Ambiguous model learning made unambiguous with 1/f priors

What happens to the optimal interpretation of noisy data when there exists more than one equally plausible interpretation of the data? In a Bayesian model-learning framework the answer depends on the prior expectations of the dynamics of the model parameter that is to be inferred from the data. Local time constraints on the priors are insufficient to pick one interpretation over another. On the other hand, nonlocal time constraints, induced by a $1/f$ noise spectrum of the priors, is shown to permit learning of a specific model parameter even when there are infinitely many equally plausible interpretations of the data. This transition is inferred by a remarkable mapping of the model estimation problem to a dissipative physical system, allowing the use of powerful statistical mechanical methods to uncover the transition from indeterminate to determinate model learning.Comment: 8 pages, 2 figure

Prediction of light aircraft interior sound pressure level using the room equation

The room equation is investigated for predicting interior sound level. The method makes use of an acoustic power balance, by equating net power flow into the cabin volume to power dissipated within the cabin using the room equation. The sound power level transmitted through the panels was calculated by multiplying the measured space averaged transmitted intensity for each panel by its surface area. The sound pressure level was obtained by summing the mean square sound pressures radiated from each panel. The data obtained supported the room equation model in predicting the cabin interior sound pressure level

Parametric inference in the large data limit using maximally informative models

Motivated by data-rich experiments in transcriptional regulation and sensory neuroscience, we consider the following general problem in statistical inference. When exposed to a high-dimensional signal S, a system of interest computes a representation R of that signal which is then observed through a noisy measurement M. From a large number of signals and measurements, we wish to infer the "filter" that maps S to R. However, the standard method for solving such problems, likelihood-based inference, requires perfect a priori knowledge of the "noise function" mapping R to M. In practice such noise functions are usually known only approximately, if at all, and using an incorrect noise function will typically bias the inferred filter. Here we show that, in the large data limit, this need for a pre-characterized noise function can be circumvented by searching for filters that instead maximize the mutual information I[M;R] between observed measurements and predicted representations. Moreover, if the correct filter lies within the space of filters being explored, maximizing mutual information becomes equivalent to simultaneously maximizing every dependence measure that satisfies the Data Processing Inequality. It is important to note that maximizing mutual information will typically leave a small number of directions in parameter space unconstrained. We term these directions "diffeomorphic modes" and present an equation that allows these modes to be derived systematically. The presence of diffeomorphic modes reflects a fundamental and nontrivial substructure within parameter space, one that is obscured by standard likelihood-based inference.Comment: To appear in Neural Computatio

Equitability, mutual information, and the maximal information coefficient

Reshef et al. recently proposed a new statistical measure, the "maximal information coefficient" (MIC), for quantifying arbitrary dependencies between pairs of stochastic quantities. MIC is based on mutual information, a fundamental quantity in information theory that is widely understood to serve this need. MIC, however, is not an estimate of mutual information. Indeed, it was claimed that MIC possesses a desirable mathematical property called "equitability" that mutual information lacks. This was not proven; instead it was argued solely through the analysis of simulated data. Here we show that this claim, in fact, is incorrect. First we offer mathematical proof that no (non-trivial) dependence measure satisfies the definition of equitability proposed by Reshef et al.. We then propose a self-consistent and more general definition of equitability that follows naturally from the Data Processing Inequality. Mutual information satisfies this new definition of equitability while MIC does not. Finally, we show that the simulation evidence offered by Reshef et al. was artifactual. We conclude that estimating mutual information is not only practical for many real-world applications, but also provides a natural solution to the problem of quantifying associations in large data sets

Kerfuffle: a web tool for multi-species gene colocalization analysis

The evolutionary pressures that underlie the large-scale functional organization of the genome are not well understood in eukaryotes. Recent evidence suggests that functionally similar genes may colocalize (cluster) in the eukaryotic genome, suggesting the role of chromatin-level gene regulation in shaping the physical distribution of coordinated genes. However, few of the bioinformatic tools currently available allow for a systematic study of gene colocalization across several, evolutionarily distant species. Kerfuffle is a web tool designed to help discover, visualize, and quantify the physical organization of genomes by identifying significant gene colocalization and conservation across the assembled genomes of available species (currently up to 47, from humans to worms). Kerfuffle only requires the user to specify a list of human genes and the names of other species of interest. Without further input from the user, the software queries the e!Ensembl BioMart server to obtain positional information and discovers homology relations in all genes and species specified. Using this information, Kerfuffle performs a multi-species clustering analysis, presents downloadable lists of clustered genes, performs Monte Carlo statistical significance calculations, estimates how conserved gene clusters are across species, plots histograms and interactive graphs, allows users to save their queries, and generates a downloadable visualization of the clusters using the Circos software. These analyses may be used to further explore the functional roles of gene clusters by interrogating the enriched molecular pathways associated with each cluster.Comment: BMC Bioinformatics, In pres

Occupational therapists' perceptions of predischarge home assessments with older adults in acute care

