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Terpenes are a widespread class of natural products with significant chemical and biological diversity and many of these molecules have already made their way into medicines. Given the thousands of molecules already described, the full characterization of this chemical space can be a challenging task when relying in classical approaches. In this work we employ a data science-based approach to identify, compile and characterize the diversity of terpenes currently known in a systematic way. We worked with a natural product database, COCONUT, from which we extracted information for nearly 60000 terpenes. For these molecules, we conducted a subclass-by-subclass analysis in which we highlight several chemical and physical properties relevant to several fields, such as natural products chemistry, medicinal chemistry and drug discovery, among others. We were also interested in assessing the potential of this data for clustering and classification tasks. For clustering, we have applied and compared k-means with agglomerative clustering, both to the original data and following a step of dimensionality reduction. To this end, PCA, FastICA, Kernel PCA, t-SNE and UMAP were used and benchmarked. We also employed a number of methods for the purpose of classifying terpene subclasses using their physico-chemical descriptors. Light gradient boosting machine, k-nearest neighbors, random forests, Gaussian naiive Bayes and Multilayer perceptron, with the best-performing algorithms yielding accuracy, F1 score, precision and other metrics all over 0.9, thus showing the capabilities of these approaches for the classification of terpene subclasses.

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在統(tong)計中(zhong)(zhong),主(zhu)成分分析(PCA)是(shi)一種通過最大化(hua)每個(ge)維度(du)的(de)方(fang)(fang)差來將較高維度(du)空(kong)間中(zhong)(zhong)的(de)數據投影到較低維度(du)空(kong)間中(zhong)(zhong)的(de)方(fang)(fang)法(fa)。給定二維,三(san)維或(huo)更高維空(kong)間中(zhong)(zhong)的(de)點(dian)集(ji)合,可以將“最佳(jia)擬合”線(xian)定義為最小化(hua)從點(dian)到線(xian)的(de)平(ping)(ping)均平(ping)(ping)方(fang)(fang)距(ju)離的(de)線(xian)。可以從垂直于第(di)一條直線(xian)的(de)方(fang)(fang)向類似(si)地選擇下一條最佳(jia)擬合線(xian)。重復此過程會產生一個(ge)正交的(de)基(ji)礎,其中(zhong)(zhong)數據的(de)不同(tong)單個(ge)維度(du)是(shi)不相關的(de)。 這(zhe)些基(ji)向量稱為主(zhu)成分。

We study a multivariate version of trend filtering, called Kronecker trend filtering or KTF, for the case in which the design points form a lattice in $d$ dimensions. KTF is a natural extension of univariate trend filtering (Steidl et al., 2006; Kim et al., 2009; Tibshirani, 2014), and is defined by minimizing a penalized least squares problem whose penalty term sums the absolute (higher-order) differences of the parameter to be estimated along each of the coordinate directions. The corresponding penalty operator can be written in terms of Kronecker products of univariate trend filtering penalty operators, hence the name Kronecker trend filtering. Equivalently, one can view KTF in terms of an $\ell_1$-penalized basis regression problem where the basis functions are tensor products of falling factorial functions, a piecewise polynomial (discrete spline) basis that underlies univariate trend filtering. This paper is a unification and extension of the results in Sadhanala et al. (2016, 2017). We develop a complete set of theoretical results that describe the behavior of $k^{\mathrm{th}}$ order Kronecker trend filtering in $d$ dimensions, for every $k \geq 0$ and $d \geq 1$. This reveals a number of interesting phenomena, including the dominance of KTF over linear smoothers in estimating heterogeneously smooth functions, and a phase transition at $d=2(k+1)$, a boundary past which (on the high dimension-to-smoothness side) linear smoothers fail to be consistent entirely. We also leverage recent results on discrete splines from Tibshirani (2020), in particular, discrete spline interpolation results that enable us to extend the KTF estimate to any off-lattice location in constant-time (independent of the size of the lattice $n$).

