Comparing Data-Driven and Mechanistic Models for Predicting Phenology in Deciduous Broadleaf Forests

Understanding the future climate is crucial for informed policy decisions on climate change prevention and mitigation. Earth system models play an important role in predicting future climate, requiring accurate representation of complex sub-processes that span multiple time scales and spatial scales. One such process that links seasonal and interannual climate variability to cyclical biological events is tree phenology in deciduous broadleaf forests. Phenological dates, such as the start and end of the growing season, are critical for understanding the exchange of carbon and water between the biosphere and the atmosphere. Mechanistic prediction of these dates is challenging. Hybrid modelling, which integrates data-driven approaches into complex models, offers a solution. In this work, as a first step towards this goal, train a deep neural network to predict a phenological index from meteorological time series. We find that this approach outperforms traditional process-based models. This highlights the potential of data-driven methods to improve climate predictions. We also analyze which variables and aspects of the time series influence the predicted onset of the season, in order to gain a better understanding of the advantages and limitations of our model.

Dozerformer: Sequence Adaptive Sparse Transformer for Multivariate Time Series Forecasting

Transformers have achieved remarkable performance in multivariate time series(MTS) forecasting due to their capability to capture long-term dependencies. However, the canonical attention mechanism has two key limitations: (1) its quadratic time complexity limits the sequence length, and (2) it generates future values from the entire historical sequence. To address this, we propose a Dozer Attention mechanism consisting of three sparse components: (1) Local, each query exclusively attends to keys within a localized window of neighboring time steps. (2) Stride, enables each query to attend to keys at predefined intervals. (3) Vary, allows queries to selectively attend to keys from a subset of the historical sequence. Notably, the size of this subset dynamically expands as forecasting horizons extend. Those three components are designed to capture essential attributes of MTS data, including locality, seasonality, and global temporal dependencies. Additionally, we present the Dozerformer Framework, incorporating the Dozer Attention mechanism for the MTS forecasting task. We evaluated the proposed Dozerformer framework with recent state-of-the-art methods on nine benchmark datasets and confirmed its superior performance. The code will be released after the manuscript is accepted.

Image-based Data Representations of Time Series: A Comparative Analysis in EEG Artifact Detection

Alternative data representations are powerful tools that augment the performance of downstream models. However, there is an abundance of such representations within the machine learning toolbox, and the field lacks a comparative understanding of the suitability of each representation method. In this paper, we propose artifact detection and classification within EEG data as a testbed for profiling image-based data representations of time series data. We then evaluate eleven popular deep learning architectures on each of six commonly-used representation methods. We find that, while the choice of representation entails a choice within the tradeoff between bias and variance, certain representations are practically more effective in highlighting features which increase the signal-to-noise ratio of the data. We present our results on EEG data, and open-source our testing framework to enable future comparative analyses in this vein.

Offshore Wind Plant Instance Segmentation Using Sentinel-1 Time Series, GIS, and Semantic Segmentation Models

Offshore wind farms represent a renewable energy source with a significant global growth trend, and their monitoring is strategic for territorial and environmental planning. This study's primary objective is to detect offshore wind plants at an instance level using semantic segmentation models and Sentinel-1 time series. The secondary objectives are: (a) to develop a database consisting of labeled data and S-1 time series; (b) to compare the performance of five deep semantic segmentation architectures (U-Net, U-Net++, Feature Pyramid Network - FPN, DeepLabv3+, and LinkNet); (c) develop a novel augmentation strategy that shuffles the positions of the images within the time series; (d) investigate different dimensions of time series intervals (1, 5, 10, and 15 images); and (e) evaluate the semantic-to-instance conversion procedure. LinkNet was the top-performing model, followed by U-Net++ and U-Net, while FPN and DeepLabv3+ presented the worst results. The evaluation of semantic segmentation models reveals enhanced Intersection over Union (IoU) (25%) and F-score metrics (18%) with the augmentation of time series images. The study showcases the augmentation strategy's capability to mitigate biases and precisely detect invariant targets. Furthermore, the conversion from semantic to instance segmentation demonstrates its efficacy in accurately isolating individual instances within classified regions - simplifying training data and reducing annotation effort and complexity.

