1. Automated analysis of bioacoustic recordings using machine learning (ML) methods has the potential to greatly scale biodiversity monitoring efforts. The use of ML for high-stakes applications, such as conservation research, demands a data-centric approach with a focus on utilizing carefully annotated and curated evaluation and training data that is relevant and representative. Creating annotated datasets of sound recordings presents a number of challenges, such as managing large collections of recordings with associated metadata, developing flexible annotation tools that can accommodate the diverse range of vocalization profiles of different organisms, and addressing the scarcity of expert annotators. 2. We present Whombat a user-friendly, browser-based interface for managing audio recordings and annotation projects, with several visualization, exploration, and annotation tools. It enables users to quickly annotate, review, and share annotations, as well as visualize and evaluate a set of machine learning predictions on a dataset. The tool facilitates an iterative workflow where user annotations and machine learning predictions feedback to enhance model performance and annotation quality. 3. We demonstrate the flexibility of Whombat by showcasing two distinct use cases: an project aimed at enhancing automated UK bat call identification at the Bat Conservation Trust (BCT), and a collaborative effort among the USDA Forest Service and Oregon State University researchers exploring bioacoustic applications and extending automated avian classification models in the Pacific Northwest, USA. 4. Whombat is a flexible tool that can effectively address the challenges of annotation for bioacoustic research. It can be used for individual and collaborative work, hosted on a shared server or accessed remotely, or run on a personal computer without the need for coding skills.
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This study investigates the potential of automated deep learning to enhance the accuracy and efficiency of multi-class classification of bird vocalizations, compared against traditional manually-designed deep learning models. Using the Western Mediterranean Wetland Birds dataset, we investigated the use of AutoKeras, an automated machine learning framework, to automate neural architecture search and hyperparameter tuning. Comparative analysis validates our hypothesis that the AutoKeras-derived model consistently outperforms traditional models like MobileNet, ResNet50 and VGG16. Our approach and findings underscore the transformative potential of automated deep learning for advancing bioacoustics research and models. In fact, the automated techniques eliminate the need for manual feature engineering and model design while improving performance. This study illuminates best practices in sampling, evaluation and reporting to enhance reproducibility in this nascent field. All the code used is available at https: //github.com/giuliotosato/AutoKeras-bioacustic Keywords: AutoKeras; automated deep learning; audio classification; Wetlands Bird dataset; comparative analysis; bioacoustics; validation dataset; multi-class classification; spectrograms.
Fast and accurate predictions for complex physical dynamics are a significant challenge across various applications. Real-time prediction on resource-constrained hardware is even more crucial in real-world problems. The deep operator network (DeepONet) has recently been proposed as a framework for learning nonlinear mappings between function spaces. However, the DeepONet requires many parameters and has a high computational cost when learning operators, particularly those with complex (discontinuous or non-smooth) target functions. This study proposes HyperDeepONet, which uses the expressive power of the hypernetwork to enable the learning of a complex operator with a smaller set of parameters. The DeepONet and its variant models can be thought of as a method of injecting the input function information into the target function. From this perspective, these models can be viewed as a particular case of HyperDeepONet. We analyze the complexity of DeepONet and conclude that HyperDeepONet needs relatively lower complexity to obtain the desired accuracy for operator learning. HyperDeepONet successfully learned various operators with fewer computational resources compared to other benchmarks.
This paper introduces a new theoretical and computational framework for a data driven Koopman mode analysis of nonlinear dynamics. To alleviate the potential problem of ill-conditioned eigenvectors in the existing implementations of the Dynamic Mode Decomposition (DMD) and the Extended Dynamic Mode Decomposition (EDMD), the new method introduces a Koopman-Schur decomposition that is entirely based on unitary transformations. The analysis in terms of the eigenvectors as modes of a Koopman operator compression is replaced with a modal decomposition in terms of a flag of invariant subspaces that correspond to selected eigenvalues. The main computational tool from the numerical linear algebra is the partial ordered Schur decomposition that provides convenient orthonormal bases for these subspaces. In the case of real data, a real Schur form is used and the computation is based on real orthogonal transformations. The new computational scheme is presented in the framework of the Extended DMD and the kernel trick is used.
Deep neural networks (DNNs) often fail silently with over-confident predictions on out-of-distribution (OOD) samples, posing risks in real-world deployments. Existing techniques predominantly emphasize either the feature representation space or the gradient norms computed with respect to DNN parameters, yet they overlook the intricate gradient distribution and the topology of classification regions. To address this gap, we introduce GRadient-aware Out-Of-Distribution detection in interpolated manifolds (GROOD), a novel framework that relies on the discriminative power of gradient space to distinguish between in-distribution (ID) and OOD samples. To build this space, GROOD relies on class prototypes together with a prototype that specifically captures OOD characteristics. Uniquely, our approach incorporates a targeted mix-up operation at an early intermediate layer of the DNN to refine the separation of gradient spaces between ID and OOD samples. We quantify OOD detection efficacy using the distance to the nearest neighbor gradients derived from the training set, yielding a robust OOD score. Experimental evaluations substantiate that the introduction of targeted input mix-upamplifies the separation between ID and OOD in the gradient space, yielding impressive results across diverse datasets. Notably, when benchmarked against ImageNet-1k, GROOD surpasses the established robustness of state-of-the-art baselines. Through this work, we establish the utility of leveraging gradient spaces and class prototypes for enhanced OOD detection for DNN in image classification.
