A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks

An explosion of high-throughput DNA sequencing in the past decade has led to a surge of interest in population-scale inference with whole-genome data. Recent work in population genetics has centered on designing inference methods for relatively simple model classes, and few scalable general-purpose inference techniques exist for more realistic, complex models. To achieve this, two inferential challenges need to be addressed: (1) population data are exchangeable, calling for methods that efficiently exploit the symmetries of the data, and (2) computing likelihoods is intractable as it requires integrating over a set of correlated, extremely high-dimensional latent variables. These challenges are traditionally tackled by likelihood-free methods that use scientific simulators to generate datasets and reduce them to hand-designed, permutation-invariant summary statistics, often leading to inaccurate inference. In this work, we develop an exchangeable neural network that performs summary statistic-free, likelihood-free inference. Our framework can be applied in a black-box fashion across a variety of simulation-based tasks, both within and outside biology. We demonstrate the power of our approach on the recombination hotspot testing problem, outperforming the state-of-the-art.Comment: 9 pages, 8 figure

Pruning Error Minimization in Least Squares Support Vector Machines

The support vector machine (SVM) is a method for classification and for function approximation. This method commonly makes use of an /spl epsi/-insensitive cost function, meaning that errors smaller than /spl epsi/ remain unpunished. As an alternative, a least squares support vector machine (LSSVM) uses a quadratic cost function. When the LSSVM method is used for function approximation, a nonsparse solution is obtained. The sparseness is imposed by pruning, i.e., recursively solving the approximation problem and subsequently omitting data that has a small error in the previous pass. However, omitting data with a small approximation error in the previous pass does not reliably predict what the error will be after the sample has been omitted. In this paper, a procedure is introduced that selects from a data set the training sample that will introduce the smallest approximation error when it will be omitted. It is shown that this pruning scheme outperforms the standard one

Computing Vertex Centrality Measures in Massive Real Networks with a Neural Learning Model

Vertex centrality measures are a multi-purpose analysis tool, commonly used in many application environments to retrieve information and unveil knowledge from the graphs and network structural properties. However, the algorithms of such metrics are expensive in terms of computational resources when running real-time applications or massive real world networks. Thus, approximation techniques have been developed and used to compute the measures in such scenarios. In this paper, we demonstrate and analyze the use of neural network learning algorithms to tackle such task and compare their performance in terms of solution quality and computation time with other techniques from the literature. Our work offers several contributions. We highlight both the pros and cons of approximating centralities though neural learning. By empirical means and statistics, we then show that the regression model generated with a feedforward neural networks trained by the Levenberg-Marquardt algorithm is not only the best option considering computational resources, but also achieves the best solution quality for relevant applications and large-scale networks. Keywords: Vertex Centrality Measures, Neural Networks, Complex Network Models, Machine Learning, Regression ModelComment: 8 pages, 5 tables, 2 figures, version accepted at IJCNN 2018. arXiv admin note: text overlap with arXiv:1810.1176