Our understanding of bird song, a model system for animal communication and the neurobiology of learning, depends critically on making reliable, validated comparisons between the complex multidimensional syllables that are used in songs. However, most assessments of song similarity are based on human inspection of spectrograms, or computational methods developed from human intuitions. Using a novel automated operant conditioning system, we collected a large corpus of zebra finches' (Taeniopygia guttata) decisions about song syllable similarity. We use this dataset to compare and externally validate similarity algorithms in widely-used publicly available software (Raven, Sound Analysis Pro, Luscinia). Although these methods all perform better than chance, they do not closely emulate the avian assessments. We then introduce a novel deep learning method that can produce perceptual similarity judgements trained on such avian decisions. We find that this new method outperforms the established methods in accuracy and more closely approaches the avian assessments. Inconsistent (hence ambiguous) decisions are a common occurrence in animal behavioural data; we show that a modification of the deep learning training that accommodates these leads to the strongest performance. We argue this approach is the best way to validate methods to compare song similarity, that our dataset can be used to validate novel methods, and that the general approach can easily be extended to other species.

Probabilistic data structures use space-efficient representations of data in order to (approximately) respond to queries about the data. Traditionally, these structures are accompanied by probabilistic bounds on query-response errors. These bounds implicitly assume benign attack models, in which the data and the queries are inputs are chosen non-adaptively, and independent of the randomness used to construct the representation. Yet probabilistic data structures are increasingly used in settings where these assumptions may be violated. This work provides a provable security treatment of probabilistic data structures in adversarial environments. We give a syntax that captures a wide variety of in-use structures, and our security notions support development of error bounds in the presence of powerful attacks. Concretely, we primarily focus on examining the widely used Bloom filter, but also consider counting (Bloom) filters and count-min sketch data structures. For the traditional version of these, our security findings are largely negative; however, we show that simple embellishments (e.g., using salts, or secret keys) yields structures that provide provable security, and with little overhead.

MOTIVATION: The invention of next-generation sequencing technology has made it possible to study the rare variants that are more likely to pinpoint causal disease genes. To make such experiments financially viable, DNA samples from several subjects are often pooled before sequencing. This induces large between-pool variation which, together with other sources of experimental error, creates over-dispersed data. Statistical analysis of pooled sequencing data needs to appropriately model this additional variance to avoid inflating the false-positive rate. RESULTS: We propose a new statistical method based on an extra-binomial model to address the over-dispersion and apply it to pooled case-control data. We demonstrate that our model provides a better fit to the data than either a standard binomial model or a traditional extra-binomial model proposed by Williams and can analyse both rare and common variants with lower or more variable pool depths compared to the other methods. AVAILABILITY: Package 'extraBinomial' is on http://cran.r-project.org/. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.