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Register a new userIntroducing a Central African Primate Vocalisation Dataset for Automated Species Classification
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Automated classification of animal vocalisations is a potentially powerful wildlife monitoring tool. Training robust classifiers requires sizable annotated datasets, which are not easily recorded in the wild. To circumvent this problem, we recorded four primate species under semi-natural conditions in a wildlife sanctuary in Cameroon with the objective to train a classifier capable of detecting species in the wild. Here, we introduce the collected dataset, describe our approach and initial results of classifier development. To increase the efficiency of the annotation process, we condensed the recordings with an energy/change based automatic vocalisation detection. Segmenting the annotated chunks into training, validation and test sets, initial results reveal up to 82% unweighted average recall (UAR) test set performance in four-class primate species classification.
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This paper focuses on a core task in computational sustainability and statistical ecology: species distribution modeling (SDM). In SDM, the occurrence pattern of a species on a landscape is predicted by environmental features based on observations at a set of locations. At first, SDM may appear to be a binary classification problem, and one might be inclined to employ classic tools (e.g., logistic regression, support vector machines, neural networks) to tackle it. However, wildlife surveys introduce structured noise (especially under-counting) in the species observations. If unaccounted for, these observation errors systematically bias SDMs. To address the unique challenges of SDM, this paper proposes a framework called StatEcoNet. Specifically, this work employs a graphical generative model in statistical ecology to serve as the skeleton of the proposed computational framework and carefully integrates neural networks under the framework. The advantages of StatEcoNet over related approaches are demonstrated on simulated datasets as well as bird species data. Since SDMs are critical tools for ecological science and natural resource management, StatEcoNet may offer boosted computational and analytical powers to a wide range of applications that have significant social impacts, e.g., the study and conservation of threatened species.
Understanding primate behavior is a mission-critical goal of both biology and biomedicine. Despite the importance of behavior, our ability to rigorously quantify it has heretofore been limited to low-information measures like preference, looking time, and reaction time, or to non-scaleable measures like ethograms. However, recent technological advances have led to a major revolution in behavioral measurement. Specifically, digital video cameras and automated pose tracking software can provide detailed measures of full body position (i.e., pose) of multiple primates over time (i.e., behavior) with high spatial and temporal resolution. Pose-tracking technology in turn can be used to detect behavioral states, such as eating, sleeping, and mating. The availability of such data has in turn spurred developments in data analysis techniques. Together, these changes are poised to lead to major advances in scientific fields that rely on behavioral as a dependent variable. In this review, we situate the tracking revolution in the history of the study of behavior, argue for investment in and development of analytical and research techniques that can profit from the advent of the era of big behavior, and propose that zoos will have a central role to play in this era.
1. Joint Species Distribution models (JSDMs) explain spatial variation in community composition by contributions of the environment, biotic associations, and possibly spatially structured residual covariance. They show great promise as a general analytical framework for community ecology and macroecology, but current JSDMs, even when approximated by latent variables, scale poorly on large datasets, limiting their usefulness for currently emerging big (e.g., metabarcoding and metagenomics) community datasets. 2. Here, we present a novel, more scalable JSDM (sjSDM) that circumvents the need to use latent variables by using a Monte-Carlo integration of the joint JSDM likelihood and allows flexible elastic net regularization on all model components. We implemented sjSDM in PyTorch, a modern machine learning framework that can make use of CPU and GPU calculations. Using simulated communities with known species-species associations and different number of species and sites, we compare sjSDM with state-of-the-art JSDM implementations to determine computational runtimes and accuracy of the inferred species-species and species-environmental associations. 3. We find that sjSDM is orders of magnitude faster than existing JSDM algorithms (even when run on the CPU) and can be scaled to very large datasets. Despite the dramatically improved speed, sjSDM produces more accurate estimates of species association structures than alternative JSDM implementations. We demonstrate the applicability of sjSDM to big community data using eDNA case study with thousands of fungi operational taxonomic units (OTU). 4. Our sjSDM approach makes the analysis of JSDMs to large community datasets with hundreds or thousands of species possible, substantially extending the applicability of JSDMs in ecology. We provide our method in an R package to facilitate its applicability for practical data analysis.
Memorization in over-parameterized neural networks could severely hurt generalization in the presence of mislabeled examples. However, mislabeled examples are hard to avoid in extremely large datasets collected with weak supervision. We address this problem by reasoning counterfactually about the loss distribution of examples with uniform random labels had they were trained with the real examples, and use this information to remove noisy examples from the training set. First, we observe that examples with uniform random labels have higher losses when trained with stochastic gradient descent under large learning rates. Then, we propose to model the loss distribution of the counterfactual examples using only the network parameters, which is able to model such examples with remarkable success. Finally, we propose to remove examples whose loss exceeds a certain quantile of the modeled loss distribution. This leads to On-the-fly Data Denoising (ODD), a simple yet effective algorithm that is robust to mislabeled examples, while introducing almost zero computational overhead compared to standard training. ODD is able to achieve state-of-the-art results on a wide range of datasets including real-world ones such as WebVision and Clothing1M.
Robotic weed control has seen increased research of late with its potential for boosting productivity in agriculture. Majority of works focus on developing robotics for croplands, ignoring the weed management problems facing rangeland stock farmers. Perhaps the greatest obstacle to widespread uptake of robotic weed control is the robust classification of weed species in their natural environment. The unparalleled successes of deep learning make it an ideal candidate for recognising various weed species in the complex rangeland environment. This work contributes the first large, public, multiclass image dataset of weed species from the Australian rangelands; allowing for the development of robust classification methods to make robotic weed control viable. The DeepWeeds dataset consists of 17,509 labelled images of eight nationally significant weed species native to eight locations across northern Australia. This paper presents a baseline for classification performance on the dataset using the benchmark deep learning models, Inception-v3 and ResNet-50. These models achieved an average classification accuracy of 95.1% and 95.7%, respectively. We also demonstrate real time performance of the ResNet-50 architecture, with an average inference time of 53.4 ms per image. These strong results bode well for future field implementation of robotic weed control methods in the Australian rangelands.
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