Statistical Learning
Estimating infectiousness throughout SARS-CoV-2 infection course
The role that individuals with asymptomatic or mildly symptomatic severe acute respiratory syndrome coronavirus 2 have in transmission of the virus is not well understood. Jones et al. investigated viral load in patients, comparing those showing few, if any, symptoms with hospitalized cases. Approximately 400,000 individuals, mostly from Berlin, were tested from February 2020 to March 2021 and about 6% tested positive. Of the 25,381 positive subjects, about 8% showed very high viral loads. People became infectious within 2 days of infection, and in hospitalized individuals, about 4 days elapsed from the start of virus shedding to the time of peak viral load, which occurred 1 to 3 days before the onset of symptoms. Overall, viral load was highly variable, but was about 10-fold higher in persons infected with the B.1.1.7 variant. Children had slightly lower viral loads than adults, although this difference may not be clinically significant. Science , abi5273, this issue p. [eabi5273][1] ### INTRODUCTION Although post facto studies have revealed the importance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission from presymptomatic, asymptomatic, and mildly symptomatic (PAMS) cases, the virological basis of their infectiousness remains largely unquantified. The reasons for the rapid spread of variant lineages of concern, such as B.1.1.7, have yet to be fully determined. ### RATIONALE Viral load (viral RNA concentration) in patient samples and the rate of isolation success of virus from clinical specimens in cell culture are the clinical parameters most directly relevant to infectiousness and hence to transmission. To increase our understanding of the infectiousness of SARS-CoV-2, especially in PAMS cases and those infected with the B.1.1.7 variant, we analyzed viral load data from 25,381 German cases, including 9519 hospitalized patients, 6110 PAMS cases from walk-in test centers, 1533 B.1.1.7 variant infections, and the viral load time series of 4434 (mainly hospitalized) patients. Viral load results were then combined with estimated cell culture isolation probabilities, producing a clinical proxy estimate of infectiousness. ### RESULTS PAMS subjects had, at the first positive test, viral loads and estimated infectiousness only slightly less than hospitalized patients. Similarly, children were found to have mean viral loads only slightly lower (0.5 log10 unitsor less) than those of adults and ~78% of the adult peak cell culture isolation probability. Eight percent of first-positive viral loads were 109 copies per swab or higher, across a wide age range (mean 37.6 years, standard deviation 13.4 years), representing a likely highly infectious minority, one-third of whom were PAMS. Relative to non-B.1.1.7 cases, patients with the B.1.1.7 variant had viral loads that were higher by a factor of 10 and estimated cell culture infectivity that was higher by a factor of 2.6. Similar ranges of viral loads from B.1.1.7 and B.1.177 samples were shown to be capable of causing infection in Caco-2 cell culture. A time-course analysis estimates that a peak viral load of 108.1 copies per swab is reached 4.3 days after onset of shedding and shows that, across the course of infection, hospitalized patients have slightly higher viral loads than nonhospitalized cases, who in turn have viral loads slightly higher than PAMS cases. Higher viral loads are observed in first-positive tests of PAMS subjects, likely as a result of systematic earlier testing. Mean culture isolation probability declines to 0.5 at 5 days after peak viral load and to 0.3 at 10 days after peak viral load. We estimate a rate of viral load decline of 0.17 log10 units per day, which, combined with reported estimates of incubation time and time to loss of successful cell culture isolation, suggests that viral load peaks 1 to 3 days before onset of symptoms (in symptomatic cases). ### CONCLUSION PAMS subjects who test positive at walk-in test centers can be expected to be approximately as infectious as hospitalized patients. The level of expected infectious viral shedding of PAMS people is of high importance because they are circulating in the community at the time of detection of infection. Although viral load and cell culture infectivity cannot be translated directly to transmission probability, it is likely that the rapid spread of the B.1.1.7 variant is partly attributable to higher viral load in these cases. Easily measured virological parameters can be used, for example, to estimate transmission risk from different groups (by age, gender, clinical status, etc.), to quantify variance, to show differences in virus variants, to highlight and quantify overdispersion, and to inform quarantine, containment, and elimination strategies. ![Figure][2] Viral load and cell culture infectivity in 25,381 SARS-CoV-2 infections. ( A ) Viral loads in presymptomatic, asymptomatic, and mildly symptomatic cases (PAMS; red), hospitalized patients (blue), and other subjects (black). ( B ) Expected first-positive viral load and cell culture isolation probability, colored as in (A). ( C ) Temporal estimation with lines representing patients, colored as in (A). ( D ) As