Small-variance asymptotics for Bayesian neural networks

Bayesian neural networks (BNNs) are a rich and flexible class of models that have several advantages over standard feedforward networks, but are typically expensive to train on large-scale data. In this thesis, we explore the use of small-variance asymptotics-an approach to yielding fast algorithms from probabilistic models-on various Bayesian neural network models. We first demonstrate how small-variance asymptotics shows precise connections between standard neural networks and BNNs; for example, particular sampling algorithms for BNNs reduce to standard backpropagation in the small-variance limit. We then explore a more complex BNN where the number of hidden units is additionally treated as a random variable in the model. While standard sampling schemes would be too slow to be practical, our asymptotic approach yields a simple method for extending standard backpropagation to the case where the number of hidden units is not fixed. We show on several data sets that the resulting algorithm has benefits over backpropagation on networks with a fixed architecture.2019-01-02T00:00:00

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity

Luminous Red Galaxies in Clusters: Central Occupation, Spatial Distributions, and Mis-centering

Luminous Red Galaxies (LRG) from the Sloan Digital Sky Survey are considered among the best understood samples of galaxies, and they are employed in a broad range of cosmological studies. Because they form a relatively homogeneous population, with high stellar masses and red colors, they are expected to occupy halos in a relatively simple way. In this paper, we study how LRGs occupy massive halos via direct counts in clusters and we reveal several unexpected trends suggesting that the connection between LRGs and dark matter halos may not be straightforward. Using the redMaPPer cluster catalog, we derive the central occupation of LRGs as a function richness, Ncen({\lambda}). Assuming no correlation between cluster mass and central galaxy luminosity at fixed richness, we show that clusters contain a significantly lower fraction of central LRGs than predicted from the two-point correlation function. At halo masses of 10^14.5 Msun, we find Ncen=0.73, compared to Ncen of 0.89 from correlation studies. Our central occupation function for LRGs converges to 0.95 at large halo masses. A strong anti-correlation between central luminosity and cluster mass at fixed richness is required to reconcile our results with those based on clustering studies. We also derive P_BNC, the probability that the brightest cluster member is not the central galaxy. We find P_BNC ~ 20-30% which is a factor of ~2 lower than the value found by Skibba et al. 2011. Finally, we study the radial offsets of bright non-central LRGs from cluster centers and show that bright non-central LRGs follow a different radial distribution compared to red cluster members, which follow a Navarro-Frank-White profile. This work demonstrates that even the most massive clusters do not always have an LRG at the center, and that the brightest galaxy in a cluster is not always the central galaxy.Comment: 18 pages, 9 figures, 4 tables, submitted to MNRAS, included the referee comment

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AMICO galaxy clusters in KiDS-DR3: sample properties and selection function

We present the first catalogue of galaxy cluster candidates derived from the third data release of the Kilo Degree Survey (KiDS-DR3). The sample of clusters has been produced using the Adaptive Matched Identifier of Clustered Objects (AMICO) algorithm. In this analysis AMICO takes advantage of the luminosity and spatial distribution of galaxies only, not considering colours. In this way, we prevent any selection effect related to the presence or absence of the red-sequence in the clusters. The catalogue contains 7988 candidate galaxy clusters in the redshift range 0.13.5 with a purity approaching 95% over the entire redshift range. In addition to the catalogue of galaxy clusters we also provide a catalogue of galaxies with their probabilistic association to galaxy clusters. We quantify the sample purity, completeness and the uncertainties of the detection properties, such as richness, redshift, and position, by means of mock galaxy catalogues derived directly from the data. This preserves their statistical properties including photo-z uncertainties, unknown absorption across the survey, missing data, spatial correlation of galaxies and galaxy clusters. Being based on the real data, such mock catalogues do not have to rely on the assumptions on which numerical simulations and semi-analytic models are based on. This paper is the first of a series of papers in which we discuss the details and physical properties of the sample presented in this work.Comment: 16 pages, 14 figures, 3 tables, submitted to MNRA

Technical Report: Distribution Temporal Logic: Combining Correctness with Quality of Estimation

We present a new temporal logic called Distribution Temporal Logic (DTL) defined over predicates of belief states and hidden states of partially observable systems. DTL can express properties involving uncertainty and likelihood that cannot be described by existing logics. A co-safe formulation of DTL is defined and algorithmic procedures are given for monitoring executions of a partially observable Markov decision process with respect to such formulae. A simulation case study of a rescue robotics application outlines our approach.Comment: More expanded version of "Distribution Temporal Logic: Combining Correctness with Quality of Estimation" to appear in IEEE CDC 201

Technical report: Distribution Temporal Logic: combining correctness with quality of estimation

We present a new temporal logic called Distribution Temporal Logic (DTL) defined over predicates of belief states and hidden states of partially observable systems. DTL can express properties involving uncertainty and likelihood that cannot be described by existing logics. A co-safe formulation of DTL is defined and algorithmic procedures are given for monitoring executions of a partially observable Markov decision process with respect to such formulae. A simulation case study of a rescue robotics application outlines our approach