Miracle-dz/UniFAR-FTUs huggingface dataset:
UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation

The state-of-the-art models for medical image segmentation are variants of U-Net and fully convolutional networks (FCN). Despite their success, these models have two limitations: (1) their optimal depth is apriori unknown, requiring extensive architecture search or inefficient ensemble of models of varying depths; and (2) their skip connections impose an unnecessarily restrictive fusion scheme, forcing aggregation only at the same-scale feature maps of the encoder and decoder sub-networks. To overcome these two limitations, we propose UNet++, a new neural architecture for semantic and instance segmentation, by (1) alleviating the unknown network depth with an efficient ensemble of U-Nets of varying depths, which partially share an encoder and co-learn simultaneously using deep supervision; (2) redesigning skip connections to aggregate features of varying semantic scales at the decoder sub-networks, leading to a highly flexible feature fusion scheme; and (3) devising a pruning scheme to accelerate the inference speed of UNet++. We have evaluated UNet++ using six different medical image segmentation datasets, covering multiple imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and electron microscopy (EM), and demonstrating that (1) UNet++ consistently outperforms the baseline models for the task of semantic segmentation across different datasets and backbone architectures; (2) UNet++ enhances segmentation quality of varying-size objects—an improvement over the fixed-depth U-Net; (3) Mask RCNN++ (Mask R-CNN with UNet++ design) outperforms the original Mask R-CNN for the task of instance segmentation; and (4) pruned UNet++ models achieve significant speedup while showing only modest performance degradation. Our implementation and pre-trained models are available at https://github.com/MrGiovanni/UNetPlusPlus.
auto-multithresh: A General Purpose Automasking Algorithm

Producing images from interferometer data requires accurate modeling of the sources in the field of view, which is typically done using the clean algorithm. Given the large number of degrees of freedom in interferometeric images, one constrains the possible model solutions for clean by masking regions that contain emission. Traditionally this process has largely been done by hand. This approach is not possible with today’s large data volumes which require automated imaging pipelines. This paper describes an automated masking algorithm that operates within clean called auto-multithresh. This algorithm was developed and validated using a set of ∼1000 Atacama Large Millimeter/submillimeter Array (ALMA) images chosen to span a range of intrinsic morphology and data characteristics. It takes a top-down approach to producing masks: it uses the residual images to identify significant peaks and then expands the mask to include emission associated with these peaks down to lower signal-to-noise noise. The auto-multithresh algorithm has been implemented in CASA and has been used in production as part of the ALMA Imaging Pipeline starting with Cycle 5. It has been shown to be able to mask a wide range of emission ranging from simple point sources to complex extended emission with minimal tuning of the parameters based on the point-spread function of the data. Although the algorithm was developed for ALMA, it is general enough to have been used successfully with data from other interferometers with appropriate parameter tuning. Integrating the algorithm more deeply within the minor cycle could lead to future performance improvements.
Neural Memory Networks for Robust Classification of Seizure Type

Classification of seizure type is a key step in the clinical process for evaluating an individual who presents with seizures. It determines the course of clinical diagnosis and treatment, and its impact stretches beyond the clinical domain to epilepsy research and the development of novel therapies. Automated identification of seizure type may facilitate understanding of the disease, and seizure detection and prediction has been the focus of recent research that has sought to exploit the benefits of machine learning and deep learning architectures. Nevertheless, there is not yet a definitive solution for automating the classification of seizure type, a task that must currently be performed by an expert epileptologist. Inspired by recent advances in neural memory networks (NMNs), we introduce a novel approach for the classification of seizure type using electrophysiological data. We first explore the performance of traditional deep learning techniques which use convolutional and recurrent neural networks, and enhance these architectures by using external memory modules with trainable neural plasticity. We show that our model achieves a state-of-the-art weighted F1 score of 0.945 for seizure type classification on the TUH EEG Seizure Corpus with the IBM TUSZ preprocessed data. This work highlights the potential of neural memory networks to support the field of epilepsy research, along with biomedical research and signal analysis more broadly.
Bayesian Framework for Simultaneous Registration and Estimation of Noisy, Sparse, and Fragmented Functional Data

Abstract In many applications, smooth processes generate data that are recorded under a variety of observational regimes, including dense sampling and sparse or fragmented observations that are often contaminated with error. The statistical goal of registering and estimating the individual underlying functions from discrete observations has thus far been mainly approached sequentially without formal uncertainty propagation, or in an application-specific manner by pooling information across subjects. We propose a unified Bayesian framework for simultaneous registration and estimation, which is flexible enough to accommodate inference on individual functions under general observational regimes. Our ability to do this relies on the specification of strongly informative prior models over the amplitude component of function variability using two strategies: a data-driven approach that defines an empirical basis for the amplitude subspace based on training data, and a shape-restricted approach when the relative location and number of extrema is well-understood. The proposed methods build on the elastic functional data analysis framework to separately model amplitude and phase variability inherent in functional data. We emphasize the importance of uncertainty quantification and visualization of these two components as they provide complementary information about the estimated functions. We validate the proposed framework using multiple simulation studies and real applications.
FootAndBall: Integrated player and ball detector

