在生物学领域中包含高通量技术在近年来产生了大量的生物数据。现在，将这些巨大的数据转化为知识是计算生物学中的主要挑战。传统的数据分析方法未能执行任务。因此，研究人员正在转向基于机器学习的方法，用于分析高维大数据。在机器学习中，一旦使用训练数据集培训模型，它可以应用于独立的测试数据集。在当前时代，深度学习算法进一步促进机器学习在包括植物病毒学的几种生物领域中的应用。考虑到在理解植物病毒学中应用机器学习的重大进展，这一综述突出了关于机器学习的介绍笔记，并全面探讨了机器学习在诊断病毒疾病中的趋势和前景，了解宿主病毒的相互作用和植物病毒的出现。

A framework for creating and updating digital twins for dynamical systems from a library of physics-based functions is proposed. The sparse Bayesian machine learning is used to update and derive an interpretable expression for the digital twin. Two approaches for updating the digital twin are proposed. The first approach makes use of both the input and output information from a dynamical system, whereas the second approach utilizes output-only observations to update the digital twin. Both methods use a library of candidate functions representing certain physics to infer new perturbation terms in the existing digital twin model. In both cases, the resulting expressions of updated digital twins are identical, and in addition, the epistemic uncertainties are quantified. In the first approach, the regression problem is derived from a state-space model, whereas in the latter case, the output-only information is treated as a stochastic process. The concepts of It\^o calculus and Kramers-Moyal expansion are being utilized to derive the regression equation. The performance of the proposed approaches is demonstrated using highly nonlinear dynamical systems such as the crack-degradation problem. Numerical results demonstrated in this paper almost exactly identify the correct perturbation terms along with their associated parameters in the dynamical system. The probabilistic nature of the proposed approach also helps in quantifying the uncertainties associated with updated models. The proposed approaches provide an exact and explainable description of the perturbations in digital twin models, which can be directly used for better cyber-physical integration, long-term future predictions, degradation monitoring, and model-agnostic control.

Dengue fever is a virulent disease spreading over 100 tropical and subtropical countries in Africa, the Americas, and Asia. This arboviral disease affects around 400 million people globally, severely distressing the healthcare systems. The unavailability of a specific drug and ready-to-use vaccine makes the situation worse. Hence, policymakers must rely on early warning systems to control intervention-related decisions. Forecasts routinely provide critical information for dangerous epidemic events. However, the available forecasting models (e.g., weather-driven mechanistic, statistical time series, and machine learning models) lack a clear understanding of different components to improve prediction accuracy and often provide unstable and unreliable forecasts. This study proposes an ensemble wavelet neural network with exogenous factor(s) (XEWNet) model that can produce reliable estimates for dengue outbreak prediction for three geographical regions, namely San Juan, Iquitos, and Ahmedabad. The proposed XEWNet model is flexible and can easily incorporate exogenous climate variable(s) confirmed by statistical causality tests in its scalable framework. The proposed model is an integrated approach that uses wavelet transformation into an ensemble neural network framework that helps in generating more reliable long-term forecasts. The proposed XEWNet allows complex non-linear relationships between the dengue incidence cases and rainfall; however, mathematically interpretable, fast in execution, and easily comprehensible. The proposal's competitiveness is measured using computational experiments based on various statistical metrics and several statistical comparison tests. In comparison with statistical, machine learning, and deep learning methods, our proposed XEWNet performs better in 75% of the cases for short-term and long-term forecasting of dengue incidence.

The promise of Mobile Health (mHealth) is the ability to use wearable sensors to monitor participant physiology at high frequencies during daily life to enable temporally-precise health interventions. However, a major challenge is frequent missing data. Despite a rich imputation literature, existing techniques are ineffective for the pulsative signals which comprise many mHealth applications, and a lack of available datasets has stymied progress. We address this gap with PulseImpute, the first large-scale pulsative signal imputation challenge which includes realistic mHealth missingness models, an extensive set of baselines, and clinically-relevant downstream tasks. Our baseline models include a novel transformer-based architecture designed to exploit the structure of pulsative signals. We hope that PulseImpute will enable the ML community to tackle this significant and challenging task.

We propose a novel model agnostic data-driven reliability analysis framework for time-dependent reliability analysis. The proposed approach -- referred to as MAntRA -- combines interpretable machine learning, Bayesian statistics, and identifying stochastic dynamic equation to evaluate reliability of stochastically-excited dynamical systems for which the governing physics is \textit{apriori} unknown. A two-stage approach is adopted: in the first stage, an efficient variational Bayesian equation discovery algorithm is developed to determine the governing physics of an underlying stochastic differential equation (SDE) from measured output data. The developed algorithm is efficient and accounts for epistemic uncertainty due to limited and noisy data, and aleatoric uncertainty because of environmental effect and external excitation. In the second stage, the discovered SDE is solved using a stochastic integration scheme and the probability failure is computed. The efficacy of the proposed approach is illustrated on three numerical examples. The results obtained indicate the possible application of the proposed approach for reliability analysis of in-situ and heritage structures from on-site measurements.

