Quantum Query Complexity for Some Graph Problems

The paper [4] by H. Buhrman and R. de Wolf contains an impressive survey of solved and open problems in quantum query complexity, including many graph problems. We use recent results by A.Ambainis [1] to prove higher lower bounds for some of these problems. Some of our new lower bounds do not close the gap between the best upper and lower bounds. We prove in these cases that it is impossible to provide a better application of Ambainis’ technique for these problems.

Characteristic Topological Features of Promoter Capture Hi-C Interaction Networks

Current Hi-C technologies for chromosome conformation capture allow to understand a broad spectrum of functional interactions between genome elements. Although significant progress has been made into analysis of Hi-C data to identify the biologically significant features, many questions still remain open. In this paper we describe analysis methods of Hi-C (specifically PCHi-C) interaction networks that are strictly focused on topological properties of these networks. The main questions we are trying to answer are: (1) can topological properties of interaction networks for different cell types alone be sufficient to distinguish between these types, and what the most important of such propert…

Architecture and Language for Semantic Reduction of Domain-Specific Models in BPMS

Nowadays each business process management system (BPMS) supports either an industry standard or its own specific modeling language. But no BPMS supports a specific language for each organization. We propose an architecture for building BPMS that allows creating a domain-specific modeling language for every client easily. The main problem is to bridge the gap between the domain-specific language and the executable language. We show that we can look at this problem as a classification of the domain-specific language constructs in the terms of the executable language. To solve this problem we present a novel model transformation language, with which this type of problem can be solved more natu…

Graph-based network analysis of transcriptional regulation pattern divergence in duplicated yeast gene pairs

The genome and interactome of Saccharomyces cerevisiae have been characterized extensively over the course of the past few decades. However, despite many insights gained over the years, both functional studies and evolutionary analyses continue to reveal many complexities and confounding factors in the construction of reliable transcriptional regulatory network models. We present here a graph-based technique for comparing transcriptional regulatory networks based on network motif similarity for gene pairs. We construct interaction graphs for duplicated transcription factor pairs traceable to the ancestral whole-genome duplication as well as other paralogues in Saccharomyces cerevisiae. We c…

Using Deep Learning to Extrapolate Protein Expression Measurements

Mass spectrometry (MS)-based quantitative proteomics experiments typically assay a subset of up to 60% of the ≈20 000 human protein coding genes. Computational methods for imputing the missing values using RNA expression data usually allow only for imputations of proteins measured in at least some of the samples. In silico methods for comprehensively estimating abundances across all proteins are still missing. Here, a novel method is proposed using deep learning to extrapolate the observed protein expression values in label-free MS experiments to all proteins, leveraging gene functional annotations and RNA measurements as key predictive attributes. This method is tested on four datasets, in…

DSL Based Platform for Business Process Management

Currently nearly all commercial and open source BPMS are based on BPMN as a process notation. In contrast, the paper proposes to build a BPMS based on a domain specific language (DSL) as a process notation – DSBPMS. In such a DSBPMS a specific business process support could be created by business analysts. A platform for creating such DSBPMS with feasible efforts is described. This platform contains a Configurator for easy creation of graphical editors for the chosen DSL and a simple mapping language for transforming processes in this DSL to a language directly executable by the execution engine of this platform. The engine includes also all typical execution support functions so no other t…

OWL Orthogonal Extension

It is critical for knowledge bases to capture the reality in direct and intuitive way. OWL ontology language was designed for this goal. In this paper we study the limitations of the OWL open world semantics for the task of knowledge capture and retrieval. We propose a new mechanism based on the closed world semantics that alleviates part of the limitations. Further we describe a system where both OWL and the new mechanisms interoperate together. Finally, we outline some immediate applications and further research directions.

Behaviour of thermal expansion of (1-x)Pb(Ni1/3Nb2/3)O3–xPbTiO3 solid solutions

The publication costs of this article were covered by the Estonian Academy of Sciences and the University of Tartu.

Graph-based characterisations of cell types and functionally related modules in promoter capture Hi-C Data

Topological structure analysis of chromatin interaction networks.

Abstract Background Current Hi-C technologies for chromosome conformation capture allow to understand a broad spectrum of functional interactions between genome elements. Although significant progress has been made into analysis of Hi-C data to identify biologically significant features, many questions still remain open, in particular regarding potential biological significance of various topological features that are characteristic for chromatin interaction networks. Results It has been previously observed that promoter capture Hi-C (PCHi-C) interaction networks tend to separate easily into well-defined connected components that can be related to certain biological functionality, however, …

Network motif-based analysis of regulatory patterns in paralogous gene pairs

Current high-throughput experimental techniques make it feasible to infer gene regulatory interactions at the whole-genome level with reasonably good accuracy. Such experimentally inferred regulatory networks have become available for a number of simpler model organisms such as S. cerevisiae, and others. The availability of such networks provides an opportunity to compare gene regulatory processes at the whole genome level, and in particular, to assess similarity of regulatory interactions for homologous gene pairs either from the same or from different species. We present here a new technique for analyzing the regulatory interaction neighborhoods of paralogous gene pairs. Our central focu…