The paper describes a deep neural network-based detector dedicated for ball and players detection in high resolution, long shot, video recordings of soccer matches. The detector, dubbed FootAndBall, has an efficient fully convolutional architecture and can operate on input video stream with an arbitrary resolution. It produces ball confidence map encoding the position of the detected ball, player confidence map and player bounding boxes tensor encoding players' positions and bounding boxes. The network uses Feature Pyramid Network desing pattern, where lower level features with higher spatial resolution are combined with higher level features with bigger receptive field. This improves discriminability of small objects (the ball) as larger visual context around the object of interest is taken into account for the classification. Due to its specialized design, the network has two orders of magnitude less parameters than a generic deep neural network-based object detector, such as SSD or YOLO. This allows real-time processing of high resolution input video stream.
Two Birds with One Stone: Investigating Invertible Neural Networks for Inverse Problems in Morphology

Most problems in natural language processing can be approximated as inverse problems such as analysis and generation at variety of levels from morphological (e.g., cat+Plural↔cats) to semantic (e.g., (call + 1 2)↔“Calculate one plus two. ”). Although the tasks in both directions are closely related, general approach in the field has been to design separate models specific for each task. However, having one shared model for both tasks, would help the researchers exploit the common knowledge among these problems with reduced time and memory requirements. We investigate a specific class of neural networks, called Invertible Neural Networks (INNs) (Ardizzone et al. 2019) that enable simultaneous optimization in both directions, hence allow addressing of inverse problems via a single model. In this study, we investigate INNs on morphological problems casted as inverse problems. We apply INNs to various morphological tasks with varying ambiguity and show that they provide competitive performance in both directions. We show that they are able to recover the morphological input parameters, i.e., predicting the lemma (e.g., cat) or the morphological tags (e.g., Plural) when run in the reverse direction, without any significant performance drop in the forward direction, i.e., predicting the surface form (e.g., cats).
Detecting Hardly Visible Roads in Low-Resolution Satellite Time Series Data

Massive amounts of satellite data have been gathered over time, holding the potential to unveil a spatiotemporal chronicle of the surface of Earth. These data allow scientists to investigate various important issues, such as land use changes, on a global scale. However, not all land-use phenomena are equally visible on satellite imagery. In particular, the creation of an inventory of the planet’s road infrastructure remains a challenge, despite being crucial to analyze urbanization patterns and their impact. Towards this end, this work advances data-driven approaches for the automatic identification of roads based on open satellite data. Given the typical resolutions of these historical satellite data, we observe that there is inherent variation in the visibility of different road types. Based on this observation, we propose two deep learning frameworks that extend state-of-the-art deep learning methods by formalizing road detection as an ordinal classification task. In contrast to related schemes, one of the two models also resorts to satellite time series data that are potentially affected by missing data and cloud occlusion. Taking these time series data into account eliminates the need to manually curate datasets of high-quality image tiles, substantially simplifying the application of such models on a global scale. We evaluate our approaches on a dataset that is based on Sentinel 2 satellite imagery and OpenStreetMap vector data. Our results indicate that the proposed models can successfully identify large and medium-sized roads. We also discuss opportunities and challenges related to the detection of roads and other infrastructure on a global scale.
Evidence for cosmic acceleration with next-generation surveys: a model-independent approach

We quantify the evidence for cosmic acceleration using simulations of $H(z)$ measurements from SKA- and Euclid-like surveys. We perform a non-parametric reconstruction of the Hubble parameters and its derivative to obtain the deceleration parameter $q(z)$ using the Gaussian Processes method. This is a completely model-independent approach, so we can determine whether the Universe is undergoing accelerated expansion {\it regardless} of any assumption of a dark energy model. We find that Euclid-like and SKA-like band 1 surveys can probe cosmic acceleration at over $3$ and $5\sigma$ confidence level, respectively. By combining them with a SKA-like band 2 survey, which reaches lower redshift ranges, the evidence for a current accelerated phase increases to over $7\sigma$. This is a significant improvement from current $H(z)$ measurements from cosmic chronometers and galaxy redshift surveys, showing that these surveys can underpin cosmic acceleration in a model-independent way.
SiamMan: Siamese Motion-aware Network for Visual Tracking

