Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. The gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological processes most pertinent to their study. Approximately 68 bioinformatics enrichment tools that are currently available in the community are collected in this survey. Tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms. The comprehensive collections, unique tool classifications and associated questions/issues will provide a more comprehensive and up-to-date view regarding the advantages, pitfalls and recent trends in a simpler tool-class level rather than by a tool-by-tool approach. Thus, the survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.

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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

Modern mobile devices have access to a wealth of data suitable for learning models, which in turn can greatly improve the user experience on the device. For example, language models can improve speech recognition and text entry, and image models can automatically select good photos. However, this rich data is often privacy sensitive, large in quantity, or both, which may preclude logging to the data center and training there using conventional approaches. We advocate an alternative that leaves the training data distributed on the mobile devices, and learns a shared model by aggregating locally-computed updates. We term this decentralized approach Federated Learning. 
We present a practical method for the federated learning of deep networks based on iterative model averaging, and conduct an extensive empirical evaluation, considering five different model architectures and four datasets. These experiments demonstrate the approach is robust to the unbalanced and non-IID data distributions that are a defining characteristic of this setting. Communication costs are the principal constraint, and we show a reduction in required communication rounds by 10-100x as compared to synchronized stochastic gradient descent.

Communication-Efficient Learning of Deep Networks from Decentralized Data

The problem of privacy-preserving data analysis has a long history spanning multiple disciplines. As electronic data about individuals becomes increasingly detailed, and as technology enables ever more powerful collection and curation of these data, the need increases for a robust, meaningful, and mathematically rigorous definition of privacy, together with a computationally rich class of algorithms that satisfy this definition. Differential Privacy is such a definition.After motivating and discussing the meaning of differential privacy, the preponderance of this monograph is devoted to fundamental techniques for achieving differential privacy, and application of these techniques in creative combinations, using the query-release problem as an ongoing example. A key point is that, by rethinking the computational goal, one can often obtain far better results than would be achieved by methodically replacing each step of a non-private computation with a differentially private implementation. Despite some astonishingly powerful computational results, there are still fundamental limitations — not just on what can be achieved with differential privacy but on what can be achieved with any method that protects against a complete breakdown in privacy. Virtually all the algorithms discussed herein maintain differential privacy against adversaries of arbitrary computational power. Certain algorithms are computationally intensive, others are efficient. Computational complexity for the adversary and the algorithm are both discussed.We then turn from fundamentals to applications other than queryrelease, discussing differentially private methods for mechanism design and machine learning. The vast majority of the literature on differentially private algorithms considers a single, static, database that is subject to many analyses. Differential privacy in other models, including distributed databases and computations on data streams is discussed.Finally, we note that this work is meant as a thorough introduction to the problems and techniques of differential privacy, but is not intended to be an exhaustive survey — there is by now a vast amount of work in differential privacy, and we can cover only a small portion of it.

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The Algorithmic Foundations of Differential Privacy

Over the past five years a new approach to privacy-preserving data analysis has born fruit [13, 18, 7, 19, 5, 37, 35, 8, 32]. This approach differs from much (but not all!) of the related literature in the statistics, databases, theory, and cryptography communities, in that a formal and ad omnia privacy guarantee is defined, and the data analysis techniques presented are rigorously proved to satisfy the guarantee. The key privacy guarantee that has emerged is differential privacy. Roughly speaking, this ensures that (almost, and quantifiably) no risk is incurred by joining a statistical database.

In this survey, we recall the definition of differential privacy and two basic techniques for achieving it. We then show some interesting applications of these techniques, presenting algorithms for three specific tasks and three general results on differentially private learning.

/pdf/differential-privacy-a-survey-of-results-36msco9vw4.pdf

Differential privacy: a survey of results

Machine learning techniques based on neural networks are achieving remarkable results in a wide variety of domains. Often, the training of models requires large, representative datasets, which may be crowdsourced and contain sensitive information. The models should not expose private information in these datasets. Addressing this goal, we develop new algorithmic techniques for learning and a refined analysis of privacy costs within the framework of differential privacy. Our implementation and experiments demonstrate that we can train deep neural networks with non-convex objectives, under a modest privacy budget, and at a manageable cost in software complexity, training efficiency, and model quality.

