Information Surfaces in Systems Biology and Applications to Engineering Sustainable Agriculture

Systems biology of plants offers myriad opportunities and many challenges in modeling. A number of technical challenges stem from paucity of computational methods for discovery of the most fundamental properties of complex dynamical systems. In systems engineering, eigen-mode analysis have proved to be a powerful approach. Following this philosophy, we introduce a new theory that has the benefits of eigen-mode analysis, while it allows investigation of complex dynamics prior to estimation of optimal scales and resolutions. Information Surfaces organizes the many intricate relationships among "eigen-modes" of gene networks at multiple scales and via an adaptable multi-resolution analytic approach that permits discovery of the appropriate scale and resolution for discovery of functions of genes in the model plant Arabidopsis. Applications are many, and some pertain developments of crops that sustainable agriculture requires.Comment: 24 Pages, DoCEIS 1

Learning from High-Dimensional Multivariate Signals.

Modern measurement systems monitor a growing number of variables at low cost. In the problem of characterizing the observed measurements, budget limitations usually constrain the number n of samples that one can acquire, leading to situations where the number p of variables is much larger than n. In this situation, classical statistical methods, founded on the assumption that n is large and p is fixed, fail both in theory and in practice. A successful approach to overcome this problem is to assume a parsimonious generative model characterized by a number k of parameters, where k is much smaller than p. In this dissertation we develop algorithms to fit low-dimensional generative models and extract relevant information from high-dimensional, multivariate signals. First, we define extensions of the well-known Scalar Shrinkage-Thresholding Operator, that we name Multidimensional and Generalized Shrinkage-Thresholding Operators, and show that these extensions arise in numerous algorithms for structured-sparse linear and non-linear regression. Using convex optimization techniques, we show that these operators, defined as the solutions to a class of convex, non-differentiable, optimization problems have an equivalent convex, low-dimensional reformulation. Our equivalence results shed light on the behavior of a general class of penalties that includes classical sparsity-inducing penalties such as the LASSO and the Group LASSO. In addition, our reformulation leads in some cases to new efficient algorithms for a variety of high-dimensional penalized estimation problems. Second, we introduce two new classes of low-dimensional factor models that account for temporal shifts commonly occurring in multivariate signals. Our first contribution, called Order Preserving Factor Analysis, can be seen as an extension of the non-negative, sparse matrix factorization model to allow for order-preserving temporal translations in the data. We develop an efficient descent algorithm to fit this model using techniques from convex and non-convex optimization. Our second contribution extends Principal Component Analysis to the analysis of observations suffering from circular shifts, and we call it Misaligned Principal Component Analysis. We quantify the effect of the misalignments in the spectrum of the sample covariance matrix in the high-dimensional regime and develop simple algorithms to jointly estimate the principal components and the misalignment parameters.Ph.D.Electrical Engineering: SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/91544/1/atibaup_1.pd

Bloggers Behavior and Emergent Communities in Blog Space

Interactions between users in cyberspace may lead to phenomena different from those observed in common social networks. Here we analyse large data sets about users and Blogs which they write and comment, mapped onto a bipartite graph. In such enlarged Blog space we trace user activity over time, which results in robust temporal patterns of user--Blog behavior and the emergence of communities. With the spectral methods applied to the projection on weighted user network we detect clusters of users related to their common interests and habits. Our results suggest that different mechanisms may play the role in the case of very popular Blogs. Our analysis makes a suitable basis for theoretical modeling of the evolution of cyber communities and for practical study of the data, in particular for an efficient search of interesting Blog clusters and further retrieval of their contents by text analysis

Algorithmic methods to infer the evolutionary trajectories in cancer progression

The genomic evolution inherent to cancer relates directly to a renewed focus on the voluminous next-generation sequencing data and machine learning for the inference of explanatory models of how the (epi)genomic events are choreographed in cancer initiation and development. However, despite the increasing availability of multiple additional -omics data, this quest has been frustrated by various theoretical and technical hurdles, mostly stemming from the dramatic heterogeneity of the disease. In this paper, we build on our recent work on the 'selective advantage' relation among driver mutations in cancer progression and investigate its applicability to the modeling problem at the population level. Here, we introduce PiCnIc (Pipeline for Cancer Inference), a versatile, modular, and customizable pipeline to extract ensemble-level progression models from cross-sectional sequenced cancer genomes. The pipeline has many translational implications because it combines state-of-the-art techniques for sample stratification, driver selection, identification of fitness-equivalent exclusive alterations, and progression model inference. We demonstrate PiCnIc's ability to reproduce much of the current knowledge on colorectal cancer progression as well as to suggest novel experimentally verifiable hypotheses

Schema-conformant memories are preferentially consolidated during REM sleep

Memory consolidation is most commonly described by the standard model, which proposes an initial binding role for the hippocampus which diminishes over time as intracortical connections are strengthened. Recent evidence suggests that slow wave sleep (SWS) plays an essential role in this process. Existing animal and human studies have suggested that memories which fit tightly into an existing knowledge framework or schema might use an alternative consolidation route in which the medial prefrontal cortex takes on the binding role. In this study we sought to investigate the role of sleep in this process using a novel melodic memory task. Participants were asked to remember 32 melodies, half of which conformed to a tonal schema present in all enculturated listeners, and half of which did not fit with this schema. After a 24-h consolidation interval, participants were asked to remember a further 32 melodies, before being given a recognition test in which melodies from both sessions were presented alongside some previously unheard foils. Participants remembered schema-conformant melodies better than non-conformant ones. This was much more strongly the case for consolidated melodies, suggesting that consolidation over a 24-h period preferentially consolidated schema-conformant items. Overnight sleep was monitored between the sessions, and the extent of the consolidation benefit for schema-conformant items was associated with both the amount of REM sleep obtained and EEG theta power in frontal and central regions during REM sleep. Overall our data suggest that REM sleep plays a crucial role in the rapid consolidation of schema-conformant items. This finding is consistent with previous results from animal studies and the SLIMM model of Van Kesteren, Ruiter, Fernández, and Henson (2012), and suggest that REM sleep, rather than SWS, may be involved in an alternative pathway of consolidation for schema-conformant memories. Copyright © 2015. Published by Elsevier Inc

Recommender Systems

The ongoing rapid expansion of the Internet greatly increases the necessity of effective recommender systems for filtering the abundant information. Extensive research for recommender systems is conducted by a broad range of communities including social and computer scientists, physicists, and interdisciplinary researchers. Despite substantial theoretical and practical achievements, unification and comparison of different approaches are lacking, which impedes further advances. In this article, we review recent developments in recommender systems and discuss the major challenges. We compare and evaluate available algorithms and examine their roles in the future developments. In addition to algorithms, physical aspects are described to illustrate macroscopic behavior of recommender systems. Potential impacts and future directions are discussed. We emphasize that recommendation has a great scientific depth and combines diverse research fields which makes it of interests for physicists as well as interdisciplinary researchers.Comment: 97 pages, 20 figures (To appear in Physics Reports