Adaptive Tag Selection for Image Annotation

Not all tags are relevant to an image, and the number of relevant tags is image-dependent. Although many methods have been proposed for image auto-annotation, the question of how to determine the number of tags to be selected per image remains open. The main challenge is that for a large tag vocabulary, there is often a lack of ground truth data for acquiring optimal cutoff thresholds per tag. In contrast to previous works that pre-specify the number of tags to be selected, we propose in this paper adaptive tag selection. The key insight is to divide the vocabulary into two disjoint subsets, namely a seen set consisting of tags having ground truth available for optimizing their thresholds and a novel set consisting of tags without any ground truth. Such a division allows us to estimate how many tags shall be selected from the novel set according to the tags that have been selected from the seen set. The effectiveness of the proposed method is justified by our participation in the ImageCLEF 2014 image annotation task. On a set of 2,065 test images with ground truth available for 207 tags, the benchmark evaluation shows that compared to the popular top-$k$ strategy which obtains an F-score of 0.122, adaptive tag selection achieves a higher F-score of 0.223. Moreover, by treating the underlying image annotation system as a black box, the new method can be used as an easy plug-in to boost the performance of existing systems

Constructing Hierarchical Image-tags Bimodal Representations for Word Tags Alternative Choice

This paper describes our solution to the multi-modal learning challenge of ICML. This solution comprises constructing three-level representations in three consecutive stages and choosing correct tag words with a data-specific strategy. Firstly, we use typical methods to obtain level-1 representations. Each image is represented using MPEG-7 and gist descriptors with additional features released by the contest organizers. And the corresponding word tags are represented by bag-of-words model with a dictionary of 4000 words. Secondly, we learn the level-2 representations using two stacked RBMs for each modality. Thirdly, we propose a bimodal auto-encoder to learn the similarities/dissimilarities between the pairwise image-tags as level-3 representations. Finally, during the test phase, based on one observation of the dataset, we come up with a data-specific strategy to choose the correct tag words leading to a leap of an improved overall performance. Our final average accuracy on the private test set is 100%, which ranks the first place in this challenge.Comment: 6 pages, 1 figure, Presented at the Workshop on Representation Learning, ICML 201

A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data

Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and high sequencing error rates of modern sequencers present many new computational challenges in data interpretation. These challenges have led to the development of new classes of mapping tools and {\em de novo} assemblers. These algorithms are challenged by the continued improvement in sequencing throughput. We here describe digital normalization, a single-pass computational algorithm that systematizes coverage in shotgun sequencing data sets, thereby decreasing sampling variation, discarding redundant data, and removing the majority of errors. Digital normalization substantially reduces the size of shotgun data sets and decreases the memory and time requirements for {\em de novo} sequence assembly, all without significantly impacting content of the generated contigs. We apply digital normalization to the assembly of microbial genomic data, amplified single-cell genomic data, and transcriptomic data. Our implementation is freely available for use and modification

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina datasets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as 1 nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures + supplement. Significantly revised for clarity, references added, results not change

Using GWAS Data to Identify Copy Number Variants Contributing to Common Complex Diseases

Copy number variants (CNVs) account for more polymorphic base pairs in the human genome than do single nucleotide polymorphisms (SNPs). CNVs encompass genes as well as noncoding DNA, making these polymorphisms good candidates for functional variation. Consequently, most modern genome-wide association studies test CNVs along with SNPs, after inferring copy number status from the data generated by high-throughput genotyping platforms. Here we give an overview of CNV genomics in humans, highlighting patterns that inform methods for identifying CNVs. We describe how genotyping signals are used to identify CNVs and provide an overview of existing statistical models and methods used to infer location and carrier status from such data, especially the most commonly used methods exploring hybridization intensity. We compare the power of such methods with the alternative method of using tag SNPs to identify CNV carriers. As such methods are only powerful when applied to common CNVs, we describe two alternative approaches that can be informative for identifying rare CNVs contributing to disease risk. We focus particularly on methods identifying de novo CNVs and show that such methods can be more powerful than case-control designs. Finally we present some recommendations for identifying CNVs contributing to common complex disorders.Comment: Published in at http://dx.doi.org/10.1214/09-STS304 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Jet Substructure by Accident

We propose a new search strategy for high-multiplicity hadronic final states. When new particles are produced at threshold, the distribution of their decay products is approximately isotropic. If there are many partons in the final state, it is likely that several will be clustered into the same large-radius jet. The resulting jet exhibits substructure, even though the parent states are not boosted. This "accidental" substructure is a powerful discriminant against background because it is more pronounced for high-multiplicity signals than for QCD multijets. We demonstrate how to take advantage of accidental substructure to reduce backgrounds without relying on the presence of missing energy. As an example, we present the expected limits for several R-parity violating gluino decay topologies. This approach allows for the determination of QCD backgrounds using data-driven methods, which is crucial for the feasibility of any search that targets signatures with many jets and suppressed missing energy.Comment: 20 + 7 pages, 8 figures; v2: references added, minor changes, journal versio