Training and Comparison of nnU-Net and DeepMedic Methods for Autosegmentation of Pediatric Brain Tumors

Brain tumors are the most common solid tumors and the leading cause of cancer-related death among children. Tumor segmentation is essential in surgical and treatment planning, and response assessment and monitoring. However, manual segmentation is time-consuming and has high inter-operator variability, underscoring the need for more efficient methods. We compared two deep learning-based 3D segmentation models, DeepMedic and nnU-Net, after training with pediatric-specific multi-institutional brain tumor data using based on multi-parametric MRI scans.Multi-parametric preoperative MRI scans of 339 pediatric patients (n=293 internal and n=46 external cohorts) with a variety of tumor subtypes, were preprocessed and manually segmented into four tumor subregions, i.e., enhancing tumor (ET), non-enhancing tumor (NET), cystic components (CC), and peritumoral edema (ED). After training, performance of the two models on internal and external test sets was evaluated using Dice scores, sensitivity, and Hausdorff distance with reference to ground truth manual segmentations. Dice score for nnU-Net internal test sets was (mean +/- SD (median)) 0.9+/-0.07 (0.94) for WT, 0.77+/-0.29 for ET, 0.66+/-0.32 for NET, 0.71+/-0.33 for CC, and 0.71+/-0.40 for ED, respectively. For DeepMedic the Dice scores were 0.82+/-0.16 for WT, 0.66+/-0.32 for ET, 0.48+/-0.27, for NET, 0.48+/-0.36 for CC, and 0.19+/-0.33 for ED, respectively. Dice scores were significantly higher for nnU-Net (p<=0.01). External validation of the trained nnU-Net model on the multi-institutional BraTS-PEDs 2023 dataset revealed high generalization capability in segmentation of whole tumor and tumor core with Dice scores of 0.87+/-0.13 (0.91) and 0.83+/-0.18 (0.89), respectively. Pediatric-specific data trained nnU-Net model is superior to DeepMedic for whole tumor and subregion segmentation of pediatric brain tumors.

Unsupervised Multi-modal Feature Alignment for Time Series Representation Learning

In recent times, the field of unsupervised representation learning (URL) for time series data has garnered significant interest due to its remarkable adaptability across diverse downstream applications. Unsupervised learning goals differ from downstream tasks, making it tricky to ensure downstream task utility by focusing only on temporal feature characterization. Researchers have proposed multiple transformations to extract discriminative patterns implied in informative time series, trying to fill the gap. Despite the introduction of a variety of feature engineering techniques, e.g. spectral domain, wavelet transformed features, features in image form and symbolic features etc. the utilization of intricate feature fusion methods and dependence on heterogeneous features during inference hampers the scalability of the solutions. To address this, our study introduces an innovative approach that focuses on aligning and binding time series representations encoded from different modalities, inspired by spectral graph theory, thereby guiding the neural encoder to uncover latent pattern associations among these multi-modal features. In contrast to conventional methods that fuse features from multiple modalities, our proposed approach simplifies the neural architecture by retaining a single time series encoder, consequently leading to preserved scalability. We further demonstrate and prove mechanisms for the encoder to maintain better inductive bias. In our experimental evaluation, we validated the proposed method on a diverse set of time series datasets from various domains. Our approach outperforms existing state-of-the-art URL methods across diverse downstream tasks.

GE-AdvGAN: Improving the transferability of adversarial samples by gradient editing-based adversarial generative model

Adversarial generative models, such as Generative Adversarial Networks (GANs), are widely applied for generating various types of data, i.e., images, text, and audio. Accordingly, its promising performance has led to the GAN-based adversarial attack methods in the white-box and black-box attack scenarios. The importance of transferable black-box attacks lies in their ability to be effective across different models and settings, more closely aligning with real-world applications. However, it remains challenging to retain the performance in terms of transferable adversarial examples for such methods. Meanwhile, we observe that some enhanced gradient-based transferable adversarial attack algorithms require prolonged time for adversarial sample generation. Thus, in this work, we propose a novel algorithm named GE-AdvGAN to enhance the transferability of adversarial samples whilst improving the algorithm's efficiency. The main approach is via optimising the training process of the generator parameters. With the functional and characteristic similarity analysis, we introduce a novel gradient editing (GE) mechanism and verify its feasibility in generating transferable samples on various models. Moreover, by exploring the frequency domain information to determine the gradient editing direction, GE-AdvGAN can generate highly transferable adversarial samples while minimizing the execution time in comparison to the state-of-the-art transferable adversarial attack algorithms. The performance of GE-AdvGAN is comprehensively evaluated by large-scale experiments on different datasets, which results demonstrate the superiority of our algorithm. The code for our algorithm is available at: https://github.com/LMBTough/GE-advGAN

