We demonstrate a PointNet-based deep learning approach to classify local structure in molecular simulations, learning features directly from atomic coordinates.

In this paper, we introduce a generalized value iteration network (GVIN), which is an end-to-end neural network planning module. GVIN emulates the value iteration algorithm by using a novel graph convolution operator, which enables GVIN to learn and plan on irregular spatial graphs. We propose three novel differentiable kernels as graph convolution operators and show that the embedding-based kernel achieves the best performance. Furthermore, we present episodic Q-learning, an improvement upon traditional n-step Q-learning that stabilizes training for VIN and GVIN. Lastly, we evaluate GVIN on planning problems in 2D mazes, irregular graphs, and real-world street networks, showing that GVIN generalizes well for both arbitrary graphs and unseen graphs of larger scaleand outperforms a naive generalization of VIN (discretizing a spatial graph into a 2D image).

Given the complex relationship between gene expression and phenotypic outcomes, computationally efficient approaches are needed to sift through large high-dimensional datasets in order to identify biologically relevant biomarkers. In this report, we describe a method of identifying the most salient biomarker genes in a dataset, which we call “candidate genes”, by evaluating the ability of gene combinations to classify samples from a dataset, which we call “classification potential”. Our algorithm, Gene Oracle, uses a neural network to test user defined gene sets for polygenic classification potential and then uses a combinatorial approach to further decompose selected gene sets into candidate and non-candidate biomarker genes. We tested this algorithm on curated gene sets from the Molecular Signatures Database (MSigDB) quantified in RNAseq gene expression matrices obtained from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) data repositories. First, we identified which MSigDB Hallmark subsets have significant classification potential for both the TCGA and GTEx datasets. Then, we identified the most discriminatory candidate biomarker genes in each Hallmark gene set and provide evidence that the improved biomarker potential of these genes may be due to reduced functional complexity.

Summary We introduce the Transcriptome State Perturbation Generator (TSPG) as a novel deep-learning method to identify changes in genomic expression that occur between tissue states using generative adversarial networks. TSPG learns the transcriptome perturbations from RNA-sequencing data required to shift from a source to a target class. We apply TSPG as an effective method of detecting biologically relevant alternate expression patterns between normal and tumor human tissue samples. We demonstrate that the application of TSPG to expression data obtained from a biopsy sample of a patient's kidney cancer can identify patient-specific differentially expressed genes between their individual tumor sample and a target class of healthy kidney gene expression. By utilizing TSPG in a precision medicine application in which the patient sample is not replicated (i.e., ), we present a novel technique of determining significant transcriptional aberrations that can be used to help identify potential targeted therapies.

In this paper, we introduce a generalized value iteration network (GVIN), which is an end-to-end neural network planning module. GVIN emulates the value iteration algorithm by using a novel graph convolution operator, which enables GVIN to learn and plan on irregular spatial graphs. We propose three novel differentiable kernels as graph convolution operators and show that the embedding-based kernel achieves the best performance. Furthermore, we present episodic Q-learning, an improvement upon traditional n-step Q-learning that stabilizes training for VIN and GVIN. Lastly, we evaluate GVIN on planning problems in 2D mazes, irregular graphs, and realworld street networks, showing that GVIN generalizes well for both arbitrary graphs and unseen graphs of larger scale and outperforms a naive generalization of VIN (discretizing a spatial graph into a 2D image).