Are Elephants Bigger than Butterflies? Reasoning about Sizes of Objects

Human vision greatly benefits from the information about sizes of objects. The role of size in several visual reasoning tasks has been thoroughly explored in human perception and cognition. However, the impact of the information about sizes of objects is yet to be determined in AI. We postulate that this is mainly attributed to the lack of a comprehensive repository of size information. In this paper, we introduce a method to automatically infer object sizes, leveraging visual and textual information from web. By maximizing the joint likelihood of textual and visual observations, our method learns reliable relative size estimates, with no explicit human supervision. We introduce the relative size dataset and show that our method outperforms competitive textual and visual baselines in reasoning about size comparisons.Comment: To appear in AAAI 201

Bayesian estimation of Differential Transcript Usage from RNA-seq data

Next generation sequencing allows the identification of genes consisting of differentially expressed transcripts, a term which usually refers to changes in the overall expression level. A specific type of differential expression is differential transcript usage (DTU) and targets changes in the relative within gene expression of a transcript. The contribution of this paper is to: (a) extend the use of cjBitSeq to the DTU context, a previously introduced Bayesian model which is originally designed for identifying changes in overall expression levels and (b) propose a Bayesian version of DRIMSeq, a frequentist model for inferring DTU. cjBitSeq is a read based model and performs fully Bayesian inference by MCMC sampling on the space of latent state of each transcript per gene. BayesDRIMSeq is a count based model and estimates the Bayes Factor of a DTU model against a null model using Laplace's approximation. The proposed models are benchmarked against the existing ones using a recent independent simulation study as well as a real RNA-seq dataset. Our results suggest that the Bayesian methods exhibit similar performance with DRIMSeq in terms of precision/recall but offer better calibration of False Discovery Rate.Comment: Revised version, accepted to Statistical Applications in Genetics and Molecular Biolog

The Effect of Nonstationarity on Models Inferred from Neural Data

Neurons subject to a common non-stationary input may exhibit a correlated firing behavior. Correlations in the statistics of neural spike trains also arise as the effect of interaction between neurons. Here we show that these two situations can be distinguished, with machine learning techniques, provided the data are rich enough. In order to do this, we study the problem of inferring a kinetic Ising model, stationary or nonstationary, from the available data. We apply the inference procedure to two data sets: one from salamander retinal ganglion cells and the other from a realistic computational cortical network model. We show that many aspects of the concerted activity of the salamander retinal neurons can be traced simply to the external input. A model of non-interacting neurons subject to a non-stationary external field outperforms a model with stationary input with couplings between neurons, even accounting for the differences in the number of model parameters. When couplings are added to the non-stationary model, for the retinal data, little is gained: the inferred couplings are generally not significant. Likewise, the distribution of the sizes of sets of neurons that spike simultaneously and the frequency of spike patterns as function of their rank (Zipf plots) are well-explained by an independent-neuron model with time-dependent external input, and adding connections to such a model does not offer significant improvement. For the cortical model data, robust couplings, well correlated with the real connections, can be inferred using the non-stationary model. Adding connections to this model slightly improves the agreement with the data for the probability of synchronous spikes but hardly affects the Zipf plot.Comment: version in press in J Stat Mec

Minimax-optimal Inference from Partial Rankings

This paper studies the problem of inferring a global preference based on the partial rankings provided by many users over different subsets of items according to the Plackett-Luce model. A question of particular interest is how to optimally assign items to users for ranking and how many item assignments are needed to achieve a target estimation error. For a given assignment of items to users, we first derive an oracle lower bound of the estimation error that holds even for the more general Thurstone models. Then we show that the Cram\'er-Rao lower bound and our upper bounds inversely depend on the spectral gap of the Laplacian of an appropriately defined comparison graph. When the system is allowed to choose the item assignment, we propose a random assignment scheme. Our oracle lower bound and upper bounds imply that it is minimax-optimal up to a logarithmic factor among all assignment schemes and the lower bound can be achieved by the maximum likelihood estimator as well as popular rank-breaking schemes that decompose partial rankings into pairwise comparisons. The numerical experiments corroborate our theoretical findings.Comment: 16 pages, 2 figure

Laboratory colonisation and genetic bottlenecks in the tsetse fly Glossina pallidipes

Background The IAEA colony is the only one available for mass rearing of Glossina pallidipes, a vector of human and animal African trypanosomiasis in eastern Africa. This colony is the source for Sterile Insect Technique (SIT) programs in East Africa. The source population of this colony is unclear and its genetic diversity has not previously been evaluated and compared to field populations.<p></p> Methodology/Principal Findings We examined the genetic variation within and between the IAEA colony and its potential source populations in north Zimbabwe and the Kenya/Uganda border at 9 microsatellites loci to retrace the demographic history of the IAEA colony. We performed classical population genetics analyses and also combined historical and genetic data in a quantitative analysis using Approximate Bayesian Computation (ABC). There is no evidence of introgression from the north Zimbabwean population into the IAEA colony. Moreover, the ABC analyses revealed that the foundation and establishment of the colony was associated with a genetic bottleneck that has resulted in a loss of 35.7% of alleles and 54% of expected heterozygosity compared to its source population. Also, we show that tsetse control carried out in the 1990's is likely reduced the effective population size of the Kenya/Uganda border population.<p></p> Conclusions/Significance All the analyses indicate that the area of origin of the IAEA colony is the Kenya/Uganda border and that a genetic bottleneck was associated with the foundation and establishment of the colony. Genetic diversity associated with traits that are important for SIT may potentially have been lost during this genetic bottleneck which could lead to a suboptimal competitiveness of the colony males in the field. The genetic diversity of the colony is lower than that of field populations and so, studies using colony flies should be interpreted with caution when drawing general conclusions about G. pallidipes biology.<p></p&gt

Interpretation of Interpersonal Utility Comparisons: Positive, Normative or Descriptive

While interpersonal utility comparisons are indispensable to the determination of utility maxima, their interpretation as either normative or positive produces awkward conclusions. This paper alternatively reinterprets interpersonal utility comparisons as descriptive and value-laden rather than as either normative or positive. On this basis they are characterized as functional concepts, and are thus argued to be objective. This treatment suggests that it is possible to derive evaluative statements from descriptive ones, contrary to the usual view of the is-ought problem. Recent philosophy of language results are employed to support these views