Efficient and Joint Hyperparameter and Architecture Search for Collaborative Filtering

Automated Machine Learning (AutoML) techniques have recently been introduced to design Collaborative Filtering (CF) models in a data-specific manner. However, existing works either search architectures or hyperparameters while ignoring the fact they are intrinsically related and should be considered together. This motivates us to consider a joint hyperparameter and architecture search method to design CF models. However, this is not easy because of the large search space and high evaluation cost. To solve these challenges, we reduce the space by screening out usefulness yperparameter choices through a comprehensive understanding of individual hyperparameters. Next, we propose a two-stage search algorithm to find proper configurations from the reduced space. In the first stage, we leverage knowledge from subsampled datasets to reduce evaluation costs; in the second stage, we efficiently fine-tune top candidate models on the whole dataset. Extensive experiments on real-world datasets show better performance can be achieved compared with both hand-designed and previous searched models. Besides, ablation and case studies demonstrate the effectiveness of our search framework.Comment: Accepted by KDD 202

High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer

Cell surface mannose 6-phosphate/insulin-like growth factor II receptors (M6P/IGF2R) bind and target exogenous insulin-like growth factor II (IGF2) to the prelysosomes where it is degraded. Loss of heterozygosity (LOH) for M6P/IGF2R is found in cancers, with mutational inactivation of the remaining allele. We exploited the normal allele-specific differential methylation of the M6P/IGF2R intron 2 CpG island to rapidly evaluate potential LOH in ovarian cancers, since every normal individual is informative. To this end, we developed a method for bisulfite modification of genomic DNA in 96-well format that allows for rapid methylation profiling. We identified ovarian cancers with M6P/IGF2R LOH, but unexpectedly also found frequent abnormal acquisition of methylation on the paternally inherited allele at intron 2. These results demonstrate the utility of our high-throughput method of bisulfite modification for analysis of large sample numbers. They further show that the methylation status of the intron 2 CpG island may be a useful indicator of LOH and biomarker of disease

Efficient Post-processing of Diffusion Tensor Cardiac Magnetic Imaging Using Texture-conserving Deformable Registration

Diffusion tensor based cardiac magnetic resonance (DT-CMR) is a method capable of providing non-invasive measurements of myocardial microstructure. Image registration is essential to correct image shifts due to intra and inter breath-hold motion. Registration is challenging in DT-CMR due to the low signal-to-noise and various contrasts induced by the diffusion encoding in the myocardial and surrounding organs. Traditional deformable registration destroys the texture information while rigid registration inefficiently discards frames with local deformation. In this study, we explored the possibility of deep learning-based deformable registration on DT- CMR. Based on the noise suppression using low-rank features and diffusion encoding suppression using variational auto encoder-decoder, a B-spline based registration network extracted the displacement fields and maintained the texture features of DT-CMR. In this way, our method improved the efficiency of frame utilization, manual cropping, and computational speed.Comment: 4 pages, 4 figures, conferenc

A Glimpse of Streptococcal Toxic Shock Syndrome from Comparative Genomics of S. suis 2 Chinese Isolates

BACKGROUND: Streptococcus suis serotype 2 (SS2) is an important zoonotic pathogen, causing more than 200 cases of severe human infection worldwide, with the hallmarks of meningitis, septicemia, arthritis, etc. Very recently, SS2 has been recognized as an etiological agent for streptococcal toxic shock syndrome (STSS), which was originally associated with Streptococcus pyogenes (GAS) in Streptococci. However, the molecular mechanisms underlying STSS are poorly understood. METHODS AND FINDINGS: To elucidate the genetic determinants of STSS caused by SS2, whole genome sequencing of 3 different Chinese SS2 strains was undertaken. Comparative genomics accompanied by several lines of experiments, including experimental animal infection, PCR assay, and expression analysis, were utilized to further dissect a candidate pathogenicity island (PAI). Here we show, for the first time, a novel molecular insight into Chinese isolates of highly invasive SS2, which caused two large-scale human STSS outbreaks in China. A candidate PAI of ∼89 kb in length, which is designated 89K and specific for Chinese SS2 virulent isolates, was investigated at the genomic level. It shares the universal properties of PAIs such as distinct GC content, consistent with its pivotal role in STSS and high virulence. CONCLUSIONS: To our knowledge, this is the first PAI candidate from S. suis worldwide. Our finding thus sheds light on STSS triggered by SS2 at the genomic level, facilitates further understanding of its pathogenesis and points to directions of development on some effective strategies to combat highly pathogenic SS2 infections

Study on the Synchronous Propulsion of New Urbanization and Ecological Civilization Construction

The construction of ecological civilization is the inevitable choice for implementing of the new urbanization strategy and is the objective requirement of promoting the new urbanization. It provides the power support for the new urbanization, and economic development has entered a new era in China. In order to better promote the new urbanization and the construction of ecological civilization, there is a need to optimize the use of land resources, provide space guarantee for new urbanization and the construction of ecological civilization; vigorously develop the financial sector to provide financial support for the new urbanization and the construction of ecological civilization; perfect information infrastructure to provide information support for the new urbanization and the construction of ecological civilization; stick to people-oriented principle and strive to build livable city of ecological civilization; establish ecological compensation mechanism to promote the coordinated development of regional new ecological town; make a blue map for cooperative promotion of new urbanization and ecological civilization construction through the establishment of a scientific and rational plan

Proton Nuclear Magnetic Resonance-Spectroscopic Discrimination of Wines Reflects Genetic Homology of Several Different Grape (V. vinifera L.) Cultivars.

Proton nuclear magnetic resonance spectroscopy coupled multivariate analysis (1H NMR-PCA/PLS-DA) is an important tool for the discrimination of wine products. Although 1H NMR has been shown to discriminate wines of different cultivars, a grape genetic component of the discrimination has been inferred only from discrimination of cultivars of undefined genetic homology and in the presence of many confounding environmental factors. We aimed to confirm the influence of grape genotypes in the absence of those factors.We applied 1H NMR-PCA/PLS-DA and hierarchical cluster analysis (HCA) to wines from five, variously genetically-related grapevine (V. vinifera) cultivars; all grown similarly on the same site and vinified similarly. We also compared the semi-quantitative profiles of the discriminant metabolites of each cultivar with previously reported chemical analyses. The cultivars were clearly distinguishable and there was a general correlation between their grouping and their genetic homology as revealed by recent genomic studies. Between cultivars, the relative amounts of several of the cultivar-related discriminant metabolites conformed closely with reported chemical analyses.Differences in grape-derived metabolites associated with genetic differences alone are a major source of 1H NMR-based discrimination of wines and 1H NMR has the capacity to discriminate between very closely related cultivars.The study confirms that genetic variation among grape cultivars alone can account for the discrimination of wine by 1H NMR-PCA/PLS and indicates that 1H NMR spectra of wine of single grape cultivars may in future be used in tandem with hierarchical cluster analysis to elucidate genetic lineages and metabolomic relations of grapevine cultivars. In the absence of genetic information, for example, where predecessor varieties are no longer extant, this may be a particularly useful approach

A Riemannian approach for computing geodesics in elastic shape analysis

"We propose a Riemannian quasi-Newton method to compute a geodesic invariant to scaling, translation, rotation and reparameterization and show that it is more efficient than the current state-of-the-art coordinate-descent/path-straightening approach.