Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology

The use of wastewater-based epidemiology (WBE) for early detection of virus circulation and response during the SARS-CoV-2 pandemic increased interest in and use of virus concentration protocols that are quick, scalable, and efficient. One such protocol involves sample clarification by size fractionation using either low-speed centrifugation to produce a clarified supernatant or membrane filtration to produce an initial filtrate depleted of solids, eukaryotes and bacterial present in wastewater (WW), followed by concentration of virus particles by ultrafiltration of the above. While this approach has been successful in identifying viruses from WW, it assumes that majority of the viruses of interest should be present in the fraction obtained by ultrafiltration of the initial filtrate, with negligible loss of viral particles and viral diversity. We used WW samples collected in a population of ~700,000 in southwest USA between October 2019 and March 2021, targeting three non-enveloped viruses (enteroviruses [EV], canine picornaviruses [CanPV], and human adenovirus 41 [Ad41]), to evaluate whether size fractionation of WW prior to ultrafiltration leads to appreciable differences in the virus presence and diversity determined. We showed that virus presence or absence in WW samples in both portions (filter trapped solids [FTS] and filtrate) are not consistent with each other. We also found that in cases where virus was detected in both fractions, virus diversity (or types) captured either in FTS or filtrate were not consistent with each other. Hence, preferring one fraction of WW over the other can undermine the capacity of WBE to function as an early warning system and negatively impact the accurate representation of virus presence and diversity in a population.
On the scaling and anisotropy of two subranges in the inertial range of solar wind turbulence

Intermittency and anisotropy are two important aspects of plasma turbulence, which the solar wind provides a natural laboratory to investigate. However, their forms and nature are still under debate, making it difficult to achieve a consensus in the theoretical interpretation. Here, we perform higher-order statistics for the observations in the fast solar wind at 1.48 au obtained by Ulysses and in the slow solar wind at 0.17 au obtained by Parker Solar Probe (PSP). We find that two subranges clearly exist in the inertial range and they present distinct features with regard to the intermittency and anisotropy. The subrange 1 with smaller scale has a multifractal scaling with the second index $\xi(2) \sim 2/3$ and the subrange 2 with larger scale is also multifractal but with $\xi(2) \sim 1/2$. The break between two subranges locates at the same spatial scale for both Ulysses and PSP observations. Subrange 1 is multifractal in the direction perpendicular to the local magnetic field with $\xi_{\perp}(2) \sim 2/3$ and seems to be monoscaling in the parallel direction with $\xi_{\parallel}(2) \sim 1$. Subrange 2 is multifractal in both parallel and perpendicular directions with $\xi_{\perp}(2) \sim 1/2$ and $\xi_{\parallel}(2) \sim 2/3$. Both subrange 1 and subrange 2 present power and wavevector anisotropies. The distinct features of two subranges suggest that a transition from weak to strong turbulence may occur and the spatial scale of the break may not evolve with the solar wind expansion. These new results update our knowledge of the inertial range and provide strong observational constraints on the understanding of intermittency and anisotropy in solar wind turbulence.
ControlVC: Zero-Shot Voice Conversion with Time-Varying Controls on Pitch and Rhythm

Recent developments in neural speech synthesis and vocoding have sparked a renewed interest in voice conversion (VC). Beyond timbre transfer, achieving controllability on para-linguistic parameters such as pitch and rhythm is critical in deploying VC systems in many application scenarios. Existing studies, however, either only provide utterance-level global control or lack interpretability on the controls. In this paper, we propose ControlVC, the ﬁrst neural voice conversion system that achieves time-varying controls on pitch and rhythm. ControlVC uses pre-trained encoders to compute pitch embeddings and linguistic embeddings from the source utterance and speaker embeddings from the target utterance. These embeddings are then concatenated and converted to speech using a vocoder. It achieves rhythm control through TD-PSOLA pre-processing on the source utter-ance, and achieves pitch control by manipulating the pitch contour before feeding it to the pitch encoder. Systematic subjective and objective evaluations are conducted to assess the speech quality and controllability. Results show that, on non-parallel and zero-shot conversion tasks, ControlVC signiﬁcantly outperforms two other self-constructed baselines on speech quality, and it can successfully achieve time-varying pitch control.
Temporally Extended Successor Representations

