Hyp-UML: Hyperbolic Image Retrieval with Uncertainty-aware Metric Learning

Metric learning plays a critical role in training image retrieval and classification. It is also a key algorithm in representation learning, e.g., for feature learning and its alignment in metric space. Hyperbolic embedding has been recently developed. Compared to the conventional Euclidean embedding in most of the previously developed models, Hyperbolic embedding can be more effective in representing the hierarchical data structure. Second, uncertainty estimation/measurement is a long-lasting challenge in artificial intelligence. Successful uncertainty estimation can improve a machine learning model's performance, robustness, and security. In Hyperbolic space, uncertainty measurement is at least with equivalent, if not more, critical importance. In this paper, we develop a Hyperbolic image embedding with uncertainty-aware metric learning for image retrieval. We call our method Hyp-UML: Hyperbolic Uncertainty-aware Metric Learning. Our contribution are threefold: we propose an image embedding algorithm based on Hyperbolic space, with their corresponding uncertainty value; we propose two types of uncertainty-aware metric learning, for the popular Contrastive learning and conventional margin-based metric learning, respectively. We perform extensive experimental validations to prove that the proposed algorithm can achieve state-of-the-art results among related methods. The comprehensive ablation study validates the effectiveness of each component of the proposed algorithm

Application of wave based method for predicting the response of coupled vibro-acoustic system with unconstrained damping layer

The Wave Based Method (WBM) is a deterministic prediction method that is computational efficiency as compared to other deterministic prediction techniques in mid-frequency problems. This paper discusses the application of WBM for predicting the dynamic displacement of plate with an unconstrained damping layer based on Kirchhoff theory. Further, the prediction of acoustic response of the coupled vibro-acoustic system with unconstrained damping is realized on the use of WBM. A numerical example is introduced, and the comparison of numerical result obtained by WBM and FEM is acquired. It is seen that the WBM is applicable for vibro-acoustic system with unconstrained damping and is expected to yield faster and more accurate predictions. The limitation of the method caused by simplify hypothesis is described in combination with modelling ways and numerical results

Machine Learning of Pair-Contact Process with Diffusion

The pair-contact process with diffusion (PCPD), a generalized model of the ordinary pair-contact process (PCP) without diffusion, exhibits a continuous absorbing phase transition. Unlike the PCP, whose nature of phase transition is clearly classified into the directed percolation (DP) universality class, the model of PCPD has been controversially discussed since its infancy. To our best knowledge, there is so far no consensus on whether the phase transition of the PCPD falls into the unknown university classes or else conveys a new kind of non-equilibrium phase transition. In this paper, both unsupervised and supervised learning are employed to study the PCPD with scrutiny. Firstly, two unsupervised learning methods, principal component analysis (PCA) and autoencoder, are taken. Our results show that both methods can cluster the original configurations of the model and provide reasonable estimates of thresholds. Therefore, no matter whether the non-equilibrium lattice model is a random process of unitary (for instance the DP) or binary (for instance the PCP), or whether it contains the diffusion motion of particles, unsupervised leaning can capture the essential, hidden information. Beyond that, supervised learning is also applied to learning the PCPD at different diffusion rates. We proposed a more accurate numerical method to determine the spatial correlation exponent $\nu_{\perp}$, which, to a large degree, avoids the uncertainty of data collapses through naked eyes. Our extensive calculations reveal that $\nu_{\perp}$ of PCPD depends continuously on the diffusion rate $D$, which supports the viewpoint that the PCPD may lead to a new type of absorbing phase transition.Comment: 15 pages, 11 figure

Immunostimulatory Activity of Protein Hydrolysate from Oviductus Ranae on Macrophage In Vitro

Oviductus Ranae is the dry oviduct of Rana chensinensis, which is also called R. chensinensis oil. Oviductus Ranae is a valuable Chinese crude drug and is recorded in the Pharmacopoeia of the People’s Republic of China. The aim of this study was to investigate the immunostimulatory activity of protein hydrolysate of Oviductus Ranae (ORPH) and to assess its possible mechanism. Immunomodulatory activity of ORPH was examined in murine macrophage RAW 264.7 cells. The effect of ORPH on the phagocytic activity of macrophages was determined by the neutral red uptake assay. After treatment with ORPH, NO production levels in the culture supernatant were investigated by Griess assay. The mRNA and protein expressions of inducible nitric oxide synthase (iNOS) were detected by RT-PCR and Western blotting. The production of TNF-α, IL-1β, and IL-6 after treatment with ORPH was measured using ELISA assay. In addition, NF-κB levels were also investigated by Western blot. The results showed that ORPH enhanced the phagocytosis of macrophage, increased productions of TNF-α, IL-1β, IL-6, and NO in RAW 264.7 cells, and upregulated the mRNA and protein expression of iNOS. Besides, NF-κB, levels in RAW 264.7 cells were elevated after ORPH treatment. These findings suggested that ORPH might stimulate macrophage activities by activating the NF-κB pathway

The <i>Sinocyclocheilus</i> cavefish genome provides insights into cave adaptation

BACKGROUND: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0223-4) contains supplementary material, which is available to authorized users

The Study on Newly Developed McAb NJ001 Specific to Non-Small Cell Lung Cancer and Its Biological Characteristics

Monoclonal antibody (McAb) is the key tool for cancer immunodiagnosis and immunotherapy. McAb-based immunotherapy that targets tumor antigens has had great achivement. In this study, a cell clone which kept secreting high-titer IgG1-type McAb named NJ001 against human non-small cell lung cancer (NSCLC) cells was obtained. The titer of purified NJ001 was 2×106. The antigen named SP70 of NSCLC specifically identified by NJ001 was proved to be a protein with the relative molecular mass (Mr) of 70 kDa. The results of immunohistochemical staining indicated that NJ001 could positively react to NSCLC, but weak positively or negatively react to human small-cell lung cancer (SCLC), pulmonary pseudotumor and other epithelial tumors. In soft agar assay, the colony formation efficiency in NJ001 groups decreased in a dose-dependent manner. For the concentration of 100 µg/ml, 200 µg/ml and 400 µg/ml, the inhibition ratio of colony formation was 23.4%, 62.5% and 100% respectively. Meanwhile, NJ001 caused significant reduction in tumor volume and tumor weight compared to control mice in lung cancer xenograft model. The tumor growth inhibition ratio in 200 µg, 400 µg and 800 µg NJ001 groups was 10.44%, 37.29% and 44.04%, respectively. NJ001 also led to cytomorphological changes and induced the apoptosis of human lung adenocarcinoma cell line SPC-A1 significantly. The newly developed NJ001 selectively reacted to NSCLC and exhibited anti-tumor activity both in vitro and in vivo. NJ001 is of great value concerning immunodiagnostics and immunotherapy for NSCLC and holds promise for further research regarding the mechanism underlying tumor progression of NSCLC