RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments. We present RSEM, an user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data. RSEM outputs abundance estimates, 95% credibility intervals, and visualization files and can also simulate RNA-Seq data. In contrast to other existing tools, the software does not require a reference genome. Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes. On simulated and real data sets, RSEM has superior or comparable performance to quantification methods that rely on a reference genome. Taking advantage of RSEM's ability to effectively use ambiguously-mapping reads, we show that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads. On the other hand, estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired-end reads, depending on the number of possible splice forms for each gene. RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.

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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

THE DESIGN AND ANALYSIS OF EXPERIMENTS. By Oscar Kempthorne. New York, John Wiley and Sons, Inc., 1952. 631 pp. $8.50. This book by a teacher of statistics (as well as a consultant for \"experimenters\") is a comprehensive study of the philosophical background for the statistical design of experiment. It is necessary to have some facility with algebraic notation and manipulation to be able to use the volume intelligently. The problems are presented from the theoretical point of view, without such practical examples as would be helpful for those not acquainted with mathematics. The mathematical justification for the techniques is given. As a somewhat advanced treatment of the design and analysis of experiments, this volume will be interesting and helpful for many who approach statistics theoretically as well as practically. With emphasis on the \"why,\" and with description given broadly, the author relates the subject matter to the general theory of statistics and to the general problem of experimental inference. MARGARET J. ROBERTSON

The Design and Analysis of Experiments

Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathematically principled analysis software. TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression analysis of high-throughput mRNA sequencing (RNA-seq) data. Together, they allow biologists to identify new genes and new splice variants of known ones, as well as compare gene and transcript expression under two or more conditions. This protocol describes in detail how to use TopHat and Cufflinks to perform such analyses. It also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-seq analysis results. Although the procedure assumes basic informatics skills, these tools assume little to no background with RNA-seq analysis and are meant for novices and experts alike. The protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results. The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time.

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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such clusters, or communities, can be considered as fairly independent compartments of a graph, playing a similar role like, e. g., the tissues or the organs in the human body. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. This problem is very hard and not yet satisfactorily solved, despite the huge effort of a large interdisciplinary community of scientists working on it over the past few years. We will attempt a thorough exposition of the topic, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists, from the discussion of crucial issues like the significance of clustering and how methods should be tested and compared against each other, to the description of applications to real networks.

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Community detection in graphs

The goal of dimensionality reduction is to embed high-dimensional data in a low-dimensional space while preserving structure in the data relevant to exploratory data analysis such as clusters. However, existing dimensionality reduction methods often either fail to separate clusters due to the crowding problem or can only separate clusters at a single resolution. We develop a new approach to dimensionality reduction: tree preserving embedding. Our approach uses the topological notion of connectedness to separate clusters at all resolutions. We provide a formal guarantee of cluster separation for our approach that holds for finite samples. Our approach requires no parameters and can handle general types of data, making it easy to use in practice and suggesting new strategies for robust data visualization.

https://www.pnas.org/content/pnas/108/41/16916.full.pdf

Tree preserving embedding

We consider the problem of quantifying the degree of coordination between transcription and translation, in yeast. Several studies have reported a surprising lack of coordination over the years, in organisms as different as yeast and humans, using diverse technologies. However, a close look at this literature suggests that the lack of reported correlation may not reflect the biology of regulation. These reports do not control for between-study biases and structure in the measurement errors, ignore key aspects of how the data connect to the estimand, and systematically underestimate the correlation as a consequence. Here, we design a careful meta-analysis of 27 yeast datasets, supported by a multilevel model, full uncertainty quantification, a suite of sensitivity analyses, and novel theory, to produce a more accurate estimate of the correlation between mRNA and protein levels—a proxy for coordination. From a statistical perspective, this problem motivates new theory on the impact of noise, model misspecif...