We present a temporally extended variation of the successor representation, which we term t-SR. t-SR captures the expected state transition dynamics of temporally extended actions by constructing successor representations over primitive action repeats. This form of temporal abstraction does not learn a top-down hierarchy of pertinent task structures, but rather a bottom-up composition of coupled actions and action repetitions. This lessens the amount of decisions required in control without learning a hierarchical policy. As such, t-SR directly considers the time horizon of temporally extended action sequences without the need for predefined or domain-specific options. We show that in environments with dynamic reward structure, t-SR is able to leverage both the flexibility of the successor representation and the abstraction afforded by temporally extended actions. Thus, in a series of sparsely rewarded gridworld environments, t-SR optimally adapts learnt policies far faster than comparable value-based, model-free reinforcement learning methods. We also show that the manner in which t-SR learns to solve these tasks requires the learnt policy to be sampled consistently less often than non-temporally extended policies.
Efficient Random Walk based Sampling with Inverse Degree

Random walk sampling methods have been widely used in graph sampling in recent years, while it has bias towards higher degree nodes in the sample. To overcome this deficiency, classical methods such as MHRW design weighted walking by repeating low-degree nodes while rejecting high-degree nodes, so that the long-term behavior of Markov chain can achieve uniform distribution. This modification, however, may make the sampler stay in the same node for several times, leading to undersampling. To address this issue, we propose a sampling framework that only need current and candidate node degree to improve the performance of graph sampling methods. We also extend our original idea to a more general framework. Our extended IDRW method finds a balance between the large deviation problem of SRW and sample rejection problem in MHRW. We evaluate our technique in simulation by running extensive experiments on various real-world datasets, and the result show that our method improves the accuracy compared with the state of art techniques. We also investigate the effect of the parameter and give the suggested range for a better usage in application.
Text Summarization with Oracle Expectation

Extractive summarization produces summaries by identifying and concatenating the most important sentences in a document. Since most summarization datasets do not come with gold labels indicating whether document sentences are summary-worthy, different labeling algorithms have been proposed to extrapolate oracle extracts for model training. In this work, we identify two flaws with the widely used greedy labeling approach: it delivers suboptimal and deterministic oracles. To alleviate both issues, we propose a simple yet effective labeling algorithm that creates soft, expectation-based sentence labels. We define a new learning objective for extractive summarization which incorporates learning signals from multiple oracle summaries and prove it is equivalent to estimating the oracle expectation for each document sentence. Without any architectural modifications, the proposed labeling scheme achieves superior performance on a variety of summarization benchmarks across domains and languages, in both supervised and zero-shot settings.
Concurrent Graph Queries on the Lucata Pathfinder

High-performance analysis of unstructured data like graphs now is critical for applications ranging from business intelligence to genome analysis. Towards this, data centers hold large graphs in memory to serve multiple concurrent queries from different users. Even a single analysis often explores multiple options. Current computing architectures often are not the most time- or energy-efficient solutions. The novel Lucata Pathfinder architecture tackles this problem, combining migratory threads for low-latency reading with memory-side processing for high-performance accumulation. One hundred to 750 concurrent breadth-first searches (BFS) all achieve end-to-end speed-ups of 81% to 97% over one-at-a-time queries on a graph with 522M edges. Comparing to RedisGraph running on a large Intel-based server, the Pathfinder achieves a 19$\times$ speed-up running 128 BFS queries concurrently. The Pathfinder also efficiently supports a mix of concurrent analyses, demonstrated with connected components and BFS.
Evaluation of Question Answering Systems: Complexity of judging a natural language

Question answering (QA) systems are among the most important and rapidly developing research topics in natural language processing (NLP). A reason, therefore, is that a QA system allows humans to interact more naturally with a machine, e.g., via a virtual assistant or search engine. In the last decades, many QA systems have been proposed to address the requirements of different question-answering tasks. Furthermore, many error scores have been introduced, e.g., based on n-gram matching, word embeddings, or contextual embeddings to measure the performance of a QA system. This survey attempts to provide a systematic overview of the general framework of QA, QA paradigms, benchmark datasets, and assessment techniques for a quantitative evaluation of QA systems. The latter is particularly important because not only is the construction of a QA system complex but also its evaluation. We hypothesize that a reason, therefore, is that the quantitative formalization of human judgment is an open problem.
Ablation Path Saliency

Various types of saliency methods have been proposed for explaining black-box classification. In image applications, this means highlighting the part of the image that is most relevant for the current decision. Unfortunately, the different methods may disagree and it can be hard to quantify how representative and faithful the explanation really is. We observe however that several of these methods can be seen as edge cases of a single, more general procedure based on finding a particular path through the classifier's domain. This offers additional geometric interpretation to the existing methods. We demonstrate furthermore that ablation paths can be directly used as a technique of its own right. This is able to compete with literature methods on existing benchmarks, while giving more fine-grained information and better opportunities for validation of the explanations' faithfulness.
Image retrieval method based on entropy and fractal coding