In this paper, we present a novel siamese motion-aware network (SiamMan) for visual tracking, which consists of the siamese feature extraction subnetwork, followed by the classification, regression, and localization branches in parallel. The classification branch is used to distinguish the foreground from background, and the regression branch is adopt to regress the bounding box of target. To reduce the impact of manually designed anchor boxes to adapt to different target motion patterns, we design the localization branch, which aims to coarsely localize the target to help the regression branch to generate accurate results. Meanwhile, we introduce the global context module into the localization branch to capture long-range dependency for more robustness in large displacement of target. In addition, we design a multi-scale learnable attention module to guide these three branches to exploit discriminative features for better performance. The whole network is trained offline in an end-to-end fashion with large-scale image pairs using the standard SGD algorithm with back-propagation. Extensive experiments on five challenging benchmarks, i.e., VOT2016, VOT2018, OTB100, UAV123 and LTB35, demonstrate that SiamMan achieves leading accuracy with high efficiency. Code can be found at this https URL.
Analysis of Cardiovascular Changes Caused by Epileptic Seizures in Human Photoplethysmogram Signal

Objectives: This study examines human Photoplethysmogram (PPG) along with Electrocardiogram (ECG) signals to study cardiac autonomic imbalance in epileptic seizures. The significance and the prevalence of changes in PPG morphological parameters have been investigated to find common patterns among subjects. Alterations in cardiovascular parameters measured by PPG/ECG signals are used to train a neural network based on LSTM for automatic seizure detection. Methods: Electroencephalogram (EEG), ECG, and PPG signals from 12 different subjects ( 8 males;4 females;age 34.3$\pm$ 13.8) were recorded including 57 seizures and 101 hours of inter-ictal data. 12 PPG features significantly changing due to epileptic seizures were extracted and normalized based on a proposed z-score metric. 7 feature are heart rate variability related and 5 features hemodynamic related. Results: A consistent pattern of ictal change was observed for all the features across the subjects/seziures. The proposed seizure detector is subject independent and works for both nocturnal and diurnal seizures. With an average of 0.52 false alarms per hour, positive predictive value of $43\%$ and sensitivity of $92\%$, the new proposed hemodynamic based seizure detector shows improvement over the the heart rate variability based detector. Conclusion: The cardiac autonomic imbalance due to seizure manifests itself in variations of peripheral hemodynamics measured by PPG signal, suggesting vasoconstriction in limbs. These variations can be used on a consumer seizure detecting devices with optical sensors for seizure detection. Significance: The stereotyped pattern is common among all the subjects which can help understand the mechanism of cardiac autonomic imbalance induced by epileptic seizures.
Learning Agent Communication under Limited Bandwidth by Message Pruning

Communication is a crucial factor for the big multi-agent world to stay organized and productive. Recently, Deep Reinforcement Learning (DRL) has been applied to learn the communication strategy and the control policy for multiple agents. However, the practical \emph{\textbf{limited bandwidth}} in multi-agent communication has been largely ignored by the existing DRL methods. Specifically, many methods keep sending messages incessantly, which consumes too much bandwidth. As a result, they are inapplicable to multi-agent systems with limited bandwidth. To handle this problem, we propose a gating mechanism to adaptively prune less beneficial messages. We evaluate the gating mechanism on several tasks. Experiments demonstrate that it can prune a lot of messages with little impact on performance. In fact, the performance may be greatly improved by pruning redundant messages. Moreover, the proposed gating mechanism is applicable to several previous methods, equipping them the ability to address bandwidth restricted settings.
Bayesian Copula Density Deconvolution for Zero-Inflated Data in Nutritional Epidemiology

Abstract Estimating the marginal and joint densities of the long-term average intakes of different dietary components is an important problem in nutritional epidemiology. Since these variables cannot be directly measured, data are usually collected in the form of 24-hr recalls of the intakes, which show marked patterns of conditional heteroscedasticity. Significantly compounding the challenges, the recalls for episodically consumed dietary components also include exact zeros. The problem of estimating the density of the latent long-time intakes from their observed measurement error contaminated proxies is then a problem of deconvolution of densities with zero-inflated data. We propose a Bayesian semiparametric solution to the problem, building on a novel hierarchical latent variable framework that translates the problem to one involving continuous surrogates only. Crucial to accommodating important aspects of the problem, we then design a copula based approach to model the involved joint distributions, adopting different modeling strategies for the marginals of the different dietary components. We design efficient Markov chain Monte Carlo algorithms for posterior inference and illustrate the efficacy of the proposed method through simulation experiments. Applied to our motivating nutritional epidemiology problems, compared to other approaches, our method provides more realistic estimates of the consumption patterns of episodically consumed dietary components. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
Marginalized State Distribution Entropy Regularization in Policy Optimization

