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Biological sequencing data consist of read counts, e.g. of specified taxa and often exhibit sparsity (zero-count inflation) and overdispersion (extra-Poisson variability). As most sequencing techniques provide an arbitrary total count, taxon-specific counts should ideally be treated as proportions under the compositional data-analytic framework. There is increasing interest in the role of the gut microbiome composition in mediating the effects of different exposures on health outcomes. Most previous approaches to compositional mediation have addressed the problem of identifying potentially mediating taxa among a large number of candidates. We here consider causal inference in compositional mediation when a priori knowledge is available about the hierarchy for a restricted number of taxa, building on a single hypothesis structured in terms of contrasts between appropriate sub-compositions. Based on the theory on multiple contemporaneous mediators and the assumed causal graph, we define non-parametric estimands for overall and coordinate-wise mediation effects, and show how these indirect effects can be estimated from empirical data based on simple parametric linear models. The mediators have straightforward and coherent interpretations, related to specific causal questions about the interrelationships between the sub-compositions. We perform a simulation study focusing on the impact of sparsity and overdispersion on estimation of mediation. While unbiased, the precision of the estimators depends, for any given magnitude of indirect effect, on sparsity and the relative magnitudes of exposure-to-mediator and mediator-to-outcome effects in a complex manner. We demonstrate the approach on empirical data, finding an inverse association of fibre intake on insulin level, mainly attributable to direct rather than indirect effects.

The efficient segmentation of foreground text information from the background in degraded color document images is a critical challenge in the preservation of ancient manuscripts. The imperfect preservation of ancient manuscripts over time has led to various types of degradation, such as staining, yellowing, and ink seepage, significantly affecting image binarization results. This work proposes a three-stage method using Generative Adversarial Networks (GAN) for enhancing and binarizing degraded color document images through Discrete Wavelet Transform (DWT). Stage-1 involves applying DWT and retaining the Low-Low (LL) subband images for image enhancement. In Stage-2, the original input image is divided into four single-channel images (Red, Green, Blue, and Gray), and each is trained with independent adversarial networks to extract color foreground information. In Stage-3, the output image from Stage-2 and the original input image are used to train independent adversarial networks for document binarization, enabling the integration of global and local features. The experimental results demonstrate that our proposed method outperforms other classic and state-of-the-art (SOTA) methods on the Document Image Binarization Contest (DIBCO) datasets. We have released our implementation code at //github.com/abcpp12383/ThreeStageBinarization.

Machine learning (ML) is becoming a critical tool for interrogation of large complex data. Labeling, defined as the process of adding meaningful annotations, is a crucial step of supervised ML. However, labeling datasets is time consuming. Here we show that convolutional neural networks (CNNs), trained on crudely labeled astronomical videos, can be leveraged to improve the quality of data labeling and reduce the need for human intervention. We use videos of the solar magnetic field, crudely labeled into two classes: emergence or non-emergence of bipolar magnetic regions (BMRs), based on their first detection on the solar disk. We train CNNs using crude labels, manually verify, correct labeling vs. CNN disagreements, and repeat this process until convergence. Traditionally, flux emergence labelling is done manually. We find that a high-quality labeled dataset, derived through this iterative process, reduces the necessary manual verification by 50%. Furthermore, by gradually masking the videos and looking for maximum change in CNN inference, we locate BMR emergence time without retraining the CNN. This demonstrates the versatility of CNNs for simplifying the challenging task of labeling complex dynamic events.

Click-based interactive segmentation aims to generate target masks via human clicking, which facilitates efficient pixel-level annotation and image editing. In such a task, target ambiguity remains a problem hindering the accuracy and efficiency of segmentation. That is, in scenes with rich context, one click may correspond to multiple potential targets, while most previous interactive segmentors only generate a single mask and fail to deal with target ambiguity. In this paper, we propose a novel interactive segmentation network named PiClick, to yield all potentially reasonable masks and suggest the most plausible one for the user. Specifically, PiClick utilizes a Transformer-based architecture to generate all potential target masks by mutually interactive mask queries. Moreover, a Target Reasoning module is designed in PiClick to automatically suggest the user-desired mask from all candidates, relieving target ambiguity and extra-human efforts. Extensive experiments on 9 interactive segmentation datasets demonstrate PiClick performs favorably against previous state-of-the-arts considering the segmentation results. Moreover, we show that PiClick effectively reduces human efforts in annotating and picking the desired masks. To ease the usage and inspire future research, we release the source code of PiClick together with a plug-and-play annotation tool at //github.com/cilinyan/PiClick.