In content-based image retrieval system, describing and extracting image's feature is a key question. An image can be characterized by its fractal codes, and fractal codes can be used as the image's feature to retrieve the images effectively. This paper proposes a novel image retrieval method using information entropy and fractal coding. First, each image in the database is classified by computing information entropy which is compared with a given threshold estimated from the inquired image. Second, the inquired image's fractal codes are generated via Jacquin method, which is applied to the same kind of database images with fractal tenth iteration decoding. Finally, the image retrieval result is obtained by matching the similar Euclidean distance between the inquired image and the iterated decoded image. Experimental results show that compared with the direct image pixels similar matching strategy, our scheme not only reduces retrieval complexity and retrieval time, but also guarantees the retrieval rate. Thus our proposed method is effective and feasible.
RetiFluidNet: A Self-Adaptive and Multi-Attention Deep Convolutional Network for Retinal OCT Fluid Segmentation

Optical coherence tomography (OCT) helps ophthalmologists assess macular edema, accumulation of fluids, and lesions at microscopic resolution. Quantification of retinal fluids is necessary for OCT-guided treatment management, which relies on a precise image segmentation step. As manual analysis of retinal fluids is a time-consuming, subjective, and error-prone task, there is increasing demand for fast and robust automatic solutions. In this study, a new convolutional neural architecture named RetiFluidNet is proposed for multi-class retinal fluid segmentation. The model benefits from hierarchical representation learning of textural, contextual, and edge features using a new self-adaptive dual-attention (SDA) module, multiple self-adaptive attention-based skip connections (SASC), and a novel multi-scale deep self-supervision learning (DSL) scheme. The attention mechanism in the proposed SDA module enables the model to automatically extract deformation-aware representations at different levels, and the introduced SASC paths further consider spatial-channel interdependencies for concatenation of counterpart encoder and decoder units, which improve representational capability. RetiFluidNet is also optimized using a joint loss function comprising a weighted version of dice overlap and edge-preserved connectivity-based losses, where several hierarchical stages of multi-scale local losses are integrated into the optimization process. The model is validated based on three publicly available datasets: RETOUCH, OPTIMA, and DUKE, with comparisons against several baselines. Experimental results on the datasets prove the effectiveness of the proposed model in retinal OCT fluid segmentation and reveal that the suggested method is more effective than existing state-of-the-art fluid segmentation algorithms in adapting to retinal OCT scans recorded by various image scanning instruments.
Joint Triplet Loss Learning for Next New POI Recommendation

Sparsity of the User-POI matrix is a well established problem for next POI recommendation, which hinders effective learning of user preferences. Focusing on a more granular extension of the problem, we propose a Joint Triplet Loss Learning (JTLL) module for the Next New ( 𝑁 2 ) POI recommendation task, which is more challenging. Our JTLL module first computes additional training samples from the users’ historical POI visit sequence, then, a designed triplet loss function is proposed to decrease and increase distances of POI and user embeddings based on their respective relations. Next, the JTLL module is jointly trained with recent approaches to additionally learn unvisited relations for the recommendation task. Experiments conducted on two known real-world LBSN datasets show that our joint training module was able to improve the performances of recent existing works.
One-Shot Learning of Stochastic Differential Equations with Computational Graph Completion

We consider the problem of learning Stochastic Diﬀerential Equations of the form dX t = f ( X t ) dt + σ ( X t ) dW t from one sample trajectory. This problem is more challenging than learning deterministic dynamical systems because one sample trajectory only provides indirect information on the unknown functions f , σ , and stochastic process dW t representing the drift, the diﬀusion, and the stochastic forcing terms, respectively. We propose a simple kernel-based solution to this problem that can be decomposed as follows: (1) Represent the time-increment map X t → X t + dt as a Computational Graph in which f , σ and dW t appear as unknown functions and random variables. (2) Complete the graph (approximate unknown functions and random variables) via Maximum a Posteriori Estimation (given the data) with Gaussian Process (GP) priors on the unknown functions. (3) Learn the covariance functions (kernels) of the GP priors from data with randomized cross-validation. Numerical experiments illustrate the eﬃcacy, robustness, and scope of our method.
Lightweight Image Codec via Multi-Grid Multi-Block-Size Vector Quantization (MGBVQ)

