 Award ID(s):
 1829681
 Publication Date:
 NSFPAR ID:
 10125764
 Journal Name:
 Advances in neural information processing systems
 ISSN:
 10495258
 Sponsoring Org:
 National Science Foundation
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Obeid, I. ; Selesnik, I. ; Picone, J. (Ed.)The Neuronix highperformance computing cluster allows us to conduct extensive machine learning experiments on big data [1]. This heterogeneous cluster uses innovative scheduling technology, Slurm [2], that manages a network of CPUs and graphics processing units (GPUs). The GPU farm consists of a variety of processors ranging from lowend consumer grade devices such as the Nvidia GTX 970 to higherend devices such as the GeForce RTX 2080. These GPUs are essential to our research since they allow extremely computeintensive deep learning tasks to be executed on massive data resources such as the TUH EEG Corpus [2]. We use TensorFlow [3] as the core machine learning library for our deep learning systems, and routinely employ multiple GPUs to accelerate the training process. Reproducible results are essential to machine learning research. Reproducibility in this context means the ability to replicate an existing experiment – performance metrics such as error rates should be identical and floatingpoint calculations should match closely. Three examples of ways we typically expect an experiment to be replicable are: (1) The same job run on the same processor should produce the same results each time it is run. (2) A job run on a CPU and GPU should producemore »

Finding overcomplete latent representations of data has applications in data analysis, signal processing, machine learning, theoretical neuroscience and many other fields. In an overcomplete representation, the number of latent features exceeds the data dimensionality, which is useful when the data is undersampled by the measurements (compressed sensing or information bottlenecks in neural systems) or composed from multiple complete sets of linear features, each spanning the data space. Independent Components Analysis (ICA) is a linear technique for learning sparse latent representations, which typically has a lower computational cost than sparse coding, a linear generative model which requires an iterative, nonlinear inference step. While well suited for finding complete representations, we show that overcompleteness poses a challenge to existing ICA algorithms. Specifically, the coherence control used in existing ICA and other dictionary learning algorithms, necessary to prevent the formation of duplicate dictionary features, is illsuited in the overcomplete case. We show that in the overcomplete case, several existing ICA algorithms have undesirable global minima that maximize coherence. We provide a theoretical explanation of these failures and, based on the theory, propose improved coherence control costs for overcomplete ICA algorithms. Further, by comparing ICA algorithms to the computationally more expensive sparse coding onmore »

The complexity, dynamics, and scale of data acquired by modern biotechnology increasingly favor modelfree computational methods that make minimal assumptions about underlying biological mechanisms. For example, singlecell transcriptome and proteome data have a throughput several orders more than bulk methods. Many modelfree statistical methods for pattern discovery such as mutual information and chisquared tests, however, require discrete data. Most discretization methods minimize squared errors for each variable independently, not necessarily retaining joint patterns. To address this issue, we present a joint grid discretization algorithm that preserves clusters in the original data. We evaluated this algorithm on simulated data to show its advantage over other methods in maintaining clusters as measured by the adjusted Rand index. We also show it promotes global functional patterns over independent patterns. On singlecell proteome and transcriptome of leukemia and healthy blood, joint grid discretization captured known proteintoRNA regulatory relationships, while revealing previously unknown interactions. As such, the joint grid discretization is applicable as a data transformation step in associative, functional, and causal inference of molecular interactions fundamental to systems biology. The developed software is publicly available at https://cran.rproject.org/package=GridOnClusters

Abstract Background Statistical geneticists employ simulation to estimate the power of proposed studies, test new analysis tools, and evaluate properties of causal models. Although there are existing trait simulators, there is ample room for modernization. For example, most phenotype simulators are limited to Gaussian traits or traits transformable to normality, while ignoring qualitative traits and realistic, nonnormal trait distributions. Also, modern computer languages, such as Julia, that accommodate parallelization and cloudbased computing are now mainstream but rarely used in older applications. To meet the challenges of contemporary big studies, it is important for geneticists to adopt new computational tools.
Results We present , an opensource Julia package that makes it trivial to quickly simulate phenotypes under a variety of genetic architectures. This package is integrated into our OpenMendel suite for easy downstream analyses. Julia was purposebuilt for scientific programming and provides tremendous speed and memory efficiency, easy access to multiCPU and GPU hardware, and to distributed and cloudbased parallelization. is designed to encourage flexible trait simulation, including via the standard devices of applied statistics, generalized linear models (GLMs) and generalized linear mixed models (GLMMs). also accommodates many study designs: unrelateds, sibships, pedigrees, or a mixture of all three. (Of course, for datamore »
Conclusion The package has three main advantages. (1) It leverages the computational efficiency and ease of use of Julia to provide extremely fast, straightforward simulation of even the most complex genetic models, including GLMs and GLMMs. (2) It can be operated entirely within, but is not limited to, the integrated analysis pipeline of OpenMendel. And finally (3), by allowing a wider range of more realistic phenotype models, brings power calculations and diagnostic tools closer to what investigators might see in realworld analyses.

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