Automated Visual Fin Identification of Individual Great White Sharks

This paper discusses the automated visual identification of individual great white sharks from dorsal fin imagery. We propose a computer vision photo ID system and report recognition results over a database of thousands of unconstrained fin images. To the best of our knowledge this line of work establishes the first fully automated contour-based visual ID system in the field of animal biometrics. The approach put forward appreciates shark fins as textureless, flexible and partially occluded objects with an individually characteristic shape. In order to recover animal identities from an image we first introduce an open contour stroke model, which extends multi-scale region segmentation to achieve robust fin detection. Secondly, we show that combinatorial, scale-space selective fingerprinting can successfully encode fin individuality. We then measure the species-specific distribution of visual individuality along the fin contour via an embedding into a global `fin space'. Exploiting this domain, we finally propose a non-linear model for individual animal recognition and combine all approaches into a fine-grained multi-instance framework. We provide a system evaluation, compare results to prior work, and report performance and properties in detail.Comment: 17 pages, 16 figures. To be published in IJCV. Article replaced to update first author contact details and to correct a Figure reference on page

Unsupervised learning of generative topic saliency for person re-identification

(c) 2014. The copyright of this document resides with its authors. It may be distributed unchanged freely in print or electronic forms.© 2014. The copyright of this document resides with its authors. Existing approaches to person re-identification (re-id) are dominated by supervised learning based methods which focus on learning optimal similarity distance metrics. However, supervised learning based models require a large number of manually labelled pairs of person images across every pair of camera views. This thus limits their ability to scale to large camera networks. To overcome this problem, this paper proposes a novel unsupervised re-id modelling approach by exploring generative probabilistic topic modelling. Given abundant unlabelled data, our topic model learns to simultaneously both (1) discover localised person foreground appearance saliency (salient image patches) that are more informative for re-id matching, and (2) remove busy background clutters surrounding a person. Extensive experiments are carried out to demonstrate that the proposed model outperforms existing unsupervised learning re-id methods with significantly simplified model complexity. In the meantime, it still retains comparable re-id accuracy when compared to the state-of-the-art supervised re-id methods but without any need for pair-wise labelled training data

Plant image retrieval using color, shape and texture features

We present a content-based image retrieval system for plant image retrieval, intended especially for the house plant identification problem. A plant image consists of a collection of overlapping leaves and possibly flowers, which makes the problem challenging.We studied the suitability of various well-known color, shape and texture features for this problem, as well as introducing some new texture matching techniques and shape features. Feature extraction is applied after segmenting the plant region from the background using the max-flow min-cut technique. Results on a database of 380 plant images belonging to 78 different types of plants show promise of the proposed new techniques and the overall system: in 55% of the queries, the correct plant image is retrieved among the top-15 results. Furthermore, the accuracy goes up to 73% when a 132-image subset of well-segmented plant images are considered

IDENTIFICATION OF COVER SONGS USING INFORMATION THEORETIC MEASURES OF SIMILARITY

13 pages, 5 figures, 4 tables. v3: Accepted version13 pages, 5 figures, 4 tables. v3: Accepted version13 pages, 5 figures, 4 tables. v3: Accepted versio

Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy.

In mass spectrometry-based untargeted metabolomics, rarely more than 30% of the compounds are identified. Without the true identity of these molecules it is impossible to draw conclusions about the biological mechanisms, pathway relationships and provenance of compounds. The only way at present to address this discrepancy is to use in silico fragmentation software to identify unknown compounds by comparing and ranking theoretical MS/MS fragmentations from target structures to experimental tandem mass spectra (MS/MS). We compared the performance of four publicly available in silico fragmentation algorithms (MetFragCL, CFM-ID, MAGMa+ and MS-FINDER) that participated in the 2016 CASMI challenge. We found that optimizing the use of metadata, weighting factors and the manner of combining different tools eventually defined the ultimate outcomes of each method. We comprehensively analysed how outcomes of different tools could be combined and reached a final success rate of 93% for the training data, and 87% for the challenge data, using a combination of MAGMa+, CFM-ID and compound importance information along with MS/MS matching. Matching MS/MS spectra against the MS/MS libraries without using any in silico tool yielded 60% correct hits, showing that the use of in silico methods is still important

Silhouette-based gait recognition using Procrustes shape analysis and elliptic Fourier descriptors

This paper presents a gait recognition method which combines spatio-temporal motion characteristics, statistical and physical parameters (referred to as STM-SPP) of a human subject for its classification by analysing shape of the subject's silhouette contours using Procrustes shape analysis (PSA) and elliptic Fourier descriptors (EFDs). STM-SPP uses spatio-temporal gait characteristics and physical parameters of human body to resolve similar dissimilarity scores between probe and gallery sequences obtained by PSA. A part-based shape analysis using EFDs is also introduced to achieve robustness against carrying conditions. The classification results by PSA and EFDs are combined, resolving tie in ranking using contour matching based on Hu moments. Experimental results show STM-SPP outperforms several silhouette-based gait recognition methods

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens.

Large-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise. To make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service. PinAPL-Py implements state-of-the-art tools and statistical models, assembled in a comprehensive workflow covering sequence quality control, automated sgRNA sequence extraction, alignment, sgRNA enrichment/depletion analysis and gene ranking. The workflow is set up to use a variety of popular sgRNA libraries as well as custom libraries that can be easily uploaded. Various analysis options are offered, suitable to analyze a large variety of CRISPR/Cas9 screening experiments. Analysis output includes ranked lists of sgRNAs and genes, and publication-ready plots. PinAPL-Py helps to advance genome-wide screening efforts by combining comprehensive functionality with user-friendly implementation. PinAPL-Py is freely accessible at http://pinapl-py.ucsd.edu with instructions and test datasets