Instance segmentation in electron microscopy (EM) volumes poses a significant challenge due to the complex morphology of instances and insufficient annotations. Self-supervised learning has recently emerged as a promising solution, enabling the acquisition of prior knowledge of cellular tissue structures that are essential for EM instance segmentation. However, existing pretraining methods often lack the ability to capture complex visual patterns and relationships between voxels, which results in the acquired prior knowledge being insufficient for downstream EM analysis tasks. In this paper, we propose a novel pretraining framework that leverages multiscale visual representations to capture both voxel-level and feature-level consistency in EM volumes. Specifically, our framework enforces voxel-level consistency between the outputs of a Siamese network by a reconstruction function, and incorporates a cross-attention mechanism for soft feature matching to achieve fine-grained feature-level consistency. Moreover, we propose a contrastive learning scheme on the feature pyramid to extract discriminative features across multiple scales. We extensively pretrain our method on four large-scale EM datasets, achieving promising performance improvements in representative tasks of neuron and mitochondria instance segmentation.
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We propose a unified dynamic tracking algorithmic framework (PLAY-CS) to reconstruct signal sequences with their intrinsic structured dynamic sparsity. By capitalizing on specific statistical assumptions concerning the dynamic filter of the signal sequences, the proposed framework exhibits versatility by encompassing various existing dynamic compressive sensing (DCS) algorithms. This is achieved through the incorporation of a newly proposed Partial-Laplacian filtering sparsity model, tailored to capture a more sophisticated dynamic sparsity. In practical scenarios such as dynamic channel tracking in wireless communications, the framework demonstrates enhanced performance compared to existing DCS algorithms.
Current multilingual semantic parsing (MSP) datasets are almost all collected by translating the utterances in the existing datasets from the resource-rich language to the target language. However, manual translation is costly. To reduce the translation effort, this paper proposes the first active learning procedure for MSP (AL-MSP). AL-MSP selects only a subset from the existing datasets to be translated. We also propose a novel selection method that prioritizes the examples diversifying the logical form structures with more lexical choices, and a novel hyperparameter tuning method that needs no extra annotation cost. Our experiments show that AL-MSP significantly reduces translation costs with ideal selection methods. Our selection method with proper hyperparameters yields better parsing performance than the other baselines on two multilingual datasets.
Neural shape representation generally refers to representing 3D geometry using neural networks, e.g., to compute a signed distance or occupancy value at a specific spatial position. Previous methods tend to rely on the auto-decoder paradigm, which often requires densely-sampled and accurate signed distances to be known during training and testing, as well as an additional optimization loop during inference. This introduces a lot of computational overhead, in addition to having to compute signed distances analytically, even during testing. In this paper, we present a novel encoder-decoder neural network for embedding 3D shapes in a single forward pass. Our architecture is based on a multi-scale hybrid system incorporating graph-based and voxel-based components, as well as a continuously differentiable decoder. Furthermore, the network is trained to solve the Eikonal equation and only requires knowledge of the zero-level set for training and inference. Additional volumetric samples can be generated on-the-fly, and incorporated in an unsupervised manner. This means that in contrast to most previous work, our network is able to output valid signed distance fields without explicit prior knowledge of non-zero distance values or shape occupancy. In other words, our network computes approximate solutions to the boundary-valued Eikonal equation. It also requires only a single forward pass during inference, instead of the common latent code optimization. We further propose a modification of the loss function in case that surface normals are not well defined, e.g., in the context of non-watertight surface-meshes and non-manifold geometry. We finally demonstrate the efficacy, generalizability and scalability of our method on datasets consisting of deforming 3D shapes, single class encoding and multiclass encoding, showcasing a wide range of possible applications.
Phase-amplitude coupling is a phenomenon observed in several neurological processes, where the phase of one signal modulates the amplitude of another signal with a distinct frequency. The modulation index (MI) is a common technique used to quantify this interaction by assessing the Kullback-Leibler divergence between a uniform distribution and the empirical conditional distribution of amplitudes with respect to the phases of the observed signals. The uniform distribution is an ideal representation that is expected to appear under the absence of coupling. However, it does not reflect the statistical properties of coupling values caused by random chance. In this paper, we propose a statistical framework for evaluating the significance of an observed MI value based on a null hypothesis that a MI value can be entirely explained by chance. Significance is obtained by comparing the value with a reference distribution derived under the null hypothesis of independence (i.e., no coupling) between signals. We derived a closed-form distribution of this null model, resulting in a scaled beta distribution. To validate the efficacy of our proposed framework, we conducted comprehensive Monte Carlo simulations, assessing the significance of MI values under various experimental scenarios, including amplitude modulation, trains of spikes, and sequences of high-frequency oscillations. Furthermore, we corroborated the reliability of our model by comparing its statistical significance thresholds with reported values from other research studies conducted under different experimental settings. Our method offers several advantages such as meta-analysis reliability, simplicity and computational efficiency, as it provides p-values and significance levels without resorting to generating surrogate data through sampling procedures.
