Inference for population genetics models is hindered by computationally intractable likelihoods. While this issue is tackled by likelihood-free methods, these approaches typically rely on hand-crafted summary statistics of the data. In complex settings, designing and selecting suitable summary statistics is problematic and results are very sensitive to such choices. In this paper, we learn the first exchangeable feature representation for population genetic data to work directly with genotype data. This is achieved by means of a novel Bayesian likelihood-free inference framework, where a permutation-invariant convolutional neural network learns the inverse functional relationship from the data to the posterior. We leverage access to scientific simulators to learn such likelihood-free function mappings, and establish a general framework for inference in a variety of simulation-based tasks. We demonstrate the power of our method on the recombination hotspot testing problem, outperforming the state-of-the-art.
The inferential accuracy and scalability of these methods can be improved by exploiting symmetries in the input data. Permutation-invariant models have been previously studied in machine learning for SVMs @cite_30 and, recently, gained a surge of interest in the deep learning literature. Recent work on designing architectures for exchangeable data include , , and , which exploit parameter sharing to encode invariances. To our knowledge, no prior work has been done on learning feature representations for exchangeable population genetic data.
@cite_30
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We study the problem of classifying actions of human subjects using depth movies generated by Kinect or other depth sensors. Representing human body as dynamical skeletons, we study the evolution of their (skeletons’) shapes as trajectories on Kendall’s shape manifold. The action data is typically corrupted by large variability in execution rates within and across subjects and, thus, causing major problems in statistical analyses. To address that issue, we adopt a recently-developed framework of [1] , [2] to this problem domain. Here, the variable execution rates correspond to re-parameterizations of trajectories, and one uses a parameterization-invariant metric for aligning, comparing, averaging, and modeling trajectories. This is based on a combination of transported square-root vector fields (TSRVFs) of trajectories and the standard Euclidean norm, that allows computational efficiency. We develop a comprehensive suite of computational tools for this application domain: smoothing and denoising skeleton trajectories using median filtering, up- and down-sampling actions in time domain, simultaneous temporal-registration of multiple actions, and extracting invertible Euclidean representations of actions. Due to invertibility these Euclidean representations allow both discriminative and generative models for statistical analysis. For instance, they can be used in a SVM-based classification of original actions, as demonstrated here using MSR Action-3D, MSR Daily Activity and 3D Action Pairs datasets. Using only the skelet al information, we achieve state-of-the-art classification results on these datasets.