The problem of estimating the structure of a graph from observed data is of growing interest in the context of high-throughput genomic data, and single-cell RNA sequencing in particular. These, however, are challenging applications, since the data consist of high-dimensional counts with high variance and over-abundance of zeros. Here, we present a general framework for learning the structure of a graph from single-cell RNA-seq data, based on the zero-inflated negative binomial distribution. We demonstrate with simulations that our approach is able to retrieve the structure of a graph in a variety of settings and we show the utility of the approach on real data.
相關內容
A technique that allows a formation-enforcing control (FEC) derived from graph rigidity theory to interface with a realistic relative localization system is proposed in this paper. Recent research in sensor-based multi-robot control has given rise to multiple modalities of mutual relative localization systems. In particular, vision-based relative localization has reached the stage where it can be carried onboard lightweight UAVs in order to retrieve the relative positions and relative orientations of cooperating units. A separate stream of development spawned distributed formation-enforcing control which can lead individual robots into a desired formation using relative localization of their neighbors. These two fields naturally complement each other by achieving real-world flights of UAVs in formation without the need for absolute localization in the world. However, real relative localization systems are, without exception, burdened by non-negligible sensory noise, which is typically not fully taken into account in formation-enforcing control algorithms. Such noise can lead to rapid changes in velocity, which further interferes with visual localization. Our approach provides a solution to these challenges, enabling practical deployment of FEC under realistic conditions, as we demonstrated in real-world experiments.
In an era where scientific experimentation is often costly, multi-fidelity emulation provides a powerful tool for predictive scientific computing. While there has been notable work on multi-fidelity modeling, existing models do not incorporate an important ``conglomerate'' property of multi-fidelity simulators, where the accuracies of different simulator components (modeling separate physics) are controlled by different fidelity parameters. Such conglomerate simulators are widely encountered in complex nuclear physics and astrophysics applications. We thus propose a new CONglomerate multi-FIdelity Gaussian process (CONFIG) model, which embeds this conglomerate structure within a novel non-stationary covariance function. We show that the proposed CONFIG model can capture prior knowledge on the numerical convergence of conglomerate simulators, which allows for cost-efficient emulation of multi-fidelity systems. We demonstrate the improved predictive performance of CONFIG over state-of-the-art models in a suite of numerical experiments and two applications, the first for emulation of cantilever beam deflection and the second for emulating the evolution of the quark-gluon plasma, which was theorized to have filled the Universe shortly after the Big Bang.
Spatially correlated data with an excess of zeros, usually referred to as zero-inflated spatial data, arise in many disciplines. Examples include count data, for instance, abundance (or lack thereof) of animal species and disease counts, as well as semi-continuous data like observed precipitation. Spatial two-part models are a flexible class of models for such data. Fitting two-part models can be computationally expensive for large data due to high-dimensional dependent latent variables, costly matrix operations, and slow mixing Markov chains. We describe a flexible, computationally efficient approach for modeling large zero-inflated spatial data using the projection-based intrinsic conditional autoregression (PICAR) framework. We study our approach, which we call PICAR-Z, through extensive simulation studies and two environmental data sets. Our results suggest that PICAR-Z provides accurate predictions while remaining computationally efficient. An important goal of our work is to allow researchers who are not experts in computation to easily build computationally efficient extensions to zero-inflated spatial models; this also allows for a more thorough exploration of modeling choices in two-part models than was previously possible. We show that PICAR-Z is easy to implement and extend in popular probabilistic programming languages such as nimble and stan.
This paper investigates in which cases continuous optimization for directed acyclic graph (DAG) structure learning can and cannot perform well and why this happens, and suggests possible directions to make the search procedure more reliable. Reisach et al. (2021) suggested that the remarkable performance of several continuous structure learning approaches is primarily driven by a high agreement between the order of increasing marginal variances and the topological order, and demonstrated that these approaches do not perform well after data standardization. We analyze this phenomenon for continuous approaches assuming equal and non-equal noise variances, and show that the statement may not hold in either case by providing counterexamples, justifications, and possible alternative explanations. We further demonstrate that nonconvexity may be a main concern especially for the non-equal noise variances formulation, while recent advances in continuous structure learning fail to achieve improvement in this case. Our findings suggest that future works should take into account the non-equal noise variances formulation to handle more general settings and for a more comprehensive empirical evaluation. Lastly, we provide insights into other aspects of the search procedure, including thresholding and sparsity, and show that they play an important role in the final solutions.
We consider a generalized poset sorting problem (GPS), in which we are given a query graph $G = (V, E)$ and an unknown poset $\mathcal{P}(V, \prec)$ that is defined on the same vertex set $V$, and the goal is to make as few queries as possible to edges in $G$ in order to fully recover $\mathcal{P}$, where each query $(u, v)$ returns the relation between $u, v$, i.e., $u \prec v$, $v \prec u$ or $u \not \sim v$. This generalizes both the poset sorting problem [Faigle et al., SICOMP 88] and the generalized sorting problem [Huang et al., FOCS 11]. We give algorithms with $\tilde{O}(n\cdot \mathrm{poly}(k))$ query complexity when $G$ is a complete bipartite graph or $G$ is stochastic under the \ER model, where $k$ is the \emph{width} of the poset, and these generalize [Daskalakis et al., SICOMP 11] which only studies complete graph $G$. Both results are based on a unified framework that reduces the poset sorting to partitioning the vertices with respect to a given pivot element, which may be of independent interest. Our study of GPS also leads to a new $\tilde{O}(n^{1 - 1 / (2W)})$ competitive ratio for the so-called weighted generalized sorting problem where $W$ is the number of distinct weights in the query graph. This problem was considered as an open question in [Charikar et al., JCSS 02], and our result makes important progress as it yields the first nontrivial $\tilde{O}(n)$ ratio for general weighted query graphs (and better ratio if $W$ is bounded). We obtain this via an $\tilde{O}(nk + n^{1.5})$ query complexity algorithm for the case where every edge in $G$ is guaranteed to be comparable in the poset, which generalizes the state-of-the-art $\tilde{O}(n^{1.5})$ bound for generalized sorting [Huang et al., FOCS 11].