Transformer layers, which use an alternating pattern of multi-head attention and multi-layer perceptron (MLP) layers, provide an effective tool for a variety of machine learning problems. As the transformer layers use residual connections to avoid the problem of vanishing gradients, they can be viewed as the numerical integration of a differential equation. In this extended abstract, we build upon this connection and propose a modification of the internal architecture of a transformer layer. The proposed model places the multi-head attention sublayer and the MLP sublayer parallel to each other. Our experiments show that this simple modification improves the performance of transformer networks in multiple tasks. Moreover, for the image classification task, we show that using neural ODE solvers with a sophisticated integration scheme further improves performance.

Consider a scenario in one-shot query-guided object localization where neither an image of the object nor the object category name is available as a query. In such a scenario, a hand-drawn sketch of the object could be a choice for a query. However, hand-drawn crude sketches alone, when used as queries, might be ambiguous for object localization, e.g., a sketch of a laptop could be confused for a sofa. On the other hand, a linguistic definition of the category, e.g., a small portable computer small enough to use in your lap" along with the sketch query, gives better visual and semantic cues for object localization. In this work, we present a multimodal query-guided object localization approach under the challenging open-set setting. In particular, we use queries from two modalities, namely, hand-drawn sketch and description of the object (also known as gloss), to perform object localization. Multimodal query-guided object localization is a challenging task, especially when a large domain gap exists between the queries and the natural images, as well as due to the challenge of combining the complementary and minimal information present across the queries. For example, hand-drawn crude sketches contain abstract shape information of an object, while the text descriptions often capture partial semantic information about a given object category. To address the aforementioned challenges, we present a novel cross-modal attention scheme that guides the region proposal network to generate object proposals relevant to the input queries and a novel orthogonal projection-based proposal scoring technique that scores each proposal with respect to the queries, thereby yielding the final localization results. ...

We consider the stochastic linear contextual bandit problem with high-dimensional features. We analyze the Thompson sampling (TS) algorithm, using special classes of sparsity-inducing priors (e.g. spike-and-slab) to model the unknown parameter, and provide a nearly optimal upper bound on the expected cumulative regret. To the best of our knowledge, this is the first work that provides theoretical guarantees of Thompson sampling in high dimensional and sparse contextual bandits. For faster computation, we use spike-and-slab prior to model the unknown parameter and variational inference instead of MCMC to approximate the posterior distribution. Extensive simulations demonstrate improved performance of our proposed algorithm over existing ones.

Labeling a module defective or non-defective is an expensive task. Hence, there are often limits on how much-labeled data is available for training. Semi-supervised classifiers use far fewer labels for training models, but there are numerous semi-supervised methods, including self-labeling, co-training, maximal-margin, and graph-based methods, to name a few. Only a handful of these methods have been tested in SE for (e.g.) predicting defects and even that, those tests have been on just a handful of projects. This paper takes a wide range of 55 semi-supervised learners and applies these to over 714 projects. We find that semi-supervised "co-training methods" work significantly better than other approaches. However, co-training needs to be used with caution since the specific choice of co-training methods needs to be carefully selected based on a user's specific goals. Also, we warn that a commonly-used co-training method ("multi-view"-- where different learners get different sets of columns) does not improve predictions (while adding too much to the run time costs 11 hours vs. 1.8 hours). Those cautions stated, we find using these "co-trainers," we can label just 2.5% of data, then make predictions that are competitive to those using 100% of the data. It is an open question worthy of future work to test if these reductions can be seen in other areas of software analytics. All the codes used and datasets analyzed during the current study are available in the https://GitHub.com/Suvodeep90/Semi_Supervised_Methods.

This work introduces the novel task of Source-free Multi-target Domain Adaptation and proposes adaptation framework comprising of \textbf{Co}nsistency with \textbf{N}uclear-Norm Maximization and \textbf{Mix}Up knowledge distillation (\textit{CoNMix}) as a solution to this problem. The main motive of this work is to solve for Single and Multi target Domain Adaptation (SMTDA) for the source-free paradigm, which enforces a constraint where the labeled source data is not available during target adaptation due to various privacy-related restrictions on data sharing. The source-free approach leverages target pseudo labels, which can be noisy, to improve the target adaptation. We introduce consistency between label preserving augmentations and utilize pseudo label refinement methods to reduce noisy pseudo labels. Further, we propose novel MixUp Knowledge Distillation (MKD) for better generalization on multiple target domains using various source-free STDA models. We also show that the Vision Transformer (VT) backbone gives better feature representation with improved domain transferability and class discriminability. Our proposed framework achieves the state-of-the-art (SOTA) results in various paradigms of source-free STDA and MTDA settings on popular domain adaptation datasets like Office-Home, Office-Caltech, and DomainNet. Project Page: https://sites.google.com/view/conmix-vcl