arXiv Computer Science @arxiv_cs@qoto.org

Surges that have been observed at different periods in the number of COVID-19 cases are associated with the emergence of multiple SARS-CoV-2 (Severe Acute Respiratory Virus) variants. The design of methods to support laboratory detection are crucial in the monitoring of these variants. Hence, in this paper, we develop a semi-automated method to design both forward and reverse primer sets to detect SARS-CoV-2 variants. To proceed, we train deep Convolution Neural Networks (CNNs) to classify labelled SARS-CoV-2 variants and identify partial genomic features needed for the forward and reverse Polymerase Chain Reaction (PCR) primer design. Our proposed approach supplements existing ones while promoting the emerging concept of neural network assisted primer design for PCR. Our CNN model was trained using a database of SARS-CoV-2 full-length genomes from GISAID and tested on a separate dataset from NCBI, with 98\% accuracy for the classification of variants. This result is based on the development of three different methods of feature extraction, and the selected primer sequences for each SARS-CoV-2 variant detection (except Omicron) were present in more than 95 \% of sequences in an independent set of 5000 same variant sequences, and below 5 \% in other independent datasets with 5000 sequences of each variant. In total, we obtain 22 forward and reverse primer pairs with flexible length sizes (18-25 base pairs) with an expected amplicon length ranging between 42 and 3322 nucleotides. Besides the feature appearance, in-silico primer checks confirmed that the identified primer pairs are suitable for accurate SARS-CoV-2 variant detection by means of PCR tests.

Simulating time-domain observations of gravitational wave (GW) detector environments will allow for a better understanding of GW sources, augment datasets for GW signal detection and help in characterizing the noise of the detectors, leading to better physics. This paper presents a novel approach to simulating fixed-length time-domain signals using a three-player Wasserstein Generative Adversarial Network (WGAN), called DVGAN, that includes an auxiliary discriminator that discriminates on the derivatives of input signals. An ablation study is used to compare the effects of including adversarial feedback from an auxiliary derivative discriminator with a vanilla two-player WGAN. We show that discriminating on derivatives can stabilize the learning of GAN components on 1D continuous signals during their training phase. This results in smoother generated signals that are less distinguishable from real samples and better capture the distributions of the training data. DVGAN is also used to simulate real transient noise events captured in the advanced LIGO GW detector.

COVID-19 poses disproportionate mental health consequences to the public during different phases of the pandemic. We use a computational approach to capture the specific aspects that trigger an online community's anxiety about the pandemic and investigate how these aspects change over time. First, we identified nine subjects of anxiety (SOAs) in a sample of Reddit posts ($N$=86) from r/COVID19\_support using thematic analysis. Then, we quantified Reddit users' anxiety by training algorithms on a manually annotated sample ($N$=793) to automatically label the SOAs in a larger chronological sample ($N$=6,535). The nine SOAs align with items in various recently developed pandemic anxiety measurement scales. We observed that Reddit users' concerns about health risks remained high in the first eight months of the pandemic. These concerns diminished dramatically despite the surge of cases occurring later. In general, users' language disclosing the SOAs became less intense as the pandemic progressed. However, worries about mental health and the future increased steadily throughout the period covered in this study. People also tended to use more intense language to describe mental health concerns than health risks or death concerns. Our results suggest that this online group's mental health condition does not necessarily improve despite COVID-19 gradually weakening as a health threat due to appropriate countermeasures. Our system lays the groundwork for population health and epidemiology scholars to examine aspects that provoke pandemic anxiety in a timely fashion.

These notes are an overview of some classical linear methods in Multivariate Data Analysis. This is an good old domain, well established since the 60's, and refreshed timely as a key step in statistical learning. It can be presented as part of statistical learning, or as dimensionality reduction with a geometric flavor. Both approaches are tightly linked: it is easier to learn patterns from data in low dimensional spaces than in high-dimensional spaces. It is shown how a diversity of methods and tools boil down to a single core methods, PCA with SVD, such that the efforts to optimize codes for analyzing massive data sets can focus on this shared core method, and benefit to all methods. An extension to the study of several arrays is presented (Canonical Analysis).

The term melodic template or skeleton refers to a basic melody which is subject to variation during a music performance. In many oral music tradition, these templates are implicitly passed throughout generations without ever being formalized in a score. In this work, we introduce a new geometric optimization problem, the spanning tube problem, to approximate a melodic template for a set of labeled performance transcriptions corresponding to an specific style in oral music traditions. Given a set of $n$ piecewise linear functions, we solve the problem of finding a continuous function, $f^*$, and a minimum value, $\varepsilon^*$, such that, the vertical segment of length $2\varepsilon^*$ centered at $(x,f^*(x))$ intersects at least $p$ functions ($p\leq n$). The method explored here also provide a novel tool for quantitatively assess the amount of melodic variation which occurs across performances.

