Dependency detection with similarity constraints

Unsupervised two-view learning, or detection of dependencies between two paired data sets, is typically done by some variant of canonical correlation analysis (CCA). CCA searches for a linear projection for each view, such that the correlations between the projections are maximized. The solution is invariant to any linear transformation of either or both of the views; for tasks with small sample size such flexibility implies overfitting, which is even worse for more flexible nonparametric or kernel-based dependency discovery methods. We develop variants which reduce the degrees of freedom by assuming constraints on similarity of the projections in the two views. A particular example is provided by a cancer gene discovery application where chromosomal distance affects the dependencies between gene copy number and activity levels. Similarity constraints are shown to improve detection performance of known cancer genes.Comment: 9 pages, 3 figures. Appeared in proceedings of the 2009 IEEE International Workshop on Machine Learning for Signal Processing XIX (MLSP'09). Implementation of the method available at http://bioconductor.org/packages/devel/bioc/html/pint.htm

Hardware Accelarated Visual Tracking Algorithms. A Systematic Literature Review

Many industrial applications need object recognition and tracking capabilities. The algorithms developed for those purposes are computationally expensive. Yet ,real time performance, high accuracy and small power consumption are essential measures of the system. When all these requirements are combined, hardware acceleration of these algorithms becomes a feasible solution. The purpose of this study is to analyze the current state of these hardware acceleration solutions, which algorithms have been implemented in hardware and what modifications have been done in order to adapt these algorithms to hardware.Siirretty Doriast

Evaluation of the GPS Accuracy of Tablets

Augmented Reality (AR) applications often require knowledge of the user’s position in some global coordinate system in order to draw the augmented content to its correct position on the screen. The most common method for coarse positioning is the Global Positioning System (GPS). One of the advantages of GPS is that GPS receivers can be found in almost every modern mobile device. This research was conducted in order to determine the accuracies of different GPS receivers. The tests included seven consumer-grade tablets, three external GPS modules and one professional-grade GPS receiver. All of the devices were tested with both static and mobile measurements. It was concluded that even the cheaper external GPS receivers were notably more accurate than the GPS receivers of the tested tablets. The absolute accuracy of the tablets is difficult to determine from the test results, since the results vary by a large margin between different measurements. The accuracy of the tested tablets in static measurements were between 0.30 meters and 13.75 meters.Siirretty Doriast

Digital Humanities and study of history

Peer reviewe

Bibliographic Data Science and the History of the Book (c. 1500–1800)

National bibliographies have been identified as a crucial resource for historical research on the publishing landscape, but using them requires addressing challenges of data quality, completeness, and interpretation. We call this approach bibliographic data science. In this article, we briefly assess the development of book formats and the vernacularization process in early modern Europe. The work undertaken paves the way for more extensive integration of library catalogs to map the history of the book.Peer reviewe

Intellectual history and the possibilities of the use of digital resources

Peer reviewe

Alchemy & algorithms : perspectives on the philosophy and history of open science

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Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors

Background Gastric adenocarcinoma is associated with H. pylori infection and inflammation that can result in the dysbiosis of gastric microbiota. The association of intestinal microbiota with gastric adenocarcinoma subtypes or with gastric gastrointestinal stromal tumors (GIST) is however not well known. Therefore, we performed 16S rRNA gene sequencing on DNA isolated from stool samples of Finnish patients and controls to study differences in microbiota among different histological subtypes of gastric adenocarcinoma, gastric GIST and healthy controls. Results We found that gut microbiota alpha diversity was lowest in diffuse adenocarcinoma patients, followed by intestinal type and GIST patients, although the differences were not significant compared to controls. Beta-diversity analysis however showed significant differences in microbiota composition for all subtypes compared to controls. Significantly higher abundance of Enterobacteriaceae was observed in both adenocarcinoma subtypes, whereas lower abundance of Bifidobacteriaceae was seen only in diffuse adenocarcinoma and of Oscillibacter in intestinal adenocarcinoma. Both GIST and adenocarcinoma patients had higher abundance of Enterobacteriaceae and lower abundance of Lactobacillaceae and Oscillibacter while lower abundance of Lachnoclostridium, Bifidobacterium, Parabacteroides and Barnesiella was seen only in the adenocarcinoma patients. Conclusions Our analysis shows association of higher Enterobacteriaceae abundance with all types of gastric tumors. Therefore it could be potentially useful as a marker of gastric malignancies. Lower gut microbiota diversity might be indicative of poorly differentiated, invasive, advanced or aggressive tumors and could possibly be a prognostic marker for gastric tumors.Peer reviewe

Gut Microbiota and Host Gene Mutations in Colorectal Cancer Patients and Controls of Iranian and Finnish Origin

Background/Aim: Gut microbiota plays an important role in colorectal cancer (CRC) and its composition in CRC patients can be influenced by ethnicity and tumour genomics. Herein, the aim was to study the possible associations of ethnicity and gene mutations with the gut microbiota in CRC patients. Materials and Methods: Bacterial composition in stool samples of 83 CRC patients and 60 controls from Iran and Finland was studied by 16S rRNA gene sequencing. The association of gut microbiota composition with CRC, host mutations in KRAS, NRAS and TP53, and ethnicity analysed. Results: Beta diversity analysis indicated significant differences between the Iranian and Finnish gut microbiota composition, in both controls and patients' groups. The Iranian controls had higher abundance of Prevotella and lower abundance of Bacteroides compared to the Finnish controls, while the Finnish patients had higher abundance of Clostridium compared to Iranian patients. Abundance of Ruminococcus was higher in patients compared to the controls. Higher abundances of Herbaspirillum, Catenibacterium and lower abundances of Barnesiella were associated with mutations in NRAS, TP53, and RAS respectively. Conclusion: A possible link of host gene mutations with gut bacterial composition is suggested.Peer reviewe