Machine learning algorithms often contain many hyperparameters (HPs) whose values affect the predictive performance of the induced models in intricate ways. Due to the high number of possibilities for these HP configurations and their complex interactions, it is common to use optimization techniques to find settings that lead to high predictive performance. However, insights into efficiently exploring this vast space of configurations and dealing with the trade-off between predictive and runtime performance remain challenging. Furthermore, there are cases where the default HPs fit the suitable configuration. Additionally, for many reasons, including model validation and attendance to new legislation, there is an increasing interest in interpretable models, such as those created by the Decision Tree (DT) induction algorithms. This paper provides a comprehensive approach for investigating the effects of hyperparameter tuning for the two DT induction algorithms most often used, CART and C4.5. DT induction algorithms present high predictive performance and interpretable classification models, though many HPs need to be adjusted. Experiments were carried out with different tuning strategies to induce models and to evaluate HPs' relevance using 94 classification datasets from OpenML. The experimental results point out that different HP profiles for the tuning of each algorithm provide statistically significant improvements in most of the datasets for CART, but only in one-third for C4.5. Although different algorithms may present different tuning scenarios, the tuning techniques generally required few evaluations to find accurate solutions. Furthermore, the best technique for all the algorithms was the IRACE. Finally, we found out that tuning a specific small subset of HPs is a good alternative for achieving optimal predictive performance.
Artificial neural networks thrive in solving the classification problem for a particular rigid task, acquiring knowledge through generalized learning behaviour from a distinct training phase. The resulting network resembles a static entity of knowledge, with endeavours to extend this knowledge without targeting the original task resulting in a catastrophic forgetting. Continual learning shifts this paradigm towards networks that can continually accumulate knowledge over different tasks without the need to retrain from scratch. We focus on task incremental classification, where tasks arrive sequentially and are delineated by clear boundaries. Our main contributions concern 1) a taxonomy and extensive overview of the state-of-the-art, 2) a novel framework to continually determine the stability-plasticity trade-off of the continual learner, 3) a comprehensive experimental comparison of 11 state-of-the-art continual learning methods and 4 baselines. We empirically scrutinize method strengths and weaknesses on three benchmarks, considering Tiny Imagenet and large-scale unbalanced iNaturalist and a sequence of recognition datasets. We study the influence of model capacity, weight decay and dropout regularization, and the order in which the tasks are presented, and qualitatively compare methods in terms of required memory, computation time, and storage.
The remarkable practical success of deep learning has revealed some major surprises from a theoretical perspective. In particular, simple gradient methods easily find near-optimal solutions to non-convex optimization problems, and despite giving a near-perfect fit to training data without any explicit effort to control model complexity, these methods exhibit excellent predictive accuracy. We conjecture that specific principles underlie these phenomena: that overparametrization allows gradient methods to find interpolating solutions, that these methods implicitly impose regularization, and that overparametrization leads to benign overfitting. We survey recent theoretical progress that provides examples illustrating these principles in simpler settings. We first review classical uniform convergence results and why they fall short of explaining aspects of the behavior of deep learning methods. We give examples of implicit regularization in simple settings, where gradient methods lead to minimal norm functions that perfectly fit the training data. Then we review prediction methods that exhibit benign overfitting, focusing on regression problems with quadratic loss. For these methods, we can decompose the prediction rule into a simple component that is useful for prediction and a spiky component that is useful for overfitting but, in a favorable setting, does not harm prediction accuracy. We focus specifically on the linear regime for neural networks, where the network can be approximated by a linear model. In this regime, we demonstrate the success of gradient flow, and we consider benign overfitting with two-layer networks, giving an exact asymptotic analysis that precisely demonstrates the impact of overparametrization. We conclude by highlighting the key challenges that arise in extending these insights to realistic deep learning settings.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
Machine-learning models have demonstrated great success in learning complex patterns that enable them to make predictions about unobserved data. In addition to using models for prediction, the ability to interpret what a model has learned is receiving an increasing amount of attention. However, this increased focus has led to considerable confusion about the notion of interpretability. In particular, it is unclear how the wide array of proposed interpretation methods are related, and what common concepts can be used to evaluate them. We aim to address these concerns by defining interpretability in the context of machine learning and introducing the Predictive, Descriptive, Relevant (PDR) framework for discussing interpretations. The PDR framework provides three overarching desiderata for evaluation: predictive accuracy, descriptive accuracy and relevancy, with relevancy judged relative to a human audience. Moreover, to help manage the deluge of interpretation methods, we introduce a categorization of existing techniques into model-based and post-hoc categories, with sub-groups including sparsity, modularity and simulatability. To demonstrate how practitioners can use the PDR framework to evaluate and understand interpretations, we provide numerous real-world examples. These examples highlight the often under-appreciated role played by human audiences in discussions of interpretability. Finally, based on our framework, we discuss limitations of existing methods and directions for future work. We hope that this work will provide a common vocabulary that will make it easier for both practitioners and researchers to discuss and choose from the full range of interpretation methods.
Deep learning constitutes a recent, modern technique for image processing and data analysis, with promising results and large potential. As deep learning has been successfully applied in various domains, it has recently entered also the domain of agriculture. In this paper, we perform a survey of 40 research efforts that employ deep learning techniques, applied to various agricultural and food production challenges. We examine the particular agricultural problems under study, the specific models and frameworks employed, the sources, nature and pre-processing of data used, and the overall performance achieved according to the metrics used at each work under study. Moreover, we study comparisons of deep learning with other existing popular techniques, in respect to differences in classification or regression performance. Our findings indicate that deep learning provides high accuracy, outperforming existing commonly used image processing techniques.
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