Automatic generation of dense non-rigid optical flow

There hardly exists any large-scale datasets with dense optical flow of non-rigid motion from real-world imagery as of today. The reason lies mainly in the difficulty of human annotation to generate optical flow ground-truth. To circumvent the need for human annotation, we propose a framework to automatically generate optical flow from real-world videos. The method extracts and matches objects from video frames to compute initial constraints, and applies a deformation over the objects of interest to obtain dense optical flow fields. We propose several ways to augment the optical flow variations. Extensive experimental results show that training on our automatically generated optical flow outperforms methods that are trained on rigid synthetic data using FlowNet-S, PWC-Net, and LiteFlowNet. Datasets and algorithms of our optical flow generation framework is available at https://github.com/lhoangan/arap_flow.Comment: The paper is under consideration at Computer Vision and Image Understandin

Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems

Background: Variable selection on high throughput biological data, such as gene expression or single nucleotide polymorphisms (SNPs), becomes inevitable to select relevant information and, therefore, to better characterize diseases or assess genetic structure. There are different ways to perform variable selection in large data sets. Statistical tests are commonly used to identify differentially expressed features for explanatory purposes, whereas Machine Learning wrapper approaches can be used for predictive purposes. In the case of multiple highly correlated variables, another option is to use multivariate exploratory approaches to give more insight into cell biology, biological pathways or complex traits.Results: A simple extension of a sparse PLS exploratory approach is proposed to perform variable selection in a multiclass classification framework.Conclusions: sPLS-DA has a classification performance similar to other wrapper or sparse discriminant analysis approaches on public microarray and SNP data sets. More importantly, sPLS-DA is clearly competitive in terms of computational efficiency and superior in terms of interpretability of the results via valuable graphical outputs. sPLS-DA is available in the R package mixOmics, which is dedicated to the analysis of large biological data sets

Adaptive learning through technology: a technical review and implementation

Purpose There is an increase globally of students using technology to support their learning. The purpose of this paper is to outline the technical aspects of adaptive learning and contribute to the development of pedagogy that incorporates this method in teaching and learning. Design/methodology/approach This is a technical review article that summarises key guidance on the application of adaptive learning and then reflects on its application in a UK and Vietnamese context. Findings Initial analysis demonstrates that learning can occur asynchronously because of students engaging with adaptive learning. Issues and recommendations were derived from the reflections and practice of both UK and Vietnamese practitioners. Recommendations focussed on the more practical elements of constructing and maintaining adaptive learning. Questions were then constructed to make the decision of whether to implement adaptive learning into teaching and learning practices. Originality/value This academic commentary reflects on the implementation of asynchronous learning adaptive technologies in both the UK and Vietnam, specifically exploring the use of a “mastery path” and “computerised adaptive testing” to enhance student understanding

Singularities and Topology of Meromorphic Functions

We present several aspects of the "topology of meromorphic functions", which we conceive as a general theory which includes the topology of holomorphic functions, the topology of pencils on quasi-projective spaces and the topology of polynomial functions.Comment: 21 pages, 1 figur

Temporal development of the oral microbiome and prediction of early childhood caries

Human microbiomes are predicted to assemble in a reproducible and ordered manner yet there is limited knowledge on the development of the complex bacterial communities that constitute the oral microbiome. The oral microbiome plays major roles in many oral diseases including early childhood caries (ECC), which afflicts up to 70% of children in some countries. Saliva contains oral bacteria that are indicative of the whole oral microbiome and may have the ability to reflect the dysbiosis in supragingival plaque communities that initiates the clinical manifestations of ECC. The aim of this study was to determine the assembly of the oral microbiome during the first four years of life and compare it with the clinical development of ECC. The oral microbiomes of 134 children enrolled in a birth cohort study were determined at six ages between two months and four years-of-age and their mother’s oral microbiome was determined at a single time point. We identified and quantified 356 operational taxonomic units (OTUs) of bacteria in saliva by sequencing the V4 region of the bacterial 16S RNA genes. Bacterial alpha diversity increased from a mean of 31 OTUs in the saliva of infants at 1.9 months-of-age to 84 OTUs at 39 months-of-age. The oral microbiome showed a distinct shift in composition as the children matured. The microbiome data were compared with the clinical development of ECC in the cohort at 39, 48, and 60 months-of-age as determined by ICDAS-II assessment. Streptococcus mutans was the most discriminatory oral bacterial species between health and current disease, with an increased abundance in disease. Overall our study demonstrates an ordered temporal development of the oral microbiome, describes a limited core oral microbiome and indicates that saliva testing of infants may help predict ECC risk

The combinatorics of plane curve singularities. How Newton polygons blossom into lotuses