In a recent article, the class of functions from the integers to the integers computable in polynomial time has been characterized using discrete ordinary differential equations (ODE), also known as finite differences. Doing so, we pointed out the fundamental role of linear (discrete) ODEs and classical ODE tools such as changes of variables to capture computability and complexity measures, or as a tool for programming. In this article, we extend the approach to a characterization of functions from the integers to the reals computable in polynomial time in the sense of computable analysis. In particular, we provide a characterization of such functions in terms of the smallest class of functions that contains some basic functions, and that is closed by composition, linear length ODEs, and a natural effective limit schema.

No existing spherical convolutional neural network (CNN) framework is both computationally scalable and rotationally equivariant. Continuous approaches capture rotational equivariance but are often prohibitively computationally demanding. Discrete approaches offer more favorable computational performance but at the cost of equivariance. We develop a hybrid discrete-continuous (DISCO) group convolution that is simultaneously equivariant and computationally scalable to high-resolution. While our framework can be applied to any compact group, we specialize to the sphere. Our DISCO spherical convolutions exhibit $\text{SO}(3)$ rotational equivariance, where $\text{SO}(n)$ is the special orthogonal group representing rotations in $n$-dimensions. When restricting rotations of the convolution to the quotient space $\text{SO}(3)/\text{SO}(2)$ for further computational enhancements, we recover a form of asymptotic $\text{SO}(3)$ rotational equivariance. Through a sparse tensor implementation we achieve linear scaling in number of pixels on the sphere for both computational cost and memory usage. For 4k spherical images we realize a saving of $10^9$ in computational cost and $10^4$ in memory usage when compared to the most efficient alternative equivariant spherical convolution. We apply the DISCO spherical CNN framework to a number of benchmark dense-prediction problems on the sphere, such as semantic segmentation and depth estimation, on all of which we achieve the state-of-the-art performance.

Operating under real world conditions is challenging due to the possibility of a wide range of failures induced by partial observability. In relatively benign settings, such failures can be overcome by retrying or executing one of a small number of hand-engineered recovery strategies. By contrast, contact-rich sequential manipulation tasks, like opening doors and assembling furniture, are not amenable to exhaustive hand-engineering. To address this issue, we present a general approach for robustifying manipulation strategies in a sample-efficient manner. Our approach incrementally improves robustness by first discovering the failure modes of the current strategy via exploration in simulation and then learning additional recovery skills to handle these failures. To ensure efficient learning, we propose an online algorithm Value Upper Confidence Limit (Value-UCL) that selects what failure modes to prioritize and which state to recover to such that the expected performance improves maximally in every training episode. We use our approach to learn recovery skills for door-opening and evaluate them both in simulation and on a real robot with little fine-tuning. Compared to open-loop execution, our experiments show that even a limited amount of recovery learning improves task success substantially from 71\% to 92.4\% in simulation and from 75\% to 90\% on a real robot.

In this work, we extend the convex body chasing problem to an adversarial setting, where a player is tasked to chase a sequence of convex bodies generated adversarially by an opponent. The Player aims to minimize the cost associated with its total movements, while the Opponent tries to maximize it. The set of feasible convex bodies is finite and known to both agents, which allows us to provide performance guarantees with max-min optimality rather than in the form of competitive ratio. Under certain assumptions, we showed the continuity of the optimal value function, based on which, we designed an algorithm that numerically generates policies with performance guarantees. Finally, the theoretical results are verified through numerical examples.

We propose a new method of adaptive piecewise approximation based on Sinc points for ordinary differential equations. The adaptive method is a piecewise collocation method which utilizes Poly-Sinc interpolation to reach a preset level of accuracy for the approximation. Our work extends the adaptive piecewise Poly-Sinc method to function approximation, for which we derived an a priori error estimate for our adaptive method and showed its exponential convergence in the number of iterations. In this work, we show the exponential convergence in the number of iterations of the a priori error estimate obtained from the piecewise collocation method, provided that a good estimate of the exact solution of the ordinary differential equation at the Sinc points exists. We use a statistical approach for partition refinement. The adaptive greedy piecewise Poly-Sinc algorithm is validated on regular and stiff ordinary differential equations.

