TROM: A Testing-based Method for Finding Transcriptomic Similarity of Biological Samples

Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic data. An important question is to understand the conservation and differentiation of biological processes in different species. We propose a testing-based method TROM (Transcriptome Overlap Measure) for comparing transcriptomes within or between different species, and provide a different perspective to interpret transcriptomic similarity in contrast to traditional correlation analyses. Specifically, the TROM method focuses on identifying associated genes that capture molecular characteristics of biological samples, and subsequently comparing the biological samples by testing the overlap of their associated genes. We use simulation and real data studies to demonstrate that TROM is more powerful in identifying similar transcriptomes and more robust to stochastic gene expression noise than Pearson and Spearman correlations. We apply TROM to compare the developmental stages of six Drosophila species, C. elegans, S. purpuratus, D. rerio and mouse liver, and find interesting correspondence patterns that imply conserved gene expression programs in the development of these species. The TROM method is available as an R package on CRAN (http://cran.r-project.org/) with manuals and source codes available at http://www.stat.ucla.edu/ jingyi.li/software-and-data/trom.html

Accelerating federated learning via momentum gradient descent

Federated learning (FL) provides a communication-efficient approach to solve machine learning problems concerning distributed data, without sending raw data to a central server. However, existing works on FL only utilize first-order gradient descent (GD) and do not consider the preceding iterations to gradient update which can potentially accelerate convergence. In this article, we consider momentum term which relates to the last iteration. The proposed momentum federated learning (MFL) uses momentum gradient descent (MGD) in the local update step of FL system. We establish global convergence properties of MFL and derive an upper bound on MFL convergence rate. Comparing the upper bounds on MFL and FL convergence rates, we provide conditions in which MFL accelerates the convergence. For different machine learning models, the convergence performance of MFL is evaluated based on experiments with MNIST and CIFAR-10 datasets. Simulation results confirm that MFL is globally convergent and further reveal significant convergence improvement over FL

Partitioned Sampling of Public Opinions Based on Their Social Dynamics

Public opinion polling is usually done by random sampling from the entire population, treating individual opinions as independent. In the real world, individuals' opinions are often correlated, e.g., among friends in a social network. In this paper, we explore the idea of partitioned sampling, which partitions individuals with high opinion similarities into groups and then samples every group separately to obtain an accurate estimate of the population opinion. We rigorously formulate the above idea as an optimization problem. We then show that the simple partitions which contain only one sample in each group are always better, and reduce finding the optimal simple partition to a well-studied Min-r-Partition problem. We adapt an approximation algorithm and a heuristic algorithm to solve the optimization problem. Moreover, to obtain opinion similarity efficiently, we adapt a well-known opinion evolution model to characterize social interactions, and provide an exact computation of opinion similarities based on the model. We use both synthetic and real-world datasets to demonstrate that the partitioned sampling method results in significant improvement in sampling quality and it is robust when some opinion similarities are inaccurate or even missing

Enabling Multi-level Trust in Privacy Preserving Data Mining

Privacy Preserving Data Mining (PPDM) addresses the problem of developing accurate models about aggregated data without access to precise information in individual data record. A widely studied \emph{perturbation-based PPDM} approach introduces random perturbation to individual values to preserve privacy before data is published. Previous solutions of this approach are limited in their tacit assumption of single-level trust on data miners. In this work, we relax this assumption and expand the scope of perturbation-based PPDM to Multi-Level Trust (MLT-PPDM). In our setting, the more trusted a data miner is, the less perturbed copy of the data it can access. Under this setting, a malicious data miner may have access to differently perturbed copies of the same data through various means, and may combine these diverse copies to jointly infer additional information about the original data that the data owner does not intend to release. Preventing such \emph{diversity attacks} is the key challenge of providing MLT-PPDM services. We address this challenge by properly correlating perturbation across copies at different trust levels. We prove that our solution is robust against diversity attacks with respect to our privacy goal. That is, for data miners who have access to an arbitrary collection of the perturbed copies, our solution prevent them from jointly reconstructing the original data more accurately than the best effort using any individual copy in the collection. Our solution allows a data owner to generate perturbed copies of its data for arbitrary trust levels on-demand. This feature offers data owners maximum flexibility.Comment: 20 pages, 5 figures. Accepted for publication in IEEE Transactions on Knowledge and Data Engineerin