—A multi-grid multi-block-size vector quantization (MGBVQ) method is proposed for image coding in this work. The fundamental idea of image coding is to remove correlations among pixels before quantization and entropy coding, e.g., the discrete cosine transform (DCT) and intra predictions, adopted by modern image coding standards. We present a new method to remove pixel correlations. First, by decomposing correlations into long- and short-range correlations, we represent long-range correlations in coarser grids due to their smoothness, thus leading to a multi-grid (MG) coding architecture. Second, we show that short-range correlations can be effectively coded by a suite of vector quantizers (VQs). Along this line, we argue the effectiveness of VQs of very large block sizes and present a convenient way to implement them. It is shown by experimental results that MGBVQ offers excellent rate-distortion (RD) performance, which is comparable with existing image coders, at much lower complexity. Besides, it provides a progressive coded bitstream.
The scattering of baby Skyrmions off potential obstructions, in a Landau-Lifshitz model

The dynamics of baby skyrmions of the (2+1) new baby Skyrme model, in a Landau - Lifshitz model, was studied in the presence of various potential obstructions of varying geometries. The potential obstructions were created by introducing a localised inhomogeneity in the new baby Skyrme model's potential coefficient. The size and shape of the potential obstruction was varied and two systems were investigated, namely the symmetric and asymmetric systems. In the symmetric system the trajectory of the baby skyrmions, as they traverse the barrier, was deformed from the normal circular trajectory, during which time the skyrmions sped up. For critical values of the barrier height, the baby skyrmions no longer formed a bound state and were free to separate. In the case of a potential hole, the baby skyrmions no longer formed a bound state and moved asymptotically along the edge of the hole. In the asymmetric barrier system the baby skyrmions behaved the same as the skyrmions of the symmetric obstructions. Away from the obstruction the baby skyrmions orbited the boundary of the system. In the potential hole system the bound skyrmions moved along the edge of the hole. For critical values of the hole depth, the bound state between the skyrmions was broken, resulting in one of the skyrmions remaining stationary and the other traversing the edge of the hole. During our investigations into this system it was found that the definition of the angular momentum must be modified to ensure overall conservation. It was shown how these modifications arise and how they are calculated.
Strong Transferable Adversarial Attacks via Ensembled Asymptotically Normal Distribution Learning

Strong adversarial examples are crucial for evaluating and enhancing the robustness of deep neural networks. However, the performance of popular attacks is usually sensitive, for instance, to minor image transformations, stemming from limited information -- typically only one input example, a handful of white-box source models, and undefined defense strategies. Hence, the crafted adversarial examples are prone to overfit the source model, which hampers their transferability to unknown architectures. In this paper, we propose an approach named Multiple Asymptotically Normal Distribution Attacks (MultiANDA) which explicitly characterize adversarial perturbations from a learned distribution. Specifically, we approximate the posterior distribution over the perturbations by taking advantage of the asymptotic normality property of stochastic gradient ascent (SGA), then employ the deep ensemble strategy as an effective proxy for Bayesian marginalization in this process, aiming to estimate a mixture of Gaussians that facilitates a more thorough exploration of the potential optimization space. The approximated posterior essentially describes the stationary distribution of SGA iterations, which captures the geometric information around the local optimum. Thus, MultiANDA allows drawing an unlimited number of adversarial perturbations for each input and reliably maintains the transferability. Our proposed method outperforms ten state-of-the-art black-box attacks on deep learning models with or without defenses through extensive experiments on seven normally trained and seven defense models.
Shrinking unit: a Graph Convolution-Based Unit for CNN-like 3D Point Cloud Feature Extractors

3D point clouds have attracted increasing attention in architecture, engineering, and construction due to their high-quality object representation and efficient acquisition methods. Consequently, many point cloud feature detection methods have been proposed in the literature to automate some workflows, such as their classification or semantic segmentation. Nevertheless, the performance of point cloud automated systems significantly lags behind their image counterparts. While part of this failure stems from the irregularity, unstructuredness, and disorder of point clouds, which makes the task of point cloud feature detection significantly more challenging than the image one, we argue that a lack of inspiration from the image domain might be the primary cause of such a gap. Indeed, given the overwhelming success of Convolutional Neural Networks (CNNs) in image feature detection, it seems reasonable to design their point cloud counterparts, but none of the proposed approaches closely resembles them. Specifically, even though many approaches generalise the convolution operation in point clouds, they fail to emulate the CNNs multiple-feature detection and pooling operations. For this reason, we propose a graph convolution-based unit, dubbed Shrinking unit, that can be stacked vertically and horizontally for the design of CNN-like 3D point cloud feature extractors. Given that self, local and global correlations between points in a point cloud convey crucial spatial geometric information, we also leverage them during the feature extraction process. We evaluate our proposal by designing a feature extractor model for the ModelNet-10 benchmark dataset and achieve 90.64% classification accuracy, demonstrating that our innovative idea is effective. Our code is available at github.com/albertotamajo/Shrinking-unit.