Predischarge occupational therapy home assessments are routinely performed with older adults in Europe, Australia and North America. Their primary aim is to facilitate a timely and safe discharge from hospital. However, there is a lack of published research on this topic, especially studies exploring occupational therapists' perceptions of home assessments. The paper aims to redress this by describing occupational therapists' perceptions of predischarge occupational therapy home assessments with older adults in acute care. All occupational therapists who undertook home assessments in an acute care hospital with older adults during the duration of the study period were invited to complete a reflective diary. In total, 15 reflective diaries were completed by six therapists. The data were analysed using thematic content analysis. The findings suggest that home assessments were carried out because of mobility or environmental concerns. Satisfaction and dissatisfaction with the outcome of the home assessment were related to the incidents that occurred during the assessment. Some of the occupational therapists' anxieties were related to the older adults' level of functioning or ill health, and the older adults' own concerns did have an impact upon the therapists' expectations of the home assessment process

Estimating mutual information and multi--information in large networks

We address the practical problems of estimating the information relations that characterize large networks. Building on methods developed for analysis of the neural code, we show that reliable estimates of mutual information can be obtained with manageable computational effort. The same methods allow estimation of higher order, multi--information terms. These ideas are illustrated by analyses of gene expression, financial markets, and consumer preferences. In each case, information theoretic measures correlate with independent, intuitive measures of the underlying structures in the system

Dietary impacts on intestinal microbial community and cardiovascular diseases

OBJECTIVE: Chapter 1: Investigate the impact that trimethylamine N-oxide (TMAO), dietary contribution of short chain fatty acids (SCFAs), and role of bile acids has on cardiovascular health and disease. Chapter 2: Evaluate the association between intakes of dietary protein from both animal and plant sources on lipid profile changes. METHODS: Chapter 1: Literature review using PubMed and EMBASE to search for published studies for dietary intake or supplementation impact on TMAO or its precursors and their role in the development or prevention of cardiovascular diseases. Chapter 2: Framingham Offspring Study, prospective cohort study using statistical methods to investigate the changes in lipid profiles with dietary animal and plant protein. PUBLISHED STUDIES/RESULTS: Chapter 1: The increased risk of cardiovascular diseases (CVD) correlates with increasing levels of circulating levels of TMAO. The risk of CVD in animal and human studies have shown to be distinct in groups with and without CVD, leading to either beneficial or adverse effects from the consumption of dietary phosphatidylcholine, choline, betaine, carnitine, or intact TMAO. A Western dietary approach has been linked with the development of dyslipidemia whereas, adherence to a Mediterranean diet reduces the risk of major CVD events. The dietary precursors involved in TMA production by the gut microbiota then respectively to TMAO through hepatic enzyme FMO3 provide both beneficial and detrimental effects. Mechanisms of action for TMAO on CVD risk involves changes associated with cholesterol and sterol metabolism leading to foam cell formation, and enhancement of scavenger receptors, CD36 and scavenger receptor-A, on macrophages affects the rate of cholesterol influx and efflux. Choline derived in a dose-dependent manner from eggs improves cardiometabolic biomarkers with no changes in fasting TMAO. Further, choline from eggs also increases the lipoprotein particle size for both HDL-cholesterol and LDL-cholesterol increasing the rate of reverse cholesterol transport (RCT). Betaine concentrations in humans are associated with health outcomes based on an individual’s overall systemic health at baseline. Supplementation with L-carnitine produced favorable effects in lean subjects compared to obese subjects, improved cardiometabolic status in patients with myocardial infarction, and improved lipid profiles among individuals with prevalent coronary heart disease (CAD). Fish consumption increases concentrations of TMAO due to its high levels of intact TMAO though, protective effects for CVD are obtained from fatty fish providing omega-3-fatty acids impacting positive changes in the lipid profiles. Antibiotic therapy suppresses the gut microbiota and eliminates the production of TMA from the dietary precursors that are required. Chapter 2: Men and women both showed a decreasing trend for LDL-cholesterol as the tertiles increased for animal protein intake. Plant protein intake showed a similar decreasing trend for LDL-cholesterol with increasing protein tertiles; however, men had inconsistency among the trend whereas women had a consistent decreasing trend. HDL-cholesterol content increases in males and females with both increasing tertiles for animal and plant protein, though plant protein presented much stronger effects when compared to animal protein. Log-transformed triglycerides were inversely associated with increasing animal protein intake, men revealing greater effects than females. Plant protein intake showed a stronger effect than animal protein intake in an increasing trend in the log of triglycerides over the 6 exams. Overall, total cholesterol content varied at each examination period, animal protein intake tertiles displayed decreased level of total cholesterol, there was a greater effect in men than women. Higher intake of plant protein had a similar trend to animal protein intake showing a decrease in the total cholesterol concentration. Women had a much greater effect in reducing total cholesterol with plant protein when compared to men. CONCLUSION: Chapter 1: Multiple human and animal trials addressed in the association between diet, dietary precursors, gut microbiota composition, and their derived metabolite TMAO on the presence or absence of CVD display contradictory results and identifies areas needing further study. Chapter 2: Regardless of the source of protein, the lipid profiles improved with the intake of either animal or plant protein as the protein intake was increased over the tertiles in each exam. The overall trend with increasing animal or plant protein intake led to decrease in LDL-cholesterol, log transformed triglycerides, and total cholesterol whereas, the HDL-cholesterol concentrations were increased. Men favored animal protein intake to show greater reductions in LDL-cholesterol and total cholesterol, whereas women favored plant protein. The increase in HDL-cholesterol concentration was stronger with the intake of plant protein in men and women. The changes in log transformed triglycerides were similar in men and women