We show how machine learning techniques can be applied for the classification of topological phases in leaky photonic lattices using limited measurement data. We propose an approach based solely on bulk intensity measurements, thus exempt from the need for complicated phase retrieval procedures. In particular, we design a fully connected neural network that accurately determines topological properties from the output intensity distribution in dimerized waveguide arrays with leaky channels, after propagation of a spatially localized initial excitation at a finite distance, in a setting that closely emulates realistic experimental conditions.

Wildfire detection using satellite images is a widely studied task in remote sensing with many applications to fire delineation and mapping. Recently, deep learning methods have become a scalable solution to automate this task, especially in the field of unsupervised learning where no training data is available. This is particularly important in the context of emergency risk monitoring where fast and effective detection is needed, generally based on high-resolution satellite data. Among various approaches, Anomaly Detection (AD) appears to be highly potential thanks to its broad applications in computer vision, medical imaging, as well as remote sensing. In this work, we build upon the framework of Vector Quantized Variational Autoencoder (VQ-VAE), a popular reconstruction-based AD method with discrete latent spaces, to perform unsupervised burnt area extraction. We integrate VQ-VAE into an end-to-end framework with an intensive post-processing step using dedicated vegetation, water and brightness indexes. Our experiments conducted on high-resolution SPOT-6/7 images provide promising results of the proposed technique, showing its high potential in future research on unsupervised burnt area extraction.

The mission of visual brain-computer interfaces (BCIs) is to enhance information transfer rate (ITR) to reach high speed towards real-life communication. Despite notable progress, noninvasive visual BCIs have encountered a plateau in ITRs, leaving it uncertain whether higher ITRs are achievable. In this study, we investigate the information rate limits of the primary visual channel to explore whether we can and how we should build visual BCI with higher information rate. Using information theory, we estimate a maximum achievable ITR of approximately 63 bits per second (bps) with a uniformly-distributed White Noise (WN) stimulus. Based on this discovery, we propose a broadband WN BCI approach that expands the utilization of stimulus bandwidth, in contrast to the current state-of-the-art visual BCI methods based on steady-state visual evoked potentials (SSVEPs). Through experimental validation, our broadband BCI outperforms the SSVEP BCI by an impressive margin of 7 bps, setting a new record of 50 bps. This achievement demonstrates the possibility of decoding 40 classes of noninvasive neural responses within a short duration of only 0.1 seconds. The information-theoretical framework introduced in this study provides valuable insights applicable to all sensory-evoked BCIs, making a significant step towards the development of next-generation human-machine interaction systems.

In many real-world settings, image observations of freely rotating 3D rigid bodies, may be available when low-dimensional measurements are not. However, the high-dimensionality of image data precludes the use of classical estimation techniques to learn the dynamics. The usefulness of standard deep learning methods is also limited because an image of a rigid body reveals nothing about the distribution of mass inside the body, which, together with initial angular velocity, is what determines how the body will rotate. We present a physics-informed neural network model to estimate and predict 3D rotational dynamics from image sequences. We achieve this using a multi-stage prediction pipeline that maps individual images to a latent representation homeomorphic to $\mathbf{SO}(3)$, computes angular velocities from latent pairs, and predicts future latent states using the Hamiltonian equations of motion. We demonstrate the efficacy of our approach on new rotating rigid-body datasets of sequences of synthetic images of rotating objects, including cubes, prisms and satellites, with unknown uniform and non-uniform mass distributions.

Hashing has been widely used in approximate nearest search for large-scale database retrieval for its computation and storage efficiency. Deep hashing, which devises convolutional neural network architecture to exploit and extract the semantic information or feature of images, has received increasing attention recently. In this survey, several deep supervised hashing methods for image retrieval are evaluated and I conclude three main different directions for deep supervised hashing methods. Several comments are made at the end. Moreover, to break through the bottleneck of the existing hashing methods, I propose a Shadow Recurrent Hashing(SRH) method as a try. Specifically, I devise a CNN architecture to extract the semantic features of images and design a loss function to encourage similar images projected close. To this end, I propose a concept: shadow of the CNN output. During optimization process, the CNN output and its shadow are guiding each other so as to achieve the optimal solution as much as possible. Several experiments on dataset CIFAR-10 show the satisfying performance of SRH.

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.