Extraction of latent sources of complex stimuli is critical for making sense of the world. While the brain solves this blind source separation (BSS) problem continuously, its algorithms remain unknown. Previous work on biologically-plausible BSS algorithms assumed that observed signals are linear mixtures of statistically independent or uncorrelated sources, limiting the domain of applicability of these algorithms. To overcome this limitation, we propose novel biologically-plausible neural networks for the blind separation of potentially dependent/correlated sources. Differing from previous work, we assume some general geometric, not statistical, conditions on the source vectors allowing separation of potentially dependent/correlated sources. Concretely, we assume that the source vectors are sufficiently scattered in their domains which can be described by certain polytopes. Then, we consider recovery of these sources by the Det-Max criterion, which maximizes the determinant of the output correlation matrix to enforce a similar spread for the source estimates. Starting from this normative principle, and using a weighted similarity matching approach that enables arbitrary linear transformations adaptable by local learning rules, we derive two-layer biologically-plausible neural network algorithms that can separate mixtures into sources coming from a variety of source domains. We demonstrate that our algorithms outperform other biologically-plausible BSS algorithms on correlated source separation problems.

Emergency Department (ED) overcrowding continues to be a public health issue as well as a patient safety issue. The underlying factors leading to ED crowding are numerous, varied, and complex. Although lack of in-hospital beds is frequently attributed as the primary reason for crowding, ED's dependencies on other ancillary resources, including imaging, consults, and labs, also contribute to crowding. Using retrospective data associated with imaging, including delays, processing time, and the number of image orders, from a large tier 1 trauma center, we developed a discrete event simulation model to identify the impact of the imaging delays and bundling image orders on patient time in the ED. Results from sensitivity analysis show that reducing the delays associated with imaging and bundling as few as 10% of imaging orders for certain patients can significantly (p-value < 0.05) reduce the time a patient spends in the ED.

We initiate the study of quantum algorithms for optimizing approximately convex functions. Given a convex set ${\cal K}\subseteq\mathbb{R}^{n}$ and a function $F\colon\mathbb{R}^{n}\to\mathbb{R}$ such that there exists a convex function $f\colon\mathcal{K}\to\mathbb{R}$ satisfying $\sup_{x\in{\cal K}}|F(x)-f(x)|\leq ε/n$, our quantum algorithm finds an $x^{*}\in{\cal K}$ such that $F(x^{*})-\min_{x\in{\cal K}} F(x)\leqε$ using $\tilde{O}(n^{3})$ quantum evaluation queries to $F$. This achieves a polynomial quantum speedup compared to the best-known classical algorithms. As an application, we give a quantum algorithm for zeroth-order stochastic convex bandits with $\tilde{O}(n^{5}\log^{2} T)$ regret, an exponential speedup in $T$ compared to the classical $Ω(\sqrt{T})$ lower bound. Technically, we achieve quantum speedup in $n$ by exploiting a quantum framework of simulated annealing and adopting a quantum version of the hit-and-run walk. Our speedup in $T$ for zeroth-order stochastic convex bandits is due to a quadratic quantum speedup in multiplicative error of mean estimation.

Increasing the layer number of on-chip photonic neural networks (PNNs) is essential to improve its model performance. However, the successively cascading of network hidden layers results in larger integrated photonic chip areas. To address this issue, we propose the optical neural ordinary differential equations (ON-ODE) architecture that parameterizes the continuous dynamics of hidden layers with optical ODE solvers. The ON-ODE comprises the PNNs followed by the photonic integrator and optical feedback loop, which can be configured to represent residual neural networks (ResNet) and recurrent neural networks with effectively reduced chip area occupancy. For the interference-based optoelectronic nonlinear hidden layer, the numerical experiments demonstrate that the single hidden layer ON-ODE can achieve approximately the same accuracy as the two-layer optical ResNet in image classification tasks. Besides, the ONODE improves the model classification accuracy for the diffraction-based all-optical linear hidden layer. The time-dependent dynamics property of ON-ODE is further applied for trajectory prediction with high accuracy.

Intelligent data-driven monitoring procedures hold enormous potential for ensuring safe operation and optimal management of the railway infrastructure in the face of increasing demands on cost and efficiency. Numerous studies have shown that the track stiffness is one of the main parameters influencing the evolution of degradation that drives maintenance processes. As such, the measurement of track stiffness is fundamental for characterizing the performance of the track in terms of deterioration rate and noise emission. This can be achieved via low-cost On Board Monitoring (OBM) sensing systems (i.e., axle-box accelerometers) that are mounted on in-service trains and enable frequent, real-time monitoring of the railway infrastructure network. Acceleration-based stiffness indicators have seldom been considered in monitoring applications. In this work, the use of a Vold-Kalman filter is proposed, for decomposing the signal into periodic wheel and track related excitation--response pairs functions. We demonstrate that these components are in turn correlated to operational conditions, such as wheel out-of-roundness and rail type. We further illustrate the relationship between the track stiffness, the measured wheel-rail forces and the sleeper passage amplitude, which can ultimately serve as an indicator for predictive track maintenance and prediction of track durability.