Entropy regularization is used to get improved optimization performance in reinforcement learning tasks. A common form of regularization is to maximize policy entropy to avoid premature convergence and lead to more stochastic policies for exploration through action space. However, this does not ensure exploration in the state space. In this work, we instead consider the distribution of discounted weighting of states, and propose to maximize the entropy of a lower bound approximation to the weighting of a state, based on latent space state representation. We propose entropy regularization based on the marginal state distribution, to encourage the policy to have a more uniform distribution over the state space for exploration. Our approach based on marginal state distribution achieves superior state space coverage on complex gridworld domains, that translate into empirical gains in sparse reward 3D maze navigation and continuous control domains compared to entropy regularization with stochastic policies.
SketchZooms: Deep Multi‐view Descriptors for Matching Line Drawings

Finding point‐wise correspondences between images is a long‐standing problem in image analysis. This becomes particularly challenging for sketch images, due to the varying nature of human drawing style, projection distortions and viewport changes. In this paper, we present the first attempt to obtain a learned descriptor for dense registration in line drawings. Based on recent deep learning techniques for corresponding photographs, we designed descriptors to locally match image pairs where the object of interest belongs to the same semantic category, yet still differ drastically in shape, form, and projection angle. To this end, we have specifically crafted a data set of synthetic sketches using non‐photorealistic rendering over a large collection of part‐based registered 3D models. After training, a neural network generates descriptors for every pixel in an input image, which are shown togeneralize correctly in unseen sketches hand‐drawn by humans. We evaluate our method against a baseline of correspondences data collected from expert designers, in addition to comparisons with other descriptors that have been proven effective in sketches. Code, data and further resources will be publicly released by the time of publication.
Chemical Properties of Two Dense Cores in a Planck Galactic Cold Clump G168.72-15.48

To deepen our understanding of the chemical properties of the Planck Galactic Cold Clump (PGCC) G168.72-15.48, we performed observations of nine molecular species, namely, c-C3H, H2CO, HC5N, HC7N, SO, CCH, N2H+, CH3OH, and CH3CCH, toward two dense cores in PGCC G168.72-15.48 using the Tianma Radio Telescope and Purple Mountain Observatory Telescope. We detected c-C3H, H2CO, HC5N, N2H+, CCH, and CH3OH in both G168-H1 and G168-H2 cores, whereas HC7N and CH3CCH were detected only in G168-H1 and SO was detected only in G168-H2. Mapping observations reveal that the CCH, N2H+, CH3OH, and CH3CCH emissions are well coupled with the dust emission in G168-H1. Additionally, N2H+ exhibits an exceptionally weak emission in the denser and more evolved G168-H2 core, which may be attributed to the N2H+ depletion. We suggest that the N2H+ depletion in G168-H2 is dominated by N2 depletion, rather than the destruction by CO. The local thermodynamic equilibrium calculations indicate that the carbon-chain molecules of CCH, HC5N, HC7N, and CH3CCH are more abundant in the younger G168-H1 core. We found that starless core G168-H1 may have the properties of cold dark clouds based on its abundances of carbon-chain molecules. While, the prestellar core G168-H2 exhibits lower carbon-chain molecular abundances than the general cold dark clouds. With our gas-grain astrochemical model calculations, we attribute the observed chemical differences between G168-H1 and G168-H2 to their different gas densities and different evolutionary stages.
Improving Land Cover Segmentation Across Satellites Using Domain Adaptation

Land use and land cover mapping is essential to various fields of study, such as forestry, agriculture, and urban management. Generally, earth observation satellites facilitate and accelerate the mapping process. Subsequently, deep learning methods have been proven to be excellent in automating the mapping via semantic image segmentation. However, because deep neural networks require large amounts of labeled data, it is not easy to exploit the full potential of satellite imagery. Additionally, land cover tends to differ in appearance from one region to another; therefore, having labeled data from one location does not necessarily help map others. Furthermore, satellite images come in various multispectral bands, which range from RGB to over 12 bands. In this study, our aim is to use domain adaptation (DA) to solve the aforementioned problems. We applied a well-performing DA approach on the DeepGlobe land cover dataset as well as datasets that we built using RGB images from Sentinel-2, WorldView-2, and Pleiades-1B satellites with CORINE Land Cover as ground truth (GT) labels. The experiments revealed significant improvements over the results obtained without using DA. In some cases, an improvement of over 20% mean intersection over union was obtained. Sometimes, our model manages to correct errors in the GT labels.