Helsinki Institute for Information Technology

About: Helsinki Institute for Information Technology is a facility organization based out in Espoo, Finland. It is known for research contribution in the topics: Population & Bayesian network. The organization has 630 authors who have published 1962 publications receiving 63426 citations.

Causal search in structural vector autoregressive models

Abstract: This paper reviews a class of methods to perform causal inference in the framework of a structural vector autoregressive model. We consider three different settings. In the first setting the underlying system is linear with normal disturbances and the structural model is identified by exploiting the information incorporated in the partial correlations of the estimated residuals. Zero partial correlations are used as input of a search algorithm formalized via graphical causal models. In the second, semi-parametric, setting the underlying system is linear with non-Gaussian disturbances. In this case the structural vector autoregressive model is identified through a search procedure based on independent component analysis. Finally, we explore the possibility of causal search in a nonparametric setting by studying the performance of conditional independence tests based on kernel density estimations.

Overlapping community detection in labeled graphs

Abstract: We present a new approach for the problem of finding overlapping communities in graphs and social networks. Our approach consists of a novel problem definition and three accompanying algorithms. We are particularly interested in graphs that have labels on their vertices, although our methods are also applicable to graphs with no labels. Our goal is to find k communities so that the total edge density over all k communities is maximized. In the case of labeled graphs, we require that each community is succinctly described by a set of labels. This requirement provides a better understanding for the discovered communities. The proposed problem formulation leads to the discovery of vertex-overlapping and dense communities that cover as many graph edges as possible. We capture these properties with a simple objective function, which we solve by adapting efficient approximation algorithms for the generalized maximum-coverage problem and the densest-subgraph problem. Our proposed algorithm is a generic greedy scheme. We experiment with three variants of the scheme, obtained by varying the greedy step of finding a dense subgraph. We validate our algorithms by comparing with other state-of-the-art community-detection methods on a variety of performance measures. Our experiments confirm that our algorithms achieve results of high quality in terms of the reported measures, and are practical in terms of performance.

DNMT Inhibitors Increase Methylation in the Cancer Genome.

Abstract: DNA methyltransferase inhibitors (DNMTi) decitabine and azacytidine are approved therapies for myelodysplastic syndrome and acute myeloid leukemia, and their combinations with other anticancer agents are being tested as therapeutic options for multiple solid cancers such as colon, ovarian, and lung cancer. However, the current therapeutic challenges of DNMTis include development of resistance, severe side effects and no or partial treatment responses, as observed in more than half of the patients. Therefore, there is a critical need to better understand the mechanisms of action of these drugs. In order to discover molecular targets of DNMTi therapy, we identified 638 novel CpGs with an increased methylation in response to decitabine treatment in HCT116 cell lines and validated the findings in multiple cancer types (e.g., bladder, ovarian, breast, and lymphoma) cell lines, bone marrow mononuclear cells from primary leukemia patients, as well as peripheral blood mononuclear cells and ascites from platinum resistance epithelial ovarian cancer patients. Azacytidine treatment also increased methylation of these CpGs in colon, ovarian, breast, and lymphoma cancer cell lines. Methylation at 166 identified CpGs strongly correlated (|r|≥ 0.80) with corresponding gene expression in HCT116 cell line. Differences in methylation at some of the identified CpGs and expression changes of the corresponding genes was observed in TCGA colon cancer tissue as compared to adjacent healthy tissue. Our analysis revealed that hypermethylated CpGs are involved in cancer cell proliferation and apoptosis by P53 and olfactory receptor pathways, hence influencing DNMTi responses. In conclusion, we showed hypermethylation of CpGs as a novel mechanism of action for DNMTi agents and identified 638 hypermethylated molecular targets (CpGs) common to decitabine and azacytidine therapy. These novel results suggest that hypermethylation of CpGs should be considered when predicting the DNMTi responses and side effects in cancer patients.

Collective creation and sense-making of mobile media

Abstract: Traditionally, mobile media sharing and messaging has been studied from the perspective of an individual author making media available to other users. With the aim of supporting spectator groups at large-scale events, we developed a messaging application for camera phones with the idea of collectively created albums called Media Stories. The field trial at a rally competition pointed out the collective and participative practices involved in the creation and sense-making of media, challenging the view of individual authorship. Members contributed actively to producing chains of messages in Media Stories, with more than half of the members as authors on average in each story. Observations indicate the centrality of collocated viewing and creation in the use of media. Design implications include providing a ""common space"" and possibilities of creating collective objects, adding features that enrich collocated collective use, and supporting the active construction of awareness and social presence through the created media.