The rapid recent progress in machine learning (ML) has raised a number of scientific questions that challenge the longstanding dogma of the field. One of the most important riddles is the good empirical generalization of overparameterized models. Overparameterized models are excessively complex with respect to the size of the training dataset, which results in them perfectly fitting (i.e., interpolating) the training data, which is usually noisy. Such interpolation of noisy data is traditionally associated with detrimental overfitting, and yet a wide range of interpolating models -- from simple linear models to deep neural networks -- have recently been observed to generalize extremely well on fresh test data. Indeed, the recently discovered double descent phenomenon has revealed that highly overparameterized models often improve over the best underparameterized model in test performance. Understanding learning in this overparameterized regime requires new theory and foundational empirical studies, even for the simplest case of the linear model. The underpinnings of this understanding have been laid in very recent analyses of overparameterized linear regression and related statistical learning tasks, which resulted in precise analytic characterizations of double descent. This paper provides a succinct overview of this emerging theory of overparameterized ML (henceforth abbreviated as TOPML) that explains these recent findings through a statistical signal processing perspective. We emphasize the unique aspects that define the TOPML research area as a subfield of modern ML theory and outline interesting open questions that remain.

Community detection, a fundamental task for network analysis, aims to partition a network into multiple sub-structures to help reveal their latent functions. Community detection has been extensively studied in and broadly applied to many real-world network problems. Classical approaches to community detection typically utilize probabilistic graphical models and adopt a variety of prior knowledge to infer community structures. As the problems that network methods try to solve and the network data to be analyzed become increasingly more sophisticated, new approaches have also been proposed and developed, particularly those that utilize deep learning and convert networked data into low dimensional representation. Despite all the recent advancement, there is still a lack of insightful understanding of the theoretical and methodological underpinning of community detection, which will be critically important for future development of the area of network analysis. In this paper, we develop and present a unified architecture of network community-finding methods to characterize the state-of-the-art of the field of community detection. Specifically, we provide a comprehensive review of the existing community detection methods and introduce a new taxonomy that divides the existing methods into two categories, namely probabilistic graphical model and deep learning. We then discuss in detail the main idea behind each method in the two categories. Furthermore, to promote future development of community detection, we release several benchmark datasets from several problem domains and highlight their applications to various network analysis tasks. We conclude with discussions of the challenges of the field and suggestions of possible directions for future research.

Deep neural networks have revolutionized many machine learning tasks in power systems, ranging from pattern recognition to signal processing. The data in these tasks is typically represented in Euclidean domains. Nevertheless, there is an increasing number of applications in power systems, where data are collected from non-Euclidean domains and represented as the graph-structured data with high dimensional features and interdependency among nodes. The complexity of graph-structured data has brought significant challenges to the existing deep neural networks defined in Euclidean domains. Recently, many studies on extending deep neural networks for graph-structured data in power systems have emerged. In this paper, a comprehensive overview of graph neural networks (GNNs) in power systems is proposed. Specifically, several classical paradigms of GNNs structures (e.g., graph convolutional networks, graph recurrent neural networks, graph attention networks, graph generative networks, spatial-temporal graph convolutional networks, and hybrid forms of GNNs) are summarized, and key applications in power systems such as fault diagnosis, power prediction, power flow calculation, and data generation are reviewed in detail. Furthermore, main issues and some research trends about the applications of GNNs in power systems are discussed.

This paper focuses on the expected difference in borrower's repayment when there is a change in the lender's credit decisions. Classical estimators overlook the confounding effects and hence the estimation error can be magnificent. As such, we propose another approach to construct the estimators such that the error can be greatly reduced. The proposed estimators are shown to be unbiased, consistent, and robust through a combination of theoretical analysis and numerical testing. Moreover, we compare the power of estimating the causal quantities between the classical estimators and the proposed estimators. The comparison is tested across a wide range of models, including linear regression models, tree-based models, and neural network-based models, under different simulated datasets that exhibit different levels of causality, different degrees of nonlinearity, and different distributional properties. Most importantly, we apply our approaches to a large observational dataset provided by a global technology firm that operates in both the e-commerce and the lending business. We find that the relative reduction of estimation error is strikingly substantial if the causal effects are accounted for correctly.

Machine learning (ML) has shown to advance the research field of quantum chemistry in almost any possible direction and has recently also entered the excited states to investigate the multifaceted photochemistry of molecules. In this paper, we pursue two goals: i) We show how ML can be used to model permanent dipole moments for excited states and transition dipole moments by adapting the charge model of [Chem. Sci., 2017, 8, 6924-6935], which was originally proposed for the permanent dipole moment vector of the electronic ground state. ii) We investigate the transferability of our excited-state ML models in chemical space, i.e., whether an ML model can predict properties of molecules that it has never been trained on and whether it can learn the different excited states of two molecules simultaneously. To this aim, we employ and extend our previously reported SchNarc approach for excited-state ML. We calculate UV absorption spectra from excited-state energies and transition dipole moments as well as electrostatic potentials from latent charges inferred by the ML model of the permanent dipole moment vectors. We train our ML models on CH$_2$NH$_2^+$ and C$_2$H$_4$, while predictions are carried out for these molecules and additionally for CHNH$_2$, CH$_2$NH, and C$_2$H$_5^+$. The results indicate that transferability is possible for the excited states.

