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Joint species distribution models (JSDM) are among the most important statistical tools in community ecology. However, existing JSDMs cannot model mutual exclusion between species. We tackle this deficiency by developing a novel hierarchical JSDM with Dirichlet-Multinomial observation process for mutually exclusive species groups. We apply non-stationary multivariate Gaussian processes to describe species niche preferences and conduct Bayesian inference using Markov chain Monte Carlo. We propose decision theoretic model comparison and validation methods to assess the goodness of the proposed model and its alternatives in a case study on modeling vegetation cover in a boreal peatland in Finland. Our results show that ignoring the interspecific interactions and competition significantly reduces models predictive performance and through that leads to biased estimates for total cover of individual species and over all species combined. Models relative predictive performance also depends on the predictive task highlighting that model comparison and assessment method should resemble the true predictive task. Our results also demonstrate that the proposed joint species distribution model can be used to simultaneously infer interspecific correlations in niche preference as well as mutual competition for space and through that provide novel insight into ecological research.

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ACM/IEEE第23屆模型驅動工程語言和系統國際會議,是模型驅動軟件和系統工程的首要會議系列,由ACM-SIGSOFT和IEEE-TCSE支持組織。自1998年以來,模型涵蓋了建模的各個方面,從語言和方法到工具和應用程序。模特的參加者來自不同的背景,包括研究人員、學者、工程師和工業專業人士。MODELS 2019是一個論壇,參與者可以圍繞建模和模型驅動的軟件和系統交流前沿研究成果和創新實踐經驗。今年的版本將為建模社區提供進一步推進建模基礎的機會,并在網絡物理系統、嵌入式系統、社會技術系統、云計算、大數據、機器學習、安全、開源等新興領域提出建模的創新應用以及可持續性。 官網鏈接: · INTERACT · Networking · · 模型評估 ·
2022 年 1 月 7 日

This article studies the estimation of community memberships from non-binary pair interactions represented by an $N$-by-$N$ tensor whose values are elements of $\mathcal S$, where $N$ is the number of nodes and $\mathcal S$ is the space of the pairwise interactions between the nodes. As an information-theoretic benchmark, we study data sets generated by a non-binary stochastic block model, and derive fundamental information criteria for the recovery of the community memberships as $N \to \infty$. Examples of applications include weighted networks ($\mathcal S = \mathbb R$), link-labeled networks $(\mathcal S = \{0, 1, \dots, L\}$), multiplex networks $(\mathcal S = \{0,1\}^M$) and temporal networks ($\mathcal S = \{0,1\}^T$). For temporal interactions, we show that (i) even a small increase in $T$ may have a big impact on the recovery of community memberships, (ii) consistent recovery is possible even for very sparse data (e.g.\ bounded average degree) when $T$ is large enough. We also present several estimation algorithms, both offline and online, which fully utilise the temporal nature of the observed data. We analyse the accuracy of the proposed estimation algorithms under various assumptions on data sparsity and identifiability. Numerical experiments show that even a poor initial estimate (e.g., blind random guess) of the community assignment leads to high accuracy obtained by the online algorithm after a small number of iterations, and remarkably so also in very sparse regimes.

Spectral clustering has been one of the widely used methods for community detection in networks. However, large-scale networks bring computational challenges to the eigenvalue decomposition therein. In this paper, we study the spectral clustering using randomized sketching algorithms from a statistical perspective, where we typically assume the network data are generated from a stochastic block model that is not necessarily of full rank. To do this, we first use the recently developed sketching algorithms to obtain two randomized spectral clustering algorithms, namely, the random projection-based and the random sampling-based spectral clustering. Then we study the theoretical bounds of the resulting algorithms in terms of the approximation error for the population adjacency matrix, the misclassification error, and the estimation error for the link probability matrix. It turns out that, under mild conditions, the randomized spectral clustering algorithms lead to the same theoretical bounds as those of the original spectral clustering algorithm. We also extend the results to degree-corrected stochastic block models. Numerical experiments support our theoretical findings and show the efficiency of randomized methods. A new R package called Rclust is developed and made available to the public.

Longitudinal and survival sub-models are two building blocks for joint modelling of longitudinal and time to event data. Extensive research indicates separate analysis of these two processes could result in biased outputs due to their associations. Conditional independence between measurements of biomarkers and event time process given latent classes or random effects is a common approach for characterising the association between the two sub-models while taking the heterogeneity among the population into account. However, this assumption is tricky to validate because of the unobservable latent variables. Thus a Gaussian copula joint model with random effects is proposed to accommodate the scenarios where the conditional independence assumption is questionable. In our proposed model, the conventional joint model assuming conditional independence is a special case when the association parameter in the Gaussian copula shrinks to zero. Simulation studies and real data application are carried out to evaluate the performance of our proposed model. In addition, personalised dynamic predictions of survival probabilities are obtained based on the proposed model and comparisons are made to the predictions obtained under the conventional joint model.

Reaction networks are often used to model interacting species in fields such as biochemistry and ecology. When the counts of the species are sufficiently large, the dynamics of their concentrations are typically modeled via a system of differential equations. However, when the counts of some species are small, the dynamics of the counts are typically modeled stochastically via a discrete state, continuous time Markov chain. A key quantity of interest for such models is the probability mass function of the process at some fixed time. Since paths of such models are relatively straightforward to simulate, we can estimate the probabilities by constructing an empirical distribution. However, the support of the distribution is often diffuse across a high-dimensional state space, where the dimension is equal to the number of species. Therefore generating an accurate empirical distribution can come with a large computational cost. We present a new Monte Carlo estimator that fundamentally improves on the "classical" Monte Carlo estimator described above. It also preserves much of classical Monte Carlo's simplicity. The idea is basically one of conditional Monte Carlo. Our conditional Monte Carlo estimator has two parameters, and their choice critically affects the performance of the algorithm. Hence, a key contribution of the present work is that we demonstrate how to approximate optimal values for these parameters in an efficient manner. Moreover, we provide a central limit theorem for our estimator, which leads to approximate confidence intervals for its error.