This survey may be seen as an introduction to the use of toric and tropical geometry in the analysis of plane curve singularities, which are germs $(C,o)$ of complex analytic curves contained in a smooth complex analytic surface $S$. The embedded topological type of such a pair $(S, C)$ is usually defined to be that of the oriented link obtained by intersecting $C$ with a sufficiently small oriented Euclidean sphere centered at the point $o$, defined once a system of local coordinates $(x,y)$ was chosen on the germ $(S,o)$. If one works more generally over an arbitrary algebraically closed field of characteristic zero, one speaks instead of the combinatorial type of $(S, C)$. One may define it by looking either at the Newton-Puiseux series associated to $C$ relative to a generic local coordinate system $(x,y)$, or at the set of infinitely near points which have to be blown up in order to get the minimal embedded resolution of the germ $(C,o)$ or, thirdly, at the preimage of this germ by the resolution. Each point of view leads to a different encoding of the combinatorial type by a decorated tree: an Eggers-Wall tree, an Enriques diagram, or a weighted dual graph. The three trees contain the same information, which in the complex setting is equivalent to the knowledge of the embedded topological type. There are known algorithms for transforming one tree into another. In this paper we explain how a special type of two-dimensional simplicial complex called a lotus allows to think geometrically about the relations between the three types of trees. Namely, all of them embed in a natural lotus, their numerical decorations appearing as invariants of it. This lotus is constructed from the finite set of Newton polygons created during any process of resolution of $(C,o)$ by successive toric modifications.Comment: 104 pages, 58 figures. Compared to the previous version, section 2 is new. The historical information, contained before in subsection 6.2, is distributed now throughout the paper in the subsections called "Historical comments''. More details are also added at various places of the paper. To appear in the Handbook of Geometry and Topology of Singularities I, Springer, 202

Evaluation of O2PLS in Omics data integration

Background: Rapid computational and technological developments made large amounts of omics data available in different biological levels. It is becoming clear that simultaneous data analysis methods are needed for better interpretation and understanding of the underlying systems biology. Different methods have been proposed for this task, among them Partial Least Squares (PLS) related methods. To also deal with orthogonal variation, systematic variation in the data unrelated to one another, we consider the Two-way Orthogonal PLS (O2PLS): an integrative data analysis method which is capable of modeling systematic variation, while providing more parsimonious models aiding interpretation. Results: A simulation study to assess the performance of O2PLS showed positive results in both low and higher dimensions. More noise (50 % of the data) only affected the systematic part estimates. A data analysis was conducted using data on metabolomics and transcriptomics from a large Finnish cohort (DILGOM). A previous sequential study, using the same data, showed significant correlations between the Lipo-Leukocyte (LL) module and lipoprotein metabolites. The O2PLS results were in agreement with these findings, identifying almost the same set of co-varying variables. Moreover, our integrative approach identified other associative genes and metabolites, while taking into account systematic variation in the data. Including orthogonal components enhanced overall fit, but the orthogonal variation was difficult to interpret. Conclusions: Simulations showed that the O2PLS estimates were close to the true parameters in both low and higher dimensions. In the presence of more noise (50 %), the orthogonal part estimates could not distinguish well between joint and unique variation. The joint estimates were not systematically affected. Simultaneous analysis with O2PLS on metabolome and transcriptome data showed that the LL module, together with VLDL and HDL metabolites, were important for the metabolomic and transcriptomic relation. This is in agreement with an earlier study. In addition more gene expression and metabolites are identified being important for the joint covariation

Integrative analysis of gene expression and copy number alterations using canonical correlation analysis

Supplementary Figure 1. Representation of the samples from the tuning set by their coordinates in the first two pairs of features (extracted from the tuning set) using regularized dual CCA, with regularization parameters tx = 0.9, ty = 0.3 (left panel), and PCA+CCA (right panel). We show the representations with respect to both the copy number features and the gene expression features in a superimposed way, where each sample is represented by two markers. The filled markers represent the coordinates in the features extracted from the copy number variables, and the open markers represent coordinates in the features extracted from the gene expression variables. Samples with different leukemia subtypes are shown with different colors. The first feature pair distinguishes the HD50 group from the rest, while the second feature pair represents the characteristics of the samples from the E2A/PBX1 subtype. The high canonical correlation obtained for the tuning samples with regularized dual CCA is apparent in the left panel, where the two points for each sample coincide. Nevertheless, the extracted features have a high generalization ability, as can be seen in the left panel of Figure 5, showing the representation of the validation samples. 1 Supplementary Figure 2. Representation of the samples from the tuning set by their coordinates in the first two pairs of features (extracted from the tuning set) using regularized dual CCA, with regularization parameters tx = 0, ty = 0 (left panel), and tx = 1, ty = 1 (right panel). We show the representations with respect to both the copy number features and the gene expression features in a superimposed way, where each sample is represented by tw

The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia

yesRecent studies portend a rising global spread and adaptation of human- or healthcare- associated pathogens. Here, we analyse an international collection of the emerging, multi-drug-resistant, opportunistic pathogen Stenotrophomonas maltophilia from 22 countries to infer population structure and clonality at a global level. We show that the S. maltophilia complex is divided into 23 monophyletic lineages, most of which harbour strains of all degrees of human virulence. Lineage Sm6 comprises the highest rate of human-associated strains, linked to key virulence and resistance genes. Transmission analysis identifies potential outbreak events of genetically closely related strains isolated within days or weeks in the same hospitals