Deep Learning with Differential Privacy

Learning problems form an important category of computational tasks that generalizes many of the computations researchers apply to large real-life data sets. We ask, What concept classes can be learned privately, namely, by an algorithm whose output does not depend too heavily on any one input or specific training example? More precisely, we investigate learning algorithms that satisfy differential privacy, a notion that provides strong confidentiality guarantees in contexts where aggregate information is released about a database containing sensitive information about individuals. Our goal is a broad understanding of the resources required for private learning in terms of samples, computation time, and interaction. We demonstrate that, ignoring computational constraints, it is possible to privately agnostically learn any concept class using a sample size approximately logarithmic in the cardinality of the concept class. Therefore, almost anything learnable is learnable privately: specifically, if a concept class is learnable by a (nonprivate) algorithm with polynomial sample complexity and output size, then it can be learned privately using a polynomial number of samples. We also present a computationally efficient private probabilistically approximately correct learner for the class of parity functions. This result dispels the similarity between learning with noise and private learning (both must be robust to small changes in inputs), since parity is thought to be very hard to learn given random classification noise. Local (or randomized response) algorithms are a practical class of private algorithms that have received extensive investigation. We provide a precise characterization of local private learning algorithms. We show that a concept class is learnable by a local algorithm if and only if it is learnable in the statistical query (SQ) model. Therefore, for local private learning algorithms, the similarity to learning with noise is stronger: local learning is equivalent to SQ learning, and SQ algorithms include most known noise-tolerant learning algorithms. Finally, we present a separation between the power of interactive and noninteractive local learning algorithms. Because of the equivalence to SQ learning, this result also separates adaptive and nonadaptive SQ learning.

What Can We Learn Privately

We present a large-scale analysis of mRNA coexpression based on 60 large human data sets containing a total of 3924 microarrays. We sought pairs of genes that were reliably coexpressed (based on the correlation of their expression profiles) in multiple data sets, establishing a high-confidence network of 8805 genes connected by 220,649 "coexpression links" that are observed in at least three data sets. Confirmed positive correlations between genes were much more common than confirmed negative correlations. We show that confirmation of coexpression in multiple data sets is correlated with functional relatedness, and show how cluster analysis of the network can reveal functionally coherent groups of genes. Our findings demonstrate how the large body of accumulated microarray data can be exploited to increase the reliability of inferences about gene function.

http://www.cs.columbia.edu/~homin/papers/LHSQP-2004.pdf

Coexpression Analysis of Human Genes Across Many Microarray Data Sets

Learning problems form an important category of computational tasks that generalizes many of the computations researchers apply to large real-life data sets. We ask: what concept classes can be learned privately, namely, by an algorithm whose output does not depend too heavily on any one input or specific training example? More precisely, we investigate learning algorithms that satisfy differential privacy, a notion that provides strong confidentiality guarantees in contexts where aggregate information is released about a database containing sensitive information about individuals. We demonstrate that, ignoring computational constraints, it is possible to privately agnostically learn any concept class using a sample size approximately logarithmic in the cardinality of the concept class. Therefore, almost anything learnable is learnable privately: specifically, if a concept class is learnable by a (non-private) algorithm with polynomial sample complexity and output size, then it can be learned privately using a polynomial number of samples. We also present a computationally efficient private PAC learner for the class of parity functions. Local (or randomized response) algorithms are a practical class of private algorithms that have received extensive investigation. We provide a precise characterization of local private learning algorithms. We show that a concept class is learnable by a local algorithm if and only if it is learnable in the statistical query (SQ) model. Finally, we present a separation between the power of interactive and noninteractive local learning algorithms.

Background: It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis uses the hypergeometric distribution (or a related technique) to look for "over-representation" of groups among genes selected as being differentially expressed or otherwise of interest based on a gene-by-gene analysis. However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported. Results: We introduce ErmineJ, a multiplatform user-friendly stand-alone software tool for the analysis of functionally-relevant sets of genes in the context of microarray gene expression data. ErmineJ implements multiple algorithms for gene set analysis, including over-representation and resampling-based methods that focus on gene scores or correlation of gene expression profiles. In addition to a graphical user interface, ErmineJ has a command line interface and an application programming interface that can be used to automate analyses. The graphical user interface includes tools for creating and modifying gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene expression data. ErmineJ comes with a complete user manual, and is open-source software licensed under the Gnu Public License. Conclusion: The availability of multiple analysis algorithms, together with a rich feature set and simple graphical interface, should make ErmineJ a useful addition to the biologist's informatics toolbox. ErmineJ is available from http://microarray.cu.genome.org.

/pdf/erminej-tool-for-functional-analysis-of-gene-expression-data-2hjzmabc5t.pdf

ErmineJ: Tool for functional analysis of gene expression data sets

Learning problems form an important category of computational tasks that generalizes many of the computations researchers apply to large real-life data sets. We ask: what concept classes can be learned privately, namely, by an algorithm whose output does not depend too heavily on any one input or specific training example? More precisely, we investigate learning algorithms that satisfy differential privacy, a notion that provides strong confidentiality guarantees in the contexts where aggregate information is released about a database containing sensitive information about individuals. We present several basic results that demonstrate general feasibility of private learning and relate several models previously studied separately in the contexts of privacy and standard learning.

http://www.cse.psu.edu/~sxr48/pubs/KLNRS-FOCS2008-published.pdf

Homin K. Lee

Papers

What Can We Learn Privately

Coexpression Analysis of Human Genes Across Many Microarray Data Sets

What Can We Learn Privately

ErmineJ: Tool for functional analysis of gene expression data sets

What Can We Learn Privately