LiDAR data acquisition and processing for ecology applications

The collection of ecological data in the field is essential to diagnose, monitor and manage ecosystems in a sustainable way. Since acquisition of this information through traditional methods are generally time-consuming, due to the capability of recording large volumes of data in short time periods, automation of data acquisition sees a growing trend. Terrestrial laser scanners (TLS), particularly LiDAR sensors, have been used in ecology, allowing to reconstruct the 3D structure of vegetation, and thus, infer ecosystem characteristics based on the spatial variation of the density of points. However, the low amount of information obtained per beam, lack of data analysis tools and the high cost of the equipment limit their use. This way, a low-cost TLS (<10k$) was developed along with data acquisition and processing mechanisms applicable in two case studies: an urban garden and a target area for ecological restoration. The orientation of LiDAR was modified to make observations in the vertical plane and a motor was integrated for its rotation, enabling the acquisition of 360 degree data with high resolution. Motion and location sensors were also integrated for automatic error correction and georeferencing. From the data generated, histograms of point density variation along the vegetation height were created, where shrub stratum was easily distinguishable from tree stratum, and maximum tree height and shrub cover were calculated. These results agreed with the field data, whereby the developed TLS has proved to be effective in calculating metrics of structural complexity of vegetation.

Efficient approximation of Earth Mover's Distance Based on Nearest Neighbor Search

Earth Mover's Distance (EMD) is an important similarity measure between two distributions, used in computer vision and many other application domains. However, its exact calculation is computationally and memory intensive, which hinders its scalability and applicability for large-scale problems. Various approximate EMD algorithms have been proposed to reduce computational costs, but they suffer lower accuracy and may require additional memory usage or manual parameter tuning. In this paper, we present a novel approach, NNS-EMD, to approximate EMD using Nearest Neighbor Search (NNS), in order to achieve high accuracy, low time complexity, and high memory efficiency. The NNS operation reduces the number of data points compared in each NNS iteration and offers opportunities for parallel processing. We further accelerate NNS-EMD via vectorization on GPU, which is especially beneficial for large datasets. We compare NNS-EMD with both the exact EMD and state-of-the-art approximate EMD algorithms on image classification and retrieval tasks. We also apply NNS-EMD to calculate transport mapping and realize color transfer between images. NNS-EMD can be 44x to 135x faster than the exact EMD implementation, and achieves superior accuracy, speedup, and memory efficiency over existing approximate EMD methods.

Self-supervised Event-based Monocular Depth Estimation using Cross-modal Consistency

An event camera is a novel vision sensor that can capture per-pixel brightness changes and output a stream of asynchronous ``events''. It has advantages over conventional cameras in those scenes with high-speed motions and challenging lighting conditions because of the high temporal resolution, high dynamic range, low bandwidth, low power consumption, and no motion blur. Therefore, several supervised monocular depth estimation from events is proposed to address scenes difficult for conventional cameras. However, depth annotation is costly and time-consuming. In this paper, to lower the annotation cost, we propose a self-supervised event-based monocular depth estimation framework named EMoDepth. EMoDepth constrains the training process using the cross-modal consistency from intensity frames that are aligned with events in the pixel coordinate. Moreover, in inference, only events are used for monocular depth prediction. Additionally, we design a multi-scale skip-connection architecture to effectively fuse features for depth estimation while maintaining high inference speed. Experiments on MVSEC and DSEC datasets demonstrate that our contributions are effective and that the accuracy can outperform existing supervised event-based and unsupervised frame-based methods.