This paper presents an alternative approach to dehomogenisation of elastic Rank-N laminate structures based on the computer graphics discipline of phasor noise. The proposed methodology offers an improvement of existing methods, where high-quality single-scale designs can be obtained efficiently without the utilisation of any least-squares problem or pre-trained models. By utilising a continuous and periodic representation of the translation at each intermediate step, appropriate length-scale and thicknesses can be obtained. Numerical tests verifies the performance of the proposed methodology compared to state-of-the-art alternatives, and the dehomogenised designs achieve structural performance within a few percentages of the optimised homogenised solution. The nature of the phasor-based dehomogenisation is inherently mesh-independent and highly parallelisable, allowing for further efficient implementations and future extensions to 3D problems on unstructured meshes.
A novel unconstrained optimization model named weighted trace-penalty minimization (WTPM) is proposed to address the extreme eigenvalue problem arising from the Full Configuration Interaction (FCI) method. Theoretical analysis shows that the global minimizers of the WTPM objective function are the desired eigenvectors, rather than the eigenspace. Analyzing the condition number of the Hessian operator in detail contributes to the determination of a near-optimal weight matrix. With the sparse feature of FCI matrices in mind, the coordinate descent (CD) method is adapted to WTPM and results in WTPM-CD method. The reduction of computational and storage costs in each iteration shows the efficiency of the proposed algorithm. Finally, the numerical experiments demonstrate the capability to address large-scale FCI matrices.
The recent proliferation of knowledge graphs (KGs) coupled with incomplete or partial information, in the form of missing relations (links) between entities, has fueled a lot of research on knowledge base completion (also known as relation prediction). Several recent works suggest that convolutional neural network (CNN) based models generate richer and more expressive feature embeddings and hence also perform well on relation prediction. However, we observe that these KG embeddings treat triples independently and thus fail to cover the complex and hidden information that is inherently implicit in the local neighborhood surrounding a triple. To this effect, our paper proposes a novel attention based feature embedding that captures both entity and relation features in any given entity's neighborhood. Additionally, we also encapsulate relation clusters and multihop relations in our model. Our empirical study offers insights into the efficacy of our attention based model and we show marked performance gains in comparison to state of the art methods on all datasets.
Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.
High spectral dimensionality and the shortage of annotations make hyperspectral image (HSI) classification a challenging problem. Recent studies suggest that convolutional neural networks can learn discriminative spatial features, which play a paramount role in HSI interpretation. However, most of these methods ignore the distinctive spectral-spatial characteristic of hyperspectral data. In addition, a large amount of unlabeled data remains an unexploited gold mine for efficient data use. Therefore, we proposed an integration of generative adversarial networks (GANs) and probabilistic graphical models for HSI classification. Specifically, we used a spectral-spatial generator and a discriminator to identify land cover categories of hyperspectral cubes. Moreover, to take advantage of a large amount of unlabeled data, we adopted a conditional random field to refine the preliminary classification results generated by GANs. Experimental results obtained using two commonly studied datasets demonstrate that the proposed framework achieved encouraging classification accuracy using a small number of data for training.
Image segmentation is considered to be one of the critical tasks in hyperspectral remote sensing image processing. Recently, convolutional neural network (CNN) has established itself as a powerful model in segmentation and classification by demonstrating excellent performances. The use of a graphical model such as a conditional random field (CRF) contributes further in capturing contextual information and thus improving the segmentation performance. In this paper, we propose a method to segment hyperspectral images by considering both spectral and spatial information via a combined framework consisting of CNN and CRF. We use multiple spectral cubes to learn deep features using CNN, and then formulate deep CRF with CNN-based unary and pairwise potential functions to effectively extract the semantic correlations between patches consisting of three-dimensional data cubes. Effective piecewise training is applied in order to avoid the computationally expensive iterative CRF inference. Furthermore, we introduce a deep deconvolution network that improves the segmentation masks. We also introduce a new dataset and experimented our proposed method on it along with several widely adopted benchmark datasets to evaluate the effectiveness of our method. By comparing our results with those from several state-of-the-art models, we show the promising potential of our method.
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