Data Fusion by Matrix Factorization

For most problems in science and engineering we can obtain data sets that describe the observed system from various perspectives and record the behavior of its individual components. Heterogeneous data sets can be collectively mined by data fusion. Fusion can focus on a specific target relation and exploit directly associated data together with contextual data and data about system's constraints. In the paper we describe a data fusion approach with penalized matrix tri-factorization (DFMF) that simultaneously factorizes data matrices to reveal hidden associations. The approach can directly consider any data that can be expressed in a matrix, including those from feature-based representations, ontologies, associations and networks. We demonstrate the utility of DFMF for gene function prediction task with eleven different data sources and for prediction of pharmacologic actions by fusing six data sources. Our data fusion algorithm compares favorably to alternative data integration approaches and achieves higher accuracy than can be obtained from any single data source alone.Comment: Short preprint, 13 pages, 3 Figures, 3 Tables. Full paper in 10.1109/TPAMI.2014.234397

Conformal Prediction with Orange

Conformal predictors estimate the reliability of outcomes made by supervised machine learning models. Instead of a point value, conformal prediction defines an outcome region that meets a user-specified reliability threshold. Provided that the data are independently and identically distributed, the user can control the level of the prediction errors and adjust it following the requirements of a given application. The quality of conformal predictions often depends on the choice of nonconformity estimate for a given machine learning method. To promote the selection of a successful approach, we have developed Orange3-Conformal, a Python library that provides a range of conformal prediction methods for classification and regression. The library also implements several nonconformity scores. It has a modular design and can be extended to add new conformal prediction methods and nonconformities

FragViz: visualization of fragmented networks

BACKGROUND Researchers in systems biology use network visualization to summarize the results of their analysis. Such networks often include unconnected components, which popular network alignment algorithms place arbitrarily with respect to the rest of the network. This can lead to misinterpretations due to the proximity of otherwise unrelated elements. RESULTS We propose a new network layout optimization technique called FragViz which can incorporate additional information on relations between unconnected network components. It uses a two-step approach by first arranging the nodes within each of the components and then placing the components so that their proximity in the network corresponds to their relatedness. In the experimental study with the leukemia gene networks we demonstrate that FragViz can obtain network layouts which are more interpretable and hold additional information that could not be exposed using classical network layout optimization algorithms. CONCLUSIONS Network visualization relies on computational techniques for proper placement of objects under consideration. These algorithms need to be fast so that they can be incorporated in responsive interfaces required by the explorative data analysis environments. Our layout optimization technique FragViz meets these requirements and specifically addresses the visualization of fragmented networks, for which standard algorithms do not consider similarities between unconnected components. The experiments confirmed the claims on speed and accuracy of the proposed solution

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions.

UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are methods to study protein-RNA interactions in untreated cells and tissues. Here, we analyzed six published and two novel data sets to confirm that both methods identify protein-RNA cross-link sites, and to identify a slight uridine preference of UV-C-induced cross-linking. Comparing Nova CLIP and iCLIP data revealed that cDNA deletions have a preference for TTT motifs, whereas iCLIP cDNA truncations are more likely to identify clusters of YCAY motifs as the primary Nova binding sites. In conclusion, we demonstrate how each method impacts the analysis of protein-RNA binding specificity.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Biomechanical and Clinical Alterations of the Hip Joint Following Femoral Neck Fracture and Implantation of Bipolar Hip Endoprosthesis