Pre-training with offline data and online fine-tuning using reinforcement learning is a promising strategy for learning control policies by leveraging the best of both worlds in terms of sample efficiency and performance. One natural approach is to initialize the policy for online learning with the one trained offline. In this work, we introduce a policy expansion scheme for this task. After learning the offline policy, we use it as one candidate policy in a policy set. We then expand the policy set with another policy which will be responsible for further learning. The two policies will be composed in an adaptive manner for interacting with the environment. With this approach, the policy previously learned offline is fully retained during online learning, thus mitigating the potential issues such as destroying the useful behaviors of the offline policy in the initial stage of online learning while allowing the offline policy participate in the exploration naturally in an adaptive manner. Moreover, new useful behaviors can potentially be captured by the newly added policy through learning. Experiments are conducted on a number of tasks and the results demonstrate the effectiveness of the proposed approach.
The study of almost surely discrete random probability measures is an active line of research in Bayesian nonparametrics. The idea of assuming interaction across the atoms of the random probability measure has recently spurred significant interest in the context of Bayesian mixture models. This allows the definition of priors that encourage well separated and interpretable clusters. In this work, we provide a unified framework for the construction and the Bayesian analysis of random probability measures with interacting atoms, encompassing both repulsive and attractive behaviors. Specifically we derive closed-form expressions for the posterior distribution, the marginal and predictive distributions, which were not previously available except for the case of measures with i.i.d. atoms. We show how these quantities are fundamental both for prior elicitation and to develop new posterior simulation algorithms for hierarchical mixture models. Our results are obtained without any assumption on the finite point process that governs the atoms of the random measure. Their proofs rely on new analytical tools borrowed from the theory of Palm calculus and that might be of independent interest. We specialize our treatment to the classes of Poisson, Gibbs, and Determinantal point processes, as well as to the case of shot-noise Cox processes.
Classic algorithms and machine learning systems like neural networks are both abundant in everyday life. While classic computer science algorithms are suitable for precise execution of exactly defined tasks such as finding the shortest path in a large graph, neural networks allow learning from data to predict the most likely answer in more complex tasks such as image classification, which cannot be reduced to an exact algorithm. To get the best of both worlds, this thesis explores combining both concepts leading to more robust, better performing, more interpretable, more computationally efficient, and more data efficient architectures. The thesis formalizes the idea of algorithmic supervision, which allows a neural network to learn from or in conjunction with an algorithm. When integrating an algorithm into a neural architecture, it is important that the algorithm is differentiable such that the architecture can be trained end-to-end and gradients can be propagated back through the algorithm in a meaningful way. To make algorithms differentiable, this thesis proposes a general method for continuously relaxing algorithms by perturbing variables and approximating the expectation value in closed form, i.e., without sampling. In addition, this thesis proposes differentiable algorithms, such as differentiable sorting networks, differentiable renderers, and differentiable logic gate networks. Finally, this thesis presents alternative training strategies for learning with algorithms.
The Q-learning algorithm is known to be affected by the maximization bias, i.e. the systematic overestimation of action values, an important issue that has recently received renewed attention. Double Q-learning has been proposed as an efficient algorithm to mitigate this bias. However, this comes at the price of an underestimation of action values, in addition to increased memory requirements and a slower convergence. In this paper, we introduce a new way to address the maximization bias in the form of a "self-correcting algorithm" for approximating the maximum of an expected value. Our method balances the overestimation of the single estimator used in conventional Q-learning and the underestimation of the double estimator used in Double Q-learning. Applying this strategy to Q-learning results in Self-correcting Q-learning. We show theoretically that this new algorithm enjoys the same convergence guarantees as Q-learning while being more accurate. Empirically, it performs better than Double Q-learning in domains with rewards of high variance, and it even attains faster convergence than Q-learning in domains with rewards of zero or low variance. These advantages transfer to a Deep Q Network implementation that we call Self-correcting DQN and which outperforms regular DQN and Double DQN on several tasks in the Atari 2600 domain.
The chronological order of user-item interactions can reveal time-evolving and sequential user behaviors in many recommender systems. The items that users will interact with may depend on the items accessed in the past. However, the substantial increase of users and items makes sequential recommender systems still face non-trivial challenges: (1) the hardness of modeling the short-term user interests; (2) the difficulty of capturing the long-term user interests; (3) the effective modeling of item co-occurrence patterns. To tackle these challenges, we propose a memory augmented graph neural network (MA-GNN) to capture both the long- and short-term user interests. Specifically, we apply a graph neural network to model the item contextual information within a short-term period and utilize a shared memory network to capture the long-range dependencies between items. In addition to the modeling of user interests, we employ a bilinear function to capture the co-occurrence patterns of related items. We extensively evaluate our model on five real-world datasets, comparing with several state-of-the-art methods and using a variety of performance metrics. The experimental results demonstrate the effectiveness of our model for the task of Top-K sequential recommendation.
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191