/pdf/estimating-a-structured-covariance-matrix-from-multilab-42v87po85c.pdf

Estimating a Structured Covariance Matrix From Multilab Measurements in High-Throughput Biology

Hidden variables, evolving over time, appear in multiple settings, where it is valuable to recover them, typically from observed sums. Our driving application is 'network tomography', where we need to estimate the origin-destination (OD) traffic flows to determine, e.g., who is communicating with whom in a local area network. This information allows network engineers and managers to solve problems in design, routing, configuration debugging, monitoring and pricing. Unfortunately the direct measurement of the OD traffic is usually difficult, or even impossible; instead, we can easily measure the loads on every link, that is, sums of desirable OD flows.In this paper we propose i-FILTER, a method to solve this problem, which improves the state-of-the-art by (a) introducing explicit time dependence, and by (b) using realistic, non-Gaussian marginals in the statistical models for the traffic flows, as never attempted before. We give experiments on real data, where i-FILTER scales linearly with new observations and out-performs the best existing solutions, in a wide variety of settings. Specifically, on real network traffic measured at CMU, and at AT&T, i-FILTER reduced the estimation errors between 15% and 46% in all cases.

/pdf/recovering-latent-time-series-from-their-observed-sums-4wzbvr662u.pdf

Recovering latent time-series from their observed sums: network tomography with particle filters.

We systematically investigate issues due to mis-specification that arise in estimating causal effects when (treatment) interference is informed by a network available pre-intervention, i.e., in situations where the outcome of a unit may depend on the treatment assigned to other units. We develop theory for several forms of interference through the concept of exposure neighborhood, and develop the corresponding semi-parametric representation for potential outcomes as a function of the exposure neighborhood. Using this representation, we extend the definition of two popular classes of causal estimands, marginal and average causal effects, to the case of network interference. We characterize the bias and variance one incurs when combining classical randomization strategies (namely, Bernoulli, Completely Randomized, and Cluster Randomized designs) and estimators (namely, difference-in-means and Horvitz-Thompson) used to estimate average treatment effect and on the total treatment effect, under misspecification due to interference. We illustrate how difference-in-means estimators can have arbitrarily large bias when estimating average causal effects, depending on the form and strength of interference, which is unknown at design stage. Horvitz-Thompson (HT) estimators are unbiased when the correct weights are specified. Here, we derive the HT weights for unbiased estimation of different estimands, and illustrate how they depend on the design, the form of interference, which is unknown at design stage, and the estimand. More importantly, we show that HT estimators are in-admissible for a large class of randomization strategies, in the presence of interference. We develop new model-assisted and model-dependent strategies to improve HT estimators, and we develop new randomization strategies for estimating the average treatment effect and total treatment effect.

A systematic investigation of classical causal inference strategies under mis-specification due to network interference.

Over the past three years I have been working on probabilistic models of multivariate attributes and relations. My work suggests a probabilistic framework and a general modeling approach to complex and evolving networks, which is based on the four concepts of mixed membership, motifs, dynamics & integration. In this thesis, I present such a framework and discuss its properties. In particular, the main goal of the research is to establish the essential elements of formal models of complexity that reconcile the global properties of a system with local phenomena of interest, in a generative fashion. 
A solution to the global/local trade-off is to express complexity through hierarchical mixtures of simple patterns, i.e., motifs, that evolve over time. Complex global behavior emerges from the combination of local interaction patterns and their dynamics. I discuss the extent to which this novel framework incorporates, generalizes, and extends other probabilistic approaches present in the literature, and argue that it provides the foundations of a statistical theory of (random) graphs. 
A major part of the effort is devoted to the analysis of modeling issues related to the four essential aspects listed above, in the context of applications to social and biological networks. I also investigate theoretical and computational issues such as the geometrical intuition of the latent allocation task---an important inference objective shared by the various models encompassed by this framework.

/pdf/bayesian-mixed-membership-models-of-complex-and-evolving-2uc78zln7d.pdf

Edoardo M. Airoldi

Papers

Tree preserving embedding

Estimating a Structured Covariance Matrix From Multilab Measurements in High-Throughput Biology

Recovering latent time-series from their observed sums: network tomography with particle filters.

A systematic investigation of classical causal inference strategies under mis-specification due to network interference.

Bayesian mixed-membership models of complex and evolving networks