The implantation of a bipolar partial hip endoprosthesis is a treatment of choice for displaced medial femoral neck fracture. We present an experimental study which asses and compare biomechanical and clinical status through period before and after hip fracture and implantation of bipolar partial hip endoprosthesis. This study encompassed 75 patients who suffered from an acute medial femoral neck fracture and were treated with the implantation of a bipolar partial hip endoprosthesis. Their biomechanical status (stress distribution on the hip joint weight bearing area) and clinical status (Harris Hip Score) were estimated for the time prior to the injury and assessed at the follow-up examination that was, on average, carried out 40 months after the operation. Despite ageing, the observed Harris Hip Score at the follow-up examination was higher than that estimated prior to the injury (77.9>69.6; p=0.006). Similarly, the hip stress distribution was reduced (2.7 MPa<2.3 MPa; p=0.001). While this reduction can be attributed to a loss of weight due to late ageing, the principal improvement came from the operative treatment and corresponding restoration of the biomechanical properties of the hip joint. The implantation of a bipolar partial hip endoprosthesis for patients with displaced medial femoral neck fractures improves the biomechanical and clinical features of the hip, what should have on mind during making decision about treatment

Škole i promicanje inovacije

The global economic crisis has demonstrated that Slovenia is lagging behind the more organised and globally competitive states as measured by a number of important indicators, and has exposed its lack of adequate strategies and policies to improve the situation. This paper presents findings on the work of enterprise circles and the current state of Slovenian primary schools in respect of the promotion of creativity, innovation and entrepreneurship. It examines those factors within schools and the broader local environment that can promote or hinder the development of creativity, innovation and entrepreneurship among pupils. The objectives are clarified by research approaches that connect empirical data to those social circumstances that affect how the issue is understood and how stakeholders explain it. The findings indicate a lack of awareness of how important it is to create links between the education system and the labour market. Teachers who have participated in activities to promote the development of creativity and innovation are more critical of their schools, while pupils still find it difficult to express themselves differently within the school system.Globalna ekonomska kriza pokazala je da Slovenija kasni za bolje organiziranim i globalno kompetitivnim državama, što je vidljivo iz mjerenja nekoliko važnih indikatora, a otkriven je i nedostatak odgovarajućih strategija i smjerova s pomoću kojih bi se situacija popravila. U radu su prikazani rezultati rada gospodarstvenih krugova i trenutno stanje osnovnih škola u Sloveniji s obzirom na promidžbu kreativnosti, inovaciju i enterprise. Proučeni su oni čimbenici unutar škola i šire lokalne okoline koji mogu promicati ili sputavati razvoj kreativnosti, inovaciju i poduzetništvo među učenicima. Ciljevi su pojašnjeni u pristupima istraživanju koje povezuju empirijske podatke s onim društvenim okolnostima koje utječu na razumijevanje tog pitanja. Rezultati ukazuju na nedostatak informiranosti o tome koliko je važno stvoriti veze između obrazovnog sustava i tržišta rada. Nastavnici koji su sudjelovali u aktivnostima koje promiču razvoj kreativnosti i inovacije puno su kritičniji prema svojim školama, dok se učenicima u okviru školskog sustava još uvijek teško izjašnjavati na drukčiji način

Characterising the RNA targets and position-dependent splicing regulation by TDP-43: implications for neurodegenerative diseases

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How Can We Advance Integrative Biology Research in Animal Science in 21st Century?:Experience at University of Ljubljana from 2002 to 2022

In this perspective analysis, we strive to answer the following question: how can we advance integrative biology research in the 21st century with lessons from animal science? At the University of Ljubljana, Biotechnical Faculty, Department of Animal Science, we share here our three lessons learned in the two decades from 2002 to 2022 that we believe could inform integrative biology, systems science, and animal science scholarship in other countries and geographies. Cultivating multiomics knowledge through a conceptual lens of integrative biology is crucial for life sciences research that can stand the test of diverse biological, clinical, and ecological contexts. Moreover, in an era of the current COVID-19 pandemic, animal nutrition and animal science, and the study of their interactions with human health (and vice versa) through integrative biology approaches hold enormous prospects and significance for systems medicine and ecosystem health

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

Transcriptome-wide analysis of protein-RNA interactions predicts the dual splicing effects of TIA proteins, showing that their local enhancing function is associated with diverse distal splicing silencing effects