748 research outputs found
Learning Latent Variable Gaussian Graphical Model for Biomolecular Network with Low Sample Complexity
Learning a Gaussian graphical model with latent variables is ill posed when there is insufficient sample complexity, thus having to be appropriately regularized. A common choice is convex l1 plus nuclear norm to regularize the searching process. However, the best estimator performance is not always achieved with these additive convex regularizations, especially when the sample complexity is low. In this paper, we consider a concave additive regularization which does not require the strong irrepresentable condition. We use concave regularization to correct the intrinsic estimation biases from Lasso and nuclear penalty as well. We establish the proximity operators for our concave regularizations, respectively, which induces sparsity and low rankness. In addition, we extend our method to also allow the decomposition of fused structure-sparsity plus low rankness, providing a powerful tool for models with temporal information. Specifically, we develop a nontrivial modified alternating direction method of multipliers with at least local convergence. Finally, we use both synthetic and real data to validate the excellence of our method. In the application of reconstructing two-stage cancer networks, “the Warburg effect” can be revealed directly
Moment-Based Variational Inference for Markov Jump Processes
We propose moment-based variational inference as a flexible framework for
approximate smoothing of latent Markov jump processes. The main ingredient of
our approach is to partition the set of all transitions of the latent process
into classes. This allows to express the Kullback-Leibler divergence between
the approximate and the exact posterior process in terms of a set of moment
functions that arise naturally from the chosen partition. To illustrate
possible choices of the partition, we consider special classes of jump
processes that frequently occur in applications. We then extend the results to
parameter inference and demonstrate the method on several examples.Comment: Accepted by the 36th International Conference on Machine Learning
(ICML 2019
Machine Learning in Molecular Dynamics Simulations of Biomolecular Systems
Machine learning (ML) has emerged as a pervasive tool in science,
engineering, and beyond. Its success has also led to several synergies with
molecular dynamics (MD) simulations, which we use to identify and characterize
the major metastable states of molecular systems. Typically, we aim to
determine the relative stabilities of these states and how rapidly they
interchange. This information allows mechanistic descriptions of molecular
mechanisms, enables a quantitative comparison with experiments, and facilitates
their rational design. ML impacts all aspects of MD simulations -- from
analyzing the data and accelerating sampling to defining more efficient or more
accurate simulation models.Comment: 36 pages, 4 figure
Tensor Regression
Regression analysis is a key area of interest in the field of data analysis
and machine learning which is devoted to exploring the dependencies between
variables, often using vectors. The emergence of high dimensional data in
technologies such as neuroimaging, computer vision, climatology and social
networks, has brought challenges to traditional data representation methods.
Tensors, as high dimensional extensions of vectors, are considered as natural
representations of high dimensional data. In this book, the authors provide a
systematic study and analysis of tensor-based regression models and their
applications in recent years. It groups and illustrates the existing
tensor-based regression methods and covers the basics, core ideas, and
theoretical characteristics of most tensor-based regression methods. In
addition, readers can learn how to use existing tensor-based regression methods
to solve specific regression tasks with multiway data, what datasets can be
selected, and what software packages are available to start related work as
soon as possible. Tensor Regression is the first thorough overview of the
fundamentals, motivations, popular algorithms, strategies for efficient
implementation, related applications, available datasets, and software
resources for tensor-based regression analysis. It is essential reading for all
students, researchers and practitioners of working on high dimensional data.Comment: 187 pages, 32 figures, 10 table
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