in (C), but colored by age. Two elementary parameters for quantifying viral infection and shedding are viral load and whether samples yield a replicating virus isolate in cell culture. We examined 25,381 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Germany, including 6110 from test centers attended by presymptomatic, asymptomatic, and mildly symptomatic (PAMS) subjects, 9519 who were hospitalized, and 1533 B.1.1.7 lineage infections. The viral load of the youngest subjects was lower than that of the older subjects by 0.5 (or fewer) log10 units, and they displayed an estimated ~78% of the peak cell culture replication probability; in part this was due to smaller swab sizes and unlikely to be clinically relevant. Viral loads above 109 copies per swab were found in 8% of subjects, one-third of whom were PAMS, with a mean age of 37.6 years. We estimate 4.3 days from onset of shedding to peak viral load (108.1 RNA copies per swab) and peak cell culture isolation probability (0.75). B.1.1.7 subjects had mean log10 viral load 1.05 higher than that of non-B.1.1.7 subjects, and the estimated cell culture replication probability of B.1.1.7 subjects was higher by a factor of 2.6. [1]: /lookup/doi/10.1126/science.abi5273 [2]: pending:yes
Gradient Descent With AdaGrad From Scratch
Gradient descent is an optimization algorithm that follows the negative gradient of an objective function in order to locate the minimum of the function. A limitation of gradient descent is that it uses the same step size (learning rate) for each input variable. This can be a problem on objective functions that have different amounts of curvature in different dimensions, and in turn, may require a different sized step to a new point. Adaptive Gradients, or AdaGrad for short, is an extension of the gradient descent optimization algorithm that allows the step size in each dimension used by the optimization algorithm to be automatically adapted based on the gradients seen for the variable (partial derivatives) seen over the course of the search. In this tutorial, you will discover how to develop the gradient descent with adaptive gradients optimization algorithm from scratch.
SSSE: Efficiently Erasing Samples from Trained Machine Learning Models
Peste, Alexandra, Alistarh, Dan, Lampert, Christoph H.
The availability of large amounts of user-provided data has been key to the success of machine learning for many real-world tasks. Recently, an increasing awareness has emerged that users should be given more control about how their data is used. In particular, users should have the right to prohibit the use of their data for training machine learning systems, and to have it erased from already trained systems. While several sample erasure methods have been proposed, all of them have drawbacks which have prevented them from gaining widespread adoption. Most methods are either only applicable to very specific families of models, sacrifice too much of the original model's accuracy, or they have prohibitive memory or computational requirements. In this paper, we propose an efficient and effective algorithm, SSSE, for samples erasure, that is applicable to a wide class of machine learning models. From a second-order analysis of the model's loss landscape we derive a closed-form update step of the model parameters that only requires access to the data to be erased, not to the original training set. Experiments on three datasets, CelebFaces attributes (CelebA), Animals with Attributes 2 (AwA2) and CIFAR10, show that in certain cases SSSE can erase samples almost as well as the optimal, yet impractical, gold standard of training a new model from scratch with only the permitted data.
A Dataset and Method for Hallux Valgus Angle Estimation Based on Deep Learing
Xu, Ningyuan, Zhuang, Jiayan, Wu, Yaojun, Xiao, Jiangjian
Angular measurements is essential to make a resonable treatment for Hallux valgus (HV), a common forefoot deformity. However, it still depends on manual labeling and measurement, which is time-consuming and sometimes unreliable. Automating this process is a thing of concern. However, it lack of dataset and the keypoints based method which made a great success in pose estimation is not suitable for this field.To solve the problems, we made a dataset and developed an algorithm based on deep learning and linear regression. It shows great fitting ability to the ground truth.
MCMC Variational Inference via Uncorrected Hamiltonian Annealing
Given an unnormalized target distribution we want to obtain approximate samples from it and a tight lower bound on its (log) normalization constant log Z. Annealed Importance Sampling (AIS) with Hamiltonian MCMC is a powerful method that can be used to do this. Its main drawback is that it uses non-differentiable transition kernels, which makes tuning its many parameters hard. We propose a framework to use an AIS-like procedure with Uncorrected Hamiltonian MCMC, called Uncorrected Hamiltonian Annealing. Our method leads to tight and differentiable lower bounds on log Z. We show empirically that our method yields better performances than other competing approaches, and that the ability to tune its parameters using reparameterization gradients may lead to large performance improvements.
