GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data

Background: Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biomarkers. While integration of differential expression statistics has been used to refine gene set enrichment analyses, such approaches are typically limited to single gene lists resulting from simple two-group comparisons or time-series analyses. In contrast, functional class scoring and machine learning approaches provide powerful alternative methods to leverage molecular measurements for pathway analyses, and to compare continuous and multi-level categorical factors. Results: We introduce GOexpress, a software package for scoring and summarising the capacity of gene ontology features to simultaneously classify samples from multiple experimental groups. GOexpress integrates normalised gene expression data (e.g., from microarray and RNA-seq experiments) and phenotypic information of individual samples with gene ontology annotations to derive a ranking of genes and gene ontology terms using a supervised learning approach. The default random forest algorithm allows interactions between all experimental factors, and competitive scoring of expressed genes to evaluate their relative importance in classifying predefined groups of samples. Conclusions: GOexpress enables rapid identification and visualisation of ontology-related gene panels that robustly classify groups of samples and supports both categorical (e.g., infection status, treatment) and continuous (e.g., time-series, drug concentrations) experimental factors. The use of standard Bioconductor extension packages and publicly available gene ontology annotations facilitates straightforward integration of GOexpress within existing computational biology pipelines.Department of Agriculture, Food and the MarineEuropean Commission - Seventh Framework Programme (FP7)Science Foundation IrelandUniversity College Dubli

Probabilistic Models over Ordered Partitions with Application in Learning to Rank

This paper addresses the general problem of modelling and learning rank data with ties. We propose a probabilistic generative model, that models the process as permutations over partitions. This results in super-exponential combinatorial state space with unknown numbers of partitions and unknown ordering among them. We approach the problem from the discrete choice theory, where subsets are chosen in a stagewise manner, reducing the state space per each stage significantly. Further, we show that with suitable parameterisation, we can still learn the models in linear time. We evaluate the proposed models on the problem of learning to rank with the data from the recently held Yahoo! challenge, and demonstrate that the models are competitive against well-known rivals.Comment: 19 pages, 2 figure

Fairness of Exposure in Rankings

Rankings are ubiquitous in the online world today. As we have transitioned from finding books in libraries to ranking products, jobs, job applicants, opinions and potential romantic partners, there is a substantial precedent that ranking systems have a responsibility not only to their users but also to the items being ranked. To address these often conflicting responsibilities, we propose a conceptual and computational framework that allows the formulation of fairness constraints on rankings in terms of exposure allocation. As part of this framework, we develop efficient algorithms for finding rankings that maximize the utility for the user while provably satisfying a specifiable notion of fairness. Since fairness goals can be application specific, we show how a broad range of fairness constraints can be implemented using our framework, including forms of demographic parity, disparate treatment, and disparate impact constraints. We illustrate the effect of these constraints by providing empirical results on two ranking problems.Comment: In Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, London, UK, 201

Optimal treatment allocations in space and time for on-line control of an emerging infectious disease

A key component in controlling the spread of an epidemic is deciding where, whenand to whom to apply an intervention.We develop a framework for using data to informthese decisionsin realtime.We formalize a treatment allocation strategy as a sequence of functions, oneper treatment period, that map up-to-date information on the spread of an infectious diseaseto a subset of locations where treatment should be allocated. An optimal allocation strategyoptimizes some cumulative outcome, e.g. the number of uninfected locations, the geographicfootprint of the disease or the cost of the epidemic. Estimation of an optimal allocation strategyfor an emerging infectious disease is challenging because spatial proximity induces interferencebetween locations, the number of possible allocations is exponential in the number oflocations, and because disease dynamics and intervention effectiveness are unknown at outbreak.We derive a Bayesian on-line estimator of the optimal allocation strategy that combinessimulation–optimization with Thompson sampling.The estimator proposed performs favourablyin simulation experiments. This work is motivated by and illustrated using data on the spread ofwhite nose syndrome, which is a highly fatal infectious disease devastating bat populations inNorth America