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In this paper, a deep learning method is proposed for human image processing that incorporates a mechanism to update target-specific parameters. The aim is to improve system performance in situations where the target can be continuously observed. Network-based algorithms typically rely on offline training processes that use large datasets, while trained networks typically operate in a one-shot fashion. That is, each input image is processed one by one in the static network. On the other hand, many practical applications can be expected to use continuous observation rather than observation of a single image. The proposed method employs dynamic use of multiple observations to improve system performance. In this paper, the effectiveness of the proposed method adopting an iterative update process is clarified through its implementation in the task of face-pose estimation. The method consists of two separate processes: 1) sequential estimation and updating of face-shape parameters (target-specific parameters) and 2) face-pose estimation for every single image using the updated parameters. Experimental results indicate the effectiveness of the proposed method. [ABSTRACT FROM AUTHOR]

Abstract Background Identification of genes whose basal mRNA expression predicts the sensitivity of tumor cells to cytotoxic treatments can play an important role in individualized cancer medicine. It enables detailed characterization of the mechanism of action of drugs. Furthermore, screening the expression of these genes in the tumor tissue may suggest the best course of chemotherapy or a combination of drugs to overcome drug resistance. Results We developed a computational method called ProGENI to identify genes most associated with the variation of drug response across different individuals, based on gene expression data. In contrast to existing methods, ProGENI also utilizes prior knowledge of protein–protein and genetic interactions, using random walk techniques. Analysis of two relatively new and large datasets including gene expression data on hundreds of cell lines and their cytotoxic responses to a large compendium of drugs reveals a significant improvement in prediction of drug sensitivity using genes identified by ProGENI compared to other methods. Our siRNA knockdown experiments on ProGENI-identified genes confirmed the role of many new genes in sensitivity to three chemotherapy drugs: cisplatin, docetaxel, and doxorubicin. Based on such experiments and extensive literature survey, we demonstrate that about 73% of our top predicted genes modulate drug response in selected cancer cell lines. In addition, global analysis of genes associated with groups of drugs uncovered pathways of cytotoxic response shared by each group. Conclusions Our results suggest that knowledge-guided prioritization of genes using ProGENI gives new insight into mechanisms of drug resistance and identifies genes that may be targeted to overcome this phenomenon.

Abstract: In this paper, the degree distributions of a bipartite network, namely Movielens, are investigated. The statistical analysis shows that the distribution of the degree product, ku ko, has an exponential from, where ku and ko denote the user and object degrees respectively. By introducing the edge weight effect on the recommendation performance, an improved recommendation algorithm based on mass diffusion (MD) process is presented. We argue that the edges weight of the user-object bipartite network should be taken into account to measure the object similarity. By taking into account the user and object degree correlations, the weighted bipartite network is constructed. The numerical results of the MD algorithms on the weighted network indicate that both of the accuracy and diversity could be increased at the optimal case. More importantly, we find that, at the optimal case, the edge weight distribution would change from the exponential form to the poisson form. This work may shed some light on how to improve the recommendation algorithm performance by considering the statistical properties. [ABSTRACT FROM AUTHOR]

Breast cancer (BC) is a heterogeneous and complex disease as witnessed by the existence of different subtypes and clinical characteristics that poses significant challenges in disease management. The complexity of this tumor may rely on the highly interconnected nature of the various biological processes as stated by the new paradigm of Network Medicine. We explored The Cancer Genome Atlas (TCGA)-BRCA data set, by applying the network-based algorithm named SWItch Miner, and mapping the findings on the human interactome to capture the molecular interconnections associated with the disease modules. To characterize BC phenotypes, we constructed protein–protein interaction modules based on "hub genes", called switch genes, both common and specific to the four tumor subtypes. Transcriptomic profiles of patients were stratified according to both clinical (immunohistochemistry) and genetic (PAM50) classifications. 266 and 372 switch genes were identified from immunohistochemistry and PAM50 classifications, respectively. Moreover, the identified switch genes were functionally characterized to select an interconnected pathway of disease genes. By intersecting the common switch genes of the two classifications, we selected a unique signature of 28 disease genes that were BC subtype-independent and classification subtype-independent. Data were validated both in vitro (10 BC cell lines) and ex vivo (66 BC tissues) experiments. Results showed that four of these hub proteins (AURKA, CDC45, ESPL1, and RAD54L) were over-expressed in all tumor subtypes. Moreover, the inhibition of one of the identified switch genes (AURKA) similarly affected all BC subtypes. In conclusion, using a network-based approach, we identified a common BC disease module which might reflect its pathological signature, suggesting a new vision to face with the disease heterogeneity. [ABSTRACT FROM AUTHOR]