Functional Equivalency Inferred from “Authoritative Sources” in Networks of Homologous Proteins

A one-on-one mapping of protein functionality across different species is a critical component of comparative analysis. This paper presents a heuristic algorithm for discovering the Most Likely Functional Counterparts (MoLFunCs) of a protein, based on simple concepts from network theory. A key feature of our algorithm is utilization of the user's knowledge to assign high confidence to selected functional identification. We show use of the algorithm to retrieve functional equivalents for 7 membrane proteins, from an exploration of almost 40 genomes form multiple online resources. We verify the functional equivalency of our dataset through a series of tests that include sequence, structure and function comparisons. Comparison is made to the OMA methodology, which also identifies one-on-one mapping between proteins from different species. Based on that comparison, we believe that incorporation of user's knowledge as a key aspect of the technique adds value to purely statistical formal methods

Animal breeding in organic farming

After a general introduction into the available breeding techniques for animal breeding and an overview of the organic principles, points for discussion are identified and scenario's for organically accepted breeding methods are discussed

Animal breeding in organic farming:Discussion paper

It is uncertain whether animals which have been bred for conventional production are capable of optimum performance in organic conditions. In conventional agriculture there is a movement towards maximum control of production conditions in order to optimise animals' yield in intensive production systems. By contrast, organic agriculture is based on natural processes and closed cycles, and takes into account the underlying connections between production factors. Following organic ideology, production capacity should be curtailed by acting in accordance with guiding principles such as naturalness, animal welfare, efficient use of fossil fuels in the farm cycle, and agri-biodiversity (IFOAM, 1994). Organic production should be tied to the land, with farms preferably being self-sufficient mixed farms with closed cycles. An additional point of concern are the reproduction techniques used in conventional breeding. Artificial insemination (AI) and embryo transfer (ET) are commonplace in conventional animal breeding. But these techniques are 'artificial' and they deprive animals of natural mating behaviour and negatively affect the animals' welfare and integrity. By bringing in animals from conventional agriculture, organic farmers are indirectly making use of these techniques. These and other concerns have led to the project 'Organic breeding: a long way to go', which aims to lay down clear visions and an action plan for an organic breeding system

Transforming Graph Representations for Statistical Relational Learning

Relational data representations have become an increasingly important topic due to the recent proliferation of network datasets (e.g., social, biological, information networks) and a corresponding increase in the application of statistical relational learning (SRL) algorithms to these domains. In this article, we examine a range of representation issues for graph-based relational data. Since the choice of relational data representation for the nodes, links, and features can dramatically affect the capabilities of SRL algorithms, we survey approaches and opportunities for relational representation transformation designed to improve the performance of these algorithms. This leads us to introduce an intuitive taxonomy for data representation transformations in relational domains that incorporates link transformation and node transformation as symmetric representation tasks. In particular, the transformation tasks for both nodes and links include (i) predicting their existence, (ii) predicting their label or type, (iii) estimating their weight or importance, and (iv) systematically constructing their relevant features. We motivate our taxonomy through detailed examples and use it to survey and compare competing approaches for each of these tasks. We also discuss general conditions for transforming links, nodes, and features. Finally, we highlight challenges that remain to be addressed

Trends in template/fragment-free protein structure prediction

Predicting the structure of a protein from its amino acid sequence is a long-standing unsolved problem in computational biology. Its solution would be of both fundamental and practical importance as the gap between the number of known sequences and the number of experimentally solved structures widens rapidly. Currently, the most successful approaches are based on fragment/template reassembly. Lacking progress in template-free structure prediction calls for novel ideas and approaches. This article reviews trends in the development of physical and specific knowledge-based energy functions as well as sampling techniques for fragment-free structure prediction. Recent physical- and knowledge-based studies demonstrated that it is possible to sample and predict highly accurate protein structures without borrowing native fragments from known protein structures. These emerging approaches with fully flexible sampling have the potential to move the field forward

Geometric analysis of macromolecule organization within cryo-electron tomograms

Cryo-electron tomography (CET) provides unprecedented views into the native cellular environment at molecular resolution. While subtomogram analysis yields high-resolution native structures of molecular complexes, it also determines the precise positions and orientations of these macromolecules within the cell. Analyzing the geometric relationships between adjacent macromolecules can offer structural insights into molecular interactions and identify supramolecular ensembles. However, computation..

Protein 3D Structure Computed from Evolutionary Sequence Variation

The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing

Proceedings, MSVSCC 2013

Proceedings of the 7th Annual Modeling, Simulation & Visualization Student Capstone Conference held on April 11, 2013 at VMASC in Suffolk, Virginia

Representation learning on relational data

Humans utilize information about relationships or interactions between objects for orientation in various situations. For example, we trust our friend circle recommendations, become friends with the people we already have shared friends with, or adapt opinions as a result of interactions with other people. In many Machine Learning applications, we also know about relationships, which bear essential information for the use-case. Recommendations in social media, scene understanding in computer vision, or traffic prediction are few examples where relationships play a crucial role in the application. In this thesis, we introduce methods taking relationships into account and demonstrate their benefits for various problems. A large number of problems, where relationship information plays a central role, can be approached by modeling data by a graph structure and by task formulation as a prediction problem on the graph. In the first part of the thesis, we tackle the problem of node classification from various directions. We start with unsupervised learning approaches, which differ by assumptions they make about the relationship's meaning in the graph. For some applications such as social networks, it is a feasible assumption that densely connected nodes are similar. On the other hand, if we want to predict passenger traffic for the airport based on its flight connections, similar nodes are not necessarily positioned close to each other in the graph and more likely have comparable neighborhood patterns. Furthermore, we introduce novel methods for classification and regression in a semi-supervised setting, where labels of interest are known for a fraction of nodes. We use the known prediction targets and information about how nodes connect to learn the relationships' meaning and their effect on the final prediction. In the second part of the thesis, we deal with the problem of graph matching. Our first use-case is the alignment of different geographical maps, where the focus lies on the real-life setting. We introduce a robust method that can learn to ignore the noise in the data. Next, our focus moves to the field of Entity Alignment in different Knowledge Graphs. We analyze the process of manual data annotation and propose a setting and algorithms to accelerate this labor-intensive process. Furthermore, we point to the several shortcomings in the empirical evaluations, make several suggestions on how to improve it, and extensively analyze existing approaches for the task. The next part of the thesis is dedicated to the research direction dealing with automatic extraction and search of arguments, known as Argument Mining. We propose a novel approach for identifying arguments and demonstrate how it can make use of relational information. We apply our method to identify arguments in peer-reviews for scientific publications and show that arguments are essential for the decision process. Furthermore, we address the problem of argument search and introduce a novel approach that retrieves relevant and original arguments for the user's queries. Finally, we propose an approach for subspace clustering, which can deal with large datasets and assign new objects to the found clusters. Our method learns the relationships between objects and performs the clustering on the resulting graph

Roadmap on structured light

Structured light refers to the generation and application of custom light fields. As the tools and technology to create and detect structured light have evolved, steadily the applications have begun to emerge. This roadmap touches on the key fields within structured light from the perspective of experts in those areas, providing insight into the current state and the challenges their respective fields face. Collectively the roadmap outlines the venerable nature of structured light research and the exciting prospects for the future that are yet to be realized.Peer ReviewedPostprint (published version