Self-supervised learning (SSL) speech models have achieved unprecedented success in speech representation learning, but some questions regarding their representation ability remain unanswered. This paper addresses two of them: (1) Can SSL speech models deal with non-speech audio?; (2) Would different SSL speech models have insights into diverse aspects of audio features? To answer the two questions, we conduct extensive experiments on abundant speech and non-speech audio datasets to evaluate the representation ability of currently state-of-the-art SSL speech models, which are wav2vec 2.0 and HuBERT in this paper. These experiments are carried out during NeurIPS 2021 HEAR Challenge as a standard evaluation pipeline provided by competition officials. Results show that (1) SSL speech models could extract meaningful features of a wide range of non-speech audio, while they may also fail on certain types of datasets; (2) different SSL speech models have insights into different aspects of audio features. The two conclusions provide a foundation for the ensemble of representation models. We further propose an ensemble framework to fuse speech representation models' embeddings. Our framework outperforms state-of-the-art SSL speech/audio models and has generally superior performance on abundant datasets compared with other teams in HEAR Challenge. Our code is available at https://github.com/tony10101105/HEAR-2021-NeurIPS-Challenge -- NTU-GURA.

In this paper we use the language of noncommutative differential geometry to formalise discrete differential calculus. We begin with a brief review of inverse limit of posets as an approximation of topological spaces. We then show how to associate a $C^*$-algebra over a poset, giving it a piecewise-linear structure. Furthermore, we explain how dually the algebra of continuous function $C(M)$ over a manifold $M$ can be approximated by a direct limit of $C^*$-algebras over posets. Finally, in the spirit of noncommutative differential geometry, we define a finite dimensional spectral triple on each poset. We show how the usual finite difference calculus is recovered as the eigenvalues of the commutator with the Dirac operator. We prove a convergence result in the case of the $d$-lattice.

A Lookahead Auction (LA), introduced by Ronen, is an auction format for the sale of a single item among multiple buyers, which is considered simpler and more fair than the optimal auction. Indeed, it anonymously selects a provisional winner by a symmetric ascending-price process, and only then uses a personalized posted price. A LA auction extracts at least 1/2 of the optimal revenue, even under a correlated value distribution. This bound is tight, even for 2 buyers with independent values. We introduce a natural extension of LA, called lookahead with pooling (LAP). A LAP auction proceeds as LA, with one difference: it allows the seller to pool together a range of values during the ascending-price stage, and treat them the same; thus, it preserves the simplicity and fairness of LA. Our main result is that this simple pooling operation improves the revenue guarantees for independent buyers from 1/2 to 4/7 of the optimal revenue. We also give a complementary negative result, showing that for arbitrary correlated priors LAP cannot do better than 1/2 approximation.

With recent advancements in artificial intelligence, its applications can be seen in every aspect of humans' daily life. From voice assistants to mobile healthcare and autonomous driving, we rely on the performance of AI methods for many critical tasks; therefore, it is essential to assert the performance of models in proper means to prevent damage. One of the shortfalls of AI models in general, and deep machine learning in particular, is a drop in performance when faced with shifts in the distribution of data. Nonetheless, these shifts are always expected in real-world applications; thus, a field of study has emerged, focusing on detecting out-of-distribution data subsets and enabling a more comprehensive generalization. Furthermore, as many deep learning based models have achieved near-perfect results on benchmark datasets, the need to evaluate these models' reliability and trustworthiness for pushing towards real-world applications is felt more strongly than ever. This has given rise to a growing number of studies in the field of out-of-distribution detection and domain generalization, which begs the need for surveys that compare these studies from various perspectives and highlight their straightens and weaknesses. This paper presents a survey that, in addition to reviewing more than 70 papers in this field, presents challenges and directions for future works and offers a unifying look into various types of data shifts and solutions for better generalization.

We consider risk-sensitive Markov decision processes (MDPs), where the MDP model is influenced by a parameter which takes values in a compact metric space. We identify sufficient conditions under which small perturbations in the model parameters lead to small changes in the optimal value function and optimal policy. We further establish the robustness of the risk-sensitive optimal policies to modeling errors. Implications of the results for data-driven decision-making, decision-making with preference uncertainty, and systems with changing noise distributions are discussed.