predictions from image classifiers results in a large improvement in final classification performance., ICCV 2019

Optical coherence tomography (OCT) has revolutionized diagnosis and prognosis of ophthalmic diseases by visualization and measurement of retinal layers. To speed up the quantitative analysis of disease biomarkers, an increasing number of automatic segmentation algorithms have been proposed to estimate the boundary locations of retinal layers. While the performance of these algorithms has significantly improved in recent years, a critical question to ask is how far we are from a theoretical limit to OCT segmentation performance. In this paper, we present the Cramer–Rao lower bounds (CRLBs) for the problem of OCT layer segmentation. In deriving the CRLBs, we address the important problem of defining statistical models that best represent the intensity distribution in each layer of the retina. Additionally, we calculate the bounds under an optimal affine bias, reflecting the use of prior knowledge in many segmentation algorithms. Experiments using in vivo images of human retina from a commercial spectral domain OCT system are presented, showing potential for improvement of automated segmentation accuracy. Our general mathematical model can be easily adapted for virtually any OCT system. Furthermore, the statistical models of signal and noise developed in this paper can be utilized for the future improvements of OCT image denoising, reconstruction, and many other applications.

The peripheral retina of the human eye offers a unique opportunity for assessment and monitoring of ocular diseases. We have developed a novel wide-field (>70°) optical coherence tomography system (WF-OCT) equipped with wavefront sensorless adaptive optics (WSAO) for enhancing the visualization of smaller (23°) retina. We demonstrated the ability of our WF-OCT system to acquire non wavefront-corrected wide-field images rapidly, which could then be used to locate regions of interest, zoom into targeted features, and visualize the same region at different time points. A pilot clinical study was conducted on seven healthy volunteers and two subjects with prodromal Alzheimer’s disease which illustrated the capability to image Drusen-like pathologies as far as 32.5° from the fovea in un-averaged volume scans. This work suggests that the proposed combination of WF-OCT and WSAO may find applications in the diagnosis and treatment of ocular, and potentially neurodegenerative, diseases of the peripheral retina, including diabetes and Alzheimer’s disease.

International audience; 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 advance the state-of-the-art in this area, a large-scale machine learning competition called GeoLifeCLEF 2020 was organized. It relied on a dataset 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. This paper presents an overview of the competition , synthesizes the approaches used by the participating groups, and analyzes the main results. In particular, we highlight the ability of remote sensing imagery and convolutional neural networks to improve predictive performance, complementary to traditional approaches.

Recent self-supervised representation learning techniques have largely closed the gap between supervised and unsupervised learning on ImageNet classification. While the particulars of pretraining on ImageNet are now relatively well understood, the field still lacks widely accepted best practices for replicating this success on other datasets. As a first step in this direction, we study contrastive self-supervised learning on four diverse large-scale datasets. By looking through the lenses of data quantity, data domain, data quality, and task granularity, we provide new insights into the necessary conditions for successful self-supervised learning. Our key findings include observations such as: (i) the benefit of additional pretraining data beyond 500k images is modest, (ii) adding pretraining images from another domain does not lead to more general representations, (iii) corrupted pretraining images have a disparate impact on supervised and self-supervised pretraining, and (iv) contrastive learning lags far behind supervised learning on fine-grained visual classification tasks., Comment: CVPR 2022