Recent advances in Knowledge Graph Embedding (KGE) allow for representing entities and relations in continuous vector spaces. Some traditional KGE models leveraging additional type information can improve the representation of entities which however totally rely on the explicit types or neglect the diverse type representations specific to various relations. Besides, none of the existing methods is capable of inferring all the relation patterns of symmetry, inversion and composition as well as the complex properties of 1-N, N-1 and N-N relations, simultaneously. To explore the type information for any KG, we develop a novel KGE framework with Automated Entity TypE Representation (AutoETER), which learns the latent type embedding of each entity by regarding each relation as a translation operation between the types of two entities with a relation-aware projection mechanism. Particularly, our designed automated type representation learning mechanism is a pluggable module which can be easily incorporated with any KGE model. Besides, our approach could model and infer all the relation patterns and complex relations. Experiments on four datasets demonstrate the superior performance of our model compared to state-of-the-art baselines on link prediction tasks, and the visualization of type clustering provides clearly the explanation of type embeddings and verifies the effectiveness of our model.

Named entity recognition (NER) and entity linking (EL) are two fundamentally related tasks, since in order to perform EL, first the mentions to entities have to be detected. However, most entity linking approaches disregard the mention detection part, assuming that the correct mentions have been previously detected. In this paper, we perform joint learning of NER and EL to leverage their relatedness and obtain a more robust and generalisable system. For that, we introduce a model inspired by the Stack-LSTM approach (Dyer et al., 2015). We observe that, in fact, doing multi-task learning of NER and EL improves the performance in both tasks when comparing with models trained with individual objectives. Furthermore, we achieve results competitive with the state-of-the-art in both NER and EL.

Most deep learning-based models for speech enhancement have mainly focused on estimating the magnitude of spectrogram while reusing the phase from noisy speech for reconstruction. This is due to the difficulty of estimating the phase of clean speech. To improve speech enhancement performance, we tackle the phase estimation problem in three ways. First, we propose Deep Complex U-Net, an advanced U-Net structured model incorporating well-defined complex-valued building blocks to deal with complex-valued spectrograms. Second, we propose a polar coordinate-wise complex-valued masking method to reflect the distribution of complex ideal ratio masks. Third, we define a novel loss function, weighted source-to-distortion ratio (wSDR) loss, which is designed to directly correlate with a quantitative evaluation measure. Our model was evaluated on a mixture of the Voice Bank corpus and DEMAND database, which has been widely used by many deep learning models for speech enhancement. Ablation experiments were conducted on the mixed dataset showing that all three proposed approaches are empirically valid. Experimental results show that the proposed method achieves state-of-the-art performance in all metrics, outperforming previous approaches by a large margin.

We propose a new method of estimation in topic models, that is not a variation on the existing simplex finding algorithms, and that estimates the number of topics K from the observed data. We derive new finite sample minimax lower bounds for the estimation of A, as well as new upper bounds for our proposed estimator. We describe the scenarios where our estimator is minimax adaptive. Our finite sample analysis is valid for any number of documents (n), individual document length (N_i), dictionary size (p) and number of topics (K), and both p and K are allowed to increase with n, a situation not handled well by previous analyses. We complement our theoretical results with a detailed simulation study. We illustrate that the new algorithm is faster and more accurate than the current ones, although we start out with a computational and theoretical disadvantage of not knowing the correct number of topics K, while we provide the competing methods with the correct value in our simulations.

Deep reinforcement learning (RL) methods generally engage in exploratory behavior through noise injection in the action space. An alternative is to add noise directly to the agent's parameters, which can lead to more consistent exploration and a richer set of behaviors. Methods such as evolutionary strategies use parameter perturbations, but discard all temporal structure in the process and require significantly more samples. Combining parameter noise with traditional RL methods allows to combine the best of both worlds. We demonstrate that both off- and on-policy methods benefit from this approach through experimental comparison of DQN, DDPG, and TRPO on high-dimensional discrete action environments as well as continuous control tasks. Our results show that RL with parameter noise learns more efficiently than traditional RL with action space noise and evolutionary strategies individually.

Discrete random structures are important tools in Bayesian nonparametrics and the resulting models have proven effective in density estimation, clustering, topic modeling and prediction, among others. In this paper, we consider nested processes and study the dependence structures they induce. Dependence ranges between homogeneity, corresponding to full exchangeability, and maximum heterogeneity, corresponding to (unconditional) independence across samples. The popular nested Dirichlet process is shown to degenerate to the fully exchangeable case when there are ties across samples at the observed or latent level. To overcome this drawback, inherent to nesting general discrete random measures, we introduce a novel class of latent nested processes. These are obtained by adding common and group-specific completely random measures and, then, normalising to yield dependent random probability measures. We provide results on the partition distributions induced by latent nested processes, and develop an Markov Chain Monte Carlo sampler for Bayesian inferences. A test for distributional homogeneity across groups is obtained as a by product. The results and their inferential implications are showcased on synthetic and real data.

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