Over the past few years, we have seen fundamental breakthroughs in core problems in machine learning, largely driven by advances in deep neural networks. At the same time, the amount of data collected in a wide array of scientific domains is dramatically increasing in both size and complexity. Taken together, this suggests many exciting opportunities for deep learning applications in scientific settings. But a significant challenge to this is simply knowing where to start. The sheer breadth and diversity of different deep learning techniques makes it difficult to determine what scientific problems might be most amenable to these methods, or which specific combination of methods might offer the most promising first approach. In this survey, we focus on addressing this central issue, providing an overview of many widely used deep learning models, spanning visual, sequential and graph structured data, associated tasks and different training methods, along with techniques to use deep learning with less data and better interpret these complex models --- two central considerations for many scientific use cases. We also include overviews of the full design process, implementation tips, and links to a plethora of tutorials, research summaries and open-sourced deep learning pipelines and pretrained models, developed by the community. We hope that this survey will help accelerate the use of deep learning across different scientific domains.

A robot that can carry out a natural-language instruction has been a dream since before the Jetsons cartoon series imagined a life of leisure mediated by a fleet of attentive robot helpers. It is a dream that remains stubbornly distant. However, recent advances in vision and language methods have made incredible progress in closely related areas. This is significant because a robot interpreting a natural-language navigation instruction on the basis of what it sees is carrying out a vision and language process that is similar to Visual Question Answering. Both tasks can be interpreted as visually grounded sequence-to-sequence translation problems, and many of the same methods are applicable. To enable and encourage the application of vision and language methods to the problem of interpreting visually-grounded navigation instructions, we present the Matterport3D Simulator -- a large-scale reinforcement learning environment based on real imagery. Using this simulator, which can in future support a range of embodied vision and language tasks, we provide the first benchmark dataset for visually-grounded natural language navigation in real buildings -- the Room-to-Room (R2R) dataset.

A robot that can carry out a natural-language instruction has been a dream since before the Jetsons cartoon series imagined a life of leisure mediated by a fleet of attentive robot helpers. It is a dream that remains stubbornly distant. However, recent advances in vision and language methods have made incredible progress in closely related areas. This is significant because a robot interpreting a natural-language navigation instruction on the basis of what it sees is carrying out a vision and language process that is similar to Visual Question Answering. Both tasks can be interpreted as visually grounded sequence-to-sequence translation problems, and many of the same methods are applicable. To enable and encourage the application of vision and language methods to the problem of interpreting visually-grounded navigation instructions, we present the Matterport3D Simulator -- a large-scale reinforcement learning environment based on real imagery. Using this simulator, which can in future support a range of embodied vision and language tasks, we provide the first benchmark dataset for visually-grounded natural language navigation in real buildings -- the Room-to-Room (R2R) dataset.

The task of {\em data fusion} is to identify the true values of data items (eg, the true date of birth for {\em Tom Cruise}) among multiple observed values drawn from different sources (eg, Web sites) of varying (and unknown) reliability. A recent survey\cite{LDL+12} has provided a detailed comparison of various fusion methods on Deep Web data. In this paper, we study the applicability and limitations of different fusion techniques on a more challenging problem: {\em knowledge fusion}. Knowledge fusion identifies true subject-predicate-object triples extracted by multiple information extractors from multiple information sources. These extractors perform the tasks of entity linkage and schema alignment, thus introducing an additional source of noise that is quite different from that traditionally considered in the data fusion literature, which only focuses on factual errors in the original sources. We adapt state-of-the-art data fusion techniques and apply them to a knowledge base with 1.6B unique knowledge triples extracted by 12 extractors from over 1B Web pages, which is three orders of magnitude larger than the data sets used in previous data fusion papers. We show great promise of the data fusion approaches in solving the knowledge fusion problem, and suggest interesting research directions through a detailed error analysis of the methods.

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