Ensembles of Randomized NNs for Pattern-based Time Series Forecasting
Dudek, Grzegorz, Peลka, Paweล
In this work, we propose an ensemble forecasting approach based on randomized neural networks. Improved randomized learning streamlines the fitting abilities of individual learners by generating network parameters in accordance with the data and target function features. A pattern-based representation of time series makes the proposed approach suitable for forecasting time series with multiple seasonality. We propose six strategies for controlling the diversity of ensemble members. Case studies conducted on four real-world forecasting problems verified the effectiveness and superior performance of the proposed ensemble forecasting approach. It outperformed statistical models as well as state-of-the-art machine learning models in terms of forecasting accuracy. The proposed approach has several advantages: fast and easy training, simple architecture, ease of implementation, high accuracy and the ability to deal with nonstationarity and multiple seasonality in time series.
Learning to Delegate for Large-scale Vehicle Routing
Li, Sirui, Yan, Zhongxia, Wu, Cathy
Vehicle routing problems (VRPs) are a class of combinatorial problems with wide practical applications. While previous heuristic or learning-based works achieve decent solutions on small problem instances of up to 100 customers, their performance does not scale to large problems. This article presents a novel learning-augmented local search algorithm to solve large-scale VRP. The method iteratively improves the solution by identifying appropriate subproblems and $\textit{delegating}$ their improvement to a black box subsolver. At each step, we leverage spatial locality to consider only a linear number of subproblems, rather than exponential. We frame subproblem selection as a regression problem and train a Transformer on a generated training set of problem instances. We show that our method achieves state-of-the-art performance, with a speed-up of up to 15 times over strong baselines, on VRPs with sizes ranging from 500 to 3000.
Multivariate functional group sparse regression: functional predictor selection
In this paper, we propose methods for functional predictor selection and the estimation of smooth functional coefficients simultaneously in a scalar-on-function regression problem under high-dimensional multivariate functional data setting. In particular, we develop two methods for functional group-sparse regression under a generic Hilbert space of infinite dimension. We show the convergence of algorithms and the consistency of the estimation and the selection (oracle property) under infinite-dimensional Hilbert spaces. Simulation studies show the effectiveness of the methods in both the selection and the estimation of functional coefficients. The applications to the functional magnetic resonance imaging (fMRI) reveal the regions of the human brain related to ADHD and IQ.
Robust Matrix Factorization with Grouping Effect
Jiang, Haiyan, Li, Shuyu, Zhang, Luwei, Xiong, Haoyi, Dou, Dejing
Although many techniques have been applied to matrix factorization (MF), they may not fully exploit the feature structure. In this paper, we incorporate the grouping effect into MF and propose a novel method called Robust Matrix Factorization with Grouping effect (GRMF). The grouping effect is a generalization of the sparsity effect, which conducts denoising by clustering similar values around multiple centers instead of just around 0. Compared with existing algorithms, the proposed GRMF can automatically learn the grouping structure and sparsity in MF without prior knowledge, by introducing a naturally adjustable non-convex regularization to achieve simultaneous sparsity and grouping effect. Specifically, GRMF uses an efficient alternating minimization framework to perform MF, in which the original non-convex problem is first converted into a convex problem through Difference-of-Convex (DC) programming, and then solved by Alternating Direction Method of Multipliers (ADMM). In addition, GRMF can be easily extended to the Non-negative Matrix Factorization (NMF) settings. Extensive experiments have been conducted using real-world data sets with outliers and contaminated noise, where the experimental results show that GRMF has promoted performance and robustness, compared to five benchmark algorithms.
Privacy Concerns in Chatbot Interactions: When to Trust and When to Worry
Saglam, Rahime Belen, Nurse, Jason R. C., Hodges, Duncan
Through advances in their conversational abilities, chatbots have started to request and process an increasing variety of sensitive personal information. The accurate disclosure of sensitive information is essential where it is used to provide advice and support to users in the healthcare and finance sectors. In this study, we explore users' concerns regarding factors associated with the use of sensitive data by chatbot providers. We surveyed a representative sample of 491 British citizens. Our results show that the user concerns focus on deleting personal information and concerns about their data's inappropriate use. We also identified that individuals were concerned about losing control over their data after a conversation with conversational agents. We found no effect from a user's gender or education but did find an effect from the user's age, with those over 45 being more concerned than those under 45. We also considered the factors that engender trust in a chatbot. Our respondents' primary focus was on the chatbot's technical elements, with factors such as the response quality being identified as the most critical factor. We again found no effect from the user's gender or education level; however, when we considered some social factors (e.g. avatars or perceived 'friendliness'), we found those under 45 years old rated these as more important than those over 45. The paper concludes with a discussion of these results within the context of designing inclusive, digital systems that support a wide range of users.